Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005946.1 Hibiscus syriacus cultivar Beakdansim tig00013960_pilon, whole genome shotgun sequence
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: 2465359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 11
Found at i:951067 original size:33 final size:33
Alignment explanation
Indices: 950996--951108 Score: 109
Period size: 33 Copynumber: 3.2 Consensus size: 33
950986 GCAACGAGAG
* * *
950996 AATCGCAACGAGAGAATCGCAACGCGAAATGAC
1 AATCGCAACCAGACAATCGCAACGCGAAATGAA
* *
951029 TATCGCGACCAGACAATCGCAACGCGAAATGAA
1 AATCGCAACCAGACAATCGCAACGCGAAATGAA
* *
951062 AATCGCAACCGCGAAATAAAAATCGCAACGCGAAATGAA
1 AATCGCAA-C-C---A-GACAATCGCAACGCGAAATGAA
951101 AATCGCAA
1 AATCGCAA
951109 TGCGATTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
33 34 0.52
34 1 0.02
35 1 0.02
38 1 0.02
39 28 0.43
ACGTcount: A:0.44, C:0.25, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACCAGACAATCGCAACGCGAAATGAA
Found at i:951131 original size:19 final size:19
Alignment explanation
Indices: 951109--951153 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
951099 AAAATCGCAA
* *
951109 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCACGT
*
951128 TGCGTTTTTTATTTCACGT
1 TGCGATTTTTATTTCACGT
951147 TGCGATT
1 TGCGATT
951154 CTCTTGTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.09, C:0.16, G:0.22, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCACGT
Found at i:951769 original size:20 final size:20
Alignment explanation
Indices: 951744--951797 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
951734 GATTTTGTAT
951744 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
951764 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
951784 TATCGCATTGCGAT
1 TATCGCATTGCGAT
951798 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:951830 original size:20 final size:21
Alignment explanation
Indices: 951786--951837 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
951776 ATAGTCAGTA
*
951786 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
**
951807 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
951827 TCGCATTGCGA
1 TCGCATTGCGA
951838 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:951837 original size:61 final size:61
Alignment explanation
Indices: 951704--951818 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 61
951694 CGCTATGTAA
* * * ** *
951704 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
*
951765 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TCGCATTGCGAT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATCGCATTGCGAT
951819 TTACTTATTC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
61 44 0.96
62 2 0.04
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
Found at i:951908 original size:21 final size:21
Alignment explanation
Indices: 951868--951908 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
951858 ACTGTATACC
**
951868 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
951889 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
951909 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:952353 original size:22 final size:21
Alignment explanation
Indices: 952288--952352 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
952278 CCCATCCCGA
952288 TTATATATATATATATAATATT
1 TTATATATA-ATATATAATATT
* ** *
952310 TTATATTTTTTATATTA-ATT
1 TTATATATAATATATAATATT
952330 TTATATATAATATATAATATT
1 TTATATATAATATATAATATT
952351 TT
1 TT
952353 TCGAGTTTGG
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
20 16 0.47
21 11 0.32
22 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATATATAATATATAATATT
Found at i:952389 original size:23 final size:25
Alignment explanation
Indices: 952349--952394 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
952339 ATATATAATA
*
952349 TTTTTCGAGTTTGGGTTC-GGGAAT
1 TTTTTCGAGGTTGGGTTCAGGGAAT
*
952373 TTTTTC-AGGTTGTGTTCAGGGA
1 TTTTTCGAGGTTGGGTTCAGGGA
952395 CGGCGCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.13, C:0.09, G:0.33, T:0.46
Consensus pattern (25 bp):
TTTTTCGAGGTTGGGTTCAGGGAAT
Found at i:953623 original size:14 final size:14
Alignment explanation
Indices: 953604--953633 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
953594 TTGTAAATAG
953604 TTAATTATTATTAT
1 TTAATTATTATTAT
*
953618 TTAATTTTTATTAT
1 TTAATTATTATTAT
953632 TT
1 TT
953634 TTATTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTAATTATTATTAT
Found at i:953998 original size:88 final size:88
Alignment explanation
Indices: 953849--954024 Score: 334
Period size: 88 Copynumber: 2.0 Consensus size: 88
953839 GTGGAGAACA
*
953849 GAGACATACACGTTCCATCTTCCGTGTAGGGAGTACGCCATTATTCTGGAAGATGTTTCAATGCA
1 GAGACACACACGTTCCATCTTCCGTGTAGGGAGTACGCCATTATTCTGGAAGATGTTTCAATGCA
*
953914 ACTAGAACTCCCGGTAGATGGAC
66 ACTAGAACTCCAGGTAGATGGAC
953937 GAGACACACACGTTCCATCTTCCGTGTAGGGAGTACGCCATTATTCTGGAAGATGTTTCAATGCA
1 GAGACACACACGTTCCATCTTCCGTGTAGGGAGTACGCCATTATTCTGGAAGATGTTTCAATGCA
954002 ACTAGAACTCCAGGTAGATGGAC
66 ACTAGAACTCCAGGTAGATGGAC
954025 ATGTTATTAT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.26
Consensus pattern (88 bp):
GAGACACACACGTTCCATCTTCCGTGTAGGGAGTACGCCATTATTCTGGAAGATGTTTCAATGCA
ACTAGAACTCCAGGTAGATGGAC
Found at i:956567 original size:20 final size:20
Alignment explanation
Indices: 956539--956579 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
956529 GGATTTTCAA
* *
956539 AAATTTATTTTTGAAATCAT
1 AAATATATTTTTAAAATCAT
956559 AAATATATTTTTAAAATCAT
1 AAATATATTTTTAAAATCAT
956579 A
1 A
956580 TTTAAACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (20 bp):
AAATATATTTTTAAAATCAT
Found at i:960486 original size:549 final size:547
Alignment explanation
Indices: 959447--961084 Score: 2041
Period size: 549 Copynumber: 3.0 Consensus size: 547
959437 AACCCACCAA
* *
959447 TTCCTCCCTCAGCTGGCCGTTCTCTTCGATTTTCGTTCTCAAGTCCTCTTCCAGTTCACCTTTCT
1 TTCCTCCCTCAGCTTGCCGTCCTCTTCGATTTTCGTTCTCAAGTCCTCTTCCAGTTCACCTTTCT
* * * * *
959512 GATTCTTAAGAGAATTGACCTCAGATTCTAGTTCCTCCGTATGTGCCAGCAAGCCCTCTTTCTCC
66 GATTCTT-AGAGAATTGACCTCAAATTCTAGTTCCTTCGTTTGTGTCAGCAAACCCTCTTTCTCC
* * *
959577 AGCAGAACTCTTTGTTGATCCTCAGTCTTGCTTACTATCTCTTCTTTTGACTTTTCTATTTCAAT
130 TGCAGAACTCTTTGCTGATCCTCAGTCTTGCTTACTATCTCTTCTTTTGACTTTTCTATCTCAAT
*
959642 CACA-AGATCTGAAACAACTTGAGTTTTACTCTCAAGCTGAACTT-CAAGTTCTGCTTTCTGGCT
195 CACATA-ATCTGAAATAACTTGAGTTTTACTCTCAAGCTGAACTTCCAA-TTCTGCTTTCTGGCT
* *
959705 ATGCAGGGACTCCAGCTCCTGCTGCAATGTATTTATCTGATCCATCAAGCTCTTTACCTGAGTCG
258 ATGCAGGGACTCCAGCTCCTGCTGCAAAGTATTTATCTGATCCATCAAGCTCTTGACCTGAGTCG
* * * * * * **
959770 ACGTTTCATCGCCTTTTACTACAATATGCTCTTCCAACTGAGCTTTCTGAGTCCGCAACAACTCC
323 ATGCTTCATCGCCTTTCACTACAATATGTTCTTCCAACTGAGCTTTCTGAGTGCGTAATGACTCC
* * * * * *
959835 ATGTCTACTAGCAGGTTATTAATCTGCATTGTCAAATTCTCCACTCTAGACAATGATTCTTTCTC
388 ATGTCTGCTACCAGATTGTTGATCTGCAATGTCAAATTCTCCACTCTAGA-AATGATTCTTTCTC
* * * *
959900 CTTGTCCTCAAAATT-ATTTGTGAGAATCAAAAGTTCTTCTTGTCTCTGCTTTGATATCATCTCT
452 ATTGTCCTCAAAATTCA-TTGTGAGAGTCAAAAGTTCTTCTTGTCTCTGTTTTGATATCATCTCG
* *
959964 AGTTCTGAAATTTGGGATTGCAGTGCTGTATT
516 AGTTCTGAAATTTGGGATTGCAGTACTCTATT
* * * *
959996 TTCCTCCCTCAACTTGCCGTCCTCTTCAATTTTCGTTCTCAAGCCCTCTTCCAGCTCACCTTTCT
1 TTCCTCCCTCAGCTTGCCGTCCTCTTCGATTTTCGTTCTCAAGTCCTCTTCCAGTTCACCTTTCT
* * * * ** ** **
960061 GATTTTTCACAGAATTTAACTCAAATTCTAGTTTGTTTATTTGTGTCAAAAAACCCTCTTTCTCC
66 GATTCTT-AGAGAATTGACCTCAAATTCTAGTTCCTTCGTTTGTGTCAGCAAACCCTCTTTCTCC
** * * * * * *
960126 TGCACCATTCTTAGCTGATCCTCGGTCTTGCTTACTATCTCTTCTTTTGTCTTTTCTACCTCGAT
130 TGCAGAACTCTTTGCTGATCCTCAGTCTTGCTTACTATCTCTTCTTTTGACTTTTCTATCTCAAT
* * * *
960191 CACATAATCTGATATATCTTG-GTTTTTCCTCTCAAGCTGCACTTCCAATTCTGCTTTCTGG-TC
195 CACATAATCTGAAATAACTTGAG-TTTTACTCTCAAGCTGAACTTCCAATTCTGCTTTCTGGCT-
* *
960254 ATTCAGGGACCCCAGCTCCTGCTGCAAAGTATTTATCTGATCCATCAAGCTCTTGACCTGAGTCG
258 ATGCAGGGACTCCAGCTCCTGCTGCAAAGTATTTATCTGATCCATCAAGCTCTTGACCTGAGTCG
* * *
960319 ATGCTTCATCGCCTTTCACTACAATATGTTCTTCCAACCGAGCTTTCTGGGTGCGTAATGATTCC
323 ATGCTTCATCGCCTTTCACTACAATATGTTCTTCCAACTGAGCTTTCTGAGTGCGTAATGACTCC
* *
960384 ATGTCTGCTACCATATTGTTGATCTGCAATGTCAAATTCTCCACTCTAGATAATGATTCTTTCTT
388 ATGTCTGCTACCAGATTGTTGATCTGCAATGTCAAATTCTCCACTCTAGA-AATGATTCTTTCTC
* * * * * * *
960449 GTTATCCTCAAACTTCATTGTGAGTGTCGACAGTTCTTCATGTCTC-GTTTTTGATATCATCTCG
452 ATTGTCCTCAAAATTCATTGTGAGAGTCAAAAGTTCTTCTTGTCTCTG-TTTTGATATCATCTCG
* * *
960513 AGCTCTAAAATTTGGGACTGCAGTACTCTATT
516 AGTTCTGAAATTTGGGATTGCAGTACTCTATT
* * *
960545 TTCCTCCCTCAGC-TGACCGTCCTCTTCGATTTTAGTTCTTAAGTCCTCTTCCAATTCACCTTTC
1 TTCCTCCCTCAGCTTG-CCGTCCTCTTCGATTTTCGTTCTCAAGTCCTCTTCCAGTTCACCTTTC
* * *
960609 TGATTCCTTAGATAATTGACCTCAAGTTCTAGTTCCTTCGTTTGTGTCAGCAAACCCTCGTTCTC
65 TGATT-CTTAGAGAATTGACCTCAAATTCTAGTTCCTTCGTTTGTGTCAGCAAACCCTCTTTCTC
* * * * * *
960674 CTGCAGGACTCTTTGCTGATCCTCAGTCATGATTAATATCTCTTCTTTCGCCTTTTCTATCTCAA
129 CTGCAGAACTCTTTGCTGATCCTCAGTCTTGCTTACTATCTCTTCTTTTGACTTTTCTATCTCAA
* * **
960739 TCACATAATCTGAGATAGCTTGAGTTTTACTCTCAAGCTGAACTTCCAGCTCTGCTTTCTGGCTA
194 TCACATAATCTGAAATAACTTGAGTTTTACTCTCAAGCTGAACTTCCAATTCTGCTTTCTGGCTA
* * * * * * *
960804 TGCAGGGACTCCATCTCCAGCTGCAAGGTATTTATTTGATCCATCAAGCTCTTGACTTCAGTTGA
259 TGCAGGGACTCCAGCTCCTGCTGCAAAGTATTTATCTGATCCATCAAGCTCTTGACCTGAGTCGA
* * * * * *
960869 TGCTTCATCACTTTTCAATGCAATATGTTCTTCCAACTGAGCTTTCTGTGTGCGTAGTGACTCCA
324 TGCTTCATCGCCTTTCACTACAATATGTTCTTCCAACTGAGCTTTCTGAGTGCGTAATGACTCCA
* * * * * *
960934 AGTCCGCTACCAGATCGCTGATCTG-AATTGTCAAATTTTCCACTCTAGACATCGATTCTTTCTC
389 TGTCTGCTACCAGATTGTTGATCTGCAA-TGTCAAATTCTCCACTCTAGAAAT-GATTCTTTCTC
* * * * * *
960998 ATTGTCCTCGAATTTCTTTGAGAGAGTCAAAAGTTCTTCTTCTCTCTGTTTTGACATCATCTCGA
452 ATTGTCCTCAAAATTCATTGTGAGAGTCAAAAGTTCTTCTTGTCTCTGTTTTGATATCATCTCGA
961063 GTTCTGAAATTTGGGATTGCAG
517 GTTCTGAAATTTGGGATTGCAG
961085 CCTTATATTT
Statistics
Matches: 921, Mismatches: 155, Indels: 26
0.84 0.14 0.02
Matches are distributed among these distances:
548 9 0.01
549 902 0.98
550 10 0.01
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (547 bp):
TTCCTCCCTCAGCTTGCCGTCCTCTTCGATTTTCGTTCTCAAGTCCTCTTCCAGTTCACCTTTCT
GATTCTTAGAGAATTGACCTCAAATTCTAGTTCCTTCGTTTGTGTCAGCAAACCCTCTTTCTCCT
GCAGAACTCTTTGCTGATCCTCAGTCTTGCTTACTATCTCTTCTTTTGACTTTTCTATCTCAATC
ACATAATCTGAAATAACTTGAGTTTTACTCTCAAGCTGAACTTCCAATTCTGCTTTCTGGCTATG
CAGGGACTCCAGCTCCTGCTGCAAAGTATTTATCTGATCCATCAAGCTCTTGACCTGAGTCGATG
CTTCATCGCCTTTCACTACAATATGTTCTTCCAACTGAGCTTTCTGAGTGCGTAATGACTCCATG
TCTGCTACCAGATTGTTGATCTGCAATGTCAAATTCTCCACTCTAGAAATGATTCTTTCTCATTG
TCCTCAAAATTCATTGTGAGAGTCAAAAGTTCTTCTTGTCTCTGTTTTGATATCATCTCGAGTTC
TGAAATTTGGGATTGCAGTACTCTATT
Found at i:969683 original size:2 final size:2
Alignment explanation
Indices: 969676--969713 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
969666 TTTCAATCAA
969676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
969714 GAAATAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:970081 original size:22 final size:22
Alignment explanation
Indices: 970056--970125 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
970046 TTCCAGTTCG
970056 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
** **
970078 CGTTGCGATTTTC-A-AAAT-T
1 CGTTGCGATAGTCTACAGTTGT
*
970097 CGTTGTGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
970119 TGTTGCG
1 CGTTGCG
970126 TTGCGAAAAT
Statistics
Matches: 34, Mismatches: 11, Indels: 6
0.67 0.22 0.12
Matches are distributed among these distances:
19 11 0.32
20 3 0.09
21 3 0.09
22 17 0.50
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.40
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:970146 original size:40 final size:40
Alignment explanation
Indices: 970056--970148 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 40
970046 TTCCAGTTCG
* *
970056 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCAAAATT
1 CGTTGTGATAGTCTACAGTTGTCGTTGCGA-TTGCAAAATT
*
970097 CGTTGTGATAGTCTACAGTTGTTGTTGCG-TTGCGAAAATT
1 CGTTGTGATAGTCTACAGTTGTCGTTGCGATTGC-AAAATT
970137 CGTTGTGATAGT
1 CGTTGTGATAGT
970149 TAAAAAAAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 3 0.06
40 18 0.38
41 27 0.56
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.40
Consensus pattern (40 bp):
CGTTGTGATAGTCTACAGTTGTCGTTGCGATTGCAAAATT
Found at i:970236 original size:6 final size:6
Alignment explanation
Indices: 970225--970258 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
970215 GACACGTATT
970225 ACCACG ACCACG ACACCACG ACCACG ACCACG AC
1 ACCACG ACCACG --ACCACG ACCACG ACCACG AC
970259 GGCGGCGGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.77
8 6 0.23
ACGTcount: A:0.35, C:0.50, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:970244 original size:14 final size:14
Alignment explanation
Indices: 970225--970252 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
970215 GACACGTATT
970225 ACCACGACCACGAC
1 ACCACGACCACGAC
970239 ACCACGACCACGAC
1 ACCACGACCACGAC
970253 CACGACGGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.50, G:0.14, T:0.00
Consensus pattern (14 bp):
ACCACGACCACGAC
Found at i:970742 original size:6 final size:6
Alignment explanation
Indices: 970733--970781 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
970723 CCGTCTCGTC
970733 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
970781 T
1 T
970782 AATACGTATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:973032 original size:19 final size:19
Alignment explanation
Indices: 973005--973041 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
972995 TAAATTTATT
*
973005 ATTTTATATTTTAAATTAA
1 ATTTAATATTTTAAATTAA
*
973024 ATTTAATATTTTTAATTA
1 ATTTAATATTTTAAATTA
973042 GCTAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTAATATTTTAAATTAA
Found at i:984177 original size:22 final size:22
Alignment explanation
Indices: 984152--984236 Score: 120
Period size: 22 Copynumber: 3.9 Consensus size: 22
984142 ATGTGAAATT
984152 TGTCCCGAA-AGACCTATGAATA
1 TGTCCCGAAGA-ACCTATGAATA
984174 TGTCCCGAAGAACCTATGAATA
1 TGTCCCGAAGAACCTATGAATA
*
984196 TGTCCTGAAGAACCTATGAATA
1 TGTCCCGAAGAACCTATGAATA
* *
984218 TGTCCTGAAG-ACTTATGAA
1 TGTCCCGAAGAACCTATGAA
984237 ACCCTCGACT
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
21 8 0.13
22 51 0.85
23 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (22 bp):
TGTCCCGAAGAACCTATGAATA
Found at i:984477 original size:2 final size:2
Alignment explanation
Indices: 984470--984507 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
984460 TCATACAAAC
984470 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
984508 CATGTGTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:985696 original size:23 final size:23
Alignment explanation
Indices: 985666--985728 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
985656 AGCTCATATA
*
985666 AATT-CACCGAAGTGCCACATAG
1 AATTGCACCGTAGTGCCACATAG
* *
985688 AATTGCACCGTAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCACATAG
985711 AATTGCACCGTAGTGCCA
1 AATTGCACCGTAGTGCCA
985729 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 4 0.11
23 32 0.89
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.21
Consensus pattern (23 bp):
AATTGCACCGTAGTGCCACATAG
Found at i:985915 original size:103 final size:103
Alignment explanation
Indices: 985744--986064 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
985734 TAATGTCCAT
985744 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
985809 GACTTCATACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
985847 AAGAACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
985912 GACTTCACACATGTTCCAAATAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
985950 AAGGACCACATATCATTCCTTAAAAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
986015 GACTTCACACATGTTCCAAAGAATACATATATGACCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
986053 AAGGACCACATA
1 AAGGACCACATA
986065 GACCCTCGAC
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:990882 original size:61 final size:61
Alignment explanation
Indices: 990806--990933 Score: 175
Period size: 61 Copynumber: 2.1 Consensus size: 61
990796 AAGGACACTA
* * *
990806 AGTGCAGGTGGTGGGCACAACCTTATGTGTTATATCTGGATTAACACTAGAGTGTAAACAT
1 AGTGCAGGTGGTGGGCACAACCTTATGTGTGATATCCGGATTAACACTAAAGTGTAAACAT
* ** * * *
990867 AGTGTAGGTGGTGGGCGTAACCTTATGTGTGATATCCGGATTAGCACTAAAGTGTAAGCTT
1 AGTGCAGGTGGTGGGCACAACCTTATGTGTGATATCCGGATTAACACTAAAGTGTAAACAT
990928 AGTGCA
1 AGTGCA
990934 AGTTTAGCAC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (61 bp):
AGTGCAGGTGGTGGGCACAACCTTATGTGTGATATCCGGATTAACACTAAAGTGTAAACAT
Found at i:993131 original size:29 final size:30
Alignment explanation
Indices: 993089--993154 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
993079 AACAAATAAA
993089 CAAAACTGAACT-CCCACTTCCCAGCGATC
1 CAAAACTGAACTCCCCACTTCCCAGCGATC
993118 CAAAACTGAACTCCCCACTTCCCAGCGATC
1 CAAAACTGAACTCCCCACTTCCCAGCGATC
993148 CAAAACT
1 CAAAACT
993155 TGCCATGGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 12 0.33
30 24 0.67
ACGTcount: A:0.33, C:0.41, G:0.09, T:0.17
Consensus pattern (30 bp):
CAAAACTGAACTCCCCACTTCCCAGCGATC
Found at i:995607 original size:7 final size:6
Alignment explanation
Indices: 995590--995698 Score: 51
Period size: 5 Copynumber: 19.2 Consensus size: 6
995580 ATCAATAGAT
* * * * *
995590 TTAATA TTAATGA TTAATA TTTAAACA TGAATA TTATTT TTTATA -TAATA
1 TTAATA TTAAT-A TTAATA -TT-AATA TTAATA TTAATA TTAATA TTAATA
995640 -TAATA -TAATA -TAATA -TAATA -TAATA -TAATA -TAATA -TATATA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTA-ATA
995681 TATAATA -TAATA -TAATA T
1 T-TAATA TTAATA TTAATA T
995699 ATATTTGATG
Statistics
Matches: 86, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
5 51 0.59
6 18 0.21
7 12 0.14
8 5 0.06
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (6 bp):
TTAATA
Found at i:995642 original size:5 final size:5
Alignment explanation
Indices: 995632--995699 Score: 122
Period size: 5 Copynumber: 14.0 Consensus size: 5
995622 ATTATTTTTT
995632 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT- ATAT-
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
995680 ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA
995700 TATTTGATGT
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.13
5 54 0.87
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:996230 original size:21 final size:20
Alignment explanation
Indices: 996206--996257 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
996196 ACTAACATCC
996206 TTAAAAAATAATTTATTAATT-
1 TTAAAAAATAA-TT-TTAATTA
* *
996227 TTAATAATTAATTTTAATTA
1 TTAAAAAATAATTTTAATTA
*
996247 TTTAAAAATAA
1 TTAAAAAATAA
996258 ATAAAATTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 6 0.24
20 10 0.40
21 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAAAAATAATTTTAATTA
Found at i:996238 original size:13 final size:13
Alignment explanation
Indices: 996220--996244 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
996210 AAAATAATTT
996220 ATTAATTTTAATA
1 ATTAATTTTAATA
996233 ATTAATTTTAAT
1 ATTAATTTTAAT
996245 TATTTAAAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTAATTTTAATA
Found at i:996715 original size:3 final size:3
Alignment explanation
Indices: 996707--996745 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
996697 ATTAAACTCC
996707 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
996746 AGATTTTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1001349 original size:185 final size:185
Alignment explanation
Indices: 1001037--1001413 Score: 666
Period size: 185 Copynumber: 2.0 Consensus size: 185
1001027 TAAAAAATTA
*
1001037 AATATTTTTTAATTTAAAAAAACAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAA
1 AATATTTTTTAATTTAAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAA
*
1001102 ATTTTATATAAAATTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTAAATTA
66 ATTTTATATAAAATTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTAGATCTTAAATTA
*
1001167 TTAATTGGGTTTTAAATGGTTTGAGCTGAGCACATATGTTATATATAATATATTT
131 TTAATTGGGTTTTAAATGGTTTGAGCTAAGCACATATGTTATATATAATATATTT
1001222 AATATTTTTTAA-TTAAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAA
1 AATATTTTTTAATTTAAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAA
** *
1001286 ATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTGGATCTTAAATT
66 ATTTTATATAA-AATTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTAGATCTTAAATT
* *
1001351 ATTAATTGGGTTTTAAATGGTTTGGGCTAAGCTCATATGTTATATATAATATATTT
130 ATTAATTGGGTTTTAAATGGTTTGAGCTAAGCACATATGTTATATATAATATATTT
1001407 AATATTT
1 AATATTT
1001414 AAAATTTAAT
Statistics
Matches: 183, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
184 62 0.34
185 121 0.66
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (185 bp):
AATATTTTTTAATTTAAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAA
ATTTTATATAAAATTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTAGATCTTAAATTA
TTAATTGGGTTTTAAATGGTTTGAGCTAAGCACATATGTTATATATAATATATTT
Found at i:1003067 original size:31 final size:31
Alignment explanation
Indices: 1003032--1003104 Score: 114
Period size: 29 Copynumber: 2.4 Consensus size: 31
1003022 TAGAATCTGA
*
1003032 CACCTCTGTGCATATAAAAGAAACGATTGAG
1 CACCTCTGTGCATATAAAAGAAACAATTGAG
1003063 CACCTCTGTGC--ATAAAAGAAACAATTGAG
1 CACCTCTGTGCATATAAAAGAAACAATTGAG
*
1003092 CACCTCTATGCAT
1 CACCTCTGTGCAT
1003105 CAATCTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 27 0.71
31 11 0.29
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.23
Consensus pattern (31 bp):
CACCTCTGTGCATATAAAAGAAACAATTGAG
Found at i:1003497 original size:13 final size:13
Alignment explanation
Indices: 1003481--1003509 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1003471 TCTTCAACCA
1003481 ATAGAGAGACATC
1 ATAGAGAGACATC
1003494 ATAGAGAGACATC
1 ATAGAGAGACATC
1003507 ATA
1 ATA
1003510 CCATCTGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.14, G:0.21, T:0.17
Consensus pattern (13 bp):
ATAGAGAGACATC
Found at i:1006739 original size:20 final size:19
Alignment explanation
Indices: 1006714--1006761 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1006704 ATTTAGTTTA
**
1006714 ATTTATTTTTAATTTAATAG
1 ATTTATTTTTAA-AAAATAG
*
1006734 ATTTATACTTTAAAAAATAG
1 ATTTAT-TTTTAAAAAATAG
1006754 ATTTATTT
1 ATTTATTT
1006762 CCTCCAATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.04
20 17 0.74
21 5 0.22
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (19 bp):
ATTTATTTTTAAAAAATAG
Found at i:1007759 original size:31 final size:30
Alignment explanation
Indices: 1007716--1007878 Score: 103
Period size: 30 Copynumber: 5.5 Consensus size: 30
1007706 ATTTTAAAAA
1007716 TATAAAAATATTTTTATTTTTATCTTAACT
1 TATAAAAATATTTTTATTTTTATCTTAACT
* * *
1007746 TAT-TAAATATATTTTATTTTTATTTTTA-T
1 TATAAAAATAT-TTTTATTTTTATCTTAACT
* * *
1007775 GTA-AAAATAAATATTTTATCTTTATCTTCACT
1 -TATAAAA-ATAT-TTTTATTTTTATCTTAACT
* *
1007807 TA-AAAAATATTTTTATTATGTA-C-CAA--
1 TATAAAAATATTTTTATT-TTTATCTTAACT
*
1007833 -A-AAAAATATTTTTATTTTTATCTTAATT
1 TATAAAAATATTTTTATTTTTATCTTAACT
*
1007861 TTTAAAGATATATTTTTA
1 TATAAA-A-ATATTTTTA
1007879 AAAAAAATAT
Statistics
Matches: 103, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
24 3 0.03
25 17 0.17
26 2 0.02
28 1 0.01
29 14 0.14
30 31 0.30
31 25 0.24
32 10 0.10
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (30 bp):
TATAAAAATATTTTTATTTTTATCTTAACT
Found at i:1009037 original size:4 final size:4
Alignment explanation
Indices: 1009028--1009076 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
1009018 AACCCCCCTC
* * * *
1009028 TCTA TCTA TCTA TCTA TCCA TCCA TCCA TCTA TTTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1009076 T
1 T
1009077 TTTCATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (4 bp):
TCTA
Found at i:1009519 original size:18 final size:19
Alignment explanation
Indices: 1009496--1009538 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1009486 TCGTGTTATA
*
1009496 TAATATTTATATAAAT-TT
1 TAATATTCATATAAATATT
1009514 TAATA-TCATATAAATATT
1 TAATATTCATATAAATATT
*
1009532 TCATATT
1 TAATATT
1009539 ATAATAGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 9 0.43
18 11 0.52
19 1 0.05
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATTCATATAAATATT
Found at i:1015452 original size:20 final size:21
Alignment explanation
Indices: 1015427--1015478 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1015417 TTTTCCCAAT
*
1015427 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1015447 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1015468 TCGCAATGCGA
1 TCGCAATGCGA
1015479 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1015492 original size:20 final size:20
Alignment explanation
Indices: 1015467--1015601 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
1015457 AATTGGGAAA
1015467 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1015487 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1015507 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1015528 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
1015548 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
1015568 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
1015588 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1015602 TTTCAAAGCG
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 66 0.69
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1015511 original size:61 final size:61
Alignment explanation
Indices: 1015464--1015595 Score: 183
Period size: 61 Copynumber: 2.2 Consensus size: 61
1015454 GCGAATTGGG
* * * * *
1015464 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
1015525 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
1015586 ATAATCGCAA
1 AAAATCGCAA
1015596 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1016129 original size:20 final size:20
Alignment explanation
Indices: 1016077--1016133 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1016067 GATTCTCTCA
**
1016077 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCATTTTCGCG
*
1016097 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCG
**
1016117 TTGCGATTTTCATTTTC
1 TTGCGATAGTCATTTTC
1016134 AGAAACTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.44
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:1016324 original size:25 final size:24
Alignment explanation
Indices: 1016270--1016324 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1016260 TGTTTATTAT
* *
1016270 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1016294 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1016320 TGTTT
1 TGTTT
1016325 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1018015 original size:19 final size:20
Alignment explanation
Indices: 1017961--1018015 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1017951 TAGTTTACTT
* *
1017961 TCGCAACACGAAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
1017981 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
*
1018001 TCGCAATGC-GAAATG
1 TCGCAACGCGGAAATG
1018016 AAAATTGCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 6 0.19
20 26 0.81
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGGCTA
Found at i:1018039 original size:14 final size:14
Alignment explanation
Indices: 1018016--1018073 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
1018006 ATGCGAAATG
*
1018016 AAAATTGCAACGAC
1 AAAATCGCAACGAC
*
1018030 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1018046 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
1018062 AAAATCACAACG
1 AAAATCGCAACG
1018074 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.53
16 8 0.22
18 9 0.25
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1018063 original size:32 final size:33
Alignment explanation
Indices: 1018000--1018090 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
1017990 GGAAATGGCT
*
1018000 ATCGCAATGCGAAATGAAAATTGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1018033 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
1018065 ATCACAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1018091 TGCGATTTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 29 0.54
33 25 0.46
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1018126 original size:14 final size:14
Alignment explanation
Indices: 1018107--1018197 Score: 65
Period size: 14 Copynumber: 5.9 Consensus size: 14
1018097 TTATGTTTCG
1018107 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1018121 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
1018137 CGCATTGCGGTTTTGT
1 CG--TTGCGATTTTGT
* *
1018153 TGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
1018170 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1018186 CGTTGCGATTTT
1 CGTTGCGATTTT
1018198 CATTTCGCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
14 26 0.43
15 3 0.05
16 11 0.18
17 3 0.05
18 11 0.18
19 6 0.10
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1018171 original size:33 final size:33
Alignment explanation
Indices: 1018102--1018213 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
1018092 GCGATTTATG
*
1018102 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
* *
1018134 TTTCGCATTGCGGTTTTGTTGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1018167 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1018200 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1018214 AGCCATTTCC
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 24 0.32
33 50 0.68
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1018179 original size:19 final size:19
Alignment explanation
Indices: 1018123--1018213 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
1018113 GATTTTGTCG
1018123 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
1018141 TTGCGGTTTT--GTT-G--
1 TTGCGATTTTCATTTCGCA
1018155 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1018174 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
1018188 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1018207 TTGCGAT
1 TTGCGAT
1018214 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 21
0.67 0.07 0.25
Matches are distributed among these distances:
14 15 0.27
15 3 0.05
16 7 0.12
17 7 0.12
18 8 0.14
19 16 0.29
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1018220 original size:19 final size:20
Alignment explanation
Indices: 1018198--1018241 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1018188 TTGCGATTTT
1018198 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
1018217 CATTTCCGCTTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
1018237 CATTT
1 CATTT
1018242 TCGCGTTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:1020141 original size:14 final size:14
Alignment explanation
Indices: 1020122--1020157 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1020112 ATTGTTTAAT
1020122 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1020136 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1020150 TGATTTGT
1 TGATTTGT
1020158 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1020675 original size:20 final size:20
Alignment explanation
Indices: 1020650--1020741 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
1020640 TTGAAGATGA
1020650 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
1020670 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* * **
1020690 TTACGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
1020711 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
1020731 TTGCGATTTTC
1 TTGCGATTTTC
1020742 CAAATTCGCA
Statistics
Matches: 52, Mismatches: 19, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 38 0.73
21 14 0.27
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:1020770 original size:20 final size:21
Alignment explanation
Indices: 1020726--1020777 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1020716 ATAGTCAGTA
*
1020726 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1020747 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1020767 TCGCATTGCGA
1 TCGCATTGCGA
1020778 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1020993 original size:12 final size:12
Alignment explanation
Indices: 1020974--1021007 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1020964 CTCTCCGGCG
1020974 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1020986 ATATCCGTTCCT
1 ACATCCGTTCCT
1020998 ACATCC-TTCC
1 ACATCCGTTCC
1021008 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1021591 original size:24 final size:24
Alignment explanation
Indices: 1021564--1021617 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1021554 GTATTCGAAA
*
1021564 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1021588 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1021612 TTTGAT
1 TTTGAT
1021618 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1021809 original size:12 final size:12
Alignment explanation
Indices: 1021792--1021816 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1021782 ATATAATCCT
1021792 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1021804 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1021816 G
1 G
1021817 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1024132 original size:19 final size:19
Alignment explanation
Indices: 1024110--1024164 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
1024100 AGAAATTACT
1024110 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1024129 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1024143 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1024162 ATC
1 ATC
1024165 ACATTGCGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 10 0.34
15 1 0.03
16 2 0.07
17 2 0.07
18 1 0.03
19 13 0.45
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1024188 original size:19 final size:19
Alignment explanation
Indices: 1024166--1024226 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
1024156 ATGAAAATCA
1024166 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
**
1024185 CATTGCGA--TTC-CCTCG
1 CATTGCGATTTTCATTTCG
1024201 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
1024218 CATTACGAT
1 CATTGCGAT
1024227 AGTACTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
14 6 0.19
16 6 0.19
17 6 0.19
19 14 0.44
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.43
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:1024352 original size:14 final size:14
Alignment explanation
Indices: 1024333--1024369 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1024323 CATCAATTAA
1024333 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1024347 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1024361 ACAAATCAA
1 ACAAATCAA
1024370 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1025793 original size:21 final size:21
Alignment explanation
Indices: 1025724--1025793 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
1025714 CATGTGAATC
*
1025724 GGACTCTTGAATGGTGGGA-G
1 GGACTCTTGAACGGTGGGAGG
* * ** *
1025744 GGACCTCTTCAACGATGACAGT
1 GGA-CTCTTGAACGGTGGGAGG
*
1025766 GGCCTCTTGAACGGTGGGAGG
1 GGACTCTTGAACGGTGGGAGG
1025787 GGACTCT
1 GGACTCT
1025794 CGAGGAATGA
Statistics
Matches: 35, Mismatches: 13, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 3 0.09
21 30 0.86
22 2 0.06
ACGTcount: A:0.20, C:0.20, G:0.37, T:0.23
Consensus pattern (21 bp):
GGACTCTTGAACGGTGGGAGG
Found at i:1025812 original size:42 final size:41
Alignment explanation
Indices: 1025727--1025849 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1025717 GTGAATCGGA
* * * *
1025727 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1025769 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1025811 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1025850 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:1026241 original size:91 final size:90
Alignment explanation
Indices: 1026067--1026251 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
1026057 ATTTCAAACT
* *
1026067 TTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
1026132 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
1026160 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTTACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
1026224 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
1026251 T
1 T
1026252 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 42 0.49
93 18 0.21
95 26 0.30
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:1027969 original size:20 final size:19
Alignment explanation
Indices: 1027938--1028059 Score: 84
Period size: 20 Copynumber: 6.8 Consensus size: 19
1027928 TCTTTTGGTT
1027938 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1027957 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1027978 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1027997 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
1028011 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1028030 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
1028044 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1028060 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 11, Indels: 24
0.70 0.10 0.21
Matches are distributed among these distances:
14 20 0.25
16 4 0.05
17 4 0.05
19 21 0.26
20 29 0.36
21 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1028006 original size:14 final size:14
Alignment explanation
Indices: 1027987--1028042 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
1027977 GGAAATGACT
1027987 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1028001 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
1028018 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
1028034 ATCGCAACG
1 ATCGCAACG
1028043 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1028020 original size:33 final size:33
Alignment explanation
Indices: 1027963--1028059 Score: 167
Period size: 33 Copynumber: 2.9 Consensus size: 33
1027953 ACGAGATAAT
1027963 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
1027997 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
1028030 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
1028060 TGCGATTTTG
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:1028093 original size:19 final size:19
Alignment explanation
Indices: 1028060--1028144 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 19
1028050 AAAATCGCAA
**
1028060 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
1028079 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
1028098 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
1028112 TGCGATAGTT-ATTTCCGCGT
1 TGCGAT-TTTCATTT-CGCGT
1028132 TGCGATTTTCATT
1 TGCGATTTTCATT
1028145 CTCGAAACTA
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
14 10 0.19
17 5 0.09
19 25 0.47
20 13 0.25
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:1028683 original size:20 final size:20
Alignment explanation
Indices: 1028659--1028772 Score: 140
Period size: 20 Copynumber: 5.7 Consensus size: 20
1028649 CGCTATGTAA
* * *
1028659 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* * *
1028679 ATCGCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
1028700 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
1028720 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1028740 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1028760 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1028773 TTTCCCAATT
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
19 3 0.04
20 66 0.80
21 12 0.14
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1029750 original size:61 final size:60
Alignment explanation
Indices: 1029685--1029838 Score: 150
Period size: 60 Copynumber: 2.5 Consensus size: 60
1029675 AAGTTTTGGG
**
1029685 GACTAATTTAAAATGAGA-TTCATAATTT-AGGGATAAAAATTGTAATACTAAAAAGTTTAAA
1 GACTAATTTAAAATGAGAGTT-ATAATTTGA-GGAT-AAAATTAAAATACTAAAAAGTTTAAA
* * * ** * *
1029746 GACTAATTTAGAATAAGAGTTATAATTTGAGGATGAAATTAAAATGTTTAAAAGTTTAAG
1 GACTAATTTAAAATGAGAGTTATAATTTGAGGATAAAATTAAAATACTAAAAAGTTTAAA
* * * *
1029806 GATTAATTTAAAATGAGGGTTATAGTTTAAGGA
1 GACTAATTTAAAATGAGAGTTATAATTTGAGGA
1029839 CCTATGATAC
Statistics
Matches: 76, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
60 46 0.61
61 27 0.36
62 3 0.04
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (60 bp):
GACTAATTTAAAATGAGAGTTATAATTTGAGGATAAAATTAAAATACTAAAAAGTTTAAA
Found at i:1029888 original size:27 final size:26
Alignment explanation
Indices: 1029851--1029901 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
1029841 TATGATACAG
*
1029851 TTAGTTTAATATAATAATATATTATT
1 TTAGTTTAATAAAATAATATATTATT
*
1029877 TTAGATTTAATAAAATAATGTATTA
1 TTAG-TTTAATAAAATAATATATTA
1029902 AGTAACTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (26 bp):
TTAGTTTAATAAAATAATATATTATT
Found at i:1036768 original size:20 final size:21
Alignment explanation
Indices: 1036743--1036782 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1036733 TAAACTTAGT
1036743 TGAA-TTTATATTTTAATTTA
1 TGAATTTTATATTTTAATTTA
*
1036763 TGAATTTTATTTTTTAATTT
1 TGAATTTTATATTTTAATTT
1036783 TAGTGAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (21 bp):
TGAATTTTATATTTTAATTTA
Found at i:1042626 original size:3 final size:3
Alignment explanation
Indices: 1042618--1042679 Score: 72
Period size: 3 Copynumber: 19.3 Consensus size: 3
1042608 CGGGTCTTTT
1042618 TTA TTA TTA TT- TATA TATA TTTA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA T-TA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA
1042666 TTTA TTA TTA TTA T
1 -TTA TTA TTA TTA T
1042680 GTTTATTAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 1 0.02
3 40 0.74
4 12 0.22
5 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1042638 original size:10 final size:10
Alignment explanation
Indices: 1042617--1042677 Score: 99
Period size: 10 Copynumber: 6.2 Consensus size: 10
1042607 CCGGGTCTTT
1042617 TTTATTATTA
1 TTTATTATTA
1042627 TTTA-TATATA
1 TTTATTAT-TA
1042637 TTTATTATTA
1 TTTATTATTA
1042647 TTTATTATTA
1 TTTATTATTA
1042657 -TTATTATTA
1 TTTATTATTA
1042666 TTTATTATTA
1 TTTATTATTA
1042676 TT
1 TT
1042678 ATGTTTATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
9 12 0.25
10 33 0.69
11 3 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATTATTA
Found at i:1042686 original size:19 final size:19
Alignment explanation
Indices: 1042618--1042679 Score: 99
Period size: 19 Copynumber: 3.2 Consensus size: 19
1042608 CGGGTCTTTT
1042618 TTATTATTATTTA-TATATA
1 TTATTATTATTTATTAT-TA
1042637 TTTATTATTATTTATTATTA
1 -TTATTATTATTTATTATTA
1042657 TTATTATTATTTATTATTA
1 TTATTATTATTTATTATTA
1042676 TTAT
1 TTAT
1042680 GTTTATTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
19 23 0.56
20 15 0.37
21 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTATTATTTATTATTA
Found at i:1042691 original size:16 final size:15
Alignment explanation
Indices: 1042621--1042687 Score: 84
Period size: 16 Copynumber: 4.4 Consensus size: 15
1042611 GTCTTTTTTA
1042621 TTATTATTTATATATAT
1 TTATTA-TTAT-TATAT
1042638 TTATTATTATT-TA-
1 TTATTATTATTATAT
1042651 TTATTATTATTATTAT
1 TTATTATTATTA-TAT
*
1042667 TTATTATTATTATGT
1 TTATTATTATTATAT
1042682 TTATTA
1 TTATTA
1042688 ATTACATATT
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
13 11 0.24
14 2 0.04
15 11 0.24
16 16 0.35
17 6 0.13
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (15 bp):
TTATTATTATTATAT
Found at i:1042691 original size:19 final size:17
Alignment explanation
Indices: 1042618--1042691 Score: 80
Period size: 19 Copynumber: 4.2 Consensus size: 17
1042608 CGGGTCTTTT
1042618 TTATTATTATTTATATATA
1 TTATTATTATTTAT-TA-A
1042637 TTTATTATTATTTATTATTA
1 -TTATTATTATTTATTA--A
1042657 TTATTATTATTTATT-A
1 TTATTATTATTTATTAA
*
1042673 TTATTA-TGTTTATTAA
1 TTATTATTATTTATTAA
1042689 TTA
1 TTA
1042692 CATATTACAA
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
15 7 0.14
16 11 0.22
19 17 0.33
20 16 0.31
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (17 bp):
TTATTATTATTTATTAA
Found at i:1042983 original size:12 final size:12
Alignment explanation
Indices: 1042966--1042990 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1042956 ACCGAACATC
1042966 CACCTACAGTGA
1 CACCTACAGTGA
1042978 CACCTACAGTGA
1 CACCTACAGTGA
1042990 C
1 C
1042991 CAAATCAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (12 bp):
CACCTACAGTGA
Found at i:1046577 original size:31 final size:32
Alignment explanation
Indices: 1046541--1046602 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1046531 ATTTTACATG
1046541 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
1046572 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1046603 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:1049066 original size:26 final size:25
Alignment explanation
Indices: 1049037--1049114 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
1049027 AATTTTTGAC
1049037 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
1049063 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
*
1049083 ATTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
1049109 ATTCTT
1 ATTCTT
1049115 TCCACCTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.12
26 14 0.35
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.42
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:1049075 original size:20 final size:20
Alignment explanation
Indices: 1049052--1049126 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
1049042 ATCTCTTTGA
1049052 GACCTTGAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
* *
1049072 GACCTTGAAACATTCCCTCTCTTTGA
1 GACCTTGAAATA-T---TCT-TTT-C
1049098 GACCTTGAAATATTC-TTTC
1 GACCTTGAAATATTCTTTTC
*
1049117 CACCTTGAAA
1 GACCTTGAAA
1049127 CACTGTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.20
20 14 0.32
21 1 0.02
22 2 0.05
24 3 0.07
25 4 0.09
26 11 0.25
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (20 bp):
GACCTTGAAATATTCTTTTC
Found at i:1050979 original size:22 final size:22
Alignment explanation
Indices: 1050951--1050998 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 22
1050941 AGAAAAGTAT
1050951 ATACATACATACA-CATGCATAC
1 ATACATACATACACCATG-ATAC
1050973 ATACATACATACATCCATGATAC
1 ATACATACATACA-CCATGATAC
1050996 ATA
1 ATA
1050999 AAATTTGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 13 0.54
23 7 0.29
24 4 0.17
ACGTcount: A:0.46, C:0.25, G:0.04, T:0.25
Consensus pattern (22 bp):
ATACATACATACACCATGATAC
Found at i:1051594 original size:105 final size:101
Alignment explanation
Indices: 1051453--1051690 Score: 264
Period size: 105 Copynumber: 2.3 Consensus size: 101
1051443 TGAGAATTTT
* * * *
1051453 AAAACAAATTGTGTTTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
** *
1051517 TAAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC-
66 T-AAAACAAAATTAATCTCA-CTT-GA-AATCGTTTC--TCA
* * * *
1051558 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGGATTTGTTTCACA
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* * *
1051623 TTAAACAAAGTTGATCTCACTTGAAATCGTTTCTCA
66 TAAAACAAAATTAATCTCACTTGAAATCGTTTCTCA
* *
1051659 AAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTC
1051691 TCTAAAAACA
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
100 2 0.02
101 29 0.25
102 6 0.05
103 2 0.02
104 3 0.03
105 71 0.62
106 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.38
Consensus pattern (101 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
TAAAACAAAATTAATCTCACTTGAAATCGTTTCTCA
Found at i:1051681 original size:35 final size:36
Alignment explanation
Indices: 1051637--1051717 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
1051627 ACAAAGTTGA
*
1051637 TCTCACTTGAAATC-GTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAAA-CAATTTCTCTAAAAACAAACTTTG
* * *
1051672 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAAACAATTTCTCTAAAAACAAACTTTG
*
1051708 TCTCATTTGA
1 TCTCACTTGA
1051718 GACTATATCT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 1 0.03
35 16 0.42
36 21 0.55
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (36 bp):
TCTCACTTGAAACAATTTCTCTAAAAACAAACTTTG
Found at i:1051708 original size:36 final size:36
Alignment explanation
Indices: 1051652--1051755 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
1051642 CTTGAAATCG
*
1051652 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
** *
1051687 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* * *
1051723 TATCT-T-AAAGCAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
1051756 TCATTTTCTC
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 22 0.38
35 7 0.12
36 29 0.50
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:1052027 original size:29 final size:29
Alignment explanation
Indices: 1051994--1052175 Score: 210
Period size: 29 Copynumber: 6.4 Consensus size: 29
1051984 TTAAAGACAA
*
1051994 TTTCTTTTGAAAAAAAATCTTTGGGTTTG
1 TTTCTTTTGAAAAAAAATCTTTGAGTTTG
*
1052023 TTTCTCTTGAAAAAAAATCTTTGAGTTTG
1 TTTCTTTTGAAAAAAAATCTTTGAGTTTG
* *
1052052 TTCCTCTTG--AAAAAATCTTTGAGTTTG
1 TTTCTTTTGAAAAAAAATCTTTGAGTTTG
* * * *
1052079 CTCCTTTTGAATAAAAATCTTGGAGTTTG
1 TTTCTTTTGAAAAAAAATCTTTGAGTTTG
* *
1052108 TTCCTTTTGAATAAAAATCTTTGAG-TTG
1 TTTCTTTTGAAAAAAAATCTTTGAGTTTG
* * *
1052136 TTTCTTTTG-AAAAATATCTTTGAGTCTA
1 TTTCTTTTGAAAAAAAATCTTTGAGTTTG
*
1052164 TTTATTTTGAAA
1 TTTCTTTTGAAA
1052176 CAAAGTTTTG
Statistics
Matches: 134, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
27 38 0.28
28 20 0.15
29 76 0.57
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (29 bp):
TTTCTTTTGAAAAAAAATCTTTGAGTTTG
Found at i:1052089 original size:56 final size:57
Alignment explanation
Indices: 1052004--1052160 Score: 212
Period size: 56 Copynumber: 2.8 Consensus size: 57
1051994 TTTCTTTTGA
* *
1052004 AAAAAAATCTTTGGGTTTGTTTCTCTTGAAAAAAAATCTTTGAGTTTGTTCCTCTTG
1 AAAAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAAATCTTTGAGTTTGTTCCTCTTG
* * * * *
1052061 -AAAAAATCTTTGAGTTTGCTCCTTTTGAATAAAAATCTTGGAGTTTGTTCCTTTTG
1 AAAAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAAATCTTTGAGTTTGTTCCTCTTG
*
1052117 AATAAAAATCTTTGAG-TTGTTTCTTTTG-AAAAATATCTTTGAGT
1 AA-AAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAAATCTTTGAGT
1052161 CTATTTATTT
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
56 62 0.72
57 11 0.13
58 13 0.15
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (57 bp):
AAAAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAAATCTTTGAGTTTGTTCCTCTTG
Found at i:1052107 original size:85 final size:85
Alignment explanation
Indices: 1051997--1052160 Score: 242
Period size: 85 Copynumber: 1.9 Consensus size: 85
1051987 AAGACAATTT
*
1051997 CTTTTGAAAAAAAATCTTTGGGTTTGTTTCTCTTGAAAAAAAATCTTTGAGTTTGTTCCTCTTGA
1 CTTTTGAAAAAAAATCTTTGGGTTTGTTCCTCTTGAAAAAAAATCTTTGAG-TTGTTCCTCTTGA
1052062 AAAA-ATCTTTGAGTTTGCTC
65 AAAATATCTTTGAGTTTGCTC
* * * * *
1052082 CTTTTGAATAAAAATC-TTGGAGTTTGTTCCTTTTGAATAAAAATCTTTGAGTTGTTTCTTTTGA
1 CTTTTGAAAAAAAATCTTTGG-GTTTGTTCCTCTTGAAAAAAAATCTTTGAGTTGTTCCTCTTGA
1052146 AAAATATCTTTGAGT
65 AAAATATCTTTGAGT
1052161 CTATTTATTT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
84 19 0.27
85 52 0.73
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (85 bp):
CTTTTGAAAAAAAATCTTTGGGTTTGTTCCTCTTGAAAAAAAATCTTTGAGTTGTTCCTCTTGAA
AAATATCTTTGAGTTTGCTC
Found at i:1052172 original size:56 final size:56
Alignment explanation
Indices: 1051997--1052175 Score: 200
Period size: 56 Copynumber: 3.2 Consensus size: 56
1051987 AAGACAATTT
* * *
1051997 CTTTTGAAAAAAAATCTTTGGGTTTGTTTCTCTTGAAAAAAAATCTTTGAGTTTGTTC
1 CTTTTG-AAAAAAATCTTTGAGTTTGTTTCTTTTG-AAAAAAATCTTTGAGTTTATTC
* * * * *
1052055 CTCTTG-AAAAAATCTTTGAGTTTGCTCCTTTTGAATAAAAATCTTGGAGTTTGTTC
1 CTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTTGAA-AAAAATCTTTGAGTTTATTC
* * *
1052111 CTTTTGAATAAAAATCTTTGAG-TTGTTTCTTTTGAAAAATATCTTTGAGTCTATTT
1 CTTTTGAA-AAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAATCTTTGAGTTTATTC
*
1052167 ATTTTGAAA
1 CTTTTGAAA
1052176 CAAAGTTTTG
Statistics
Matches: 103, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
55 3 0.03
56 69 0.67
57 13 0.13
58 18 0.17
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.46
Consensus pattern (56 bp):
CTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAATCTTTGAGTTTATTC
Found at i:1052172 original size:85 final size:85
Alignment explanation
Indices: 1051993--1052175 Score: 235
Period size: 85 Copynumber: 2.2 Consensus size: 85
1051983 CTTAAAGACA
*
1051993 ATTTCTTTTGAAAAAAAATCTTTGGGTTTGTTTCTCTTGAAAAAAAATCTTTGAGTTTGTTCCTC
1 ATTTCTTTTGAAAAAAAATCTTTGGGTTTGTTCCTCTTGAAAAAAAATCTTTGAGTTTGTTCCTC
*
1052058 TTGAAAAAATCTTTGAGTTT
66 TTGAAAAAATCTTTGAGTCT
** * * * * *
1052078 GCTCCTTTTGAATAAAAATC-TTGGAGTTTGTTCCTTTTGAATAAAAATCTTTGAG-TTGTTTCT
1 ATTTCTTTTGAAAAAAAATCTTTGG-GTTTGTTCCTCTTGAAAAAAAATCTTTGAGTTTGTTCCT
*
1052141 TTTGAAAAATATCTTTGAGTCT
65 CTTGAAAAA-ATCTTTGAGTCT
*
1052163 ATTTATTTTGAAA
1 ATTTCTTTTGAAA
1052176 CAAAGTTTTG
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
84 19 0.23
85 62 0.77
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.46
Consensus pattern (85 bp):
ATTTCTTTTGAAAAAAAATCTTTGGGTTTGTTCCTCTTGAAAAAAAATCTTTGAGTTTGTTCCTC
TTGAAAAAATCTTTGAGTCT
Found at i:1052249 original size:52 final size:53
Alignment explanation
Indices: 1052171--1052274 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
1052161 CTATTTATTT
1052171 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
1052223 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAATCTTTGAG
1052275 ATTGTTTCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 36 0.73
54 13 0.27
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:1052298 original size:27 final size:27
Alignment explanation
Indices: 1052261--1052317 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
1052251 AATTTTGTGA
*
1052261 AAAAAATCTTTGAGATT-GTTTCTTTTG
1 AAAAAATCTTTGAG-TTGGTTTCTTTGG
1052288 AAAAAATCTTTGAGTTGGTTTCTTTGG
1 AAAAAATCTTTGAGTTGGTTTCTTTGG
1052315 AAA
1 AAA
1052318 TAAAATTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.44
Consensus pattern (27 bp):
AAAAAATCTTTGAGTTGGTTTCTTTGG
Found at i:1052348 original size:37 final size:37
Alignment explanation
Indices: 1052306--1052426 Score: 112
Period size: 37 Copynumber: 3.5 Consensus size: 37
1052296 TTTGAGTTGG
*
1052306 TTTCTTTGGAAATAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
* * * * **
1052343 TTTCTTTTGAAACAAAA------ATCT-TTGAGTTTG
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1052373 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
* *
1052410 TTTCTTTTGAAAAAAAA
1 TTTCTTTGGAAACAAAA
1052427 AAATCTTTGA
Statistics
Matches: 62, Mismatches: 15, Indels: 14
0.68 0.16 0.15
Matches are distributed among these distances:
30 21 0.34
31 3 0.05
36 3 0.05
37 35 0.56
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (37 bp):
TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
Found at i:1052367 original size:67 final size:68
Alignment explanation
Indices: 1052288--1052436 Score: 255
Period size: 67 Copynumber: 2.2 Consensus size: 68
1052278 GTTTCTTTTG
*
1052288 AAAAAATCTTTGAGTTGGTTTCTTTGGAAATAAAATTTTGTCTCTCTTAAGATAATTTCTTTTG-
1 AAAAAATCTTTGAGTTGGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
1052352 AAA
66 AAA
* *
1052355 CAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
1 AAAAAATCTTTGAGTTGGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTG-
1052420 AAAA
65 AAAA
1052424 AAAAAATCTTTGA
1 AAAAAATCTTTGA
1052437 ATCTGTTTCT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
67 61 0.80
69 15 0.20
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (68 bp):
AAAAAATCTTTGAGTTGGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
AAA
Found at i:1052770 original size:63 final size:62
Alignment explanation
Indices: 1052668--1052790 Score: 183
Period size: 63 Copynumber: 2.0 Consensus size: 62
1052658 GATGTAATCC
* * *
1052668 ATCTTTGAGTCTGTTTCTTTTAAAACAAAATTTTATCTCTTAACGACAATTTCTTTTGAAAAA
1 ATCTTTGAGTCTGTTTCTTTGAAAACAAAATTTTATCTCTCAA-GACAACTTCTTTTGAAAAA
* * *
1052731 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAA
1 ATCTTTGAGTCTGTTTCTTTGAAAACAAAATTTTATCTCTCAAGACAACTTCTTTTGAAA
1052791 CCACCCACAT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
62 16 0.30
63 38 0.70
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (62 bp):
ATCTTTGAGTCTGTTTCTTTGAAAACAAAATTTTATCTCTCAAGACAACTTCTTTTGAAAAA
Found at i:1052998 original size:34 final size:35
Alignment explanation
Indices: 1052899--1052998 Score: 105
Period size: 38 Copynumber: 2.8 Consensus size: 35
1052889 CAAAGTTCAC
*
1052899 CATCTTTGAGTCTGTTTC-CTTTGAAACAAAACAAA
1 CATCTTTGAGTATGTTTCTC-TTGAAACAAAACAAA
* *
1052934 CAAAGTCTTTGAGTATGTTTTTCTTAAAACAAAA-AAA
1 C--A-TCTTTGAGTATGTTTCTCTTGAAACAAAACAAA
* *
1052971 CATCTTTGAGTTTGTTTCTCTCGAAACA
1 CATCTTTGAGTATGTTTCTCTTGAAACA
1052999 CTAATCTTTG
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
34 22 0.41
35 2 0.04
37 5 0.09
38 24 0.44
39 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (35 bp):
CATCTTTGAGTATGTTTCTCTTGAAACAAAACAAA
Found at i:1053370 original size:43 final size:43
Alignment explanation
Indices: 1053317--1053643 Score: 226
Period size: 43 Copynumber: 7.6 Consensus size: 43
1053307 AGACCAGATT
*
1053317 TCCTTATCACGTAGGAGCCGTGTCA-ACCATAGATAACCAGCC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGCC
* * * ** **
1053359 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCATAAC
1 -TCCTCATCACGTAGGAGCCGTGTCAT-ACC-ATAGATAACCA-GCC
* * * * *
1053406 TCTTCATCACGTATGAGCCGTGTCATTCC-CAG---ACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAG-CC
* *
1053446 TCCTTATCACGTAGGAGCCGTGTCA-ACCATAGATAACCAGCTG
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGC-C
* * * *
1053489 TCCTCATCACGTATGAGCCGTGTCATTCC-CAG---ACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAG-CC
*
1053529 TCCTTATCACGTAGGAGCCGTGTCA-ACCATAGATAACCAGCC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGCC
* * * ** *
1053571 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCAT-ACC-ATAGATAACCAG-CC
* *
1053618 TCTTCATCACGTATGAGCCGTGTCAT
1 TCCTCATCACGTAGGAGCCGTGTCAT
1053644 TCCCCGACCA
Statistics
Matches: 217, Mismatches: 46, Indels: 39
0.72 0.15 0.13
Matches are distributed among these distances:
39 4 0.02
40 58 0.27
42 1 0.00
43 81 0.37
44 2 0.01
45 8 0.04
46 61 0.28
47 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (43 bp):
TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGCC
Found at i:1053466 original size:40 final size:39
Alignment explanation
Indices: 1053411--1053673 Score: 170
Period size: 40 Copynumber: 6.3 Consensus size: 39
1053401 ATAACTCTTC
*
1053411 ATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTT
1 ATCACGTAGGAGCCGTGTCA-TCCCAGACCAGATCTCCTT
* * * * *
1053451 ATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCTGTCCTC
1 ATCACGTAGGAGCCGTGTCATCC-CAG---ACCAGATCTCCTT
*
1053494 ATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTT
1 ATCACGTAGGAGCCGTGTCA-TCCCAGACCAGATCTCCTT
* * * *
1053534 ATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CCGTCCTC
1 ATCACGTAGGAGCCGTGTCATCC-CAG---ACCAGATC-TCCTT
* * *
1053577 ATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACT-CTT
1 ATCACGTAGGAGCCGTGTCATC-CC---AGA---CCAGATCTCCTT
* * * *
1053622 CATCACGTATGAGCCGTGTCATTCCCCGACCAGATGTCCTC
1 -ATCACGTAGGAGCCGTGTCA-TCCCAGACCAGATCTCCTT
1053663 ATCACGTAGGA
1 ATCACGTAGGA
1053674 ACCGCGTTAA
Statistics
Matches: 171, Mismatches: 31, Indels: 42
0.70 0.13 0.17
Matches are distributed among these distances:
39 4 0.02
40 68 0.40
41 2 0.01
42 1 0.01
43 62 0.36
44 3 0.02
45 2 0.01
46 26 0.15
47 3 0.02
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (39 bp):
ATCACGTAGGAGCCGTGTCATCCCAGACCAGATCTCCTT
Found at i:1053508 original size:83 final size:83
Alignment explanation
Indices: 1053409--1053594 Score: 345
Period size: 83 Copynumber: 2.2 Consensus size: 83
1053399 CCATAACTCT
1053409 TCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACGTAGGAGCCGTGTCAACC
*
1053474 ATAGATAACCAGCTGTCC
66 ATAGATAACCAGCCGTCC
1053492 TCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACGTAGGAGCCGTGTCAACC
1053557 ATAGATAACCAGCCGTCC
66 ATAGATAACCAGCCGTCC
* *
1053575 TCATCACGTAGGAACCGTGT
1 TCATCACGTATGAGCCGTGT
1053595 TATCACCTTT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 100 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (83 bp):
TCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACGTAGGAGCCGTGTCAACC
ATAGATAACCAGCCGTCC
Found at i:1053643 original size:212 final size:212
Alignment explanation
Indices: 1053271--1053673 Score: 716
Period size: 212 Copynumber: 1.9 Consensus size: 212
1053261 TAAAGATGGT
* *
1053271 CAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATTTCCTTATCACGTAGGAGCC
1 CAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTTATCACGTAGGAGCC
1053336 GTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCC
66 GTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCC
* *
1053401 ATAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACGTAGGAGCCG
131 AGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTCATCACGTAGGAGCCG
1053466 TGTCAACCATAGATAAC
196 TGTCAACCATAGATAAC
* * * *
1053483 CAGCTGTCCTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACGTAGGAGCC
1 CAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTTATCACGTAGGAGCC
1053548 GTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCC
66 GTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCC
* *
1053613 AGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATGTCCTCATCACGTAGGA
131 AGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTCATCACGTAGGA
1053674 ACCGCGTTAA
Statistics
Matches: 181, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
212 181 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (212 bp):
CAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTTATCACGTAGGAGCC
GTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCC
AGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTCATCACGTAGGAGCCG
TGTCAACCATAGATAAC
Found at i:1053878 original size:3 final size:3
Alignment explanation
Indices: 1053870--1053934 Score: 78
Period size: 3 Copynumber: 20.3 Consensus size: 3
1053860 CGGGTCTTTT
1053870 TTA TTA TTA TT- TATA TATA TTTA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA T-TA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA
1053918 TTA TTTA TTA TTA TTA T
1 TTA -TTA TTA TTA TTA T
1053935 GTTTATTAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.02
3 43 0.75
4 12 0.21
5 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1053890 original size:10 final size:10
Alignment explanation
Indices: 1053869--1053932 Score: 94
Period size: 10 Copynumber: 6.2 Consensus size: 10
1053859 CCGGGTCTTT
1053869 TTTATTATTA
1 TTTATTATTA
1053879 TTTA-TATATA
1 TTTATTAT-TA
1053889 TTTATTATTA
1 TTTATTATTA
1053899 TTTATTATTA
1 TTTATTATTA
1053909 TTATTATTATTA
1 -T-TTATTATTA
1053921 TTTATTATTA
1 TTTATTATTA
1053931 TT
1 TT
1053933 ATGTTTATTA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
9 3 0.06
10 33 0.66
11 5 0.10
12 9 0.18
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATTATTA
Found at i:1053933 original size:16 final size:16
Alignment explanation
Indices: 1053873--1053934 Score: 83
Period size: 16 Copynumber: 3.8 Consensus size: 16
1053863 GTCTTTTTTA
1053873 TTATTATT-TATATATAT
1 TTATTATTAT-TAT-TAT
1053890 TTATTATTATTTATTA-
1 TTATTATTA-TTATTAT
1053906 TTATTATTATTATTAT
1 TTATTATTATTATTAT
1053922 TTATTATTATTAT
1 TTATTATTATTAT
1053935 GTTTATTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.14
16 22 0.52
17 10 0.24
18 3 0.07
19 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:1054238 original size:12 final size:12
Alignment explanation
Indices: 1054221--1054245 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1054211 ACCGAACATC
1054221 CACCTACAGTGA
1 CACCTACAGTGA
1054233 CACCTACAGTGA
1 CACCTACAGTGA
1054245 C
1 C
1054246 CAAATCAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (12 bp):
CACCTACAGTGA
Found at i:1060003 original size:5 final size:5
Alignment explanation
Indices: 1059993--1060018 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1059983 AGTGAATAAA
1059993 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
1060019 AAAAATATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:1062366 original size:28 final size:28
Alignment explanation
Indices: 1062312--1062376 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
1062302 TAACCGAATG
*
1062312 GTGACACGTGACACGAAATATGATACCA
1 GTGACACGTGACACGAAACATGATACCA
* * *
1062340 GTGACACGTGACACGATACATGGTACCG
1 GTGACACGTGACACGAAACATGATACCA
*
1062368 GTGAGACGT
1 GTGACACGT
1062377 TACATCATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.18
Consensus pattern (28 bp):
GTGACACGTGACACGAAACATGATACCA
Found at i:1065441 original size:2 final size:2
Alignment explanation
Indices: 1065434--1065466 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1065424 ATAAATTTAA
1065434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1065467 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1065471 original size:2 final size:2
Alignment explanation
Indices: 1065466--1065517 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1065456 ATATATATAT
1065466 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1065508 AG AG AG AG AG
1 AG AG AG AG AG
1065518 GATTCAGTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1071571 original size:18 final size:18
Alignment explanation
Indices: 1071548--1071583 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1071538 TACAAATGTT
1071548 AATAAATCATTTGAGATC
1 AATAAATCATTTGAGATC
1071566 AATAAATCATTTGAGATC
1 AATAAATCATTTGAGATC
1071584 GATTATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
AATAAATCATTTGAGATC
Found at i:1085970 original size:5 final size:5
Alignment explanation
Indices: 1085960--1085994 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
1085950 GGTTATGGGT
1085960 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1085995 ATGGGATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:1088114 original size:317 final size:316
Alignment explanation
Indices: 1087530--1088487 Score: 1577
Period size: 317 Copynumber: 3.0 Consensus size: 316
1087520 TTGTCAGTTG
* * *
1087530 TGTGCTTGTTATTATTAGATTATTGAATTGGGAAAAACTTTTAGCGGTTAGTTAG--A-AATATA
1 TGTGTTTGTTATTATTAGATTATTGAATTGAGAAAAACTTTTAGCGGTTAGTTAGTAACAATATG
* * *
1087592 TGATGCATGTTTTAATGGAGGAATTTCAGTTTAGGTCTATTGATAATTGAATTTGAATGTTGATT
66 TGATGCATGTTTTAATGGAGGAATTTCAGTTTAGGTCTTTTGCTAATTGAATTCGAATGTTGATT
1087657 TTGTTTTTTTTTCCAGAAAGTTACTTGGATGATAGGCTGGACCTGGTTAGTTTTGAAATTAGGCT
131 TTG-TTTTTTTT-CAGAAAGTTACTTGGATGATA----GG--CTGGTTAGTTTTGAAATTAGGCT
* * * *
1087722 CGTTAGTTGATTAAGATTTTGAATTTCTGTGAGAAGCAATGTTCAATGCTTGACTATCTTGTGGA
188 TGTTAGTTGATCAAGACTTTGAATTTCTGTGAGAAGCAATGTTCAATGCTTAACTATCTTGTGGA
1087787 TGTTGGTAATGGAAATTTTTGGTTTGATAACCTGTGATATGTAACTGAGAGGCTTCTGTTGTTC
253 TGTTGGTAATGGAAATTTTTGGTTTGATAACCTGTGATATGTAACTGAGAGGCTTCTGTTGTTC
*
1087851 TGTGTTTGTTATTATTAGATTATTGAATTGAGAAAAACTTCTAGCGGTTAGTTAGTTAACAATAT
1 TGTGTTTGTTATTATTAGATTATTGAATTGAGAAAAACTTTTAGCGGTTAGTTAG-TAACAATAT
1087916 GTGATGCATGTTTTAATGGAGGAATTTCAGTTTAGGTCTTTTGCTAATTGAATTCGAATGTTGAT
65 GTGATGCATGTTTTAATGGAGGAATTTCAGTTTAGGTCTTTTGCTAATTGAATTCGAATGTTGAT
* *
1087981 TTTGTTTTTTTTCAGAAAGTTGCTTGGATGATAGGCTGGTTAGTTTTGAAATTAGGTTTGTTAGT
130 TTTGTTTTTTTTCAGAAAGTTACTTGGATGATAGGCTGGTTAGTTTTGAAATTAGGCTTGTTAGT
* * *
1088046 TGATCAAGACTTTGAATTTTTTTGAGAAGCAATGTTCAATGCTTAACTATCTTGTGAATGTTGGT
195 TGATCAAGACTTTGAATTTCTGTGAGAAGCAATGTTCAATGCTTAACTATCTTGTGGATGTTGGT
1088111 AATGGAAATTTTTGGTTTGATAACCTGTGATATGTAACTGAGAGGCTTCTGTTGTTC
260 AATGGAAATTTTTGGTTTGATAACCTGTGATATGTAACTGAGAGGCTTCTGTTGTTC
1088168 TGTGTTTGTTATTATTAGATTATTGAATTGAGAAAAACTTTTAGCGGTTAGTTAGTAACAATATG
1 TGTGTTTGTTATTATTAGATTATTGAATTGAGAAAAACTTTTAGCGGTTAGTTAGTAACAATATG
1088233 TGATGCATGTTTTAATGGAGGAATTTCAGTTTAGGTCTTTTGCTAATTGAATTCGAATGTTGA--
66 TGATGCATGTTTTAATGGAGGAATTTCAGTTTAGGTCTTTTGCTAATTGAATTCGAATGTTGATT
* *
1088296 TT-TTTTTTTTAAGAAAGTTACTTGGATGATAGGGTGGTTAGTTTTGAAATTAGGCTTGTTAGTT
131 TTGTTTTTTTTCAGAAAGTTACTTGGATGATAGGCTGGTTAGTTTTGAAATTAGGCTTGTTAGTT
1088360 GATCAAGACTTTGAATTTCTGTGAGAAGCAATGTTCAATGCTTAACTATCTTGTGGATGTTGGTA
196 GATCAAGACTTTGAATTTCTGTGAGAAGCAATGTTCAATGCTTAACTATCTTGTGGATGTTGGTA
* * * * * *
1088425 ATGAAAATTTTTGGTTTGATAACTTGTGATATGTAATTGAGTGGCTTCTTTTGTTG
261 ATGGAAATTTTTGGTTTGATAACCTGTGATATGTAACTGAGAGGCTTCTGTTGTTC
1088481 TGTGTTT
1 TGTGTTT
1088488 AAGGGAGCGG
Statistics
Matches: 603, Mismatches: 30, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
313 177 0.29
314 2 0.00
316 73 0.12
317 198 0.33
319 2 0.00
321 52 0.09
323 20 0.03
324 9 0.01
325 70 0.12
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43
Consensus pattern (316 bp):
TGTGTTTGTTATTATTAGATTATTGAATTGAGAAAAACTTTTAGCGGTTAGTTAGTAACAATATG
TGATGCATGTTTTAATGGAGGAATTTCAGTTTAGGTCTTTTGCTAATTGAATTCGAATGTTGATT
TTGTTTTTTTTCAGAAAGTTACTTGGATGATAGGCTGGTTAGTTTTGAAATTAGGCTTGTTAGTT
GATCAAGACTTTGAATTTCTGTGAGAAGCAATGTTCAATGCTTAACTATCTTGTGGATGTTGGTA
ATGGAAATTTTTGGTTTGATAACCTGTGATATGTAACTGAGAGGCTTCTGTTGTTC
Found at i:1094275 original size:23 final size:23
Alignment explanation
Indices: 1094235--1094278 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1094225 GTATTTATTT
*
1094235 AATTATTTAGTTATAAATATATA
1 AATTATTTAATTATAAATATATA
1094258 AATTATTATAATTA-AAATATA
1 AATTATT-TAATTATAAATATA
1094279 ACTAAAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
AATTATTTAATTATAAATATATA
Found at i:1097364 original size:34 final size:34
Alignment explanation
Indices: 1097326--1097396 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
1097316 ACATTAACTT
*
1097326 ACAGTCCAAAAATTAACAAGCACGGTCCTTAATC
1 ACAGTCCAAAAATTAACAAGCACAGTCCTTAATC
1097360 ACAGTCCAAAAATTAACAAGCACAGTCCTTAATC
1 ACAGTCCAAAAATTAACAAGCACAGTCCTTAATC
1097394 ACA
1 ACA
1097397 AATCAAGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.44, C:0.27, G:0.10, T:0.20
Consensus pattern (34 bp):
ACAGTCCAAAAATTAACAAGCACAGTCCTTAATC
Found at i:1097930 original size:15 final size:17
Alignment explanation
Indices: 1097904--1097941 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1097894 AAATCAACAT
*
1097904 AAAATTACCTAG-ATTA
1 AAAATTACCTAGCATGA
1097920 AAAATTA-CTAGCATGA
1 AAAATTACCTAGCATGA
1097936 AAAATT
1 AAAATT
1097942 GAAACGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.53, C:0.11, G:0.08, T:0.29
Consensus pattern (17 bp):
AAAATTACCTAGCATGA
Found at i:1100255 original size:12 final size:13
Alignment explanation
Indices: 1100238--1100271 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
1100228 CCAAACAACC
1100238 AAAAAAGAAA-AG
1 AAAAAAGAAACAG
1100250 AAAAAAGAAACAG
1 AAAAAAGAAACAG
1100263 AATAAAAGA
1 AA-AAAAGA
1100272 TACCTTTAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.50
13 4 0.20
14 6 0.30
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (13 bp):
AAAAAAGAAACAG
Found at i:1101084 original size:22 final size:22
Alignment explanation
Indices: 1101056--1101097 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1101046 CGGAAATGTT
*
1101056 TAAAAAACATTAATGTTTTAAG
1 TAAAAAACAATAATGTTTTAAG
*
1101078 TAAAAAATAATAATGTTTTA
1 TAAAAAACAATAATGTTTTA
1101098 TATAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (22 bp):
TAAAAAACAATAATGTTTTAAG
Found at i:1101634 original size:2 final size:2
Alignment explanation
Indices: 1101622--1101661 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1101612 ATTATAGAAA
* *
1101622 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1101662 TATTATCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:1102392 original size:21 final size:21
Alignment explanation
Indices: 1102310--1102392 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1102300 CGCAAATCAG
1102310 TTTCCAAAATCGCAACGCGAT
1 TTTCCAAAATCGCAACGCGAT
* *
1102331 TCTT-GAAAATCGCAATGCGAT
1 T-TTCCAAAATCGCAACGCGAT
** * * **
1102352 AGTACAAATTCGCATTGCGAT
1 TTTCCAAAATCGCAACGCGAT
1102373 TTTCCAAAATCGCAACGCGA
1 TTTCCAAAATCGCAACGCGA
1102393 ACACATAAAT
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (21 bp):
TTTCCAAAATCGCAACGCGAT
Found at i:1102421 original size:20 final size:20
Alignment explanation
Indices: 1102379--1102552 Score: 208
Period size: 20 Copynumber: 8.7 Consensus size: 20
1102369 CGATTTTCCA
* *
1102379 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1102399 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
1102419 AAATTGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1102439 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1102459 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1102479 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1102499 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1102519 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1102540 AAATCGCAACGCG
1 AAATCGCAACGCG
1102553 ATATTTAAAG
Statistics
Matches: 130, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
19 1 0.01
20 111 0.85
21 17 0.13
22 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1103117 original size:20 final size:20
Alignment explanation
Indices: 1103073--1103182 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
1103063 TTTGCAGAAG
*
1103073 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
1103094 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
1103114 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
1103135 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
1103149 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
1103168 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
1103183 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:1103130 original size:41 final size:38
Alignment explanation
Indices: 1103071--1103182 Score: 144
Period size: 41 Copynumber: 3.0 Consensus size: 38
1103061 AATTTGCAGA
*
1103071 AGTCGCAACGAGATAAATGAAAATCGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1103109 GACTGTCGCAACGAGAGAAATGAAAATCGCAACGAGAG-A-
1 -A--GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
*
1103148 A-TCGCAAC--GCGAAATGAAAATCGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1103183 CGCAACGCGA
Statistics
Matches: 67, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
33 23 0.34
34 1 0.01
35 7 0.10
38 1 0.01
39 1 0.01
40 1 0.01
41 33 0.49
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.12
Consensus pattern (38 bp):
AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
Found at i:1103152 original size:14 final size:14
Alignment explanation
Indices: 1103133--1103189 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1103123 GAGAAATGAA
1103133 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1103147 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1103166 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1103180 AATCGCAACG
1 AATCGCAACG
1103190 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1103165 original size:33 final size:33
Alignment explanation
Indices: 1103125--1103205 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1103115 CGCAACGAGA
1103125 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1103158 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1103191 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1103206 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Done.