Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 23 of 32
Found at i:3160063 original size:19 final size:20
Alignment explanation
Indices: 3160033--3160070 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
3160023 TTTTCCTCTT
3160033 TTTTGTTGTTTTTTTTTTGG
1 TTTTGTTGTTTTTTTTTTGG
3160053 TTTTGTT-TTTTTTTTTTG
1 TTTTGTTGTTTTTTTTTTG
3160071 TTTAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (20 bp):
TTTTGTTGTTTTTTTTTTGG
Found at i:3171119 original size:79 final size:79
Alignment explanation
Indices: 3171008--3171214 Score: 236
Period size: 79 Copynumber: 2.6 Consensus size: 79
3170998 GAGATAATAA
* * * * * * * *
3171008 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTCGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
3171073 -TTAGAAAAAAAAAT
65 TTTAGAAAAAAAAAC
* *
3171087 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
* ** * *
3171152 TTTGGGAATAAAGC
66 TTAGAAAAAAAAAC
* *
3171166 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
3171215 GAAATAACGA
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
78 1 0.01
79 106 0.99
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAAC
Found at i:3171206 original size:28 final size:28
Alignment explanation
Indices: 3171166--3171237 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
3171156 GGAATAAAGC
** *
3171166 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
3171194 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
3171222 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
3171238 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:3171295 original size:52 final size:51
Alignment explanation
Indices: 3171226--3171395 Score: 171
Period size: 52 Copynumber: 3.3 Consensus size: 51
3171216 AAATAACGAG
* * *
3171226 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGG-AGTTTTGAAAATAAAACCGGA
* ** * * *
3171278 GTTTGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGAGTTTTGAAAATAAAACCGGA
* * * * *
3171330 GTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCAATAAAACTGGG
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGAGTTTTGA-AAATAAAACCGGA
3171382 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
3171396 TCGGAAATAA
Statistics
Matches: 98, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
51 1 0.01
52 88 0.90
53 9 0.09
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGAGTTTTGAAAATAAAACCGGA
Found at i:3171405 original size:184 final size:185
Alignment explanation
Indices: 3171195--3171537 Score: 519
Period size: 185 Copynumber: 1.9 Consensus size: 185
3171185 CGGAAGTAAC
* * *
3171195 GGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAA-AAATTGGT-A
1 GGGGTTGGAGTATCCCCGAGGAAATAACGAGGTTGGAGTATCCCCGATTATGAAGAAATTGGTGA
* * *
3171258 TTTTTGAAAATAAAATCGGAGTTTGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAA
66 TTTTTGAAAATAAAATCGAAGTTAGAGTATCCCCGATTAAA-GAAAATTAGCGTTTTGAAAATAA
* *
3171323 AACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACT
130 AACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACT
** * *
3171379 GGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAGAAATTGGTGT
1 GGGGTTGGAGTATCCCCGAGGAAATAACGAGGTTGGAGTATCCCCGATTATGAAGAAATTGGTGA
* * *
3171444 TTTTTGGAAATAAAATCGAAGTTAGAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAA
66 TTTTTGAAAATAAAATCGAAGTTAGAGTATCCCCGATTAAAGAAAATTAGCGTTTTGAAAATAAA
*
3171509 ATCGGAGTTGGAATATCCCCGATTGTGGA
131 ACCGGAGTTGGAATATCCCCGATTGTGGA
3171538 GAATTGAGAA
Statistics
Matches: 141, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
184 48 0.34
185 56 0.40
186 37 0.26
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (185 bp):
GGGGTTGGAGTATCCCCGAGGAAATAACGAGGTTGGAGTATCCCCGATTATGAAGAAATTGGTGA
TTTTTGAAAATAAAATCGAAGTTAGAGTATCCCCGATTAAAGAAAATTAGCGTTTTGAAAATAAA
ACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACT
Found at i:3171506 original size:51 final size:53
Alignment explanation
Indices: 3171414--3171532 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
3171404 AACGGGGTTG
* *
3171414 GAGTATCCCCGATTATGAAGAAATTGGTGTTTTTTGGAAATAAAATCGAAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGAAGTTA
* *
3171468 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGAAGTTA
*
3171519 GAATATCCCCGATT
1 GAGTATCCCCGATT
3171533 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 33 0.56
52 2 0.03
53 8 0.14
54 16 0.27
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGAAGTTA
Found at i:3171526 original size:133 final size:132
Alignment explanation
Indices: 3171282--3171528 Score: 306
Period size: 133 Copynumber: 1.9 Consensus size: 132
3171272 ATCGGAGTTT
** *
3171282 GAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGAT
1 GAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGAAGTTAGAGTATCCCCGAT
* * * * *
3171347 TGTGGAAAAATTAGTGTTTTAGCAATAAAACTGGGGTTGGAGTATCCCCTCGGAAATAACGGGGT
66 TATAGAAAAATTAGTGTTTTAGAAATAAAACTGGAGTTGGAATATCCCCTCGGAAATAACGGGGT
3171412 TG
131 TG
* * *
3171414 GAGTATCCCCGATTATGAA-G-AAATTGGTGTTTTTTGGAAATAAAATCGAAGTTAGAGTATCCC
1 GAGTATCCCCGATTA--AAGGAAAATTGGCG--TTTTGAAAATAAAACCGAAGTTAGAGTATCCC
3171477 CGATTATAG-AAAATTAGTGTTTT-GAAAATAAAA-TCGGAGTTGGAATATCCCC
62 CGATTATAGAAAAATTAGTGTTTTAG-AAATAAAACT-GGAGTTGGAATATCCCC
3171529 GATTGTGGAG
Statistics
Matches: 98, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
132 25 0.26
133 37 0.38
134 36 0.37
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (132 bp):
GAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGAAGTTAGAGTATCCCCGAT
TATAGAAAAATTAGTGTTTTAGAAATAAAACTGGAGTTGGAATATCCCCTCGGAAATAACGGGGT
TG
Found at i:3173900 original size:21 final size:21
Alignment explanation
Indices: 3173874--3173938 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 21
3173864 ATCTGGGTAA
3173874 AATTTCCAAATGTATCGATAC
1 AATTTCCAAATGTATCGATAC
3173895 AATTTCCAAATGTATCGATAC
1 AATTTCCAAATGTATCGATAC
**
3173916 AAAGATCC--ATGTATCGATAC
1 -AATTTCCAAATGTATCGATAC
3173936 AAT
1 AAT
3173939 GTATCGATAC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.05
20 12 0.30
21 21 0.52
22 5 0.12
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (21 bp):
AATTTCCAAATGTATCGATAC
Found at i:3173942 original size:13 final size:13
Alignment explanation
Indices: 3173924--3173949 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3173914 ACAAAGATCC
3173924 ATGTATCGATACA
1 ATGTATCGATACA
3173937 ATGTATCGATACA
1 ATGTATCGATACA
3173950 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3173945 original size:33 final size:33
Alignment explanation
Indices: 3173903--3173969 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3173893 ACAATTTCCA
***
3173903 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
3173936 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
3173969 A
1 A
3173970 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:3174013 original size:19 final size:18
Alignment explanation
Indices: 3173989--3174056 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
3173979 CAGTAGCTAA
3173989 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
3174008 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
3174023 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
3174040 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
3174057 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:3174029 original size:13 final size:13
Alignment explanation
Indices: 3174011--3174035 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3174001 ACAATACTTA
3174011 TGTATCGATACAT
1 TGTATCGATACAT
3174024 TGTATCGATACA
1 TGTATCGATACA
3174036 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3174033 original size:32 final size:32
Alignment explanation
Indices: 3173992--3174054 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3173982 TAGCTAATTA
*
3173992 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
3174024 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
3174055 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:3176576 original size:39 final size:38
Alignment explanation
Indices: 3176522--3176597 Score: 116
Period size: 39 Copynumber: 2.0 Consensus size: 38
3176512 TCAAAAATGC
*
3176522 CTAGATGTATCGATACATTGAAAAATGTATCGATACAT
1 CTAGATGTATCGATACAATGAAAAATGTATCGATACAT
* *
3176560 CTAGAATGTATTGATACAATGAATAATGTATCGATACA
1 CTAG-ATGTATCGATACAATGAAAAATGTATCGATACA
3176598 AATTGTGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 4 0.12
39 30 0.88
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.32
Consensus pattern (38 bp):
CTAGATGTATCGATACAATGAAAAATGTATCGATACAT
Found at i:3176598 original size:20 final size:20
Alignment explanation
Indices: 3176526--3176598 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
3176516 AAATGCCTAG
*
3176526 ATGTATCGATACATTGAAAA
1 ATGTATCGATACAATGAAAA
** *
3176546 ATGTATCGATAC-ATCTAGA
1 ATGTATCGATACAATGAAAA
* *
3176565 ATGTATTGATACAATGAATA
1 ATGTATCGATACAATGAAAA
3176585 ATGTATCGATACAA
1 ATGTATCGATACAA
3176599 ATTGTGAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
19 14 0.33
20 29 0.67
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAATGAAAA
Found at i:3181252 original size:17 final size:17
Alignment explanation
Indices: 3181230--3181263 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3181220 TGTGTGATAA
3181230 TATTAAAAAAAATTTAT
1 TATTAAAAAAAATTTAT
**
3181247 TATTAAATTAAATTTAT
1 TATTAAAAAAAATTTAT
3181264 ATTTATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTAAAAAAAATTTAT
Found at i:3194053 original size:75 final size:76
Alignment explanation
Indices: 3193908--3194070 Score: 201
Period size: 75 Copynumber: 2.2 Consensus size: 76
3193898 TTGAAAAGAT
3193908 CTTTAAATAGCTAGTAATCGCTCGATACCAGAACAATCTCCCAAACTGAATCTCCTAGCTTCCCC
1 CTTTAAATAGCTAGTAATCGCTCGATACCAGAACAATCTCCCAAACTGAATCTCCTAGCTTCCCC
3193973 GAATTTAGAAC
66 GAATTTAGAAC
* * * *
3193984 CTTTAACTAGCTAGTAATGGTTC-ACTACCA-AACAATCTCCCGAACTG-ATCTCCTAGGC-TCC
1 CTTTAAATAGCTAGTAATCGCTCGA-TACCAGAACAATCTCCCAAACTGAATCTCCTA-GCTTCC
*
3194045 TACC-AATTTAGAAT
64 --CCGAATTTAGAAC
*
3194059 CTTTAAGTAGCT
1 CTTTAAATAGCT
3194071 GTATGCCACA
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
74 11 0.14
75 39 0.51
76 27 0.35
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (76 bp):
CTTTAAATAGCTAGTAATCGCTCGATACCAGAACAATCTCCCAAACTGAATCTCCTAGCTTCCCC
GAATTTAGAAC
Found at i:3198053 original size:65 final size:65
Alignment explanation
Indices: 3197972--3198102 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
3197962 TATCCTTAAC
* *
3197972 TTCCACTAGTGATTGCTCCCCCTGAAGGTCAGGTTGAGTAAAGTAGGGTGTTCTCCCTTCAAAAG
1 TTCCACTAGTGATTGCTCCCCCTGAAGGTAAGGCTGAGTAAAGTAGGGTGTTCTCCCTTCAAAAG
3198037 TTCCACTAGTGATTGCTCCCCCTGAAGGTAAGGCTGAGTAAAGTAGGGTGTTCTCCCTTCAAAAG
1 TTCCACTAGTGATTGCTCCCCCTGAAGGTAAGGCTGAGTAAAGTAGGGTGTTCTCCCTTCAAAAG
3198102 T
1 T
3198103 GACGTCAGGA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (65 bp):
TTCCACTAGTGATTGCTCCCCCTGAAGGTAAGGCTGAGTAAAGTAGGGTGTTCTCCCTTCAAAAG
Found at i:3208603 original size:14 final size:14
Alignment explanation
Indices: 3208584--3208611 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3208574 TTTATGAGTA
3208584 TAAAAAAGGCTTGC
1 TAAAAAAGGCTTGC
3208598 TAAAAAAGGCTTGC
1 TAAAAAAGGCTTGC
3208612 ACACCTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
TAAAAAAGGCTTGC
Found at i:3216011 original size:2 final size:2
Alignment explanation
Indices: 3216004--3216051 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
3215994 GATTTGTTTC
*
3216004 AT AT AT AT AT AT AC 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 AT AT AT
3216046 AT AT AT
1 AT AT AT
3216052 CTACCTACAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3224762 original size:39 final size:39
Alignment explanation
Indices: 3224659--3224908 Score: 189
Period size: 39 Copynumber: 6.4 Consensus size: 39
3224649 GTAGAATTGC
** *
3224659 CAAAATGACCTTAAAAGACATTTTTATGCAT-AGAATGA-
1 CAAAATGACCTTAATGGACATTTTTATGCATGA-AATTAT
* *
3224697 CTAAAATGA-CTCAAATGAACATTTTTATGCATGAAATTAT
1 C-AAAATGACCT-TAATGGACATTTTTATGCATGAAATTAT
* * *
3224737 CAAAATGACCTTAATGGATACTTTTATGCATGAAA-TAA
1 CAAAATGACCTTAATGGACATTTTTATGCATGAAATTAT
* * *
3224775 CTAAAATGAACC-TAATGGACATTTTTGTTCATGAAATGA-
1 C-AAAATG-ACCTTAATGGACATTTTTATGCATGAAATTAT
*
3224814 CTAAAATGACCCTT-ATGGACATTTTTATGCATAAAATTAAT
1 C-AAAATGA-CCTTAATGGACATTTTTATGCATGAAATT-AT
* * *
3224855 -AAAATGATCC-TAATTGACATTGTCATGCATGAAA-TAGGT
1 CAAAATGA-CCTTAATGGACATTTTTATGCATGAAATTA--T
3224894 -AAAATGACCTTAATG
1 CAAAATGACCTTAATG
3224909 TAATGCATGC
Statistics
Matches: 171, Mismatches: 25, Indels: 31
0.75 0.11 0.14
Matches are distributed among these distances:
37 1 0.01
38 11 0.06
39 149 0.87
40 10 0.06
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (39 bp):
CAAAATGACCTTAATGGACATTTTTATGCATGAAATTAT
Found at i:3224797 original size:78 final size:77
Alignment explanation
Indices: 3224659--3224908 Score: 251
Period size: 78 Copynumber: 3.2 Consensus size: 77
3224649 GTAGAATTGC
** * * *
3224659 CAAAATGACCTTAAAAGACATTTTTATGCATAGAATGACTAAAATG-ACTCAAATGAACATTTTT
1 CAAAATGACCTTAATGGACATTTTTATGCATA-AATAACTAAAATGAAC-CTAATGGACATTTTT
3224723 ATGCATGAAATTAT
64 ATGCATGAAATTAT
* * *
3224737 CAAAATGACCTTAATGGATACTTTTATGCATGAAATAACTAAAATGAACCTAATGGACATTTTTG
1 CAAAATGACCTTAATGGACATTTTTATGCAT-AAATAACTAAAATGAACCTAATGGACATTTTTA
* *
3224802 TTCATGAAATGA-
65 TGCATGAAATTAT
* * *
3224814 CTAAAATGACCCTT-ATGGACATTTTTATGCATAAAATTAA-TAAAATGATCCTAATTGACATTG
1 C-AAAATGA-CCTTAATGGACATTTTTATGCAT-AAA-TAACTAAAATGAACCTAATGGACATTT
*
3224877 TCATGCATGAAA-TAGGT
62 TTATGCATGAAATTA--T
3224894 -AAAATGACCTTAATG
1 CAAAATGACCTTAATG
3224909 TAATGCATGC
Statistics
Matches: 143, Mismatches: 20, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
77 6 0.04
78 127 0.89
79 10 0.07
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (77 bp):
CAAAATGACCTTAATGGACATTTTTATGCATAAATAACTAAAATGAACCTAATGGACATTTTTAT
GCATGAAATTAT
Found at i:3224841 original size:117 final size:117
Alignment explanation
Indices: 3224660--3224908 Score: 292
Period size: 117 Copynumber: 2.1 Consensus size: 117
3224650 TAGAATTGCC
** *
3224660 AAAATGACCTTAAAAGACATTTTTATGCATAGAATGACTAAAATGACTCAAATGAACATTTTTAT
1 AAAATGACCTTAATGGACATTTTTATGCATAGAATGACTAAAATGACCCAAATGAACATTTTTAT
* * *
3224725 GCATGAAATT-ATCAAAATGA-CCTTAATGGATACTT-TTATGCATGAAATAACT
66 GCATAAAATTAAT-AAAATGATCC-TAATGGACA-TTGTCATGCATGAAATAACT
* * ** *
3224777 AAAATGAACC-TAATGGACATTTTTGTTCAT-GAAATGACTAAAATGACCCTTATGGACATTTTT
1 AAAATG-ACCTTAATGGACATTTTTATGCATAG-AATGACTAAAATGACCCAAATGAACATTTTT
* **
3224840 ATGCATAAAATTAATAAAATGATCCTAATTGACATTGTCATGCATGAAATAGGT
64 ATGCATAAAATTAATAAAATGATCCTAATGGACATTGTCATGCATGAAATAACT
3224894 AAAATGACCTTAATG
1 AAAATGACCTTAATG
3224909 TAATGCATGC
Statistics
Matches: 112, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
116 6 0.05
117 99 0.88
118 7 0.06
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (117 bp):
AAAATGACCTTAATGGACATTTTTATGCATAGAATGACTAAAATGACCCAAATGAACATTTTTAT
GCATAAAATTAATAAAATGATCCTAATGGACATTGTCATGCATGAAATAACT
Found at i:3232207 original size:7 final size:7
Alignment explanation
Indices: 3232197--3232228 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
3232187 AAAAACATAA
3232197 AAAAAAG
1 AAAAAAG
3232204 AAAAAAG
1 AAAAAAG
3232211 AAAAAAG
1 AAAAAAG
*
3232218 AGAAAAG
1 AAAAAAG
3232225 AAAA
1 AAAA
3232229 GAACCTACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:3233291 original size:61 final size:60
Alignment explanation
Indices: 3233194--3233377 Score: 296
Period size: 61 Copynumber: 3.0 Consensus size: 60
3233184 AACCTTTTAT
* *
3233194 CCTTTCAGTCCTCAAAGAGCAGGATGTCTTTTCCTTTGAAAGCCCACACGAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAAGATGTCTTTTCCTTT-AAAGCCCACACAAGTTGGTGGCA
*
3233255 CCTTTCAGTCCTCAAAGAGCAAGATGTCTTTCCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAAGATGTCTTTTCC-TTTAAAGCCCACACAAGTTGGTGGCA
* *
3233316 CCTTTCGGTCCTCAAAGAGCAAGATGCCTTTTCCTCTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAAGATGTCTTTTCCT-TTAAAGCCCACACAAGTTGGTGGCA
3233377 C
1 C
3233378 GTATCTACTT
Statistics
Matches: 115, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
60 1 0.01
61 111 0.97
62 3 0.03
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.27
Consensus pattern (60 bp):
CCTTTCAGTCCTCAAAGAGCAAGATGTCTTTTCCTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:3233827 original size:20 final size:20
Alignment explanation
Indices: 3233802--3233857 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
3233792 GTTTTACCCA
3233802 GATGTATTGATACATTTTTC
1 GATGTATTGATACATTTTTC
3233822 GATGTATTGATACATTTTTC
1 GATGTATTGATACATTTTTC
* *
3233842 AATGTATCGATACATT
1 GATGTATTGATACATT
3233858 CAGGCATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (20 bp):
GATGTATTGATACATTTTTC
Found at i:3236336 original size:79 final size:79
Alignment explanation
Indices: 3236224--3236404 Score: 256
Period size: 79 Copynumber: 2.3 Consensus size: 79
3236214 TAAAATACCG
* * * * *
3236224 ATTTTTCACCATCGAGGATAATCAAATCCCGTTATTT-TCGAGGGGATACTCCAACCTCGATTTT
1 ATTTTTCACAATCGGGGATACTCAAATCCCGTTATTTAT-AAAGGGATACTCCAACCTCGATTTT
3236288 ATTTTTAAAACATTA
65 ATTTTTAAAACATTA
* **
3236303 ATTTTTCACAATCGGGGATACTCAAATCCCGTTATTTATAAAGGGATACTCTAACCTTTATTTTA
1 ATTTTTCACAATCGGGGATACTCAAATCCCGTTATTTATAAAGGGATACTCCAACCTCGATTTTA
*
3236368 TTTTTAAAACATTG
66 TTTTTAAAACATTA
*
3236382 ATTTTTCACAATTGGGGATACTC
1 ATTTTTCACAATCGGGGATACTC
3236405 CAACCCTAGT
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
79 90 0.99
80 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (79 bp):
ATTTTTCACAATCGGGGATACTCAAATCCCGTTATTTATAAAGGGATACTCCAACCTCGATTTTA
TTTTTAAAACATTA
Found at i:3236418 original size:130 final size:131
Alignment explanation
Indices: 3236265--3236541 Score: 337
Period size: 130 Copynumber: 2.1 Consensus size: 131
3236255 TTATTTTCGA
* * * * *
3236265 GGGGATACTCCAA-CCTCGATTTTATTTTTAAAACATTAATTTTTCACAATCGGGGATACTCAAA
1 GGGGATACTCCAACCCTAGATTTTATTTCTAAAACATCAATTTTTCACAATCGAGAATACTCAAA
* * * ** *
3236329 TCCC-GTTATTTATAAAGGGATACTCTAACCTTTA-TTTTATTTTTAAAACATTGATTTTTCACA
66 -CCCTGTTATTTATAAAGGGATACTCCAACC-TCAGTTTTATTTCTAAAACACCGATTTTCCACA
*
3236392 ATT
129 ATC
* *
3236395 GGGGATACTCCAACCCTAG-TTTTATTTCTAAAACATCGATTTTTCACAATCGAGAATACTCCAA
1 GGGGATACTCCAACCCTAGATTTTATTTCTAAAACATCAATTTTTCACAATCGAGAATACTCAAA
* *
3236459 CCCTGTTATTTCTGAAGGGATACTCCAACCTCAGTTTTTATTTCTAAAACACCGATTTTCCACAA
66 CCCTGTTATTTATAAAGGGATACTCCAACCTCAG-TTTTATTTCTAAAACACCGATTTTCCACAA
3236524 TC
130 TC
**
3236526 GAAGATACTCCAACCC
1 GGGGATACTCCAACCC
3236542 CGTTATTTCC
Statistics
Matches: 125, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
129 5 0.04
130 75 0.60
131 45 0.36
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (131 bp):
GGGGATACTCCAACCCTAGATTTTATTTCTAAAACATCAATTTTTCACAATCGAGAATACTCAAA
CCCTGTTATTTATAAAGGGATACTCCAACCTCAGTTTTATTTCTAAAACACCGATTTTCCACAAT
C
Found at i:3236421 original size:51 final size:50
Alignment explanation
Indices: 3236345--3236462 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 50
3236335 TATTTATAAA
* * * * *
3236345 GGGATACTCTAACCTTTATTTTATTTTTAAAACATTGATTTTTCACAATTG
1 GGGATACTCCAACC-CTATTTTATTTCTAAAACATCGATTTTTCACAATCG
3236396 GGGATACTCCAACCCTAGTTTTATTTCTAAAACATCGATTTTTCACAATCG
1 GGGATACTCCAACCCTA-TTTTATTTCTAAAACATCGATTTTTCACAATCG
* *
3236447 AGAATACTCCAACCCT
1 GGGATACTCCAACCCT
3236463 GTTATTTCTG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 2 0.03
51 57 0.97
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (50 bp):
GGGATACTCCAACCCTATTTTATTTCTAAAACATCGATTTTTCACAATCG
Found at i:3236579 original size:209 final size:209
Alignment explanation
Indices: 3236205--3236620 Score: 514
Period size: 209 Copynumber: 2.0 Consensus size: 209
3236195 TCATTCATGT
* * * *
3236205 TTTTATTTCTAAAATACCGATTTTTCACCATCGAGGATAATCAAATCCCGTTATTTTCGAGGGGA
1 TTTTATTTCTAAAACACCGATTTTTCACAATCGAGAATAATCAAATCCCGTTATTTTCGAAGGGA
* ** * ** *
3236270 TACTCCAACCTCGATTTTATTTTTAAAACATTAATTTTTCACAATCGGGGATACTCAAATCCCGT
66 TACTCCAACCTCGATTTTATTTCTAAAACACCAATTTTCCACAATCGAAGATACTCAAACCCCGT
* * ** * * * * ***
3236335 TATTTATAAAGGGATACTCTAACCTTTATTTTATTTTTAAAACATTGATTTTTCACAATTGGGGA
131 TATTTACAAAGGGATACTCCAACCTCGACTTTATTTCTAAAACATAGAATTTTCACAATTAAAGA
3236400 TACTCCAACCCTAG
196 TACTCCAACCCTAG
* * *
3236414 TTTTATTTCTAAAACATCGATTTTTCACAATCGAGAATACTCCAA-CCCTGTTA-TTTCTGAAGG
1 TTTTATTTCTAAAACACCGATTTTTCACAATCGAGAATAATCAAATCCC-GTTATTTTC-GAAGG
* * *
3236477 GATACTCCAACCTCAGTTTTTATTTCTAAAACACCGATTTTCCACAATCGAAGATACTCCAACCC
64 GATACTCCAACCTC-GATTTTATTTCTAAAACACCAATTTTCCACAATCGAAGATACTCAAACCC
* *
3236542 CGTTATTT-CCAAGGGATACTCCAACCTCGGCTTTATTTCTAAAACATAGAATTTTCACAATTAA
128 CGTTATTTACAAAGGGATACTCCAACCTCGACTTTATTTCTAAAACATAGAATTTTCACAATTAA
3236606 AGATACTCCAACCCT
193 AGATACTCCAACCCT
3236621 GTTATTTCCG
Statistics
Matches: 174, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
208 7 0.04
209 119 0.68
210 48 0.28
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (209 bp):
TTTTATTTCTAAAACACCGATTTTTCACAATCGAGAATAATCAAATCCCGTTATTTTCGAAGGGA
TACTCCAACCTCGATTTTATTTCTAAAACACCAATTTTCCACAATCGAAGATACTCAAACCCCGT
TATTTACAAAGGGATACTCCAACCTCGACTTTATTTCTAAAACATAGAATTTTCACAATTAAAGA
TACTCCAACCCTAG
Found at i:3236743 original size:79 final size:79
Alignment explanation
Indices: 3236397--3236735 Score: 400
Period size: 79 Copynumber: 4.3 Consensus size: 79
3236387 TCACAATTGG
*
3236397 GGATACTCCAACC-CTAGTTTTATTTCTAAAACATCGATTTTTCACAATCG-AGAATACTCCAAC
1 GGATACTCCAACCTC-AGTTTTATTTCTAAAACATCGATTTTCCACAATCGAAG-ATACTCCAAC
* *
3236460 CCTGTTATTTCTGA-A
64 CCCGTTATTTCCGAGA
*
3236475 GGGATACTCCAACCTCAGTTTTTATTTCTAAAACACCGATTTTCCACAATCGAAGATACTCCAAC
1 -GGATACTCCAACCTCAG-TTTTATTTCTAAAACATCGATTTTCCACAATCGAAGATACTCCAAC
*
3236540 CCCGTTATTTCCAAG-
64 CCCGTTATTTCCGAGA
* * * **
3236555 GGATACTCCAACCTCGGCTTTATTTCTAAAACATAGAATTTT-CACAATTAAAGATACTCCAACC
1 GGATACTCCAACCTCAGTTTTATTTCTAAAACATCG-ATTTTCCACAATCGAAGATACTCCAACC
*
3236619 CTGTTATTTCCGAGA
65 CCGTTATTTCCGAGA
* * * * * * ** *
3236634 GGATACTCTAACCCCAATTTTATTTCCAAAACATCGATTCTCCACCATCGGGGATACTCTAACCC
1 GGATACTCCAACCTCAGTTTTATTTCTAAAACATCGATTTTCCACAATCGAAGATACTCCAACCC
3236699 CGTTATTTCCGAGA
66 CGTTATTTCCGAGA
* *
3236713 AGATACTCCAACCTCATTTTTAT
1 GGATACTCCAACCTCAGTTTTAT
3236736 CTCCAAAATA
Statistics
Matches: 221, Mismatches: 32, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
78 52 0.24
79 114 0.52
80 53 0.24
81 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (79 bp):
GGATACTCCAACCTCAGTTTTATTTCTAAAACATCGATTTTCCACAATCGAAGATACTCCAACCC
CGTTATTTCCGAGA
Found at i:3240757 original size:7 final size:6
Alignment explanation
Indices: 3240747--3240784 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
3240737 TAAAAAACCC
*
3240747 AAAATT AAAA-A AAAATTT AAAATT AAAATT AAAATT AA
1 AAAATT AAAATT AAAA-TT AAAATT AAAATT AAAATT AA
3240785 TAATAGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 4 0.14
6 20 0.71
7 4 0.14
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:3241813 original size:82 final size:80
Alignment explanation
Indices: 3241699--3241847 Score: 228
Period size: 82 Copynumber: 1.8 Consensus size: 80
3241689 TAAAGTAGAC
* * *
3241699 ATGTCTTAAAGGTAATATGGATATAGTTGTCTTAATAAGACAATGTCTAAAGTAGACATGTCTTA
1 ATGTCTTAAAGATAATATGGATATAGTTGTCTTAATAAAACAACGTCTAAAGTAGACATGTCTTA
3241764 AGATAAGTTAGCTTG
66 AGATAAGTTAGCTTG
*
3241779 ATGTCTTAATAAGATAATGTGGATA-AGTTTGTCTTAATAAAACAACGTCTAAAGTAGACATGTC
1 ATGTCTT-A-AAGATAATATGGATATAG-TTGTCTTAATAAAACAACGTCTAAAGTAGACATGTC
3241843 TTAAG
63 TTAAG
3241848 GTAAATTGTC
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
80 7 0.11
81 3 0.05
82 52 0.84
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (80 bp):
ATGTCTTAAAGATAATATGGATATAGTTGTCTTAATAAAACAACGTCTAAAGTAGACATGTCTTA
AGATAAGTTAGCTTG
Found at i:3243810 original size:79 final size:79
Alignment explanation
Indices: 3243678--3243829 Score: 200
Period size: 79 Copynumber: 1.9 Consensus size: 79
3243668 CTTTGAGATG
* * *
3243678 AAAAATTTAATATTTTTAAAATAAAAACGAGGTTGGAGTATTCTCTCAGAAATAAC-GGTGTTAG
1 AAAAATTTAATATTTTAAAAATAAAAACGAGGTTGGAGTATCCCCTCAGAAATAACAGG-GTTAG
3243742 AGTATCCCCAAAATC
65 AGTATCCCCAAAATC
** * * *
3243757 AAAAATTTAATATTTTAAAAATAAAAGTGGGGTTGGAGTATCCCCTC-GAAAATAGCAGGGTTGG
1 AAAAATTTAATATTTTAAAAATAAAAACGAGGTTGGAGTATCCCCTCAG-AAATAACAGGGTTAG
3243821 AGTATCCCC
65 AGTATCCCC
3243830 TCAGAAATAA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
78 1 0.02
79 60 0.95
80 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (79 bp):
AAAAATTTAATATTTTAAAAATAAAAACGAGGTTGGAGTATCCCCTCAGAAATAACAGGGTTAGA
GTATCCCCAAAATC
Found at i:3243837 original size:28 final size:27
Alignment explanation
Indices: 3243786--3243855 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 27
3243776 AATAAAAGTG
*
3243786 GGGTTGGAGTATCCCCTCGAAAATAGC
1 GGGTTGGAGTATCCCCTCGAAAATAAC
3243813 AGGGTTGGAGTATCCCCTC-AGAAATAAC
1 -GGGTTGGAGTATCCCCTCGA-AAATAAC
*
3243841 GGGTTTAGAGTATCC
1 GGG-TTGGAGTATCC
3243856 TCGAGATGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 4 0.11
28 34 0.89
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCTCGAAAATAAC
Found at i:3243916 original size:28 final size:28
Alignment explanation
Indices: 3243881--3243934 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
3243871 AGTATTTCGA
*
3243881 AAATAAAAATAAGGTTGGAGTATCCCCT
1 AAATAAAAACAAGGTTGGAGTATCCCCT
*
3243909 AAA-AAAAACGAGGTTGGAGTATCCCC
1 AAATAAAAACAAGGTTGGAGTATCCCC
3243935 GAGATGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (28 bp):
AAATAAAAACAAGGTTGGAGTATCCCCT
Found at i:3244029 original size:79 final size:78
Alignment explanation
Indices: 3243813--3244030 Score: 271
Period size: 78 Copynumber: 2.8 Consensus size: 78
3243803 CGAAAATAGC
* * * * * *
3243813 AGGGTTGGAGTATCCCCTCAGAAATAACGGGTTTAGAGTATCCTCGAGATG-ATAGTTTAGTATT
1 AGGGTTGGAGTATCCCCTCAGAAATAAAGGG-TTGGAGTATCCCCGAGATGAAAACTTTAATATT
3243877 TCGAAAATAAAAAT
65 TCGAAAATAAAAAT
* * *
3243891 AAGGTTGGAGTATCCCCT-A-AAAAAAACGAGGTTGGAGTATCCCCGAGATGAAAATTTTAATAT
1 AGGGTTGGAGTATCCCCTCAGAAATAAA-G-GGTTGGAGTATCCCCGAGATGAAAACTTTAATAT
3243954 TTCGAAAATAAAAAT
64 TTCGAAAATAAAAAT
* * *
3243969 GGGGTTAGAGTATCTCCTCAGAAATAAAGGGATTGGAGTATCCCCGAGATGAAAACTTTAAT
1 AGGGTTGGAGTATCCCCTCAGAAATAAAGGG-TTGGAGTATCCCCGAGATGAAAACTTTAAT
3244031 GTTATAAAAG
Statistics
Matches: 120, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
76 5 0.04
77 19 0.16
78 59 0.49
79 31 0.26
80 6 0.05
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (78 bp):
AGGGTTGGAGTATCCCCTCAGAAATAAAGGGTTGGAGTATCCCCGAGATGAAAACTTTAATATTT
CGAAAATAAAAAT
Found at i:3246432 original size:13 final size:13
Alignment explanation
Indices: 3246414--3246439 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3246404 CAGGGTTGTT
3246414 TTGTATCGATACA
1 TTGTATCGATACA
3246427 TTGTATCGATACA
1 TTGTATCGATACA
3246440 AAACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3247879 original size:198 final size:198
Alignment explanation
Indices: 3247541--3247914 Score: 703
Period size: 198 Copynumber: 1.9 Consensus size: 198
3247531 ATGCCGTTGT
* *
3247541 ATTTAAAATATGTGCATTGTTGGTGTAAACTTTTGAAGCTAATCACAATTACTTGTAAAACACTA
1 ATTTAAAATATATGCATTGTTGGTGTAAACTTTCGAAGCTAATCACAATTACTTGTAAAACACTA
3247606 TTAATTGTTATTTCATGTATTAGACATTTTAATTTCTTTATTTACATTGAAGATATTTTTCATCT
66 TTAATTGTTATTTCATGTATTAGACATTTTAATTTCTTTATTTACATTGAAGATATTTTTCATCT
3247671 ATAAGTTTATAATAATACGTTATAAATAACTTATGTAGATAAAGTTTCGAAGCTAATCACAATTA
131 ATAAGTTTATAATAATACGTTATAAATAACTTATGTAGATAAAGTTTCGAAGCTAATCACAATTA
3247736 CTA
196 CTA
*
3247739 ATTTAAAATATATTCATTGTTGGTGTAAACTTTCGAAGCTAATCACAATTACTTGTAAAACACTA
1 ATTTAAAATATATGCATTGTTGGTGTAAACTTTCGAAGCTAATCACAATTACTTGTAAAACACTA
* *
3247804 TTAATTGTTATTTCATGTATTATACATTTTAATTTCTTTATTTACATTGAGGATATTTTTCATCT
66 TTAATTGTTATTTCATGTATTAGACATTTTAATTTCTTTATTTACATTGAAGATATTTTTCATCT
3247869 ATAAGTTTATAATAATACGTTATAAATAACTTATGTAGATAAAGTT
131 ATAAGTTTATAATAATACGTTATAAATAACTTATGTAGATAAAGTT
3247915 CATGCAACAT
Statistics
Matches: 171, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
198 171 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (198 bp):
ATTTAAAATATATGCATTGTTGGTGTAAACTTTCGAAGCTAATCACAATTACTTGTAAAACACTA
TTAATTGTTATTTCATGTATTAGACATTTTAATTTCTTTATTTACATTGAAGATATTTTTCATCT
ATAAGTTTATAATAATACGTTATAAATAACTTATGTAGATAAAGTTTCGAAGCTAATCACAATTA
CTA
Found at i:3249672 original size:50 final size:51
Alignment explanation
Indices: 3249609--3249754 Score: 213
Period size: 50 Copynumber: 2.9 Consensus size: 51
3249599 GATTCATATT
* * *
3249609 TTTTTACCAAGATGTATCAATATATTTTTCAATGTATCGATACATTCTGTC
1 TTTTTACCCAGATGTATCGATATATTTTTCAATGTATCGATACATTCGGTC
* * *
3249660 -TTTTACCCAGATGTATCGATACATTTTTCAATGTGTCTATACATTCGGTC
1 TTTTTACCCAGATGTATCGATATATTTTTCAATGTATCGATACATTCGGTC
* *
3249710 TTTTTATCCAGATGTATCGATATATTTTTTAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATATATTTTTCAATGTATCGATACAT
3249755 CTAGTTAAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
50 44 0.53
51 39 0.47
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (51 bp):
TTTTTACCCAGATGTATCGATATATTTTTCAATGTATCGATACATTCGGTC
Found at i:3253359 original size:19 final size:19
Alignment explanation
Indices: 3253335--3253373 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3253325 TGTAAACCAG
3253335 TTTTAAAACATGAGTGCTA
1 TTTTAAAACATGAGTGCTA
3253354 TTTTAAAACATGAGTGCTA
1 TTTTAAAACATGAGTGCTA
3253373 T
1 T
3253374 CAAGAGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTTAAAACATGAGTGCTA
Found at i:3254909 original size:20 final size:20
Alignment explanation
Indices: 3254884--3254934 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3254874 ACCCTAAAAA
*
3254884 GTATCGATACACATTTAAAT
1 GTATCGATACACATTGAAAT
* * *
3254904 GTATCGATACAGATTGCATT
1 GTATCGATACACATTGAAAT
3254924 GTATCGATACA
1 GTATCGATACA
3254935 TTGTATCGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (20 bp):
GTATCGATACACATTGAAAT
Found at i:3254938 original size:13 final size:13
Alignment explanation
Indices: 3254920--3254948 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3254910 ATACAGATTG
3254920 CATTGTATCGATA
1 CATTGTATCGATA
3254933 CATTGTATCGATA
1 CATTGTATCGATA
3254946 CAT
1 CAT
3254949 GACCAAATGT
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:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:3254980 original size:21 final size:20
Alignment explanation
Indices: 3254936--3254984 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3254926 ATCGATACAT
**
3254936 TGTATCGATACATGACCAAA
1 TGTATCGATACATGAAAAAA
*
3254956 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAA-AA
3254977 TGTATCGA
1 TGTATCGA
3254985 CAAAAATTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:3258333 original size:13 final size:13
Alignment explanation
Indices: 3258315--3258341 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3258305 TAAAAAACTT
3258315 ATGTATCGATACA
1 ATGTATCGATACA
3258328 ATGTATCGATACA
1 ATGTATCGATACA
3258341 A
1 A
3258342 CACTTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3258338 original size:32 final size:33
Alignment explanation
Indices: 3258297--3258361 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3258287 TAGCTTAAAT
3258297 TGTATCGATAAAAAAC-TTATGTATCGATACAA
1 TGTATCGATAAAAAACTTTATGTATCGATACAA
* *
3258329 TGTATCGATACAACACTTTATGTATCGATACAA
1 TGTATCGATAAAAAACTTTATGTATCGATACAA
3258362 ATCGTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (33 bp):
TGTATCGATAAAAAACTTTATGTATCGATACAA
Found at i:3259288 original size:49 final size:47
Alignment explanation
Indices: 3259219--3259613 Score: 379
Period size: 49 Copynumber: 8.2 Consensus size: 47
3259209 CAAGACAGAA
* * *
3259219 AAGGTGCCCATATGCTGATTCAAGGCCAGCGCTATTGGAATTAAAGAT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGC-ATTGGACTTAAAGAT
* *
3259267 GAAGGTGCCAATGTGTTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 -AAGGTGCCAATGTGCTGATTCAAGGCCAGC-GCATTGGACTTAAAGAT
* * *
3259316 GAGGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT
1 -AAGGTGCCAATGTGCTGATTCAAGGCCAGCG-CATTGGACTTAAAGAT
* * ** * *
3259365 AAGGGTGCCAATATGCTGATTCAAGGCAAGCTATATTAGAGTTAAAGAT
1 AA-GGTGCCAATGTGCTGATTCAAGGCCAGC-GCATTGGACTTAAAGAT
* *
3259414 GAAGGTGCCAATGTGCTGATTTAAGGCCAGCTACATTGGACTTAAAGAT
1 -AAGGTGCCAATGTGCTGATTCAAGGCCAGC-GCATTGGACTTAAAGAT
* * * *
3259463 GAGGGTACCAGTGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT
1 -AAGGTGCCAATGTGCTGATTCAAGGCCAGCG-CATTGGACTTAAAGAT
* * **
3259512 AAGGGTGCCAATATACTGATTCAAGGCCAGCTATATTGGACTT----A-
1 AA-GGTGCCAATGTGCTGATTCAAGGCCAGC-GCATTGGACTTAAAGAT
*
3259556 AAGGTGCCAATGTGCTGAGTCAAGGCCAGC-CATATTGGACTTAAAGAT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGC--ATTGGACTTAAAGAT
3259604 AAGGGTGCCA
1 AA-GGTGCCA
3259614 CGGACTTGTG
Statistics
Matches: 289, Mismatches: 41, Indels: 32
0.80 0.11 0.09
Matches are distributed among these distances:
43 34 0.12
44 2 0.01
45 1 0.00
47 1 0.00
48 4 0.01
49 244 0.84
50 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (47 bp):
AAGGTGCCAATGTGCTGATTCAAGGCCAGCGCATTGGACTTAAAGAT
Found at i:3259347 original size:98 final size:96
Alignment explanation
Indices: 3259221--3259613 Score: 438
Period size: 98 Copynumber: 4.1 Consensus size: 96
3259211 AGACAGAAAA
* * * *
3259221 GGTGCCCATATGCTGATTCAAGGCCAGCGCTATTGGAATTAAAGATGAAGGTGCCAATGTGTTGA
1 GGTGCCAATGTGCTGATTCAAGGCCAGCGC-ATTGGACTTAAAGAT-AAGGTGCCAATGTGCTGA
*
3259286 TTCAAGGCCAGCTACATTGGACTTAAAGATGAG
64 TTCAAGGCCAGCTACATTGGACTTAAAGATAAG
* * *
3259319 GGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAGGGTGCCAATATGCTGA
1 GGTGCCAATGTGCTGATTCAAGGCCAGCG-CATTGGACTTAAAGATAA-GGTGCCAATGTGCTGA
* * * *
3259384 TTCAAGGCAAGCTATATTAGAGTTAAAGATGAA-
64 TTCAAGGCCAGCTACATTGGACTTAAAGAT-AAG
* * * * *
3259417 GGTGCCAATGTGCTGATTTAAGGCCAGCTACATTGGACTTAAAGATGAGGGTACCAGTGTGCTGA
1 GGTGCCAATGTGCTGATTCAAGGCCAGC-GCATTGGACTTAAAGAT-AAGGTGCCAATGTGCTGA
* *
3259482 TTCAAGGCCAGCGACATTGGTCTTAAAGATAAG
64 TTCAAGGCCAGCTACATTGGACTTAAAGATAAG
* * ** *
3259515 GGTGCCAATATACTGATTCAAGGCCAGCTATATTGGACTT----A-AAGGTGCCAATGTGCTGAG
1 GGTGCCAATGTGCTGATTCAAGGCCAGC-GCATTGGACTTAAAGATAAGGTGCCAATGTGCTGAT
* *
3259575 TCAAGGCCAGCCATATTGGACTTAAAGATAAG
65 TCAAGGCCAGCTACATTGGACTTAAAGATAAG
3259607 GGTGCCA
1 GGTGCCA
3259614 CGGACTTGTG
Statistics
Matches: 252, Mismatches: 37, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
92 51 0.20
94 1 0.00
97 4 0.02
98 193 0.77
99 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.25
Consensus pattern (96 bp):
GGTGCCAATGTGCTGATTCAAGGCCAGCGCATTGGACTTAAAGATAAGGTGCCAATGTGCTGATT
CAAGGCCAGCTACATTGGACTTAAAGATAAG
Found at i:3259413 original size:147 final size:147
Alignment explanation
Indices: 3259221--3259613 Score: 591
Period size: 147 Copynumber: 2.7 Consensus size: 147
3259211 AGACAGAAAA
* ** *
3259221 GGTGCCCATATGCTGATTCAAGGCCAGCGCTATTGGAATTAAAGATGAAGGTGCCAATGTGTTGA
1 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAATTAAAGATGAAGGTGCCAATGTGCTGA
*
3259286 TTCAAGGCCAGCTACATTGGACTTAAAGATGAGGGTGCCAATGTGTTGATTCAAGGCCAGCGACA
66 TTCAAGGCCAGCTACATTGGACTTAAAGATGAGGGTGCCAATGTGCTGATTCAAGGCCAGCGACA
3259351 TTGGTCTTAAAGATAAG
131 TTGGTCTTAAAGATAAG
* * *
3259368 GGTGCCAATATGCTGATTCAAGGCAAGCTATATTAGAGTTAAAGATGAAGGTGCCAATGTGCTGA
1 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAATTAAAGATGAAGGTGCCAATGTGCTGA
* * *
3259433 TTTAAGGCCAGCTACATTGGACTTAAAGATGAGGGTACCAGTGTGCTGATTCAAGGCCAGCGACA
66 TTCAAGGCCAGCTACATTGGACTTAAAGATGAGGGTGCCAATGTGCTGATTCAAGGCCAGCGACA
3259498 TTGGTCTTAAAGATAAG
131 TTGGTCTTAAAGATAAG
* *
3259515 GGTGCCAATATACTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGCTGA
1 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAATTAAAGATGAAGGTGCCAATGTGCTGA
* * * *
3259574 GTCAAGGCCAGCCATATTGGACTTAAAGATAAGGGTGCCA
66 TTCAAGGCCAGCTACATTGGACTTAAAGATGAGGGTGCCA
3259614 CGGACTTGTG
Statistics
Matches: 225, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
141 52 0.23
143 1 0.00
147 172 0.76
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.25
Consensus pattern (147 bp):
GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAATTAAAGATGAAGGTGCCAATGTGCTGA
TTCAAGGCCAGCTACATTGGACTTAAAGATGAGGGTGCCAATGTGCTGATTCAAGGCCAGCGACA
TTGGTCTTAAAGATAAG
Found at i:3259741 original size:35 final size:34
Alignment explanation
Indices: 3259608--3259765 Score: 192
Period size: 34 Copynumber: 4.6 Consensus size: 34
3259598 AAAGATAAGG
* * * * *
3259608 GTGCCACGGACTTGTGGACTTAGAAGGAAAAAAA
1 GTGCCACAGAGTTGTGGGCTTAAAAGGAAAAAGA
* *
3259642 GTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGA
1 GTGCCACAGAGTTGTGGGCTTAAAAGGAAAAAGA
3259676 GTGCCACAGAGTTGTGGGCTTAAAAGGAAAAAGA
1 GTGCCACAGAGTTGTGGGCTTAAAAGGAAAAAGA
* *
3259710 GTGCCACAGAGTTGTGGGTTTTAAAAAGAAAAACGA
1 GTGCCACAGAGTTGTGGG-CTTAAAAGGAAAAA-GA
* *
3259746 -TGCCACAGAATTATGGGCTT
1 GTGCCACAGAGTTGTGGGCTT
3259766 CGGAAAAAGG
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
34 83 0.74
35 27 0.24
36 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.20
Consensus pattern (34 bp):
GTGCCACAGAGTTGTGGGCTTAAAAGGAAAAAGA
Found at i:3259839 original size:27 final size:27
Alignment explanation
Indices: 3259772--3259914 Score: 153
Period size: 30 Copynumber: 5.1 Consensus size: 27
3259762 GCTTCGGAAA
* *
3259772 AAGG-TGCCACTGACTTGTGGGTTTTTTTT
1 AAGGTTGCCACTGACTTGTGGG---CTTTG
*
3259801 AAGGTTGCCACTGATTTGTGGGCTTTG
1 AAGGTTGCCACTGACTTGTGGGCTTTG
* *
3259828 AAGGTTGCCACTAACTTGTGGGTTTTGG
1 AAGGTTGCCACTGACTTGTGGGCTTT-G
*
3259856 AAAAGGGTGCCACTGACTTGTGGGCTTTTG
1 --AAGGTTGCCACTGACTTGTGGGC-TTTG
*
3259886 AAGGTTGCCACTGATTTGTGGGCTTTG
1 AAGGTTGCCACTGACTTGTGGGCTTTG
3259913 AA
1 AA
3259915 AAAGGGTGAG
Statistics
Matches: 98, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
27 32 0.33
28 22 0.22
29 4 0.04
30 37 0.38
31 3 0.03
ACGTcount: A:0.17, C:0.15, G:0.31, T:0.36
Consensus pattern (27 bp):
AAGGTTGCCACTGACTTGTGGGCTTTG
Found at i:3259846 original size:57 final size:58
Alignment explanation
Indices: 3259772--3259922 Score: 198
Period size: 57 Copynumber: 2.6 Consensus size: 58
3259762 GCTTCGGAAA
**** * *
3259772 AAGG-TGCCACTGACTTGTGGGTTTTTTTTAAGGTTGCCACTGATTTGTGGGC-TTTG
1 AAGGTTGCCACTGACTTGTGGGTTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
*
3259828 AAGGTTGCCACTAACTTGTGGGTTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
1 AAGGTTGCCACTGACTTGTGGGTTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
* * *
3259886 AAGGTTGCCACTGATTTGTGGGCTTTGAAAAAGGGTG
1 AAGGTTGCCACTGACTTGTGGGTTTTGGAAAAGGGTG
3259923 AGGGATGTCT
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
56 4 0.05
57 41 0.50
58 37 0.45
ACGTcount: A:0.19, C:0.14, G:0.32, T:0.35
Consensus pattern (58 bp):
AAGGTTGCCACTGACTTGTGGGTTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
Found at i:3259918 original size:58 final size:57
Alignment explanation
Indices: 3259801--3259922 Score: 181
Period size: 58 Copynumber: 2.1 Consensus size: 57
3259791 GGTTTTTTTT
* * * *
3259801 AAGGTTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTAACTTGTGGGTTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAAGGTTGCCACTAACTTGTGGGCTTTGAAA
* *
3259858 AAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGATTTGTGGGCTTTGAAA
1 AAGGGTGCCACTGACTTGTGGGC-TTTGAAGGTTGCCACTAACTTGTGGGCTTTGAAA
3259916 AAGGGTG
1 AAGGGTG
3259923 AGGGATGTCT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 21 0.36
58 37 0.64
ACGTcount: A:0.20, C:0.14, G:0.34, T:0.33
Consensus pattern (57 bp):
AAGGGTGCCACTGACTTGTGGGCTTTGAAGGTTGCCACTAACTTGTGGGCTTTGAAA
Found at i:3261398 original size:15 final size:15
Alignment explanation
Indices: 3261350--3261405 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
3261340 ATCCGGACCC
*
3261350 TTTTTGTTGTTGTTGT
1 TTTTTTTTGTTGTT-T
3261366 TTTTGTTTTGTT-TTT
1 TTTT-TTTTGTTGTTT
3261381 TTTTTTTTGTTGTTT
1 TTTTTTTTGTTGTTT
3261396 TTTTTTTTGT
1 TTTTTTTTGT
3261406 GGAGGACGCC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
14 7 0.19
15 18 0.49
16 6 0.16
17 6 0.16
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (15 bp):
TTTTTTTTGTTGTTT
Found at i:3274685 original size:52 final size:52
Alignment explanation
Indices: 3274536--3274664 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
3274526 CGAAATATGA
3274536 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
3274588 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
3274640 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
3274665 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:3274742 original size:13 final size:13
Alignment explanation
Indices: 3274724--3274750 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3274714 TACAAAACTT
3274724 ATGTATCGATACA
1 ATGTATCGATACA
3274737 ATGTATCGATACA
1 ATGTATCGATACA
3274750 A
1 A
3274751 CACTTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3274747 original size:32 final size:33
Alignment explanation
Indices: 3274706--3274770 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
3274696 TAGCTTAAAT
3274706 TGTATCGATACAAAAC-TTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
* *
3274738 TGTATCGATACAACACTTTATGTGTCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
3274771 ATCGTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAAAACTTTATGTATCGATACAA
Found at i:3276423 original size:3 final size:3
Alignment explanation
Indices: 3276409--3276442 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3276399 CATCAAAGAC
*
3276409 GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
3276443 GTGACTCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:3280938 original size:22 final size:21
Alignment explanation
Indices: 3280895--3280935 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3280885 TAAAATTCTT
3280895 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAATACATC
3280917 GTTTTTCA-TCAAAAT-CATC
1 GTTTTTCACTCAAAATACATC
3280936 ATCAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (21 bp):
GTTTTTCACTCAAAATACATC
Found at i:3281208 original size:20 final size:21
Alignment explanation
Indices: 3281176--3281227 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
3281166 CTCCTAGGCA
*
3281176 GCACCCACCAGGTCGCGACC-G
1 GCACCC-CCAGGTCGCAACCGG
3281197 GCACCCCCAGGTCGCAACCGG
1 GCACCCCCAGGTCGCAACCGG
3281218 GCAGCCCCCA
1 GCA-CCCCCA
3281228 CACTAGTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.43
21 10 0.36
22 6 0.21
ACGTcount: A:0.19, C:0.50, G:0.27, T:0.04
Consensus pattern (21 bp):
GCACCCCCAGGTCGCAACCGG
Found at i:3282605 original size:21 final size:21
Alignment explanation
Indices: 3282579--3282620 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3282569 AGAAATGGTT
3282579 AATGTTTGATTAAGGGGGAGA
1 AATGTTTGATTAAGGGGGAGA
3282600 AATGTTTGATTAAGGGGGAGA
1 AATGTTTGATTAAGGGGGAGA
3282621 GAAAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.29
Consensus pattern (21 bp):
AATGTTTGATTAAGGGGGAGA
Found at i:3283178 original size:20 final size:20
Alignment explanation
Indices: 3283130--3283186 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
3283120 GTCAAAACCC
*
3283130 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
3283150 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* * *
3283170 TGCATTGTATCAATACA
1 TGAAATGTATCGATACA
3283187 TTGTATCGAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:3283232 original size:21 final size:20
Alignment explanation
Indices: 3283188--3283236 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3283178 ATCAATACAT
**
3283188 TGTATCGATACATGACCAAA
1 TGTATCGATACATGAAAAAA
*
3283208 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAA-AA
3283229 TGTATCGA
1 TGTATCGA
3283237 CAAAAATTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:3285191 original size:13 final size:13
Alignment explanation
Indices: 3285173--3285197 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3285163 AAAATTTCCA
3285173 AATGTATCGATAC
1 AATGTATCGATAC
3285186 AATGTATCGATA
1 AATGTATCGATA
3285198 TATGGAATAA
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:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:3285275 original size:19 final size:19
Alignment explanation
Indices: 3285251--3285300 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
3285241 AGCGATACAT
3285251 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
3285270 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
3285289 TGTATCGATACA
1 TGTATCGATACA
3285301 TTGTATCGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:3285307 original size:13 final size:13
Alignment explanation
Indices: 3285289--3285313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3285279 ACAACACTTA
3285289 TGTATCGATACAT
1 TGTATCGATACAT
3285302 TGTATCGATACA
1 TGTATCGATACA
3285314 AATTGTTGAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3291276 original size:17 final size:18
Alignment explanation
Indices: 3291254--3291301 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
3291244 ACTGTATTTG
3291254 TATTTAAAATTT-TAATA
1 TATTTAAAATTTATAATA
* *
3291271 TATTTAATAATTTATATTT
1 TATTTAA-AATTTATAATA
3291290 TATTT-AAATTTA
1 TATTTAAAATTTA
3291302 AAGAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 13 0.48
18 6 0.22
19 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTAAAATTTATAATA
Found at i:3291295 original size:19 final size:17
Alignment explanation
Indices: 3291248--3291297 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
3291238 TATATTACTG
3291248 TATTTGTATTTAAAATTT
1 TATTT-TATTTAAAATTT
* *
3291266 TAATATATTTAATAATTT
1 TATTTTATTTAA-AATTT
3291284 ATATTTTATTTAAA
1 -TATTTTATTTAAA
3291298 TTTAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 7 0.27
18 9 0.35
19 10 0.38
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTTTATTTAAAATTT
Found at i:3294662 original size:87 final size:87
Alignment explanation
Indices: 3294508--3294678 Score: 249
Period size: 87 Copynumber: 2.0 Consensus size: 87
3294498 TGCATCAAAT
*
3294508 AATTTAGATTAGCAAACAACTTAAAAAACAATAGTTACAACGTATGTTACATGCACTCTTCATTT
1 AATTTAGATTAGCAAACAACTTAAAAAACAATAGTTACAACGTATGTTACAAGCACTCTTCATTT
*
3294573 TTTTCTAAAATACTCATGTTAG
66 TTTCCTAAAATACTCATGTTAG
*
3294595 AATTTAGATTAGCAAACAACTTAAAAAAACAATAGTTACCATC-TATGTTACACAG-ACTCTTCA
1 AATTTAGATTAGCAAACAACTT-AAAAAACAATAGTTA-CAACGTATGTTACA-AGCACTCTTCA
* *
3294658 -TTTTTCCTAAAGTACTTATGT
63 TTTTTTCCTAAAATACTCATGT
3294679 ATGGCATATG
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
87 40 0.53
88 32 0.42
89 4 0.05
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (87 bp):
AATTTAGATTAGCAAACAACTTAAAAAACAATAGTTACAACGTATGTTACAAGCACTCTTCATTT
TTTCCTAAAATACTCATGTTAG
Found at i:3299034 original size:17 final size:17
Alignment explanation
Indices: 3299012--3299046 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3299002 TCACTATTAT
3299012 TTCACTTATTCACCATC
1 TTCACTTATTCACCATC
3299029 TTCACTTATTCACCATC
1 TTCACTTATTCACCATC
3299046 T
1 T
3299047 CCAACATACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.43
Consensus pattern (17 bp):
TTCACTTATTCACCATC
Found at i:3299280 original size:2 final size:2
Alignment explanation
Indices: 3299273--3299297 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3299263 AATGCTAGAA
3299273 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
3299298 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3301128 original size:23 final size:21
Alignment explanation
Indices: 3301088--3301129 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
3301078 GTTTACATAA
*
3301088 AAATATAAATTTTTAAATTAT
1 AAATATAAATTTTAAAATTAT
3301109 AAATATATAATATTTAAAATT
1 AAATATA-AAT-TTTAAAATT
3301130 TTTAAACACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 3 0.17
23 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATATAAATTTTAAAATTAT
Found at i:3301137 original size:155 final size:155
Alignment explanation
Indices: 3300889--3301190 Score: 550
Period size: 155 Copynumber: 1.9 Consensus size: 155
3300879 TATATTATTT
* *
3300889 TCATATACGAGTATATATTACATACATTTTAAATGTTTACGTAAAAATATAAATTTTTAAATTAT
1 TCATATACGAATATATATTACATACATTTTAAATGTTTACATAAAAATATAAATTTTTAAATTAT
*
3300954 AAATATATAATATTTAAAATATTTAAACACTTAATAAATAAAATAAAATATTTGAAATATATAAT
66 AAATATATAATATTTAAAATATTTAAACACTTAATAAATAAAATAAAATATTTAAAATATATAAT
*
3301019 AAATATAATTGTTAATCTCAATAAA
131 AAATATAATTATTAATCTCAATAAA
*
3301044 TCATATATGAATATATATTACATACATTTTAAATGTTTACATAAAAATATAAATTTTTAAATTAT
1 TCATATACGAATATATATTACATACATTTTAAATGTTTACATAAAAATATAAATTTTTAAATTAT
*
3301109 AAATATATAATATTTAAAATTTTTAAACACTTAATAAATAAAATAAAATATTTAAAATATATAAT
66 AAATATATAATATTTAAAATATTTAAACACTTAATAAATAAAATAAAATATTTAAAATATATAAT
3301174 AAATATAATTATTAATC
131 AAATATAATTATTAATC
3301191 AAGTTAGGCT
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
155 141 1.00
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (155 bp):
TCATATACGAATATATATTACATACATTTTAAATGTTTACATAAAAATATAAATTTTTAAATTAT
AAATATATAATATTTAAAATATTTAAACACTTAATAAATAAAATAAAATATTTAAAATATATAAT
AAATATAATTATTAATCTCAATAAA
Found at i:3303614 original size:13 final size:13
Alignment explanation
Indices: 3303596--3303621 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3303586 CATTTTGGGA
3303596 TGTATCGATACAT
1 TGTATCGATACAT
3303609 TGTATCGATACAT
1 TGTATCGATACAT
3303622 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3303618 original size:33 final size:32
Alignment explanation
Indices: 3303576--3303639 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
3303566 TACAAGCCAA
*
3303576 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
3303609 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
3303640 ATAGTTAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:3303791 original size:19 final size:20
Alignment explanation
Indices: 3303754--3303792 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3303744 CTGTGCATTA
3303754 TGTATCGATACATTTTAAGG
1 TGTATCGATACATTTTAAGG
*
3303774 TGTATCGATATA-TTTAAGG
1 TGTATCGATACATTTTAAGG
3303793 GTTTTGATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTTTAAGG
Found at i:3312225 original size:32 final size:33
Alignment explanation
Indices: 3312166--3312227 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
3312156 CAAGCCAATG
*
3312166 TATCGATACATTTTGGGATGTATCGATACATTA
1 TATCGATACATCTTGGGATGTATCGATACATTA
*
3312199 TATCGATACATCTTGTG-TGTATCGATACA
1 TATCGATACATCTTGGGATGTATCGATACA
3312228 AACAGTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.39
Consensus pattern (33 bp):
TATCGATACATCTTGGGATGTATCGATACATTA
Found at i:3312305 original size:20 final size:21
Alignment explanation
Indices: 3312258--3312310 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
3312248 GCCAATGACC
*
3312258 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
3312279 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
3312299 TGTATCGATACA
1 TGTATCGATACA
3312311 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:3312316 original size:13 final size:13
Alignment explanation
Indices: 3312298--3312322 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3312288 ACATTTGGTC
3312298 ATGTATCGATACA
1 ATGTATCGATACA
3312311 ATGTATCGATAC
1 ATGTATCGATAC
3312323 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3312369 original size:19 final size:20
Alignment explanation
Indices: 3312332--3312370 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3312322 CTGTGCATTA
3312332 TGTATCGATACATTTTAAGG
1 TGTATCGATACATTTTAAGG
*
3312352 TGTATTGATACA-TTTAAGG
1 TGTATCGATACATTTTAAGG
3312371 GTTTTGACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTTTAAGG
Found at i:3322904 original size:13 final size:13
Alignment explanation
Indices: 3322886--3322911 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3322876 TACACAAAGT
3322886 ATGTATCGATACA
1 ATGTATCGATACA
3322899 ATGTATCGATACA
1 ATGTATCGATACA
3322912 CCAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3327404 original size:52 final size:52
Alignment explanation
Indices: 3327256--3327384 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
3327246 TGAAATATGA
3327256 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
3327308 AAATTTGCCTGCATGTATCGCTACATTTCATAGTATATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
3327360 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
3327385 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:3327411 original size:13 final size:13
Alignment explanation
Indices: 3327393--3327417 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3327383 CAAAGATCAG
3327393 TGTATCGATACAA
1 TGTATCGATACAA
3327406 TGTATCGATACA
1 TGTATCGATACA
3327418 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3327483 original size:13 final size:13
Alignment explanation
Indices: 3327465--3327526 Score: 70
Period size: 13 Copynumber: 4.3 Consensus size: 13
3327455 TTCGTAACCG
3327465 TACATTGTATCGA
1 TACATTGTATCGA
3327478 TACATTGTATCGA
1 TACATTGTATCGA
3327491 TACAAATCTTATGTATCGA
1 TAC--A---T-TGTATCGA
3327510 TACATTGTATCGA
1 TACATTGTATCGA
3327523 TACA
1 TACA
3327527 ACACTTATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 28 0.65
14 1 0.02
15 1 0.02
17 1 0.02
18 1 0.02
19 11 0.26
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:3327507 original size:19 final size:18
Alignment explanation
Indices: 3327483--3327547 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
3327473 ATCGATACAT
3327483 TGTATCGATACAAATCTTA
1 TGTATCGATACAAA-CTTA
3327502 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
3327515 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
3327534 TGTATCGATACAAA
1 TGTATCGATACAAA
3327548 TCGTTGAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 1 0.03
17 1 0.03
18 2 0.05
19 24 0.60
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:3327511 original size:32 final size:32
Alignment explanation
Indices: 3327470--3327545 Score: 136
Period size: 32 Copynumber: 2.4 Consensus size: 32
3327460 AACCGTACAT
3327470 TGTATCGATACATTGTATCGATACAA-ATCTTA
1 TGTATCGATACATTGTATCGATACAACA-CTTA
3327502 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
3327534 TGTATCGATACA
1 TGTATCGATACA
3327546 AATCGTTGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
32 42 0.98
33 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:3328734 original size:20 final size:20
Alignment explanation
Indices: 3328709--3328786 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
3328699 ACTACCAAGG
*
3328709 AAATGTATCGATACATTAAT
1 AAATGTATCGATACATTATT
* **
3328729 AAATGTATCAATACATGCTT
1 AAATGTATCGATACATTATT
* *
3328749 CAGATTGTATCGATACAATATT
1 -A-AATGTATCGATACATTATT
*
3328771 CAATGTATCGATACAT
1 AAATGTATCGATACAT
3328787 GCAGGTAAAT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 29 0.66
21 1 0.02
22 14 0.32
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.35
Consensus pattern (20 bp):
AAATGTATCGATACATTATT
Found at i:3333526 original size:13 final size:13
Alignment explanation
Indices: 3333508--3333532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3333498 ATACATAGGA
3333508 CATTGTATCGATG
1 CATTGTATCGATG
3333521 CATTGTATCGAT
1 CATTGTATCGAT
3333533 ATATAGTAAA
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:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATG
Found at i:3333532 original size:33 final size:33
Alignment explanation
Indices: 3333490--3333559 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
3333480 CTACCACTAT
* * *
3333490 TTGTATCGATACATAGGACATTGTATCGATGCA
1 TTGTATCGATACATAGGAAAATGTATCGATACA
* *
3333523 TTGTATCGATATATAGTAAAATGTATCGATACA
1 TTGTATCGATACATAGGAAAATGTATCGATACA
3333556 TTGT
1 TTGT
3333560 GCCCAACAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (33 bp):
TTGTATCGATACATAGGAAAATGTATCGATACA
Found at i:3339729 original size:13 final size:13
Alignment explanation
Indices: 3339711--3339740 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3339701 AAGGATCTTA
3339711 GTATCGATACATT
1 GTATCGATACATT
3339724 GTATCGATACATT
1 GTATCGATACATT
3339737 GTAT
1 GTAT
3339741 TAGGACTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:3341709 original size:43 final size:44
Alignment explanation
Indices: 3341631--3341717 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 44
3341621 TTATTTTTTG
*
3341631 GAAACAAAAAGGGGGAGAGATATTTTATAATGGGAAAATTTTAT
1 GAAACAAAAAGGGGGAGAGATATTTTATAAAGGGAAAATTTTAT
*
3341675 GAAACAAAAA-GGGGAGAGATATTTTTTAAAGGGAAAATTTTAT
1 GAAACAAAAAGGGGGAGAGATATTTTATAAAGGGAAAATTTTAT
3341718 TAAGGGGGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 31 0.76
44 10 0.24
ACGTcount: A:0.46, C:0.02, G:0.24, T:0.28
Consensus pattern (44 bp):
GAAACAAAAAGGGGGAGAGATATTTTATAAAGGGAAAATTTTAT
Found at i:3342045 original size:57 final size:57
Alignment explanation
Indices: 3341977--3342092 Score: 196
Period size: 57 Copynumber: 2.0 Consensus size: 57
3341967 CGATAGGGAG
* * *
3341977 TAAAGTTAACCAAATTTATTTTTTAAAGTTTTGTTATATCAAAAAGGGGGAGATTGT
1 TAAAGTCAACCAAATTTATTTTTCAAAGTTTTGTTATATAAAAAAGGGGGAGATTGT
*
3342034 TAAAGTCAACCAAATTTATTTTTCACAGTTTTGTTATATAAAAAAGGGGGAGATTGT
1 TAAAGTCAACCAAATTTATTTTTCAAAGTTTTGTTATATAAAAAAGGGGGAGATTGT
3342091 TA
1 TA
3342093 GGATCTTGGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (57 bp):
TAAAGTCAACCAAATTTATTTTTCAAAGTTTTGTTATATAAAAAAGGGGGAGATTGT
Found at i:3342380 original size:20 final size:21
Alignment explanation
Indices: 3342349--3342387 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
3342339 AGGTCAAAAC
3342349 CCTAGAAAGTATCGATACAAG
1 CCTAGAAAGTATCGATACAAG
3342370 CCTAG-AAGTATCGATACA
1 CCTAGAAAGTATCGATACA
3342388 TATTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (21 bp):
CCTAGAAAGTATCGATACAAG
Found at i:3352701 original size:25 final size:24
Alignment explanation
Indices: 3352661--3352742 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 24
3352651 CCTTTGCAAA
*
3352661 AAAAAAATCAACAAAAAAACAAAAC
1 AAAAAAAT-AAAAAAAAAACAAAAC
*
3352686 AAAAAAATTAAAAAAAAACAAAACC
1 AAAAAAATAAAAAAAAAACAAAA-C
*
3352711 AAAAAAA-AAATAAAAAACAAACAAC
1 AAAAAAATAAAAAAAAAAC-AA-AAC
3352736 AAAAAAA
1 AAAAAAA
3352743 GGTCCAGATG
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
24 22 0.44
25 26 0.52
26 2 0.04
ACGTcount: A:0.83, C:0.12, G:0.00, T:0.05
Consensus pattern (24 bp):
AAAAAAATAAAAAAAAAACAAAAC
Found at i:3352714 original size:12 final size:12
Alignment explanation
Indices: 3352657--3352741 Score: 63
Period size: 12 Copynumber: 7.0 Consensus size: 12
3352647 GCATCCTTTG
3352657 CAAAA-AAAAAA
1 CAAAACAAAAAA
*
3352668 TCAACA-AAAAAA
1 -CAAAACAAAAAA
3352680 CAAAACAAAAAA
1 CAAAACAAAAAA
3352692 -ATTAAA-AAAAAA
1 CA--AAACAAAAAA
3352704 CAAAACCAAAAAA
1 CAAAA-CAAAAAA
*
3352717 -AAAATAAAAAA
1 CAAAACAAAAAA
3352728 CAAACAACAAAAAA
1 C-AA-AACAAAAAA
3352742 AGGTCCAGAT
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
11 14 0.23
12 26 0.43
13 12 0.20
14 8 0.13
ACGTcount: A:0.82, C:0.13, G:0.00, T:0.05
Consensus pattern (12 bp):
CAAAACAAAAAA
Found at i:3352726 original size:18 final size:17
Alignment explanation
Indices: 3352658--3352742 Score: 64
Period size: 18 Copynumber: 4.6 Consensus size: 17
3352648 CATCCTTTGC
**
3352658 AAAAAAAAAATCAACAA
1 AAAAAAAAAAAAAACAA
3352675 AAAAACAAAACAAAAA-AA
1 AAAAA-AAAA-AAAAACAA
*
3352693 TTAAAAAAAAACAAAACCAA
1 --AAAAAAAAA-AAAAACAA
3352713 AAAAAAAATAAAAAACAA
1 AAAAAAAA-AAAAAACAA
3352731 ACAACAAAAAAA
1 A-AA-AAAAAAA
3352743 GGTCCAGATG
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
17 5 0.09
18 22 0.39
19 17 0.30
20 12 0.21
ACGTcount: A:0.84, C:0.12, G:0.00, T:0.05
Consensus pattern (17 bp):
AAAAAAAAAAAAAACAA
Found at i:3354316 original size:32 final size:32
Alignment explanation
Indices: 3354275--3354358 Score: 132
Period size: 32 Copynumber: 2.6 Consensus size: 32
3354265 GTATTTTCTC
*
3354275 CTTCTAAAGCCCACAGAAGTCGATGGCAACCT
1 CTTCTAAAGCCCACACAAGTCGATGGCAACCT
* *
3354307 CTTCTAAAGCTCACACAAGTCGATGGCAACTT
1 CTTCTAAAGCCCACACAAGTCGATGGCAACCT
*
3354339 CTTCTAAAGTCCACACAAGT
1 CTTCTAAAGCCCACACAAGT
3354359 TGGTGGAAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (32 bp):
CTTCTAAAGCCCACACAAGTCGATGGCAACCT
Found at i:3354344 original size:64 final size:64
Alignment explanation
Indices: 3354275--3354414 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 64
3354265 GTATTTTCTC
* * *
3354275 CTTCTAAAGCCCACAGAAGTCGATGGCAA-CCTCTTCTAAAGCTCACACAAGTC-GATGGCAACT
1 CTTCTAAAGCCCACACAAGTCGATGGAAACCCTC-TCAAAAGCTCACACAAGTCAG-TGGCAACT
*
3354338 T
64 A
* * * * *
3354339 CTTCTAAAGTCCACACAAGTTGGTGGAAACCCTCTCAAAAGCTCACACATGTCAGTGGCATCTA
1 CTTCTAAAGCCCACACAAGTCGATGGAAACCCTCTCAAAAGCTCACACAAGTCAGTGGCAACTA
3354403 CTTCT-AAGCCCA
1 CTTCTAAAGCCCA
3354415 ATGTCGTTGG
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
63 6 0.09
64 53 0.83
65 5 0.08
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (64 bp):
CTTCTAAAGCCCACACAAGTCGATGGAAACCCTCTCAAAAGCTCACACAAGTCAGTGGCAACTA
Found at i:3354476 original size:52 final size:53
Alignment explanation
Indices: 3354403--3354502 Score: 150
Period size: 52 Copynumber: 1.9 Consensus size: 53
3354393 GTGGCATCTA
*
3354403 CTTCTAAGCCCAATGTCGTTGGCCTTGAATCAACACCTTGGCACCTTTTTTTT
1 CTTCTAAGCCCAATGTCGTTGGCCTTGAATCAACACATTGGCACCTTTTTTTT
* *
3354456 CTTC-AAGTCCAATG-CTGTTGGCCTTGAATCAGCACATTGGCACCTTT
1 CTTCTAAGCCCAATGTC-GTTGGCCTTGAATCAACACATTGGCACCTTT
3354503 GTCATCTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
51 1 0.02
52 38 0.88
53 4 0.09
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (53 bp):
CTTCTAAGCCCAATGTCGTTGGCCTTGAATCAACACATTGGCACCTTTTTTTT
Found at i:3354528 original size:52 final size:52
Alignment explanation
Indices: 3354418--3354654 Score: 160
Period size: 52 Copynumber: 4.4 Consensus size: 52
3354408 AAGCCCAATG
* * * ** *
3354418 TCGTTGGCCTTGAATCAACACCTTGGCACCTTTTTTTTCTTCAAGTCCA--A
1 TCGTTGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGTCCAGTA
*
3354468 TGCTGTTGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGTTCAGTA
1 T-C-GTTGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGTCCAGTA
* * * * *
3354522 TCGTTGGCCTTGAATTAGCATATCGGCACCTTTATCCTTCTTCTAA-TCTTCAAGTCTAA
1 TCGTTGGCCTTGAATCAGCACATTGGCACCTTTGT-CATCTT-TAAGTC--C-AG--T-A
* * * *
3354581 T-GTTGCCGGCCTTGAATCAGCATATTGTCACCTTTGTCATCTTTAAGCCCAATA
1 TCGTT---GGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGTCCAGTA
*
3354635 -CTGCTGGCCTTGAATCAGCA
1 TC-GTTGGCCTTGAATCAGCA
3354655 TATTAGCATC
Statistics
Matches: 148, Mismatches: 21, Indels: 34
0.73 0.10 0.17
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
52 84 0.57
53 7 0.05
54 6 0.04
55 4 0.03
56 2 0.01
57 1 0.01
58 5 0.03
59 5 0.03
60 6 0.04
61 26 0.18
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (52 bp):
TCGTTGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGTCCAGTA
Found at i:3354655 original size:52 final size:51
Alignment explanation
Indices: 3354588--3354828 Score: 195
Period size: 52 Copynumber: 4.6 Consensus size: 51
3354578 TAATGTTGCC
* * * *
3354588 GGCCTTGAATCAGCATATTGTCACCTTTGTCATCTTTAAGCCCAAT-ACTGCT
1 GGCCTTGAATCAGCATATTG-CATCTTTATCATCTTTAAGCCCAATGTC-ACT
* * * *
3354640 GGCCTTGAATCAGCATATTAGCATCTTTAACAT-TCCTAAACCTAATGTCACT
1 GGCCTTGAATCAGCATATT-GCATCTTTATCATCT-TTAAGCCCAATGTCACT
* * * * * *
3354692 GGCTTTGAATCAGTATATTGACATTCTTT-TCATCTTCAAGTCTAATGTCGCT
1 GGCCTTGAATCAGCATATTG-CA-TCTTTATCATCTTTAAGCCCAATGTCACT
* *
3354744 GG-CTATGAATCAGCATATTGGCATTCTTT-GCATCTTTAAGCCCAATATCACT
1 GGCCT-TGAATCAGCATATT-GCA-TCTTTATCATCTTTAAGCCCAATGTCACT
* *
3354796 GGCCTTGAATCAGCATGTTAGCACCTTTATCAT
1 GGCCTTGAATCAGCATATT-GCATCTTTATCAT
3354829 TTTTCTCATC
Statistics
Matches: 151, Mismatches: 28, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
51 7 0.05
52 133 0.88
53 11 0.07
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.36
Consensus pattern (51 bp):
GGCCTTGAATCAGCATATTGCATCTTTATCATCTTTAAGCCCAATGTCACT
Found at i:3354668 original size:113 final size:113
Alignment explanation
Indices: 3354455--3354668 Score: 286
Period size: 113 Copynumber: 1.9 Consensus size: 113
3354445 ACCTTTTTTT
** ** *
3354455 TCTTCAAGTCCAATGCTGTTGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGTTCAG
1 TCTTCAAGTCCAATGCTGCCGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGCCCAA
* * *
3354520 TATCGTTGGCCTTGAATTAGCATATCGGCACCTTTATCCTTCTTCTAA
66 TATCGCTGGCCTTGAATCAGCATATCAGCACCTTTATCCTTCTTCTAA
* * * *
3354568 TCTTCAAGTCTAATGTTGCCGGCCTTGAATCAGCATATTGTCACCTTTGTCATCTTTAAGCCCAA
1 TCTTCAAGTCCAATGCTGCCGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGCCCAA
* *
3354633 TA-CTGCTGGCCTTGAATCAGCATATTAGCATCTTTA
66 TATC-GCTGGCCTTGAATCAGCATATCAGCACCTTTA
3354669 ACATTCCTAA
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
112 1 0.01
113 85 0.99
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.36
Consensus pattern (113 bp):
TCTTCAAGTCCAATGCTGCCGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGCCCAA
TATCGCTGGCCTTGAATCAGCATATCAGCACCTTTATCCTTCTTCTAA
Found at i:3354882 original size:61 final size:61
Alignment explanation
Indices: 3354765--3354901 Score: 179
Period size: 61 Copynumber: 2.2 Consensus size: 61
3354755 AGCATATTGG
*** * *
3354765 CATTCTT-TGCATCTTTAAGCCCAATATCACTGGCCTTGAATCAGCATGTTAGCACCTTTAT
1 CATTCTTCT-CATCTTTAAGCCCAATATCACTGGCCCAAAATCAACATATTAGCACCTTTAT
* *
3354826 CATTTTTCTCATCTTTAAGCCCAATATCGCTGGCCCAAAATCAACATATT-GACACCTTTAT
1 CATTCTTCTCATCTTTAAGCCCAATATCACTGGCCCAAAATCAACATATTAG-CACCTTTAT
3354887 CATTCTTCTCATCTT
1 CATTCTTCTCATCTT
3354902 CATCACTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
60 1 0.02
61 64 0.97
62 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.37
Consensus pattern (61 bp):
CATTCTTCTCATCTTTAAGCCCAATATCACTGGCCCAAAATCAACATATTAGCACCTTTAT
Found at i:3359695 original size:58 final size:58
Alignment explanation
Indices: 3359605--3359714 Score: 193
Period size: 58 Copynumber: 1.9 Consensus size: 58
3359595 GGTAATGTAC
**
3359605 TCTCTAAAAGTGTTTCATTAGCCTATTGAGGTTATTACCTTAAGAACGCATAGAAACT
1 TCTCTAAAAGTGTTTCATTAGCCTATCAAGGTTATTACCTTAAGAACGCATAGAAACT
*
3359663 TCTCTAAAAGTGTTTCATTAGCCTATCAAGGTTATTACCTTAAGAAGGCATA
1 TCTCTAAAAGTGTTTCATTAGCCTATCAAGGTTATTACCTTAAGAACGCATA
3359715 TAAATTTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (58 bp):
TCTCTAAAAGTGTTTCATTAGCCTATCAAGGTTATTACCTTAAGAACGCATAGAAACT
Found at i:3362714 original size:19 final size:18
Alignment explanation
Indices: 3362689--3362756 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
3362679 AATTCAACAA
3362689 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
3362707 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
3362723 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
3362739 TATTGTACCGATACATAA
1 T-TTGTATCGATACATAA
3362757 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
18 1 0.02
19 26 0.62
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:3362728 original size:13 final size:13
Alignment explanation
Indices: 3362710--3362734 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3362700 ACATAAGTGT
3362710 TGTATCGATACAA
1 TGTATCGATACAA
3362723 TGTATCGATACA
1 TGTATCGATACA
3362735 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3362728 original size:32 final size:32
Alignment explanation
Indices: 3362691--3362753 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
3362681 TTCAACAATT
* *
3362691 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTACCGATACAA
3362723 TGTATCGATACATAAGTATTGTACCGATACA
1 TGTATCGATACATAAGTATTGTACCGATACA
3362754 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTACCGATACAA
Found at i:3362814 original size:13 final size:13
Alignment explanation
Indices: 3362796--3362821 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3362786 CATTTTTCTG
3362796 TGTATCGATACAT
1 TGTATCGATACAT
3362809 TGTATCGATACAT
1 TGTATCGATACAT
3362822 CTATTCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3362839 original size:34 final size:33
Alignment explanation
Indices: 3362776--3362842 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
3362766 GCCAAGGAAA
*
3362776 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTATTCTGTGTATCGATACAT
*
3362809 TGTATCGATACATCTATTCTTTGTATCGATACAT
1 TGTATCGATACAT-TATTCTGTGTATCGATACAT
3362843 CTAGGAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGTATCGATACAT
Found at i:3363368 original size:11 final size:11
Alignment explanation
Indices: 3363354--3363384 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3363344 AATCCTTTAG
3363354 CAAAAAAAAAC
1 CAAAAAAAAAC
*
3363365 CAAAAAAACAC
1 CAAAAAAAAAC
3363376 CAAAAAAAA
1 CAAAAAAAA
3363385 CACTATTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAC
Found at i:3363385 original size:12 final size:12
Alignment explanation
Indices: 3363354--3363387 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3363344 AATCCTTTAG
3363354 CAAAAAAAA-AC
1 CAAAAAAAACAC
3363365 C-AAAAAAACAC
1 CAAAAAAAACAC
3363376 CAAAAAAAACAC
1 CAAAAAAAACAC
3363388 TATTCCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.33
11 4 0.19
12 10 0.48
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (12 bp):
CAAAAAAAACAC
Found at i:3365252 original size:51 final size:52
Alignment explanation
Indices: 3365195--3365580 Score: 191
Period size: 52 Copynumber: 7.4 Consensus size: 52
3365185 CAATTCTCCG
* * * * *
3365195 CAATCGGGGATATTCCATCTCTGATTTTATTTTC-AAAACACTAA-TTTTCTA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-A
* *
3365246 TAATCGGGGATACCCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTTTTCA
* * * *** ** *
3365299 CAATCGGGGATACTCCAACCCCG-TTAATCATTGGGGATACTCCAAC-CCCGTTATTT-T
1 CAATCGGGGATACTCCAACTCCGATT--TTATT-----TCCAAAAACACCAATT-TTTCA
* * * ** * *** *
3365356 CGA--GGGGATACTCCAACCCCTG-CTTTA-TTCTTAAAATATTGATTTATCA
1 CAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAATTTTTCA
* * * * * *
3365405 TAATCGGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTTCCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT-CA
* * * * * *
3365457 CAATCGGGGATTCTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTTCCTT
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-A
* * *
3365509 TAATCAGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTTTCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAA-TTTTTCA
*
3365562 CAATCGAGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
3365581 CTCGTTATTT
Statistics
Matches: 253, Mismatches: 60, Indels: 42
0.71 0.17 0.12
Matches are distributed among these distances:
48 6 0.02
49 3 0.01
50 1 0.00
51 64 0.25
52 71 0.28
53 59 0.23
54 16 0.06
55 17 0.07
56 2 0.01
57 6 0.02
58 6 0.02
59 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (52 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCA
Found at i:3365371 original size:28 final size:26
Alignment explanation
Indices: 3365304--3365375 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 26
3365294 TTTCACAATC
3365304 GGGGATACTCCAACCCCGTTAATCATT
1 GGGGATACTCCAACCCCGTTAATCA-T
*
3365331 GGGGATACTCCAACCCCGTTATTTTCGA-
1 GGGGATACTCCAACCCCGTTA--ATC-AT
3365359 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
3365376 TGCTTTATTC
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 21 0.51
28 17 0.41
29 2 0.05
30 1 0.02
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (26 bp):
GGGGATACTCCAACCCCGTTAATCAT
Found at i:3365484 original size:52 final size:51
Alignment explanation
Indices: 3365359--3365581 Score: 198
Period size: 52 Copynumber: 4.3 Consensus size: 51
3365349 TTATTTTCGA
* * * *** * *
3365359 GGGGATACTCCAACCCCTGCTTTATTCTTAAAATATTGATTTAT-CATAATC
1 GGGGATACTCCAACCCCGGTTTTATTC-TAAAACACCAATTTTTCCACAATC
*
3365410 GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGGTTTTATT-CTAAAACACCAATTTTTCCACAATC
* * **
3365462 GGGGATTCTCCAACCCCGGTTTTATTTTCAAAACACCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTCT-AAAACACCAATTTTTCC-ACAATC
* * * * * *
3365514 AGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTTTCACAATC
1 GGGGATACTCCAACCCCGGTTTTA-TT-CTAAAACACCAATTTTTCCACAATC
*
3365567 GAGGATACTCCAACC
1 GGGGATACTCCAACC
3365582 TCGTTATTTC
Statistics
Matches: 139, Mismatches: 26, Indels: 12
0.79 0.15 0.07
Matches are distributed among these distances:
51 43 0.31
52 64 0.46
53 27 0.19
54 5 0.04
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGTTTTATTCTAAAACACCAATTTTTCCACAATC
Found at i:3365592 original size:31 final size:28
Alignment explanation
Indices: 3365569--3365640 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
3365559 TCACAATCGA
*
3365569 GGATACTCCAACCTCGTTATTTCATCAG
1 GGATACTCCAACCCCGTTATTTCATCAG
**
3365597 GGATACTCCAACCCCGTTACCTC--CGAGG
1 GGATACTCCAACCCCGTTATTTCATC-A-G
3365625 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
3365641 GCTTTATTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 1 0.03
27 1 0.03
28 37 0.95
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTATTTCATCAG
Found at i:3372478 original size:16 final size:16
Alignment explanation
Indices: 3372459--3372610 Score: 108
Period size: 16 Copynumber: 9.4 Consensus size: 16
3372449 TTCAAACTGA
*
3372459 AAATGACCCAAACCCG
1 AAATGACCCGAACCCG
* * *
3372475 AAATAACTCGAATCC-
1 AAATGACCCGAACCCG
* * *
3372490 AGAATGACCTGCACCTG
1 A-AATGACCCGAACCCG
* * *
3372507 AATTGACCCAAACTCG
1 AAATGACCCGAACCCG
**
3372523 AAATGACCCGAACTTG
1 AAATGACCCGAACCCG
* *
3372539 AAATAACCCAAAACCCG
1 AAATGACCC-GAACCCG
* *
3372556 AAATGACCTGAACCCA
1 AAATGACCCGAACCCG
** *
3372572 AAATGACTTGAATCCG
1 AAATGACCCGAACCCG
3372588 AAATGACCCGAACCCG
1 AAATGACCCGAACCCG
3372604 AAATGAC
1 AAATGAC
3372611 TTGAACTTAA
Statistics
Matches: 100, Mismatches: 33, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
15 1 0.01
16 87 0.87
17 12 0.12
ACGTcount: A:0.41, C:0.30, G:0.14, T:0.14
Consensus pattern (16 bp):
AAATGACCCGAACCCG
Found at i:3372595 original size:81 final size:80
Alignment explanation
Indices: 3372459--3372610 Score: 182
Period size: 81 Copynumber: 1.9 Consensus size: 80
3372449 TTCAAACTGA
* * * * * *
3372459 AAATGACCCAAACCCGAAATAACTCGAATCCAGAATGACCTGCACCTGAATTGACCCAAACTCGA
1 AAATAACCCAAACCCGAAATAACTCGAACCCAAAATGACCTGAACCTGAAATGACCCAAACCCGA
3372524 AATGACCCGAACTTG
66 AATGACCCGAACTTG
* * *
3372539 AAATAACCCAAAACCCGAAATGAC-CTGAACCCAAAATGACTTGAATCC-GAAATGACCCGAACC
1 AAATAACCC-AAACCCGAAATAACTC-GAACCCAAAATGACCTGAA-CCTGAAATGACCCAAACC
3372602 CGAAATGAC
63 CGAAATGAC
3372611 TTGAACTTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
80 9 0.15
81 49 0.82
82 2 0.03
ACGTcount: A:0.41, C:0.30, G:0.14, T:0.14
Consensus pattern (80 bp):
AAATAACCCAAACCCGAAATAACTCGAACCCAAAATGACCTGAACCTGAAATGACCCAAACCCGA
AATGACCCGAACTTG
Found at i:3388663 original size:37 final size:37
Alignment explanation
Indices: 3388622--3388706 Score: 170
Period size: 37 Copynumber: 2.3 Consensus size: 37
3388612 TGCCACAATC
3388622 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
3388659 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
3388696 ATGCATTTGTG
1 ATGCATTTGTG
3388707 CTTTGTTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (37 bp):
ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
Found at i:3389123 original size:28 final size:28
Alignment explanation
Indices: 3389047--3389378 Score: 323
Period size: 28 Copynumber: 11.6 Consensus size: 28
3389037 GGCATTCCTC
*
3389047 ACCTTCCAAAGCCCACAAGTCAGTGGCA
1 ACCTTCAAAAGCCCACAAGTCAGTGGCA
* * * * *
3389075 TCTTTTTCTAAAGCCAACAAGTCAGTGACA
1 AC--CTTCAAAAGCCCACAAGTCAGTGGCA
3389105 ACCTTCAAAAGCCCACAAGTCAGTGGCA
1 ACCTTCAAAAGCCCACAAGTCAGTGGCA
3389133 ACCTTCAAAAGCCCACAAGTCAGTGGCA
1 ACCTTCAAAAGCCCACAAGTCAGTGGCA
*
3389161 ACCTTCAAAAGCCCACAAGTTAGTGGCA
1 ACCTTCAAAAGCCCACAAGTCAGTGGCA
* *
3389189 ACCTTCAGAAGCCCACAAATC-GATGGCA
1 ACCTTCAAAAGCCCACAAGTCAG-TGGCA
* *
3389217 CCCCCTT-TAAAGCCCACAAGTCAGTGGC-
1 --ACCTTCAAAAGCCCACAAGTCAGTGGCA
* *
3389245 ACCTTTTTC-AAAGCCCACAAGTCAATGGGA
1 ACC---TTCAAAAGCCCACAAGTCAGTGGCA
* * *
3389275 TCTTTTCAAAAGCCTACAAGTCAGTGGC-
1 AC-CTTCAAAAGCCCACAAGTCAGTGGCA
* * *
3389303 ATCTTCTCAAAGCCCACAAGTTAGTGGCA
1 ACCTTC-AAAAGCCCACAAGTCAGTGGCA
*
3389332 ACCTTCAAAAAACCCACAAGTCAGTGGCA
1 ACCTTC-AAAAGCCCACAAGTCAGTGGCA
* *
3389361 TCTTCTCAAAAGCCCACA
1 ACCT-TCAAAAGCCCACA
3389379 CAAGTTCGTG
Statistics
Matches: 248, Mismatches: 40, Indels: 31
0.78 0.13 0.10
Matches are distributed among these distances:
26 2 0.01
27 4 0.02
28 122 0.49
29 89 0.36
30 31 0.12
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.20
Consensus pattern (28 bp):
ACCTTCAAAAGCCCACAAGTCAGTGGCA
Found at i:3389318 original size:86 final size:85
Alignment explanation
Indices: 3389046--3389397 Score: 333
Period size: 86 Copynumber: 4.1 Consensus size: 85
3389036 AGGCATTCCT
* * * * *
3389046 CACCTTC-CAAAGCCCACAAGTCAGTGGCATCTTTTTCTAAAGCCAACAAGTCAGTGACAACCTT
1 CACCTTCTCAAAGCCCACAAGTCAGTGGCAACCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTT
3389110 CAAAAGCCCACAAGTCAGTGG
66 CAAAAGCCCACAAGTC-GTGG
* *
3389131 CAACCTTC-AAAAGCCCACAAGTCAGTGGCAACC--TTCAAAAGCCCACAAGTTAGTGGCAACCT
1 C-ACCTTCTCAAAGCCCACAAGTCAGTGGCAACCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
* *
3389193 TCAGAAGCCCACAAATCGATGG
65 TCAAAAGCCCACAAGTCG-TGG
** * * * *
3389215 CACCCCCTTTAAAGCCCACAAGTCAGTGGC-ACCTTTTTC-AAAGCCCACAAGTCAATGGGATCT
1 CACCTTC-TCAAAGCCCACAAGTCAGTGGCAACC-TTTTCAAAAGCCCACAAGTCAGTGGCAAC-
* *
3389278 TTTCAAAAGCCTACAAGTCAGTGG
63 CTTCAAAAGCCCACAAGTC-GTGG
* * * * *
3389302 CATCTTCTCAAAGCCCACAAGTTAGTGGCAACC--TTCAAAAAACCCACAAGTCAGTGGCATCTT
1 CACCTTCTCAAAGCCCACAAGTCAGTGGCAACCTTTTC-AAAAGCCCACAAGTCAGTGGCAACCT
3389365 CTCAAAAGCCCACACAAGTTCGTGG
65 -TCAAAAG-CC-CACAAG-TCGTGG
*
3389390 CATCTTCT
1 CACCTTCT
3389398 TCTAAGTCCA
Statistics
Matches: 222, Mismatches: 29, Indels: 29
0.79 0.10 0.10
Matches are distributed among these distances:
83 5 0.02
84 50 0.23
85 23 0.10
86 94 0.42
87 30 0.14
88 18 0.08
89 2 0.01
ACGTcount: A:0.32, C:0.31, G:0.16, T:0.20
Consensus pattern (85 bp):
CACCTTCTCAAAGCCCACAAGTCAGTGGCAACCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTT
CAAAAGCCCACAAGTCGTGG
Done.