Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 40 of 135
Found at i:10303156 original size:18 final size:18
Alignment explanation
Indices: 10303135--10303171 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10303125 ATTCGATTAA
*
10303135 TCGATCAATTAATCGAAT
1 TCGATCAATTAACCGAAT
*
10303153 TCGATCGATTAACCGAAT
1 TCGATCAATTAACCGAAT
10303171 T
1 T
10303172 AATTCGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (18 bp):
TCGATCAATTAACCGAAT
Found at i:10304177 original size:25 final size:25
Alignment explanation
Indices: 10304149--10304206 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
10304139 TTAAGTTTGA
10304149 ATATATTACAATTATTAATTC-GATT
1 ATATATTACAA-TATTAATTCTGATT
10304174 ATATTATGT--AATATTAATTCTGATT
1 ATA-TAT-TACAATATTAATTCTGATT
10304199 ATA-ATTAC
1 ATATATTAC
10304207 TTGAATGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 11
0.72 0.00 0.28
Matches are distributed among these distances:
22 1 0.04
23 2 0.07
24 9 0.32
25 12 0.43
26 3 0.11
27 1 0.04
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (25 bp):
ATATATTACAATATTAATTCTGATT
Found at i:10305047 original size:23 final size:23
Alignment explanation
Indices: 10305007--10305055 Score: 62
Period size: 27 Copynumber: 2.0 Consensus size: 23
10304997 ATTGAGAGGT
10305007 TTCAAAAAAATAATTAATAAATA
1 TTCAAAAAAATAATTAATAAATA
10305030 TTCACAAAAAATGATAATTAATAAAT
1 TT--CAAAAAA--ATAATTAATAAAT
10305056 CAAATTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 2 0.09
25 7 0.32
27 13 0.59
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (23 bp):
TTCAAAAAAATAATTAATAAATA
Found at i:10308282 original size:20 final size:17
Alignment explanation
Indices: 10308234--10308283 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
10308224 TATATGTATT
10308234 ATAATAATTAAATAAAA
1 ATAATAATTAAATAAAA
10308251 ATAATAATTAAATAAAA
1 ATAATAATTAAATAAAA
10308268 ATAATAATT-AATAAAA
1 ATAATAATTAAATAAAA
10308284 TTTTAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 7 0.21
17 26 0.79
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAATAATTAAATAAAA
Found at i:10334974 original size:24 final size:24
Alignment explanation
Indices: 10334946--10335008 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
10334936 AGAAATAATC
10334946 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
10334970 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
10334994 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
10335009 TATTACTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTG
Found at i:10336980 original size:24 final size:24
Alignment explanation
Indices: 10336929--10336983 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
10336919 TCTTTCAGTT
* *
10336929 AAACTCTGTTTATTTGTTTTAATT
1 AAACTCTGTTTATTTGTTTGAATC
*
10336953 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTATTTGTTTGAATC
10336977 AAACTCT
1 AAACTCT
10336984 TATTACTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTGAATC
Found at i:10340847 original size:14 final size:14
Alignment explanation
Indices: 10340828--10340859 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
10340818 AAATTATGTG
10340828 TGTTCATGTTCGTT
1 TGTTCATGTTCGTT
10340842 TGTTCATGTTCGTT
1 TGTTCATGTTCGTT
10340856 TGTT
1 TGTT
10340860 TAATGTTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.22, T:0.59
Consensus pattern (14 bp):
TGTTCATGTTCGTT
Found at i:10340867 original size:15 final size:14
Alignment explanation
Indices: 10340828--10340867 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
10340818 AAATTATGTG
*
10340828 TGTTCATGTTCGTT
1 TGTTAATGTTCGTT
*
10340842 TGTTCATGTTCGTT
1 TGTTAATGTTCGTT
10340856 TGTTTAATGTTC
1 TG-TTAATGTTC
10340868 ACGAACATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.57
Consensus pattern (14 bp):
TGTTAATGTTCGTT
Found at i:10341959 original size:4 final size:4
Alignment explanation
Indices: 10341934--10341986 Score: 54
Period size: 4 Copynumber: 12.5 Consensus size: 4
10341924 ACGGGAGAAG
*
10341934 AAGA AGGA AAGGA AAGGA AAGA AAGA AAGA AGGAGA AA-A AAGA AAGA
1 AAGA AAGA AA-GA AA-GA AAGA AAGA AAGA A--AGA AAGA AAGA AAGA
10341981 AAGA AA
1 AAGA AA
10341987 AAGGAGAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
3 3 0.07
4 27 0.63
5 9 0.21
6 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:10341961 original size:18 final size:18
Alignment explanation
Indices: 10341932--10341983 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
10341922 TTACGGGAGA
*
10341932 AGAAGAAGGAAAGGAAAGG
1 AGAAGAAAGAAA-GAAAGG
10341951 A-AAGAAAGAAAG-AAGG
1 AGAAGAAAGAAAGAAAGG
*
10341967 AGAAAAAAGAAAGAAAG
1 AGAAGAAAGAAAGAAAG
10341984 AAAAAGGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 5 0.17
17 11 0.38
18 12 0.41
19 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AGAAGAAAGAAAGAAAGG
Found at i:10341966 original size:21 final size:21
Alignment explanation
Indices: 10341942--10341997 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
10341932 AGAAGAAGGA
10341942 AAGGAAAGGAAAGAAAGAAAG
1 AAGGAAAGGAAAGAAAGAAAG
*
10341963 AAGGAGAA-AAAAGAAAGAAAG
1 AAGGA-AAGGAAAGAAAGAAAG
10341984 AA--AAAGGAGAAGAA
1 AAGGAAAGGA-AAGAA
10341998 TGTTATTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 2 0.07
19 2 0.07
20 5 0.17
21 19 0.63
22 2 0.07
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (21 bp):
AAGGAAAGGAAAGAAAGAAAG
Found at i:10341997 original size:16 final size:15
Alignment explanation
Indices: 10341940--10341988 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 15
10341930 GAAGAAGAAG
10341940 GAAAGGAAAGGAAAGAAA
1 GAAA-GAAA-GAAA-AAA
10341958 GAAAGAAGGAGAAAAAA
1 GAAAGAA--AGAAAAAA
10341975 GAAAGAAAGAAAAA
1 GAAAGAAAGAAAAA
10341989 GGAGAAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.24
17 13 0.45
18 8 0.28
19 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (15 bp):
GAAAGAAAGAAAAAA
Found at i:10342311 original size:25 final size:23
Alignment explanation
Indices: 10342261--10342315 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
10342251 TTATTATAAG
*
10342261 TTATTTGTTTTGTTTAATTTAATTT
1 TTATTTGATTTGTTTAA-TT-ATTT
10342286 TTATTTGATTTGTTATTAATT-TTT
1 TTATTTGATTTG-T-TTAATTATTT
10342310 TTATTT
1 TTATTT
10342316 AGTAGAGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 9 0.33
25 11 0.41
26 3 0.11
27 4 0.15
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (23 bp):
TTATTTGATTTGTTTAATTATTT
Found at i:10342398 original size:21 final size:20
Alignment explanation
Indices: 10342374--10342417 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
10342364 TAATTTAATT
10342374 TAATTTAATTTTGTTAGTAAG
1 TAATTTAATTTTGTTAGT-AG
*
10342395 TAATTTTATTTTGTTAGTAG
1 TAATTTAATTTTGTTAGTAG
10342415 TAA
1 TAA
10342418 GTAAGTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (20 bp):
TAATTTAATTTTGTTAGTAG
Found at i:10344426 original size:43 final size:43
Alignment explanation
Indices: 10344328--10344432 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 43
10344318 GGTATGTCAT
10344328 TCCT-TGACATGTTATTAAATCATATTACTGAACCCGTGTTAA
1 TCCTGTGACATGTTATTAAATCATATTACTGAACCCGTGTTAA
* * * *
10344370 T-ATCGTGACATGTTATTAAATTATATTACTTG-ACTCTTGTTAA
1 TCCT-GTGACATGTTATTAAATCATATTAC-TGAACCCGTGTTAA
*
10344413 TCCTGTGATATGTTTATTAA
1 TCCTGTGACATG-TTATTAA
10344433 TTGTGCAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
41 1 0.02
42 1 0.02
43 40 0.77
44 10 0.19
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (43 bp):
TCCTGTGACATGTTATTAAATCATATTACTGAACCCGTGTTAA
Found at i:10344897 original size:6 final size:6
Alignment explanation
Indices: 10344886--10344921 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
10344876 CCTCCTGCAC
* *
10344886 AAGAGG AAGAGG AAGAGA AAGAGG AAGAGA AAGAGG
1 AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG
10344922 CATTGGATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (6 bp):
AAGAGG
Found at i:10344907 original size:12 final size:12
Alignment explanation
Indices: 10344886--10344921 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
10344876 CCTCCTGCAC
*
10344886 AAGAGGAAGAGG
1 AAGAGAAAGAGG
10344898 AAGAGAAAGAGG
1 AAGAGAAAGAGG
10344910 AAGAGAAAGAGG
1 AAGAGAAAGAGG
10344922 CATTGGATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (12 bp):
AAGAGAAAGAGG
Found at i:10344909 original size:18 final size:18
Alignment explanation
Indices: 10344886--10344920 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10344876 CCTCCTGCAC
*
10344886 AAGAGGAAGAGGAAGAGA
1 AAGAGGAAGAGAAAGAGA
10344904 AAGAGGAAGAGAAAGAG
1 AAGAGGAAGAGAAAGAG
10344921 GCATTGGATG
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:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (18 bp):
AAGAGGAAGAGAAAGAGA
Found at i:10345384 original size:21 final size:21
Alignment explanation
Indices: 10345344--10345401 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
10345334 AAATTTTATA
*
10345344 TATGATTTAGGG-TTAGGGTTT
1 TATG-TTTAGGGTTTAAGGTTT
10345365 TATGTTTAGGGTTTAAGGTTT
1 TATGTTTAGGGTTTAAGGTTT
*
10345386 CATGTTTAGGGTTTAA
1 TATGTTTAGGGTTTAA
10345402 AACTAAATCC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.21
21 27 0.79
ACGTcount: A:0.21, C:0.02, G:0.29, T:0.48
Consensus pattern (21 bp):
TATGTTTAGGGTTTAAGGTTT
Found at i:10346409 original size:20 final size:21
Alignment explanation
Indices: 10346365--10346415 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
10346355 AATAAATAAG
10346365 TAATAAATAT-ATAATAAACA
1 TAATAAATATAATAATAAACA
* *
10346385 TAATAAATATAATATTAAATA
1 TAATAAATATAATAATAAACA
10346406 -AATAAA-ATAA
1 TAATAAATATAA
10346416 AAAGAAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 16 0.57
21 8 0.29
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
TAATAAATATAATAATAAACA
Found at i:10347491 original size:30 final size:28
Alignment explanation
Indices: 10347464--10347684 Score: 189
Period size: 29 Copynumber: 7.6 Consensus size: 28
10347454 CATATTTTGG
10347464 CCCTCAAACTTTTCCAAAATTACATTTTAA
1 CCCTCAAAC-TTTCCAAAATTACATTTT-A
* * *
10347494 CCCTTAAGCTTTACAAAATTACATTTATA
1 CCCTCAAACTTTCCAAAATTACATTT-TA
* * *
10347523 CCCT-GAACTTTCTAAAAATTATATTTTAA
1 CCCTCAAACTTTC-CAAAATTACATTTT-A
*
10347552 CCCTCAAACTTTCAAAAATTACATTTTTA
1 CCCTCAAACTTTCCAAAATTACA-TTTTA
* *
10347581 -CCTCTGAACTTTCCAAAAATTACGTTTTGA
1 CCCTC-AAACTTTCC-AAAATTACATTTT-A
* *
10347611 CCCTCGAACTTTCCATAATTACATTTTTA
1 CCCTCAAACTTTCCAAAATTACA-TTTTA
* *
10347640 CCCTTAAACTTTTCCAAAATTACATTTTG
1 CCCTCAAAC-TTTCCAAAATTACATTTTA
*
10347669 CCC-CAAACATT-CAAAA
1 CCCTCAAACTTTCCAAAA
10347685 GTTCGATTTT
Statistics
Matches: 159, Mismatches: 21, Indels: 26
0.77 0.10 0.13
Matches are distributed among these distances:
26 5 0.03
27 2 0.01
28 14 0.09
29 80 0.50
30 54 0.34
31 4 0.03
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.37
Consensus pattern (28 bp):
CCCTCAAACTTTCCAAAATTACATTTTA
Found at i:10347513 original size:29 final size:28
Alignment explanation
Indices: 10347474--10347667 Score: 192
Period size: 29 Copynumber: 6.6 Consensus size: 28
10347464 CCCTCAAACT
*
10347474 TTTCCAAAATTACATTTTAACCCTTAAGC
1 TTTCCAAAATTACATTTTAACCCTGAA-C
*
10347503 TTTACAAAATTACA-TTTATACCCTGAAC
1 TTTCCAAAATTACATTTTA-ACCCTGAAC
* * *
10347531 TTTCTAAAAATTATATTTTAACCCTCAAAC
1 TTTC-CAAAATTACATTTTAACCCT-GAAC
* *
10347561 TTTCAAAAATTACATTTTTACCTCTGAAC
1 TTTCCAAAATTACATTTTAACC-CTGAAC
* *
10347590 TTTCCAAAAATTACGTTTTGACCCTCGAAC
1 TTTCC-AAAATTACATTTTAACCCT-GAAC
* * *
10347620 TTTCCATAATTACATTTTTACCCTTAAAC
1 TTTCCAAAATTACATTTTAACCC-TGAAC
10347649 TTTTCCAAAATTACATTTT
1 -TTTCCAAAATTACATTTT
10347668 GCCCCAAACA
Statistics
Matches: 139, Mismatches: 17, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
28 8 0.06
29 76 0.55
30 55 0.40
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (28 bp):
TTTCCAAAATTACATTTTAACCCTGAAC
Found at i:10347614 original size:59 final size:57
Alignment explanation
Indices: 10347474--10347684 Score: 230
Period size: 59 Copynumber: 3.6 Consensus size: 57
10347464 CCCTCAAACT
* * *
10347474 TTTCCAAAATTACATTTTAACCCTTAAGCTTT-ACAAAATTACATTTATACCCTGAAC
1 TTTCCAAAATTACATTTTAACCCTCAAACTTTCA-AAAATTACATTTTTACCCTGAAC
* *
10347531 TTTCTAAAAATTATATTTTAACCCTCAAACTTTCAAAAATTACATTTTTACCTCTGAAC
1 TTTC-CAAAATTACATTTTAACCCTCAAACTTTCAAAAATTACATTTTTACC-CTGAAC
* * * * * *
10347590 TTTCCAAAAATTACGTTTTGACCCTCGAACTTTCCATAATTACATTTTTACCCTTAAAC
1 TTTCC-AAAATTACATTTTAACCCTCAAACTTTCAAAAATTACATTTTTACCC-TGAAC
* *
10347649 TTTTCCAAAATTACATTTT-GCCC-CAAACATTCAAAA
1 -TTTCCAAAATTACATTTTAACCCTCAAACTTTCAAAA
10347685 GTTCGATTTT
Statistics
Matches: 129, Mismatches: 19, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
57 13 0.10
58 44 0.34
59 67 0.52
60 5 0.04
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (57 bp):
TTTCCAAAATTACATTTTAACCCTCAAACTTTCAAAAATTACATTTTTACCCTGAAC
Found at i:10354331 original size:27 final size:27
Alignment explanation
Indices: 10354293--10354346 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
10354283 TTATGGGTCG
10354293 GATCGAGATACAATTATTAATCGATCC
1 GATCGAGATACAATTATTAATCGATCC
10354320 GATCGAGATACAATTATTAATCGATCC
1 GATCGAGATACAATTATTAATCGATCC
10354347 AAACTCATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (27 bp):
GATCGAGATACAATTATTAATCGATCC
Found at i:10358958 original size:42 final size:42
Alignment explanation
Indices: 10358898--10359004 Score: 99
Period size: 42 Copynumber: 2.5 Consensus size: 42
10358888 CCTAAAATTG
* *
10358898 AGATGAAAACCTGTAAAGGGGGT-CTCGAAAACAAAAGGTTCA
1 AGATGAAAACCCGCAAAGGGGGTCCT-GAAAACAAAAGGTTCA
* * * **
10358940 AGATGAAAGCCCGCAAAGGGTGTCCTGAAACCAAAAGGAATTTTG
1 AGATGAAAACCCGCAAAGGGGGTCCTGAAAACAAAAGG---TTCA
*
10358985 AGTTGAAAACCCGCAAAGGG
1 AGATGAAAACCCGCAAAGGG
10359005 CGACTGAAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
42 30 0.58
43 2 0.04
45 20 0.38
ACGTcount: A:0.40, C:0.17, G:0.27, T:0.16
Consensus pattern (42 bp):
AGATGAAAACCCGCAAAGGGGGTCCTGAAAACAAAAGGTTCA
Found at i:10359903 original size:39 final size:39
Alignment explanation
Indices: 10359858--10360028 Score: 130
Period size: 39 Copynumber: 4.4 Consensus size: 39
10359848 GATTGAAGAT
*
10359858 TCCGATCTCTTACCCTGATCATGGAGCAGATCACAATCA
1 TCCGATCTCTTACCCTGAGCATGGAGCAGATCACAATCA
* ** * *
10359897 TCCGATCTTTTACCCTGAGGTTGGGGCAGATCACTATCA
1 TCCGATCTCTTACCCTGAGCATGGAGCAGATCACAATCA
* * * * * *
10359936 GCCAATCTCTTACCCTGAGCCTGG-GACAGATTATAACCA
1 TCCGATCTCTTACCCTGAGCATGGAG-CAGATCACAATCA
* * * * * *
10359975 TTCGACCTTTTACCCCGAGCCT-GAGGCAGATCACTATCA
1 TCCGATCTCTTACCCTGAGCATGGA-GCAGATCACAATCA
* *
10360014 ACCAATCTCTTACCC
1 TCCGATCTCTTACCC
10360029 CATGTTTGGG
Statistics
Matches: 99, Mismatches: 30, Indels: 6
0.73 0.22 0.04
Matches are distributed among these distances:
38 2 0.02
39 96 0.97
40 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (39 bp):
TCCGATCTCTTACCCTGAGCATGGAGCAGATCACAATCA
Found at i:10359948 original size:78 final size:76
Alignment explanation
Indices: 10359862--10360108 Score: 264
Period size: 78 Copynumber: 3.2 Consensus size: 76
10359852 GAAGATTCCG
* * * * **
10359862 ATCTCTTACCCTGATCATGGAGCAGATCACAATCATCCGATCTTTTACCCTGAGGTTGGGGCAGA
1 ATCTCTTACCCTGATCATGG-GCAGATTATAACCATTCGATCTTTTACCC-GAGCCTGGGGCAGA
10359927 TCACTATCAGCCA
64 TCACTATCAGCCA
* * * *
10359940 ATCTCTTACCCTGAGCCTGGGACAGATTATAACCATTCGACCTTTTACCCCGAGCCTGAGGCAGA
1 ATCTCTTACCCTGATCATGGG-CAGATTATAACCATTCGATCTTTTA-CCCGAGCCTGGGGCAGA
*
10360005 TCACTATCAACCA
64 TCACTATCAGCCA
* * * *
10360018 ATCTCTTACCCCATG-T-TTGGGGCAGATTGTAACCATTCGATCTTTTACCCGAGCCTAGGGTAG
1 ATCTCTTA-CCC-TGATCAT-GGGCAGATTATAACCATTCGATCTTTTACCCGAGCCTGGGGCAG
**
10360081 ATCACTATCAGATA
63 ATCACTATCAGCCA
10360095 ATCTCTTACCCTGA
1 ATCTCTTACCCTGA
10360109 GCTTGGGGCA
Statistics
Matches: 142, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
75 2 0.01
76 3 0.02
77 33 0.23
78 93 0.65
79 9 0.06
80 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.28
Consensus pattern (76 bp):
ATCTCTTACCCTGATCATGGGCAGATTATAACCATTCGATCTTTTACCCGAGCCTGGGGCAGATC
ACTATCAGCCA
Found at i:10360231 original size:133 final size:132
Alignment explanation
Indices: 10359989--10360249 Score: 371
Period size: 133 Copynumber: 2.0 Consensus size: 132
10359979 ACCTTTTACC
* * * *
10359989 CCGAGCCTGAGGCAGATCACTATCAACCAATCTCTTACCCCATGTTTGGGGCAGATTGTAACCAT
1 CCGAGCCTGAGGCAAATCACTATCAACCAATCTCTTACCCCATGCTTGAGGCAGATTGCAACCAT
* * * * *
10360054 TCGATCTTTTACCCGAGCCTAGGGTAGATCACTATCAGATAATCTCTTACCCTGAGCTTGGGGCA
66 TCGATCTCTTACCCGAGCCTAGGGTAGATCACCATCAGACAATCTCTTACCCCGAGCCTGGGGCA
10360119 AT
131 AT
* * *
10360121 CCGAGCCTGAGGCAAATCACTATCAGCCAATCTCTTACCCCCGTGCTTGAGGCAGATTGCAGCCA
1 CCGAGCCTGAGGCAAATCACTATCAACCAATCTCTTA-CCCCATGCTTGAGGCAGATTGCAACCA
* *
10360186 TTCGATCTCTTACCCTGAGCCTA-GGTAGATCGCCATCAGCCAATCTCTTACCCCGAGCCTGGGG
65 TTCGATCTCTTACCC-GAGCCTAGGGTAGATCACCATCAGACAATCTCTTACCCCGAGCCTGGGG
10360250 TAGTTTGTAG
Statistics
Matches: 113, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
132 35 0.31
133 71 0.63
134 7 0.06
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (132 bp):
CCGAGCCTGAGGCAAATCACTATCAACCAATCTCTTACCCCATGCTTGAGGCAGATTGCAACCAT
TCGATCTCTTACCCGAGCCTAGGGTAGATCACCATCAGACAATCTCTTACCCCGAGCCTGGGGCA
AT
Found at i:10360238 original size:38 final size:39
Alignment explanation
Indices: 10360190--10360331 Score: 137
Period size: 39 Copynumber: 3.7 Consensus size: 39
10360180 CAGCCATTCG
* *
10360190 ATCTCTTACCCTGAGCCT-AGGTAGATCGCCATCAGCCA
1 ATCTCTTACCCCGAGCCTGAGGTAGATCGCCATCAACCA
* * * * * *
10360228 ATCTCTTACCCCGAGCCTGGGGTAGTTTG-TAGCCATCCA
1 ATCTCTTACCCCGAGCCTGAGGTAGATCGCCA-TCAACCA
* * * *
10360267 ATCTCTTACCCCAAGCTTGAGGCAGATCACCATCAACCA
1 ATCTCTTACCCCGAGCCTGAGGTAGATCGCCATCAACCA
*
10360306 ATCTCTTACCCCGAGCCT-AGGAAGAT
1 ATCTCTTACCCCGAGCCTGAGGTAGAT
10360332 TACAGCCATT
Statistics
Matches: 81, Mismatches: 20, Indels: 6
0.76 0.19 0.06
Matches are distributed among these distances:
38 25 0.31
39 55 0.68
40 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGAGGTAGATCGCCATCAACCA
Found at i:10360275 original size:77 final size:78
Alignment explanation
Indices: 10360123--10360396 Score: 320
Period size: 77 Copynumber: 3.5 Consensus size: 78
10360113 GGGGCAATCC
* * * * * *
10360123 GAGCCTGAGGCAAATCACTATCAGCCAATCTCTTACCCCCGTGCTTGAGGCAGATTGCAGCCATT
1 GAGCTTGAGGCAGATCACCATCAGCCAATCTCTTA-CCCCGAGCCTGAGGAAGATTGCAGCCATT
10360188 CGATCTCTTACCCT
65 CGATCTCTTACCCT
* * * * * * * *
10360202 GAGCCT-AGGTAGATCGCCATCAGCCAATCTCTTACCCCGAGCCTGGGGTAGTTTGTAGCCATCC
1 GAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGAAGATTGCAGCCATTC
* *
10360266 AATCTCTTACCCC
66 GATCTCTTACCCT
* * *
10360279 AAGCTTGAGGCAGATCACCATCAACCAATCTCTTACCCCGAGCCT-AGGAAGATTACAGCCATTC
1 GAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGAAGATTGCAGCCATTC
10360343 GATCT-TTCACCCT
66 GATCTCTT-ACCCT
* *
10360356 GAGCTTGGGGCAGATCACCATCAGCCAATCCCTTACCCCGA
1 GAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCCCGA
10360397 TCATGAGGCA
Statistics
Matches: 163, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
76 2 0.01
77 96 0.59
78 59 0.36
79 6 0.04
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.23
Consensus pattern (78 bp):
GAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGAAGATTGCAGCCATTC
GATCTCTTACCCT
Found at i:10361566 original size:20 final size:21
Alignment explanation
Indices: 10361522--10361572 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
10361512 AATAAAAATG
10361522 TAATAAATAT-ATAATAAACA
1 TAATAAATATAATAATAAACA
* *
10361542 TAATAAATATAATATTAAATA
1 TAATAAATATAATAATAAACA
10361563 -AATAAA-ATAA
1 TAATAAATATAA
10361573 AAAGAAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 16 0.57
21 8 0.29
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
TAATAAATATAATAATAAACA
Found at i:10362606 original size:30 final size:29
Alignment explanation
Indices: 10362571--10362970 Score: 191
Period size: 29 Copynumber: 13.6 Consensus size: 29
10362561 GTCCCTGAAT
*
10362571 TTTCCAAAAATCATATTTTGATCCCAAAC
1 TTTCCAAAAATCATATTTTGACCCCAAAC
* ** *
10362600 TTTTCC-AAAATTATATTTAAACCCTTAAAC
1 -TTTCCAAAAATCATATTTTGACCC-CAAAC
*
10362630 -TTCACAAAATTACAT-TTTT-ACCCCTAAAC
1 TTTC-CAAAAAT-CATATTTTGACCCC-AAAC
* ** *
10362659 TTTCCAAAAATCATGTTTCAACCCTCGAAC
1 TTTCCAAAAATCATATTTTGACCC-CAAAC
* *
10362689 TTTCTAAAATTACAT-TTTT-ACCCTCAAAC
1 TTTCCAAAAAT-CATATTTTGACCC-CAAAC
** **
10362718 TTTTTAAAAATCATATTTTTCCCCCAAAC
1 TTTCCAAAAATCATATTTTGACCCCAAAC
* *
10362747 TTTCTAAAAATCACATTTTGACCCCCAAAC
1 TTTCCAAAAATCATATTTTGA-CCCCAAAC
* *
10362777 TTTCCAAAAATCATGTTTTGAACCCTAAAC
1 TTTCCAAAAATCATATTTTG-ACCCCAAAC
* * * **
10362807 TTTTCATAATTACAT-TTTT-ACTCTTAAAC
1 TTTCCAAAAAT-CATATTTTGAC-CCCAAAC
* * * *
10362836 TTTCCAAAAATCACATATTAACCCTTAAAC
1 TTTCCAAAAATCATATTTTGACCC-CAAAC
*
10362866 TTTCC-AAAATTATATTTT-ACCCCTAAAC
1 TTTCCAAAAATCATATTTTGACCCC-AAAC
* * *
10362894 TTTTTCAAAATTACAT-TTTTGCCCCCTAAA-
1 -TTTCCAAAAAT-CATATTTTGACCCC-AAAC
* *
10362924 TATCCAAAAA-CTACCATTTTG-CCCTCAAA-
1 TTTCCAAAAATC-A-TATTTTGACCC-CAAAC
*
10362953 TTTCCAAAAATCACATTT
1 TTTCCAAAAATCATATTT
10362971 CCAACTTCAA
Statistics
Matches: 291, Mismatches: 50, Indels: 60
0.73 0.12 0.15
Matches are distributed among these distances:
27 1 0.00
28 27 0.09
29 131 0.45
30 112 0.38
31 20 0.07
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (29 bp):
TTTCCAAAAATCATATTTTGACCCCAAAC
Found at i:10362659 original size:59 final size:58
Alignment explanation
Indices: 10362571--10362896 Score: 288
Period size: 59 Copynumber: 5.6 Consensus size: 58
10362561 GTCCCTGAAT
* * *
10362571 TTTCCAAAAAT-CATATTTTGATCCC-AAACTTTTCC-AAAATTATATTTAAACCCTTAAAC
1 TTTCCAAAATTACAT-TTTT-ACCCCTAAAC-TTTCCAAAAATCATATTT-AACCCTTAAAC
* **
10362630 -TTCACAAAATTACATTTTTACCCCTAAACTTTCCAAAAATCATGTTTCAACCCTCGAAC
1 TTTC-CAAAATTACATTTTTACCCCTAAACTTTCCAAAAATCATATTT-AACCCTTAAAC
* ** ** **
10362689 TTTCTAAAATTACATTTTTA-CCCTCAAACTTTTTAAAAATCATATTTTTCCCCCAAAC
1 TTTCCAAAATTACATTTTTACCCCT-AAACTTTCCAAAAATCATATTTAACCCTTAAAC
* * * * *
10362747 TTTCTAAAAATCACATTTTGACCCCCAAACTTTCCAAAAATCATGTTTTGAACCC-TAAAC
1 TTTC-CAAAATTACATTTTTACCCCTAAACTTTCCAAAAATCAT-ATTT-AACCCTTAAAC
* * * * *
10362807 TTTTCATAATTACATTTTTACTCTTAAACTTTCCAAAAATCACATATTAACCCTTAAAC
1 TTTCCAAAATTACATTTTTACCCCTAAACTTTCCAAAAATCATAT-TTAACCCTTAAAC
*
10362866 TTTCCAAAATTATA-TTTTACCCCTAAACTTT
1 TTTCCAAAATTACATTTTTACCCCTAAACTTT
10362897 TTCAAAATTA
Statistics
Matches: 215, Mismatches: 40, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
58 48 0.22
59 145 0.67
60 19 0.09
61 3 0.01
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (58 bp):
TTTCCAAAATTACATTTTTACCCCTAAACTTTCCAAAAATCATATTTAACCCTTAAAC
Found at i:10364411 original size:112 final size:112
Alignment explanation
Indices: 10364276--10364477 Score: 334
Period size: 112 Copynumber: 1.8 Consensus size: 112
10364266 TATGACATAT
* *
10364276 CGAAATAACTCACATAACTACCGATACAACAAACTCCAGAGAGCTAAGAAGCTTACCCTGAAACT
1 CGAAACAACTCACATAACTACCGATACAACAAACTCAAGAGAGCTAAGAAGCTTACCCTGAAACT
*
10364341 TCTACCGATACAAGTATTCGAACTACTGATACAATTATAACTTCTAC
66 TCTACCGATACAAGTACTCGAACTACTGATACAATTATAACTTCTAC
* * *
10364388 CGAAACAACTCACACTAA-TACCGATACAACAAACTCAAGAGAGCTAGGAAGCTTACTCTGCAAC
1 CGAAACAACTCACA-TAACTACCGATACAACAAACTCAAGAGAGCTAAGAAGCTTACCCTGAAAC
10364452 TTCTACCGATACAAGTACTCGAACTA
65 TTCTACCGATACAAGTACTCGAACTA
10364478 TCGATAGAAC
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
112 80 0.96
113 3 0.04
ACGTcount: A:0.40, C:0.27, G:0.12, T:0.21
Consensus pattern (112 bp):
CGAAACAACTCACATAACTACCGATACAACAAACTCAAGAGAGCTAAGAAGCTTACCCTGAAACT
TCTACCGATACAAGTACTCGAACTACTGATACAATTATAACTTCTAC
Found at i:10366978 original size:24 final size:24
Alignment explanation
Indices: 10366951--10367021 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
10366941 ACCATACACG
10366951 GAGTTGGATCTTCATTTTCTACTA
1 GAGTTGGATCTTCATTTTCTACTA
* *
10366975 GAGTTGGATCTTCATTTTTTACTC
1 GAGTTGGATCTTCATTTTCTACTA
*
10366999 GAGTTGGATATTCATTTTCTACT
1 GAGTTGGATCTTCATTTTCTACT
10367022 GGTTCCACAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (24 bp):
GAGTTGGATCTTCATTTTCTACTA
Found at i:10368010 original size:44 final size:44
Alignment explanation
Indices: 10367943--10368029 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
10367933 AGACATATTG
* *
10367943 GTAATTAAGGGTGTAGATTCCATTTTGATAGATAAATAATTTTC
1 GTAATTAAGGGTGGAGATACCATTTTGATAGATAAATAATTTTC
*
10367987 GTAATTAAGGGTGGGGATACCATTTTGATAGATAAATAATTTT
1 GTAATTAAGGGTGGAGATACCATTTTGATAGATAAATAATTTT
10368030 TTTATATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.39
Consensus pattern (44 bp):
GTAATTAAGGGTGGAGATACCATTTTGATAGATAAATAATTTTC
Found at i:10381596 original size:4 final size:4
Alignment explanation
Indices: 10381589--10381623 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
10381579 TATATATATA
*
10381589 TATG TATG TTTG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
10381624 TGAATGATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (4 bp):
TATG
Found at i:10382029 original size:16 final size:17
Alignment explanation
Indices: 10381986--10382031 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
10381976 GAGCATACTT
10381986 TAATA-GTATAT-ATTA
1 TAATATGTATATGATTA
*
10382001 TAATATG-AAATGATTA
1 TAATATGTATATGATTA
10382017 T-ATATGTATATGATT
1 TAATATGTATATGATT
10382032 TCGGTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (17 bp):
TAATATGTATATGATTA
Found at i:10386018 original size:15 final size:15
Alignment explanation
Indices: 10385995--10386025 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10385985 GACGGCTTCG
*
10385995 TGTGTTCTGATTCAT
1 TGTGCTCTGATTCAT
10386010 TGTGCTCTGATTCAT
1 TGTGCTCTGATTCAT
10386025 T
1 T
10386026 ACTAATACAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.16, G:0.19, T:0.52
Consensus pattern (15 bp):
TGTGCTCTGATTCAT
Found at i:10386638 original size:21 final size:21
Alignment explanation
Indices: 10386587--10386645 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
10386577 AGAAACAGTG
*
10386587 CAGACTTCTACTGATACAACT
1 CAGACTTCTACCGATACAACT
* * *
10386608 GAGACATCTACCGATACAAGT
1 CAGACTTCTACCGATACAACT
* *
10386629 CATACTTCTATCGATAC
1 CAGACTTCTACCGATAC
10386646 TAAAAACTCT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (21 bp):
CAGACTTCTACCGATACAACT
Found at i:10390270 original size:38 final size:38
Alignment explanation
Indices: 10390219--10390295 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
10390209 ATTATATGTT
10390219 AATCTTAGTATAAATAATAAAACAAAAACATTTACTTC
1 AATCTTAGTATAAATAATAAAACAAAAACATTTACTTC
10390257 AATCTTAGTATAAATAATAAAACAAAAACATTTACTTC
1 AATCTTAGTATAAATAATAAAACAAAAACATTTACTTC
10390295 A
1 A
10390296 CCATTCTCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.31
Consensus pattern (38 bp):
AATCTTAGTATAAATAATAAAACAAAAACATTTACTTC
Found at i:10392991 original size:16 final size:16
Alignment explanation
Indices: 10392967--10393034 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
10392957 AACATCTAAA
*
10392967 GTTTGGAATAACTCTT
1 GTTTAGAATAACTCTT
**
10392983 GTTTAGAATAA-TAGT
1 GTTTAGAATAACTCTT
* *
10392998 GTTTCAAAAATAGCT-TT
1 GTTT--AGAATAACTCTT
*
10393015 GTTTAGAACAACTCTT
1 GTTTAGAATAACTCTT
10393031 GTTT
1 GTTT
10393035 GTAACAATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
15 12 0.31
16 16 0.41
17 10 0.26
18 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (16 bp):
GTTTAGAATAACTCTT
Found at i:10393835 original size:23 final size:23
Alignment explanation
Indices: 10393791--10393835 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
10393781 GTCTTCCTTT
* *
10393791 TTGTCTTTTTTCAATACATTCCA
1 TTGTCTTTTTGCAACACATTCCA
10393814 TTGTCTTGTTTGCAACAC-TTCC
1 TTGTCTT-TTTGCAACACATTCC
10393836 TTTCTCCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.18, C:0.24, G:0.09, T:0.49
Consensus pattern (23 bp):
TTGTCTTTTTGCAACACATTCCA
Found at i:10398168 original size:2 final size:2
Alignment explanation
Indices: 10398161--10398196 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10398151 CCACAAGTAC
10398161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10398197 TACAGATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10405833 original size:24 final size:24
Alignment explanation
Indices: 10405791--10405853 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
10405781 TACAACCTTT
**
10405791 CACCTTTCATCTCCCTTAACATTC
1 CACCTTTCATCTTTCTTAACATTC
* * *
10405815 CACCTTTCATCTTTTTTAACCTTT
1 CACCTTTCATCTTTCTTAACATTC
* *
10405839 CACATTTCACCTTTC
1 CACCTTTCATCTTTC
10405854 ATCTTCCTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.19, C:0.37, G:0.00, T:0.44
Consensus pattern (24 bp):
CACCTTTCATCTTTCTTAACATTC
Found at i:10406335 original size:34 final size:34
Alignment explanation
Indices: 10406287--10406363 Score: 136
Period size: 34 Copynumber: 2.2 Consensus size: 34
10406277 TGTTTTTGTG
10406287 TTATGTTATGCTTGAAAGTTTTGTTAAGGGATTAC
1 TTATGTT-TGCTTGAAAGTTTTGTTAAGGGATTAC
10406322 TTATGTTTGCTTGAAAGTTTTGTTAAGGGATTAC
1 TTATGTTTGCTTGAAAGTTTTGTTAAGGGATTAC
*
10406356 TCATGTTT
1 TTATGTTT
10406364 ATATTAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 34 0.83
35 7 0.17
ACGTcount: A:0.23, C:0.06, G:0.22, T:0.48
Consensus pattern (34 bp):
TTATGTTTGCTTGAAAGTTTTGTTAAGGGATTAC
Found at i:10411800 original size:27 final size:26
Alignment explanation
Indices: 10411750--10411813 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 26
10411740 AAATCTTCTC
10411750 TAAATTAATAAATATTAATTTATCAA
1 TAAATTAATAAATATTAATTTATCAA
*
10411776 TAAATTAATAAATTATTCATTTATCAA
1 TAAATTAATAAA-TATTAATTTATCAA
*
10411803 TAAACTAATAA
1 TAAATTAATAA
10411814 CCTCGATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 12 0.34
27 23 0.66
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (26 bp):
TAAATTAATAAATATTAATTTATCAA
Found at i:10414578 original size:22 final size:23
Alignment explanation
Indices: 10414553--10414605 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
10414543 GAGCACCAAG
*
10414553 GTGCTATACGAAGAGAAC-AAAC
1 GTGCTAAACGAAGAGAACTAAAC
* * *
10414575 GTGCAAAACGGAGAGCACTAAAC
1 GTGCTAAACGAAGAGAACTAAAC
10414598 GTGCTAAA
1 GTGCTAAA
10414606 TAATGGAGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (23 bp):
GTGCTAAACGAAGAGAACTAAAC
Found at i:10416540 original size:28 final size:28
Alignment explanation
Indices: 10416508--10416571 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
10416498 AAATACTACT
* * *
10416508 TTTGTGGTAAAATTTTGTAAGGTAAGCC
1 TTTGTGGTAAAACTCTATAAGGTAAGCC
* *
10416536 TTTGTTGCAAAACTCTATAAGGTAAGCC
1 TTTGTGGTAAAACTCTATAAGGTAAGCC
10416564 TTTGTGGT
1 TTTGTGGT
10416572 GAACCTCTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (28 bp):
TTTGTGGTAAAACTCTATAAGGTAAGCC
Found at i:10416579 original size:28 final size:28
Alignment explanation
Indices: 10416525--10416636 Score: 84
Period size: 28 Copynumber: 4.0 Consensus size: 28
10416515 TAAAATTTTG
*
10416525 TAAGGTAAGCCTTTGTTGCAAAACTCTA
1 TAAGGTAAGCCTTTGTGGCAAAACTCTA
** *
10416553 TAAGGTAAGCCTTTGTGGTGAACCTCT-
1 TAAGGTAAGCCTTTGTGGCAAAACTCTA
* * *
10416580 TAAAGG-ATTGCATTTGTGGCAAATCTCTA
1 T-AAGGTA-AGCCTTTGTGGCAAAACTCTA
* * * *
10416609 GAAAGGTAAGTCTTGGTGGCAAACCTCT
1 -TAAGGTAAGCCTTTGTGGCAAAACTCT
10416637 TAAAGTATGT
Statistics
Matches: 64, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
27 2 0.03
28 42 0.66
29 19 0.30
30 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (28 bp):
TAAGGTAAGCCTTTGTGGCAAAACTCTA
Found at i:10416627 original size:29 final size:28
Alignment explanation
Indices: 10416594--10416683 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 28
10416584 GGATTGCATT
10416594 TGTGGCAAATCTCTAGAAAGGTAAGTCT-
1 TGTGGCAAATCTCT-GAAAGGTAAGTCTA
* * *
10416622 TGGTGGCAAACCTCTTAAA-GTATGTCTA
1 T-GTGGCAAATCTCTGAAAGGTAAGTCTA
* * **
10416650 TGTGGCAAGTCTCTGAAAGGAAAACCTA
1 TGTGGCAAATCTCTGAAAGGTAAGTCTA
10416678 TGTGGC
1 TGTGGC
10416684 GAGTACTAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
27 21 0.43
28 16 0.33
29 12 0.24
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (28 bp):
TGTGGCAAATCTCTGAAAGGTAAGTCTA
Found at i:10416905 original size:27 final size:27
Alignment explanation
Indices: 10416810--10416906 Score: 90
Period size: 27 Copynumber: 3.6 Consensus size: 27
10416800 GTTAAATTCT
**
10416810 GTAAATGAAGCCTTTGTGGCT-ACTTT
1 GTAAATGAAGCCTTTGTGGCTAACTAA
*
10416836 GTAAAGTGAA-CCTTTGTGGCGAACTCTAA
1 GTAAA-TGAAGCCTTTGTGGCTAA--CTAA
* ** *
10416865 ATAAGGGAATCCTTTGTGGCTAACTAA
1 GTAAATGAAGCCTTTGTGGCTAACTAA
10416892 GTAAATGAAGCCTTT
1 GTAAATGAAGCCTTT
10416907 TTGTTGCGTA
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
26 15 0.27
27 20 0.36
28 3 0.05
29 17 0.31
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (27 bp):
GTAAATGAAGCCTTTGTGGCTAACTAA
Found at i:10430048 original size:19 final size:19
Alignment explanation
Indices: 10430026--10430094 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
10430016 AAAATCAACA
10430026 GTCAAAGTCAAAGTCAATG
1 GTCAAAGTCAAAGTCAATG
* *
10430045 GTCAACGATCAAAGTTAACAT-
1 GTCAAAG-TCAAAG-TCA-ATG
* *
10430066 GTC-TAGTCAAAGTCAACG
1 GTCAAAGTCAAAGTCAATG
10430084 GTCAAAGTCAA
1 GTCAAAGTCAA
10430095 TAGGTCGATT
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
17 1 0.03
18 5 0.13
19 18 0.47
20 7 0.18
21 5 0.13
22 2 0.05
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (19 bp):
GTCAAAGTCAAAGTCAATG
Found at i:10438928 original size:31 final size:29
Alignment explanation
Indices: 10438861--10438931 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
10438851 AAATTAAAAT
* *
10438861 TTCATATATAAAATTGCACAAAATCAAAG
1 TTCATGTATAAAATTGCACAAAACCAAAG
*
10438890 TTCATGTATACAATTGCACATTAAACCATAA-
1 TTCATGTATAAAATTGCACA--AAACCA-AAG
10438921 TTCATGTATAA
1 TTCATGTATAA
10438932 TTTTGAGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 18 0.51
31 15 0.43
32 2 0.06
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (29 bp):
TTCATGTATAAAATTGCACAAAACCAAAG
Found at i:10442878 original size:20 final size:20
Alignment explanation
Indices: 10442853--10442893 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
10442843 CAATGACATG
10442853 CAAAACAAGAAGAAAAATCT
1 CAAAACAAGAAGAAAAATCT
10442873 CAAAACAAGAAGAAAAATCT
1 CAAAACAAGAAGAAAAATCT
10442893 C
1 C
10442894 GCAATTGCTA
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:0.63, C:0.17, G:0.10, T:0.10
Consensus pattern (20 bp):
CAAAACAAGAAGAAAAATCT
Found at i:10454354 original size:12 final size:12
Alignment explanation
Indices: 10454337--10454363 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
10454327 TTGATGTTGC
10454337 AGCTAAGATAAA
1 AGCTAAGATAAA
10454349 AGCTAAGATAAA
1 AGCTAAGATAAA
10454361 AGC
1 AGC
10454364 AATATAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.11, G:0.19, T:0.15
Consensus pattern (12 bp):
AGCTAAGATAAA
Found at i:10462183 original size:15 final size:16
Alignment explanation
Indices: 10462163--10462192 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10462153 TTTAATTTTT
10462163 TTATTT-ACTTTTCAG
1 TTATTTCACTTTTCAG
10462178 TTATTTCACTTTTCA
1 TTATTTCACTTTTCA
10462193 TCATGTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.17, G:0.03, T:0.60
Consensus pattern (16 bp):
TTATTTCACTTTTCAG
Found at i:10471804 original size:17 final size:18
Alignment explanation
Indices: 10471784--10471817 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10471774 AAAATGAGCA
*
10471784 TGTA-AATTAAATACGAG
1 TGTACAATTAAAGACGAG
10471801 TGTACAATTAAAGACGA
1 TGTACAATTAAAGACGA
10471818 AATCGAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (18 bp):
TGTACAATTAAAGACGAG
Found at i:10472246 original size:29 final size:29
Alignment explanation
Indices: 10472215--10472308 Score: 107
Period size: 31 Copynumber: 3.1 Consensus size: 29
10472205 AAAAATGGAA
*
10472215 TTTTAAAAAGTTCGAGGGTTAAATTCAAAT
1 TTTTAAAAAGTTAG-GGGTTAAATTCAAAT
* * *
10472245 TTTTAGAAAGTTTGGGGTCAAATTCAAAT
1 TTTTAAAAAGTTAGGGGTTAAATTCAAAT
* *
10472274 TTTTGGAAAGGTTAGGGGGTTAAATTCAAAT
1 TTTT-AAAAAGTTA-GGGGTTAAATTCAAAT
10472305 TTTT
1 TTTT
10472309 GGAAAATTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 18 0.33
30 17 0.31
31 19 0.35
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.39
Consensus pattern (29 bp):
TTTTAAAAAGTTAGGGGTTAAATTCAAAT
Found at i:10472255 original size:30 final size:30
Alignment explanation
Indices: 10472221--10472356 Score: 159
Period size: 30 Copynumber: 4.5 Consensus size: 30
10472211 GGAATTTTAA
* * *
10472221 AAAGTTCGAGGGTTAAATTCAAATTTTTAG
1 AAAGTTTGAGGGTCAAATTCAAATTTTTGG
10472251 AAAGTTTG-GGGTCAAATTCAAATTTTTGG
1 AAAGTTTGAGGGTCAAATTCAAATTTTTGG
* * *
10472280 AAAGGTTAGGGGGTTAAATTCAAATTTTTGG
1 AAA-GTTTGAGGGTCAAATTCAAATTTTTGG
* *
10472311 AAAATTTGAGGGCCAAATT-AGAATTTTTGG
1 AAAGTTTGAGGGTCAAATTCA-AATTTTTGG
*
10472341 AAAGTTTAAGGGTCAA
1 AAAGTTTGAGGGTCAA
10472357 GTTTGAATTT
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
29 23 0.26
30 44 0.49
31 23 0.26
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (30 bp):
AAAGTTTGAGGGTCAAATTCAAATTTTTGG
Found at i:10472299 original size:31 final size:29
Alignment explanation
Indices: 10472221--10472346 Score: 128
Period size: 29 Copynumber: 4.2 Consensus size: 29
10472211 GGAATTTTAA
* *
10472221 AAAGTTCGAGGGTTAAATTCAAATTTTTAG
1 AAAGTT-GGGGGTTAAATTCAAATTTTTGG
* *
10472251 AAAGTTTGGGGTCAAATTCAAATTTTTGG
1 AAAGTTGGGGGTTAAATTCAAATTTTTGG
10472280 AAAGGTTAGGGGGTTAAATTCAAATTTTTGG
1 AAA-GTT-GGGGGTTAAATTCAAATTTTTGG
* * **
10472311 AAAATTTGAGGGCCAAATT-AGAATTTTTGG
1 -AAAGTTGGGGGTTAAATTCA-AATTTTTGG
10472341 AAAGTT
1 AAAGTT
10472347 TAAGGGTCAA
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
29 28 0.35
30 27 0.33
31 23 0.28
32 3 0.04
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (29 bp):
AAAGTTGGGGGTTAAATTCAAATTTTTGG
Found at i:10472299 original size:60 final size:61
Alignment explanation
Indices: 10472230--10472344 Score: 180
Period size: 60 Copynumber: 1.9 Consensus size: 61
10472220 AAAAGTTCGA
* *
10472230 GGGTTAAATTCAAATTTTTAGAAAGTTTG-GGGTCAAATTCA-AATTTTTGGAAAGGTTAGG
1 GGGTTAAATTCAAATTTTTAGAAAATTTGAGGGCCAAATT-AGAATTTTTGGAAAGGTTAGG
*
10472290 GGGTTAAATTCAAATTTTTGGAAAATTTGAGGGCCAAATTAGAATTTTTGGAAAG
1 GGGTTAAATTCAAATTTTTAGAAAATTTGAGGGCCAAATTAGAATTTTTGGAAAG
10472345 TTTAAGGGTC
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
60 28 0.56
61 22 0.44
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (61 bp):
GGGTTAAATTCAAATTTTTAGAAAATTTGAGGGCCAAATTAGAATTTTTGGAAAGGTTAGG
Found at i:10483768 original size:6 final size:6
Alignment explanation
Indices: 10483757--10483791 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
10483747 TCAGATTCAC
* *
10483757 ATACAG ATACAG ATACAG ATACAA AAACAG ATACA
1 ATACAG ATACAG ATACAG ATACAG ATACAG ATACA
10483792 TGTGCAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.57, C:0.17, G:0.11, T:0.14
Consensus pattern (6 bp):
ATACAG
Found at i:10486380 original size:19 final size:18
Alignment explanation
Indices: 10486358--10486393 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10486348 CCCTTCTCCT
*
10486358 TTCTTTCTTTCTTTCTCTC
1 TTCTATCTTTC-TTCTCTC
10486377 TTCTATCTTTCTTCTCT
1 TTCTATCTTTCTTCTCT
10486394 TCTACTAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.67
Consensus pattern (18 bp):
TTCTATCTTTCTTCTCTC
Found at i:10490417 original size:2 final size:2
Alignment explanation
Indices: 10490410--10490455 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
10490400 TCCGATGTCA
10490410 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
10490452 TC TC
1 TC TC
10490456 GGCGTGAAGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:10491578 original size:13 final size:13
Alignment explanation
Indices: 10491548--10491579 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
10491538 AGCGCAATAA
*
10491548 AAAAATATTTTTG
1 AAAAGTATTTTTG
10491561 AAAAGTATTTTTG
1 AAAAGTATTTTTG
10491574 AAAAGT
1 AAAAGT
10491580 TTGATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (13 bp):
AAAAGTATTTTTG
Found at i:10494773 original size:6 final size:6
Alignment explanation
Indices: 10494752--10494814 Score: 63
Period size: 6 Copynumber: 10.0 Consensus size: 6
10494742 AAATTATGTC
* * *
10494752 AAAATT AAAATAT AAAATT AAATTT AAAATT AAAAAATA AAAATA AAAATT
1 AAAATT AAAAT-T AAAATT AAAATT AAAATT --AAAATT AAAATT AAAATT
*
10494803 AAAACT AAAATT
1 AAAATT AAAATT
10494815 TAATCATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
6 37 0.77
7 6 0.12
8 5 0.10
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:10494817 original size:13 final size:13
Alignment explanation
Indices: 10494752--10494817 Score: 71
Period size: 13 Copynumber: 5.2 Consensus size: 13
10494742 AAATTATGTC
*
10494752 AAAATTAAAATAT
1 AAAATTAAAATTT
10494765 AAAATT-AAATTT
1 AAAATTAAAATTT
**
10494777 AAAATTAAAAAAT
1 AAAATTAAAATTT
* *
10494790 AAAAATAAAAATT
1 AAAATTAAAATTT
*
10494803 AAAACTAAAATTT
1 AAAATTAAAATTT
10494816 AA
1 AA
10494818 TCATTATTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
12 11 0.24
13 34 0.76
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:10495351 original size:458 final size:457
Alignment explanation
Indices: 10494476--10495375 Score: 1059
Period size: 458 Copynumber: 2.0 Consensus size: 457
10494466 TATTTTCAAG
* * * * * * *
10494476 AATTTAGTCTTTTCATTTTTTAAATTTAAAAATTTAAATCCATTTGTTAACATTATTATGATTCT
1 AATTTAGTCCTTTCATTTTTCAAAATTAAAAATTTAAAGCCATTTGTTAACATCATTATAATTAT
* * * * * * **
10494541 TCTATTAAATTTGTTGATATGATATTTTGAAATTAAAAAAAATTTACTCACTTTTTATCCATGTA
66 TCTATAAAATTTATCGATATCATATTTTAAAATTAAAAAAAA-TTACTCAATTAATATCCATGTA
* * * * * * * * * *
10494606 ACAAAAATGACTTTGTAATTTACTTGAATTTAATAGAGAATTTTAATAGTGTTACAATTTTTAAA
130 AAAAAAATGACTTTCTAATATACTTAAATTTAATAAAAAAATTTAATAATATTACAATTCTTAAA
* * * * * * * * *
10494671 ATTTTACATAAAGATTTTAATCATAATAAAATATTTAAATTAACTAATGATATTATAAGAATTGA
195 AATTCAAATAAAGATTTTAATCATAACAAAATATTTAAACTAACTAATAACATTATAAAAATTAA
* *
10494736 GATATCAAATTATGTCAAAATTAAAATATAAAATTAAATTTAAAATTAAAAAATAAAAATAAAAA
260 GACATCAAATTATGTCAAAATTAAAATATAAAATCAAATTTAAAA-TAAAAAATAAAAATAAAAA
* *
10494801 TTAAAACTAAAATTTAATCATTATTATATAATCTAAAAAAAGAAGAGAACTAAAATTGAAATTTA
324 TTAAAACTAAAATTTAATCATTATTATATAAACTAAAAAAAGAAGAGAACTAAAATTAAAATTTA
* *
10494866 GACATATCTTTTGATATAAAGAAAAGTACAAATGTCATGTAAGGAAGCCTTTCTTTTATATACAG
389 GACATATCTTTTGATATAAACAAAAGTACAAATGTCATATAAGGAAGCCTTTCTTTTATATACAG
10494931 TAGT
454 TAGT
* * *
10494935 AATTTAGCTCCTTT-ATTTTTCAAAATTAAAAATTT-AAGCGTATTTGTTAATATCGTTATAATT
1 AATTTAG-TCCTTTCATTTTTCAAAATTAAAAATTTAAAGC-CATTTGTTAACATCATTATAATT
* **
10494998 ATTTTATAAAATTTATCGATATCATATTTTAAAATT-AAAAAAA-TACTCAATTAATATTTATGT
64 ATTCTATAAAATTTATCGATATCATATTTTAAAATTAAAAAAAATTACTCAATTAATATCCATGT
10495061 AATAAAAAATGA-TATTCTAATATACTTAAATTTAATAAAAAAATTTAATAATATTAACAATTCT
129 AA-AAAAAATGACT-TTCTAATATACTTAAATTTAATAAAAAAATTTAATAATATT-ACAATTCT
10495125 TAAAAATTCAAATCAAA-ATTTTAATCATAACAAAATATTTAAACTAACTAATAACATTATAAAA
191 TAAAAATTCAAAT-AAAGATTTTAATCATAACAAAATATTTAAACTAACTAATAACATTATAAAA
***
10495189 ATTAA-AGCATCAAATTATGTCAAAATTAAAATATAAATATCAAATTTAAAA-ACTGAA-AAAAA
255 ATTAAGA-CATCAAATTATGTCAAAATTAAAATATAAA-ATCAAATTTAAAATAAAAAATAAAAA
* * * * * * *
10495251 TAAGAATTAAAACTGAAATTTAATCGTTCTTATATAAACTGAAAAGAGTAA-AGAGATTAAAATT
318 TAAAAATTAAAACTAAAATTTAATCATTATTATATAAACTAAAAAAAG-AAGAGA-ACTAAAATT
* *
10495315 AAAATTTAGAC-TATCATCTTTGCATA-AAACAAAAGTACAAGTGTCATATAAGGAAGGCTTT
381 AAAATTTAGACATATC-T-TTTG-ATATAAACAAAAGTACAAATGTCATATAAGGAAGCCTTT
10495376 AGGGCCTTCC
Statistics
Matches: 370, Mismatches: 58, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
456 71 0.19
457 66 0.18
458 137 0.37
459 91 0.25
460 5 0.01
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (457 bp):
AATTTAGTCCTTTCATTTTTCAAAATTAAAAATTTAAAGCCATTTGTTAACATCATTATAATTAT
TCTATAAAATTTATCGATATCATATTTTAAAATTAAAAAAAATTACTCAATTAATATCCATGTAA
AAAAAATGACTTTCTAATATACTTAAATTTAATAAAAAAATTTAATAATATTACAATTCTTAAAA
ATTCAAATAAAGATTTTAATCATAACAAAATATTTAAACTAACTAATAACATTATAAAAATTAAG
ACATCAAATTATGTCAAAATTAAAATATAAAATCAAATTTAAAATAAAAAATAAAAATAAAAATT
AAAACTAAAATTTAATCATTATTATATAAACTAAAAAAAGAAGAGAACTAAAATTAAAATTTAGA
CATATCTTTTGATATAAACAAAAGTACAAATGTCATATAAGGAAGCCTTTCTTTTATATACAGTA
GT
Found at i:10497031 original size:20 final size:21
Alignment explanation
Indices: 10497006--10497054 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
10496996 TAAAATTATT
10497006 TAAAAAAAGG-AATAAAAAAG-
1 TAAAAAAAGGTAA-AAAAAAGA
10497026 TAAAAAAAGGTAAAAAAAAGA
1 TAAAAAAAGGTAAAAAAAAGA
10497047 TAAAAAAA
1 TAAAAAAA
10497055 TATAATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (21 bp):
TAAAAAAAGGTAAAAAAAAGA
Found at i:10500267 original size:25 final size:24
Alignment explanation
Indices: 10500197--10500326 Score: 103
Period size: 23 Copynumber: 5.5 Consensus size: 24
10500187 ACACTAGCGC
10500197 GCCCTCTG-T-TTAGCACGTT-TCGT
1 GCCCTCTGTTATTAGCAC-TTGT-GT
* *
10500220 GCCCTCTG-T-TCAGCATTGTGTGT
1 GCCCTCTGTTATTAGCACT-TGTGT
10500243 GCCCTCTGTTATTAGCACTTCGTGT
1 GCCCTCTGTTATTAGCACTT-GTGT
10500268 GCCCTCTG--ATTAGCACTTTGTGT
1 GCCCTCTGTTATTAGCAC-TTGTGT
* ** *
10500291 GCCCTCTATTACCCAGCACTTATGT
1 GCCCTCTGTTA-TTAGCACTTGTGT
10500316 GCCCTCTGTTA
1 GCCCTCTGTTA
10500327 AGTACTTCGG
Statistics
Matches: 89, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
22 1 0.01
23 44 0.49
24 5 0.06
25 34 0.38
26 5 0.06
ACGTcount: A:0.12, C:0.30, G:0.20, T:0.38
Consensus pattern (24 bp):
GCCCTCTGTTATTAGCACTTGTGT
Found at i:10500274 original size:48 final size:47
Alignment explanation
Indices: 10500218--10500326 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 47
10500208 AGCACGTTTC
* ** *
10500218 GTGCCCTCTGTTCAGCA-TTGTGTGTGCCCTCTGTTA-TTAGCACTTCGT
1 GTGCCCTCTGTT-AGCACTT-TGTGTGCCCTCTATTACCCAGCACTT-AT
10500266 GTGCCCTCTGATTAGCACTTTGTGTGCCCTCTATTACCCAGCACTTAT
1 GTGCCCTCTG-TTAGCACTTTGTGTGCCCTCTATTACCCAGCACTTAT
10500314 GTGCCCTCTGTTA
1 GTGCCCTCTGTTA
10500327 AGTACTTCGG
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
47 3 0.06
48 40 0.74
49 11 0.20
ACGTcount: A:0.13, C:0.29, G:0.20, T:0.38
Consensus pattern (47 bp):
GTGCCCTCTGTTAGCACTTTGTGTGCCCTCTATTACCCAGCACTTAT
Found at i:10507382 original size:23 final size:23
Alignment explanation
Indices: 10507352--10507430 Score: 74
Period size: 23 Copynumber: 3.3 Consensus size: 23
10507342 ACTAGCGCAA
10507352 CCTCTGTTTAGCACGTTTCGTGC
1 CCTCTGTTTAGCACGTTTCGTGC
* *
10507375 CCTCTGTTCAGCACTGTGT-GTGC
1 CCTCTGTTTAGCAC-GTTTCGTGC
10507398 CCTCTGTTATTAGCAC--TTCGTGTGC
1 CCTCTG-T-TTAGCACGTTTC--GTGC
10507423 CCTCTGTT
1 CCTCTGTT
10507431 ACCCAGCACT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
22 1 0.02
23 24 0.52
24 5 0.11
25 16 0.35
ACGTcount: A:0.09, C:0.30, G:0.22, T:0.39
Consensus pattern (23 bp):
CCTCTGTTTAGCACGTTTCGTGC
Found at i:10507447 original size:26 final size:25
Alignment explanation
Indices: 10507371--10507478 Score: 114
Period size: 25 Copynumber: 4.4 Consensus size: 25
10507361 AGCACGTTTC
* *
10507371 GTGCCCTCTGTT--CAGCACTGTGT
1 GTGCCCTCTGTTACCAGCACTTTAT
** **
10507394 GTGCCCTCTGTTATTAGCACTTCGT
1 GTGCCCTCTGTTACCAGCACTTTAT
10507419 GTGCCCTCTGTTACCCAGCACTTTAT
1 GTGCCCTCTGTTA-CCAGCACTTTAT
10507445 GTGCCCTCTGTTACCCAGCAC-TTAT
1 GTGCCCTCTGTTA-CCAGCACTTTAT
*
10507470 GTTCCCTCT
1 GTGCCCTCT
10507479 TTTAAGTACT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.16
25 33 0.45
26 29 0.39
ACGTcount: A:0.12, C:0.33, G:0.19, T:0.36
Consensus pattern (25 bp):
GTGCCCTCTGTTACCAGCACTTTAT
Found at i:10509474 original size:20 final size:20
Alignment explanation
Indices: 10509446--10509483 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10509436 TATCATAAAA
*
10509446 ATAACAAATGAATAAAATAC
1 ATAACAAATAAATAAAATAC
*
10509466 ATAATAAATAAATAAAAT
1 ATAACAAATAAATAAAAT
10509484 TAAATAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (20 bp):
ATAACAAATAAATAAAATAC
Found at i:10515432 original size:17 final size:17
Alignment explanation
Indices: 10515390--10515424 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
10515380 CACCAAAAAA
10515390 AATAACAAACAAATAAAT
1 AATAA-AAACAAATAAAT
10515408 AATAAAAAC-AATAAAT
1 AATAAAAACAAATAAAT
10515424 A
1 A
10515425 TATGAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 4 0.24
18 5 0.29
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (17 bp):
AATAAAAACAAATAAAT
Found at i:10516116 original size:29 final size:28
Alignment explanation
Indices: 10516051--10516117 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 28
10516041 TTGTAAAGCT
*
10516051 ATTAAAATTAAAAGGCTAAATTAAAATAA
1 ATTAAAA-TAAAAGGCTAAATTAAAACAA
*
10516080 ATTAAAAATAAAAGGACTAAATTAAAACAC
1 ATT-AAAATAAAAGG-CTAAATTAAAACAA
*
10516110 CTTAAAAT
1 ATTAAAAT
10516118 GCGAAAAGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 15 0.45
30 18 0.55
ACGTcount: A:0.61, C:0.07, G:0.06, T:0.25
Consensus pattern (28 bp):
ATTAAAATAAAAGGCTAAATTAAAACAA
Found at i:10516116 original size:30 final size:29
Alignment explanation
Indices: 10516051--10516108 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
10516041 TTGTAAAGCT
* *
10516051 ATTAAAATTAAAAGGCTAAATTAAAATAA
1 ATTAAAAATAAAAGGCTAAATTAAAACAA
10516080 ATTAAAAATAAAAGGACTAAATTAAAACA
1 ATTAAAAATAAAAGG-CTAAATTAAAACA
10516109 CCTTAAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.24
Consensus pattern (29 bp):
ATTAAAAATAAAAGGCTAAATTAAAACAA
Found at i:10527663 original size:17 final size:18
Alignment explanation
Indices: 10527623--10527665 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
10527613 TTTAAAAGCC
10527623 TAAAACCGAAAAACAATA
1 TAAAACCGAAAAACAATA
**
10527641 TGAAAACCGAAACTCAA-A
1 T-AAAACCGAAAAACAATA
10527659 TAAAACC
1 TAAAACC
10527666 AATTCAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 3 0.14
19 13 0.59
ACGTcount: A:0.60, C:0.21, G:0.07, T:0.12
Consensus pattern (18 bp):
TAAAACCGAAAAACAATA
Found at i:10534665 original size:3 final size:3
Alignment explanation
Indices: 10534657--10534700 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
10534647 TTGATATGTT
10534657 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
10534701 GTCGAAATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:10537448 original size:18 final size:18
Alignment explanation
Indices: 10537427--10537463 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
10537417 ATTTTGGATG
10537427 TAAATGAAATTTTAAAAT
1 TAAATGAAATTTTAAAAT
*
10537445 TAAATTAAATTTTAAAAT
1 TAAATGAAATTTTAAAAT
10537463 T
1 T
10537464 TGGATTTTAT
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:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
TAAATGAAATTTTAAAAT
Found at i:10537585 original size:3 final size:3
Alignment explanation
Indices: 10537577--10537614 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
10537567 GATCTTTACA
* *
10537577 ATT ATT ATT GTT GTT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
10537615 GACTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:10548115 original size:327 final size:327
Alignment explanation
Indices: 10547521--10548178 Score: 1127
Period size: 327 Copynumber: 2.0 Consensus size: 327
10547511 CACGATGATC
* * *
10547521 TTGAAGATCCTCTTATCGGTTGGAAATCTAAACTTTTCAAGAATATCAAGAGTAGTGATGAAGAT
1 TTGAAGATCCTCTTATCGGATGGAAATCTAAACGTTTCAAGAATATCAAGAGTAGCGATGAAGAT
**
10547586 TTGCTTGAACTAAATCGGGATTGGCCTGTGCCTATTGATGTTAAAGTTGAGGATCCTGAAAGTGA
66 TTGCTTGAACTAAATCGGGATTGGCCTGCACCTATTGATGTTAAAGTTGAGGATCCTGAAAGTGA
* * * ** *
10547651 AACTGCTAATGTAAATATTTTGAAGACTGACGTGTCTTATCCTACAACGGAACCTGAATACTGTA
131 AACCGCTAATGTAAATATTTTGAAGACTGACGTGCCTTATCATACAACGGAACCCCAATACAGTA
* * *
10547716 CTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGACCTGGCTTGACGTGGGGCTTTCT
196 CTATTAATGAAGTGTCATATGAATACACGGAAGATTCTGAGACCAGGCTTGACGTGGGGCTTTCT
*
10547781 GGTTGTGAAACAAGGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATATAGGGAAAA
261 GGTTGTGAAACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATATAGGGAAAA
10547846 TT
326 TT
*
10547848 TTGAAGATCCTCTTATCGGATGGAAATCTAAACGTTTCAAGAATATCAAGAGTAGCGATGAGGAT
1 TTGAAGATCCTCTTATCGGATGGAAATCTAAACGTTTCAAGAATATCAAGAGTAGCGATGAAGAT
* *
10547913 TTGCTTGAATTAAATCGGGATTGGCCTGCACCTATTGATGTTAAAGTTGAGGTTCCTGAAAGTGA
66 TTGCTTGAACTAAATCGGGATTGGCCTGCACCTATTGATGTTAAAGTTGAGGATCCTGAAAGTGA
* * *
10547978 AACCGCTAATGTAAATATTTTGAGGACTGATGTGCCTTATCATACAACGGAACCCCAATACAGTT
131 AACCGCTAATGTAAATATTTTGAAGACTGACGTGCCTTATCATACAACGGAACCCCAATACAGTA
10548043 CTATTAATGAAGTGTCATATGAATACACGGAAGATTCTGAGACCAGGCTTGACGTGGGGCTTTCT
196 CTATTAATGAAGTGTCATATGAATACACGGAAGATTCTGAGACCAGGCTTGACGTGGGGCTTTCT
10548108 GGTTGTGAAACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATATAGGGAAAA
261 GGTTGTGAAACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATATAGGGAAAA
10548173 TT
326 TT
10548175 TTGA
1 TTGA
10548179 GACCAAGTTT
Statistics
Matches: 310, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
327 310 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (327 bp):
TTGAAGATCCTCTTATCGGATGGAAATCTAAACGTTTCAAGAATATCAAGAGTAGCGATGAAGAT
TTGCTTGAACTAAATCGGGATTGGCCTGCACCTATTGATGTTAAAGTTGAGGATCCTGAAAGTGA
AACCGCTAATGTAAATATTTTGAAGACTGACGTGCCTTATCATACAACGGAACCCCAATACAGTA
CTATTAATGAAGTGTCATATGAATACACGGAAGATTCTGAGACCAGGCTTGACGTGGGGCTTTCT
GGTTGTGAAACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATATAGGGAAAA
TT
Found at i:10552514 original size:12 final size:12
Alignment explanation
Indices: 10552497--10552521 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10552487 ATTAATATAT
10552497 GCACAGTTCCTG
1 GCACAGTTCCTG
10552509 GCACAGTTCCTG
1 GCACAGTTCCTG
10552521 G
1 G
10552522 GATCCAGTAA
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:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (12 bp):
GCACAGTTCCTG
Found at i:10557020 original size:23 final size:23
Alignment explanation
Indices: 10556967--10557024 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
10556957 ATTTTTTTTC
*
10556967 AGAGAATCTTCACAATTCATTGT
1 AGAGAATCTTCACAATTCATTAT
* * *
10556990 AAAAAATCTTCACAGTTC-TTCAT
1 AGAGAATCTTCACAATTCATT-AT
10557013 AGAGAATCTTCA
1 AGAGAATCTTCA
10557025 TTATTCATGT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
22 2 0.07
23 26 0.93
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (23 bp):
AGAGAATCTTCACAATTCATTAT
Found at i:10557112 original size:10 final size:9
Alignment explanation
Indices: 10557083--10557121 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
10557073 TTAAAAAGAA
10557083 ATAATTTTTT
1 ATAA-TTTTT
*
10557093 ATAATATTT
1 ATAATTTTT
10557102 ATACATTTTT
1 ATA-ATTTTT
10557112 ATAATTTTT
1 ATAATTTTT
10557121 A
1 A
10557122 AAAAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 14 0.54
10 12 0.46
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:10557130 original size:19 final size:19
Alignment explanation
Indices: 10557089--10557131 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
10557079 AGAAATAATT
* * *
10557089 TTTTATAATATTTATACAT
1 TTTTATAATATTTAAAAAA
*
10557108 TTTTATAATTTTTAAAAAA
1 TTTTATAATATTTAAAAAA
10557127 TTTTA
1 TTTTA
10557132 AAAAATTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTATAATATTTAAAAAA
Found at i:10557709 original size:30 final size:30
Alignment explanation
Indices: 10557675--10557773 Score: 180
Period size: 30 Copynumber: 3.3 Consensus size: 30
10557665 CGCCTCCAAA
* *
10557675 GCTTCCCTTACCATCTATCTCTGCTTTTCC
1 GCTTCTCTTATCATCTATCTCTGCTTTTCC
10557705 GCTTCTCTTATCATCTATCTCTGCTTTTCC
1 GCTTCTCTTATCATCTATCTCTGCTTTTCC
10557735 GCTTCTCTTATCATCTATCTCTGCTTTTCC
1 GCTTCTCTTATCATCTATCTCTGCTTTTCC
10557765 GCTTCTCTT
1 GCTTCTCTT
10557774 CTCCTTTCTA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.09, C:0.35, G:0.07, T:0.48
Consensus pattern (30 bp):
GCTTCTCTTATCATCTATCTCTGCTTTTCC
Found at i:10562148 original size:30 final size:30
Alignment explanation
Indices: 10562110--10562513 Score: 223
Period size: 30 Copynumber: 13.7 Consensus size: 30
10562100 CCCAAAAGGT
*
10562110 CCCT-AAACTTTCTAAAAATTACATTTTAA
1 CCCTCAAACTTTCCAAAAATTACATTTTAA
*
10562139 CCCTCAAACTTTCCAAAAATTACATTTTGA
1 CCCTCAAACTTTCCAAAAATTACATTTTAA
* * * *
10562169 CCC-CTAAAATTTCCATAAATCATATTTTAA
1 CCCTC-AAACTTTCCAAAAATTACATTTTAA
* * * *
10562199 CCCTTAAACTTTTCTAAAATTACATTTTGA
1 CCCTCAAACTTTCCAAAAATTACATTTTAA
*
10562229 -CCTCTAAACTTTCCAAAAATTACATTTTGA
1 CCCTC-AAACTTTCCAAAAATTACATTTTAA
*
10562259 CCC-CTAAAC-TT-CACAATATTACATTTTTAA
1 CCCTC-AAACTTTCCA-AAAATTACA-TTTTAA
* *
10562289 CCCTC-AACTTTTCTAAAATTACCATTTT-A
1 CCCTCAAACTTTCCAAAAATTA-CATTTTAA
* * *
10562318 CCCCCAAACATTTCCAAAAATTTCCATTTT-G
1 CCCTCAAAC-TTTCCAAAAA-TTACATTTTAA
* * * *
10562349 CCCCCGAAC-ATCCAAAAATTACCATTTT-T
1 CCCTCAAACTTTCCAAAAATTA-CATTTTAA
* * * *
10562378 CCCCCGAACATT-CAAAAATTACCATTTT-G
1 CCCTCAAACTTTCCAAAAATTA-CATTTTAA
* * * *
10562407 CCCCCGAA-TATCCAAAAATTACCATTTT-G
1 CCCTCAAACTTTCCAAAAATTA-CATTTTAA
* * *
10562436 CCCTCAAA-TTTCCAAAAGTCACATTTTCGA
1 CCCTCAAACTTTCCAAAAATTACATTTT-AA
* * * **
10562466 -CCTCGAATTTTCCAAAAGTTTGATTTTAA
1 CCCTCAAACTTTCCAAAAATTACATTTTAA
* *
10562495 TCCT-AAATTTTCCAAAAAT
1 CCCTCAAACTTTCCAAAAAT
10562514 CTCAATTGTG
Statistics
Matches: 306, Mismatches: 48, Indels: 42
0.77 0.12 0.11
Matches are distributed among these distances:
28 11 0.04
29 126 0.41
30 139 0.45
31 28 0.09
32 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (30 bp):
CCCTCAAACTTTCCAAAAATTACATTTTAA
Found at i:10562266 original size:90 final size:87
Alignment explanation
Indices: 10562110--10562353 Score: 289
Period size: 90 Copynumber: 2.7 Consensus size: 87
10562100 CCCAAAAGGT
10562110 CCCTAAAC-TTTCTAAAAATTACATTTTAACCCTCAAACTTTCCAAAAATTACATTTTGACCCCT
1 CCCTAAACTTTTCT-AAAATTACATTTT-ACCCT-AAACTTTCCAAAAATTACATTTTGACCCCT
*
10562174 AAAATTTC-C-ATAA-ATCATATTTTAA
63 -AAACTTCACAATAATA-CAT-TTTTAA
10562199 CCCTTAAACTTTTCTAAAATTACATTTTGACCTCTAAACTTTCCAAAAATTACATTTTGACCCCT
1 CCC-TAAACTTTTCTAAAATTACATTTT-ACC-CTAAACTTTCCAAAAATTACATTTTGACCCCT
*
10562264 AAACTTCACAATATTACATTTTTAA
63 AAACTTCACAATAATACATTTTTAA
* * * *
10562289 CCCTCAACTTTTCTAAAATTACCATTTTACCCCCAAACATTTCCAAAAATTTCCATTTTGCCCCC
1 CCCTAAACTTTTCTAAAATTA-CATTTTA-CCCTAAAC-TTTCCAAAAA-TTACATTTTGACCCC
10562354 GAACATCCAA
Statistics
Matches: 138, Mismatches: 7, Indels: 18
0.85 0.04 0.11
Matches are distributed among these distances:
89 32 0.23
90 79 0.57
91 26 0.19
92 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (87 bp):
CCCTAAACTTTTCTAAAATTACATTTTACCCTAAACTTTCCAAAAATTACATTTTGACCCCTAAA
CTTCACAATAATACATTTTTAA
Found at i:10562373 original size:29 final size:29
Alignment explanation
Indices: 10562303--10562438 Score: 200
Period size: 29 Copynumber: 4.6 Consensus size: 29
10562293 CAACTTTTCT
* *
10562303 AAAATTACCATTTTACCCCCAAACATTTCCA
1 AAAATTACCATTTTGCCCCCGAACA--TCCA
*
10562334 AAAATTTCCATTTTGCCCCCGAACATCCA
1 AAAATTACCATTTTGCCCCCGAACATCCA
* *
10562363 AAAATTACCATTTTTCCCCCGAACATTCA
1 AAAATTACCATTTTGCCCCCGAACATCCA
*
10562392 AAAATTACCATTTTGCCCCCGAATATCCA
1 AAAATTACCATTTTGCCCCCGAACATCCA
10562421 AAAATTACCATTTTGCCC
1 AAAATTACCATTTTGCCC
10562439 TCAAATTTCC
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
29 74 0.77
31 22 0.23
ACGTcount: A:0.35, C:0.32, G:0.04, T:0.29
Consensus pattern (29 bp):
AAAATTACCATTTTGCCCCCGAACATCCA
Found at i:10562473 original size:58 final size:59
Alignment explanation
Indices: 10562303--10562462 Score: 195
Period size: 58 Copynumber: 2.7 Consensus size: 59
10562293 CAACTTTTCT
*
10562303 AAAATTACCATTTTACCCCCAAACATTTCCAAAAATTTC-CATTTTGCCCCCGAACATCCA
1 AAAATTACCATTTTACCCCCAAACATTTCCAAAAA--TCACATTTTGCCCCCGAATATCCA
* * *
10562363 AAAATTACCATTTTTCCCCCGAACA-TT-CAAAAATTACCATTTTGCCCCCGAATATCCA
1 AAAATTACCATTTTACCCCCAAACATTTCCAAAAATCA-CATTTTGCCCCCGAATATCCA
* * *
10562421 AAAATTACCATTTTGCCCTC-AA-ATTTCCAAAAGTCACATTTT
1 AAAATTACCATTTTACCCCCAAACATTTCCAAAAATCACATTTT
10562463 CGACCTCGAA
Statistics
Matches: 88, Mismatches: 8, Indels: 11
0.82 0.07 0.10
Matches are distributed among these distances:
56 2 0.02
57 10 0.11
58 51 0.58
59 2 0.02
60 23 0.26
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.31
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCAAACATTTCCAAAAATCACATTTTGCCCCCGAATATCCA
Found at i:10565979 original size:25 final size:23
Alignment explanation
Indices: 10565939--10565984 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
10565929 CCAATTAGAA
10565939 AATTATTGTTTAAATTTAATTCT
1 AATTATTGTTTAAATTTAATTCT
*
10565962 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTA-AATTTAATT
10565985 TGAATCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
AATTATTGTTTAAATTTAATTCT
Found at i:10567424 original size:5 final size:6
Alignment explanation
Indices: 10567408--10567483 Score: 53
Period size: 6 Copynumber: 11.8 Consensus size: 6
10567398 TAATTTAGCC
* * *
10567408 ATTTTT ATTTTT ATTTTT ATTTTCAT ATTTTTT GTTTTT AATTTA ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTT--T A-TTTTT ATTTTT ATTTTT ATTTTT
* * *
10567459 ACATTTA ATTTTT TTATTTT ATTTT
1 A-TTTTT ATTTTT AT-TTTT ATTTT
10567484 ATAGGTTCTT
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
6 37 0.70
7 10 0.19
8 2 0.04
9 4 0.08
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (6 bp):
ATTTTT
Found at i:10567447 original size:27 final size:25
Alignment explanation
Indices: 10567407--10567483 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 25
10567397 TTAATTTAGC
*
10567407 CATTTTTATTTTTATTTTTATTTTCA
1 CATTTTTTTTTTTA-TTTTATTTTCA
* * *
10567433 TATTTTTTGTTTTTAATTTAATTTTTA
1 CATTTTTT-TTTTT-ATTTTATTTTCA
*
10567460 CATTTAATTTTTTTATTTTATTTT
1 CATTT-TTTTTTTTATTTTATTTT
10567484 ATAGGTTCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 15 0.37
27 23 0.56
28 3 0.07
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (25 bp):
CATTTTTTTTTTTATTTTATTTTCA
Found at i:10567464 original size:13 final size:12
Alignment explanation
Indices: 10567442--10567471 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
10567432 ATATTTTTTG
10567442 TTTTTAATTTAA
1 TTTTTAATTTAA
10567454 TTTTTACATTTAA
1 TTTTTA-ATTTAA
10567467 TTTTT
1 TTTTT
10567472 TTATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTAATTTAA
Found at i:10567472 original size:33 final size:33
Alignment explanation
Indices: 10567408--10567478 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
10567398 TAATTTAGCC
* * * *
10567408 ATTTTTATTTTTATTTTTATTTTCATATTTTTT
1 ATTTTTAATTTAATTTTTAATTTAATATTTTTT
*
10567441 GTTTTTAATTTAATTTTTACATTTAAT-TTTTTT
1 ATTTTTAATTTAATTTTTA-ATTTAATATTTTTT
10567474 ATTTT
1 ATTTT
10567479 ATTTTATAGG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (33 bp):
ATTTTTAATTTAATTTTTAATTTAATATTTTTT
Found at i:10567477 original size:13 final size:13
Alignment explanation
Indices: 10567442--10567483 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
10567432 ATATTTTTTG
10567442 TTTTTAATTTAA-
1 TTTTTAATTTAAT
10567454 TTTTTACATTTAAT
1 TTTTTA-ATTTAAT
* *
10567468 TTTTTTATTTTAT
1 TTTTTAATTTAAT
10567481 TTT
1 TTT
10567484 ATAGGTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 6 0.23
13 15 0.58
14 5 0.19
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:10569479 original size:10 final size:10
Alignment explanation
Indices: 10569460--10569504 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
10569450 ATGTTTTTTT
10569460 AAAAAA-TGA
1 AAAAAATTGA
10569469 AAAAAATTGA
1 AAAAAATTGA
*
10569479 AAAAAAATG-
1 AAAAAATTGA
*
10569488 AAAAAATTAA
1 AAAAAATTGA
10569498 AAAAAAT
1 AAAAAAT
10569505 AGTATATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 13 0.42
10 18 0.58
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.16
Consensus pattern (10 bp):
AAAAAATTGA
Found at i:10569484 original size:19 final size:19
Alignment explanation
Indices: 10569460--10569503 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
10569450 ATGTTTTTTT
*
10569460 AAAAAATGAAAAAAATTGAA
1 AAAAAATG-AAAAAATTAAA
10569480 AAAAAATGAAAAAATTAAA
1 AAAAAATGAAAAAATTAAA
10569499 AAAAA
1 AAAAA
10569504 TAGTATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.14
Consensus pattern (19 bp):
AAAAAATGAAAAAATTAAA
Found at i:10569485 original size:20 final size:18
Alignment explanation
Indices: 10569460--10569504 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
10569450 ATGTTTTTTT
10569460 AAAAAATGAAAAAAATTGAA
1 AAAAAATG-AAAAAATT-AA
10569480 AAAAAATGAAAAAATTAA
1 AAAAAATGAAAAAATTAA
10569498 AAAAAAT
1 AAAAAAT
10569505 AGTATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 9 0.36
19 8 0.32
20 8 0.32
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.16
Consensus pattern (18 bp):
AAAAAATGAAAAAATTAA
Found at i:10569531 original size:12 final size:11
Alignment explanation
Indices: 10569511--10569553 Score: 59
Period size: 12 Copynumber: 3.7 Consensus size: 11
10569501 AAATAGTATA
10569511 TTTATTTTCAT
1 TTTATTTTCAT
10569522 TTTCATTTTCAT
1 TTT-ATTTTCAT
*
10569534 TTTATTATTAAT
1 TTTATT-TTCAT
10569546 TTTATTTT
1 TTTATTTT
10569554 AATTATGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 8 0.28
12 21 0.72
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTATTTTCAT
Found at i:10570526 original size:18 final size:19
Alignment explanation
Indices: 10570513--10570548 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
10570503 AAAAAAAATT
10570513 AAAAAAATT-GAAAAAAGG
1 AAAAAAATTGGAAAAAAGG
10570531 AAAAAAATTGGAAAAAAG
1 AAAAAAATTGGAAAAAAG
10570549 AAGAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAAAAATTGGAAAAAAGG
Found at i:10572737 original size:20 final size:20
Alignment explanation
Indices: 10572695--10572737 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
10572685 AATTTAGACA
*
10572695 TTTTTATTTTTATTTCATAT
1 TTTTTATTTTTATTTAATAT
*
10572715 TTTTTGTTTTTAATTTAAT-T
1 TTTTTATTTTT-ATTTAATAT
10572735 TTT
1 TTT
10572738 ACAATTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTTATTTTTATTTAATAT
Found at i:10574791 original size:12 final size:11
Alignment explanation
Indices: 10574768--10574816 Score: 62
Period size: 11 Copynumber: 4.3 Consensus size: 11
10574758 TAGTATATTT
*
10574768 ATTTATTTTTA
1 ATTTAATTTTA
10574779 ATTTAAATTTTA
1 ATTT-AATTTTA
10574791 ATTTTAATTTTA
1 A-TTTAATTTTA
*
10574803 ATTTTATTTTA
1 ATTTAATTTTA
10574814 ATT
1 ATT
10574817 ATGCACTGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 16 0.47
12 15 0.44
13 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTAATTTTA
Found at i:10574813 original size:5 final size:6
Alignment explanation
Indices: 10574769--10574816 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
10574759 AGTATATTTA
* *
10574769 TTTATT TTTAAT TTAAAT TTTAAT TTTAAT TTTAAT TTT-AT TTTAAT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT
10574816 T
1 T
10574817 ATGCACTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTAAT
Found at i:10575761 original size:9 final size:9
Alignment explanation
Indices: 10575747--10575794 Score: 69
Period size: 9 Copynumber: 5.3 Consensus size: 9
10575737 ATTTAAAAAG
10575747 AAAAAAGAA
1 AAAAAAGAA
10575756 AAAAAAGAA
1 AAAAAAGAA
10575765 AAAAAAGAA
1 AAAAAAGAA
**
10575774 AAAAATTAA
1 AAAAAAGAA
*
10575783 AAAAAGGAA
1 AAAAAAGAA
10575792 AAA
1 AAA
10575795 TTGGAAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.04
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:10575762 original size:16 final size:16
Alignment explanation
Indices: 10575741--10575777 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
10575731 TTTTATATTT
10575741 AAAAAGAAAAAAGAAA
1 AAAAAGAAAAAAGAAA
10575757 AAAAAGAAAAAA-AAGA
1 AAAAAGAAAAAAGAA-A
10575773 AAAAA
1 AAAAA
10575778 ATTAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAGAAA
Found at i:10575767 original size:17 final size:17
Alignment explanation
Indices: 10575741--10575794 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
10575731 TTTTATATTT
*
10575741 AAAAAGAAAAAAGA-AA
1 AAAAAGAAAAAAAAGAA
10575757 AAAAAGAAAAAAAAGAA
1 AAAAAGAAAAAAAAGAA
** *
10575774 AAAAATTAAAAAAAGGA
1 AAAAAGAAAAAAAAGAA
10575791 AAAA
1 AAAA
10575795 TTGGAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
16 13 0.39
17 20 0.61
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (17 bp):
AAAAAGAAAAAAAAGAA
Found at i:10576875 original size:23 final size:24
Alignment explanation
Indices: 10576849--10576894 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
10576839 CCAATTAGGG
10576849 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATAT-TTTAGAATTTAATTCT
10576872 AATTATCATTTTAGAATTTAATT
1 AATTAT-ATTTTAGAATTTAATT
10576895 TGGATCTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (24 bp):
AATTATATTTTAGAATTTAATTCT
Found at i:10577986 original size:21 final size:19
Alignment explanation
Indices: 10577957--10578012 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
10577947 AATTTAGCCA
*
10577957 TTTTATTTTTATTTTCATAT
1 TTTTTTTTTTATTTTCAT-T
* *
10577977 TTTTTGTTTTTAATTTGATT
1 TTTTT-TTTTTATTTTCATT
10577997 TTTTTTATTTTATTTT
1 TTTTTT-TTTTATTTT
10578013 ATAGGTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 18 0.60
21 11 0.37
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.79
Consensus pattern (19 bp):
TTTTTTTTTTATTTTCATT
Found at i:10580062 original size:6 final size:5
Alignment explanation
Indices: 10580045--10580109 Score: 58
Period size: 6 Copynumber: 11.4 Consensus size: 5
10580035 AAAATTAGTA
10580045 TATTT TATTTT TCATTT TCATTT TCATTTT TAGTTT TATTT TATTTT TATTT
1 TATTT TA-TTT T-ATTT T-ATTT T-A-TTT TA-TTT TATTT TA-TTT TATTT
10580097 TAATTT TATTT TA
1 T-ATTT TATTT TA
10580110 ATTATGCAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
5 17 0.31
6 32 0.59
7 5 0.09
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:10580068 original size:35 final size:35
Alignment explanation
Indices: 10580028--10580104 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
10580018 AAAAAATGAA
10580028 AATTTTAAAAATTAG-TATATTTTATTTTTCATTTT
1 AATTTTAAAAATTAGTTATATTTTATTTTT-ATTTT
* * *** *
10580063 CATTTTCATTTTTAGTTTTATTTTATTTTTATTTT
1 AATTTTAAAAATTAGTTATATTTTATTTTTATTTT
10580098 AATTTTA
1 AATTTTA
10580105 TTTTAATTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
35 20 0.61
36 13 0.39
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.66
Consensus pattern (35 bp):
AATTTTAAAAATTAGTTATATTTTATTTTTATTTT
Found at i:10580110 original size:11 final size:11
Alignment explanation
Indices: 10580045--10580112 Score: 73
Period size: 11 Copynumber: 5.9 Consensus size: 11
10580035 AAAATTAGTA
*
10580045 TATTTTATTTT
1 TATTTTAATTT
*
10580056 TCATTTTCATTT
1 T-ATTTTAATTT
*
10580068 TCATTTTTAGTTT
1 T-A-TTTTAATTT
*
10580081 TATTTTATTTT
1 TATTTTAATTT
10580092 TATTTTAATTT
1 TATTTTAATTT
10580103 TATTTTAATT
1 TATTTTAATT
10580113 ATGCAATGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
11 29 0.59
12 12 0.24
13 8 0.16
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (11 bp):
TATTTTAATTT
Found at i:10581053 original size:10 final size:9
Alignment explanation
Indices: 10581033--10581102 Score: 70
Period size: 9 Copynumber: 7.6 Consensus size: 9
10581023 TTATTATTAG
10581033 AAAAAAGAA
1 AAAAAAGAA
10581042 AAAAAAGAA
1 AAAAAAGAA
**
10581051 AAAGAAAGTCG
1 AAA-AAAG-AA
10581062 AAAAAAGAA
1 AAAAAAGAA
*
10581071 AAAAACTGAA
1 AAAAA-AGAA
*
10581081 AAAAATG-A
1 AAAAAAGAA
10581089 AAAAAAGAA
1 AAAAAAGAA
10581098 AAAAA
1 AAAAA
10581103 TTGGAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
8 7 0.14
9 25 0.49
10 16 0.31
11 3 0.06
ACGTcount: A:0.80, C:0.03, G:0.13, T:0.04
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:10581092 original size:27 final size:29
Alignment explanation
Indices: 10581062--10581130 Score: 88
Period size: 27 Copynumber: 2.4 Consensus size: 29
10581052 AAGAAAGTCG
*
10581062 AAAAAAGAAAAAAACT-GAAAAAA-ATGA
1 AAAAAAGAAAAAAACTGGAAAAAAGAAGA
*
10581089 AAAAAAGAAAAAAATTGGAAAAAAGAAGA
1 AAAAAAGAAAAAAACTGGAAAAAAGAAGA
* *
10581118 AGAAAAGATAAAA
1 AAAAAAGAAAAAA
10581131 TTGGGTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 15 0.42
28 7 0.19
29 14 0.39
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.07
Consensus pattern (29 bp):
AAAAAAGAAAAAAACTGGAAAAAAGAAGA
Found at i:10581110 original size:18 final size:17
Alignment explanation
Indices: 10581033--10581115 Score: 69
Period size: 18 Copynumber: 4.5 Consensus size: 17
10581023 TTATTATTAG
*
10581033 AAAAAAGAAAAAAAAGAA
1 AAAAAAGAAAAAAATG-A
*
10581051 AAAGAAAGTCGAAAAAA-GA
1 AAA-AAAG--AAAAAAATGA
10581070 AAAAAACTGAAAAAAATGA
1 AAAAAA--GAAAAAAATGA
*
10581089 AAAAAAGAAAAAAATTGG
1 AAAAAAGAAAAAAA-TGA
10581107 AAAAAAGAA
1 AAAAAAGAA
10581116 GAAGAAAAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
17 8 0.15
18 23 0.42
19 16 0.29
20 2 0.04
21 6 0.11
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.06
Consensus pattern (17 bp):
AAAAAAGAAAAAAATGA
Found at i:10581112 original size:19 final size:18
Alignment explanation
Indices: 10581062--10581103 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
10581052 AAGAAAGTCG
10581062 AAAAAA-GAAAAAAACTGA
1 AAAAAATGAAAAAAAC-GA
10581080 AAAAAATGAAAAAAA-GA
1 AAAAAATGAAAAAAACGA
10581097 AAAAAAT
1 AAAAAAT
10581104 TGGAAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 6 0.26
19 8 0.35
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.07
Consensus pattern (18 bp):
AAAAAATGAAAAAAACGA
Found at i:10582199 original size:25 final size:23
Alignment explanation
Indices: 10582158--10582203 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
10582148 CCAATTAGAG
10582158 AATTATTATTTAGATTTAATTCT
1 AATTATTATTTAGATTTAATTCT
*
10582181 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
10582204 TGGATCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCT
Found at i:10583315 original size:12 final size:13
Alignment explanation
Indices: 10583298--10583327 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
10583288 ATATTTTTTG
10583298 TTTTTA-ATTTAA
1 TTTTTACATTTAA
10583310 TTTTTACATTTAA
1 TTTTTACATTTAA
10583323 TTTTT
1 TTTTT
10583328 TTTATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTACATTTAA
Done.