Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold15
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: 4011073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 11440 characters in sequence are not A, C, G, or T
File 8 of 25
Found at i:1198712 original size:21 final size:21
Alignment explanation
Indices: 1198671--1198714 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1198661 CTCTCTTTTA
* *
1198671 TCTCCCCCATTTATTAATAAT
1 TCTCCCCCATTAATCAATAAT
1198692 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCATTAATCAA-TAAT
1198713 TC
1 TC
1198715 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (21 bp):
TCTCCCCCATTAATCAATAAT
Found at i:1200378 original size:21 final size:21
Alignment explanation
Indices: 1200354--1200400 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1200344 TTTGATGCTG
1200354 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
1200374 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
1200395 ATTTTG
1 ATTTTG
1200401 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:1200539 original size:13 final size:13
Alignment explanation
Indices: 1200521--1200559 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1200511 ATAATCACCC
* *
1200521 TGTATCGATATAG
1 TGTATCGATACAA
1200534 TGTATCGATACAA
1 TGTATCGATACAA
1200547 TGTATCGATACAA
1 TGTATCGATACAA
1200560 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1202657 original size:15 final size:15
Alignment explanation
Indices: 1202637--1202667 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1202627 ATTTCGTTTG
*
1202637 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1202652 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1202667 G
1 G
1202668 GACATTTTTA
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:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1204500 original size:21 final size:21
Alignment explanation
Indices: 1204471--1204515 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1204461 AAGTTTTCAT
*
1204471 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1204491 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1204513 TTT
1 TTT
1204516 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1206751 original size:13 final size:13
Alignment explanation
Indices: 1206733--1206758 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1206723 CAATTTTTTG
1206733 TGTATCGATACAT
1 TGTATCGATACAT
1206746 TGTATCGATACAT
1 TGTATCGATACAT
1206759 ACTTGCTGTA
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:1219239 original size:79 final size:78
Alignment explanation
Indices: 1219105--1219306 Score: 201
Period size: 79 Copynumber: 2.6 Consensus size: 78
1219095 GATAATAACG
* * * * * * ** * *
1219105 GGGTTGGAGTGTTCCTTTGAAAATAACGGGGCTGGAGTATCCTCGGTTGTGAGAAATCGATGA-T
1 GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATT
*
1219169 TAGAAAAAAAAATC
65 TAGAAAAAAAAATA
1219183 GGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATT
1 GGG-TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATA-T
* * * **
1219248 TTGGGAATAAAGTTA
64 TTAGAAAAAAAAATA
*
1219263 GGGTTGGAGTATCCCCTC-AGAAGTAACGGGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCC
1219307 GATGAAATAA
Statistics
Matches: 103, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
78 5 0.05
79 86 0.83
80 12 0.12
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (78 bp):
GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTT
AGAAAAAAAAATA
Found at i:1219295 original size:28 final size:28
Alignment explanation
Indices: 1219263--1219332 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
1219253 AATAAAGTTA
*
1219263 GGGTTGGAGTATCCCCTCA-GAAGTAACG
1 GGGTTGGAGTATCCCC-CATGAAATAACG
*
1219291 GGGTTGGAGTATCCCCGATGAAATAACG
1 GGGTTGGAGTATCCCCCATGAAATAACG
*
1219319 AGGTTGGAGTATCC
1 GGGTTGGAGTATCC
1219333 TCGACTGTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 1 0.03
28 37 0.97
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.23
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCCATGAAATAACG
Found at i:1221271 original size:17 final size:17
Alignment explanation
Indices: 1221249--1221282 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1221239 ATGGAATAGT
1221249 GTTTTTCTTTGTTTTTG
1 GTTTTTCTTTGTTTTTG
* *
1221266 GTTTTTTTTTTTTTTTG
1 GTTTTTCTTTGTTTTTG
1221283 CTAAAGGATT
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:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (17 bp):
GTTTTTCTTTGTTTTTG
Found at i:1221829 original size:13 final size:13
Alignment explanation
Indices: 1221811--1221836 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1221801 ACAAAGATCC
1221811 ATGTATCGATACA
1 ATGTATCGATACA
1221824 ATGTATCGATACA
1 ATGTATCGATACA
1221837 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:1221832 original size:33 final size:33
Alignment explanation
Indices: 1221790--1221856 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1221780 AAAGTTTCCA
***
1221790 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1221823 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1221856 A
1 A
1221857 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:1221900 original size:19 final size:18
Alignment explanation
Indices: 1221876--1221940 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
1221866 CAGTAGCTAA
1221876 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1221895 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1221910 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1221927 TTATGTATCGATAC
1 TTATGTATCGATAC
1221941 GAATTGTTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 1 0.03
19 25 0.62
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1221916 original size:13 final size:13
Alignment explanation
Indices: 1221898--1221922 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1221888 ACAATACTTA
1221898 TGTATCGATACAT
1 TGTATCGATACAT
1221911 TGTATCGATACA
1 TGTATCGATACA
1221923 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:1221920 original size:32 final size:32
Alignment explanation
Indices: 1221879--1221940 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
1221869 TAGCTAATTA
*
1221879 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1221911 TGTATCGATACAAAACTTATGTATCGATAC
1 TGTATCGATACAAAACTTATGTATCGATAC
1221941 GAATTGTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1222023 original size:21 final size:21
Alignment explanation
Indices: 1221999--1222055 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1221989 CATTTGTAGG
1221999 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
1222020 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
1222041 ATGTATCGATACATT
1 ATGTATCGATACATT
1222056 TGGATAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:1223647 original size:155 final size:155
Alignment explanation
Indices: 1223339--1223866 Score: 530
Period size: 155 Copynumber: 3.4 Consensus size: 155
1223329 TAAAGTTTCA
* * * * * *
1223339 AAAAAATTATGAAATTGCCCCTAAGGGATATCTTCTATGTAAAAATACCCGATACCCCTAAA-GA
1 AAAAAATTACGAAAATGCCCCTAAGGGATACCTTCGACGTAAAAATACCTGATACCCCTAAAGGA
* ** * *
1223403 TCTTAAAAATGATTTTAAAAT-AGGTGAACCTATCCTAAATATCTACCTTCAGCAAAAAAGCAAA
66 -CTTAAAAAAGATAAT-AAATGAGATGAACCTATCCTAAATATCTACCTTCAGCATAAAAGCAAA
* * *
1223467 CCCGGTGATAATCTAAGACTCGGTTCT
129 CCCAGTGACAATCTAAGACTAGGTTCT
* *
1223494 AAAAAATTACGAAAATACCCCTAAGGGATACCTTCGACGTAAAAATACCTGAGACCCCTAAAGGA
1 AAAAAATTACGAAAATGCCCCTAAGGGATACCTTCGACGTAAAAATACCTGATACCCCTAAAGGA
* * * ** *
1223559 CTTAAAAAGGATAATAAATGAAATGAACCTATCCTAAATATCTACCTTCGGCATAAAAGTGAACT
66 CTTAAAAAAGATAATAAATGAGATGAACCTATCCTAAATATCTACCTTCAGCATAAAAGCAAACC
*
1223624 CAGTGACAA-CTTAGGACTAGGTTCT
131 CAGTGACAATC-TAAGACTAGGTTCT
* * * * * *
1223649 AAAAAATTACGAAAATGCTCTTAAAGGATACTTTCGACGTAAAAGTA-CTCGATACCCCTTAAGG
1 AAAAAATTACGAAAATGCCCCTAAGGGATACCTTCGACGTAAAAATACCT-GATACCCCTAAAGG
* *
1223713 ACTTAAAAAAGATAATAGATGAGATGAACCTATCCT-AA-ATCTACCTTCAGCATAAAAGCAGAC
65 ACTTAAAAAAGATAATAAATGAGATGAACCTATCCTAAATATCTACCTTCAGCATAAAAGCAAAC
* * * ** *
1223776 CCAATGATAACCTTGGACTCA-GTTTT
130 CCAGTGACAATCTAAGACT-AGGTTCT
* * * * * ** * **
1223802 AAAAAAAATATGAAAATGCTCTTAGGGGATACCTTTAACGTAAAAGTGTCTGATACCCCTAAAGG
1 -AAAAAATTACGAAAATGCCCCTAAGGGATACCTTCGACGTAAAAATACCTGATACCCCTAAAGG
1223867 TCTTGAGATA
Statistics
Matches: 314, Mismatches: 51, Indels: 17
0.82 0.13 0.04
Matches are distributed among these distances:
153 38 0.12
154 63 0.20
155 211 0.67
156 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (155 bp):
AAAAAATTACGAAAATGCCCCTAAGGGATACCTTCGACGTAAAAATACCTGATACCCCTAAAGGA
CTTAAAAAAGATAATAAATGAGATGAACCTATCCTAAATATCTACCTTCAGCATAAAAGCAAACC
CAGTGACAATCTAAGACTAGGTTCT
Found at i:1225482 original size:14 final size:13
Alignment explanation
Indices: 1225441--1225484 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1225431 GCCAGCCAAA
*
1225441 AAAAATGATATTT
1 AAAAATTATATTT
*
1225454 AAAAATTATAATT
1 AAAAATTATATTT
*
1225467 AATAAATTATTTTT
1 AA-AAATTATATTT
1225481 AAAA
1 AAAA
1225485 TTTTAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (13 bp):
AAAAATTATATTT
Found at i:1228753 original size:2 final size:2
Alignment explanation
Indices: 1228746--1228785 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1228736 GAACAAATGT
*
1228746 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1228786 ATTGATCTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1228902 original size:14 final size:15
Alignment explanation
Indices: 1228865--1228902 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1228855 AAGAGAAAAG
* *
1228865 AAAATAAAAGTCTGA
1 AAAAAAAAAGTCTCA
1228880 AAAAAAAAAG-CTCA
1 AAAAAAAAAGTCTCA
1228894 AAAAAAAAA
1 AAAAAAAAA
1228903 TTCCGGATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.74, C:0.08, G:0.08, T:0.11
Consensus pattern (15 bp):
AAAAAAAAAGTCTCA
Found at i:1229318 original size:23 final size:22
Alignment explanation
Indices: 1229261--1229323 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 22
1229251 TCGTGTTTAG
*
1229261 AATATTTATTATTTATAAATTTT
1 AATATTTA-TATATATAAATTTT
1229284 AATAATTTATATGATATAAATTTT
1 AAT-ATTTATAT-ATATAAATTTT
1229308 AATATTTATATTATAT
1 AATATTTATA-TATAT
1229324 TCGTATTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
23 17 0.47
24 19 0.53
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
AATATTTATATATATAAATTTT
Found at i:1230573 original size:20 final size:19
Alignment explanation
Indices: 1230541--1230578 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
1230531 ATAAAATTAT
1230541 TAAAATATCAAAAATAAAAC
1 TAAAATATC-AAAATAAAAC
1230561 TAAAATAAT-AAAATAAAA
1 TAAAAT-ATCAAAATAAAA
1230579 TTTTAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 6 0.35
21 2 0.12
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (19 bp):
TAAAATATCAAAATAAAAC
Found at i:1237159 original size:23 final size:22
Alignment explanation
Indices: 1237123--1237167 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1237113 AGGTAAGTAA
*
1237123 ATTTTTTTTCTAACTTTATATT
1 ATTTTTTTTCTAACTATATATT
*
1237145 ATTTTATTTTTTAACTATATATT
1 ATTTT-TTTTCTAACTATATATT
1237168 TATGTTGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTTTTTTCTAACTATATATT
Found at i:1241948 original size:79 final size:79
Alignment explanation
Indices: 1241848--1242049 Score: 221
Period size: 79 Copynumber: 2.6 Consensus size: 79
1241838 AATAACGGGG
* * * * *
1241848 TTGGAGTACCCCCTT-GAAAATAACGGGGTTGGAGTATCCTCGGTTGTGAAAAATCGATGA-TTA
1 TTGGAGTA-TCCCTTCGGAAATAACGGGGTTGGAGTATCCTCGATTATGAAAAATCAAT-ATTTA
*
1241911 GGAAATAAAATCGAGA
64 GGAAATAAAACCGAGA
* * *
1241927 TTGGAGTATCCCTTCGGAAATAACGGGGTTGGAGTATCC-CTAATTATGAGAAATCAATATTTTG
1 TTGGAGTATCCCTTCGGAAATAACGGGGTTGGAGTATCCTC-GATTATGAAAAATCAATATTTAG
* * *
1241991 GAAATAAAGCCGGGG
65 GAAATAAAACCGAGA
* **
1242006 TTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCTCGAT
1 TTGGAGTATCCCTTCGGAAATAACGGGGTTGGAGTATCCTCGAT
1242050 GAAATAACGA
Statistics
Matches: 103, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
78 7 0.07
79 95 0.92
80 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (79 bp):
TTGGAGTATCCCTTCGGAAATAACGGGGTTGGAGTATCCTCGATTATGAAAAATCAATATTTAGG
AAATAAAACCGAGA
Found at i:1242057 original size:28 final size:28
Alignment explanation
Indices: 1242001--1242077 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
1241991 GAAATAAAGC
**
1242001 CGGGGTTGGAGTATCCCCTCG--GAGGTAA
1 CGGGGTTGGAGTAT--CCTCGATGAAATAA
1242029 CGGGGTTGGAGTATCCTCGATGAAATAA
1 CGGGGTTGGAGTATCCTCGATGAAATAA
*
1242057 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCTCGAT
1242078 TGAAGGAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 5 0.11
28 39 0.89
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCTCGATGAAATAA
Found at i:1244520 original size:13 final size:13
Alignment explanation
Indices: 1244502--1244527 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1244492 ACAAAGATCG
1244502 ATGTATCGATACA
1 ATGTATCGATACA
1244515 ATGTATCGATACA
1 ATGTATCGATACA
1244528 TTTCCTTAAT
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:1244538 original size:21 final size:21
Alignment explanation
Indices: 1244514--1244555 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1244504 GTATCGATAC
1244514 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
1244535 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
1244556 GGCAGTAGCT
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:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:1244604 original size:19 final size:19
Alignment explanation
Indices: 1244580--1244693 Score: 144
Period size: 19 Copynumber: 6.6 Consensus size: 19
1244570 AGCAATACAT
1244580 TGTATCGATACAACACCTA
1 TGTATCGATACAACACCTA
1244599 TGTATCGATACAACACCTA
1 TGTATCGATACAACACCTA
1244618 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACCTA
1244631 TGTATCGATACAACACCTA
1 TGTATCGATACAACACCTA
1244650 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACCTA
1244663 TGTATCGATACAACACCTA
1 TGTATCGATACAACACCTA
1244682 TGTATCGATACA
1 TGTATCGATACA
1244694 TTTTCTGTTT
Statistics
Matches: 83, Mismatches: 0, Indels: 24
0.78 0.00 0.22
Matches are distributed among these distances:
13 18 0.22
14 2 0.02
16 12 0.14
18 2 0.02
19 49 0.59
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAACACCTA
Found at i:1244635 original size:32 final size:32
Alignment explanation
Indices: 1244599--1244695 Score: 194
Period size: 32 Copynumber: 3.0 Consensus size: 32
1244589 ACAACACCTA
1244599 TGTATCGATACAACACCTATGTATCGATACAT
1 TGTATCGATACAACACCTATGTATCGATACAT
1244631 TGTATCGATACAACACCTATGTATCGATACAT
1 TGTATCGATACAACACCTATGTATCGATACAT
1244663 TGTATCGATACAACACCTATGTATCGATACAT
1 TGTATCGATACAACACCTATGTATCGATACAT
1244695 T
1 T
1244696 TTCTGTTTGT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (32 bp):
TGTATCGATACAACACCTATGTATCGATACAT
Found at i:1244636 original size:13 final size:13
Alignment explanation
Indices: 1244618--1244674 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1244608 ACAACACCTA
1244618 TGTATCGATACAT
1 TGTATCGATACAT
1244631 TGTATCGATACAACACCT
1 TGTATCGAT---ACA--T
1244649 ATGTATCGATACAT
1 -TGTATCGATACAT
1244663 TGTATCGATACA
1 TGTATCGATACA
1244675 ACACCTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1244693 original size:51 final size:48
Alignment explanation
Indices: 1244574--1244674 Score: 154
Period size: 51 Copynumber: 2.1 Consensus size: 48
1244564 CTTCGTAGCA
1244574 ATACATTGTATCGATACAACACCTATGTATCGATACAACACCTATGTATCG
1 ATACATTGTATCGATACAACACCTATGTATCGAT--AACA-CTATGTATCG
1244625 ATACATTGTATCGATACAACACCTATGTATCGAT-ACA-T-TGTATCG
1 ATACATTGTATCGATACAACACCTATGTATCGATAACACTATGTATCG
1244670 ATACA
1 ATACA
1244675 ACACCTATGT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
45 12 0.24
46 1 0.02
48 3 0.06
51 34 0.68
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.31
Consensus pattern (48 bp):
ATACATTGTATCGATACAACACCTATGTATCGATAACACTATGTATCG
Found at i:1245530 original size:42 final size:42
Alignment explanation
Indices: 1245495--1245579 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
1245485 AGGACAAAGG
*
1245495 AAAAAG-GG-AAATGAAA-TACGTCCTGCTCTTTGAGGACGAA
1 AAAAAGAGGAAAAT-AAAGTACATCCTGCTCTTTGAGGACGAA
* *
1245535 AAAAAGAGGAAAATAAAGTGCATCCTGCTCTTTGAGGACTAA
1 AAAAAGAGGAAAATAAAGTACATCCTGCTCTTTGAGGACGAA
1245577 AAA
1 AAA
1245580 GAGAAAAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 6 0.15
41 5 0.13
42 28 0.72
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (42 bp):
AAAAAGAGGAAAATAAAGTACATCCTGCTCTTTGAGGACGAA
Found at i:1245696 original size:61 final size:61
Alignment explanation
Indices: 1245603--1246024 Score: 358
Period size: 55 Copynumber: 7.3 Consensus size: 61
1245593 AAGGAAGTGT
* *
1245603 GTCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGT
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGC
* * * *
1245664 GTCCTGCCCTTTGATGACTAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAA-AGAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGA-AAAGGC
* * * * * * * * *
1245725 GTCTTGCTTTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTTGCAAAGGAAAGAC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGC
* * *
1245786 GTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGC
* * *
1245841 GTCCTGCTCTTTGAAGATTGGAAAA-TGCCACCAACTGGTGTGGGCTTT-----G-AAAGGC
1 GTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGC
* * * *
1245896 GTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTT-----G-AAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGC
* * ** *
1245951 ATCTTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTATGTTGGCTTT------AAAAGGC
1 GTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGC
1246006 GTCCTGCTCTTTGAGGACT
1 GTCCTGCTCTTTGAGGACT
1246025 AAAGGGTGAA
Statistics
Matches: 313, Mismatches: 42, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
54 3 0.01
55 157 0.50
56 7 0.02
60 1 0.00
61 145 0.46
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (61 bp):
GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGC
Found at i:1245863 original size:55 final size:55
Alignment explanation
Indices: 1245718--1246024 Score: 416
Period size: 55 Copynumber: 5.5 Consensus size: 55
1245708 CTTTGAAAAA
* *
1245718 GAAAGGCGTCTTGCTTTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTT
1 GAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTT
*
1245773 GCAAAGGAAAGACGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT
1 G-AAA-G---G-CGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTT
* * ** * *
1245834 GAAAGGCGTCCTGCTCTTTGAAGATTGGAAAATGCCACCAACTGGTGTGGGCTTT
1 GAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTT
1245889 GAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTT
1 GAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTT
* * ** * *
1245944 GAAAGGCATCTTGCTCTTTGAGGACTGGAAAATGCCACCAACTTATGTTGGCTTT
1 GAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTT
*
1245999 AAAAGGCGTCCTGCTCTTTGAGGACT
1 GAAAGGCGTCCTGCTCTTTGAGGACT
1246025 AAAGGGTGAA
Statistics
Matches: 223, Mismatches: 23, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
55 166 0.74
56 4 0.02
57 1 0.00
59 1 0.00
60 4 0.02
61 47 0.21
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (55 bp):
GAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTT
Found at i:1246164 original size:149 final size:149
Alignment explanation
Indices: 1245894--1246178 Score: 491
Period size: 149 Copynumber: 1.9 Consensus size: 149
1245884 GCTTTGAAAG
1245894 GCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTTGAAAGGCATCTTGCT
1 GCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTTGAAAGGCATCTTGCT
* * *
1245959 CTTTGAGGACTGGAAAATGCCACCAACTTATGTTGGCTTTAAAAGGCGTCCTGCTCTTTGAGGAC
66 CTTTGAGGACTGAAAAATGCCACCAACTTATGTGGGCTTTAAAAGACGTCCTGCTCTTTGAGGAC
1246024 TAAAGGGTGAAAGGAGAGA
131 TAAAGGGTGAAAGGAGAGA
* *
1246043 GCGTCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCTTGC
1 GCGTCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTAGGCTTTGAAAGGCATCTTGC
* *
1246107 TCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGACGTCCTGCTCTTTGAGGA
65 TCTTTGAGGACTGAAAAATGCCACCAACTTATGTGGGCTTTAAAAGACGTCCTGCTCTTTGAGGA
1246172 CTAAAGG
130 CTAAAGG
1246179 TGCCACCAAC
Statistics
Matches: 128, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
149 124 0.97
150 4 0.03
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (149 bp):
GCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTTGAAAGGCATCTTGCT
CTTTGAGGACTGAAAAATGCCACCAACTTATGTGGGCTTTAAAAGACGTCCTGCTCTTTGAGGAC
TAAAGGGTGAAAGGAGAGA
Found at i:1246259 original size:61 final size:59
Alignment explanation
Indices: 1246043--1246589 Score: 560
Period size: 61 Copynumber: 9.4 Consensus size: 59
1246033 AAAGGAGAGA
1246043 GCGTCCTGCTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTT----GAAAG
1 GCGTCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAG
* * *
1246098 GCGTCTTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT----GAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAG
*
1246153 ACGTCCTGCTCTTTGAGGACT--AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAA-GA-AAG
* * * *
1246213 GCGTCCTGCTTTTTGAGGACTGGGAAGTGCCACCAACTTGTATGGGCTTTAAACAGAGAAA
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAA-AGA-AAG
* * * *
1246274 ACATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTCTGGGCTTT---A-AAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAG
* * *
1246329 GTGTCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAA
1 GCGTCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTT-AAAAG-AAAG
* * *
1246390 GCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAG-AAAG
* * * *
1246451 GCATCCTGTTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGGAAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAA---AGAAAG
* * * *
1246514 GTGTCCTGCTCTTTCAGGACT-AAAAGGTGCCACCAACTTGTGTGCGCTTT---A-AAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAG
*
1246569 GCGTCTTGCTCTTTGAGGACT
1 GCGTCCTGCTCTTTGAGGACT
1246590 AAAGGGTGAA
Statistics
Matches: 426, Mismatches: 43, Indels: 46
0.83 0.08 0.09
Matches are distributed among these distances:
53 3 0.01
54 28 0.07
55 132 0.31
56 2 0.00
57 1 0.00
59 3 0.01
60 22 0.05
61 181 0.42
62 10 0.02
63 43 0.10
64 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (59 bp):
GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAG
Found at i:1246426 original size:177 final size:173
Alignment explanation
Indices: 1246046--1246568 Score: 678
Period size: 177 Copynumber: 3.0 Consensus size: 173
1246036 GGAGAGAGCG
* * *
1246046 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTGAAAG-G---CGTCTTGC
1 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAACATCCTGC
* * **
1246107 TCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGACGTCCTGCTCTTTGAGGA
66 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGA
* * *
1246172 CTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
131 CTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAAGCA
* * *
1246216 TCCTGCTTTTTGAGGACTGGGAAGTGCCACCAACTTGTATGGGCTTTAAACAGAGAAAACATCCT
1 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAA-AGAG-AAACATCCT
* *
1246281 GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTCTGGGCTTTAAAAGGTGTCCTGCTCTTTGGG
64 GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAG
1246346 GACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
129 GACT-AAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGCA
* *
1246393 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGA-AAAGGCATCC
1 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGAGAAA--CATCC
*
1246457 TGTTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGGAAAAAGGTGTCCTG
63 TGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT--------AAAAGGTGTCCTG
* *
1246522 CTCTTTCAGGACTAAAAGGTGCCACCAACTTGTGTGCGCTTTAAAAG
120 CTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
1246569 GCGTCTTGCT
Statistics
Matches: 308, Mismatches: 26, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
170 46 0.15
171 2 0.01
172 1 0.00
175 3 0.01
176 67 0.22
177 126 0.41
178 7 0.02
184 5 0.02
185 51 0.17
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (173 bp):
TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAACATCCTGC
TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGA
CTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCA
Found at i:1246440 original size:36 final size:36
Alignment explanation
Indices: 1246400--1246502 Score: 93
Period size: 36 Copynumber: 3.2 Consensus size: 36
1246390 GCATCCTGCT
1246400 CTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGG
1 CTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGG
* * *
1246436 CTTTGA--A-AAGAAAA-GGCATC--C-TGT-T---
1 CTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGG
*
1246461 CTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGG
1 CTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGG
1246497 CTTTGA
1 CTTTGA
1246503 AAGGGAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 22
0.63 0.09 0.28
Matches are distributed among these distances:
25 6 0.12
27 1 0.02
28 6 0.12
29 7 0.14
30 1 0.02
31 1 0.02
32 7 0.14
33 7 0.14
34 1 0.02
36 12 0.24
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (36 bp):
CTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGG
Found at i:1246772 original size:61 final size:60
Alignment explanation
Indices: 1246608--1247403 Score: 829
Period size: 61 Copynumber: 13.4 Consensus size: 60
1246598 AAAAGAGAGA
* *
1246608 GCGTCTTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGC-TT----TG-AAAG
1 GCGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAATGAAAAG
*
1246663 GCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAATGAGAAG
1 GCGTCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAATGAAAAG
* * *
1246723 GTGTCCTGCTCTTTGAGGACTGGGAAGTGCGACCAACTTGTGTGGGCTTTAAACA-GAGAAA-
1 GCGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAA-ATGA-AAAG
* * *
1246784 ACATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGC-TT----TG-AAAG
1 GCGTCCTGCTCTTTGAGGACTG-AAAGTGCCACCAACTTGTGTGGGCTTTAAAATGAAAAG
* * *
1246839 GTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAT-AAAAA
1 GCGTCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTT-AAAATGAAAAG
* * * *
1246900 GCATCCTGCTCTTTGAGGACTAGAAAATGCCATCAACTTGTGTGGGCTTTGAAAA-GAAAAA
1 GCGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAATGAAAAG
* * *
1246961 GCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAAG
1 GCGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAATG-AAAAG
* * *
1247024 GTGTCATGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT----T-AAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAATGAAAAG
* * * * *
1247080 GCGTCTTACTCTTTGAGAACTGAAA--GCCACCAACTTGTGTGGGCTTTAAAAAGAAAAA
1 GCGTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAATGAAAAG
* * *
1247138 GCGTCCTGCTTTTTGAGGACT-AAAGGTGCCCCCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAATGAAAAG
* * *
1247198 GTGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAATG-AAAAG
* * * * *
1247259 GTGTCCTGCTCTTTGAGGACTGGAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAA
1 GCGTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAATG--AAAAG
* * *
1247321 GTGTCCTGCTCTTTGAGGA-TTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAGAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTT-AAAATGA-AAAG
1247382 GCGTCCTGCTCTTTGAGGACTG
1 GCGTCCTGCTCTTTGAGGACTG
1247404 GAAGGGCTAA
Statistics
Matches: 636, Mismatches: 63, Indels: 77
0.82 0.08 0.10
Matches are distributed among these distances:
53 24 0.04
54 27 0.04
55 60 0.09
56 28 0.04
57 3 0.00
58 21 0.03
59 2 0.00
60 107 0.17
61 252 0.40
62 63 0.10
63 49 0.08
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (60 bp):
GCGTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAATGAAAAG
Found at i:1246892 original size:29 final size:29
Alignment explanation
Indices: 1246811--1246892 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 29
1246801 GACTGAAAAA
1246811 TGCCACCAACTTGTGTGGGCTTTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAGG
** *
1246840 TGTCCTGC-TCTT-TG-GGGAC--TGAAAGG
1 TG-CCACCAACTTGTGTGGG-CTTTGAAAGG
1246866 TGCCACCAACTTGTGTGGGCTTTGAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAA
1246893 ATAAAAAGCA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
25 3 0.08
26 12 0.30
27 6 0.15
28 6 0.15
29 10 0.25
30 3 0.08
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (29 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGG
Found at i:1246943 original size:177 final size:173
Alignment explanation
Indices: 1246614--1247373 Score: 906
Period size: 177 Copynumber: 4.3 Consensus size: 173
1246604 GAGAGCGTCT
* *
1246614 TGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGA
1 TGCTCTTTGAGGACTA-AAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGA
* * *
1246679 GGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAATGAGAAGGTGTCCTGCTCTTTGAGGACT
65 GGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAT-AAAAAGCGTCCTGCTCTTTGAGGACT
* * *
1246744 GGGAAGTGCGACCAACTTGTGTGGGCTTTAAACAGAGAAAA-CATCC
129 -GGAAATGCCACCAACTTGTGTGGGCTTTAAAAAGA-AAAAGCATCC
* *
1246790 TGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGG
1 TGCTCTTTGAGGACT-AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGA
*
1246855 GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAATAAAAAGCATCCTGCTCTTTGAGGAC
65 GGACT-AAAGGTGCCACCAACTTGTGTGGGCTTT-AAAATAAAAAGCGTCCTGCTCTTTGAGGAC
* * *
1246920 TAGAAAATGCCATCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
128 T-GGAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGCATCC
*
1246967 TGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAAGGTGTCAT
1 TGCTCTTTGAGGACT--AAAAGTGCCACCAACTTGTGTGGGCTTT------G--AAAGGTGTCCT
* * *
1247031 GCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT----TAAAAGGCGTCTTACTCT
56 GCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAATAAAAAGCGTCCTGCTCT
* *
1247092 TTGAGAACT-GAAA-GCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGCGTCC
120 TTGAGGACTGGAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGCATCC
* * *
1247144 TGCTTTTTGAGGACTAAAGGTGCCCCCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTC
1 TGCTCTTTGAGGACTAAAAGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGTGTCCTGCTC
* * *
1247209 TTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTGCTCTTTG
60 TTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAATAAAAA-GCGTCCTGCTCTTTG
** **
1247274 AGGACTGGAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGTGTCC
123 AGGACTGGAAATGCCACCAACTTGTGTGGGCTTTAAAAAG--AAAAAGCATCC
* * *
1247327 TGCTCTTTGAGGATTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAA
1 TGCTCTTTGAGGACTAAAAGTGCCACCAACTTGTGTGGGCTTTGAAA
1247374 AGAGAAAGGC
Statistics
Matches: 515, Mismatches: 45, Indels: 47
0.85 0.07 0.08
Matches are distributed among these distances:
173 27 0.05
174 25 0.05
175 9 0.02
176 90 0.17
177 176 0.34
178 18 0.03
179 17 0.03
180 24 0.05
181 28 0.05
183 50 0.10
185 51 0.10
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (173 bp):
TGCTCTTTGAGGACTAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAG
GACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAATAAAAAGCGTCCTGCTCTTTGAGGACTGG
AAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGCATCC
Found at i:1246951 original size:36 final size:36
Alignment explanation
Indices: 1246910--1247012 Score: 84
Period size: 36 Copynumber: 3.2 Consensus size: 36
1246900 GCATCCTGCT
1246910 CTTTGAGGACTAGAAAATGCCATCAACTTGTGTGGG
1 CTTTGAGGACTAGAAAATGCCATCAACTTGTGTGGG
* * *
1246946 CTTTGA--A-AAGAAAAAG-CATC--C-TG-CT---
1 CTTTGAGGACTAGAAAATGCCATCAACTTGTGTGGG
* *
1246971 CTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGG
1 CTTTGAGGACTAGAAAATGCCATCAACTTGTGTGGG
1247007 CTTTGA
1 CTTTGA
1247013 AAAGGAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 22
0.62 0.10 0.28
Matches are distributed among these distances:
25 6 0.12
27 1 0.02
28 7 0.15
29 5 0.10
30 1 0.02
31 1 0.02
32 6 0.12
33 8 0.17
34 1 0.02
36 12 0.25
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (36 bp):
CTTTGAGGACTAGAAAATGCCATCAACTTGTGTGGG
Found at i:1246967 original size:510 final size:515
Alignment explanation
Indices: 1246098--1247373 Score: 1906
Period size: 510 Copynumber: 2.4 Consensus size: 515
1246088 GCTTTGAAAG
* * *
1246098 GCGTCTTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGACGTCCTGCT
1 GCGTCTTGCTCTTTGAGGACT-AGAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCT
* * *
1246163 CTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGCTTTTTG
65 CTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGTGTCCTGCTCTTTG
*
1246228 AGGACTGGGAAGTGCCACCAACTTGTATGGGCTTTAAACAGAGAAAACATCCTGCTCTTTGAGGA
130 AGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAACAGAGAAAACATCCTGCTCTTTGAGGA
* * *
1246293 CTGGAAAATGCCACCAACTTGTCTGGGCTTTAAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTG
195 CTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTG
1246358 CCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTAGAAAATGCCAC
260 CCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTAGAAAATGCCAC
* *
1246423 CAACTTGTGTGGGCTTTGAAAAGAAAAGGCATCCTGTTCTTTGAGGACTGGAAAATGCCACCAAC
325 CAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
* *
1246488 TTGTGTGGGCTTTGAAAGGGAAAAAGGTGTCCTGCTCTTTCAGGACTAAAAGGTGCCACCAACTT
390 TTGTGTGGGCTTTGAAAAGGAAAAAGGTGTCATGCTCTTTCAGGACTAAAAGGTGCCACCAACTT
* * * *
1246553 GTGTGCGC-TTTAAAAGGCGTCTTGCTCTTTGAGGACT-AAAG-G-GT-G-AAAAGAGAGA
455 GTGTGCGCTTTTAAAAGGCGTCTTACTCTTTGAGAACTGAAAGCGTGTGGTAAAAGAAAAA
1246608 GCGTCTTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCT
1 GCGTCTTGCTCTTTGAGGACTA-GAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCT
*
1246673 CTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAATGAGAAGGTGTCCTGCTCTTTG
65 CTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGTGTCCTGCTCTTTG
*
1246738 AGGACTGGGAAGTGCGACCAACTTGTGTGGGCTTTAAACAGAGAAAACATCCTGCTCTTTGAGGA
130 AGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAACAGAGAAAACATCCTGCTCTTTGAGGA
1246803 CTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTG
195 CTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTG
* *
1246868 CCACCAACTTGTGTGGGCTTTGAAAATAAAAAGCATCCTGCTCTTTGAGGACTAGAAAATGCCAT
260 CCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTAGAAAATGCCAC
1246933 CAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
325 CAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
*
1246998 TTGTGTGGGCTTTGAAAAGGAAAAAGGTGTCATGCTCTTTGAGGACTAAAAGGTGCCACCAACTT
390 TTGTGTGGGCTTTGAAAAGGAAAAAGGTGTCATGCTCTTTCAGGACTAAAAGGTGCCACCAACTT
*
1247063 GTGTGGGCTTTTAAAAGGCGTCTTACTCTTTGAGAACTGAAAGCCACCAACTTGTGTGGGCTTTA
455 GTGTGCGCTTTTAAAAGGCGTCTTACTCTTTGAGAACTGAAAG-------C--GTGT-GG---T-
1247128 AAAAGAAAAA
506 AAAAGAAAAA
* * * *
1247138 GCGTCCTGCTTTTTGAGGACTA-AAGGTGCCCCCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGT
1 GCGTCTTGCTCTTTGAGGACTAGAA-GTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGT
* *
1247202 CCTGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTG
59 CCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AGAAGGTGTCCTG
* * *
1247267 CTCTTTGAGGACT-GGAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGA-AAAAAAGTGTCCTGC
123 CTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAACAGAGAAAACA---TCCTGC
* ** *
1247330 TCTTTGAGGA-TTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAA
185 TCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAA
1247374 AGAGAAAGGC
Statistics
Matches: 696, Mismatches: 38, Indels: 38
0.90 0.05 0.05
Matches are distributed among these distances:
509 1 0.00
510 442 0.64
511 27 0.04
512 4 0.01
522 1 0.00
523 2 0.00
525 1 0.00
528 2 0.00
529 23 0.03
530 28 0.04
534 6 0.01
535 88 0.13
536 55 0.08
537 16 0.02
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (515 bp):
GCGTCTTGCTCTTTGAGGACTAGAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTC
TTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGTGTCCTGCTCTTTGA
GGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAACAGAGAAAACATCCTGCTCTTTGAGGAC
TGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGC
CACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTAGAAAATGCCACC
AACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACT
TGTGTGGGCTTTGAAAAGGAAAAAGGTGTCATGCTCTTTCAGGACTAAAAGGTGCCACCAACTTG
TGTGCGCTTTTAAAAGGCGTCTTACTCTTTGAGAACTGAAAGCGTGTGGTAAAAGAAAAA
Found at i:1247111 original size:238 final size:235
Alignment explanation
Indices: 1246608--1247402 Score: 911
Period size: 238 Copynumber: 3.3 Consensus size: 235
1246598 AAAAGAGAGA
* *
1246608 GCGTCTTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTG-----AAAGGCGTC
1 GCGTCTTGCTCTTTGAGGACT--GAA-AGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAGCGTC
* *
1246668 CTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAATGAGAAGGTGTCCTGCT
63 CTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCT
* *
1246733 CTTTGAGGACTGGGAAGTGCGACCAACTTGTGTGGGCTTTAAACAGAGAAAACA----TCCTGCT
128 CTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAA-AG-GAAAA-AGGTGTCCTGCT
* *
1246794 CTTTGAGGACTGAAAA-ATGCCACCAACTTGTGTGGGC-TTTGAAAG
190 CTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTTAAAAG
* * * *
1246839 GTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAATAAAAAGCAT
1 GCGTCTTGCTCTTTGAGGACTGAAA---GCCACCAACTTGTGTGGGCTTTGAAAA-AAAAAGCGT
** * * **
1246904 CCTGCTCTTTGAGGACTAGAAAATGCCATCAACTTGTGTGGGCTTTGAAAA-GAAAAAGCATCCT
62 CCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGTGTCCT
* *
1246968 GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAAGGTGTCATGC
125 GCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAAGGTGTCCTGC
1247033 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTTAAAAG
189 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTTAAAAG
* * *
1247080 GCGTCTTACTCTTTGAGAACTGAAAGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGCGTCCT
1 GCGTCTTGCTCTTTGAGGACTGAAAGCCACCAACTTGTGTGGGCTTTGAAAA-AAAAAGCGTCCT
* *
1247145 GCTTTTTGAGGACTAAAGGTGCCCCCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCT
65 GCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCT
* *
1247210 TTGAGGACT--AAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTGCTCTTT
130 TTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGGTGTCCTGCTCTTT
** *
1247273 GAGGACT-GGAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG
194 GAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTTAAAAG
* * * *
1247314 AAAAAAAGTGTCCTGCTCTTTGAGGA-TTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAG
1 -------GCGTCTTGCTCTTTGAGGACTGAAA---GCCACCAACTTGTGTGGGCTTTGAAAA-A-
*
1247378 AAAGGCGTCCTGCTCTTTGAGGACT
54 AAAAGCGTCCTGCTCTTTGAGGACT
1247403 GGAAGGGCTA
Statistics
Matches: 482, Mismatches: 51, Indels: 49
0.83 0.09 0.08
Matches are distributed among these distances:
229 3 0.01
231 41 0.09
234 31 0.06
235 34 0.07
236 27 0.06
237 76 0.16
238 126 0.26
239 11 0.02
240 41 0.09
241 42 0.09
243 27 0.06
244 23 0.05
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (235 bp):
GCGTCTTGCTCTTTGAGGACTGAAAGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAGCGTCCTG
CTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTT
TGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGGTGTCCTGCTCTTTGA
GGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTTAAAAG
Found at i:1247375 original size:123 final size:121
Alignment explanation
Indices: 1246614--1247408 Score: 885
Period size: 116 Copynumber: 6.7 Consensus size: 121
1246604 GAGAGCGTCT
*
1246614 TGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTT-----G--AAAGGCGTCCTG
1 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTG
* * *
1246671 CTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAATGAGAAGGTGTCC
65 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAAGTGTCC
* * *
1246729 TGCTCTTTGAGGACTGGGAA-GTGCGACCAACTTGTGTGGGCTTT-AAACAGAGAAAA--CATCC
1 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA-AGA-AAAAGGCGTCC
** *
1246790 TGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCC
63 TGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGTGTCC
* * *
1246845 TGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAATAAAAA-GCATCCTGC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGC
** * **
1246909 TCTTTGAGGACTAGAAAATGCCATCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
66 TCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGTGTCC
* * *
1246967 TGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAAGGTGTCAT
1 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAA-GAAAAAGGCGTCCT
* * *
1247031 GCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTTAAAAG-----GCGTCT
64 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGC-TTTAAAAGAAAAAGTGTCC
* * *
1247086 TACTCTTTGAGAACTGAAA---GCCACCAACTTGTGTGGGCTTTAAAAAGAAAAA-GCGTCCTGC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGC
* * * *
1247147 TTTTTGAGGACTAAAGGTGCCCCCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCC
66 TCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAAGTGTCC
* * *
1247204 TGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTGC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGC
*
1247268 TCTTTGAGGACTGGAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGTGTCC
66 TCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG--AAAAAGTGTCC
* * *
1247327 TGCTCTTTGAGGA-TTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAGAAAGGCGTCCTGC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGC
1247391 TCTTTGAGGACTGGAAGG
66 TCTTTGAGGACT-GAAGG
1247409 GCTAAAAGAG
Statistics
Matches: 593, Mismatches: 49, Indels: 67
0.84 0.07 0.09
Matches are distributed among these distances:
112 7 0.01
113 25 0.04
114 18 0.03
115 55 0.09
116 120 0.20
117 8 0.01
118 21 0.04
119 17 0.03
120 33 0.06
121 65 0.11
122 79 0.13
123 93 0.16
124 49 0.08
125 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (121 bp):
TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGC
TCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGTGTCC
Found at i:1251204 original size:13 final size:13
Alignment explanation
Indices: 1251186--1251211 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1251176 TACAGCAAGT
1251186 ATGTATCGATACA
1 ATGTATCGATACA
1251199 ATGTATCGATACA
1 ATGTATCGATACA
1251212 CAAAAAAATT
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:1253461 original size:21 final size:21
Alignment explanation
Indices: 1253428--1253472 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1253418 TTGCAAGTTG
*
1253428 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1253450 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1253470 AAA
1 AAA
1253473 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1255298 original size:15 final size:15
Alignment explanation
Indices: 1255278--1255308 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1255268 TAAAAATGTC
*
1255278 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1255293 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1255308 C
1 C
1255309 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1257398 original size:13 final size:13
Alignment explanation
Indices: 1257380--1257418 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1257370 ACATTTTTCT
1257380 TTGTATCGATACA
1 TTGTATCGATACA
1257393 TTGTATCGATACA
1 TTGTATCGATACA
1257406 TTGTATCGATACA
1 TTGTATCGATACA
1257419 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1257582 original size:20 final size:20
Alignment explanation
Indices: 1257539--1257584 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1257529 AAATCTTTTG
1257539 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1257560 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1257580 CAAAA
1 CAAAA
1257585 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1274381 original size:21 final size:21
Alignment explanation
Indices: 1274352--1274396 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1274342 AAGTTTTCAT
*
1274352 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1274372 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1274394 TTT
1 TTT
1274397 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1276628 original size:13 final size:13
Alignment explanation
Indices: 1276610--1276635 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1276600 CAATTTTTTG
1276610 TGTATCGATACAT
1 TGTATCGATACAT
1276623 TGTATCGATACAT
1 TGTATCGATACAT
1276636 ACTTGCTGTA
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:1276700 original size:21 final size:21
Alignment explanation
Indices: 1276674--1276749 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1276664 CTGCCAAGAA
1276674 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
1276695 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1276715 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1276736 ATGTATCGATACAT
1 ATGTATCGATACAT
1276750 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1276719 original size:20 final size:20
Alignment explanation
Indices: 1276694--1276767 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1276684 ACATCTTTTT
1276694 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
1276714 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
1276735 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
1276755 CATGTATCGATAC
1 CATGTATCGATAC
1276768 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:1276731 original size:41 final size:41
Alignment explanation
Indices: 1276674--1276767 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
1276664 CTGCCAAGAA
1276674 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1276715 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1276756 ATGTATCGATAC
1 ATGTATCGATAC
1276768 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1278676 original size:47 final size:47
Alignment explanation
Indices: 1278612--1278712 Score: 184
Period size: 47 Copynumber: 2.1 Consensus size: 47
1278602 ATCGATACAT
* *
1278612 TTTTCAATGTATTGATACATCTAGTTAATTTTGAGCATTTCGGGCCA
1 TTTTCAATGTATCGATACATCTAGGTAATTTTGAGCATTTCGGGCCA
1278659 TTTTCAATGTATCGATACATCTAGGTAATTTTGAGCATTTCGGGCCA
1 TTTTCAATGTATCGATACATCTAGGTAATTTTGAGCATTTCGGGCCA
1278706 TTTTCAA
1 TTTTCAA
1278713 CCTTGGCTCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.42
Consensus pattern (47 bp):
TTTTCAATGTATCGATACATCTAGGTAATTTTGAGCATTTCGGGCCA
Found at i:1279418 original size:13 final size:13
Alignment explanation
Indices: 1279400--1279424 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1279390 TTTTACAATT
1279400 TGTATCGATACAA
1 TGTATCGATACAA
1279413 TGTATCGATACA
1 TGTATCGATACA
1279425 TAAGTTTTGT
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:1281729 original size:27 final size:27
Alignment explanation
Indices: 1281699--1281754 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
1281689 ATACCAAATT
**
1281699 TTATTCATCGGGGATACTCCAACCCCA
1 TTATTCAGAGGGGATACTCCAACCCCA
* *
1281726 TTATTCCGAGGGGATACTCCAATCCCA
1 TTATTCAGAGGGGATACTCCAACCCCA
1281753 TT
1 TT
1281755 TTTGAATTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (27 bp):
TTATTCAGAGGGGATACTCCAACCCCA
Found at i:1283405 original size:13 final size:13
Alignment explanation
Indices: 1283387--1283445 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 13
1283377 AAGCTTTGGG
1283387 ATGTATCGATACA
1 ATGTATCGATACA
1283400 ATGTATCGATACA
1 ATGTATCGATACA
1283413 TTTTGGGATGTATCGATACA
1 -------ATGTATCGATACA
1283433 ATGTATCGATACA
1 ATGTATCGATACA
1283446 TATTGTGTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 26 0.67
20 13 0.33
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1283423 original size:33 final size:33
Alignment explanation
Indices: 1283381--1283465 Score: 145
Period size: 33 Copynumber: 2.6 Consensus size: 33
1283371 CGTTACAAGC
1283381 TTTGGGATGTATCGATACAATGTATCGATACAT
1 TTTGGGATGTATCGATACAATGTATCGATACAT
1283414 TTTGGGATGTATCGATACAATGTATCGATACAT
1 TTTGGGATGTATCGATACAATGTATCGATACAT
* *
1283447 ATTGTG-TGTATCGATACAA
1 TTTGGGATGTATCGATACAA
1283466 ACAGTTAAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 13 0.26
33 37 0.74
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (33 bp):
TTTGGGATGTATCGATACAATGTATCGATACAT
Found at i:1283563 original size:13 final size:13
Alignment explanation
Indices: 1283545--1283569 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1283535 TAGATTGGTC
1283545 ATGTATCGATACA
1 ATGTATCGATACA
1283558 ATGTATCGATAC
1 ATGTATCGATAC
1283570 TATGCAATCT
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:1284152 original size:22 final size:22
Alignment explanation
Indices: 1284125--1284169 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1284115 TTTTCTTTTC
1284125 TCTCCCCCTTAATCAAAA-AATT
1 TCTCCCCCTTAAT-AAAATAATT
1284147 TCTCCCCCTTAATAAAATAATT
1 TCTCCCCCTTAATAAAATAATT
1284169 T
1 T
1284170 AACAATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (22 bp):
TCTCCCCCTTAATAAAATAATT
Found at i:1285574 original size:21 final size:21
Alignment explanation
Indices: 1285543--1285594 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
1285533 GCTGCTAGTG
* *
1285543 TGGGGGCTGCCCGGTTGCGACT
1 TGGGGG-TGCCCGGTCGCGACC
1285565 TGGGGGTG-CCGGTCGCGACC
1 TGGGGGTGCCCGGTCGCGACC
1285585 TGGTGGGTGC
1 TGG-GGGTGC
1285595 TACCTAGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 13 0.50
21 7 0.27
22 6 0.23
ACGTcount: A:0.04, C:0.25, G:0.50, T:0.21
Consensus pattern (21 bp):
TGGGGGTGCCCGGTCGCGACC
Found at i:1292112 original size:13 final size:13
Alignment explanation
Indices: 1292094--1292119 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1292084 ACATTTTGGG
1292094 ATGTATCGATACA
1 ATGTATCGATACA
1292107 ATGTATCGATACA
1 ATGTATCGATACA
1292120 TATTGTGTGT
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:1292114 original size:33 final size:32
Alignment explanation
Indices: 1292072--1292139 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
1292062 CGTTACAAGG
*
1292072 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCGATA
*
1292105 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGGGTGTATCGATA
1292137 CAA
1 CAA
1292140 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCGATA
Found at i:1292227 original size:20 final size:21
Alignment explanation
Indices: 1292180--1292231 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1292170 GCCAATGACC
*
1292180 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
1292201 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
1292221 TGTATCGATAC
1 TGTATCGATAC
1292232 TGTGCAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:1297417 original size:20 final size:20
Alignment explanation
Indices: 1297384--1297550 Score: 111
Period size: 20 Copynumber: 7.8 Consensus size: 20
1297374 TTTTTACCCA
*
1297384 AATGTATTGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * * *
1297404 AATATATCGATACATGTATG
1 AATGTATCGATACATTTTTC
*
1297424 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTTTTC
*
1297444 AATGTATTGATACATTCTATCTTTTTACCC
1 AATGTATCGAT--A--C-A--TTTTT---C
*
1297474 AGATGTATGGATACATTTTTC
1 A-ATGTATCGATACATTTTTC
* * * *
1297495 AATATATCGATACATGTATG
1 AATGTATCGATACATTTTTC
1297515 AATGTATCGATACATTCTTT-
1 AATGTATCGATACATT-TTTC
1297535 AATGTATCGATACATT
1 AATGTATCGATACATT
1297551 CTGTCTTTTT
Statistics
Matches: 114, Mismatches: 21, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
20 84 0.74
21 4 0.04
22 1 0.01
24 6 0.05
25 1 0.01
26 1 0.01
27 5 0.04
29 1 0.01
30 2 0.02
31 9 0.08
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:1297439 original size:40 final size:40
Alignment explanation
Indices: 1297384--1297549 Score: 145
Period size: 40 Copynumber: 3.9 Consensus size: 40
1297374 TTTTTACCCA
*
1297384 AATGTATTGATACATTTTTCAATATATCGATACATGTATG
1 AATGTATCGATACATTTTTCAATATATCGATACATGTATG
* * * * *
1297424 AATGTATCGATACATTCTTCAATGTATTGATACATTCTATCTTTTTACCC
1 AATGTATCGATACATTTTTCAATATATCGATACA-TGTA------T---G
*
1297474 AGATGTATGGATACATTTTTCAATATATCGATACATGTATG
1 A-ATGTATCGATACATTTTTCAATATATCGATACATGTATG
*
1297515 AATGTATCGATACATTCTTT-AATGTATCGATACAT
1 AATGTATCGATACATT-TTTCAATATATCGATACAT
1297550 TCTGTCTTTT
Statistics
Matches: 100, Mismatches: 14, Indels: 24
0.72 0.10 0.17
Matches are distributed among these distances:
40 58 0.58
41 7 0.07
44 1 0.01
47 1 0.01
50 4 0.04
51 29 0.29
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.42
Consensus pattern (40 bp):
AATGTATCGATACATTTTTCAATATATCGATACATGTATG
Found at i:1297507 original size:51 final size:51
Alignment explanation
Indices: 1297425--1297600 Score: 187
Period size: 51 Copynumber: 3.7 Consensus size: 51
1297415 ACATGTATGA
* *
1297425 ATGTATCGATACATTCTTCAATGTATTGATACATTCTATCTTTTTACCCAG
1 ATGTATCGATACATTTTTCAATGTATCGATACATTCTATCTTTTTACCCAG
* * * *
1297476 ATGTATGGATACATTTTTCAATATATCGATACA-TGTA------T---GA-
1 ATGTATCGATACATTTTTCAATGTATCGATACATTCTATCTTTTTACCCAG
*
1297516 ATGTATCGATACATTCTTT-AATGTATCGATACATTCTGTCTTTTTACCCAG
1 ATGTATCGATACATT-TTTCAATGTATCGATACATTCTATCTTTTTACCCAG
*
1297567 ATGTATCGATACATTTTTCAATGTATCAATACAT
1 ATGTATCGATACATTTTTCAATGTATCGATACAT
1297601 CTAGTTAAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
40 27 0.27
41 6 0.06
44 1 0.01
47 1 0.01
50 7 0.07
51 58 0.58
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.42
Consensus pattern (51 bp):
ATGTATCGATACATTTTTCAATGTATCGATACATTCTATCTTTTTACCCAG
Found at i:1297529 original size:91 final size:91
Alignment explanation
Indices: 1297374--1297600 Score: 382
Period size: 91 Copynumber: 2.5 Consensus size: 91
1297364 AAAAATCATA
* *
1297374 TTTTTACCCAAATGTATTGATACATTTTTCAATATATCGATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATATATCGATACATGTATGAATGTATCGATACAT
*
1297439 TCTTCAATGTATTGATACATTCTATC
66 TCTTCAATGTATCGATACATTCTATC
*
1297465 TTTTTACCCAGATGTATGGATACATTTTTCAATATATCGATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATATATCGATACATGTATGAATGTATCGATACAT
* *
1297530 TCTTTAATGTATCGATACATTCTGTC
66 TCTTCAATGTATCGATACATTCTATC
* *
1297556 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCAATACAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATATATCGATACAT
1297601 CTAGTTAAAA
Statistics
Matches: 128, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 128 1.00
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (91 bp):
TTTTTACCCAGATGTATCGATACATTTTTCAATATATCGATACATGTATGAATGTATCGATACAT
TCTTCAATGTATCGATACATTCTATC
Found at i:1311338 original size:14 final size:13
Alignment explanation
Indices: 1311253--1311340 Score: 81
Period size: 14 Copynumber: 6.6 Consensus size: 13
1311243 CAGTTCGCCA
1311253 TTTGTCAAGAAAT
1 TTTGTCAAGAAAT
*
1311266 GGTTGTCAAGAAAT
1 -TTTGTCAAGAAAT
*
1311280 TATTGTCAAGAACT
1 T-TTGTCAAGAAAT
*
1311294 TTTGTCGAG-AAT
1 TTTGTCAAGAAAT
* *
1311306 GTTCGTC-AGAAAC
1 -TTTGTCAAGAAAT
1311319 TTTGTCAAGAAAAT
1 TTTGTCAAG-AAAT
1311333 TTTGTCAA
1 TTTGTCAA
1311341 TACGACCTCT
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
12 9 0.15
13 16 0.27
14 35 0.58
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.35
Consensus pattern (13 bp):
TTTGTCAAGAAAT
Found at i:1311397 original size:28 final size:28
Alignment explanation
Indices: 1311349--1311836 Score: 528
Period size: 28 Copynumber: 17.6 Consensus size: 28
1311339 AATACGACCT
* *
1311349 CTTTTCAAAGCTCACTAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
1311377 CTTTTCAAAGCCCATATGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
*
1311406 C-TTTCAAAGCCCACAAGTTAGTGGCA-
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
1311432 TTCTTTCGAAGCCCATAAGTCAGTGGCAT
1 CT-TTTCAAAGCCCACAAGTCAGTGGCAC
* *
1311461 C-TTTCAAAGCTCACAAGTCAATGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
1311488 CTTCTCAAAGCCCACAAGTCAATGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
1311516 CTTTTCAAAGCCCACATGTCAGTGGTATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
1311545 C-TTTCAAAGCCCACAAGTTAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * *
1311572 CTTCTCAAAGCCCATATGTAAGTGGCTC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
1311600 C-TTTCAAAGCCCACAAGTCAGTGACAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
1311627 CCTTTCAAAGCCCACAAGTCAGCGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
1311656 C-TTTCAAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * *
1311683 CTTCTC-AAGCTCATATGTTAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
1311711 C-TTTCAAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
1311738 CTTTTCAAAGCCCACAAGTCAGTGGAAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
1311766 ATTTTTAAAGCCCACAAGTTAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
1311794 CTTTTCAAAG-CCACAAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
1311822 C-TTTCAAAGCCCACA
1 CTTTTCAAAGCCCACA
1311837 CAAGTCGATG
Statistics
Matches: 381, Mismatches: 64, Indels: 30
0.80 0.13 0.06
Matches are distributed among these distances:
27 90 0.24
28 286 0.75
29 5 0.01
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.25
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:1311505 original size:83 final size:83
Alignment explanation
Indices: 1311351--1311836 Score: 551
Period size: 83 Copynumber: 5.8 Consensus size: 83
1311341 TACGACCTCT
* * * * *
1311351 TTTCAAAGCTCACTAGTCAGTGGCACCTTTTCAAAGCCCATATGTCAGTGGCATCCTTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCATC-TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
*
1311416 CCACAAGTTAGTGGCATTC
65 CCACAAGTCAGTGGCATTC
* * * *
1311435 TTTCGAAGCCCATAAGTCAGTGGCATCTTTCAAAGCTCACAAGTCAATGGCA-CCTTCTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCATCTTTCAAAGCCCACAAGTCAGTGGCATCCTT-TCAAAGC
*
1311499 CCACAAGTCAATGGCA-TC
65 CCACAAGTCAGTGGCATTC
* * *
1311517 TTTTCAAAGCCCACATGTCAGTGGTATCCTTTCAAAGCCCACAAGTTAGTGGCAT-CTTCTCAAA
1 -TTTCAAAGCCCACAAGTCAGTGGCAT-CTTTCAAAGCCCACAAGTCAGTGGCATCCTT-TCAAA
* * * *
1311581 GCCCATATGTAAGTGGC-TCC
63 GCCCACAAGTCAGTGGCATTC
* * *
1311601 TTTCAAAGCCCACAAGTCAGTGACACCCTTTCAAAGCCCACAAGTCAGCGGCATCCTTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCA-TCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
*
1311666 CCACAAGTCAGTGGCA-CC
65 CCACAAGTCAGTGGCATTC
* * * *
1311684 TTCTC-AAGCTCATATGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAA
1 TT-TCAAAGCCCACAAGTCAGTGGCAT-CTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAA
1311747 GCCCACAAGTCAGTGGAACATT-
63 GCCCACAAGTCAGTGG--CATTC
*
1311769 TTT-AAAGCCCACAAGTTAGTGGCATCTTTTCAAAG-CCACAAGTCAGTGGCATCCTTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCATC-TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
1311832 CCACA
65 CCACA
1311837 CAAGTCGATG
Statistics
Matches: 342, Mismatches: 43, Indels: 35
0.81 0.10 0.08
Matches are distributed among these distances:
82 8 0.02
83 228 0.67
84 102 0.30
85 4 0.01
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (83 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
CACAAGTCAGTGGCATTC
Found at i:1311549 original size:111 final size:110
Alignment explanation
Indices: 1311351--1311836 Score: 604
Period size: 111 Copynumber: 4.4 Consensus size: 110
1311341 TACGACCTCT
* * *
1311351 TTTCAAAGCTCACTAGTCAGTGGCACCTTTTCAAAGCCCATATGTCAGTGGCATCC-TTTCAAAG
1 TTTCAAAGCTCACAAGTCAGTGGCACC-TTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAG
* * * *
1311415 CCCACAAGTTAGTGGCATTCTTTCGAAGCCCATAAGTCAGTGGCATC
64 CCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATC
* * *
1311462 TTTCAAAGCTCACAAGTCAATGGCACCTTCTCAAAGCCCACAAGTCAATGGCATCTTTTCAAAGC
1 TTTCAAAGCTCACAAGTCAGTGGCACCTT-TCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGC
* * *
1311527 CCACATGTCAGTGGTATCCTTTCAAAGCCCACAAGTTAGTGGCATC
65 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATC
* * * * * * *
1311573 TTCTCAAAGCCCATATGTAAGTGGCTCCTTTCAAAGCCCACAAGTCAGTGACACCCTTTCAAAGC
1 TT-TCAAAGCTCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGC
* *
1311638 CCACAAGTCAGCGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACC
65 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATC
* * *
1311684 TTCTC-AAGCTCATATGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAG
1 TT-TCAAAGCTCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAG
* *
1311748 CCCACAAGTCAGTGGAACAT--TTTTAAAGCCCACAAGTTAGTGGCATC
64 CCCACAAGTCAGTGG--CATCCTTTCAAAGCCCACAAGTCAGTGGCATC
1311795 TTTTCAAAGC-CACAAGTCAGTGGCATCCTTTCAAAGCCCACA
1 -TTTCAAAGCTCACAAGTCAGTGGCA-CCTTTCAAAGCCCACA
1311837 CAAGTCGATG
Statistics
Matches: 327, Mismatches: 40, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
110 20 0.06
111 277 0.85
112 27 0.08
113 3 0.01
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (110 bp):
TTTCAAAGCTCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
CACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATC
Found at i:1311604 original size:139 final size:137
Alignment explanation
Indices: 1311351--1311836 Score: 638
Period size: 139 Copynumber: 3.5 Consensus size: 137
1311341 TACGACCTCT
* * * * *
1311351 TTTCAAAGCTCACTAGTCAGTGGCACCTTTTCAAAGCCCATATGTCAGTGGCATCCTTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
* *
1311416 CCACAAGTTAGTGGCATTCTTTCGAAGCCCATAAGTCAGTGGCAT-CTTTCAAAGCTCACAAGTC
66 CCACAAGTTAGTGGCA-TCTTTCAAAGCCCATAAGTCAGTGGC-TCCTTTCAAAGCCCACAAGTC
*
1311480 AATGGCACC
129 AGTGGCACC
* * *
1311489 TTCTCAAAGCCCACAAGTCAATGGCATCTTTTCAAAGCCCACATGTCAGTGGTATCCTTTCAAAG
1 TT-TCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG
* *
1311554 CCCACAAGTTAGTGGCATCTTCTCAAAGCCCATATGTAAGTGGCTCCTTTCAAAGCCCACAAGTC
65 CCCACAAGTTAGTGGCATCTT-TCAAAGCCCATAAGTCAGTGGCTCCTTTCAAAGCCCACAAGTC
*
1311619 AGTGACACCC
129 AGTGGCA-CC
* *
1311629 TTTCAAAGCCCACAAGTCAGCGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTCTC-AAG
1 TTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTT-TCAAAG
* * * * *
1311692 CTCATATGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGT
65 CCCACAAGTTAGTGGCAT-CTTTCAAAGCCCATAAGTCAGTGGCTCC-TTTCAAAGCCCACAAGT
* *
1311757 CAGTGGAACAT
128 CAGTGGCAC-C
* *
1311768 TTTTAAAGCCCACAAGTTAGTGGCATCTTTTCAAAG-CCACAAGTCAGTGGCATCCTTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
1311832 CCACA
66 CCACA
1311837 CAAGTCGATG
Statistics
Matches: 305, Mismatches: 33, Indels: 19
0.85 0.09 0.05
Matches are distributed among these distances:
138 69 0.23
139 232 0.76
140 4 0.01
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (137 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
CCACAAGTTAGTGGCATCTTTCAAAGCCCATAAGTCAGTGGCTCCTTTCAAAGCCCACAAGTCAG
TGGCACC
Found at i:1313892 original size:20 final size:20
Alignment explanation
Indices: 1313854--1313892 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1313844 TATCCTTTGA
*
1313854 TCATGCATTTTCACTATGTT
1 TCATGCATTTTAACTATGTT
1313874 TCATGCATTGTTAAC-ATGT
1 TCATGCATT-TTAACTATGT
1313893 CTGGCATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (20 bp):
TCATGCATTTTAACTATGTT
Found at i:1325990 original size:21 final size:19
Alignment explanation
Indices: 1325966--1326019 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 19
1325956 TTTCAACAAT
1325966 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAA-AGT-A
* *
1325987 TTGTATCGATACATAAGTG
1 TTGTATCGATACAAAAGTA
1326006 TTGTATCGATACAA
1 TTGTATCGATACAA
1326020 TGTATCGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (19 bp):
TTGTATCGATACAAAAGTA
Found at i:1326011 original size:19 final size:19
Alignment explanation
Indices: 1325966--1326050 Score: 83
Period size: 19 Copynumber: 4.7 Consensus size: 19
1325956 TTTCAACAAT
* *
1325966 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACATA-AGT-G
1325987 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1326006 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
1326020 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
1326038 TTGTATCAATACA
1 TTGTATCGATACA
1326051 ATGTATCGAT
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
13 11 0.20
15 2 0.04
17 2 0.04
19 23 0.42
20 3 0.05
21 14 0.25
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1326025 original size:13 final size:13
Alignment explanation
Indices: 1326007--1326096 Score: 66
Period size: 13 Copynumber: 6.9 Consensus size: 13
1325997 ACATAAGTGT
1326007 TGTATCGATACAA
1 TGTATCGATACAA
1326020 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
1326035 GTGTTGTATCAATACAA
1 ----TGTATCGATACAA
1326052 TGTATCGATAC-A
1 TGTATCGATACAA
1326064 T-TA-C--T-CAA
1 TGTATCGATACAA
*
1326072 TGTATCGATACAT
1 TGTATCGATACAA
1326085 TGTATCGATACA
1 TGTATCGATACA
1326097 TTAATCTTTG
Statistics
Matches: 62, Mismatches: 3, Indels: 24
0.70 0.03 0.27
Matches are distributed among these distances:
7 1 0.02
8 3 0.05
9 2 0.03
10 2 0.03
11 2 0.03
12 3 0.05
13 35 0.56
15 2 0.03
17 2 0.03
19 10 0.16
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1326029 original size:32 final size:33
Alignment explanation
Indices: 1325988--1326116 Score: 165
Period size: 32 Copynumber: 4.0 Consensus size: 33
1325978 AAACAGTAAT
1325988 TGTATCGATACATAAGT-GTTGTATCGATACAA
1 TGTATCGATACATAAGTCGTTGTATCGATACAA
*
1326020 TGTATCGATACATAAGT-GTTGTATCAATACAA
1 TGTATCGATACATAAGTCGTTGTATCGATACAA
* * ** *
1326052 TGTATCGATACATTACTCAATGTATCGATACAT
1 TGTATCGATACATAAGTCGTTGTATCGATACAA
*
1326085 TGTATCGATACATTAA-TCTTTGTATCGATACA
1 TGTATCGATACA-TAAGTCGTTGTATCGATACA
1326117 TGCATGCAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
32 46 0.54
33 37 0.44
34 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAGTCGTTGTATCGATACAA
Found at i:1326711 original size:13 final size:13
Alignment explanation
Indices: 1326693--1326718 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1326683 TACACAAAGT
1326693 ATGTATCGATACA
1 ATGTATCGATACA
1326706 ATGTATCGATACA
1 ATGTATCGATACA
1326719 TAAAAAATTG
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:1326716 original size:32 final size:33
Alignment explanation
Indices: 1326675--1326738 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1326665 TAGCCAAACT
**
1326675 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
*
1326707 TGTATCGATACATAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1326739 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1328969 original size:22 final size:21
Alignment explanation
Indices: 1328944--1328995 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
1328934 TTGCAAGTTG
1328944 AAATAAAAAATTTAGCTAATG-A
1 AAATAAAAAA-TTAGCTAA-GAA
**
1328966 AAATAATGAATTAGCTAAGAA
1 AAATAAAAAATTAGCTAAGAA
1328987 AAATAAAAA
1 AAATAAAAA
1328996 CTTGCATGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 16 0.64
22 8 0.32
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.23
Consensus pattern (21 bp):
AAATAAAAAATTAGCTAAGAA
Found at i:1330810 original size:15 final size:15
Alignment explanation
Indices: 1330790--1330820 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1330780 TAAAAATGTC
*
1330790 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1330805 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1330820 C
1 C
1330821 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1332920 original size:13 final size:13
Alignment explanation
Indices: 1332902--1332939 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1332892 CATTTTTCTT
1332902 TGTATCGATACAA
1 TGTATCGATACAA
*
1332915 TGTATCGATACAC
1 TGTATCGATACAA
1332928 TGTATCGATACA
1 TGTATCGATACA
1332940 GGGGGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1333417 original size:21 final size:20
Alignment explanation
Indices: 1333380--1333422 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1333370 GCAGCACCCA
*
1333380 CCAGGTCACGACCGGCACTC
1 CCAGGTCACAACCGGCACTC
* *
1333400 CCAGGTCGCAACCTGGCAGTC
1 CCAGGTCACAACC-GGCACTC
1333421 CC
1 CC
1333423 CATACTAGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.19, C:0.44, G:0.26, T:0.12
Consensus pattern (20 bp):
CCAGGTCACAACCGGCACTC
Found at i:1333701 original size:156 final size:157
Alignment explanation
Indices: 1333417--1333729 Score: 553
Period size: 156 Copynumber: 2.0 Consensus size: 157
1333407 GCAACCTGGC
*
1333417 AGTCCCCATACTAGCCGCCTAGTTCATCCGAAAAACCTCGATTTTACGCCAAAACACTTTCGATT
1 AGTCCCCATACTACCCGCCTAGTTCATCCGAAAAACCTCGATTTTACGCCAAAACACTTTCGATT
*
1333482 CATTTCGATGGCCCCTCGGATGAAATCTACAGCTCAAAAACGTCTCGATGTGCCTCCACCTCG-A
66 CATTTCGATGGCCCCTCGGATGAAATCTACAGCTCAAAAACGTCTCGAGGTGCCTCCACCTCGAA
1333546 TCCACCAAAATCAAA-CTTCTTCGAAGG
131 TCCA-CAAAATCAAACCTTCTTCGAAGG
1333573 AGTCCCCATACTAACCCGCCTAGTTCATCCGAAAAACCTCGATTTTACGCCAAAAACACTTTCGA
1 AGTCCCCATACT-ACCCGCCTAGTTCATCCGAAAAACCTCGATTTTACGCC-AAAACACTTTCGA
1333638 -TCA-TTCGATGGCCCCTCGGATGAAATCTACAGCTCAAAAACGTCTCGAGGTGCCTCCACCTCG
64 TTCATTTCGATGGCCCCTCGGATGAAATCTACAGCTCAAAAACGTCTCGAGGTGCCTCCACCTCG
1333701 AATCCACAAAATCAAACCTTCTTCGAAGG
129 AATCCACAAAATCAAACCTTCTTCGAAGG
1333730 TTGTTTTCGT
Statistics
Matches: 151, Mismatches: 2, Indels: 7
0.94 0.01 0.04
Matches are distributed among these distances:
156 81 0.54
157 57 0.38
158 13 0.09
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (157 bp):
AGTCCCCATACTACCCGCCTAGTTCATCCGAAAAACCTCGATTTTACGCCAAAACACTTTCGATT
CATTTCGATGGCCCCTCGGATGAAATCTACAGCTCAAAAACGTCTCGAGGTGCCTCCACCTCGAA
TCCACAAAATCAAACCTTCTTCGAAGG
Found at i:1334747 original size:22 final size:20
Alignment explanation
Indices: 1334705--1334747 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
1334695 GTGTTTAATG
*
1334705 TATTTGCTTGACTTTGTTTT
1 TATTTGCTTGACTTTGATTT
1334725 TATTTGCATTGTACTTTGATTT
1 TATTTGC-TTG-ACTTTGATTT
1334747 T
1 T
1334748 TTAATCTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 3 0.15
22 10 0.50
ACGTcount: A:0.14, C:0.09, G:0.14, T:0.63
Consensus pattern (20 bp):
TATTTGCTTGACTTTGATTT
Found at i:1335634 original size:13 final size:13
Alignment explanation
Indices: 1335616--1335641 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1335606 TACACAAAGT
1335616 ATGTATCGATACA
1 ATGTATCGATACA
1335629 ATGTATCGATACA
1 ATGTATCGATACA
1335642 CAAAAAATTG
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:1335639 original size:32 final size:33
Alignment explanation
Indices: 1335598--1335661 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1335588 TAGCCAAACT
**
1335598 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1335630 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1335662 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1342269 original size:58 final size:56
Alignment explanation
Indices: 1342176--1342295 Score: 197
Period size: 58 Copynumber: 2.1 Consensus size: 56
1342166 TACATAATAG
1342176 GCTTTTAAAAATTCTGATTTCATGGTCGAACATTGCCAAAGGAAATTCCTTAATTTGA
1 GCTTTTAAAAATTCTGATTTCATGGTCGAACATTGCCAAAGGAAATTCCTTAA--TGA
*
1342234 GCTTTTAAAAATTCTGATTTCATGGTC-AGATATTGCCAAAGGAAATTCCTTAATGA
1 GCTTTTAAAAATTCTGATTTCATGGTCGA-ACATTGCCAAAGGAAATTCCTTAATGA
1342290 GCTTTT
1 GCTTTT
1342296 TGCATCTGTT
Statistics
Matches: 60, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
56 9 0.15
57 1 0.02
58 50 0.83
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.38
Consensus pattern (56 bp):
GCTTTTAAAAATTCTGATTTCATGGTCGAACATTGCCAAAGGAAATTCCTTAATGA
Found at i:1346407 original size:13 final size:13
Alignment explanation
Indices: 1346389--1346452 Score: 92
Period size: 13 Copynumber: 4.9 Consensus size: 13
1346379 ATAATCCCCC
1346389 TGTATCGATACAG
1 TGTATCGATACAG
*
1346402 TGTATCGATACAT
1 TGTATCGATACAG
*
1346415 TATATCGATACAG
1 TGTATCGATACAG
*
1346428 TGTATCGATACAT
1 TGTATCGATACAG
*
1346441 TATATCGATACA
1 TGTATCGATACA
1346453 AAGAAAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1346420 original size:26 final size:26
Alignment explanation
Indices: 1346391--1346452 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
1346381 AATCCCCCTG
1346391 TATCGATACAGTGTATCGATACATTA
1 TATCGATACAGTGTATCGATACATTA
1346417 TATCGATACAGTGTATCGATACATTA
1 TATCGATACAGTGTATCGATACATTA
1346443 TATCGATACA
1 TATCGATACA
1346453 AAGAAAAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (26 bp):
TATCGATACAGTGTATCGATACATTA
Found at i:1348554 original size:15 final size:15
Alignment explanation
Indices: 1348534--1348564 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1348524 ATTTCGTTTG
*
1348534 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1348549 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1348564 G
1 G
1348565 GACATTTTTA
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:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1352627 original size:13 final size:13
Alignment explanation
Indices: 1352609--1352634 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1352599 CAATTTTTTG
1352609 TGTATCGATACAT
1 TGTATCGATACAT
1352622 TGTATCGATACAT
1 TGTATCGATACAT
1352635 ACTTGGTGTA
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:1352649 original size:32 final size:33
Alignment explanation
Indices: 1352589--1352652 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1352579 TACAAGCCAA
** *
1352589 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1352622 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1352653 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1354899 original size:20 final size:20
Alignment explanation
Indices: 1354869--1354980 Score: 120
Period size: 20 Copynumber: 5.6 Consensus size: 20
1354859 GTACCTAGAC
1354869 GTATCGATACATTTTTCAAT
1 GTATCGATACATTTTTCAAT
* * *
1354889 GTAAT-GATACATGTATGAAT
1 GT-ATCGATACATTTTTCAAT
*
1354909 GTATCGATACATTCTTCAAT
1 GTATCGATACATTTTTCAAT
1354929 GTATCGATACATTTTTCAAT
1 GTATCGATACATTTTTCAAT
****
1354949 GTAAT-GATACATTGAAAAAT
1 GT-ATCGATACATTTTTCAAT
1354969 GTATCGATACAT
1 GTATCGATACAT
1354981 CTAGTTAAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
19 4 0.05
20 68 0.89
21 4 0.05
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.38
Consensus pattern (20 bp):
GTATCGATACATTTTTCAAT
Found at i:1365945 original size:15 final size:15
Alignment explanation
Indices: 1365925--1365961 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1365915 TATCAAACCT
1365925 GCCAGTGTTGATACC
1 GCCAGTGTTGATACC
1365940 GCCAGTGTTGATACC
1 GCCAGTGTTGATACC
*
1365955 GTCAGTG
1 GCCAGTG
1365962 CTTGGTTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (15 bp):
GCCAGTGTTGATACC
Found at i:1371332 original size:19 final size:20
Alignment explanation
Indices: 1371300--1371356 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
1371290 TTGTATCAAT
* *
1371300 ACAA-TGTATTGATACATGC
1 ACAATTGTATCGATACATGA
*
1371319 TC-ATTGTATCGATACATGA
1 ACAATTGTATCGATACATGA
*
1371338 ACAATTGCATCGATACATG
1 ACAATTGTATCGATACATG
1371357 GAACTGGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 15 0.48
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (20 bp):
ACAATTGTATCGATACATGA
Found at i:1373487 original size:15 final size:15
Alignment explanation
Indices: 1373466--1373503 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
1373456 AAATAAATAA
1373466 AAAATTATTGAAAATG
1 AAAATTATTGAAAA-G
1373482 -AAATTATTGAAAAG
1 AAAATTATTGAAAAG
1373496 AAAATTAT
1 AAAATTAT
1373504 CGAACTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.32
Consensus pattern (15 bp):
AAAATTATTGAAAAG
Found at i:1377051 original size:50 final size:51
Alignment explanation
Indices: 1376976--1377114 Score: 203
Period size: 50 Copynumber: 2.8 Consensus size: 51
1376966 TTTCACAATT
* * *
1376976 TGTATTGATACATCCTTCATTGTATCGATACATTCTAGGTCTT-ACCTAGA
1 TGTATCGATACATCTTTCATTGTATCGATACATTCTAGGTCTTAACCCAGA
*
1377026 TGTATCGATACATCTTTCATTGTATCGATACATTCTAGGTTTTAACCCAGA
1 TGTATCGATACATCTTTCATTGTATCGATACATTCTAGGTCTTAACCCAGA
*
1377077 TGTATCGATACAT-TTCTCAATGTATCGATACATT-TAGG
1 TGTATCGATACATCTT-TCATTGTATCGATACATTCTAGG
1377115 CATTTTTGAC
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
50 46 0.56
51 36 0.44
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (51 bp):
TGTATCGATACATCTTTCATTGTATCGATACATTCTAGGTCTTAACCCAGA
Found at i:1391768 original size:22 final size:22
Alignment explanation
Indices: 1391743--1391791 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1391733 ATATATAGTG
*
1391743 ATGAACAATGATATATTGATAC
1 ATGAACAATGATATATCGATAC
* *
1391765 ATGAACAGTGATGTATCGATAC
1 ATGAACAATGATATATCGATAC
1391787 ATGAA
1 ATGAA
1391792 TAGTAATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (22 bp):
ATGAACAATGATATATCGATAC
Found at i:1393477 original size:120 final size:121
Alignment explanation
Indices: 1393207--1393843 Score: 680
Period size: 120 Copynumber: 5.3 Consensus size: 121
1393197 TTTCGAGCAT
* * * * * *
1393207 AAGTTGGTGGCATCTTTCAGTCCTTAAAGAGTATGACGCATTTTTC-TTTAAAGCCCACACAAGT
1 AAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGT
* * * * * * *
1393271 TGGTGGTACCTTTCAATCCTCAAAGAACAAGATGTCTTTTCCTTTTAAAGCCCACAC
66 TGGTGGCACCTTTCAGTCCTTAAAGAGCAGGACG-CTTTTCCTTTCAAAGCCCACAC
* * * * *
1393328 AAGTTGGTGGCATCTTTCAGTACTTAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAAGT
1 AAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGT
* *
1393393 TGGTGGCACCTTCCAATCCTTAAAGAGCAGGACGC-TTTCCTTTCAAAGCCCACAC
66 TGGTGGCACCTTTCAGTCCTTAAAGAGCAGGACGCTTTTCCTTTCAAAGCCCACAC
* * * *
1393448 AAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGAACACCTTTTCCTTTTAAAGCCCACATAAGT
1 AAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGT
* * * * *
1393513 TAGTGGCACCTTTCAGTCCATAAAGAGAAGGACACTTTTTCCTTT-AAGGCCCACAC
66 TGGTGGCACCTTTCAGTCCTTAAAGAGCAGGACGC-TTTTCCTTTCAAAGCCCACAC
* * ** *
1393569 AAG-TGGCTGGCACCTTTCAGTCCTCAAAGAGAAAGACGTATTTTCCTCTTAAAGCCCACACAAG
1 AAGTTGG-TGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAG
* * * * *
1393633 TTGGTGGCATCTTTCAGTACTTAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCATAC
65 TTGGTGGCACCTTTCAGTCCTTAAAGAGCAGGAC-GCTTTTCCTTTCAAAGCCCACAC
* * * * *
1393691 AAGTTGGTGACACC-TTCTGGTCCTCAAAGAGCAGGAC-AC-TTTACTTTCAAAGCCCACACAAG
1 AAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAG
* * * * * * *
1393753 TTGGTGACACC-TTCTAGTCCTCAAAGAGTAGGATGCATTCTCCTTACAAAGCCCATAC
65 TTGGTGGCACCTTTC-AGTCCTTAAAGAGCAGGACGC-TTTTCCTTTCAAAGCCCACAC
1393811 AAGTTGGTGGCACC-TTCTAGTCCTCAAAGAGCA
1 AAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCA
1393844 TGATGCACTT
Statistics
Matches: 440, Mismatches: 66, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
119 4 0.01
120 200 0.45
121 144 0.33
122 89 0.20
123 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (121 bp):
AAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGT
TGGTGGCACCTTTCAGTCCTTAAAGAGCAGGACGCTTTTCCTTTCAAAGCCCACAC
Found at i:1393806 original size:302 final size:302
Alignment explanation
Indices: 1393204--1393826 Score: 874
Period size: 302 Copynumber: 2.1 Consensus size: 302
1393194 GCCTTTCGAG
* * * * *
1393204 CATAAGTTGGTGGCATCTTTCAGTCCTTAAAGAGTATGACGCATTTTTCTTTAAAGCCCACACAA
1 CATAAGTTGGTGGCACCTTTCAGTCCATAAAGAGAAGGACACATTTTTCTTTAAAGCCCACACAA
* * * *
1393269 GTTGGTGGTACCTTTCAATCCTCAAAGAACAAGATGTCTTTTCCTTTTAAAGCCCACACAAGTTG
66 GTTGGTGGCACCTTTCAATCCTCAAAGAACAAGACGTATTTTCCTCTTAAAGCCCACACAAGTTG
* ** *
1393334 GTGGCATCTTTCAGTACTTAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
131 GTGGCATCTTTCAGTACTTAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGA
* * * *
1393399 CACCTTCCAATCCTTAAAGAGCAGGACGCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
196 CACCTTCCAATCCTCAAAGAGCAGGACACTTTACTTTCAAAGCCCACACAAGTTGGTGACACCTT
* * * **
1393464 TTAGTCCTCAAAGAGCAGAACACCTTTTCCTTTTAAAGCCCA
261 CTAGTCCTCAAAGAGCAGAACACATTCTCCTTACAAAGCCCA
* *
1393506 CATAAGTTAGTGGCACCTTTCAGTCCATAAAGAGAAGGACAC-TTTTTCCTTTAAGGCCCACACA
1 CATAAGTTGGTGGCACCTTTCAGTCCATAAAGAGAAGGACACATTTTT-CTTTAAAGCCCACACA
*
1393570 AG-TGGCTGGCACCTTTCAGTCCTCAAAGAGA-AAGACGTATTTTCCTCTTAAAGCCCACACAAG
65 AGTTGG-TGGCACCTTTCAATCCTCAAAGA-ACAAGACGTATTTTCCTCTTAAAGCCCACACAAG
* *
1393633 TTGGTGGCATCTTTCAGTACTTAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCATACAAGTTGG
128 TTGGTGGCATCTTTCAGTACTTAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGG
***
1393698 TGACACCTTCTGGTCCTCAAAGAGCAGGACACTTTACTTTCAAAGCCCACACAAGTTGGTGACAC
193 TGACACCTTCCAATCCTCAAAGAGCAGGACACTTTACTTTCAAAGCCCACACAAGTTGGTGACAC
* * **
1393763 CTTCTAGTCCTCAAAGAGTAGGATGCATTCTCCTTACAAAGCCCA
258 CTTCTAGTCCTCAAAGAGCAGAACACATTCTCCTTACAAAGCCCA
* *
1393808 TACAAGTTGGTGGCACCTT
1 CATAAGTTGGTGGCACCTT
1393827 CTAGTCCTCA
Statistics
Matches: 281, Mismatches: 37, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
301 8 0.03
302 272 0.97
303 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (302 bp):
CATAAGTTGGTGGCACCTTTCAGTCCATAAAGAGAAGGACACATTTTTCTTTAAAGCCCACACAA
GTTGGTGGCACCTTTCAATCCTCAAAGAACAAGACGTATTTTCCTCTTAAAGCCCACACAAGTTG
GTGGCATCTTTCAGTACTTAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGA
CACCTTCCAATCCTCAAAGAGCAGGACACTTTACTTTCAAAGCCCACACAAGTTGGTGACACCTT
CTAGTCCTCAAAGAGCAGAACACATTCTCCTTACAAAGCCCA
Found at i:1393850 original size:61 final size:61
Alignment explanation
Indices: 1393207--1393843 Score: 661
Period size: 61 Copynumber: 10.5 Consensus size: 61
1393197 TTTCGAGCAT
* * * * *
1393207 AAGTTGGTGGCATCTTTCAGTCCTTAAAGAGTATGACGCATTTTTC-TTTAAAGCCCACAC
1 AAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCATTTTCCTTTTAAAGCCCACAC
* * * * *
1393267 AAGTTGGTGGTACCTTTCAATCCTCAAAGAACAAGATGTC-TTTTCCTTTTAAAGCCCACAC
1 AAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG-CATTTTCCTTTTAAAGCCCACAC
* * * * * *
1393328 AAGTTGGTGGCATCTTTCAGTACTTAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACAC
1 AAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCATTTTCCTTTTAAAGCCCACAC
* * * *
1393389 AAGTTGGTGGCACCTTCCAATCCTTAAAGAGCAGGACGC--TTTCCTTTCAAAGCCCACAC
1 AAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCATTTTCCTTTTAAAGCCCACAC
* * * * *
1393448 AAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGAACACCTTTTCCTTTTAAAGCCCACAT
1 AAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCATTTTCCTTTTAAAGCCCACAC
* * * * *
1393509 AAGTTAGTGGCACCTTTCAGTCCAT-AAAGAGAAGGACACTTTTTCC-TTTAAGGCCCACAC
1 AAGTTGGTGGCACCTTTCAGTCC-TCAAAGAGCAGGACGCATTTTCCTTTTAAAGCCCACAC
* * * *
1393569 AAG-TGGCTGGCACCTTTCAGTCCTCAAAGAGAAAGACGTATTTTCCTCTTAAAGCCCACAC
1 AAGTTGG-TGGCACCTTTCAGTCCTCAAAGAGCAGGACGCATTTTCCTTTTAAAGCCCACAC
* * * * *
1393630 AAGTTGGTGGCATCTTTCAGTACTTAAAGAGCAGGACATC-TTTTCCTTTTAAAGCCCATAC
1 AAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAC-GCATTTTCCTTTTAAAGCCCACAC
* * * * *
1393691 AAGTTGGTGACACC-TTCTGGTCCTCAAAGAGCAGGA--CACTTTACTTTCAAAGCCCACAC
1 AAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCATTTTCCTTTTAAAGCCCACAC
* * * * ** *
1393750 AAGTTGGTGACACC-TTCTAGTCCTCAAAGAGTAGGATGCATTCTCCTTACAAAGCCCATAC
1 AAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCATTTTCCTTTTAAAGCCCACAC
1393811 AAGTTGGTGGCACC-TTCTAGTCCTCAAAGAGCA
1 AAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCA
1393844 TGATGCACTT
Statistics
Matches: 489, Mismatches: 73, Indels: 29
0.83 0.12 0.05
Matches are distributed among these distances:
58 1 0.00
59 106 0.22
60 87 0.18
61 291 0.60
62 4 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (61 bp):
AAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCATTTTCCTTTTAAAGCCCACAC
Found at i:1396841 original size:78 final size:79
Alignment explanation
Indices: 1396731--1396883 Score: 211
Period size: 78 Copynumber: 1.9 Consensus size: 79
1396721 TCATTCATAT
* *
1396731 TTTTATTTTTAAAACACCAATTTTCTACAATCGGGGATACTTCAACCCCATTATTT-TCAAGGGG
1 TTTTATTTTTAAAACACCAATTTTCTACAATCGAGGATACTCCAACCCCATTATTTCT-AAGGGG
1396795 ATACTCCAACCCCGA
65 ATACTCCAACCCCGA
* * * ** *
1396810 TTTT-TTTTTGAAACACCAATTTTTTATAATCGAGGATACTCCAACCTTATTATTTCTGAGGGGA
1 TTTTATTTTTAAAACACCAATTTTCTACAATCGAGGATACTCCAACCCCATTATTTCTAAGGGGA
1396874 TACTCCAACC
66 TACTCCAACC
1396884 TTGGTTTTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
78 60 0.92
79 5 0.08
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (79 bp):
TTTTATTTTTAAAACACCAATTTTCTACAATCGAGGATACTCCAACCCCATTATTTCTAAGGGGA
TACTCCAACCCCGA
Found at i:1401314 original size:19 final size:20
Alignment explanation
Indices: 1401290--1401345 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
1401280 ACATATTGCT
**
1401290 TTGTATCGATACATGCTC-A
1 TTGTATCGATACATGAACAA
*
1401309 TTGTATCGATATATGAACAA
1 TTGTATCGATACATGAACAA
1401329 TTGTATCGATACATGAA
1 TTGTATCGATACATGAA
1401346 ACTGGCAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (20 bp):
TTGTATCGATACATGAACAA
Found at i:1401417 original size:33 final size:33
Alignment explanation
Indices: 1401373--1401435 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1401363 AATCACTATT
* *
1401373 TGTATCAATACATAGGACATTGTATCGATATAA
1 TGTATCAATACATAGGAAAATGTATCGATATAA
* *
1401406 TGTATCGATACATAGTAAAATGTATCGATA
1 TGTATCAATACATAGGAAAATGTATCGATA
1401436 CATTGTGCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (33 bp):
TGTATCAATACATAGGAAAATGTATCGATATAA
Found at i:1402420 original size:24 final size:24
Alignment explanation
Indices: 1402393--1402440 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1402383 AAAGACTCTG
1402393 GCTTATAAGGTTTAGAGAGATTGA
1 GCTTATAAGGTTTAGAGAGATTGA
1402417 GCTTATAAGGTTTAGAGAGATTGA
1 GCTTATAAGGTTTAGAGAGATTGA
1402441 TTGGTCAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.33
Consensus pattern (24 bp):
GCTTATAAGGTTTAGAGAGATTGA
Found at i:1404868 original size:36 final size:36
Alignment explanation
Indices: 1404815--1404885 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
1404805 CTGTTGTGTG
*
1404815 CTGGAGCTGTCGCCGCTGCTAGAGTTGCTGCTGCTA
1 CTGGAGCTGTCACCGCTGCTAGAGTTGCTGCTGCTA
* * *
1404851 CTGGAGCTGTCATCGCTGCTGGATTTGCTGCTGCT
1 CTGGAGCTGTCACCGCTGCTAGAGTTGCTGCTGCT
1404886 GCTGTGGAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.10, C:0.27, G:0.32, T:0.31
Consensus pattern (36 bp):
CTGGAGCTGTCACCGCTGCTAGAGTTGCTGCTGCTA
Found at i:1408665 original size:13 final size:13
Alignment explanation
Indices: 1408647--1408672 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1408637 CATTTTTCTG
1408647 TGTATCGATACAT
1 TGTATCGATACAT
1408660 TGTATCGATACAT
1 TGTATCGATACAT
1408673 GGATCTTTGT
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:1408669 original size:33 final size:33
Alignment explanation
Indices: 1408627--1408693 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1408617 GCCAAGGAAA
***
1408627 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1408660 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1408693 T
1 T
1408694 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1411827 original size:20 final size:21
Alignment explanation
Indices: 1411797--1411836 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
1411787 ATCTGGATTT
1411797 TTCAGATGTATCGATACATTA
1 TTCAGATGTATCGATACATTA
1411818 TTCA-ATGTATCGATACATT
1 TTCAGATGTATCGATACATT
1411837 CTAGAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (21 bp):
TTCAGATGTATCGATACATTA
Found at i:1413467 original size:18 final size:17
Alignment explanation
Indices: 1413444--1413491 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 17
1413434 TAATAATAAC
1413444 AAAAAAAGAAAAAGAAGA
1 AAAAAAAGAAAAAGAA-A
1413462 AAAAAAATG-AAAAGAAA
1 AAAAAAA-GAAAAAGAAA
1413479 AAAAGAAAGAAAA
1 AAAA-AAAGAAAA
1413492 TTCAGATACT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 6 0.22
18 20 0.74
19 1 0.04
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (17 bp):
AAAAAAAGAAAAAGAAA
Found at i:1413484 original size:23 final size:24
Alignment explanation
Indices: 1413447--1413492 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
1413437 TAATAACAAA
1413447 AAAAGAAAAAGAAGAAAAAAAATG
1 AAAAGAAAAAGAAGAAAAAAAATG
*
1413471 AAAAGAAAAA-AAGAAAGAAAAT
1 AAAAGAAAAAGAAGAAAAAAAAT
1413493 TCAGATACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.04
Consensus pattern (24 bp):
AAAAGAAAAAGAAGAAAAAAAATG
Found at i:1413848 original size:13 final size:13
Alignment explanation
Indices: 1413826--1413860 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 13
1413816 ATAACAAACC
1413826 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
1413839 AAAAAGAAAAAAAAG
1 -AAAA-AAAAAAAAG
1413854 AAAAAAA
1 AAAAAAA
1413861 TCAAATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.15
14 8 0.40
15 9 0.45
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:1413851 original size:9 final size:9
Alignment explanation
Indices: 1413826--1413860 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1413816 ATAACAAACC
*
1413826 AAAAAAAAA
1 AAAAAAAAG
1413835 AAAGAAAAAG
1 AAA-AAAAAG
1413845 AAAAAAAAG
1 AAAAAAAAG
1413854 AAAAAAA
1 AAAAAAA
1413861 TCAAATGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1414916 original size:89 final size:89
Alignment explanation
Indices: 1414760--1414959 Score: 305
Period size: 89 Copynumber: 2.3 Consensus size: 89
1414750 TAAAGGAAAA
*
1414760 CACAT-TTCCTAATCATATTCC-CTTCATCCAACCACTAGATGGTATTGATGCATCACTAAGCCT
1 CACATATTCCTAATCATA-TCCTTTTCATCCAACCACTAGATGGTATTGATGCATCACTAAGCCT
*
1414823 AATTTCCTTGGGGTAAGGTGTAGCC
65 AATTTCCTTGGAGTAAGGTGTAGCC
* * * *
1414848 TACATATTCCTAATTATATCCTTTTCCTCCAACCACTAGATGGTATTGGTGCATCACTAAGCCTA
1 CACATATTCCTAATCATATCCTTTTCATCCAACCACTAGATGGTATTGATGCATCACTAAGCCTA
1414913 ATTTCCTTGGAGTAAGGTGTAGCC
66 ATTTCCTTGGAGTAAGGTGTAGCC
* *
1414937 CATATATTCCCAATCATATCCTT
1 CACATATTCCTAATCATATCCTT
1414960 CCTTACCAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
88 7 0.07
89 93 0.93
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.34
Consensus pattern (89 bp):
CACATATTCCTAATCATATCCTTTTCATCCAACCACTAGATGGTATTGATGCATCACTAAGCCTA
ATTTCCTTGGAGTAAGGTGTAGCC
Found at i:1414999 original size:89 final size:88
Alignment explanation
Indices: 1414760--1414992 Score: 254
Period size: 89 Copynumber: 2.6 Consensus size: 88
1414750 TAAAGGAAAA
* * * * * * * *
1414760 CACAT-TTCCTAATCATATTCCCTTCATCCAACCACTAGATGGTATTGATGCATCACTAAGCCTA
1 CACATATTCCCAATCATA-TCCTTTCCTCCAAACACCAAATGATATTGGTGCATCACTAAGCCTA
*
1414824 ATTTCCTTGGGGTAAGGTGTAGCC
65 ATTTCCTTGGAGTAAGGTGTAGCC
* * * * * * *
1414848 TACATATTCCTAATTATATCCTTTTCCTCCAACCACTAGATGGTATTGGTGCATCACTAAGCCTA
1 CACATATTCCCAATCATATCC-TTTCCTCCAAACACCAAATGATATTGGTGCATCACTAAGCCTA
1414913 ATTTCCTTGGAGTAAGGTGTAGCC
65 ATTTCCTTGGAGTAAGGTGTAGCC
* *
1414937 CATATATTCCCAATCATATCC-TTCCTTACCAAATACCAAATGATATTGGTGCATCA
1 CACATATTCCCAATCATATCCTTTCC-T-CCAAACACCAAATGATATTGGTGCATCA
1414993 TAAAGCCAAA
Statistics
Matches: 126, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
87 4 0.03
88 8 0.06
89 114 0.90
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (88 bp):
CACATATTCCCAATCATATCCTTTCCTCCAAACACCAAATGATATTGGTGCATCACTAAGCCTAA
TTTCCTTGGAGTAAGGTGTAGCC
Found at i:1415646 original size:42 final size:42
Alignment explanation
Indices: 1415530--1415732 Score: 160
Period size: 42 Copynumber: 4.8 Consensus size: 42
1415520 CAAGCCTTAT
* * * *
1415530 TCTCTTCATCTTTTGTCTGCACGTCGGCTTAGACTCGGGAGAC
1 TCTC-TCATCTTTTGTCTGCCCATCGGCTTAGACCCGAGAGAC
* * * * * * *
1415573 TTTTTTTACCCTTTGTCTGCCCACCGACTTAGACCCGAGAGAC
1 -TCTCTCATCTTTTGTCTGCCCATCGGCTTAGACCCGAGAGAC
**
1415616 -CTCTCTATCTTTTGT-TCGCCCATCGGCTTAGACTTGAGAGAC
1 TCTCTC-ATCTTTTGTCT-GCCCATCGGCTTAGACCCGAGAGAC
* * *
1415658 TTTTTCATCTTTTGTCTGCCCATCGGCTTAGGCCC-AGGAGAC
1 TCTCTCATCTTTTGTCTGCCCATCGGCTTAGACCCGA-GAGAC
* * * *
1415700 TTTTTCATCCTTTGCCTGCCCATCGGCTTAGAC
1 TCTCTCATCTTTTGTCTGCCCATCGGCTTAGAC
1415733 TTAGGAGACT
Statistics
Matches: 126, Mismatches: 28, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
41 4 0.03
42 87 0.69
43 33 0.26
44 2 0.02
ACGTcount: A:0.15, C:0.30, G:0.19, T:0.35
Consensus pattern (42 bp):
TCTCTCATCTTTTGTCTGCCCATCGGCTTAGACCCGAGAGAC
Found at i:1415739 original size:42 final size:42
Alignment explanation
Indices: 1415633--1415746 Score: 167
Period size: 42 Copynumber: 2.7 Consensus size: 42
1415623 TCTTTTGTTC
* *
1415633 GCCCATCGGCTTAGACTT-GAGAGACTTTTTCATCTTTTGTCT
1 GCCCATCGGCTTAGACTTAG-GAGACTTTTTCATCCTTTGCCT
* **
1415675 GCCCATCGGCTTAGGCCCAGGAGACTTTTTCATCCTTTGCCT
1 GCCCATCGGCTTAGACTTAGGAGACTTTTTCATCCTTTGCCT
1415717 GCCCATCGGCTTAGACTTAGGAGACTTTTT
1 GCCCATCGGCTTAGACTTAGGAGACTTTTT
1415747 TTGTTAATCG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 62 0.98
43 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (42 bp):
GCCCATCGGCTTAGACTTAGGAGACTTTTTCATCCTTTGCCT
Done.