Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 82 of 226
Found at i:29626487 original size:34 final size:34
Alignment explanation
Indices: 29626378--29626487 Score: 98
Period size: 34 Copynumber: 3.1 Consensus size: 34
29626368 TATATTTTTA
29626378 AATTTT-CATTACTAAAAACTCACAAAACACAAC
1 AATTTTACATTACTAAAAACTCACAAAACACAAC
* * *** * *
29626411 AATTTATAATAAATTACTAACAAAAT-ATTTAACAAAAT
1 AA-TT-T--TACATTACTAA-AAACTCACAAAACACAAC
29626449 AATTTTACATTACTAAAAACTCACAAAACACAAC
1 AATTTTACATTACTAAAAACTCACAAAACACAAC
29626483 AATTT
1 AATTT
29626488 ATAATAAATT
Statistics
Matches: 56, Mismatches: 14, Indels: 13
0.67 0.17 0.16
Matches are distributed among these distances:
33 6 0.11
34 24 0.43
35 1 0.02
36 1 0.02
37 3 0.05
38 17 0.30
39 4 0.07
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (34 bp):
AATTTTACATTACTAAAAACTCACAAAACACAAC
Found at i:29626517 original size:38 final size:38
Alignment explanation
Indices: 29626403--29626520 Score: 129
Period size: 38 Copynumber: 3.2 Consensus size: 38
29626393 AAACTCACAA
29626403 AACACAACAATTTATAATAAATTACTAACAAAATATTT
1 AACACAACAATTTATAATAAATTACTAACAAAATATTT
* * * * ***
29626441 AACAAAATAA-TT-T--TACATTACTAA-AAACTCACAA
1 AACACAACAATTTATAATAAATTACTAACAAAAT-ATTT
29626475 AACACAACAATTTATAATAAATTACTAACAAAATATTT
1 AACACAACAATTTATAATAAATTACTAACAAAATATTT
29626513 AACACAAC
1 AACACAAC
29626521 CAGTGGCGCC
Statistics
Matches: 60, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
33 4 0.07
34 19 0.32
35 2 0.03
36 2 0.03
37 2 0.03
38 27 0.45
39 4 0.07
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (38 bp):
AACACAACAATTTATAATAAATTACTAACAAAATATTT
Found at i:29626575 original size:27 final size:27
Alignment explanation
Indices: 29626522--29626576 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
29626512 TAACACAACC
* *
29626522 AGTGGCGCCTATCAGATAGGAGTCACT
1 AGTGGCGCCTACCAGATAGGAGCCACT
29626549 AGTGGCGCCTACCAGATAGGCA-CCACT
1 AGTGGCGCCTACCAGATAGG-AGCCACT
29626576 A
1 A
29626577 ACCCCATACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (27 bp):
AGTGGCGCCTACCAGATAGGAGCCACT
Found at i:29627208 original size:24 final size:25
Alignment explanation
Indices: 29627176--29627230 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
29627166 CACTTTTTTT
* *
29627176 AATAATATTTTTTTACTTT-TAAAA
1 AATATTATTATTTTACTTTATAAAA
*
29627200 AATATTATTATTTTATTTTATAAAA
1 AATATTATTATTTTACTTTATAAAA
29627225 AATATT
1 AATATT
29627231 TAAATAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
AATATTATTATTTTACTTTATAAAA
Found at i:29627402 original size:7 final size:7
Alignment explanation
Indices: 29627390--29627426 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
29627380 CACAGCCCCT
29627390 CCCTCTG
1 CCCTCTG
29627397 CCCTCTG
1 CCCTCTG
29627404 CCCTCTG
1 CCCTCTG
29627411 CCCTCTG
1 CCCTCTG
29627418 CCCTCTG
1 CCCTCTG
29627425 CC
1 CC
29627427 GTGGACTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.00, C:0.59, G:0.14, T:0.27
Consensus pattern (7 bp):
CCCTCTG
Found at i:29627737 original size:11 final size:11
Alignment explanation
Indices: 29627723--29627807 Score: 53
Period size: 11 Copynumber: 7.5 Consensus size: 11
29627713 TTTTTTTGTT
29627723 TTTTATAATTA
1 TTTTATAATTA
*
29627734 TTTTAAAATTA
1 TTTTATAATTA
* * *
29627745 TTTTGTTAGTA
1 TTTTATAATTA
* **
29627756 ATTTAGGATTA
1 TTTTATAATTA
* *
29627767 TGTTATAAATTG
1 TTTTAT-AATTA
29627779 TGTTTATAATTA
1 T-TTTATAATTA
*
29627791 TTTTAAAATTA
1 TTTTATAATTA
*
29627802 ATTTAT
1 TTTTAT
29627808 TAGTAATTTA
Statistics
Matches: 52, Mismatches: 20, Indels: 4
0.68 0.26 0.05
Matches are distributed among these distances:
11 39 0.75
12 9 0.17
13 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.56
Consensus pattern (11 bp):
TTTTATAATTA
Found at i:29627788 original size:57 final size:57
Alignment explanation
Indices: 29627724--29627836 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 57
29627714 TTTTTTGTTT
* *
29627724 TTTATAATTATTTTAAAATTATTTTGTTAGTAATTTAGGATTATGTTATAAATTGTG
1 TTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTG
29627781 TTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGT
1 TTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGT
29627837 TGTGTTTAGT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (57 bp):
TTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTG
Found at i:29628041 original size:60 final size:59
Alignment explanation
Indices: 29627909--29628022 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 59
29627899 ATGGTAAATC
**
29627909 ATTATAAATTGTTGTATTTTGTGAGTTTTTAGTAATGTAAAATTATTTTGTTAGTAATTT
1 ATTATAAATTGTTGTATTTTGTGAGTTTTTAGTAATGT-AAATTATTTTGTTAAAAATTT
* *
29627969 ATTATAAATTGTTGTGTTTTGTTAGTTTTTAGTAATGT-AATTATTTT-TTAAAAA
1 ATTATAAATTGTTGTATTTTGTGAGTTTTTAGTAATGTAAATTATTTTGTTAAAAA
29628023 ATTTTATGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 5 0.10
58 9 0.18
60 36 0.72
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (59 bp):
ATTATAAATTGTTGTATTTTGTGAGTTTTTAGTAATGTAAATTATTTTGTTAAAAATTT
Found at i:29628095 original size:97 final size:96
Alignment explanation
Indices: 29627980--29628283 Score: 367
Period size: 103 Copynumber: 3.0 Consensus size: 96
29627970 TTATAAATTG
* * *
29627980 TTGTGTTTTGTTAGTTTTTAGTAATGTAATTATTTTTTAAAAAATTTTATGGTTATTTTGTTAGT
1 TTGTGTTTTGTTATTTTTTAGTAATGTAATT-TTTTTAAAAAAATTTTATAGTTATTTTGTTAGT
*
29628045 AGTTTATGATTAGGTTATAAATTGTTAGTGTT
65 AATTTATGATTAGGTTATAAATTGTTAGTGTT
*
29628077 TTGTGTTTTGTTATTTTTTAGTAATGTAATTTCTTTTAAAAAAATGTTATAGTTATTTATTTTGT
1 TTGTGTTTTGTTATTTTTTAGTAATGTAATTT-TTTTAAAAAAAT-TT-TA--TAGTTATTTTGT
*
29628142 TAGTAATTTATGGGATTAGGTTAGAAATTGTTAGTGTTTAGT
61 TAGTAATTTAT--GATTAGGTTATAAATTGTTAGTG--T--T
* * * *
29628184 TTAGGGTTTTGTGATTTTTTAGTAATGTAA-TTTTTAAAAAATAATTTTATAGTTGTTTTGTTAG
1 TT-GTGTTTTGTTATTTTTTAGTAATGTAATTTTTTTAAAAA-AATTTTATAGTTATTTTGTTAG
29628248 TAATTTATGATTAGGTTATATAAATTGTTAGTGTT
64 TAATTTATGATTAGG-T-TATAAATTGTTAGTGTT
29628283 T
1 T
29628284 AGTTTAGTGT
Statistics
Matches: 180, Mismatches: 12, Indels: 28
0.82 0.05 0.13
Matches are distributed among these distances:
96 1 0.01
97 41 0.23
98 2 0.01
99 4 0.02
101 28 0.16
102 1 0.01
103 57 0.32
105 3 0.02
106 10 0.06
107 8 0.04
108 25 0.14
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.55
Consensus pattern (96 bp):
TTGTGTTTTGTTATTTTTTAGTAATGTAATTTTTTTAAAAAAATTTTATAGTTATTTTGTTAGTA
ATTTATGATTAGGTTATAAATTGTTAGTGTT
Found at i:29630798 original size:76 final size:77
Alignment explanation
Indices: 29630684--29630976 Score: 416
Period size: 76 Copynumber: 3.8 Consensus size: 77
29630674 AATAATTTCA
* * *
29630684 TATTTATATAATGACTTTTTTTCCATTTTA-GTATTTAATTTTATGGTTTTTTTTTGCTATTTAA
1 TATTTATGTAATGACTTTTTTTCCATTTTATTTA-TTAATTTTATGGTTTTTTTTTGCAATTTAA
29630748 ATAGTCAACTTTG
65 ATAGTCAACTTTG
* * *
29630761 TATTTATGTAATGA-TTTTTTTCCATTTTATTTATTAATTTTAAGGGTTTTTTTTACAATTTAAA
1 TATTTATGTAATGACTTTTTTTCCATTTTATTTATTAATTTTATGGTTTTTTTTTGCAATTTAAA
29630825 TAGTCAACTTTG
66 TAGTCAACTTTG
29630837 TATTTATGTAATGACTTTTTTGT-CATTTTATTTATTAATTTTATGGGTTTTTTTTTGCAATTTA
1 TATTTATGTAATGACTTTTTT-TCCATTTTATTTATTAATTTTAT-GGTTTTTTTTTGCAATTTA
29630901 AATAGTCAACTTTG
64 AATAGTCAACTTTG
** * * * *
29630915 TATTTATGTAATGACTTTTTCGCTATTTCAGTTATTAATTTTA-GG-ATTTTTTTGCAATTTAA
1 TATTTATGTAATGACTTTTTTTCCATTTTATTTATTAATTTTATGGTTTTTTTTTGCAATTTAA
29630977 TAATAAAATT
Statistics
Matches: 196, Mismatches: 15, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
75 16 0.08
76 70 0.36
77 41 0.21
78 69 0.35
ACGTcount: A:0.26, C:0.07, G:0.10, T:0.57
Consensus pattern (77 bp):
TATTTATGTAATGACTTTTTTTCCATTTTATTTATTAATTTTATGGTTTTTTTTTGCAATTTAAA
TAGTCAACTTTG
Found at i:29634092 original size:27 final size:27
Alignment explanation
Indices: 29634045--29634101 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
29634035 ACCTATTAGG
* *
29634045 TAGGAGTCACCAGTAGTGCCTACCAGA
1 TAGGAGTCACCAATAGCGCCTACCAGA
* *
29634072 TAGGAGTCACCAATGGCGCCTACTAGA
1 TAGGAGTCACCAATAGCGCCTACCAGA
29634099 TAG
1 TAG
29634102 ATACCACCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (27 bp):
TAGGAGTCACCAATAGCGCCTACCAGA
Found at i:29635532 original size:29 final size:31
Alignment explanation
Indices: 29635472--29635533 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 31
29635462 TCCGCCACTA
29635472 ATCACAATTAAAATTTCATATATATAATTAT
1 ATCACAATTAAAATTTCATATATATAATTAT
29635503 ATCA-AATTAAAATTTC-TATATCA-AATTAT
1 ATCACAATTAAAATTTCATATAT-ATAATTAT
29635532 AT
1 AT
29635534 ATTCAATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 13 0.43
30 13 0.43
31 4 0.13
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (31 bp):
ATCACAATTAAAATTTCATATATATAATTAT
Found at i:29636209 original size:23 final size:25
Alignment explanation
Indices: 29636179--29636233 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 25
29636169 ATTTTATTTG
29636179 ATAT-AAATTAAA-AAT-TATCTACA
1 ATATAAAATTAAATAATATAT-TACA
29636202 A-ATAAAATTAAATAATATATTACA
1 ATATAAAATTAAATAATATATTACA
29636226 ATATAAAA
1 ATATAAAA
29636234 AAACCAGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 2 0.07
23 9 0.32
24 8 0.29
25 9 0.32
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (25 bp):
ATATAAAATTAAATAATATATTACA
Found at i:29636422 original size:20 final size:20
Alignment explanation
Indices: 29636397--29636435 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
29636387 ATTCAACTAT
29636397 TATTAT-TATTTTATAAAATA
1 TATTATATATTTT-TAAAATA
29636417 TATTATAATATTTTTAAAA
1 TATTAT-ATATTTTTAAAA
29636436 AAAACTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 5 0.29
22 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTATATATTTTTAAAATA
Found at i:29638784 original size:60 final size:60
Alignment explanation
Indices: 29638712--29638833 Score: 217
Period size: 60 Copynumber: 2.0 Consensus size: 60
29638702 AAATAAATAT
29638712 ATCCTATAATTTCATATGTTCTTAAGAGCTCCGATTACCCACGGTACTTTGAGGAGACAA
1 ATCCTATAATTTCATATGTTCTTAAGAGCTCCGATTACCCACGGTACTTTGAGGAGACAA
* * *
29638772 ATCCTATAATTTCATATGTTCTTAGGAGCTCCGTTTACCTACGGTACTTTGAGGAGACAA
1 ATCCTATAATTTCATATGTTCTTAAGAGCTCCGATTACCCACGGTACTTTGAGGAGACAA
29638832 AT
1 AT
29638834 TTAGGCAAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (60 bp):
ATCCTATAATTTCATATGTTCTTAAGAGCTCCGATTACCCACGGTACTTTGAGGAGACAA
Found at i:29641606 original size:16 final size:16
Alignment explanation
Indices: 29641578--29641621 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
29641568 GAAAAAAAAT
*
29641578 TAATAATA-GTATAAA
1 TAATAATATATATAAA
* *
29641593 TGATAATATATATACA
1 TAATAATATATATAAA
29641609 TAATAATATATAT
1 TAATAATATATAT
29641622 TAAGCAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (16 bp):
TAATAATATATATAAA
Found at i:29641921 original size:3 final size:3
Alignment explanation
Indices: 29641861--29641906 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
29641851 ATATATAAAC
29641861 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
29641907 GGTAGTAGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:29642904 original size:14 final size:16
Alignment explanation
Indices: 29642882--29642919 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
29642872 TTCGCTCTTA
*
29642882 TTTTATTTTATTT-C-
1 TTTTCTTTTATTTGCT
29642896 TTTTCTTTTATTTGCT
1 TTTTCTTTTATTTGCT
29642912 TTTTCTTT
1 TTTTCTTT
29642920 GTCTGTGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.57
15 1 0.05
16 8 0.38
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTCTTTTATTTGCT
Found at i:29649180 original size:43 final size:43
Alignment explanation
Indices: 29649095--29649261 Score: 194
Period size: 43 Copynumber: 3.9 Consensus size: 43
29649085 GACATCACCG
* **
29649095 CTAA-CTTTAGCGGCGTTTTTCGAAATAAACGCCGCTAAAGACC
1 CTAATCTTTAGCGGCGCTTTTCCTAA-AAACGCCGCTAAAGACC
* * * *
29649138 ATGACCTTTAGCGGCGCTTTTCCTAAAAACGCCGCTAGAGACC
1 CTAATCTTTAGCGGCGCTTTTCCTAAAAACGCCGCTAAAGACC
* *
29649181 CTAATCTTTAGCGGCGCTTTTTCTACAAACGCCGCTAAAGACC
1 CTAATCTTTAGCGGCGCTTTTCCTAAAAACGCCGCTAAAGACC
* * *
29649224 CTAATCTTTAGCGGTGCTTTT-TTAAAAAACGCCACTAA
1 CTAATCTTTAGCGGCGCTTTTCCT-AAAAACGCCGCTAA
29649262 TTTTGGCAGA
Statistics
Matches: 106, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
42 1 0.01
43 87 0.82
44 18 0.17
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (43 bp):
CTAATCTTTAGCGGCGCTTTTCCTAAAAACGCCGCTAAAGACC
Found at i:29651274 original size:25 final size:25
Alignment explanation
Indices: 29651240--29651288 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
29651230 ATACAAATAT
*
29651240 AAGTTGTGTATAATGTAAGTTATGA
1 AAGTTATGTATAATGTAAGTTATGA
*
29651265 AAGTTATGTATTATGTAAGTTATG
1 AAGTTATGTATAATGTAAGTTATG
29651289 TATTATGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (25 bp):
AAGTTATGTATAATGTAAGTTATGA
Found at i:29651278 original size:16 final size:16
Alignment explanation
Indices: 29651259--29651353 Score: 86
Period size: 16 Copynumber: 5.8 Consensus size: 16
29651249 ATAATGTAAG
*
29651259 TTATGAAAGTTATGTA
1 TTATGTAAGTTATGTA
29651275 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
29651291 TTATGTAAGTTATTTAA
1 TTATGTAAGTTATGT-A
*
29651308 GTTGTGT-A-TTATGTAA
1 -TTATGTAAGTTATGT-A
* * *
29651324 GTCATGTAGGCTATGTA
1 -TTATGTAAGTTATGTA
29651341 TTATGTAAGTTAT
1 TTATGTAAGTTAT
29651354 AATAAGTAAG
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
16 51 0.80
17 3 0.05
18 10 0.16
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:29651287 original size:9 final size:9
Alignment explanation
Indices: 29651252--29651644 Score: 109
Period size: 9 Copynumber: 47.0 Consensus size: 9
29651242 GTTGTGTATA
29651252 ATGTAAGTT
1 ATGTAAGTT
*
29651261 ATGAAAGTT
1 ATGTAAGTT
29651270 ATGT-A-TT
1 ATGTAAGTT
29651277 ATGTAAGTT
1 ATGTAAGTT
29651286 ATGT-A-TT
1 ATGTAAGTT
29651293 ATGTAAGTT
1 ATGTAAGTT
*
29651302 ATTTAAGTT
1 ATGTAAGTT
*
29651311 GTGT-A-TT
1 ATGTAAGTT
*
29651318 ATGTAAGTC
1 ATGTAAGTT
* *
29651327 ATGTAGGCT
1 ATGTAAGTT
29651336 ATGT-A-TT
1 ATGTAAGTT
29651343 ATGTAAGTT
1 ATGTAAGTT
29651352 A--TAA--T
1 ATGTAAGTT
*
29651357 AAGTAAGTT
1 ATGTAAGTT
*
29651366 ATGAAAGTTAT
1 ATGTAAG-T-T
*
29651377 ATATAAGTTTAT
1 ATGTAAG--T-T
*
29651389 ATATAAGTT
1 ATGTAAGTT
29651398 ATGTAAGTT
1 ATGTAAGTT
29651407 A--T-A--T
1 ATGTAAGTT
29651411 ATGTAAGTT
1 ATGTAAGTT
29651420 ATGT--GTT
1 ATGTAAGTT
*
29651427 GTGTAAGTT
1 ATGTAAGTT
*
29651436 -TAT-A-TAT
1 ATGTAAGT-T
*
29651443 AT-TAAATTT
1 ATGT-AAGTT
29651452 AT-TCAAGTT
1 ATGT-AAGTT
29651461 ATG--A---
1 ATGTAAGTT
29651465 ATGTAAGTT
1 ATGTAAGTT
*
29651474 ATGTAAATT
1 ATGTAAGTT
* *
29651483 GTGT-A-TA
1 ATGTAAGTT
*
29651490 ACGTAAGTT
1 ATGTAAGTT
* *
29651499 AAGAAAGTT
1 ATGTAAGTT
29651508 ATGT-A-TT
1 ATGTAAGTT
29651515 ATGTAAGTT
1 ATGTAAGTT
*
29651524 ATTTAAGTT
1 ATGTAAGTT
*
29651533 GTGT-A-TT
1 ATGTAAGTT
29651540 ATGTAAGTCT
1 ATGTAAGT-T
* *
29651550 -TGTAGGCT
1 ATGTAAGTT
29651558 ATGT--GTT
1 ATGTAAGTT
29651565 ATGTAAGTT
1 ATGTAAGTT
29651574 AT-T-A--T
1 ATGTAAGTT
29651579 ATGTAAGTT
1 ATGTAAGTT
*
29651588 ATGAAAGTTAT
1 ATGTAAG-T-T
*
29651599 ATATAAGTTTAT
1 ATGTAAG--T-T
*
29651611 ATATAAGTT
1 ATGTAAGTT
29651620 ATGTAAGTT
1 ATGTAAGTT
29651629 ATGT--GTT
1 ATGTAAGTT
*
29651636 GTGTAAGTT
1 ATGTAAGTT
29651645 TATATATAAA
Statistics
Matches: 289, Mismatches: 43, Indels: 104
0.66 0.10 0.24
Matches are distributed among these distances:
4 5 0.02
5 5 0.02
6 5 0.02
7 68 0.24
8 18 0.06
9 148 0.51
10 6 0.02
11 12 0.04
12 22 0.08
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:29651297 original size:41 final size:41
Alignment explanation
Indices: 29651239--29651331 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 41
29651229 AATACAAATA
*
29651239 TAAGTTGTGTATAATGTAAGTTATGAAAGTTATGTATTATG
1 TAAGTTATGTATAATGTAAGTTATGAAAGTTATGTATTATG
* ** *
29651280 TAAGTTATGTATTATGTAAGTTATTTAAGTTGTGTATTATG
1 TAAGTTATGTATAATGTAAGTTATGAAAGTTATGTATTATG
*
29651321 TAAGTCATGTA
1 TAAGTTATGTA
29651332 GGCTATGTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.46
Consensus pattern (41 bp):
TAAGTTATGTATAATGTAAGTTATGAAAGTTATGTATTATG
Found at i:29651303 original size:25 final size:25
Alignment explanation
Indices: 29651239--29651322 Score: 77
Period size: 25 Copynumber: 3.4 Consensus size: 25
29651229 AATACAAATA
* *
29651239 TAAGTTGTGTATAATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
*
29651264 AAAGTTATGTATTATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
* *
29651289 T-A-TTATGTAAGTTATTTAAGTTGTG
1 TAAGTTATGT-A-TTATGTAAGTTATG
29651314 T-A-TTATGTA
1 TAAGTTATGTA
29651323 AGTCATGTAG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
23 6 0.12
24 3 0.06
25 42 0.82
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (25 bp):
TAAGTTATGTATTATGTAAGTTATG
Found at i:29651340 original size:25 final size:25
Alignment explanation
Indices: 29651277--29651350 Score: 94
Period size: 25 Copynumber: 3.0 Consensus size: 25
29651267 GTTATGTATT
* *
29651277 ATGTAAGTTATGTATTATGTAAGTT
1 ATGTAAGCTATGTATTATGTAAGTC
* * *
29651302 ATTTAAGTTGTGTATTATGTAAGTC
1 ATGTAAGCTATGTATTATGTAAGTC
*
29651327 ATGTAGGCTATGTATTATGTAAGT
1 ATGTAAGCTATGTATTATGTAAGT
29651351 TATAATAAGT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.46
Consensus pattern (25 bp):
ATGTAAGCTATGTATTATGTAAGTC
Found at i:29651350 original size:41 final size:41
Alignment explanation
Indices: 29651252--29651353 Score: 127
Period size: 41 Copynumber: 2.5 Consensus size: 41
29651242 GTTGTGTATA
* * *
29651252 ATGTAAGTTATGAAAGTTATGTATTATGTAAGTTATGTATT
1 ATGTAAGTTATGTAAGTTATGTATTATGTAAGTCATGTACT
* *
29651293 ATGTAAGTTATTTAAGTTGTGTATTATGTAAGTCATGTAGGCT
1 ATGTAAGTTATGTAAGTTATGTATTATGTAAGTCATGTA--CT
29651336 ATGT-A-TTATGTAAGTTAT
1 ATGTAAGTTATGTAAGTTAT
29651354 AATAAGTAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
41 46 0.88
42 1 0.02
43 5 0.10
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (41 bp):
ATGTAAGTTATGTAAGTTATGTATTATGTAAGTCATGTACT
Found at i:29651384 original size:34 final size:34
Alignment explanation
Indices: 29651345--29651421 Score: 97
Period size: 32 Copynumber: 2.3 Consensus size: 34
29651335 TATGTATTAT
29651345 GTAAGTTATA-ATAAGTAAGTTATGAAAGTTATATA
1 GTAAGTTATATAT-A-TAAGTTATGAAAGTTATATA
*
29651380 -TAAGTT-TATATATAAGTTATGTAAGTTATATA
1 GTAAGTTATATATATAAGTTATGAAAGTTATATA
29651412 TGTAAGTTAT
1 -GTAAGTTAT
29651422 GTGTTGTGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
32 19 0.51
33 3 0.08
34 14 0.38
35 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.43
Consensus pattern (34 bp):
GTAAGTTATATATATAAGTTATGAAAGTTATATA
Found at i:29651391 original size:10 final size:11
Alignment explanation
Indices: 29651370--29651412 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 11
29651360 TAAGTTATGA
29651370 AAGTTATATAT
1 AAGTTATATAT
29651381 AAGTTTATATAT
1 AAG-TTATATAT
*
29651393 AAG-T-TATGT
1 AAGTTATATAT
29651402 AAGTTATATAT
1 AAGTTATATAT
29651413 GTAAGTTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
11 7 0.26
12 11 0.41
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (11 bp):
AAGTTATATAT
Found at i:29651415 original size:13 final size:13
Alignment explanation
Indices: 29651397--29651421 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29651387 ATATATAAGT
29651397 TATGTAAGTTATA
1 TATGTAAGTTATA
29651410 TATGTAAGTTAT
1 TATGTAAGTTAT
29651422 GTGTTGTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TATGTAAGTTATA
Found at i:29651495 original size:25 final size:25
Alignment explanation
Indices: 29651465--29651547 Score: 96
Period size: 25 Copynumber: 3.3 Consensus size: 25
29651455 CAAGTTATGA
*
29651465 ATGTAAGTTATGTAAATTGTGTATA
1 ATGTAAGTTATGTAAATTGTGTATT
* * *
29651490 ACGTAAGTTAAG-AAAGTTATGTATT
1 ATGTAAGTTATGTAAA-TTGTGTATT
* *
29651515 ATGTAAGTTATTTAAGTTGTGTATT
1 ATGTAAGTTATGTAAATTGTGTATT
29651540 ATGTAAGT
1 ATGTAAGT
29651548 CTTGTAGGCT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
24 3 0.06
25 42 0.89
26 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.20, T:0.43
Consensus pattern (25 bp):
ATGTAAGTTATGTAAATTGTGTATT
Found at i:29651524 original size:16 final size:16
Alignment explanation
Indices: 29651503--29651590 Score: 51
Period size: 16 Copynumber: 5.5 Consensus size: 16
29651493 TAAGTTAAGA
29651503 AAGTTATGTATTATGT
1 AAGTTATGTATTATGT
* *
29651519 AAGTTATTTAAGTTGTGT
1 AAGTTATGT-A-TTATGT
29651537 -A-TTATGTAAGTCT-TGT
1 AAGTTATGT-A-T-TATGT
* * *
29651553 AGGCTATGTGTTATGT
1 AAGTTATGTATTATGT
29651569 AAGTTAT-TA-TATGT
1 AAGTTATGTATTATGT
29651583 AAGTTATG
1 AAGTTATG
29651591 AAAGTTATAT
Statistics
Matches: 56, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
14 12 0.21
15 2 0.04
16 29 0.52
17 3 0.05
18 10 0.18
ACGTcount: A:0.28, C:0.02, G:0.22, T:0.48
Consensus pattern (16 bp):
AAGTTATGTATTATGT
Found at i:29651612 original size:12 final size:12
Alignment explanation
Indices: 29651595--29651619 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29651585 GTTATGAAAG
29651595 TTATATATAAGT
1 TTATATATAAGT
29651607 TTATATATAAGT
1 TTATATATAAGT
29651619 T
1 T
29651620 ATGTAAGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TTATATATAAGT
Found at i:29651613 original size:10 final size:11
Alignment explanation
Indices: 29651575--29651621 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
29651565 ATGTAAGTTA
*
29651575 TTATATGTAAG
1 TTATATATAAG
*
29651586 TTAT-GA-AAG
1 TTATATATAAG
29651595 TTATATATAAG
1 TTATATATAAG
29651606 TTTATATATAAG
1 -TTATATATAAG
29651618 TTAT
1 TTAT
29651622 GTAAGTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 7 0.23
10 1 0.03
11 11 0.37
12 11 0.37
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (11 bp):
TTATATATAAG
Found at i:29651715 original size:19 final size:19
Alignment explanation
Indices: 29651693--29651733 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
29651683 GATATGATTG
*
29651693 ATAAATTTTTCAA-ATATAT
1 ATAAAATTTT-AATATATAT
29651712 ATAAAATTTTAATATATAT
1 ATAAAATTTTAATATATAT
29651731 ATA
1 ATA
29651734 TATATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAAAATTTTAATATATAT
Found at i:29651753 original size:27 final size:27
Alignment explanation
Indices: 29651706--29651765 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
29651696 AATTTTTCAA
* * *
29651706 ATATATATAAAATTTTAATATATATAT
1 ATATATATAAAAATGTAATATAAATAT
29651733 ATATATATTAAAAATGT-ATATAAATAT
1 ATATATA-TAAAAATGTAATATAAATAT
29651760 ATATAT
1 ATATAT
29651766 CAAAGATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (27 bp):
ATATATATAAAAATGTAATATAAATAT
Found at i:29651785 original size:25 final size:25
Alignment explanation
Indices: 29651724--29651774 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
29651714 AAAATTTTAA
* *
29651724 TATATATATATATATATTAAAAATG
1 TATATAAATATATATATCAAAAATG
*
29651749 TATATAAATATATATATCAAAGATG
1 TATATAAATATATATATCAAAAATG
29651774 T
1 T
29651775 TTTAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (25 bp):
TATATAAATATATATATCAAAAATG
Found at i:29652855 original size:18 final size:18
Alignment explanation
Indices: 29652807--29652855 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
29652797 GACATTCGCA
*
29652807 TATCAATTTATCAAATAC
1 TATCAATTTATCCAATAC
29652825 TATCAATTTATCCAATAC
1 TATCAATTTATCCAATAC
29652843 TATCAATTTATCC
1 TATCAATTTATCC
29652856 TTCCCACCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (18 bp):
TATCAATTTATCCAATAC
Found at i:29654834 original size:512 final size:502
Alignment explanation
Indices: 29653811--29654792 Score: 1673
Period size: 512 Copynumber: 1.9 Consensus size: 502
29653801 CAAACGCCTC
29653811 TATTGGATTCACATTTGCGGCGTTTTAAACAAAAACGCCACTAATATTTTAAAGCACGTAAAGAA
1 TATTGGATTCACATTTGCGGCGTTTTAAACAAAAACGCCACTAATATTTTAAAGCACGTAAAGAA
*
29653876 ACAGCGCCGTTTTAATAAATTATAGTGCATGTTGTGGCGTTTTCTGAAAAAACGCCACAAAAATT
66 ACAGCGCCGTTTTAATAAATTATAGTGCATGTTGTGGCGTTTTCTGAAAAAACACCACAAAAATT
29653941 AATTACCTGAATTGAACCGGCGCCGTTTTTACAAACACTTATATATCCTTGCGGCGTTTTCAATA
131 AATTACCTGAATTGAACCGGCGCCGTTTTTACAAACACTTATATATCCTTGCGGCGTTTTCAATA
*
29654006 AAACGCCAGTAACAGATTCTATTCTTCCACTGAAACGGCGCCGTTTTTCCAAATTTTAAATTTTA
196 AAACGCCAGTAACAGATTCTATTCTTCCACTGAAACGGCGCCATTTTTCCAAATTTTAAATTTTA
29654071 TCCCTAAACTAAAACGACGTCGTATCAAAACAGCTTGGAAATTTTTTGTGGCGTTTTTTATAAAA
261 TCCCTAAACTAAAACGACGTCGTATCAAAACAGCTTGGAAATTTTTTGTGGCGTTTTTTATAAAA
* * *
29654136 ACGCCGGTAATGTCTACCTTTAGTGACGTTTTTGGAAAAACGCCACTAAGGAATTTAAATTCTTT
326 ACGCAGGTAATGTCTACCTTTAGCGACGTTTTTGAAAAAACGCCACTAAGGAATTTAAATTCTTT
*
29654201 TACCAAAATGGTGCCGTTTTGGAAAATTTGTATATATAGTAGCGGCGTTTTTTCTAAAAACGCCA
391 TACCAAAATGGTGCCGTTTTGGAAAATTTGTATATATAGTA---G-G-----T-AAAAAACGCCA
29654266 CTAAATTTCACATTATTTATTTATTGTATGTTTCATTAAAATTTTTAGTAAATTATT
446 CTAAATTTCACATTATTTATTTATTGTATGTTTCATTAAAATTTTTAGTAAATTATT
* * *
29654323 TATTGTATTCACATTTGCGGCGTTTTAAACAAAAACGGCACTAATATTTTAAGGCACGTAAAGAA
1 TATTGGATTCACATTTGCGGCGTTTTAAACAAAAACGCCACTAATATTTTAAAGCACGTAAAGAA
* * *
29654388 ACGGTGCCGTTTTAATAAATTATAGTGCATGTTGTGGCGTTTTCTGAAAAAACACCAGAAAAATT
66 ACAGCGCCGTTTTAATAAATTATAGTGCATGTTGTGGCGTTTTCTGAAAAAACACCACAAAAATT
29654453 AATTACCTGAATTGAACCGGCGCCGTTTTTACAAACACTTATATATCCTTGCGGCGTTTTCAATA
131 AATTACCTGAATTGAACCGGCGCCGTTTTTACAAACACTTATATATCCTTGCGGCGTTTTCAATA
29654518 AAACGCCAGTAACAGATTCTATTCTTCCACTGAAACGGCGCCATTTTTCCAAATTTTAAATTTTA
196 AAACGCCAGTAACAGATTCTATTCTTCCACTGAAACGGCGCCATTTTTCCAAATTTTAAATTTTA
* *
29654583 TCCCTAAACTGAAACGATGTCGTATCAAAACAGCTTGGAAATTTTTTGTGGCGTTTTTTATAAAA
261 TCCCTAAACTAAAACGACGTCGTATCAAAACAGCTTGGAAATTTTTTGTGGCGTTTTTTATAAAA
*
29654648 ACGCAGGTAATGTCTACCTTTAGCGGCGTTTTTTGCAAAAAACGCCACTAAGGAATTTAAATTCT
326 ACGCAGGTAATGTCTACCTTTAGCGACG-TTTTTG-AAAAAACGCCACTAAGGAATTTAAATTCT
* *
29654713 TTTACCAAAACT-GTGCTGTTTTGGAAAATTTGTATATATAGTA-G-AAAAAACGCCGCTAAATT
389 TTTACCAAAA-TGGTGCCGTTTTGGAAAATTTGTATATATAGTAGGTAAAAAACGCCACTAAATT
29654775 TCACATTATTTATTTATT
453 TCACATTATTTATTTATT
29654793 TATTTATTGT
Statistics
Matches: 450, Mismatches: 17, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
502 34 0.08
509 1 0.00
512 340 0.76
513 6 0.01
514 68 0.15
515 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (502 bp):
TATTGGATTCACATTTGCGGCGTTTTAAACAAAAACGCCACTAATATTTTAAAGCACGTAAAGAA
ACAGCGCCGTTTTAATAAATTATAGTGCATGTTGTGGCGTTTTCTGAAAAAACACCACAAAAATT
AATTACCTGAATTGAACCGGCGCCGTTTTTACAAACACTTATATATCCTTGCGGCGTTTTCAATA
AAACGCCAGTAACAGATTCTATTCTTCCACTGAAACGGCGCCATTTTTCCAAATTTTAAATTTTA
TCCCTAAACTAAAACGACGTCGTATCAAAACAGCTTGGAAATTTTTTGTGGCGTTTTTTATAAAA
ACGCAGGTAATGTCTACCTTTAGCGACGTTTTTGAAAAAACGCCACTAAGGAATTTAAATTCTTT
TACCAAAATGGTGCCGTTTTGGAAAATTTGTATATATAGTAGGTAAAAAACGCCACTAAATTTCA
CATTATTTATTTATTGTATGTTTCATTAAAATTTTTAGTAAATTATT
Found at i:29654850 original size:22 final size:22
Alignment explanation
Indices: 29654809--29654862 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
29654799 TTGTATTTTC
* *
29654809 ATTAAAATTTTTAGTAAATAATT
1 ATTAAAGTTTTAAGTAAAT-ATT
29654832 ATTAAAGTTTTAAGT-AATATT
1 ATTAAAGTTTTAAGTAAATATT
*
29654853 -TAAAAGTTTT
1 ATTAAAGTTTT
29654863 TGATAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.32
21 3 0.11
22 3 0.11
23 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
ATTAAAGTTTTAAGTAAATATT
Found at i:29654877 original size:21 final size:21
Alignment explanation
Indices: 29654811--29654877 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 21
29654801 GTATTTTCAT
*
29654811 TAAAA-TTTTTAGTAAATAATTA
1 TAAAAGTTTTAAGT-AA-AATTA
* *
29654833 TTAAAGTTTTAAGTAATATT-
1 TAAAAGTTTTAAGTAAAATTA
*
29654853 TAAAAGTTTT-TGATAAAATTA
1 TAAAAGTTTTAAG-TAAAATTA
29654874 TAAA
1 TAAA
29654878 TTTTAGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.42
21 7 0.19
22 6 0.17
23 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
TAAAAGTTTTAAGTAAAATTA
Found at i:29654910 original size:21 final size:20
Alignment explanation
Indices: 29654884--29654928 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
29654874 TAAATTTTAG
29654884 TTTTTTTATTTCCTTT-TTATA
1 TTTTTTTATTT--TTTCTTATA
29654905 TTTTTTTATTTTTTCTTATA
1 TTTTTTTATTTTTTCTTATA
29654925 TTTT
1 TTTT
29654929 GGTCTTGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.13
20 9 0.39
21 11 0.48
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTTATTTTTTCTTATA
Found at i:29655123 original size:2 final size:2
Alignment explanation
Indices: 29655116--29655144 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29655106 TAAAGTGATC
29655116 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29655145 CTTAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29655573 original size:15 final size:13
Alignment explanation
Indices: 29655542--29655589 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
29655532 AATCTGAGCT
29655542 TAAACCTTAATCTC
1 TAAACCTTAATC-C
29655556 TAAACCTTAAATCAC
1 TAAACCTT-AATC-C
29655571 T-AACTCTTAATCC
1 TAAAC-CTTAATCC
29655584 TAAACC
1 TAAACC
29655590 CCAAACCCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 3 0.10
14 18 0.60
15 9 0.30
ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACCTTAATCC
Found at i:29655671 original size:23 final size:25
Alignment explanation
Indices: 29655618--29655676 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 25
29655608 CCCCTAACCC
* *
29655618 CTAAACATTATTTAATATATAAATT
1 CTAAACACTAATTAATATATAAATT
**
29655643 AAAAACACTAATTAAT-T-TAAATT
1 CTAAACACTAATTAATATATAAATT
*
29655666 CTAAACCCTAA
1 CTAAACACTAA
29655677 CTCGACCCCG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 14 0.52
24 1 0.04
25 12 0.44
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.36
Consensus pattern (25 bp):
CTAAACACTAATTAATATATAAATT
Found at i:29655830 original size:89 final size:88
Alignment explanation
Indices: 29655609--29655943 Score: 555
Period size: 89 Copynumber: 3.8 Consensus size: 88
29655599 AAACCCCTAC
* *
29655609 CCCTAACCCCTAAACATTATTTAATATATAAATT-AAAAACACTAATTAATTTAAATTCTAAACC
1 CCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACC
* * *
29655673 CTAACTCGACCCCGAACCCCTAC
66 CTAACTCGACCCCGAATCACTAA
29655696 CCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACC
1 CCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACC
* *
29655761 TTAACTCGACCCCAAATCACTAA
66 CTAACTCGACCCCGAATCACTAA
* **
29655784 TCCCTAACCCCTAAACATTATTTAAAATATAAATTAAAAAACACTAATTAATCTAAATTTTAAAC
1 -CCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAAC
29655849 CCTAACTCGACCCCGAATCACTAA
65 CCTAACTCGACCCCGAATCACTAA
29655873 CCCTTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAAC
1 CCC-TAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAAC
29655938 CCTAAC
65 CCTAAC
29655944 CCTAAATCCC
Statistics
Matches: 230, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
87 34 0.15
88 49 0.21
89 147 0.64
ACGTcount: A:0.44, C:0.26, G:0.01, T:0.28
Consensus pattern (88 bp):
CCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACC
CTAACTCGACCCCGAATCACTAA
Found at i:29655950 original size:20 final size:21
Alignment explanation
Indices: 29655925--29655963 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29655915 ACTAATTAAT
29655925 CTAAAT-CCTAAACCCTAACC
1 CTAAATCCCTAAACCCTAACC
*
29655945 CTAAATCCCTAACCCCTAA
1 CTAAATCCCTAAACCCTAA
29655964 ACATTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (21 bp):
CTAAATCCCTAAACCCTAACC
Found at i:29656008 original size:80 final size:77
Alignment explanation
Indices: 29655782--29656024 Score: 252
Period size: 89 Copynumber: 3.0 Consensus size: 77
29655772 CCAAATCACT
* ***
29655782 AATCCCTAACCCCTAAACATTATTTAAAATATAAATTAAAAAACACTAATTAATCTAAATTTTAA
1 AATCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAA
*
29655847 ACCCTAACTCGACCCCGA
66 ACCCT-A----A-CCCTA
29655865 ATCACTAACCCTTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAA
1 A--A-T--CCC-TAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAA
*
29655930 TCCTAAACCCTAACCCTA
60 CCCTAAACCCTAACCCTA
* * * *
29655948 AATCCCTAACCCCTAAACATTATTTAATATTATATAAATTAAAATATATTAATTAGTCTAAACCC
1 AATCCCTAACCCCTAAACATTATTT-A-A-TATATAAATTAAAAAACACTAATTAATCTAAACCC
*
29656013 TAAACTCTAACC
63 TAAACCCTAACC
29656025 TAACACCGAA
Statistics
Matches: 141, Mismatches: 10, Indels: 21
0.82 0.06 0.12
Matches are distributed among these distances:
77 19 0.13
78 4 0.03
79 1 0.01
80 42 0.30
81 1 0.01
83 6 0.04
84 1 0.01
85 1 0.01
86 1 0.01
88 4 0.03
89 61 0.43
ACGTcount: A:0.45, C:0.23, G:0.01, T:0.30
Consensus pattern (77 bp):
AATCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAA
ACCCTAACCCTA
Found at i:29656585 original size:41 final size:40
Alignment explanation
Indices: 29656525--29656802 Score: 351
Period size: 41 Copynumber: 6.8 Consensus size: 40
29656515 AAATGTTTTT
* * *
29656525 GCGGCGCTTCTTCACAAACGCCGCTAAAGGCCTCAGCATTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGGCC-GAGCATTA
* * *
29656566 GCGGCGCTTCTTCAAAAACGCCGCTAACGGCCCGAGCAGTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGG-CCGAGCATTA
29656607 GCGGCGCATT-TTCAAAAACGCCGCTAAAGGTCCGAGCATTA
1 GCGGCGC-TTATTCAAAAACGCCGCTAAAGG-CCGAGCATTA
* * *
29656648 CCGGCGCTTATGCAAAAACGCCGCTACAGGTCCGAGCATTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGG-CCGAGCATTA
*
29656689 GCGGCGCTTATGCAAAAACGCCGCTAAAGGTCCGAGCATTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGG-CCGAGCATTA
*** *
29656730 GCGGCGCTTATTCAAAATTTCCGCTAAAGACCTGAGCATTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGGCC-GAGCATTA
*
29656771 GCGGCGCTTTTTCAAAAACGCCGCTAAAGGCC
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGGCC
29656803 CCAAAAACTC
Statistics
Matches: 211, Mismatches: 22, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
40 4 0.02
41 203 0.96
42 4 0.02
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (40 bp):
GCGGCGCTTATTCAAAAACGCCGCTAAAGGCCGAGCATTA
Found at i:29656910 original size:39 final size:40
Alignment explanation
Indices: 29656856--29656974 Score: 143
Period size: 40 Copynumber: 3.0 Consensus size: 40
29656846 GGCGCTTTCC
*
29656856 AAAAAACGCCACTAATGCTT-ATTTTTAGCGGCGTTTTTT
1 AAAAAACGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTT
* * ** *
29656895 AAAAATCGCCGCTAATTCTTGACCTTTAGCGGCGTTTTTG
1 AAAAAACGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTT
* *
29656935 AAAAAGA-GCCGCTACTGCTTGATTTTTAGTGGCGTTTTTT
1 AAAAA-ACGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTT
29656975 GTCCAAATGC
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
39 17 0.26
40 48 0.74
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.38
Consensus pattern (40 bp):
AAAAAACGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTT
Found at i:29658875 original size:114 final size:112
Alignment explanation
Indices: 29658514--29658878 Score: 407
Period size: 113 Copynumber: 3.2 Consensus size: 112
29658504 CCTGAACAAC
* *
29658514 TAGTGGCGTTTCTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTA-TTGTAAGCGCCGC
1 TAGTGGCGTTTC-GATAAAACGCCGTAAAAGAACAT-ATTAGTGGCGTTTATTTGTAAGCGCCGC
* *
29658578 AAAATACCTTAACCAAAACGCAGCGTTTGG-TTCAATTGTATATTAGAAT
64 AAAATACCTTAACCAAAACGCAGCGTTTGGTTTCGA-GGTATATTAGAAT
* * ****
29658627 TAGTGGCGTTTTCGATAAAACGCCGCT-AAAGAATAGTATTAGCGGCGTTT-TACAAAAAGCGCC
1 TAGTGGCG-TTTCGATAAAACGCCG-TAAAAGAACA-TATTAGTGGCGTTTAT-TTGTAAGCGCC
* * * * * *
29658690 GC-AAATATCTTAACGAAAATGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
62 GCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTCGAGGTATATTAGAAT
* ** *
29658740 TAGTGGCATTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCGCCGC
1 TAGTGGCGTTTCGATA-AAACGCCGTAAAAGAACAT-ATTAGTGGCGTTTATTTGTAAGCGCCGC
* *
29658805 AAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAAAAT
64 AAAATACCTTAACCAAAACGCAGCGTTTGGTTTCGAGGTATATTAGAAT
29658854 TAGTGGCGTTTACGATAAAACGCCG
1 TAGTGGCGTTT-CGATAAAACGCCG
29658879 CAAATATCTT
Statistics
Matches: 202, Mismatches: 38, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
112 7 0.03
113 116 0.57
114 77 0.38
115 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (112 bp):
TAGTGGCGTTTCGATAAAACGCCGTAAAAGAACATATTAGTGGCGTTTATTTGTAAGCGCCGCAA
AATACCTTAACCAAAACGCAGCGTTTGGTTTCGAGGTATATTAGAAT
Found at i:29658906 original size:74 final size:75
Alignment explanation
Indices: 29658799--29658938 Score: 201
Period size: 74 Copynumber: 1.9 Consensus size: 75
29658789 TATTTGTAAG
* * *
29658799 CGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAAAATTAGTGGCGTT
1 CGCCGCAAAATACCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAAAATTAGTGGCGTT
29658864 TACGATAAAA
66 TACGATAAAA
* * ***
29658874 CGCCGC-AAATATCTTAACGAAAACGCACCGTTTGGTCTTGAGGTAGATTAGTGTTAGTGGCGTT
1 CGCCGCAAAATACCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAAAATTAGTGGCGTT
29658938 T
66 T
29658939 TTAAAAAAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
74 51 0.89
75 6 0.11
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (75 bp):
CGCCGCAAAATACCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAAAATTAGTGGCGTT
TACGATAAAA
Found at i:29658948 original size:74 final size:75
Alignment explanation
Indices: 29658799--29658957 Score: 194
Period size: 74 Copynumber: 2.1 Consensus size: 75
29658789 TATTTGTAAG
* * *
29658799 CGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAAAATTAGTGGCGTT
1 CGCCGCAAAATACCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAAAATTAGTGGCGTT
* *
29658864 TACGATAAAA
66 TACAAAAAAA
* * ***
29658874 CGCCGC-AAATATCTTAACGAAAACGCACCGTTTGGTCTTGAGGTAGATTAGTGTTAGTGGCGTT
1 CGCCGCAAAATACCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAAAATTAGTGGCGTT
**
29658938 TTTAAAAAAA
66 TACAAAAAAA
*
29658948 CGCCGTAAAA
1 CGCCGCAAAA
29658958 GAACATAATT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
74 61 0.87
75 9 0.13
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (75 bp):
CGCCGCAAAATACCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAAAATTAGTGGCGTT
TACAAAAAAA
Found at i:29658995 original size:188 final size:188
Alignment explanation
Indices: 29658664--29659022 Score: 580
Period size: 188 Copynumber: 1.9 Consensus size: 188
29658654 AAAGAATAGT
* *
29658664 ATTAGCGGCGTTTTACAAAAAGCGCCGCAAATATCTTAACGAAAATGCAGCGTTTGGTCTCGAGG
1 ATTAGCGGCGTTTTACAAAAAGCGCCGCAAATATCTTAACGAAAACGCACCGTTTGGTCTCGAGG
* *
29658729 TAGATTAGTATTAGTGGCATTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTT
66 TAGATTAGTATTAGTGGCATTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
*
29658794 GTAAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAAA
131 GTAAGCACCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAAA
* *
29658852 ATTAGTGGCG-TTTACGATAAAA-CGCCGCAAATATCTTAACGAAAACGCACCGTTTGGTCTTGA
1 ATTAGCGGCGTTTTAC-A-AAAAGCGCCGCAAATATCTTAACGAAAACGCACCGTTTGGTCTCGA
* *
29658915 GGTAGATTAGTGTTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTAC
64 GGTAGATTAGTATTAGTGGCATTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTA-
*
29658980 TTT-TAAGCACCGCAAAATACCTTAACCAAAACGTAGCGTTTGG
128 TTTGTAAGCACCGCAAAATACCTTAACCAAAACGCAGCGTTTGG
29659023 ATCAATTGTA
Statistics
Matches: 158, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
187 5 0.03
188 146 0.92
189 7 0.04
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (188 bp):
ATTAGCGGCGTTTTACAAAAAGCGCCGCAAATATCTTAACGAAAACGCACCGTTTGGTCTCGAGG
TAGATTAGTATTAGTGGCATTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
GTAAGCACCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAAA
Found at i:29659036 original size:188 final size:187
Alignment explanation
Indices: 29658664--29659067 Score: 571
Period size: 188 Copynumber: 2.1 Consensus size: 187
29658654 AAAGAATAGT
* * *
29658664 ATTAGCGGCGTTTTACA-AAAAGCGCCGCAAATATCTTAACGAAAATGCAGCGTTTGGTCTCGAG
1 ATTAGTGGCG-TTTACATAAAA-CGCCGCAAATATCTTAACGAAAACGCACCGTTTGGTCTCGAG
* *
29658728 GTAGATTAGTATTAGTGGCATTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATT
64 GTAGATTAGTATTAGTGGCATTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATT
* * **
29658793 TGTAAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAAA
129 TGTAAGCACCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTATCAAGGTATATTAAA
*
29658852 ATTAGTGGCGTTTACGATAAAACGCCGCAAATATCTTAACGAAAACGCACCGTTTGGTCTTGAGG
1 ATTAGTGGCGTTTAC-ATAAAACGCCGCAAATATCTTAACGAAAACGCACCGTTTGGTCTCGAGG
* *
29658917 TAGATTAGTGTTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTACTT
65 TAGATTAGTATTAGTGGCATTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTA-TT
* * *
29658982 T-TAAGCACCGCAAAATACCTTAACCAAAACGTAGCGTTTGG-ATCAATTGTATATTAGA
129 TGTAAGCACCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTATCAA-GGTATATTAAA
* * *
29659040 ATTCGTGGCGTTTTCTATAAAACACCGC
1 ATTAGTGGCGTTTAC-ATAAAACGCCGC
29659068 TAAAGAATAG
Statistics
Matches: 193, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
187 7 0.04
188 179 0.93
189 7 0.04
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (187 bp):
ATTAGTGGCGTTTACATAAAACGCCGCAAATATCTTAACGAAAACGCACCGTTTGGTCTCGAGGT
AGATTAGTATTAGTGGCATTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTG
TAAGCACCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTATCAAGGTATATTAAA
Found at i:29659317 original size:208 final size:208
Alignment explanation
Indices: 29658913--29659297 Score: 569
Period size: 208 Copynumber: 1.9 Consensus size: 208
29658903 GTTTGGTCTT
* *
29658913 GAGGTAGATTAGTGTTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTT
1 GAGGTAGATTAGTATTAGTGGCGTTTTTAAAAAAACGCAGTAAAAGAACATAATTAGTGGCGTTT
* * *
29658978 ACTTTTAAGCACCGCAAAATACCTTAACCAAAACGTAGCGTTTGGATCAATTGTATATTAGAATT
66 ACTTTTAAGCACCGCAAAATACCTTAACCAAAACGCAGAGTTTGGATCAATGGTATATTAGAATT
* * *
29659043 CGTGGCGTTTTCTATAAAACACCGCTAAAGAATAGTATTAGCGGCGTATCACAAGAAGCGCCGCA
131 AGTGGCGTTTTCGATAAAACACAGCTAAAGAATAGTATTAGCGGCGTATCACAAGAAGCGCCGCA
29659108 AATATCTTAACCA
196 AATATCTTAACCA
* *
29659121 GAGGTAGATTAGTATTAGTGGCGTTTTTAAACAAACGCAGTAAAAGAACATCATTAGTGGCGTTT
1 GAGGTAGATTAGTATTAGTGGCGTTTTTAAAAAAACGCAGTAAAAGAACATAATTAGTGGCGTTT
* * **
29659186 A-TTTGTAAGCGCCGCAAAATACCTTAACCAAAACGCAGAGTTTGGTTTTGA-GGTATATTAGAA
66 ACTTT-TAAGCACCGCAAAATACCTTAACCAAAACGCAGAGTTTGG-ATCAATGGTATATTAGAA
* * *
29659249 TTAGTGGCGTTTAT-GGTGAAACGCAGCTAAAGAATAGTATTAGCGGCGT
129 TTAGTGGCGTTT-TCGATAAAACACAGCTAAAGAATAGTATTAGCGGCGT
29659298 TTTTGGGAAA
Statistics
Matches: 157, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
207 3 0.02
208 151 0.96
209 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (208 bp):
GAGGTAGATTAGTATTAGTGGCGTTTTTAAAAAAACGCAGTAAAAGAACATAATTAGTGGCGTTT
ACTTTTAAGCACCGCAAAATACCTTAACCAAAACGCAGAGTTTGGATCAATGGTATATTAGAATT
AGTGGCGTTTTCGATAAAACACAGCTAAAGAATAGTATTAGCGGCGTATCACAAGAAGCGCCGCA
AATATCTTAACCA
Found at i:29659662 original size:14 final size:15
Alignment explanation
Indices: 29659629--29659662 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
29659619 TAAGTTTTAT
29659629 AGATTATGGAATTAG
1 AGATTATGGAATTAG
29659644 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
*
29659658 GGATT
1 AGATT
29659663 CTGGTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:29659709 original size:7 final size:7
Alignment explanation
Indices: 29659699--29659742 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
29659689 GGTTTATGGA
29659699 TTAGGGG
1 TTAGGGG
29659706 TTAGGGG
1 TTAGGGG
*
29659713 TTATGGG
1 TTAGGGG
29659720 TTAGGGG
1 TTAGGGG
*
29659727 TTA--AG
1 TTAGGGG
29659732 TTAGGGG
1 TTAGGGG
29659739 TTAG
1 TTAG
29659743 ATGTTAAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 4 0.13
7 27 0.87
ACGTcount: A:0.18, C:0.00, G:0.48, T:0.34
Consensus pattern (7 bp):
TTAGGGG
Found at i:29659748 original size:14 final size:13
Alignment explanation
Indices: 29659705--29659748 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
29659695 TGGATTAGGG
*
29659705 GTTAGGGGTTATGG
1 GTTAGGGGTTA-GA
29659719 GTTAGGGGTTA-A
1 GTTAGGGGTTAGA
29659731 GTTAGGGGTTAGA
1 GTTAGGGGTTAGA
29659744 TGTTA
1 -GTTA
29659749 AGAGTTAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 11 0.41
13 1 0.04
14 15 0.56
ACGTcount: A:0.20, C:0.00, G:0.43, T:0.36
Consensus pattern (13 bp):
GTTAGGGGTTAGA
Found at i:29659748 original size:19 final size:19
Alignment explanation
Indices: 29659712--29659750 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
29659702 GGGGTTAGGG
* *
29659712 GTTATGGGTTAGGGGTTAA
1 GTTAGGGGTTAGAGGTTAA
*
29659731 GTTAGGGGTTAGATGTTAA
1 GTTAGGGGTTAGAGGTTAA
29659750 G
1 G
29659751 AGTTAGGGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.41, T:0.36
Consensus pattern (19 bp):
GTTAGGGGTTAGAGGTTAA
Found at i:29659854 original size:7 final size:7
Alignment explanation
Indices: 29659842--29659924 Score: 71
Period size: 7 Copynumber: 11.9 Consensus size: 7
29659832 TAAATAAGGT
29659842 TTAGGGG
1 TTAGGGG
29659849 TTAGGGG
1 TTAGGGG
*
29659856 TTAGAGG
1 TTAGGGG
* *
29659863 TCATGGG
1 TTAGGGG
*
29659870 TTAAGGGT
1 TT-AGGGG
* *
29659878 TTAGAGT
1 TTAGGGG
29659885 TTA-GGG
1 TTAGGGG
*
29659891 TTAAGGGT
1 TT-AGGGG
29659899 TTA-GGG
1 TTAGGGG
29659905 TTAGGGG
1 TTAGGGG
29659912 TTAGGGG
1 TTAGGGG
29659919 TTAGGG
1 TTAGGG
29659925 ATTGGGTTAT
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
6 8 0.13
7 43 0.72
8 9 0.15
ACGTcount: A:0.19, C:0.01, G:0.47, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:29659870 original size:21 final size:21
Alignment explanation
Indices: 29659846--29659922 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
29659836 TAAGGTTTAG
*
29659846 GGGTT-AGGGGTTAGAGGTCA
1 GGGTTAAGGGGTTAGAGGTTA
* *
29659866 TGGGTTAAGGGTTTAGAGTTTA
1 -GGGTTAAGGGGTTAGAGGTTA
*
29659888 GGGTTAAGGGTTTAG-GGTTA
1 GGGTTAAGGGGTTAGAGGTTA
29659908 GGGGTT-AGGGGTTAG
1 -GGGTTAAGGGGTTAG
29659923 GGATTGGGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.24
21 25 0.51
22 12 0.24
ACGTcount: A:0.19, C:0.01, G:0.47, T:0.32
Consensus pattern (21 bp):
GGGTTAAGGGGTTAGAGGTTA
Found at i:29660021 original size:89 final size:88
Alignment explanation
Indices: 29659897--29660072 Score: 237
Period size: 89 Copynumber: 2.0 Consensus size: 88
29659887 AGGGTTAAGG
* * * * * *
29659897 GTTTAGGGTTAGGGGTTAGGGGTTAGGGATTGGGTTATGGTTTAAGGTTTAGATTAATTAGTATT
1 GTTTAGGGTTAGGGGTTAGGAGTTAGAGATTGGGTTAGGGATTAAGATTTAGATTAATTAGTACT
* *
29659962 TTTTAATTTATATATTAAATAAA
66 TTTTAATTAACATATTAAATAAA
* *
29659985 GTTTAGGGGTTAGGGGTTATGGATTTAGAG-TTGGGTTAGGGATTAAGATTTGGATTAATTAGTA
1 GTTTA-GGGTTAGGGGTTA-GGAGTTAGAGATTGGGTTAGGGATTAAGATTTAGATTAATTAGTA
29660049 CTTTTTAATTAACATATTAAATAA
64 CTTTTTAATTAACATATTAAATAA
29660073 GTTCTTTATA
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
88 5 0.07
89 64 0.84
90 7 0.09
ACGTcount: A:0.30, C:0.01, G:0.27, T:0.43
Consensus pattern (88 bp):
GTTTAGGGTTAGGGGTTAGGAGTTAGAGATTGGGTTAGGGATTAAGATTTAGATTAATTAGTACT
TTTTAATTAACATATTAAATAAA
Found at i:29660037 original size:19 final size:19
Alignment explanation
Indices: 29659998--29660037 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29659988 TAGGGGTTAG
* *
29659998 GGGTTATGGATTTAGAGTT
1 GGGTTAGGGATTAAGAGTT
*
29660017 GGGTTAGGGATTAAGATTT
1 GGGTTAGGGATTAAGAGTT
29660036 GG
1 GG
29660038 ATTAATTAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.38
Consensus pattern (19 bp):
GGGTTAGGGATTAAGAGTT
Found at i:29660174 original size:21 final size:21
Alignment explanation
Indices: 29660121--29660174 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
29660111 TAAAGATTAT
29660121 TAATTTAAAA-TTGATATGCAA
1 TAATTTAAAATTTGATAT-CAA
*
29660142 T-ATATAATAATTTGAATAT-AA
1 TAATTTAA-AATTTG-ATATCAA
29660163 TAATTTAAAATT
1 TAATTTAAAATT
29660175 GTAAAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
20 5 0.19
21 10 0.37
22 8 0.30
23 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (21 bp):
TAATTTAAAATTTGATATCAA
Found at i:29660209 original size:20 final size:20
Alignment explanation
Indices: 29660169--29660212 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
29660159 ATAATAATTT
**
29660169 AAAATTGTAAAAATTGTAAA
1 AAAATTGTAAAAATTACAAA
*
29660189 AAAATTGTCAAAATTACAAA
1 AAAATTGTAAAAATTACAAA
29660209 AAAA
1 AAAA
29660213 AATGAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.25
Consensus pattern (20 bp):
AAAATTGTAAAAATTACAAA
Found at i:29660220 original size:19 final size:18
Alignment explanation
Indices: 29660198--29660246 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
29660188 AAAAATTGTC
*
29660198 AAAATTACAAAAAAAAATG
1 AAAATTA-AAAAAAAAAAG
*
29660217 AAAATAAAAAATAAAAAAG
1 AAAATTAAAAA-AAAAAAG
29660236 -AAATTAAAAAA
1 AAAATTAAAAAA
29660247 CTAAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 13 0.50
19 12 0.46
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (18 bp):
AAAATTAAAAAAAAAAAG
Found at i:29660245 original size:13 final size:12
Alignment explanation
Indices: 29660198--29660246 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
29660188 AAAAATTGTC
29660198 AAAATTACAAAAA
1 AAAATTA-AAAAA
*
29660211 AAAATGAAAATAA
1 AAAATTAAAA-AA
29660224 AAAA-TAAAAAA
1 AAAATTAAAAAA
*
29660235 GAAATTAAAAAA
1 AAAATTAAAAAA
29660247 CTAAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 5 0.16
12 14 0.45
13 12 0.39
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (12 bp):
AAAATTAAAAAA
Found at i:29660252 original size:19 final size:20
Alignment explanation
Indices: 29660209--29660252 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
29660199 AAATTACAAA
29660209 AAAAAATGAAAATAAAAAAT
1 AAAAAATGAAAATAAAAAAT
*
29660229 AAAAAA-GAAATTAAAAAACT
1 AAAAAATGAAAATAAAAAA-T
29660249 AAAA
1 AAAA
29660253 TTTTTATTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.14
Consensus pattern (20 bp):
AAAAAATGAAAATAAAAAAT
Found at i:29661088 original size:198 final size:198
Alignment explanation
Indices: 29660750--29661175 Score: 676
Period size: 198 Copynumber: 2.2 Consensus size: 198
29660740 GCCTAATATT
* * * * *
29660750 TAGTGGCGCTTATGTATAAATGCCACAATTTACAGAAATTGTTTAGGAAAACGGCTCCGTTTTCT
1 TAGTGGCGCTTGTATATAAACGCCGCAAATTACAGAAATTGTTTAGGAAAACGGCTCCGTTTTCT
*
29660815 TATTTAACTTTAGTGGCGCTTTTAGTAAACGCCGCAAAATGGTTTTAATTTTTATGGAGACGATG
66 TATTTAACTTTAGTGGCGCTTTTAGTAAACGCCGAAAAATGGTTTTAATTTTTATGGAGACGATG
* * * * * *
29660880 CCGTTTTCTCTAAAATGCCATGAGTTTTAGTTAACTAATCTGGAAACGATAGCGTTTGATCATAT
131 CCGTTTTCTCTAAAACGCAATGACTTTGAGTTAACTAATCGGGAAACGACAGCGTTTGATCATAT
29660945 TAC
196 TAC
* *
29660948 TAGTGGCGCTGGTATATAAACGCCGCAAATTACAGAAATTGTTTAGGAAAACGGCTTCGTTTTCT
1 TAGTGGCGCTTGTATATAAACGCCGCAAATTACAGAAATTGTTTAGGAAAACGGCTCCGTTTTCT
29661013 TATTT-ACTTTTAGTGGCGCTTTTAGTAAACGCCGTAAAAAT-GTTTTAATTTTTATGGAGACGA
66 TATTTAAC-TTTAGTGGCGCTTTTAGTAAACGCCG-AAAAATGGTTTTAATTTTTATGGAGACGA
* *
29661076 TGCCGTTTTCTCTAAAACGTAATGACTTTGAGTTAACTGATCGGGAAACGACAGCGTTTGATCAT
129 TGCCGTTTTCTCTAAAACGCAATGACTTTGAGTTAACTAATCGGGAAACGACAGCGTTTGATCAT
29661141 ATTAC
194 ATTAC
29661146 TAGTGGCGCTTGTATATAAACGCCGCAAAT
1 TAGTGGCGCTTGTATATAAACGCCGCAAAT
29661176 GGGTTAATTA
Statistics
Matches: 209, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
197 2 0.01
198 202 0.97
199 5 0.02
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (198 bp):
TAGTGGCGCTTGTATATAAACGCCGCAAATTACAGAAATTGTTTAGGAAAACGGCTCCGTTTTCT
TATTTAACTTTAGTGGCGCTTTTAGTAAACGCCGAAAAATGGTTTTAATTTTTATGGAGACGATG
CCGTTTTCTCTAAAACGCAATGACTTTGAGTTAACTAATCGGGAAACGACAGCGTTTGATCATAT
TAC
Found at i:29662530 original size:18 final size:19
Alignment explanation
Indices: 29662507--29662550 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
29662497 TAGAAATTTC
*
29662507 TGTTTCTCTAGCA-TGTTA
1 TGTTTCTCTACCATTGTTA
* *
29662525 TGTTTCTGTACCATTTTTA
1 TGTTTCTCTACCATTGTTA
29662544 TGTTTCT
1 TGTTTCT
29662551 TTATTTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.57
Consensus pattern (19 bp):
TGTTTCTCTACCATTGTTA
Found at i:29662567 original size:7 final size:7
Alignment explanation
Indices: 29662555--29662641 Score: 111
Period size: 7 Copynumber: 12.3 Consensus size: 7
29662545 GTTTCTTTAT
*
29662555 TTTTCTA
1 TTTTCTG
29662562 TTTTCTG
1 TTTTCTG
29662569 TTTTCTG
1 TTTTCTG
*
29662576 TTTTCTA
1 TTTTCTG
29662583 TTTTCTG
1 TTTTCTG
29662590 TTTTCTG
1 TTTTCTG
*
29662597 TTTTCTA
1 TTTTCTG
*
29662604 TTTTCTA
1 TTTTCTG
*
29662611 TTTTTTG
1 TTTTCTG
29662618 TTTTCTG
1 TTTTCTG
*
29662625 TTTTGCTA
1 TTTT-CTG
29662633 TTTTCTG
1 TTTTCTG
29662640 TT
1 TT
29662642 GAATGAAGTG
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
7 64 0.91
8 6 0.09
ACGTcount: A:0.06, C:0.13, G:0.09, T:0.72
Consensus pattern (7 bp):
TTTTCTG
Found at i:29662581 original size:21 final size:21
Alignment explanation
Indices: 29662555--29662641 Score: 129
Period size: 21 Copynumber: 4.1 Consensus size: 21
29662545 GTTTCTTTAT
*
29662555 TTTTCTATTTTCTGTTTTCTG
1 TTTTCTATTTTCTATTTTCTG
*
29662576 TTTTCTATTTTCTGTTTTCTG
1 TTTTCTATTTTCTATTTTCTG
*
29662597 TTTTCTATTTTCTATTTTTTG
1 TTTTCTATTTTCTATTTTCTG
*
29662618 TTTTCTGTTTTGCTATTTTCTG
1 TTTTCTATTTT-CTATTTTCTG
29662640 TT
1 TT
29662642 GAATGAAGTG
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
21 50 0.82
22 11 0.18
ACGTcount: A:0.06, C:0.13, G:0.09, T:0.72
Consensus pattern (21 bp):
TTTTCTATTTTCTATTTTCTG
Found at i:29663368 original size:13 final size:13
Alignment explanation
Indices: 29663350--29663401 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
29663340 TTTTACTCTT
*
29663350 AATATATTACTTG
1 AATATATTACTTA
29663363 AATATATTACTTA
1 AATATATTACTTA
29663376 AATA-AGTTACTTA
1 AATATA-TTACTTA
*
29663389 AATACATTACTTA
1 AATATATTACTTA
29663402 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
12 1 0.03
13 34 0.94
14 1 0.03
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (13 bp):
AATATATTACTTA
Found at i:29663426 original size:53 final size:53
Alignment explanation
Indices: 29663369--29663504 Score: 211
Period size: 53 Copynumber: 2.6 Consensus size: 53
29663359 CTTGAATATA
*
29663369 TTACTTAAATAAGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT
1 TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT
* * *
29663422 TTACTTAAATATGTTA-TTCAGATACATTAATTACTAAAATTTGGTTAAATTTT
1 TTACTTAAATATGTTACTT-AAATACATTACTTACTAAAATTTCGTTAAATTTT
*
29663475 TTACTTAAGTATGTTACTTAAATACATTAC
1 TTACTTAAATATGTTACTTAAATACATTAC
29663505 CCGCTATAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
52 2 0.03
53 70 0.95
54 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (53 bp):
TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT
Found at i:29663673 original size:9 final size:9
Alignment explanation
Indices: 29663649--29663899 Score: 166
Period size: 9 Copynumber: 28.8 Consensus size: 9
29663639 TATGTACAAG
29663649 AACTTACAT
1 AACTTACAT
* *
29663658 AATTTACAC
1 AACTTACAT
29663667 AACTTACAT
1 AACTTACAT
*
29663676 AACCTACAT
1 AACTTACAT
29663685 AACTTACAT
1 AACTTACAT
29663694 AA--TACA-
1 AACTTACAT
29663700 AAGCTTACAT
1 AA-CTTACAT
* *
29663710 AACTGAAAT
1 AACTTACAT
* *
29663719 AGCTTACAC
1 AACTTACAT
29663728 AACTTACAT
1 AACTTACAT
29663737 AACTTACAT
1 AACTTACAT
*
29663746 AACTTACAG
1 AACTTACAT
* *
29663755 AAGTTATAT
1 AACTTACAT
*
29663764 AATACATA-AT
1 -A-ACTTACAT
29663774 AACTTAC--
1 AACTTACAT
29663781 AACTTACAT
1 AACTTACAT
*
29663790 AACATACAT
1 AACTTACAT
* **
29663799 TACTTTGAT
1 AACTTACAT
29663808 AACTTACAT
1 AACTTACAT
*
29663817 AAGTTACAT
1 AACTTACAT
*
29663826 AA--TACAC
1 AACTTACAT
29663833 AACTTACAT
1 AACTTACAT
** *
29663842 AGTTTACTT
1 AACTTACAT
*
29663851 AA--TACAA
1 AACTTACAT
*
29663858 AACTTAAAT
1 AACTTACAT
29663867 AACTT--AT
1 AACTTACAT
*
29663874 ACACGTACAT
1 A-ACTTACAT
29663884 AACTTACAT
1 AACTTACAT
*
29663893 AATTTAC
1 AACTTAC
29663900 TTAATACATA
Statistics
Matches: 183, Mismatches: 43, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
6 2 0.01
7 25 0.14
8 7 0.04
9 138 0.75
10 8 0.04
11 3 0.02
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:29663842 original size:25 final size:25
Alignment explanation
Indices: 29663808--29663907 Score: 87
Period size: 25 Copynumber: 4.0 Consensus size: 25
29663798 TTACTTTGAT
* * *
29663808 AACTTACATAAGTTACATAATACAC
1 AACTTACATAACTTACTTAATACAA
**
29663833 AACTTACATAGTTTACTTAATACAA
1 AACTTACATAACTTACTTAATACAA
* *
29663858 AACTTAAATAACTTA--TACACGTACAT
1 AACTTACATAACTTACTTA-A--TACAA
*
29663884 AACTTACATAATTTACTTAATACA
1 AACTTACATAACTTACTTAATACA
29663908 TAAATATATA
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
23 2 0.03
24 1 0.02
25 37 0.62
26 17 0.28
27 1 0.02
28 2 0.03
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.33
Consensus pattern (25 bp):
AACTTACATAACTTACTTAATACAA
Found at i:29666568 original size:43 final size:41
Alignment explanation
Indices: 29666515--29666638 Score: 133
Period size: 42 Copynumber: 2.9 Consensus size: 41
29666505 ATTTCTGAAC
* *
29666515 AAGCACCGCTATAGAACATTA-CTTTTAAAGGCGTTTTCTTCCA
1 AAGCGCCGCTA-AGAACATGATC-TTTAAAGGCGTTTT-TTCCA
** *
29666558 AAGCGCCGCTAAGTAACATGATCTTTAGCGGCGTTTTTTCCT
1 AAGCGCCGCTAAG-AACATGATCTTTAAAGGCGTTTTTTCCA
**
29666600 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
1 AAGCGCCGCT-AAGAACATGATCTTTAAAGGCGTTTTTT
29666639 TCTGTAAGCG
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
42 41 0.56
43 31 0.42
44 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (41 bp):
AAGCGCCGCTAAGAACATGATCTTTAAAGGCGTTTTTTCCA
Found at i:29666618 original size:42 final size:43
Alignment explanation
Indices: 29666544--29666658 Score: 162
Period size: 42 Copynumber: 2.7 Consensus size: 43
29666534 TACTTTTAAA
*
29666544 GGCGTTTTCTTCCAAAGCGCCGCT-AAGTAACATGATCTTTAGC
1 GGCGTTTT-TTCCTAAGCGCCGCTAAAGTAACATGATCTTTAGC
29666587 GGCGTTTTTTCCTAAGCGCCGCTAAAG-AACATGATCTTTAGC
1 GGCGTTTTTTCCTAAGCGCCGCTAAAGTAACATGATCTTTAGC
* *
29666629 GGCGTTTTTTTCTGTAAGCGCCGCAAAAGT
1 GGCG-TTTTTTC-CTAAGCGCCGCTAAAGT
29666659 TAGCGACGTT
Statistics
Matches: 65, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
42 33 0.51
43 18 0.28
44 14 0.22
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (43 bp):
GGCGTTTTTTCCTAAGCGCCGCTAAAGTAACATGATCTTTAGC
Found at i:29666912 original size:182 final size:182
Alignment explanation
Indices: 29666605--29666968 Score: 683
Period size: 182 Copynumber: 2.0 Consensus size: 182
29666595 TTCCTAAGCG
* *
29666605 CCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTGTAAGCGCCGCAAAAGTTAGCGACGTTG
1 CCGCTAAAGAACATGATCTTTAGCGGCATTTTTTCCTGTAAGCGCCGCAAAAGTTAGCGACGTTG
29666670 TTGTTAACGGCATTTTTTGTGGCGCTTCTTCAAGCGCCGGAAATGGATTTAGTGGCGTTAAAAAG
66 TTGTTAACGGCATTTTTTGTGGCGCTTCTTCAAGCGCCGGAAATGGATTTAGTGGCGTTAAAAAG
29666735 CGCCGCTAAAGGCCTAAAAAACGCCGCTAAAAACCTGTTCTGGTGTAGTGTT
131 CGCCGCTAAAGGCCTAAAAAACGCCGCTAAAAACCTGTTCTGGTGTAGTGTT
* *
29666787 CCGCTAAAGAACATGATCTTTTGCGGTATTTTTTCCTGTAAGCGCCGCAAAAGTTAGCGACGTTG
1 CCGCTAAAGAACATGATCTTTAGCGGCATTTTTTCCTGTAAGCGCCGCAAAAGTTAGCGACGTTG
*
29666852 TTGTTAGCGGCATTTTTTGTGGCGCTTCTTCAAGCGCCGGAAATGGATTTAGTGGCGTTAAAAAG
66 TTGTTAACGGCATTTTTTGTGGCGCTTCTTCAAGCGCCGGAAATGGATTTAGTGGCGTTAAAAAG
29666917 CGCCGCTAAAGGCCTAAAAAACGCCGCTAAAAACCTGTTCTGGTGTAGTGTT
131 CGCCGCTAAAGGCCTAAAAAACGCCGCTAAAAACCTGTTCTGGTGTAGTGTT
29666969 TTTACGGGAA
Statistics
Matches: 177, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
182 177 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (182 bp):
CCGCTAAAGAACATGATCTTTAGCGGCATTTTTTCCTGTAAGCGCCGCAAAAGTTAGCGACGTTG
TTGTTAACGGCATTTTTTGTGGCGCTTCTTCAAGCGCCGGAAATGGATTTAGTGGCGTTAAAAAG
CGCCGCTAAAGGCCTAAAAAACGCCGCTAAAAACCTGTTCTGGTGTAGTGTT
Found at i:29669954 original size:68 final size:64
Alignment explanation
Indices: 29669830--29669959 Score: 163
Period size: 68 Copynumber: 2.0 Consensus size: 64
29669820 TGATTAAACT
* * *
29669830 TAATCATTTTAATATTAAAATAATATAATGTTAGATAAACATTAAATTAAATTTAATATTAAGA
1 TAATCACTTTAATATTAAAATAAAATAATGTTAGATAAACATTAAATTAAAATTAATATTAAGA
* *
29669894 TAATCACTTTAATATTAATTTAATAAAATACTTTTAAGATAAGA-ATTAAATTAAAATTAATATT
1 TAATCACTTTAATATTAA---AATAAAATAATGTT-AGATAA-ACATTAAATTAAAATTAATATT
29669958 AA
61 AA
29669960 AATATTAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
64 17 0.30
67 11 0.20
68 27 0.48
69 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (64 bp):
TAATCACTTTAATATTAAAATAAAATAATGTTAGATAAACATTAAATTAAAATTAATATTAAGA
Found at i:29679482 original size:44 final size:44
Alignment explanation
Indices: 29679419--29679624 Score: 234
Period size: 40 Copynumber: 4.9 Consensus size: 44
29679409 NNNNNNNNNN
* *
29679419 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTATGT-GA
*
29679463 TCTGCTCCACTACTGCTTAGGGAGATAAGA-C---TTGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTATGTGA
* * * *
29679503 TCTGCTCCACTACTGCTTAGAGACATAAGATCTGGTTTCTTTCG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTATGT-GA
*
29679547 TCTGCTCCACTACTGCTTAGGGAGATAAGA-C---TTGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTATGTGA
* *
29679587 TCTGCTCCACTACTACCTAGGGAGATAAGATCTGGTTT
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTT
29679625 TAATCCTTTT
Statistics
Matches: 135, Mismatches: 16, Indels: 22
0.78 0.09 0.13
Matches are distributed among these distances:
39 2 0.01
40 64 0.47
41 2 0.01
43 2 0.01
44 64 0.47
45 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (44 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTATGTGA
Found at i:29679560 original size:84 final size:84
Alignment explanation
Indices: 29679419--29679624 Score: 376
Period size: 84 Copynumber: 2.5 Consensus size: 84
29679409 NNNNNNNNNN
29679419 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGG
29679484 GAGATAAGACTTGATGTGA
66 GAGATAAGACTTGATGTGA
* *
29679503 TCTGCTCCACTACTGCTTAGAGACATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGG
29679568 GAGATAAGACTTGATGTGA
66 GAGATAAGACTTGATGTGA
* *
29679587 TCTGCTCCACTACTACCTAGGGAGATAAGATCTGGTTT
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTT
29679625 TAATCCTTTT
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 116 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (84 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGG
GAGATAAGACTTGATGTGA
Found at i:29679888 original size:44 final size:44
Alignment explanation
Indices: 29679826--29679964 Score: 147
Period size: 44 Copynumber: 3.2 Consensus size: 44
29679816 TCAGAGAGAT
* *
29679826 AAGATCTGTTTTCTTCGATCTACTTCGCCACCAATAT-GAGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTC-CCACCAATATAG-GAAGAC
* * *
29679871 AAGATCTGC-ATCTTCGATCCACTTCCTACCAATATAGGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTCCCACCAATATAGGAAGAC
* * * * * *
29679914 AGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCCCACCAATATAGGAAGAC
29679958 AAGATCT
1 AAGATCT
29679965 NNNNNNNNNN
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
43 21 0.28
44 47 0.62
45 8 0.11
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (44 bp):
AAGATCTGCTATCTTCGATCTACTTCCCACCAATATAGGAAGAC
Found at i:29680128 original size:43 final size:43
Alignment explanation
Indices: 29680067--29680493 Score: 452
Period size: 43 Copynumber: 9.8 Consensus size: 43
29680057 NNNNNNNNTT
29680067 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCCGCA
1 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCCGCA
29680110 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCCGCA
1 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCCGCA
* *
29680153 TCTTCGATCCACTTCCTACCAATATAGGAAGATAGGA-CCTGCTA
1 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCC-GC-A
* * * * * *
29680197 TCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCAGCTT
1 TCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGATCCGC-A
* * * *
29680241 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCCGCA
1 TCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGATCCGCA
*
29680285 TCTTCGATCCACTTCCTACCAATATAGGAAGACAGGA-CCTGCTA
1 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCC-GC-A
* * * * *
29680329 TCTTCGATCTACTT-C-ACGCTAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCCACTTCCTAC-C-AATATAGGAAGACAAGATCCGC-A
* * * * * *
29680373 TCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCA
1 TCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGATCCGCA
* * * *
29680417 TCTTTGATCCACTTCCTACCAATATAGGAATAC-AGAACTTGCA
1 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATC-CGCA
29680460 TCTTCGATCCACTTCCTACCAATATAGGAAGACA
1 TCTTCGATCCACTTCCTACCAATATAGGAAGACA
29680494 GGACCTGCTA
Statistics
Matches: 324, Mismatches: 45, Indels: 29
0.81 0.11 0.07
Matches are distributed among these distances:
42 10 0.03
43 151 0.47
44 119 0.37
45 40 0.12
46 2 0.01
47 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (43 bp):
TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCCGCA
Found at i:29680302 original size:132 final size:132
Alignment explanation
Indices: 29680067--29680518 Score: 612
Period size: 132 Copynumber: 3.4 Consensus size: 132
29680057 NNNNNNNNTT
* * * * *
29680067 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCCGC-ATCTTCGATCCACTTC-CTACC
1 TCTTCGATCCACTTCCTACCAATACAGGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
* * *
29680130 AATATAGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGACCTGC
66 AGTATGGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGC
29680195 TA
131 TA
* * * *
29680197 TCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCAGCTTTCTTCGATCTACTTCGCCAC
1 TCTTCGATCCACTTC-CTACCAATACAGGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCAC
29680261 CAGTATGGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTG
65 CAGTATGGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTG
29680326 CTA
130 CTA
* * *
29680329 TCTTCGATCTACTT-C-ACGCTAATACATGAAGACAAGATCTGCTTTCTTCAATCTACTTCGCCA
1 TCTTCGATCCACTTCCTAC-C-AATACAGGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCA
* * * * *
29680392 CCAGTATGGGAAGACAAGATCTGCATCTTTGATCCACTTCCTACCAATATAGGAATACAGAACTT
64 CCAGTATGGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCT
29680457 GC-A
129 GCTA
* * *
29680460 TCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATT-TTCGATCTACTTC
1 TCTTCGATCCACTTCCTACCAATACAGGAAGACAAGATCTGCT-TTCTTCGATCTACTTC
29680519 ACGCTAATAC
Statistics
Matches: 289, Mismatches: 25, Indels: 15
0.88 0.08 0.05
Matches are distributed among these distances:
130 37 0.13
131 61 0.21
132 189 0.65
133 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (132 bp):
TCTTCGATCCACTTCCTACCAATACAGGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
AGTATGGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGC
TA
Found at i:29680463 original size:175 final size:175
Alignment explanation
Indices: 29680067--29680552 Score: 642
Period size: 175 Copynumber: 2.8 Consensus size: 175
29680057 NNNNNNNNTT
29680067 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACCAA
1 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACCAA
* * * * * * *
29680132 TATAGGAAGACAAGATCC-GC-ATCTTCGATCCACTTCCTAC-C-AATATAGGAAGATAGGACCT
66 TATAGGAAGACAGGA-CCTGCTATCTTCGATCTACTT-C-ACGCTAATACATGAAGACAAGATCT
* * * * *
29680193 GCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCAGCTT
128 GCTTTCTTCAATCTACTTCACACCAATACAGGAAGACAAGATCAGCTA
* * * *
29680241 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACCA
1 TCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACCA
29680306 ATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCTAATACATGAAGACAAGATCTGC
65 ATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCTAATACATGAAGACAAGATCTGC
* * ** *
29680371 TTTCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC-A
130 TTTCTTCAATCTACTTC-ACACCAATACAGGAAGACAAGATCAGCTA
* * * *
29680417 TCTTTGATCCACTTCCTACCAATATAGGAATAC-AGAACTTGCATCTTCGATCCACTTCCTACCA
1 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATC-CGCATCTTCGATCCACTTCCTACCA
*
29680481 ATATAGGAAGACAGGACCTGCTATTTTCGATCTACTTCACGCTAATACATGAAGACAAGATCTGC
65 ATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCTAATACATGAAGACAAGATCTGC
29680546 TTTCTTC
130 TTTCTTC
29680553 GACCAGCTCC
Statistics
Matches: 275, Mismatches: 30, Indels: 13
0.86 0.09 0.04
Matches are distributed among these distances:
174 22 0.08
175 174 0.63
176 59 0.21
177 20 0.07
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (175 bp):
TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACCAA
TATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCTAATACATGAAGACAAGATCTGCT
TTCTTCAATCTACTTCACACCAATACAGGAAGACAAGATCAGCTA
Found at i:29680640 original size:88 final size:87
Alignment explanation
Indices: 29680531--29681070 Score: 637
Period size: 88 Copynumber: 6.2 Consensus size: 87
29680521 GCTAATACAT
* * ** *
29680531 GAAGACAAGATCTGCTT-TCTTCGACCAGCTCCACTACAAATGAGGGAGGCAAGGTTTGTATCTT
1 GAAGGCAAGATCTG-TTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGT-TCTT
29680595 CGATCTGCTTCGATGTCAATGCAG
64 CGATCTGCTTCGATGTCAATGCAG
**
29680619 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGAGTT-TT
1 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTT--GTTCTT
* *
29680683 CGATCTGCTTCGCTGTCAACGCAG
64 CGATCTGCTTCGATGTCAATGCAG
**
29680707 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGTCTTC
1 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGT-TCTTC
29680772 GATCTGCTTC-ACTGTCAATGCAG
65 GATCTGCTTCGA-TGTCAATGCAG
**
29680795 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGTCTTC
1 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGT-TCTTC
* * *
29680860 GATCTGCTTTGCTGTCAAGGCAG
65 GATCTGCTTCGATGTCAATGCAG
* * * *
29680883 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGA-AGGCAAGGCTTTGTT-TT
1 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAAGG-TTTGTTCTT
* *
29680946 CGATCTGCTTC-ACTGTTAATGCAT
64 CGATCTGCTTCGA-TGTCAATGCAG
* * * *
29680970 GAAGGCAAGATCTGCTATCTTTAACCATCTCCACTACAACCGATG-GAGGCAAGGCTTTGTT-TT
1 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAAGG-TTTGTTCTT
* * ** *
29681033 CGATCTGCTTCGCTGTTAACACAA
64 CGATCTGCTTCGATGTCAATGCAG
29681057 GAAGGCAAGATCTG
1 GAAGGCAAGATCTG
29681071 ATGTATTAAT
Statistics
Matches: 409, Mismatches: 31, Indels: 25
0.88 0.07 0.05
Matches are distributed among these distances:
86 2 0.00
87 116 0.28
88 281 0.69
89 8 0.02
90 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (87 bp):
GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTTCTTCG
ATCTGCTTCGATGTCAATGCAG
Found at i:29680669 original size:44 final size:44
Alignment explanation
Indices: 29680621--29680847 Score: 184
Period size: 44 Copynumber: 5.2 Consensus size: 44
29680611 CAATGCAGGA
29680621 AGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAG
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAG
* * * * * * * *
29680665 AGGCAAGGTTTG-AGTTTTCGATCTGCT-TCGCTGTCAA-CGCAG-G
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCT-GCT-ACAACCG-AGAG
29680708 AAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAG
1 -AGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAG
* * * * * *
29680753 AGGCAAGGTTTG-TGTCTTCGATCTGCTTCACTG-T-CAA-TGCAG-G
1 AGGCAAGATCTGTTGTCTTCAACCAGC-T--CTGCTACAACCG-AGAG
29680796 AAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAG
1 -AGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAG
29680841 AGGCAAG
1 AGGCAAG
29680848 GTTTGTGTCT
Statistics
Matches: 137, Mismatches: 28, Indels: 36
0.68 0.14 0.18
Matches are distributed among these distances:
42 4 0.03
43 30 0.22
44 69 0.50
45 30 0.22
46 4 0.03
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (44 bp):
AGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAG
Found at i:29680830 original size:176 final size:173
Alignment explanation
Indices: 29680531--29681070 Score: 721
Period size: 176 Copynumber: 3.1 Consensus size: 173
29680521 GCTAATACAT
* * ** *
29680531 GAAGACAAGATCTGCTTTCTTCGACCAGCTCCACTACAAATGAGGGAGGCAAGGTTTGTATCTTC
1 GAAGGCAAGATCTG-TTTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGT-TCTTC
29680596 GATCTGCTTCGA-TGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACC
64 GATCTGCTTC-ACTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACC
29680660 GAGAGAGGCAAGGTTTGAGTTTTCGATCTGCTTCGCTGTCAACGCAG
128 GAGAGAGGCAAGGTTTG-GTTTTCGATCTGCTTCGCTGTCAACGCAG
**
29680707 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGTCTTC
1 GAAGGCAAGATCTGTT-TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGT-TCTTC
29680772 GATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCG
64 GATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCG
* * *
29680837 AGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAAGGCAG
129 AGAGAGGCAAGGTTTG-GTTTTCGATCTGCTTCGCTGTCAACGCAG
* * *
29680883 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGA-AGGCAAGGCTTTGTT-TT
1 GAAGGCAAGATCTG-TTTCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAAGG-TTTGTTCTT
* * * * * * **
29680946 CGATCTGCTTCACTGTTAATGCATGAAGGCAAGATCTGCTATCTTTAACCATCTCCACTACAACC
63 CGATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACC
* * *
29681011 GATG-GAGGCAAGGCTTT-GTTTTCGATCTGCTTCGCTGTTAACACAA
128 GA-GAGAGGCAAGG-TTTGGTTTTCGATCTGCTTCGCTGTCAACGCAG
29681057 GAAGGCAAGATCTG
1 GAAGGCAAGATCTG
29681071 ATGTATTAAT
Statistics
Matches: 326, Mismatches: 31, Indels: 16
0.87 0.08 0.04
Matches are distributed among these distances:
174 37 0.11
175 73 0.22
176 208 0.64
177 8 0.02
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (173 bp):
GAAGGCAAGATCTGTTTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTTCTTCGA
TCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAG
AGAGGCAAGGTTTGGTTTTCGATCTGCTTCGCTGTCAACGCAG
Found at i:29680885 original size:264 final size:262
Alignment explanation
Indices: 29680504--29681070 Score: 707
Period size: 264 Copynumber: 2.2 Consensus size: 262
29680494 GGACCTGCTA
* * * *
29680504 TTTTCGATCTACTTCAC-G-CTAATACATGAAGACAAGATCTGCTTTCTTCGACCAGCTCCACTA
1 TTTTCGATCTGCTTCACTGTC-AATACAAGAAGGCAAGATCTGCTTTCTTCAACCAGCTCCACTA
* * *
29680567 CAAATGAGGGAGGCAAGGTTTGTATCTTCGATCTGCTTCGATGTCAATGCAGGAAGGCAAGATCT
65 CAAACGAGAGAGGCAAGGTTTGTATCTTCGATCTGCTTCGATGTCAAGGCAGGAAGGCAAGATCT
* * ** *
29680632 GTTGTCTTCAACCAGCTCTGCTACAACCGA-GAGAGGCAAGG-TTTGAGTTTTCGATCTGCTTCG
130 GCTATCTTCAACCAGCTCCACTACAACCGATGA-AGGCAAGGCTTT--GTTTTCGATCTGCTTCA
* * **
29680695 CTGTCAACGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGA-GAGAGGCAA
192 CTGTCAACGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATG-GAGGCAA
29680759 GG-TTTG
256 GGCTTTG
* * **
29680765 TGTCTTCGATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTG-TTGTCTTCAACCAGCTCTGC
1 T-T-TTCGATCTGCTTCACTGTCAATACAAGAAGGCAAGATCTGCTT-TCTTCAACCAGCTCCAC
* * * *
29680829 TACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAAGGCAGGAAGGCAAGAT
63 TACAAACGAGAGAGGCAAGGTTTGTATCTTCGATCTGCTTCGATGTCAAGGCAGGAAGGCAAGAT
* *
29680894 CTGCTATCTTTAACCAGCTCCACTGCAACCGATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCAC
128 CTGCTATCTTCAACCAGCTCCACTACAACCGATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCAC
* * * * *
29680959 TGTTAATGCATGAAGGCAAGATCTGCTATCTTTAACCATCTCCACTACAACCGATGGAGGCAAGG
193 TGTCAACGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGG
29681024 CTTTG
258 CTTTG
* * *
29681029 TTTTCGATCTGCTTCGCTGTTAACACAAGAAGGCAAGATCTG
1 TTTTCGATCTGCTTCACTGTCAATACAAGAAGGCAAGATCTG
29681071 ATGTATTAAT
Statistics
Matches: 262, Mismatches: 35, Indels: 17
0.83 0.11 0.05
Matches are distributed among these distances:
261 1 0.00
262 36 0.14
263 88 0.34
264 131 0.50
265 6 0.02
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (262 bp):
TTTTCGATCTGCTTCACTGTCAATACAAGAAGGCAAGATCTGCTTTCTTCAACCAGCTCCACTAC
AAACGAGAGAGGCAAGGTTTGTATCTTCGATCTGCTTCGATGTCAAGGCAGGAAGGCAAGATCTG
CTATCTTCAACCAGCTCCACTACAACCGATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCACTGT
CAACGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGCTT
TG
Found at i:29680889 original size:44 final size:43
Alignment explanation
Indices: 29680577--29680891 Score: 183
Period size: 44 Copynumber: 7.2 Consensus size: 43
29680567 CAAATGAGGG
* * *
29680577 AGGCAAGGTTTGTATCTTCGATCTGCTTCGATGTCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAA-GCAGGA
* * * * * * * *
29680621 AGGCAAGATCTGTTGTCTTCAACCAGCTCTGCT-ACAA-CCGAGA
1 AGGCAAGGTTTG-TGTCTTCGATCTGCTTTGCTGTCAAGCAG-GA
* * *
29680664 GAGGCAAGGTTTGAGTTTTCGATCTGCTTCGCTGTCAACGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAA-GCAGGA
* * * * * * * *
29680709 AGGCAAGATCTGTTGTCTTCAACCAGCTCTGCT-ACAA-CCGAGA
1 AGGCAAGGTTTG-TGTCTTCGATCTGCTTTGCTGTCAAGCAG-GA
**
29680752 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCACTGTCAATGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAA-GCAGGA
* * * * * * * *
29680797 AGGCAAGATCTGTTGTCTTCAACCAGCTCTGCT-ACAA-CCGAGA
1 AGGCAAGGTTTG-TGTCTTCGATCTGCTTTGCTGTCAAGCAG-GA
29680840 GAGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAAGGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAA-GCAGGA
29680885 AGGCAAG
1 AGGCAAG
29680892 ATCTGCTATC
Statistics
Matches: 192, Mismatches: 61, Indels: 36
0.66 0.21 0.12
Matches are distributed among these distances:
42 6 0.03
43 49 0.26
44 85 0.44
45 46 0.24
46 6 0.03
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (43 bp):
AGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAAGCAGGA
Found at i:29680931 original size:44 final size:44
Alignment explanation
Indices: 29680883--29681022 Score: 117
Period size: 44 Copynumber: 3.2 Consensus size: 44
29680873 GTCAAGGCAG
29680883 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGAT
1 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGAT
* * ** * * * * *
29680927 GAAGGCAAGGCTTTG-T-T-TTCGATCTGCTTCACTGTTAA-TGCAT
1 GAAGGCAA-GATCTGCTATCTTTAACCAGCTCCACTG-CAACCG-AT
* *
29680970 GAAGGCAAGATCTGCTATCTTTAACCATCTCCACTACAACCGAT
1 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGAT
*
29681014 GGAGGCAAG
1 GAAGGCAAG
29681023 GCTTTGTTTT
Statistics
Matches: 68, Mismatches: 21, Indels: 14
0.66 0.20 0.14
Matches are distributed among these distances:
42 17 0.25
43 14 0.21
44 22 0.32
45 15 0.22
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (44 bp):
GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGAT
Found at i:29682098 original size:6 final size:6
Alignment explanation
Indices: 29682043--29682090 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
29682033 TTGGCCTCTC
* * *
29682043 CTTTTT CTTTTT -TTGTT CTTCTT CTCTTTT CTTTTT CTTTTT GTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CT-TTTT CTTTTT CTTTTT CTTTTT
29682091 TTCTTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 4 0.11
6 27 0.75
7 5 0.14
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:29682548 original size:9 final size:8
Alignment explanation
Indices: 29682522--29682575 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
29682512 AGGTCTTTTC
29682522 TTTTATTT
1 TTTTATTT
* *
29682530 TTGGTCTTT
1 TT-TTATTT
29682539 TTTTATTT
1 TTTTATTT
29682547 TTTTACTTT
1 TTTTA-TTT
29682556 TTTTATTT
1 TTTTATTT
*
29682564 TTTTGTTT
1 TTTTATTT
29682572 TTTT
1 TTTT
29682576 TGTTTTTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
8 25 0.64
9 14 0.36
ACGTcount: A:0.07, C:0.04, G:0.06, T:0.83
Consensus pattern (8 bp):
TTTTATTT
Found at i:29682556 original size:25 final size:25
Alignment explanation
Indices: 29682522--29682575 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
29682512 AGGTCTTTTC
* *
29682522 TTTTATTTTTGGTCTTTTTTTATTT
1 TTTTACTTTTGGTATTTTTTTATTT
** *
29682547 TTTTACTTTTTTTATTTTTTTGTTT
1 TTTTACTTTTGGTATTTTTTTATTT
29682572 TTTT
1 TTTT
29682576 TGTTTTTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.07, C:0.04, G:0.06, T:0.83
Consensus pattern (25 bp):
TTTTACTTTTGGTATTTTTTTATTT
Found at i:29682576 original size:17 final size:17
Alignment explanation
Indices: 29682517--29682585 Score: 77
Period size: 17 Copynumber: 4.0 Consensus size: 17
29682507 CGGTGAGGTC
*
29682517 TTTTCTTTTA-TTTTTGG
1 TTTT-TTTTATTTTTTTG
*
29682534 TCTTTTTTTATTTTTTTA
1 T-TTTTTTTATTTTTTTG
*
29682552 CTTTTTTTATTTTTTTG
1 TTTTTTTTATTTTTTTG
*
29682569 TTTTTTTTGTTTTTTTG
1 TTTTTTTTATTTTTTTG
29682586 CCTCCACTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
17 36 0.82
18 8 0.18
ACGTcount: A:0.06, C:0.04, G:0.07, T:0.83
Consensus pattern (17 bp):
TTTTTTTTATTTTTTTG
Found at i:29682581 original size:8 final size:8
Alignment explanation
Indices: 29682536--29682585 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
29682526 ATTTTTGGTC
*
29682536 TTTTTTTA
1 TTTTTTTG
*
29682544 TTTTTTTAC
1 TTTTTTT-G
*
29682553 TTTTTTTA
1 TTTTTTTG
29682561 TTTTTTTG
1 TTTTTTTG
29682569 TTTTTTTTG
1 -TTTTTTTG
29682578 TTTTTTTG
1 TTTTTTTG
29682586 CCTCCACTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
8 22 0.59
9 15 0.41
ACGTcount: A:0.06, C:0.02, G:0.06, T:0.86
Consensus pattern (8 bp):
TTTTTTTG
Found at i:29685849 original size:126 final size:126
Alignment explanation
Indices: 29685624--29685918 Score: 515
Period size: 126 Copynumber: 2.3 Consensus size: 126
29685614 NNNNNNNNNN
* * *
29685624 CGAATTTTCTAAATACGAAATATTGCCTTTATTTTCGAAATTTTTATTTTTGGAAATTTAAAAGG
1 CGAATTTTCTAAATATGAAATATTGCCTTTATTTTCGAAATTTTTACTTTTGGAAATTTAAAAAG
29685689 ATATTTTGCTATTTAGGTTTAACGAGAAAATCGAGACCCAGTAAGTTAGGGTACAATTTCT
66 ATATTTTGCTATTTAGGTTTAACGAGAAAATCGAGACCCAGTAAGTTAGGGTACAATTTCT
29685750 CGAATTTTCTAAATATGAAATATTGCCTTTATTTTCGAAATTTTTACTTTTGGAAATTTAAAAAG
1 CGAATTTTCTAAATATGAAATATTGCCTTTATTTTCGAAATTTTTACTTTTGGAAATTTAAAAAG
29685815 ATATTTTGCTATTTAGGTTTAACGAGAAAATCGAGACCCAGTAAGTTAGGGTACAATTTCT
66 ATATTTTGCTATTTAGGTTTAACGAGAAAATCGAGACCCAGTAAGTTAGGGTACAATTTCT
*
29685876 CGAA-TTTCTAAA-ATGCAAAATATTACC-TTATTTTCGAAATTTT
1 CGAATTTTCTAAATATG--AAATATTGCCTTTATTTTCGAAATTTT
29685919 ACCCTTTTGA
Statistics
Matches: 163, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
124 3 0.02
125 24 0.15
126 136 0.83
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (126 bp):
CGAATTTTCTAAATATGAAATATTGCCTTTATTTTCGAAATTTTTACTTTTGGAAATTTAAAAAG
ATATTTTGCTATTTAGGTTTAACGAGAAAATCGAGACCCAGTAAGTTAGGGTACAATTTCT
Found at i:29686184 original size:45 final size:45
Alignment explanation
Indices: 29686133--29686223 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
29686123 AACATGCATG
* * *
29686133 ACAAAGACAATAATAAGAGTACAAATAATAATATGGGGAACAATA
1 ACAAAGACAATAATAACAATACAAATAATAATATGGAGAACAATA
* * * *
29686178 ACAAAGAGAATAATAACAATATAAATGATAATATGGAGAATAATA
1 ACAAAGACAATAATAACAATACAAATAATAATATGGAGAACAATA
29686223 A
1 A
29686224 GAGCGATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.20
Consensus pattern (45 bp):
ACAAAGACAATAATAACAATACAAATAATAATATGGAGAACAATA
Found at i:29687993 original size:84 final size:84
Alignment explanation
Indices: 29687881--29688339 Score: 688
Period size: 84 Copynumber: 5.5 Consensus size: 84
29687871 GAGATAGAAT
*
29687881 TGGTTTCTTTCGTATGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTAC
1 TGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTAC
29687946 TGCTTAGGGAGATAAGATC
66 TGCTTAGGGAGATAAGATC
29687965 TGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTAC
1 TGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTAC
*
29688030 TACTTAGGGAGATAAGA-C
66 TGCTTAGGGAGATAAGATC
29688048 TTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTA
1 -TGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTA
29688113 CTGCTTAGGGAGATAAGATC
65 CTGCTTAGGGAGATAAGATC
29688133 TGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTAC
1 TGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTAC
*
29688198 TGCTTAGAGAGATAAGATC
66 TGCTTAGGGAGATAAGATC
** *
29688217 TGGTTTC-TT--TC-GCTCCACTACTGCTTAGGGAGATAAGACCTGGTTTCTTTCG-TCTGCTCC
1 TGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGA-C---TTGATGT-GATCTGCTCC
*
29688277 ACTACTGCTTAGGAAGATAAGA-C
61 ACTACTGCTTAGGGAGATAAGATC
** *
29688300 ---TTGATGT-GATCTGCTCCACTACTGCTTAGGGAGATAAGAC
1 TGGTTTCTTTCG-TCTGCTCCACTACTGCTTAGGGAGATAAGAC
29688340 CTAGTTTCTT
Statistics
Matches: 352, Mismatches: 12, Indels: 23
0.91 0.03 0.06
Matches are distributed among these distances:
80 29 0.08
81 4 0.01
83 7 0.02
84 310 0.88
85 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (84 bp):
TGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTAC
TGCTTAGGGAGATAAGATC
Found at i:29688340 original size:84 final size:79
Alignment explanation
Indices: 29687895--29688506 Score: 618
Period size: 84 Copynumber: 7.4 Consensus size: 79
29687885 TTCTTTCGTA
29687895 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
1 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
** *
29687960 AGATCTGGTTTCTTTCGTC
66 AGA-C---TTGATGT-GTC
*
29687979 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTACTTAGGGAGATA
1 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
* *
29688044 AGACTTGGTTTCTTTCGTC
66 AGACTT-G---ATGT-GTC
29688063 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
1 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
** *
29688128 AGATCTGGTTTCTTTCGTC
66 AGA-C---TTGATGT-GTC
*
29688147 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGAGAGATA
1 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
* * * *
29688212 AGA-TCTGGTTTCTT
66 AGACT-TGATGTGTC
** *
29688226 TCGCTCCACTACTGCTTAGGGAGATAAGACCTGGTTTCTTTCG-TCTGCTCCACTACTGCTTAGG
1 T-GCTCCACTACTGCTTAGGGAGATAAGA-C---TTGATGT-GATCTGCTCCACTACTGCTTAGG
*
29688290 AAGATAAGACTTGATGTGATC
60 GAGATAAGACTTGATGTG-TC
** * * *
29688311 TGCTCCACTACTGCTTAGGGAGATAAGACCTAGTTTCTTTCATCTACTCCACTACTGCTTAGGGA
1 TGCTCCACTACTGCTTAGGGAGATAAGA-C---TTGATGTGATCTGCTCCACTACTGCTTAGGGA
*
29688376 GATAGGACTTGATGTGATC
62 GATAAGACTTGATGTG-TC
* * ** *
29688395 TGCTCCACTACTGCTTAGAGACATAAGATCTGGTTTCTTTCG-TCTGCTCCACTACTGCTTAGGG
1 TGCTCCACTACTGCTTAGGGAGATAAGA-C---TTGATGT-GATCTGCTCCACTACTGCTTAGGG
29688459 AGATAAGACTTGATGTGATC
61 AGATAAGACTTGATGTG-TC
* *
29688479 TGCTCCACTACTACCTAGGGAGATAAGA
1 TGCTCCACTACTGCTTAGGGAGATAAGA
29688507 TCTGGTTTTA
Statistics
Matches: 475, Mismatches: 34, Indels: 38
0.87 0.06 0.07
Matches are distributed among these distances:
79 3 0.01
80 33 0.07
81 1 0.00
83 1 0.00
84 430 0.91
85 5 0.01
88 2 0.00
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (79 bp):
TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
AGACTTGATGTGTC
Found at i:29688423 original size:292 final size:292
Alignment explanation
Indices: 29687895--29688514 Score: 1055
Period size: 292 Copynumber: 2.1 Consensus size: 292
29687885 TTCTTTCGTA
* *
29687895 TGCTCCACTACTGCTTAGGGAGATAAGA-CTTGATGTGATCTGCTCCACTACTGCTTAGGGAGAT
1 TGCTCCACTACTGCTTAGGGAGATAAGATC-TGGTTTGATCTGCTCCACTACTGCTTAGGGAGAT
* *
29687959 AAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTC
65 AAGACCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGAAGATAAGACTTGATGTGATCTGCTC
* * * *
29688024 CACTACTACTTAGGGAGATAAGACTTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAA
130 CACTACTACTTAGGGAGATAAGACCTAGTTTCTTTCATCTACTCCACTACTGCTTAGGGAGATAA
* *
29688089 GACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCA
195 GACTTGATGTGATCTGCTCCACTACTGCTTAGAGACATAAGATCTGGTTTCTTTCGTCTGCTCCA
29688154 CTACTGCTTAGGGAGATAAGACTTGATGTGATC
260 CTACTGCTTAGGGAGATAAGACTTGATGTGATC
* * *
29688187 TGCTCCACTACTGCTTAGAGAGATAAGATCTGGTTT-CTTTCGCTCCACTACTGCTTAGGGAGAT
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTGATCT-GCTCCACTACTGCTTAGGGAGAT
29688251 AAGACCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGAAGATAAGACTTGATGTGATCTGCTC
65 AAGACCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGAAGATAAGACTTGATGTGATCTGCTC
* *
29688316 CACTACTGCTTAGGGAGATAAGACCTAGTTTCTTTCATCTACTCCACTACTGCTTAGGGAGATAG
130 CACTACTACTTAGGGAGATAAGACCTAGTTTCTTTCATCTACTCCACTACTGCTTAGGGAGATAA
29688381 GACTTGATGTGATCTGCTCCACTACTGCTTAGAGACATAAGATCTGGTTTCTTTCGTCTGCTCCA
195 GACTTGATGTGATCTGCTCCACTACTGCTTAGAGACATAAGATCTGGTTTCTTTCGTCTGCTCCA
29688446 CTACTGCTTAGGGAGATAAGACTTGATGTGATC
260 CTACTGCTTAGGGAGATAAGACTTGATGTGATC
* *
29688479 TGCTCCACTACTACCTAGGGAGATAAGATCTGGTTT
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTT
29688515 TAATCCTTTT
Statistics
Matches: 308, Mismatches: 18, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
291 2 0.01
292 305 0.99
293 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (292 bp):
TGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTGATCTGCTCCACTACTGCTTAGGGAGATA
AGACCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGAAGATAAGACTTGATGTGATCTGCTCC
ACTACTACTTAGGGAGATAAGACCTAGTTTCTTTCATCTACTCCACTACTGCTTAGGGAGATAAG
ACTTGATGTGATCTGCTCCACTACTGCTTAGAGACATAAGATCTGGTTTCTTTCGTCTGCTCCAC
TACTGCTTAGGGAGATAAGACTTGATGTGATC
Found at i:29688483 original size:208 final size:205
Alignment explanation
Indices: 29687895--29688506 Score: 756
Period size: 208 Copynumber: 2.9 Consensus size: 205
29687885 TTCTTTCGTA
** * * *
29687895 TGCTCCACTACTGCTTAGGGAGATAAGA-C---TTGATGTGATCTGCTCCACTACTGCTTAGGGA
1 TGCTCCACTACTGCTTAGGGAGATAAGACCTAGTTTCTTTCATCTACTCCACTACTGCTTAGGGA
** * * * * * **
29687956 GATAAGATCTGGTTTCTTTCG-TCTGCTCCACTACTGCTTAGGGAGATAAGA-CTTGATGT-GAT
66 GATAAGA-C---TTGATGT-GATCTGCTCCACTACTGCTTAGAGACATAAGATC-TGGTTTCTTT
*
29688018 CTGCTCCACTACTACTTAGGGAGATAAGACTTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGG
125 CTGCTCCACTACTGCTTAGGGAGATAAGACTT-G---CTTTCGTCTGCTCCACTACTGCTTAGGG
29688083 AGATAAGACTTGATGTGATC
186 AGATAAGACTTGATGTGATC
* * * *
29688103 TGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGA
1 TGCTCCACTACTGCTTAGGGAGATAAGACCTAGTTTCTTTCATCTACTCCACTACTGCTTAGGGA
*
29688168 GATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGGTTTCTTTC-GCTC
66 GATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGAGACATAAGATCTGGTTTCTTTCTGCTC
* *
29688232 CACTACTGCTTAGGGAGATAAGACCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGAAGATAA
131 CACTACTGCTTAGGGAGATAAGA-C---TTGCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAA
29688297 GACTTGATGTGATC
192 GACTTGATGTGATC
29688311 TGCTCCACTACTGCTTAGGGAGATAAGACCTAGTTTCTTTCATCTACTCCACTACTGCTTAGGGA
1 TGCTCCACTACTGCTTAGGGAGATAAGACCTAGTTTCTTTCATCTACTCCACTACTGCTTAGGGA
*
29688376 GATAGGACTTGATGTGATCTGCTCCACTACTGCTTAGAGACATAAGATCTGGTTTCTTTCGTCTG
66 GATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGAGACATAAGATCTGGTTTC-TT--TCTG
* * * *
29688441 CTCCACTACTGCTTAGGGAGATAAGACTTGATGT-GATCTGCTCCACTACTACCTAGGGAGATAA
128 CTCCACTACTGCTTAGGGAGATAAGACTTGCTTTCG-TCTGCTCCACTACTGCTTAGGGAGATAA
29688505 GA
192 GA
29688507 TCTGGTTTTA
Statistics
Matches: 360, Mismatches: 28, Indels: 32
0.86 0.07 0.08
Matches are distributed among these distances:
207 2 0.01
208 284 0.79
209 7 0.02
211 4 0.01
212 63 0.17
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (205 bp):
TGCTCCACTACTGCTTAGGGAGATAAGACCTAGTTTCTTTCATCTACTCCACTACTGCTTAGGGA
GATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGAGACATAAGATCTGGTTTCTTTCTGCTC
CACTACTGCTTAGGGAGATAAGACTTGCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGACT
TGATGTGATC
Found at i:29689023 original size:175 final size:175
Alignment explanation
Indices: 29688727--29689259 Score: 650
Period size: 175 Copynumber: 3.0 Consensus size: 175
29688717 AGATCTGTTT
29688727 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCA
1 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCA
* * * * * *
29688792 ATATAGGAAGACAGAACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTG
66 ATATAGGAAGACAGAACC-GC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGACCTG
* *
29688856 CTTTCTTCGATCCACTTCCTAC-C-AATATAGGAAGACAAGATCCGC-A
128 CTTTCTTCGATCTACTTCC-ACGCTAATACAGGAAGACAAGATCCGCTA
* * * * * * * *
29688902 TCTTCGATCCACTTC-CTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCGCCAC
1 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTAC
* * *
29688966 CAGTATGGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTG
64 CAATATAGGAAGAC-AGAACCGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTG
* * * *
29689031 CTATCTTCGATCTACTT-CACGCTAATACATGAAGACAAGATCTGCTT
128 CTTTCTTCGATCTACTTCCACGCTAATACAGGAAGACAAGATCCGCTA
* * *
29689078 TCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTTGATCCACTTCCTACCA
1 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCA
* *
29689143 ATATAGGAATACAGAACTTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCT
66 ATATAGGAAGACAGAAC-CGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCT
* * *
29689208 ATT-TTCGATCTACTT-CACGCTAATACATGAAGACAAGATCTGCTT
130 -TTCTTCGATCTACTTCCACGCTAATACAGGAAGACAAGATCCGCTA
29689253 TCTTCGA
1 TCTTCGA
29689260 CCAGCTCCAC
Statistics
Matches: 307, Mismatches: 41, Indels: 20
0.83 0.11 0.05
Matches are distributed among these distances:
173 2 0.01
174 29 0.09
175 205 0.67
176 45 0.15
177 26 0.08
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (175 bp):
TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCA
ATATAGGAAGACAGAACCGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTT
TCTTCGATCTACTTCCACGCTAATACAGGAAGACAAGATCCGCTA
Found at i:29689170 original size:219 final size:219
Alignment explanation
Indices: 29688727--29689198 Score: 759
Period size: 219 Copynumber: 2.2 Consensus size: 219
29688717 AGATCTGTTT
*
29688727 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCA
1 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACCA
29688792 ATATAGGAAGACAGAACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
66 ATATAGGAAGACAGAACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* *
29688857 TTTCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACC
131 TTTCTTCAATCCACTTCCCACCAATATAGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACC
* *
29688922 AATATAGGAAGATAGGACCTGCTA
196 AATATAGGAAGACAGAACCTGCTA
*
29688946 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACCA
1 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACCA
* *
29689011 ATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCTAATACATGAAGACAAGATCTGC
66 ATATAGGAAGACAGAACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* * * * *
29689076 TTTCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTTGATCCACTTCCTAC
131 TTTCTTCAATCCACTTC-CCACCAATATAGGAAGACAAGATCCGCATCTTCGATCCACTTCCTAC
* *
29689141 CAATATAGGAATACAGAACTTGC-A
195 CAATATAGGAAGACAGAACCTGCTA
* * *
29689165 TCTTCGATCCACTTC-CTACCAATATAGGAAGACA
1 TCTTCGATCTACTTCGCCACCAATATGGGAAGACA
29689199 GGACCTGCTA
Statistics
Matches: 233, Mismatches: 19, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
218 16 0.07
219 156 0.67
220 61 0.26
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (219 bp):
TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACCA
ATATAGGAAGACAGAACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
TTTCTTCAATCCACTTCCCACCAATATAGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACC
AATATAGGAAGACAGAACCTGCTA
Found at i:29689240 original size:44 final size:44
Alignment explanation
Indices: 29688727--29689259 Score: 518
Period size: 44 Copynumber: 12.2 Consensus size: 44
29688717 AGATCTGTTT
* * * *
29688727 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-A
1 TCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGACCTGCTA
29688771 TCTTCGATCCACTTCCTACCAATATAGGAAGAC-AGAACCTGCTA
1 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAG-ACCTGCTA
* * * * * *
29688815 TCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGACCTGCTA
29688859 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCC-GC-A
1 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGA-CCTGCTA
* *
29688902 TCTTCGATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTA
1 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGACCTGCTA
* * * *
29688946 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCC-GC-A
1 TCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGA-CCTGCTA
*
29688990 TCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTA
1 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGACCTGCTA
* * * * *
29689034 TCTTCGATCTACTT-C-ACGCTAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCCACTTCCTAC-C-AATATAGGAAGACAAGACCTGCTA
* * * * * *
29689078 TCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC-A
1 TCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGACCTGCTA
* * *
29689122 TCTTTGATCCACTTCCTACCAATATAGGAATAC-AGAACTTGC-A
1 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAG-ACCTGCTA
*
29689165 TCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTA
1 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGACCTGCTA
* * * * * *
29689209 TTTTCGATCTACTT-C-ACGCTAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCCACTTCCTAC-C-AATATAGGAAGACAAGACCTGCTA
29689253 TCTTCGA
1 TCTTCGA
29689260 CCAGCTCCAC
Statistics
Matches: 405, Mismatches: 62, Indels: 44
0.79 0.12 0.09
Matches are distributed among these distances:
42 12 0.03
43 138 0.34
44 208 0.51
45 41 0.10
46 4 0.01
47 2 0.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (44 bp):
TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGACCTGCTA
Found at i:29689259 original size:219 final size:219
Alignment explanation
Indices: 29688727--29689259 Score: 745
Period size: 219 Copynumber: 2.4 Consensus size: 219
29688717 AGATCTGTTT
*
29688727 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCA
1 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGACCTGCATCTTCGATCCACTTCCTACCA
29688792 ATATAGGAAGAC-AGAACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
66 ATATAGGAAGACAAG-ACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
* *
29688856 CTTTCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCCGCATCTTCGATCCACTTCCTAC
130 CTTTCTTCAATCCACTTCCCACCAATATAGGAAGACAAGATCCGCATCTTCGATCCACTTCCTAC
* *
29688921 CAATATAGGAAGATAGGACCTGCTA
195 CAATATAGGAAGACAGAACCTGCTA
*
29688946 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCC-GCATCTTCGATCCACTTCCTACC
1 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGA-CCTGCATCTTCGATCCACTTCCTACC
* *
29689010 AATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCTAATACATGAAGACAAGATCTG
65 AATATAGGAAGACAAGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
* * * * *
29689075 CTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTTGATCCACTTCCTA
130 CTTTCTTCAATCCACTTC-CCACCAATATAGGAAGACAAGATCCGCATCTTCGATCCACTTCCTA
* *
29689140 CCAATATAGGAATACAGAACTTGC-A
194 CCAATATAGGAAGACAGAACCTGCTA
* * * * * *
29689165 TCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGACCTGCTATTTTCGATCTACTT-C-ACG
1 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGACCTGC-ATCTTCGATCCACTTCCTAC-
* * * *
29689227 CTAATACATGAAGACAAGATCTGCTTTCTTCGA
64 C-AATATAGGAAGACAAGACCTGCTATCTTCGA
29689260 CCAGCTCCAC
Statistics
Matches: 280, Mismatches: 27, Indels: 14
0.87 0.08 0.04
Matches are distributed among these distances:
217 4 0.01
218 22 0.08
219 191 0.68
220 63 0.22
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (219 bp):
TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGACCTGCATCTTCGATCCACTTCCTACCA
ATATAGGAAGACAAGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
TTTCTTCAATCCACTTCCCACCAATATAGGAAGACAAGATCCGCATCTTCGATCCACTTCCTACC
AATATAGGAAGACAGAACCTGCTA
Found at i:29689345 original size:88 final size:87
Alignment explanation
Indices: 29689236--29689775 Score: 637
Period size: 88 Copynumber: 6.2 Consensus size: 87
29689226 GCTAATACAT
* * ** *
29689236 GAAGACAAGATCTGCTT-TCTTCGACCAGCTCCACTACAAATGAGGGAGGCAAGGTTTGTATCTT
1 GAAGGCAAGATCTG-TTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGT-TCTT
29689300 CGATCTGCTTCGATGTCAATGCAG
64 CGATCTGCTTCGATGTCAATGCAG
**
29689324 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGAGTT-TT
1 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTT--GTTCTT
* *
29689388 CGATCTGCTTCGCTGTCAACGCAG
64 CGATCTGCTTCGATGTCAATGCAG
**
29689412 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGTCTTC
1 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGT-TCTTC
29689477 GATCTGCTTC-ACTGTCAATGCAG
65 GATCTGCTTCGA-TGTCAATGCAG
**
29689500 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGTCTTC
1 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGT-TCTTC
* * *
29689565 GATCTGCTTTGCTGTCAAGGCAG
65 GATCTGCTTCGATGTCAATGCAG
* * * *
29689588 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGA-AGGCAAGGCTTTGTT-TT
1 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAAGG-TTTGTTCTT
* *
29689651 CGATCTGCTTC-ACTGTTAATGCAT
64 CGATCTGCTTCGA-TGTCAATGCAG
* * * *
29689675 GAAGGCAAGATCTGCTATCTTTAACCATCTCCACTACAACCGATG-GAGGCAAGGCTTTGTT-TT
1 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAAGG-TTTGTTCTT
* * ** *
29689738 CGATCTGCTTCGCTGTTAACACAA
64 CGATCTGCTTCGATGTCAATGCAG
29689762 GAAGGCAAGATCTG
1 GAAGGCAAGATCTG
29689776 ATGTATTAAT
Statistics
Matches: 409, Mismatches: 31, Indels: 25
0.88 0.07 0.05
Matches are distributed among these distances:
86 2 0.00
87 116 0.28
88 281 0.69
89 8 0.02
90 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (87 bp):
GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTTCTTCG
ATCTGCTTCGATGTCAATGCAG
Found at i:29689374 original size:44 final size:44
Alignment explanation
Indices: 29689326--29689552 Score: 184
Period size: 44 Copynumber: 5.2 Consensus size: 44
29689316 CAATGCAGGA
29689326 AGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAG
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAG
* * * * * * * *
29689370 AGGCAAGGTTTG-AGTTTTCGATCTGCT-TCGCTGTCAA-CGCAG-G
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCT-GCT-ACAACCG-AGAG
29689413 AAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAG
1 -AGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAG
* * * * * *
29689458 AGGCAAGGTTTG-TGTCTTCGATCTGCTTCACTG-T-CAA-TGCAG-G
1 AGGCAAGATCTGTTGTCTTCAACCAGC-T--CTGCTACAACCG-AGAG
29689501 AAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAG
1 -AGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAG
29689546 AGGCAAG
1 AGGCAAG
29689553 GTTTGTGTCT
Statistics
Matches: 137, Mismatches: 28, Indels: 36
0.68 0.14 0.18
Matches are distributed among these distances:
42 4 0.03
43 30 0.22
44 69 0.50
45 30 0.22
46 4 0.03
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (44 bp):
AGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAG
Found at i:29689535 original size:176 final size:173
Alignment explanation
Indices: 29689236--29689775 Score: 721
Period size: 176 Copynumber: 3.1 Consensus size: 173
29689226 GCTAATACAT
* * ** *
29689236 GAAGACAAGATCTGCTTTCTTCGACCAGCTCCACTACAAATGAGGGAGGCAAGGTTTGTATCTTC
1 GAAGGCAAGATCTG-TTTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGT-TCTTC
29689301 GATCTGCTTCGA-TGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACC
64 GATCTGCTTC-ACTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACC
29689365 GAGAGAGGCAAGGTTTGAGTTTTCGATCTGCTTCGCTGTCAACGCAG
128 GAGAGAGGCAAGGTTTG-GTTTTCGATCTGCTTCGCTGTCAACGCAG
**
29689412 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGTCTTC
1 GAAGGCAAGATCTGTT-TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGT-TCTTC
29689477 GATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCG
64 GATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCG
* * *
29689542 AGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAAGGCAG
129 AGAGAGGCAAGGTTTG-GTTTTCGATCTGCTTCGCTGTCAACGCAG
* * *
29689588 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGA-AGGCAAGGCTTTGTT-TT
1 GAAGGCAAGATCTG-TTTCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAAGG-TTTGTTCTT
* * * * * * **
29689651 CGATCTGCTTCACTGTTAATGCATGAAGGCAAGATCTGCTATCTTTAACCATCTCCACTACAACC
63 CGATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACC
* * *
29689716 GATG-GAGGCAAGGCTTT-GTTTTCGATCTGCTTCGCTGTTAACACAA
128 GA-GAGAGGCAAGG-TTTGGTTTTCGATCTGCTTCGCTGTCAACGCAG
29689762 GAAGGCAAGATCTG
1 GAAGGCAAGATCTG
29689776 ATGTATTAAT
Statistics
Matches: 326, Mismatches: 31, Indels: 16
0.87 0.08 0.04
Matches are distributed among these distances:
174 37 0.11
175 73 0.22
176 208 0.64
177 8 0.02
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (173 bp):
GAAGGCAAGATCTGTTTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTTCTTCGA
TCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAG
AGAGGCAAGGTTTGGTTTTCGATCTGCTTCGCTGTCAACGCAG
Found at i:29689590 original size:264 final size:262
Alignment explanation
Indices: 29689209--29689775 Score: 707
Period size: 264 Copynumber: 2.2 Consensus size: 262
29689199 GGACCTGCTA
* * * *
29689209 TTTTCGATCTACTTCAC-G-CTAATACATGAAGACAAGATCTGCTTTCTTCGACCAGCTCCACTA
1 TTTTCGATCTGCTTCACTGTC-AATACAAGAAGGCAAGATCTGCTTTCTTCAACCAGCTCCACTA
* * *
29689272 CAAATGAGGGAGGCAAGGTTTGTATCTTCGATCTGCTTCGATGTCAATGCAGGAAGGCAAGATCT
65 CAAACGAGAGAGGCAAGGTTTGTATCTTCGATCTGCTTCGATGTCAAGGCAGGAAGGCAAGATCT
* * ** *
29689337 GTTGTCTTCAACCAGCTCTGCTACAACCGA-GAGAGGCAAGG-TTTGAGTTTTCGATCTGCTTCG
130 GCTATCTTCAACCAGCTCCACTACAACCGATGA-AGGCAAGGCTTT--GTTTTCGATCTGCTTCA
* * **
29689400 CTGTCAACGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGA-GAGAGGCAA
192 CTGTCAACGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATG-GAGGCAA
29689464 GG-TTTG
256 GGCTTTG
* * **
29689470 TGTCTTCGATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTG-TTGTCTTCAACCAGCTCTGC
1 T-T-TTCGATCTGCTTCACTGTCAATACAAGAAGGCAAGATCTGCTT-TCTTCAACCAGCTCCAC
* * * *
29689534 TACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAAGGCAGGAAGGCAAGAT
63 TACAAACGAGAGAGGCAAGGTTTGTATCTTCGATCTGCTTCGATGTCAAGGCAGGAAGGCAAGAT
* *
29689599 CTGCTATCTTTAACCAGCTCCACTGCAACCGATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCAC
128 CTGCTATCTTCAACCAGCTCCACTACAACCGATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCAC
* * * * *
29689664 TGTTAATGCATGAAGGCAAGATCTGCTATCTTTAACCATCTCCACTACAACCGATGGAGGCAAGG
193 TGTCAACGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGG
29689729 CTTTG
258 CTTTG
* * *
29689734 TTTTCGATCTGCTTCGCTGTTAACACAAGAAGGCAAGATCTG
1 TTTTCGATCTGCTTCACTGTCAATACAAGAAGGCAAGATCTG
29689776 ATGTATTAAT
Statistics
Matches: 262, Mismatches: 35, Indels: 17
0.83 0.11 0.05
Matches are distributed among these distances:
261 1 0.00
262 36 0.14
263 88 0.34
264 131 0.50
265 6 0.02
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (262 bp):
TTTTCGATCTGCTTCACTGTCAATACAAGAAGGCAAGATCTGCTTTCTTCAACCAGCTCCACTAC
AAACGAGAGAGGCAAGGTTTGTATCTTCGATCTGCTTCGATGTCAAGGCAGGAAGGCAAGATCTG
CTATCTTCAACCAGCTCCACTACAACCGATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCACTGT
CAACGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGCTT
TG
Found at i:29689594 original size:44 final size:43
Alignment explanation
Indices: 29689282--29689596 Score: 183
Period size: 44 Copynumber: 7.2 Consensus size: 43
29689272 CAAATGAGGG
* * *
29689282 AGGCAAGGTTTGTATCTTCGATCTGCTTCGATGTCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAA-GCAGGA
* * * * * * * *
29689326 AGGCAAGATCTGTTGTCTTCAACCAGCTCTGCT-ACAA-CCGAGA
1 AGGCAAGGTTTG-TGTCTTCGATCTGCTTTGCTGTCAAGCAG-GA
* * *
29689369 GAGGCAAGGTTTGAGTTTTCGATCTGCTTCGCTGTCAACGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAA-GCAGGA
* * * * * * * *
29689414 AGGCAAGATCTGTTGTCTTCAACCAGCTCTGCT-ACAA-CCGAGA
1 AGGCAAGGTTTG-TGTCTTCGATCTGCTTTGCTGTCAAGCAG-GA
**
29689457 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCACTGTCAATGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAA-GCAGGA
* * * * * * * *
29689502 AGGCAAGATCTGTTGTCTTCAACCAGCTCTGCT-ACAA-CCGAGA
1 AGGCAAGGTTTG-TGTCTTCGATCTGCTTTGCTGTCAAGCAG-GA
29689545 GAGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAAGGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAA-GCAGGA
29689590 AGGCAAG
1 AGGCAAG
29689597 ATCTGCTATC
Statistics
Matches: 192, Mismatches: 61, Indels: 36
0.66 0.21 0.12
Matches are distributed among these distances:
42 6 0.03
43 49 0.26
44 85 0.44
45 46 0.24
46 6 0.03
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (43 bp):
AGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAAGCAGGA
Found at i:29689636 original size:44 final size:44
Alignment explanation
Indices: 29689588--29689727 Score: 117
Period size: 44 Copynumber: 3.2 Consensus size: 44
29689578 GTCAAGGCAG
29689588 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGAT
1 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGAT
* * ** * * * * *
29689632 GAAGGCAAGGCTTTG-T-T-TTCGATCTGCTTCACTGTTAA-TGCAT
1 GAAGGCAA-GATCTGCTATCTTTAACCAGCTCCACTG-CAACCG-AT
* *
29689675 GAAGGCAAGATCTGCTATCTTTAACCATCTCCACTACAACCGAT
1 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGAT
*
29689719 GGAGGCAAG
1 GAAGGCAAG
29689728 GCTTTGTTTT
Statistics
Matches: 68, Mismatches: 21, Indels: 14
0.66 0.20 0.14
Matches are distributed among these distances:
42 17 0.25
43 14 0.21
44 22 0.32
45 15 0.22
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (44 bp):
GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGAT
Found at i:29690803 original size:6 final size:6
Alignment explanation
Indices: 29690748--29690795 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
29690738 TTGGCCTCTC
* * *
29690748 CTTTTT CTTTTT -TTGTT CTTCTT CTCTTTT CTTTTT CTTTTT GTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CT-TTTT CTTTTT CTTTTT CTTTTT
29690796 TTCTTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 4 0.11
6 27 0.75
7 5 0.14
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:29691253 original size:9 final size:8
Alignment explanation
Indices: 29691227--29691280 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
29691217 AGGTCTTTTC
29691227 TTTTATTT
1 TTTTATTT
* *
29691235 TTGGTCTTT
1 TT-TTATTT
29691244 TTTTATTT
1 TTTTATTT
29691252 TTTTACTTT
1 TTTTA-TTT
29691261 TTTTATTT
1 TTTTATTT
*
29691269 TTTTGTTT
1 TTTTATTT
29691277 TTTT
1 TTTT
29691281 TGTTTTTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
8 25 0.64
9 14 0.36
ACGTcount: A:0.07, C:0.04, G:0.06, T:0.83
Consensus pattern (8 bp):
TTTTATTT
Found at i:29691261 original size:25 final size:25
Alignment explanation
Indices: 29691227--29691280 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
29691217 AGGTCTTTTC
* *
29691227 TTTTATTTTTGGTCTTTTTTTATTT
1 TTTTACTTTTGGTATTTTTTTATTT
** *
29691252 TTTTACTTTTTTTATTTTTTTGTTT
1 TTTTACTTTTGGTATTTTTTTATTT
29691277 TTTT
1 TTTT
29691281 TGTTTTTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.07, C:0.04, G:0.06, T:0.83
Consensus pattern (25 bp):
TTTTACTTTTGGTATTTTTTTATTT
Found at i:29691281 original size:17 final size:17
Alignment explanation
Indices: 29691222--29691290 Score: 77
Period size: 17 Copynumber: 4.0 Consensus size: 17
29691212 CGGTGAGGTC
*
29691222 TTTTCTTTTA-TTTTTGG
1 TTTT-TTTTATTTTTTTG
*
29691239 TCTTTTTTTATTTTTTTA
1 T-TTTTTTTATTTTTTTG
*
29691257 CTTTTTTTATTTTTTTG
1 TTTTTTTTATTTTTTTG
*
29691274 TTTTTTTTGTTTTTTTG
1 TTTTTTTTATTTTTTTG
29691291 CCTCCACTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
17 36 0.82
18 8 0.18
ACGTcount: A:0.06, C:0.04, G:0.07, T:0.83
Consensus pattern (17 bp):
TTTTTTTTATTTTTTTG
Found at i:29691286 original size:8 final size:8
Alignment explanation
Indices: 29691241--29691290 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
29691231 ATTTTTGGTC
*
29691241 TTTTTTTA
1 TTTTTTTG
*
29691249 TTTTTTTAC
1 TTTTTTT-G
*
29691258 TTTTTTTA
1 TTTTTTTG
29691266 TTTTTTTG
1 TTTTTTTG
29691274 TTTTTTTTG
1 -TTTTTTTG
29691283 TTTTTTTG
1 TTTTTTTG
29691291 CCTCCACTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
8 22 0.59
9 15 0.41
ACGTcount: A:0.06, C:0.02, G:0.06, T:0.86
Consensus pattern (8 bp):
TTTTTTTG
Found at i:29694452 original size:126 final size:126
Alignment explanation
Indices: 29694227--29694591 Score: 540
Period size: 126 Copynumber: 2.9 Consensus size: 126
29694217 TTTAATTTTC
* * * * * *
29694227 AAAGGATATTTGGTTATTTAGGATCAACGCGAGAAAAATCGA-AGCTCAGTAAGTTAGGGCACGA
1 AAAGGATATTTTGCTATTTAGGTTTAA--CGAG-AAAATCGAGA-CCCAGTAAGTTAGGGTAC-A
* * *
29694291 TTTTCTCGAATTTTCTAAATACGAAATATTGCCTTTATTTTCGAAATTTTTATTTTTGGAAATTT
61 ATTTCTCGAATTTTCTAAATATGAAATATTGCCTTTATTTTCGAAATTTTTACTTTTGGAAATTT
29694356 A
126 A
29694357 AAAGGATATTTTGCTATTTAGGTTTAACGAGAAAATCGAGACCCAGTAAGTTAGGGTACAATTTC
1 AAAGGATATTTTGCTATTTAGGTTTAACGAGAAAATCGAGACCCAGTAAGTTAGGGTACAATTTC
29694422 TCGAATTTTCTAAATATGAAATATTGCCTTTATTTTCGAAATTTTTACTTTTGGAAATTTA
66 TCGAATTTTCTAAATATGAAATATTGCCTTTATTTTCGAAATTTTTACTTTTGGAAATTTA
*
29694483 AAAAGATATTTTGCTATTTAGGTTTAACGAGAAAATCGAGACCCAGTAAGTTAGGGTACAATTTC
1 AAAGGATATTTTGCTATTTAGGTTTAACGAGAAAATCGAGACCCAGTAAGTTAGGGTACAATTTC
*
29694548 TCGAA-TTTCTAAA-ATGCAAAATATTACC-TTATTTTCGAAATTTT
66 TCGAATTTTCTAAATATG--AAATATTGCCTTTATTTTCGAAATTTT
29694592 ACCCTTTTGA
Statistics
Matches: 221, Mismatches: 11, Indels: 11
0.91 0.05 0.05
Matches are distributed among these distances:
124 3 0.01
125 24 0.11
126 142 0.64
127 24 0.11
128 5 0.02
130 23 0.10
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (126 bp):
AAAGGATATTTTGCTATTTAGGTTTAACGAGAAAATCGAGACCCAGTAAGTTAGGGTACAATTTC
TCGAATTTTCTAAATATGAAATATTGCCTTTATTTTCGAAATTTTTACTTTTGGAAATTTA
Found at i:29694857 original size:45 final size:45
Alignment explanation
Indices: 29694806--29694896 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
29694796 AACATGCATG
* * *
29694806 ACAAAGACAATAATAAGAGTACAAATAATAATATGGGGAACAATA
1 ACAAAGACAATAATAACAATACAAATAATAATATGGAGAACAATA
* * * *
29694851 ACAAAGAGAATAATAACAATATAAATGATAATATGGAGAATAATA
1 ACAAAGACAATAATAACAATACAAATAATAATATGGAGAACAATA
29694896 A
1 A
29694897 GAGCGATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.20
Consensus pattern (45 bp):
ACAAAGACAATAATAACAATACAAATAATAATATGGAGAACAATA
Done.