Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 7 of 204
Found at i:2220567 original size:29 final size:29
Alignment explanation
Indices: 2220534--2220597 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
2220524 TAATCCACCA
2220534 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
2220563 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
2220593 CCCAA
1 CCCAA
2220598 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:2220571 original size:30 final size:30
Alignment explanation
Indices: 2220541--2220597 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2220531 CCACCCAACT
2220541 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
2220570 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
2220598 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:2227522 original size:69 final size:71
Alignment explanation
Indices: 2227403--2227551 Score: 223
Period size: 69 Copynumber: 2.1 Consensus size: 71
2227393 GGGGAATCAT
* *
2227403 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTTCATTTC-AA-ATACAATGG
1 CACTTAGCAACCCCTCGGAGGAATCAGCACATAGCAACCCCCTTTACATTTCAAAGATACAATGG
2227466 ATATCG
66 ATATCG
***
2227472 CACTTAGCAACCCCTCGGAGGAATCAGCACATAGCAA-CCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGAGGAATCAGCACATAGCAACCCCCTTT-ACATTTCAAAGATACAATG
2227536 GATATCG
65 GATATCG
2227543 CACTTAGCA
1 CACTTAGCA
2227552 CCACCAATGA
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
68 7 0.10
69 42 0.58
70 2 0.03
71 21 0.29
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.23
Consensus pattern (71 bp):
CACTTAGCAACCCCTCGGAGGAATCAGCACATAGCAACCCCCTTTACATTTCAAAGATACAATGG
ATATCG
Found at i:2227598 original size:103 final size:104
Alignment explanation
Indices: 2227471--2227693 Score: 360
Period size: 104 Copynumber: 2.2 Consensus size: 104
2227461 AATGGATATC
2227471 GCACTTAGCAACCCCTCGGAGGAATCAGCACATAGCAA-CCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGAGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
2227535 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
*
2227574 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGAGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
2227639 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
2227678 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
2227694 TTTATATACA
Statistics
Matches: 111, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
103 37 0.33
104 73 0.66
105 1 0.01
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGAGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:2228061 original size:30 final size:29
Alignment explanation
Indices: 2228027--2228091 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
2228017 TAATCCACCA
2228027 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
2228057 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
2228087 CCCAA
1 CCCAA
2228092 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:2228065 original size:31 final size:30
Alignment explanation
Indices: 2228034--2228091 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2228024 CCACCCAACT
2228034 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
2228064 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
2228092 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:2237092 original size:32 final size:32
Alignment explanation
Indices: 2237056--2237119 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2237046 GTATCTAATC
2237056 TCACCGCCACCGTTGTTTTTACACTAACTGCA
1 TCACCGCCACCGTTGTTTTTACACTAACTGCA
2237088 TCACCGCCACCGTTGTTTTTACACTAACTGCA
1 TCACCGCCACCGTTGTTTTTACACTAACTGCA
2237120 GGGAAATACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.34, G:0.12, T:0.31
Consensus pattern (32 bp):
TCACCGCCACCGTTGTTTTTACACTAACTGCA
Found at i:2237934 original size:112 final size:113
Alignment explanation
Indices: 2237766--2237968 Score: 273
Period size: 112 Copynumber: 1.8 Consensus size: 113
2237756 AATAGATTTG
* * * ** * * *
2237766 AGGTGATGAAGAGGAGGATAGACCATTTGAGATTTGGCCTTTTATGCATCATTGATGTGGTGGGT
1 AGGTGATGAAGAGGAGAATAGACAATTTGAAACGTGGCCTTTTACGCATCACTGATGCGGTGGGT
2237831 CTCTT-GGGGCTTTTGACAGTTTTTTCAACCATGATGTGATAAATCTA
66 CTCTTGGGGGCTTTTGACAGTTTTTTCAACCATGATGTGATAAATCTA
* * * *
2237878 AGGTGATGAAGAGGAGAATAGGCAATTTGAAACGTGGCTTTTTGCGCATTACTGATGCGGTGGGT
1 AGGTGATGAAGAGGAGAATAGACAATTTGAAACGTGGCCTTTTACGCATCACTGATGCGGTGGGT
* *
2237943 CTCTTGGGGGTTTTTGATAGTTTTTT
66 CTCTTGGGGGCTTTTGACAGTTTTTT
2237969 TTTTGTTAAT
Statistics
Matches: 76, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
112 58 0.76
113 18 0.24
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.36
Consensus pattern (113 bp):
AGGTGATGAAGAGGAGAATAGACAATTTGAAACGTGGCCTTTTACGCATCACTGATGCGGTGGGT
CTCTTGGGGGCTTTTGACAGTTTTTTCAACCATGATGTGATAAATCTA
Found at i:2245413 original size:20 final size:20
Alignment explanation
Indices: 2245390--2245429 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2245380 TTGTATTTTA
*
2245390 TTATTAT-CATTATTATTATT
1 TTATTATGCA-TATTAGTATT
2245410 TTATTATGCATATTAGTATT
1 TTATTATGCATATTAGTATT
2245430 ATGATTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (20 bp):
TTATTATGCATATTAGTATT
Found at i:2245424 original size:23 final size:23
Alignment explanation
Indices: 2245383--2245431 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2245373 TGTGCTTTTG
* *
2245383 TATTTTATTATTATCATTATTAT
1 TATTTTATTATCATCATTAGTAT
2245406 TATTTTATTATGCAT-ATTAGTAT
1 TATTTTATTAT-CATCATTAGTAT
2245429 TAT
1 TAT
2245432 GATTTGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (23 bp):
TATTTTATTATCATCATTAGTAT
Found at i:2247537 original size:3 final size:3
Alignment explanation
Indices: 2247529--2247559 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2247519 AGCACAATCT
2247529 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2247560 GCAATTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2247641 original size:5 final size:5
Alignment explanation
Indices: 2247631--2247656 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2247621 TTTCAATTCT
2247631 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
2247657 ATTTTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:2249826 original size:21 final size:21
Alignment explanation
Indices: 2249768--2249826 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
2249758 TATTTGGAAC
*
2249768 TACAATAACAAGAGTACTGAAG
1 TACAA-AACAAGAGTACCGAAG
*
2249790 TGCCAGAAACAAGAGTACCGAAG
1 T-ACA-AAACAAGAGTACCGAAG
*
2249813 TACAAAATAAGAGT
1 TACAAAACAAGAGT
2249827 CTCCTATTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 9 0.29
22 3 0.10
23 18 0.58
24 1 0.03
ACGTcount: A:0.49, C:0.15, G:0.20, T:0.15
Consensus pattern (21 bp):
TACAAAACAAGAGTACCGAAG
Found at i:2254651 original size:21 final size:22
Alignment explanation
Indices: 2254621--2254676 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
2254611 ACATAGATCT
* *
2254621 AACCAAACACACCAGAATATTC
1 AACCTAACACACCAGAATATCC
2254643 AACCT-ACACACCAGAATATCC
1 AACCTAACACACCAGAATATCC
2254664 AACCTAACACACC
1 AACCTAACACACC
2254677 CGGAATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.46, C:0.38, G:0.04, T:0.12
Consensus pattern (22 bp):
AACCTAACACACCAGAATATCC
Found at i:2258046 original size:27 final size:27
Alignment explanation
Indices: 2258016--2258068 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2258006 ATATAATCTA
* * *
2258016 AAAAATATTTAAAATTTAATAAAATTC
1 AAAAATATATAAAATTCAAAAAAATTC
2258043 AAAAATATATAAAATTCAAAAAAATT
1 AAAAATATATAAAATTCAAAAAAATT
2258069 ATGATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (27 bp):
AAAAATATATAAAATTCAAAAAAATTC
Found at i:2281564 original size:25 final size:25
Alignment explanation
Indices: 2281517--2281565 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2281507 GACGTCAATA
*
2281517 AATAAAATAATAATATATTTTTTTG
1 AATAAAATAATAATATATATTTTTG
*
2281542 AATAAAAT-ATAATTTTATATTTTT
1 AATAAAATAATAA-TATATATTTTT
2281566 TTAATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
AATAAAATAATAATATATATTTTTG
Found at i:2282008 original size:19 final size:19
Alignment explanation
Indices: 2281984--2282322 Score: 169
Period size: 19 Copynumber: 18.5 Consensus size: 19
2281974 GTTTAGATTA
*
2281984 TAATTTTGTATGAATATTC
1 TAATTTTGTATGAATATTG
2282003 TAATTTTTTTGTATGAATATTG
1 TAA---TTTTGTATGAATATTG
*
2282025 TAATTTTTTATGAATATTG
1 TAATTTTGTATGAATATTG
*
2282044 TAATGTTGTATGAATATTG
1 TAATTTTGTATGAATATTG
*
2282063 TAATTATTTTAT-AATTAAATTTG
1 TAATT-TTGTATGAA-T--A-TTG
* * *
2282086 T-ATTTATAGTTTTGGAT-TAG
1 TAATTT-T-G-TATGAATATTG
2282106 TAA-TTTGTATGAATATTG
1 TAATTTTGTATGAATATTG
2282124 TAATTTTTTGTATGAATATTG
1 TAA--TTTTGTATGAATATTG
*
2282145 TAATTTT-TTTG--TA-TG
1 TAATTTTGTATGAATATTG
* *
2282160 -AATATTG--T-AATATTA
1 TAATTTTGTATGAATATTG
*
2282175 TAGTTTTGTATGAATATTG
1 TAATTTTGTATGAATATTG
* *
2282194 CAATTTT-TTTG--TA-TG
1 TAATTTTGTATGAATATTG
* *
2282209 -AATATTG--T-AATTTTG
1 TAATTTTGTATGAATATTG
2282224 TAATTTTGTATGAATATTG
1 TAATTTTGTATGAATATTG
2282243 TAATTTT-T-TG--TA-TG
1 TAATTTTGTATGAATATTG
* *
2282257 -AATATTG--T-AATATTA
1 TAATTTTGTATGAATATTG
2282272 TAATTTTGTATGAATATTG
1 TAATTTTGTATGAATATTG
*
2282291 CAATTTTTTTGTATGAATATTG
1 TAA---TTTTGTATGAATATTG
2282313 TAATTTTGTA
1 TAATTTTGTA
2282323 ATTTTGTATG
Statistics
Matches: 244, Mismatches: 32, Indels: 88
0.67 0.09 0.24
Matches are distributed among these distances:
13 8 0.03
14 17 0.07
15 10 0.04
16 21 0.09
17 7 0.03
18 16 0.07
19 85 0.35
20 11 0.05
21 20 0.08
22 41 0.17
23 4 0.02
24 3 0.01
25 1 0.00
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATGAATATTG
Found at i:2282015 original size:22 final size:22
Alignment explanation
Indices: 2281987--2282343 Score: 289
Period size: 22 Copynumber: 15.9 Consensus size: 22
2281977 TAGATTATAA
*
2281987 TTTTGTATGAATATTCTAATTT
1 TTTTGTATGAATATTGTAATTT
2282009 TTTTGTATGAATATTGTAA--T
1 TTTTGTATGAATATTGTAATTT
2282029 TTTT-TATGAATATTGTAA---
1 TTTTGTATGAATATTGTAATTT
* *
2282047 TGTTGTATGAATATTGTAATTA
1 TTTTGTATGAATATTGTAATTT
* *
2282069 TTTTATAATTAA-ATTTGT-ATTT
1 TTTTGT-ATGAATA-TTGTAATTT
* * *
2282091 ATAGTT-T-TGGAT-TAGTAA---
1 -T-TTTGTATGAATATTGTAATTT
2282109 -TTTGTATGAATATTGTAA-TT
1 TTTTGTATGAATATTGTAATTT
2282129 TTTTGTATGAATATTGTAATTT
1 TTTTGTATGAATATTGTAATTT
2282151 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-ATT-T
*
2282176 AGTTTTGTATGAATATTGCAATTT
1 --TTTTGTATGAATATTGTAATTT
2282200 TTTTGTATGAATATTGTAATTTTGT
1 TTTTGTATGAATATTGTAA--TT-T
2282225 AATTTTGTATGAATATTGTAA-TT
1 --TTTTGTATGAATATTGTAATTT
2282248 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-ATT-T
*
2282273 AATTTTGTATGAATATTGCAATTT
1 --TTTTGTATGAATATTGTAATTT
2282297 TTTTGTATGAATATTGTAATTTTGT
1 TTTTGTATGAATATTGTAA--TT-T
2282322 AATTTTGTATGAATATTGTAAT
1 --TTTTGTATGAATATTGTAAT
2282344 GTCGGGATAT
Statistics
Matches: 280, Mismatches: 17, Indels: 73
0.76 0.05 0.20
Matches are distributed among these distances:
15 2 0.01
16 1 0.00
17 4 0.01
18 8 0.03
19 28 0.10
20 8 0.03
21 38 0.14
22 82 0.29
23 13 0.05
24 13 0.05
25 11 0.04
26 2 0.01
27 70 0.25
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.55
Consensus pattern (22 bp):
TTTTGTATGAATATTGTAATTT
Found at i:2282023 original size:61 final size:60
Alignment explanation
Indices: 2281958--2282311 Score: 188
Period size: 60 Copynumber: 6.1 Consensus size: 60
2281948 TAAATTATCT
*
2281958 ATATTTAGTGTTTATAGTTTAGATTATAATTTTGTATGAATATTCTAATTTTTTTGTATGA
1 ATATTTAGT-TTTATAGTTTAGATTATAATTTTGTATGAATATTGTAATTTTTTTGTATGA
* * ** * * * * * *
2282019 ATATTGTAATTTTTTA-TGAATATTGTAATGTTGTATGAATATTGTAATTATTTTATAATTA
1 ATATT-TAGTTTTATAGTTTAGATTATAATTTTGTATGAATATTGTAATTTTTTTGT-ATGA
*
2282080 A-ATTT-GTATTTATAGTTTTGGATTAGTAA-TTTGTATGAATATTGTAA-TTTTTTGTATGA
1 ATATTTAGT-TTTATAG-TTTAGATTA-TAATTTTGTATGAATATTGTAATTTTTTTGTATGA
* * * * *
2282139 ATATTGTAATTTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTGCAATTTTTTT
1 ATATT-T-A---GTTT-TAT--A-GTT-T-AGATTATAATTTTGTATGAATATTGTAATTTTTTT
2282204 GTATGA
55 GTATGA
*
2282210 ATA-TT-G---TA-A--TT---TTGTAATTTTGTATGAATATTGTAATTTTTT-GTATGA
1 ATATTTAGTTTTATAGTTTAGATTATAATTTTGTATGAATATTGTAATTTTTTTGTATGA
*
2282258 ATA-TT-G---TA-A---T--ATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGA
1 ATATTTAGTTTTATAGTTTAGATTATAATTTTGTATGAATATTGTAATTTTTTTGTATGA
2282307 ATATT
1 ATATT
2282312 GTAATTTTGT
Statistics
Matches: 235, Mismatches: 34, Indels: 59
0.72 0.10 0.18
Matches are distributed among these distances:
47 1 0.00
48 44 0.19
49 37 0.16
50 1 0.00
53 1 0.00
54 1 0.00
57 1 0.00
58 1 0.00
59 10 0.04
60 46 0.20
61 36 0.15
62 6 0.03
65 2 0.01
66 4 0.02
68 3 0.01
69 4 0.02
70 22 0.09
71 15 0.06
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.55
Consensus pattern (60 bp):
ATATTTAGTTTTATAGTTTAGATTATAATTTTGTATGAATATTGTAATTTTTTTGTATGA
Found at i:2282078 original size:49 final size:49
Alignment explanation
Indices: 2282025--2282391 Score: 273
Period size: 49 Copynumber: 7.5 Consensus size: 49
2282015 ATGAATATTG
* *
2282025 TAATTTTTTATGAATATTGTAA-TGTTGTATGAATATTGTAATTATTTTA
1 TAATTTTGTATGAATATTGTAATTTTTGTATGAATATTGTAA-TATTTTA
*** * * * *
2282074 TAATTAAATTTG--TATT-TATAGTTTTGGATTAGTAAT-TTGTATGAATATTGTA
1 TAATTTTGTATGAATATTGTA-ATTTTTGTA-T-G-AATATTG--T-AATATTTTA
*
2282126 -ATTTTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATA--TTA
1 TAATTT-TGTATGAATATTGTAA--TTTTTGTATGAATATTGTAATATTTTA
* * *
2282175 TAGTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT-A-ATTTTG
1 TAATTTTGTATGAATATTGTAA--TTTTTGTATGAATATTGTAATATTTTA
2282224 TAATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATA--TTA
1 TAATTTTGTATGAATATTGTAA-TTTTTGTATGAATATTGTAATATTTTA
* *
2282272 TAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT-A-ATTTTG
1 TAATTTTGTATGAATATTGTAA--TTTTTGTATGAATATTGTAATATTTTA
* ** * *
2282321 TAATTTTGTATGAATATTGTAATGTCGGGAT--ATATTGTAATATTGTA
1 TAATTTTGTATGAATATTGTAATTTTTGTATGAATATTGTAATATTTTA
*
2282368 -ATTTTTTGTATGAATATTGTAATT
1 TA-ATTTTGTATGAATATTGTAATT
2282392 ATTTTATAAT
Statistics
Matches: 260, Mismatches: 32, Indels: 54
0.75 0.09 0.16
Matches are distributed among these distances:
45 7 0.03
46 4 0.02
47 36 0.14
48 49 0.19
49 111 0.43
50 9 0.03
51 10 0.04
52 11 0.04
53 5 0.02
54 9 0.03
55 3 0.01
56 6 0.02
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (49 bp):
TAATTTTGTATGAATATTGTAATTTTTGTATGAATATTGTAATATTTTA
Found at i:2282183 original size:27 final size:24
Alignment explanation
Indices: 2282109--2282343 Score: 242
Period size: 27 Copynumber: 9.8 Consensus size: 24
2282099 GGATTAGTAA
2282109 TTTGTATGAATATTGT-A-A-TTT
1 TTTGTATGAATATTGTAATATTTT
2282130 TTTGTATGAATATTGT-A-ATTTT
1 TTTGTATGAATATTGTAATATTTT
2282152 TTTGTATGAATATTGTAATATTATAGT
1 TTTGTATGAATATTGTAATATT-T--T
*
2282179 TTTGTATGAATATTG-CA-ATTTT
1 TTTGTATGAATATTGTAATATTTT
*
2282201 TTTGTATGAATATTGTAATTTTGTAAT
1 TTTGTATGAATATTGTAATATT-T--T
2282228 TTTGTATGAATATTGT-A-A-TTT
1 TTTGTATGAATATTGTAATATTTT
2282249 TTTGTATGAATATTGTAATATTATAAT
1 TTTGTATGAATATTGTAATATT-T--T
*
2282276 TTTGTATGAATATTG-CA-ATTTT
1 TTTGTATGAATATTGTAATATTTT
*
2282298 TTTGTATGAATATTGTAATTTTGTAAT
1 TTTGTATGAATATTGTAATATT-T--T
2282325 TTTGTATGAATATTGTAAT
1 TTTGTATGAATATTGTAAT
2282344 GTCGGGATAT
Statistics
Matches: 185, Mismatches: 7, Indels: 38
0.80 0.03 0.17
Matches are distributed among these distances:
21 35 0.19
22 52 0.28
23 5 0.03
24 11 0.06
25 10 0.05
26 3 0.02
27 69 0.37
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (24 bp):
TTTGTATGAATATTGTAATATTTT
Found at i:2282263 original size:97 final size:97
Alignment explanation
Indices: 2282129--2282396 Score: 416
Period size: 97 Copynumber: 2.8 Consensus size: 97
2282119 TATTGTAATT
*
2282129 TTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTG
1 TTTTGTATGAATATTGTAA-TTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTG
2282194 CAATTTTTTTGTATGAATATTGTAATTTTGTAA
65 CAATTTTTTTGTATGAATATTGTAATTTTGTAA
2282227 TTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGC
1 TTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGC
2282292 AATTTTTTTGTATGAATATTGTAATTTTGTAA
66 AATTTTTTTGTATGAATATTGTAATTTTGTAA
* ** * *
2282324 TTTTGTATGAATATTGTAA-TGTCGGGAT--ATATTGTAATATTGTAATTTTTTGTATGAATATT
1 TTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTATAA--TTTTGTATGAATATT
* *
2282386 GTAATTATTTT
64 GCAATTTTTTT
2282397 ATAATTAATT
Statistics
Matches: 160, Mismatches: 8, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
94 16 0.10
96 29 0.18
97 96 0.60
98 19 0.12
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.54
Consensus pattern (97 bp):
TTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGC
AATTTTTTTGTATGAATATTGTAATTTTGTAA
Found at i:2282465 original size:60 final size:60
Alignment explanation
Indices: 2282384--2282505 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 60
2282374 TGTATGAATA
* * ** * * *
2282384 TTGTAATTATTTTATAATTAATTTGTTAGTAATTTGGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTAAAATTAATTTATTAGTAATTCAGGATTAAGCTATAAATTGTTGTGT
*
2282444 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTCAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTTAAAA-TTAATTTATTAGTAATTCAGGATTAAGCTATAAATTGTTGTGT
2282504 TT
1 TT
2282506 AGTTTAGTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 6 0.11
60 47 0.89
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (60 bp):
TTGTAATTATTTTAAAATTAATTTATTAGTAATTCAGGATTAAGCTATAAATTGTTGTGT
Found at i:2282584 original size:38 final size:38
Alignment explanation
Indices: 2282539--2282620 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
2282529 CATATAAAGT
2282539 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
*
2282577 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
2282615 TTATAA
1 TTATAA
2282621 CTGACTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:2282698 original size:15 final size:15
Alignment explanation
Indices: 2282657--2282698 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
2282647 GTTAACTCAT
*
2282657 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
2282672 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
2282688 TTAAATTTTAT
1 TTAAATTTTAT
2282699 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:2284338 original size:12 final size:12
Alignment explanation
Indices: 2284321--2284359 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2284311 GCATCATGCA
2284321 CCAGAGCCAAAG
1 CCAGAGCCAAAG
*
2284333 CCAGAGCCAATG
1 CCAGAGCCAAAG
*
2284345 CCAGAGCCAGAG
1 CCAGAGCCAAAG
2284357 CCA
1 CCA
2284360 AAACTACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.36, C:0.36, G:0.26, T:0.03
Consensus pattern (12 bp):
CCAGAGCCAAAG
Found at i:2284340 original size:6 final size:6
Alignment explanation
Indices: 2284321--2284359 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
2284311 GCATCATGCA
*
2284321 CCAGAG CCAAAG CCAGAG CCA-ATG CCAGAG CCAGAG CCA
1 CCAGAG CCAGAG CCAGAG CCAGA-G CCAGAG CCAGAG CCA
2284360 AAACTACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 1 0.03
6 27 0.93
7 1 0.03
ACGTcount: A:0.36, C:0.36, G:0.26, T:0.03
Consensus pattern (6 bp):
CCAGAG
Found at i:2284352 original size:18 final size:18
Alignment explanation
Indices: 2284326--2284360 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2284316 ATGCACCAGA
2284326 GCCAAAGCCAGAGCCAAT
1 GCCAAAGCCAGAGCCAAT
*
2284344 GCCAGAGCCAGAGCCAA
1 GCCAAAGCCAGAGCCAA
2284361 AACTACATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.34, G:0.26, T:0.03
Consensus pattern (18 bp):
GCCAAAGCCAGAGCCAAT
Found at i:2287697 original size:22 final size:23
Alignment explanation
Indices: 2287672--2287724 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
2287662 AATACCTTAT
*
2287672 TTTTTCTTCT-TTTCCTTCCTTC
1 TTTTTCTTCTGCTTCCTTCCTTC
2287694 -TTTTCTTCTGCTTCCTTCCTTC
1 TTTTTCTTCTGCTTCCTTCCTTC
2287716 TTATTTCTT
1 TT-TTTCTT
2287725 TCGTTTCTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 9 0.33
22 11 0.41
23 1 0.04
24 6 0.22
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTTTCTTCTGCTTCCTTCCTTC
Found at i:2295099 original size:14 final size:14
Alignment explanation
Indices: 2295080--2295108 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2295070 AATGAAGCTT
2295080 ACTTCATACATTGA
1 ACTTCATACATTGA
2295094 ACTTCATACATTGA
1 ACTTCATACATTGA
2295108 A
1 A
2295109 AAGGGAGTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (14 bp):
ACTTCATACATTGA
Found at i:2295270 original size:13 final size:14
Alignment explanation
Indices: 2295239--2295271 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2295229 GTCAAATATT
*
2295239 AATATTTTATGTCA
1 AATATTTTATGTAA
2295253 AATATTTTAT-TAA
1 AATATTTTATGTAA
2295266 AATATT
1 AATATT
2295272 CTTAAAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (14 bp):
AATATTTTATGTAA
Found at i:2296897 original size:18 final size:19
Alignment explanation
Indices: 2296859--2296897 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
2296849 TTAATAATGA
2296859 TTGAAACTAGACGTTCAAT
1 TTGAAACTAGACGTTCAAT
2296878 TTGAAACT-GA-GTTACAAT
1 TTGAAACTAGACGTT-CAAT
2296896 TT
1 TT
2296898 ATTTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 8 0.42
19 8 0.42
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (19 bp):
TTGAAACTAGACGTTCAAT
Found at i:2304234 original size:25 final size:25
Alignment explanation
Indices: 2304200--2304251 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
2304190 CGAGTGATTC
2304200 AAAGTGCATTTCGAAGCTAAGAGAT
1 AAAGTGCATTTCGAAGCTAAGAGAT
2304225 AAAGTGCATTTCGAAGCTAAGAGAT
1 AAAGTGCATTTCGAAGCTAAGAGAT
2304250 AA
1 AA
2304252 CTCTTCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (25 bp):
AAAGTGCATTTCGAAGCTAAGAGAT
Found at i:2306594 original size:29 final size:28
Alignment explanation
Indices: 2306553--2306616 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
2306543 CCGAATATAA
* *
2306553 TAAATATA-TTTTTTTCAATTTTTAATTT
1 TAAA-ATACTTTTTTTAATTTTTTAATTT
*
2306581 TAAAATACTTTTTTTAATTTTTTTATTTT
1 TAAAATACTTTTTTTAA-TTTTTTAATTT
2306610 TAAAATA
1 TAAAATA
2306617 AATTTTTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 3 0.10
28 12 0.39
29 16 0.52
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (28 bp):
TAAAATACTTTTTTTAATTTTTTAATTT
Found at i:2307521 original size:43 final size:43
Alignment explanation
Indices: 2307467--2307552 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
2307457 GAAATAAATG
* *
2307467 AAAATTTTAAGAACATGATATACATGTGGATTATTATATGGAC
1 AAAAATTTAAGAACATGACATACATGTGGATTATTATATGGAC
2307510 AAAAATTTAAGAACATGACATACATGTGGATTATTATATGGAC
1 AAAAATTTAAGAACATGACATACATGTGGATTATTATATGGAC
2307553 CACATGTTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (43 bp):
AAAAATTTAAGAACATGACATACATGTGGATTATTATATGGAC
Found at i:2309082 original size:13 final size:13
Alignment explanation
Indices: 2309061--2309123 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
2309051 TTAGCGATGC
2309061 TTTTAAAAAGTAT
1 TTTTAAAAAGTAT
*
2309074 TTTTTAAAAGTAT
1 TTTTAAAAAGTAT
*** *
2309087 TACAAAAAAATAT
1 TTTTAAAAAGTAT
2309100 TTTTAAGAAA-TAT
1 TTTTAA-AAAGTAT
2309113 TTTTAAAAAGT
1 TTTTAAAAAGT
2309124 TTAGTTTAAG
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
12 3 0.08
13 33 0.85
14 3 0.08
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (13 bp):
TTTTAAAAAGTAT
Found at i:2309451 original size:19 final size:20
Alignment explanation
Indices: 2309418--2309456 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2309408 CACATTTGTA
2309418 TTATTTTAAAAAAT-ATTTT
1 TTATTTTAAAAAATAATTTT
**
2309437 TTATTTTAATTAATAATTTT
1 TTATTTTAAAAAATAATTTT
2309457 AACATATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTTAAAAAATAATTTT
Found at i:2311871 original size:12 final size:12
Alignment explanation
Indices: 2311848--2311883 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
2311838 TATATATATT
2311848 TAAAAATT-ATA
1 TAAAAATTAATA
2311859 TAAAAATTAATA
1 TAAAAATTAATA
2311871 TAAAAATTAATA
1 TAAAAATTAATA
2311883 T
1 T
2311884 GGCCGAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAAATTAATA
Found at i:2314258 original size:18 final size:18
Alignment explanation
Indices: 2314162--2314258 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
2314152 TACGACCGTT
2314162 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
2314180 TACAGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
2314198 TACGGTACTATTTACGTA
1 TACGGTACTATTCACGTA
* *
2314216 TATGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
2314234 TATGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
2314252 TACGGTA
1 TACGGTA
2314259 GTTGGGATTG
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:2320288 original size:21 final size:19
Alignment explanation
Indices: 2320244--2320289 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
2320234 ACATTTAATT
*
2320244 AATTTTTAAATTTTTTTTA
1 AATTTTTAAATTTTTTTAA
*
2320263 TATTTTTCAGAATTTTTTTAA
1 AATTTTT-A-AATTTTTTTAA
2320284 AATTTT
1 AATTTT
2320290 AAAAAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 1 0.05
21 15 0.68
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
AATTTTTAAATTTTTTTAA
Found at i:2321300 original size:37 final size:37
Alignment explanation
Indices: 2321259--2321369 Score: 101
Period size: 37 Copynumber: 3.1 Consensus size: 37
2321249 AGAAGAAAAG
2321259 GAAAATAAAGAAATAAAAAGGAAAAATTAAATTGTTC
1 GAAAATAAAGAAATAAAAAGGAAAAATTAAATTGTTC
* ** * * *
2321296 GAAAA-AAATAAA-AGTAAGGGGAAGAA-GAAA-AG---
1 GAAAATAAAGAAATA--AAAAGGAAAAATTAAATTGTTC
2321328 GAAAATAAAGAAATAAAAAGGAAAAATTAAATTGTTC
1 GAAAATAAAGAAATAAAAAGGAAAAATTAAATTGTTC
2321365 GAAAA
1 GAAAA
2321370 AAATAAAAGT
Statistics
Matches: 53, Mismatches: 12, Indels: 18
0.64 0.14 0.22
Matches are distributed among these distances:
32 13 0.25
33 9 0.17
34 2 0.04
35 2 0.04
36 9 0.17
37 18 0.34
ACGTcount: A:0.64, C:0.02, G:0.18, T:0.16
Consensus pattern (37 bp):
GAAAATAAAGAAATAAAAAGGAAAAATTAAATTGTTC
Found at i:2321332 original size:32 final size:32
Alignment explanation
Indices: 2321296--2321401 Score: 81
Period size: 32 Copynumber: 3.2 Consensus size: 32
2321286 TAAATTGTTC
2321296 GAAAAAAATAAAAGTAAGGGGAAGAAGAAAAG
1 GAAAAAAATAAAAGTAAGGGGAAGAAGAAAAG
* ** * * *
2321328 GAAAATAAA-GAAA-TAAAAAGGAAAAATTAAATTG
1 GAAAA-AAATAAAAGT-AAGGGGAAGAA-GAAA-AG
2321362 TTCGAAAAAAATAAAAGTAAGGGGAAGAAGAAAAG
1 ---GAAAAAAATAAAAGTAAGGGGAAGAAGAAAAG
2321397 GAAAA
1 GAAAA
2321402 TAAAGAAATA
Statistics
Matches: 53, Mismatches: 12, Indels: 18
0.64 0.14 0.22
Matches are distributed among these distances:
31 1 0.02
32 21 0.40
33 6 0.11
34 1 0.02
35 1 0.02
36 6 0.11
37 16 0.30
38 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.23, T:0.11
Consensus pattern (32 bp):
GAAAAAAATAAAAGTAAGGGGAAGAAGAAAAG
Found at i:2321353 original size:69 final size:69
Alignment explanation
Indices: 2321242--2321454 Score: 399
Period size: 69 Copynumber: 3.1 Consensus size: 69
2321232 GTTAAATCTA
2321242 AAGGGGAAGAAGAAAAGGAAAATAAAGAAATAAAAAGGAAAAATTAAATTGTTCGAAAAAAATAA
1 AAGGGGAAGAAGAAAAGGAAAATAAAGAAATAAAAAGGAAAAATTAAATTGTTCGAAAAAAATAA
2321307 AAGT
66 AAGT
2321311 AAGGGGAAGAAGAAAAGGAAAATAAAGAAATAAAAAGGAAAAATTAAATTGTTCGAAAAAAATAA
1 AAGGGGAAGAAGAAAAGGAAAATAAAGAAATAAAAAGGAAAAATTAAATTGTTCGAAAAAAATAA
2321376 AAGT
66 AAGT
* *
2321380 AAGGGGAAGAAGAAAAGGAAAATAAAGAAATAAAAAGAAAAAATTAAATTTTTCGAAAAAAATAA
1 AAGGGGAAGAAGAAAAGGAAAATAAAGAAATAAAAAGGAAAAATTAAATTGTTCGAAAAAAATAA
2321445 AAGT
66 AAGT
2321449 ATAGGG
1 A-AGGG
2321455 ACTAGTTTTA
Statistics
Matches: 141, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
69 137 0.97
70 4 0.03
ACGTcount: A:0.63, C:0.01, G:0.20, T:0.15
Consensus pattern (69 bp):
AAGGGGAAGAAGAAAAGGAAAATAAAGAAATAAAAAGGAAAAATTAAATTGTTCGAAAAAAATAA
AAGT
Found at i:2322239 original size:23 final size:22
Alignment explanation
Indices: 2322210--2322256 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
2322200 CAAAGAAAAC
* *
2322210 AATATGAATATACAAATATATAT
1 AATATGAATAAAAAAATATA-AT
2322233 AATATGAATAAAAAAATATAAT
1 AATATGAATAAAAAAATATAAT
2322255 AA
1 AA
2322257 AATAAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (22 bp):
AATATGAATAAAAAAATATAAT
Found at i:2322257 original size:13 final size:15
Alignment explanation
Indices: 2322233--2322264 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2322223 AAATATATAT
2322233 AATATGAATAAAA-A
1 AATATGAATAAAATA
2322247 AATAT-AATAAAATA
1 AATATGAATAAAATA
2322261 AATA
1 AATA
2322265 CATGATTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (15 bp):
AATATGAATAAAATA
Found at i:2328869 original size:30 final size:31
Alignment explanation
Indices: 2328828--2328891 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
2328818 TTTAAATATT
*
2328828 TAAAATATTTAA-AATT-ATTTATTATTTTAA
1 TAAAATATTTAATAATTCAATT-TTATTTTAA
* *
2328858 TAAATTATTTAATATTTCAATTTTATTTTAA
1 TAAAATATTTAATAATTCAATTTTATTTTAA
2328889 TAA
1 TAA
2328892 TAAATTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 11 0.38
31 15 0.52
32 3 0.10
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (31 bp):
TAAAATATTTAATAATTCAATTTTATTTTAA
Found at i:2328922 original size:16 final size:17
Alignment explanation
Indices: 2328886--2328922 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
2328876 AATTTTATTT
2328886 TAATAATAAATTTTAAA
1 TAATAATAAATTTTAAA
2328903 -AATAATAAA-TTTAAA
1 TAATAATAAATTTTAAA
2328918 TAATA
1 TAATA
2328923 TTCAATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:2330695 original size:21 final size:23
Alignment explanation
Indices: 2330650--2330699 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
2330640 GATTTATAAA
2330650 AATATATATTGATAAATATTGAT
1 AATATATATTGATAAATATTGAT
*
2330673 AATATATATTTATAAAT-TT-AT
1 AATATATATTGATAAATATTGAT
2330694 AATATA
1 AATATA
2330700 AAAATTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 8 0.31
22 2 0.08
23 16 0.62
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
AATATATATTGATAAATATTGAT
Found at i:2330750 original size:14 final size:14
Alignment explanation
Indices: 2330731--2330771 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2330721 GTAAGCCATT
2330731 ATAATATTTTTATA
1 ATAATATTTTTATA
*
2330745 ATAATA--TATATA
1 ATAATATTTTTATA
*
2330757 ATATTATTTTTATA
1 ATAATATTTTTATA
2330771 A
1 A
2330772 ATGTACTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
12 10 0.45
14 12 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATAATATTTTTATA
Found at i:2338479 original size:20 final size:21
Alignment explanation
Indices: 2338454--2338497 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
2338444 ATTTTTCACC
*
2338454 ATCTAGGA-AAAAGTATCGAT
1 ATCTAGGACAAAAATATCGAT
2338474 ATCTAGGACCAAAAATATCGAT
1 ATCTAGGA-CAAAAATATCGAT
2338496 AT
1 AT
2338498 TTTTACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
22 13 0.62
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (21 bp):
ATCTAGGACAAAAATATCGAT
Found at i:2344434 original size:20 final size:20
Alignment explanation
Indices: 2344409--2344449 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2344399 AAAATATTTA
2344409 AATGCTGAATATTTATTGAT
1 AATGCTGAATATTTATTGAT
2344429 AATGCTGAATATTTATTGAT
1 AATGCTGAATATTTATTGAT
2344449 A
1 A
2344450 TGTAGAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (20 bp):
AATGCTGAATATTTATTGAT
Found at i:2344473 original size:22 final size:22
Alignment explanation
Indices: 2344447--2344489 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2344437 ATATTTATTG
*
2344447 ATAT-GTAGAGTATTTTAGATTA
1 ATATGGTAGAG-ATGTTAGATTA
2344469 ATATGGTAGAGATGTTAGATT
1 ATATGGTAGAGATGTTAGATT
2344490 GATTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (22 bp):
ATATGGTAGAGATGTTAGATTA
Found at i:2363463 original size:50 final size:50
Alignment explanation
Indices: 2363409--2363654 Score: 150
Period size: 50 Copynumber: 5.1 Consensus size: 50
2363399 TCCTTAGCAG
* * *
2363409 TGCAACGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCAGATAT
1 TGCAATGGAAAAGATTGAAGCTACGACGGCGGATCTGGTTTCCCAGACAT
** * * * **
2363459 TGCAATTAAAAAGATTGAAGCCACAACAGCGGATC----TTAGCAG-CA-
1 TGCAATGGAAAAGATTGAAGCTACGACGGCGGATCTGGTTTCCCAGACAT
* * * * *
2363503 --CAATGGAATAGATTGAAGCTACGACGGTGGATCTAGTTTTCCTGACAT
1 TGCAATGGAAAAGATTGAAGCTACGACGGCGGATCTGGTTTCCCAGACAT
** * * *** **
2363551 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTA-ACGG
1 TGCAATGGAAAAGATTGAAGCTACGACGGCGGATCTGGTTTCCC-AGACAT
*** * * *
2363601 TGTGGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCGATAT
1 TGCAATGGAAAAGATTGAAGCTACGACGGCGGATCTGGTTTCCCAGACAT
2363651 TGCA
1 TGCA
2363655 GTTAAACAAA
Statistics
Matches: 136, Mismatches: 50, Indels: 20
0.66 0.24 0.10
Matches are distributed among these distances:
42 26 0.19
45 1 0.01
46 9 0.07
47 2 0.01
50 98 0.72
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (50 bp):
TGCAATGGAAAAGATTGAAGCTACGACGGCGGATCTGGTTTCCCAGACAT
Found at i:2363558 original size:92 final size:92
Alignment explanation
Indices: 2363401--2363588 Score: 286
Period size: 92 Copynumber: 2.0 Consensus size: 92
2363391 ATCTTACTTC
** * *
2363401 CTTAGCAGTGCAACGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCAGATATTGCAATT
1 CTTAGCAGCACAACGGAACAGATTGAAGCTACGACGGCGGATCTAGTTTCCCAGACATTGCAATT
2363466 AAAAAGATTGAAGCCACAACAGCGGAT
66 AAAAAGATTGAAGCCACAACAGCGGAT
* * * * *
2363493 CTTAGCAGCACAATGGAATAGATTGAAGCTACGACGGTGGATCTAGTTTTCCTGACATTGCAATT
1 CTTAGCAGCACAACGGAACAGATTGAAGCTACGACGGCGGATCTAGTTTCCCAGACATTGCAATT
*
2363558 AAAAAGATTGAAGCCACAACGGCGGAT
66 AAAAAGATTGAAGCCACAACAGCGGAT
2363585 CTTA
1 CTTA
2363589 CTTCCCTAAC
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
92 86 1.00
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (92 bp):
CTTAGCAGCACAACGGAACAGATTGAAGCTACGACGGCGGATCTAGTTTCCCAGACATTGCAATT
AAAAAGATTGAAGCCACAACAGCGGAT
Found at i:2363861 original size:44 final size:44
Alignment explanation
Indices: 2363805--2363938 Score: 135
Period size: 44 Copynumber: 3.0 Consensus size: 44
2363795 GATCCGAAAA
* * * *
2363805 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTGGATCGAAGAT
1 AGCAGATTTTGTCTTCCTATATTGGAGTGAAGTGGATCGAAGAT
* * * *
2363849 AGCAGATTTTGTCTTCCTATATCGATAGCGAAGTGGATCGAATAT
1 AGCAGATTTTGTCTTCCTATATTG-GAGTGAAGTGGATCGAAGAT
* * * *
2363894 A-CAGATTTTATCTTCCCATATTGGTGGTGAAGTAGATCGAAGAT
1 AGCAGATTTTGTCTTCCTATATTGG-AGTGAAGTGGATCGAAGAT
2363938 A
1 A
2363939 CAAGTCTTAT
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
44 55 0.76
45 17 0.24
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (44 bp):
AGCAGATTTTGTCTTCCTATATTGGAGTGAAGTGGATCGAAGAT
Found at i:2363940 original size:44 final size:44
Alignment explanation
Indices: 2363831--2363940 Score: 139
Period size: 44 Copynumber: 2.5 Consensus size: 44
2363821 ATGTATTGGC
* *
2363831 GTGAAGTGGATCGAAGATAGCAGATTTTGTCTTCCTATATCGATA
1 GTGAAGTGGATCGAAGATA-CAGATTTTATCTTCCCATATCGATA
* * * * *
2363876 GCGAAGTGGATCGAATATACAGATTTTATCTTCCCATATTGGTG
1 GTGAAGTGGATCGAAGATACAGATTTTATCTTCCCATATCGATA
*
2363920 GTGAAGTAGATCGAAGATACA
1 GTGAAGTGGATCGAAGATACA
2363941 AGTCTTATCT
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 38 0.69
45 17 0.31
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (44 bp):
GTGAAGTGGATCGAAGATACAGATTTTATCTTCCCATATCGATA
Found at i:2365401 original size:20 final size:20
Alignment explanation
Indices: 2365377--2365415 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2365367 CCTTTTTTTT
*
2365377 GTTTTTTT-TTTCTAAATTC
1 GTTTTTTTGTTTTTAAATTC
2365396 GTTTTTTTGTTTTTAAATTC
1 GTTTTTTTGTTTTTAAATTC
2365416 AATTCAGTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (20 bp):
GTTTTTTTGTTTTTAAATTC
Found at i:2365483 original size:15 final size:16
Alignment explanation
Indices: 2365465--2365497 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2365455 TAAATATTTA
*
2365465 TTATTGTTAT-ATTAT
1 TTATTATTATCATTAT
2365480 TTATTATTATCATTAT
1 TTATTATTATCATTAT
2365496 TT
1 TT
2365498 CCATATTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (16 bp):
TTATTATTATCATTAT
Found at i:2367761 original size:7 final size:7
Alignment explanation
Indices: 2367749--2367774 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2367739 GGTCTGTTAT
2367749 AAAAATA
1 AAAAATA
2367756 AAAAATA
1 AAAAATA
2367763 AAAAATA
1 AAAAATA
2367770 AAAAA
1 AAAAA
2367775 CAGTTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:2369351 original size:18 final size:18
Alignment explanation
Indices: 2369313--2369348 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2369303 TTATTATTTT
*
2369313 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
2369331 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
2369349 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:2369521 original size:39 final size:35
Alignment explanation
Indices: 2369432--2369521 Score: 81
Period size: 41 Copynumber: 2.4 Consensus size: 35
2369422 TATGTATATT
* *
2369432 TAATAATATTAAAAATATAATATTTTATATTAATA
1 TAATAATATTAAAAATAAAATATTTTATATCAATA
**
2369467 TTTTAAATATTTTAAAAATAAAAATAAATTTTATTATCAATA
1 TAAT-AATA--TTAAAAAT-AAAAT--ATTTTA-TATCAATA
2369509 TAATAATATTAAA
1 TAATAATATTAAA
2369522 CTTGATTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
35 2 0.05
36 4 0.10
38 8 0.19
39 9 0.21
41 10 0.24
42 9 0.21
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (35 bp):
TAATAATATTAAAAATAAAATATTTTATATCAATA
Found at i:2376424 original size:14 final size:14
Alignment explanation
Indices: 2376405--2376435 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2376395 GGCTTAGCTG
2376405 ACATCATTATTATT
1 ACATCATTATTATT
2376419 ACATCATTATTATT
1 ACATCATTATTATT
2376433 ACA
1 ACA
2376436 GCAATCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (14 bp):
ACATCATTATTATT
Found at i:2381622 original size:3 final size:3
Alignment explanation
Indices: 2381614--2381641 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2381604 TTTACTCAAC
2381614 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2381642 TTCATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2383430 original size:3 final size:3
Alignment explanation
Indices: 2383422--2383454 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2383412 GCAACATGCT
2383422 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG- TGC T
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC T
2383455 CTCCCTCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.00, C:0.30, G:0.33, T:0.36
Consensus pattern (3 bp):
TGC
Found at i:2389730 original size:14 final size:15
Alignment explanation
Indices: 2389686--2389736 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
2389676 TTACCTTAGG
2389686 TTACGTTTTAGTCAC
1 TTACGTTTTAGTCAC
* * **
2389701 TTATGTTTGAAACA-
1 TTACGTTTTAGTCAC
*
2389715 TTACGTTTTAGTCAT
1 TTACGTTTTAGTCAC
2389730 TTACGTT
1 TTACGTT
2389737 ATCATGTTGT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (15 bp):
TTACGTTTTAGTCAC
Found at i:2395759 original size:2 final size:2
Alignment explanation
Indices: 2395746--2395777 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2395736 ATAAATCTGA
*
2395746 GT GT GT GA GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2395778 ATACAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.50, T:0.47
Consensus pattern (2 bp):
GT
Found at i:2399768 original size:30 final size:30
Alignment explanation
Indices: 2399723--2399789 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
2399713 AATCAAGATG
2399723 TCATATATAAAATTGCACGA-AAATCAAAGT
1 TCATATATAAAATTGCAC-ATAAATCAAAGT
* * *
2399753 TCATGTATAACATTGCACATTAAATCGAAGT
1 TCATATATAAAATTGCACA-TAAATCAAAGT
2399784 TCATAT
1 TCATAT
2399790 GTAATCTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 1 0.03
30 16 0.52
31 14 0.45
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.31
Consensus pattern (30 bp):
TCATATATAAAATTGCACATAAATCAAAGT
Found at i:2416137 original size:14 final size:15
Alignment explanation
Indices: 2416113--2416141 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2416103 AGGTATTTTA
2416113 ATTTTTCTAAAAAAT
1 ATTTTTCTAAAAAAT
2416128 ATTTTT-TAAAAAAT
1 ATTTTTCTAAAAAAT
2416142 TAATTTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTTTCTAAAAAAT
Found at i:2417150 original size:30 final size:30
Alignment explanation
Indices: 2417093--2417151 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
2417083 TTATAAACTT
* * * *
2417093 ATAAATTGATTATTTGAATTCAGTAACTCG
1 ATAAATTAATTAATTAAATTCAATAACTCG
*
2417123 ATAAATTAATTAATTAAATTTAATAACTC
1 ATAAATTAATTAATTAAATTCAATAACTC
2417152 ATACTGATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (30 bp):
ATAAATTAATTAATTAAATTCAATAACTCG
Found at i:2417819 original size:21 final size:22
Alignment explanation
Indices: 2417778--2417827 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
2417768 GAAATGACAA
*
2417778 CAAAACAGTGAGAAAATAACAG
1 CAAAACAGTGAGAAAACAACAG
* *
2417800 TAAAATAGTG-GAAAACAACAG
1 CAAAACAGTGAGAAAACAACAG
2417821 CAAAACA
1 CAAAACA
2417828 ACAATTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.60, C:0.14, G:0.16, T:0.10
Consensus pattern (22 bp):
CAAAACAGTGAGAAAACAACAG
Found at i:2419072 original size:116 final size:116
Alignment explanation
Indices: 2418868--2419100 Score: 466
Period size: 116 Copynumber: 2.0 Consensus size: 116
2418858 CTTCTTCTTT
2418868 TATGTTTATTAATAGACTAACAGTCTAAACCGGTATAAGATAGGGTTAATTTTTGTTTTAATGTA
1 TATGTTTATTAATAGACTAACAGTCTAAACCGGTATAAGATAGGGTTAATTTTTGTTTTAATGTA
2418933 TTTTTTTACTTTCTAATCTAAACTTTCCCACCTCTTTTATCGTGAAAATCA
66 TTTTTTTACTTTCTAATCTAAACTTTCCCACCTCTTTTATCGTGAAAATCA
2418984 TATGTTTATTAATAGACTAACAGTCTAAACCGGTATAAGATAGGGTTAATTTTTGTTTTAATGTA
1 TATGTTTATTAATAGACTAACAGTCTAAACCGGTATAAGATAGGGTTAATTTTTGTTTTAATGTA
2419049 TTTTTTTACTTTCTAATCTAAACTTTCCCACCTCTTTTATCGTGAAAATCA
66 TTTTTTTACTTTCTAATCTAAACTTTCCCACCTCTTTTATCGTGAAAATCA
2419100 T
1 T
2419101 GTTGTTGAGG
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 117 1.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (116 bp):
TATGTTTATTAATAGACTAACAGTCTAAACCGGTATAAGATAGGGTTAATTTTTGTTTTAATGTA
TTTTTTTACTTTCTAATCTAAACTTTCCCACCTCTTTTATCGTGAAAATCA
Found at i:2424347 original size:39 final size:38
Alignment explanation
Indices: 2424304--2424421 Score: 141
Period size: 39 Copynumber: 2.9 Consensus size: 38
2424294 TAAATTTTTT
2424304 TTAAAAAGTTTTAAAAATATTTTAAAATTTAAAAAAAAA
1 TTAAAAAGTTTTAAAAATATTTTAAAA-TTAAAAAAAAA
2424343 TTAAAAAAAGTATTTTAAAAATATTTTAAAATT--AAAAAAA
1 TT--AAAAAG--TTTTAAAAATATTTTAAAATTAAAAAAAAA
*
2424383 TTAAAACAGTATGTAAAAAATATTTTAAAATTAAAAAAA
1 TTAAAA-AGT-T-TTAAAAATATTTTAAAATTAAAAAAA
2424422 TAAATATATT
Statistics
Matches: 69, Mismatches: 1, Indels: 16
0.80 0.01 0.19
Matches are distributed among these distances:
37 1 0.01
38 5 0.07
39 22 0.32
40 9 0.13
41 11 0.16
42 2 0.03
43 19 0.28
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (38 bp):
TTAAAAAGTTTTAAAAATATTTTAAAATTAAAAAAAAA
Found at i:2424362 original size:12 final size:11
Alignment explanation
Indices: 2424302--2424373 Score: 60
Period size: 11 Copynumber: 6.7 Consensus size: 11
2424292 ATTAAATTTT
*
2424302 TTTTAAAAA-G
1 TTTTAAAAATA
2424312 TTTTAAAAATA
1 TTTTAAAAATA
2424323 TTTT-AAAAT-
1 TTTTAAAAATA
** *
2424332 TTAAAAAAAAA
1 TTTTAAAAATA
**
2424343 TTAAAAAAAGTA
1 TTTTAAAAA-TA
2424355 TTTTAAAAATA
1 TTTTAAAAATA
2424366 TTTTAAAA
1 TTTTAAAA
2424374 TTAAAAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
9 2 0.04
10 18 0.35
11 23 0.45
12 8 0.16
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:2424422 original size:39 final size:40
Alignment explanation
Indices: 2424316--2424422 Score: 153
Period size: 39 Copynumber: 2.6 Consensus size: 40
2424306 AAAAAGTTTT
* *
2424316 AAAAATATTTTAAAATTTAAAAAAAAATTAAAAAAAGTATTTT
1 AAAAATATTTTAAAA-TT--AAAAAAATTAAAAAAAGTATGTA
*
2424359 AAAAATATTTTAAAATTAAAAAAATT-AAAACAGTATGTA
1 AAAAATATTTTAAAATTAAAAAAATTAAAAAAAGTATGTA
2424398 AAAAATATTTTAAAATTAAAAAAAT
1 AAAAATATTTTAAAATTAAAAAAAT
2424423 AAATATATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
39 35 0.57
40 9 0.15
42 2 0.03
43 15 0.25
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.33
Consensus pattern (40 bp):
AAAAATATTTTAAAATTAAAAAAATTAAAAAAAGTATGTA
Found at i:2424691 original size:28 final size:26
Alignment explanation
Indices: 2424615--2424693 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 26
2424605 CATATACATA
2424615 TATATATACATATCTATATTTTATAATC
1 TATATATACATA-C-ATATTTTATAATC
* * * *
2424643 TATGTATATATGCATGCATTTTATTATC
1 TATATATACATACAT--ATTTTATAATC
2424671 TGAATATATACATACATATTTTA
1 T--ATATATACATACATATTTTA
2424694 GGATATATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
26 2 0.05
27 1 0.03
28 26 0.65
30 11 0.28
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (26 bp):
TATATATACATACATATTTTATAATC
Found at i:2425461 original size:14 final size:15
Alignment explanation
Indices: 2425442--2425471 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2425432 AATGAAATGA
2425442 TTAATATATTA-TAT
1 TTAATATATTACTAT
2425456 TTAATATATTACTAT
1 TTAATATATTACTAT
2425471 T
1 T
2425472 ACTTATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TTAATATATTACTAT
Found at i:2434463 original size:22 final size:24
Alignment explanation
Indices: 2434432--2434476 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2434422 CTTTTAAATA
2434432 ATTTAATAAATTTA-ATCCTTCAC
1 ATTTAATAAATTTATATCCTTCAC
*
2434455 ATTT-ATAAATTTATTTCCTTCA
1 ATTTAATAAATTTATATCCTTCA
2434477 AGGTACATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTAATAAATTTATATCCTTCAC
Found at i:2436020 original size:5 final size:5
Alignment explanation
Indices: 2436010--2436041 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
2436000 TATATATATG
2436010 TATAA TATAA TA-AA TATAA TATAA TATAA TAT
1 TATAA TATAA TATAA TATAA TATAA TATAA TAT
2436042 CTAGATTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:2436029 original size:14 final size:15
Alignment explanation
Indices: 2436010--2436041 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
2436000 TATATATATG
2436010 TATAATATAATA-AA
1 TATAATATAATATAA
2436024 TATAATATAATATAA
1 TATAATATAATATAA
2436039 TAT
1 TAT
2436042 CTAGATTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TATAATATAATATAA
Found at i:2437505 original size:13 final size:13
Alignment explanation
Indices: 2437487--2437515 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2437477 TAAGTTGCTT
2437487 CCATTGTGATGGA
1 CCATTGTGATGGA
2437500 CCATTGTGATGGA
1 CCATTGTGATGGA
2437513 CCA
1 CCA
2437516 CATATGATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (13 bp):
CCATTGTGATGGA
Found at i:2442896 original size:29 final size:30
Alignment explanation
Indices: 2442863--2442930 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
2442853 ATTATGGGAC
2442863 TAGATCAAATTAGTACCTT-CATTA-TTAAA
1 TAGATCAAATTAGT-CCTTGCATTATTTAAA
* *
2442892 TAGATCAATTTAGTCTTTGCATTATTTAAA
1 TAGATCAAATTAGTCCTTGCATTATTTAAA
2442922 -AGAATCAAA
1 TAG-ATCAAA
2442931 CAAGGTCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 3 0.09
29 20 0.61
30 10 0.30
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (30 bp):
TAGATCAAATTAGTCCTTGCATTATTTAAA
Found at i:2444595 original size:20 final size:20
Alignment explanation
Indices: 2444572--2444632 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2444562 TATTTTGAAG
2444572 TTGTAAAAATTCTAAAAAAT
1 TTGTAAAAATTCTAAAAAAT
* * *
2444592 TTGTAAAAATTATAATAATT
1 TTGTAAAAATTCTAAAAAAT
* *
2444612 TTTTAAAAATTACAAAAAAAT
1 TTGTAAAAATT-CTAAAAAAT
2444633 ATTAAAACTA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 27 0.84
21 5 0.16
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
TTGTAAAAATTCTAAAAAAT
Found at i:2445226 original size:20 final size:20
Alignment explanation
Indices: 2445201--2445238 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2445191 TTCTAAATAA
*
2445201 ATTTTTAAACTAATTTTTAT
1 ATTTTTAAAATAATTTTTAT
2445221 ATTTTTAAAATAATTTTT
1 ATTTTTAAAATAATTTTT
2445239 GCAAGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTTAAAATAATTTTTAT
Found at i:2457226 original size:21 final size:21
Alignment explanation
Indices: 2457202--2457255 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
2457192 TATATATTTT
2457202 AAATTTAAAAGTA-ATAAATAA
1 AAATTTAAAAGTATATAAA-AA
2457223 AAATTTAAAA-TATATAAAAA
1 AAATTTAAAAGTATATAAAAA
*
2457243 AAACTTAAAAGTA
1 AAATTTAAAAGTA
2457256 CGTTTAGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (21 bp):
AAATTTAAAAGTATATAAAAA
Found at i:2457250 original size:20 final size:21
Alignment explanation
Indices: 2457206--2457255 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
2457196 TATTTTAAAT
*
2457206 TTAAAAGTAATAAATAAAAAT
1 TTAAAAGTAATAAATAAAAAC
2457227 TTAAAA-TATATAAA-AAAAAC
1 TTAAAAGTA-ATAAATAAAAAC
2457247 TTAAAAGTA
1 TTAAAAGTA
2457256 CGTTTAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (21 bp):
TTAAAAGTAATAAATAAAAAC
Found at i:2462886 original size:77 final size:77
Alignment explanation
Indices: 2462759--2462913 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
2462749 GATTAGCAGG
2462759 GGCAGTATTAGCCTACTGTTACAGTATGGTCAGTTGACCAGTCAACGGTTAGTTGTTAGTGGTTA
1 GGCAGTATTAGCCTACTGTTACAGTATGGTCAGTTGACCAGTCAACGGTTAGTTGTTAGTGGTTA
2462824 ATAAGATGGTTA
66 ATAAGATGGTTA
2462836 GGCAGTATTAGCCTACTGTTACAGTATGGTCAGTTGACCAGTCAACGGTTAGTTGTTAGTGGTTA
1 GGCAGTATTAGCCTACTGTTACAGTATGGTCAGTTGACCAGTCAACGGTTAGTTGTTAGTGGTTA
2462901 ATAAGATGGTTA
66 ATAAGATGGTTA
2462913 G
1 G
2462914 CTCATAACCG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.34
Consensus pattern (77 bp):
GGCAGTATTAGCCTACTGTTACAGTATGGTCAGTTGACCAGTCAACGGTTAGTTGTTAGTGGTTA
ATAAGATGGTTA
Found at i:2462939 original size:19 final size:19
Alignment explanation
Indices: 2462909--2462954 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2462899 TAATAAGATG
2462909 GTTAGCTCATAACCGTTTTA
1 GTTAG-TCATAACCGTTTTA
*
2462929 GTTAGTCATAACTGTTTTA
1 GTTAGTCATAACCGTTTTA
2462948 GTTAGTC
1 GTTAGTC
2462955 GGTTGAAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.43
Consensus pattern (19 bp):
GTTAGTCATAACCGTTTTA
Found at i:2463409 original size:19 final size:19
Alignment explanation
Indices: 2463385--2463455 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
2463375 AATCTTGTAA
2463385 TATAATATATATGTAAATT
1 TATAATATATATGTAAATT
* * **
2463404 TATAATTTATAATGTGAACA
1 TATAATATAT-ATGTAAATT
* *
2463424 TA-AATATCTATTTACAACTT
1 TATAATATATATGTA-AA-TT
2463444 TATAATATATAT
1 TATAATATATAT
2463456 AAATATATTC
Statistics
Matches: 37, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
18 3 0.08
19 16 0.43
20 10 0.27
21 8 0.22
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (19 bp):
TATAATATATATGTAAATT
Found at i:2465177 original size:43 final size:42
Alignment explanation
Indices: 2465115--2465304 Score: 263
Period size: 43 Copynumber: 4.5 Consensus size: 42
2465105 AGAAATAAAT
*
2465115 GCCGCTATAGATCATGACCTTTAGCGGCGCCTTTTCCACAAAC
1 GCCGCTATAGATCAAGACCTTTAGCGGCG-CTTTTCCACAAAC
* * * *
2465158 GCCGCTATAAATCAGGACCTTTAGCAGCGCTTTTACACAAAC
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCACAAAC
* * * *
2465200 GCCGCTATAGCTCAAGATCTTTAGCGACGCTTTTTCCACAAAT
1 GCCGCTATAGATCAAGACCTTTAGCGGCGC-TTTTCCACAAAC
2465243 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTT-CCACAAAC
*
2465286 GCCGCTATAGCTCAAGACC
1 GCCGCTATAGATCAAGACC
2465305 CTCACAAACG
Statistics
Matches: 128, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
42 40 0.31
43 88 0.69
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (42 bp):
GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCACAAAC
Found at i:2465223 original size:85 final size:86
Alignment explanation
Indices: 2465115--2465304 Score: 283
Period size: 85 Copynumber: 2.2 Consensus size: 86
2465105 AGAAATAAAT
* * * *
2465115 GCCGCTATAGATCATGACCTTTAGCGGCGCCTTTTCCACAAACGCCGCTATAAATCAGGACCTTT
1 GCCGCTATAGCTCAAGACCTTTAGCGACGCCTTTTCCACAAACGCCGCTATAAATCAAGACCTTT
2465180 AGCAGCGCTTTT-ACACAAAC
66 AGCAGCGCTTTTCACACAAAC
* * * *
2465200 GCCGCTATAGCTCAAGATCTTTAGCGACGCTTTTTCCACAAATGCCGCTATAGATCAAGACCTTT
1 GCCGCTATAGCTCAAGACCTTTAGCGACGCCTTTTCCACAAACGCCGCTATAAATCAAGACCTTT
* *
2465265 AGCGGCGCTTTTCCCACAAAC
66 AGCAGCGCTTTTCACACAAAC
2465286 GCCGCTATAGCTCAAGACC
1 GCCGCTATAGCTCAAGACC
2465305 CTCACAAACG
Statistics
Matches: 93, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
85 68 0.73
86 25 0.27
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (86 bp):
GCCGCTATAGCTCAAGACCTTTAGCGACGCCTTTTCCACAAACGCCGCTATAAATCAAGACCTTT
AGCAGCGCTTTTCACACAAAC
Found at i:2465458 original size:16 final size:16
Alignment explanation
Indices: 2465437--2465470 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2465427 ATTTATTAAA
*
2465437 TATTAAAATCAAACAT
1 TATTAAAATCAAAAAT
*
2465453 TATTAATATCAAAAAT
1 TATTAAAATCAAAAAT
2465469 TA
1 TA
2465471 ATTAGTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAAAATCAAAAAT
Found at i:2477963 original size:20 final size:18
Alignment explanation
Indices: 2477935--2477974 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
2477925 TTAATTTTAA
2477935 TTTTTAAAATGTTCTAATT
1 TTTTTAAAATGTTC-AATT
*
2477954 TTTTTAAAAATTTTCAATT
1 TTTTT-AAAATGTTCAATT
2477973 TT
1 TT
2477975 CATCATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTTAAAATGTTCAATT
Found at i:2483671 original size:31 final size:31
Alignment explanation
Indices: 2483636--2483702 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
2483626 GTTACAAAAT
* ** *
2483636 AGTCATTGAATTATTTGAGAGTTTTCATTTA
1 AGTCATTGAACTATTCAAAAGTTTTCATTTA
*
2483667 AGTCATTGAACTATTCAAAAGTTTTTATTTA
1 AGTCATTGAACTATTCAAAAGTTTTCATTTA
2483698 AGTCA
1 AGTCA
2483703 CTGGGATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (31 bp):
AGTCATTGAACTATTCAAAAGTTTTCATTTA
Found at i:2488039 original size:31 final size:29
Alignment explanation
Indices: 2488004--2488080 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
2487994 TTAATAGCTC
*
2488004 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* * ***
2488035 AGTGACAAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
2488064 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
2488081 CTAAGGTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 21 0.55
30 1 0.03
31 16 0.42
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:2493196 original size:25 final size:25
Alignment explanation
Indices: 2493162--2493210 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
2493152 ATTTATTTTT
* *
2493162 TATAATTTTTATAATTTTTTTAAAA
1 TATAATTTTTATAATATTTATAAAA
*
2493187 TATAATTTTTTTAATATTTATAAA
1 TATAATTTTTATAATATTTATAAA
2493211 TATTTTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TATAATTTTTATAATATTTATAAAA
Found at i:2493203 original size:14 final size:15
Alignment explanation
Indices: 2493171--2493200 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2493161 TTATAATTTT
2493171 TATAATTTTTTTAAAA
1 TATAATTTTTTT-AAA
2493187 TATAATTTTTTTAA
1 TATAATTTTTTTAA
2493201 TATTTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 2 0.14
16 12 0.86
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATAATTTTTTTAAA
Found at i:2494563 original size:25 final size:26
Alignment explanation
Indices: 2494530--2494583 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
2494520 CTAAATTTTG
*
2494530 AATTACTTT-TAATTTTAATATGGAAC
1 AATTACTTTCTAATTATAA-ATGGAAC
*
2494556 AATT-CTTTCTAATTATAAATTGAAC
1 AATTACTTTCTAATTATAAATGGAAC
2494581 AAT
1 AAT
2494584 GGTAGCAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (26 bp):
AATTACTTTCTAATTATAAATGGAAC
Found at i:2502576 original size:27 final size:26
Alignment explanation
Indices: 2502524--2502581 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
2502514 CTAAAAATAA
2502524 TATTATAATAATTAATATATTAAAATT
1 TATTATAATAATTAATATATTAAAA-T
*
2502551 TATTATAA-ATATATAATAT-TTTAAAT
1 TATTATAATA-AT-TAATATATTAAAAT
2502577 TATTA
1 TATTA
2502582 CATTACAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 7 0.25
27 15 0.54
28 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TATTATAATAATTAATATATTAAAAT
Found at i:2502766 original size:7 final size:7
Alignment explanation
Indices: 2502749--2502780 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
2502739 AGGATCTCCC
2502749 TTTTC-T
1 TTTTCTT
2502755 TTTTCTT
1 TTTTCTT
2502762 TTTTCTT
1 TTTTCTT
2502769 TTTTCTT
1 TTTTCTT
2502776 TTTTC
1 TTTTC
2502781 ATTCACGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTCTT
Found at i:2504845 original size:16 final size:18
Alignment explanation
Indices: 2504811--2504853 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
2504801 TTTAGACGAA
*
2504811 TTTTTAATTAATTTAATT
1 TTTTTATTTAATTTAATT
2504829 TTTTTATTTAA-TT-ATT
1 TTTTTATTTAATTTAATT
*
2504845 TTTTGATTT
1 TTTTTATTT
2504854 TATAATATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 11 0.48
17 2 0.09
18 10 0.43
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTTTATTTAATTTAATT
Found at i:2510319 original size:15 final size:15
Alignment explanation
Indices: 2510288--2510326 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2510278 TCTTTTTATA
2510288 TTTTTA-AAAAATAT
1 TTTTTATAAAAATAT
* *
2510302 TTTTTATAAGAATTT
1 TTTTTATAAAAATAT
2510317 TTTTTATAAA
1 TTTTTATAAA
2510327 TTTGTTACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TTTTTATAAAAATAT
Found at i:2511566 original size:38 final size:38
Alignment explanation
Indices: 2511490--2511566 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 38
2511480 AATCAAGACT
*
2511490 TTCATTATTTATATTAAATTTCGATAAACAACACAATA
1 TTCATTATTTATATTAAATTTCGATAAACAACAAAATA
2511528 TTCATTATTTATATTAAATTTCGATAAACAA-ATAAATA
1 TTCATTATTTATATTAAATTTCGATAAACAACA-AAATA
2511566 T
1 T
2511567 ATATCAACTA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
37 1 0.03
38 36 0.97
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (38 bp):
TTCATTATTTATATTAAATTTCGATAAACAACAAAATA
Found at i:2517350 original size:42 final size:42
Alignment explanation
Indices: 2517282--2517383 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 42
2517272 AGGCTGCACA
* ** * *
2517282 GAAGCACATAAGTGCTAAACGGAAACCCGTAAGGGTTTAACG
1 GAAGCACATAAGAGCTAAACAAAAACCCATAAGGGTTAAACG
*
2517324 GAAGCACAT-AGAAGCTAAACAAAAACCCATTAGGGTTAAACG
1 GAAGCACATAAG-AGCTAAACAAAAACCCATAAGGGTTAAACG
* * * *
2517366 AAAACATATATGAGCTAA
1 GAAGCACATAAGAGCTAA
2517384 TTGAAGCTCA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
41 2 0.04
42 45 0.94
43 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.17
Consensus pattern (42 bp):
GAAGCACATAAGAGCTAAACAAAAACCCATAAGGGTTAAACG
Found at i:2519255 original size:17 final size:17
Alignment explanation
Indices: 2519233--2519265 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2519223 AATGTAAGAT
*
2519233 ATTAATTATTATAAAAA
1 ATTAATCATTATAAAAA
2519250 ATTAATCATTATAAAA
1 ATTAATCATTATAAAA
2519266 TAAATTCCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTAATCATTATAAAAA
Found at i:2519344 original size:18 final size:18
Alignment explanation
Indices: 2519323--2519357 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2519313 ATTTTACTAA
2519323 AAATATTTTTT-TTAAATG
1 AAAT-TTTTTTATTAAATG
2519341 AAATTTTTTTATTAAAT
1 AAATTTTTTTATTAAAT
2519358 AACACAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
AAATTTTTTTATTAAATG
Found at i:2519420 original size:18 final size:18
Alignment explanation
Indices: 2519393--2519427 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2519383 ATCCAACACA
*
2519393 AAAAAAAAATTATTTTTC
1 AAAAAAAAATAATTTTTC
*
2519411 AAAAATAAATAATTTTT
1 AAAAAAAAATAATTTTT
2519428 AATGAAACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAAAAAAATAATTTTTC
Found at i:2526769 original size:18 final size:18
Alignment explanation
Indices: 2526748--2526787 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2526738 TTAAAATTAA
2526748 AAATATATAAAAAAATAG
1 AAATATATAAAAAAATAG
* * *
2526766 AAATTTATAAAATATTAG
1 AAATATATAAAAAAATAG
2526784 AAAT
1 AAAT
2526788 GTTATTTCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
AAATATATAAAAAAATAG
Found at i:2527365 original size:68 final size:68
Alignment explanation
Indices: 2527256--2527465 Score: 370
Period size: 68 Copynumber: 3.1 Consensus size: 68
2527246 TCAAGTTTAT
* *
2527256 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAGTTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
2527321 AAA
66 AAA
*
2527324 TTTACTAATCAAATTTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
2527389 AAA
66 AAA
2527392 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
2527455 AAT
66 AAA
2527458 TTTACTAA
1 TTTACTAA
2527466 CAATTAATTT
Statistics
Matches: 137, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
66 27 0.20
67 1 0.01
68 109 0.80
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:2527366 original size:9 final size:9
Alignment explanation
Indices: 2527354--2527381 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2527344 TTTTATTACA
2527354 ACAATTAAT
1 ACAATTAAT
2527363 ACAATTAAT
1 ACAATTAAT
2527372 ACAATTAAT
1 ACAATTAAT
2527381 A
1 A
2527382 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:2527475 original size:16 final size:16
Alignment explanation
Indices: 2527454--2527495 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2527444 AATAATTTGA
*
2527454 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
2527470 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
2527486 TAGTTTTAAT
1 TAATTTTAAT
2527496 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:2529008 original size:2 final size:2
Alignment explanation
Indices: 2529001--2529045 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
2528991 TTCTTCACGA
*
2529001 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT CAT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
2529043 AT A
1 AT A
2529046 CCTTCATTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2530431 original size:13 final size:13
Alignment explanation
Indices: 2530413--2530437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2530403 AATCGACATG
2530413 TTTATTTTATTTA
1 TTTATTTTATTTA
2530426 TTTATTTTATTT
1 TTTATTTTATTT
2530438 GGTGAATTAT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:2532842 original size:27 final size:28
Alignment explanation
Indices: 2532814--2532866 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2532804 AGCCGTAACT
2532814 TTTTATAA-ATAAATA-TATTATAATAC
1 TTTTATAACATAAATATTATTATAATAC
* *
2532840 TTTTATAACATATATATTTTTATAATA
1 TTTTATAACATAAATATTATTATAATA
2532867 AGCTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
27 6 0.26
28 9 0.39
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTTATAACATAAATATTATTATAATAC
Found at i:2540709 original size:18 final size:18
Alignment explanation
Indices: 2540688--2540750 Score: 55
Period size: 18 Copynumber: 3.8 Consensus size: 18
2540678 AGAAGAATGG
2540688 TGGAAACAGGGAGTAGCA
1 TGGAAACAGGGAGTAGCA
* *
2540706 TGG----AGGG-TTATCA
1 TGGAAACAGGGAGTAGCA
* *
2540719 GGGAAACGGGGAGTAGCA
1 TGGAAACAGGGAGTAGCA
2540737 TGGAAACAGGGAGT
1 TGGAAACAGGGAGT
2540751 TGATTTCTTG
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
13 6 0.19
14 4 0.12
17 3 0.09
18 19 0.59
ACGTcount: A:0.33, C:0.10, G:0.43, T:0.14
Consensus pattern (18 bp):
TGGAAACAGGGAGTAGCA
Found at i:2554589 original size:19 final size:20
Alignment explanation
Indices: 2554562--2554612 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
2554552 CAAATAATTT
* **
2554562 AAAATTTATAAAAATAT-CC
1 AAAAATTATAAAAATATAAA
*
2554581 AAAAATTATAAAATTATAAA
1 AAAAATTATAAAAATATAAA
2554601 AAAAATTATAAA
1 AAAAATTATAAA
2554613 CATCCGCATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAATTATAAAAATATAAA
Found at i:2555800 original size:29 final size:27
Alignment explanation
Indices: 2555768--2555827 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 27
2555758 TGTCAACATA
2555768 CTTTTCATAATATAATTAATATAAATATG
1 CTTTT-ATAA-ATAATTAATATAAATATG
*
2555797 CTTTTTTAAATAATTAATATAAATATG
1 CTTTTATAAATAATTAATATAAATATG
2555824 CTTT
1 CTTT
2555828 CCAATAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 22 0.73
28 3 0.10
29 5 0.17
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (27 bp):
CTTTTATAAATAATTAATATAAATATG
Found at i:2555838 original size:27 final size:28
Alignment explanation
Indices: 2555776--2555838 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
2555766 TACTTTTCAT
**
2555776 AATATAATTAATATAAATATGCTTTTTT
1 AATATAATTAATATAAATATGCTTTTCC
2555804 AA-ATAATTAATATAAATATGC-TTTCC
1 AATATAATTAATATAAATATGCTTTTCC
*
2555830 AATAAAATT
1 AATATAATT
2555839 GCAATTGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 5 0.16
27 24 0.77
28 2 0.06
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (28 bp):
AATATAATTAATATAAATATGCTTTTCC
Found at i:2558493 original size:22 final size:23
Alignment explanation
Indices: 2558466--2558508 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2558456 AAACATATGA
**
2558466 AATAACTTTAAAT-TTTAAAAAT
1 AATAACTACAAATATTTAAAAAT
2558488 AATAACTACAAATATTTAAAA
1 AATAACTACAAATATTTAAAA
2558509 TTTTATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (23 bp):
AATAACTACAAATATTTAAAAAT
Found at i:2563545 original size:139 final size:137
Alignment explanation
Indices: 2563358--2563744 Score: 467
Period size: 139 Copynumber: 2.8 Consensus size: 137
2563348 TCTTCTACTG
* *
2563358 ACATTTGTATTTTTTATTTCACGTTGCTTCAAGCTTTTTAAATCTTTAATTAATTTTTTTAACAT
1 ACATTTGTATTTTTTATTTCATGTTGCTTCAAGC-TTTTAAAT-TTTAATTAATATTTTTAACAT
* * * * *
2563423 ATTAGTTCTTTGGTTAGATGGTTAAATAGTTACAATTACATCCTTGAGTCTCAAGTTTAATTCAT
64 ATTAATTCTTTCGTTAGATGGTTAGATAGTTGCAATTACATCCTTGAGTCTCAAGTTCAATTCAT
*
2563488 CTCCGACTC
129 CTACGACTC
* * * *
2563497 ATATTTGTATTTTCTATTTCATGTTACTTCAAGCATTTTCAAATTTTAATTAATATTTTTAACTT
1 ACATTTGTATTTTTTATTTCATGTTGCTTCAAGC-TTTT-AAATTTTAATTAATATTTTTAACAT
* * * * * * * *
2563562 TTTAATTCTTTCGTTAGATGGTTAGATAGTCGTAAGTACATTCTTGAGTCTCGAGTTCGATTCCT
64 ATTAATTCTTTCGTTAGATGGTTAGATAGTTGCAATTACATCCTTGAGTCTCAAGTTCAATTCAT
*
2563627 CTACTACTC
129 CTACGACTC
*
2563636 ACATTTGTATTTTTTATTTCATGTTGCTTCAAG-TTTT---TTTTAATTAATATTTCTAACATAT
1 ACATTTGTATTTTTTATTTCATGTTGCTTCAAGCTTTTAAATTTTAATTAATATTTTTAACATAT
** * *
2563697 TACCTCTTTTCGTTAGATGGTTAGATAATTGCTATTACATCCTTGAGT
66 TAATTC-TTTCGTTAGATGGTTAGATAGTTGCAATTACATCCTTGAGT
2563745 ATGAGGTTTC
Statistics
Matches: 210, Mismatches: 36, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
133 25 0.12
134 35 0.17
137 4 0.02
139 142 0.68
140 4 0.02
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (137 bp):
ACATTTGTATTTTTTATTTCATGTTGCTTCAAGCTTTTAAATTTTAATTAATATTTTTAACATAT
TAATTCTTTCGTTAGATGGTTAGATAGTTGCAATTACATCCTTGAGTCTCAAGTTCAATTCATCT
ACGACTC
Found at i:2566974 original size:18 final size:18
Alignment explanation
Indices: 2566953--2566989 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2566943 TAACCAACCA
*
2566953 AATCGATTTAATTCGGTT
1 AATCGATTTAATTCAGTT
2566971 AATCGATTTAATTCAGTT
1 AATCGATTTAATTCAGTT
2566989 A
1 A
2566990 GAGGTCGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (18 bp):
AATCGATTTAATTCAGTT
Done.