Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 122 of 187
Found at i:36879249 original size:20 final size:20
Alignment explanation
Indices: 36879224--36879271 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
36879214 TCCATGCGAT
*
36879224 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCACACGAGCTCAAG
* *
36879244 TCAGCTCGCACGAGCTCAAT
1 TCAGCTCACACGAGCTCAAG
36879264 TCAGCTCA
1 TCAGCTCA
36879272 TTTAGCTCGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (20 bp):
TCAGCTCACACGAGCTCAAG
Found at i:36886219 original size:23 final size:23
Alignment explanation
Indices: 36886187--36886298 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
36886177 CTTTTTGAAC
* *
36886187 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
36886210 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * *
36886233 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
36886256 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
36886279 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
36886299 CCCAAAACCG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:36886263 original size:46 final size:46
Alignment explanation
Indices: 36886187--36886298 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
36886177 CTTTTTGAAC
* *
36886187 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
36886233 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
36886279 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
36886299 CCCAAAACCG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:36892734 original size:28 final size:29
Alignment explanation
Indices: 36892703--36892774 Score: 110
Period size: 28 Copynumber: 2.5 Consensus size: 29
36892693 TTAGATATTA
*
36892703 TTAAATATGTCCTAATTAGTTTA-GGGTT
1 TTAAATATGTCCTAATTAGTTCATGGGTT
* *
36892731 TTAATTATGTCCTAATTAGTTCATGTGTT
1 TTAAATATGTCCTAATTAGTTCATGGGTT
36892760 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
36892775 ACTAATACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 21 0.54
29 18 0.46
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCATGGGTT
Found at i:36904866 original size:20 final size:20
Alignment explanation
Indices: 36904843--36904889 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
36904833 GGGTTGAGGT
36904843 TGAGCTGAATTCAACTCGAA
1 TGAGCTGAATTCAACTCGAA
* * * *
36904863 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTCAACTCGAA
36904883 TGAGCTG
1 TGAGCTG
36904890 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTCAACTCGAA
Found at i:36930244 original size:21 final size:21
Alignment explanation
Indices: 36930218--36930280 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
36930208 TTGGTATTTG
36930218 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
36930239 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
** *
36930260 GGTGTTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
36930281 ATGGTTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 22 0.61
22 14 0.39
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:36930249 original size:11 final size:11
Alignment explanation
Indices: 36930229--36930261 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
36930219 GAATTGGTAC
36930229 GAAATGGTATG
1 GAAATGGTATG
*
36930240 GAATTGGTAT-
1 GAAATGGTATG
36930250 GAAATGGTATG
1 GAAATGGTATG
36930261 G
1 G
36930262 TGTTTGGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (11 bp):
GAAATGGTATG
Found at i:36931470 original size:30 final size:30
Alignment explanation
Indices: 36931412--36931470 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
36931402 TTGAAAAGGT
* *
36931412 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
36931442 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
36931471 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:36933629 original size:29 final size:29
Alignment explanation
Indices: 36933592--36933664 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
36933582 TTAGATATTA
* *
36933592 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
*
36933621 TTAATTATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
36933650 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
36933665 ACTAATACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:36936451 original size:34 final size:34
Alignment explanation
Indices: 36936389--36936495 Score: 162
Period size: 34 Copynumber: 3.1 Consensus size: 34
36936379 TGCTTTCTTC
* *
36936389 AACAACTCATTGAATGGCCG-TCCATTTGCATGTGG
1 AACATCTCATT-AATTGCCGTTCC-TTTGCATGTGG
36936424 AACATCTCATTAATTGCCGTTCCTTTGCATGTGG
1 AACATCTCATTAATTGCCGTTCCTTTGCATGTGG
*
36936458 AACATCTCATTAATTGCCGTTCCTTTGCATGTAG
1 AACATCTCATTAATTGCCGTTCCTTTGCATGTGG
36936492 AACA
1 AACA
36936496 ACATCTTCAA
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
34 55 0.81
35 13 0.19
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (34 bp):
AACATCTCATTAATTGCCGTTCCTTTGCATGTGG
Found at i:36936732 original size:16 final size:16
Alignment explanation
Indices: 36936692--36936733 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
36936682 TTCTGCTTTA
36936692 AACAACAGCATTAAAC
1 AACAACAGCATTAAAC
* *
36936708 AATAGCAGCATTAAAC
1 AACAACAGCATTAAAC
*
36936724 AGCAACAGCA
1 AACAACAGCA
36936734 AAACACATTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.12, T:0.12
Consensus pattern (16 bp):
AACAACAGCATTAAAC
Found at i:36939028 original size:12 final size:12
Alignment explanation
Indices: 36938995--36939076 Score: 55
Period size: 12 Copynumber: 6.9 Consensus size: 12
36938985 TTTCCACTCG
36938995 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
36939006 AGCTCTCTTTCA
1 ATTTCTTTTTCA
36939018 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
*
36939031 CTCTTTCTTTTTC-
1 --ATTTCTTTTTCA
36939044 --TTCTTTTTCA
1 ATTTCTTTTTCA
*
36939054 ATTTATTTTTCA
1 ATTTCTTTTTCA
*
36939066 ATCTCTTTTTC
1 ATTTCTTTTTC
36939077 TTTTTTAATT
Statistics
Matches: 54, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
9 9 0.17
11 3 0.06
12 30 0.56
13 2 0.04
14 1 0.02
15 9 0.17
ACGTcount: A:0.13, C:0.23, G:0.01, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:36939101 original size:14 final size:13
Alignment explanation
Indices: 36939072--36939108 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
36939062 TTCAATCTCT
36939072 TTTTCTTTTTTAA
1 TTTTCTTTTTTAA
*
36939085 TTTTCTTTTCTTCA
1 TTTTCTTTT-TTAA
36939099 TTTTCTTTTT
1 TTTTCTTTTT
36939109 CTCTCACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTCTTTTTTAA
Found at i:36939136 original size:18 final size:18
Alignment explanation
Indices: 36939059--36939156 Score: 70
Period size: 18 Copynumber: 5.3 Consensus size: 18
36939049 TTTCAATTTA
*
36939059 TTTTTCAATCTCTTTTTC
1 TTTTTCAATTTCTTTTTC
*
36939077 TTTTTTAATTTTCTTTTCTTC
1 TTTTTCAA-TTTC-TTT-TTC
* ** * **
36939098 ATTTTCTTTTTCTCTCAC
1 TTTTTCAATTTCTTTTTC
**
36939116 TTTTTTGATTTCTTTTTC
1 TTTTTCAATTTCTTTTTC
*
36939134 TTTTGCAATTTCTTTTTC
1 TTTTTCAATTTCTTTTTC
36939152 TTTTT
1 TTTTT
36939157 GTTTACTTTC
Statistics
Matches: 57, Mismatches: 20, Indels: 6
0.69 0.24 0.07
Matches are distributed among these distances:
18 38 0.67
19 5 0.09
20 7 0.12
21 7 0.12
ACGTcount: A:0.09, C:0.17, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTTCAATTTCTTTTTC
Found at i:36939187 original size:57 final size:61
Alignment explanation
Indices: 36939049--36939187 Score: 134
Period size: 57 Copynumber: 2.4 Consensus size: 61
36939039 TTTTCTTCTT
* ** *
36939049 TTTCAATTTATTTTTCAATCTCTTTTTCTTTTTTAATTTTCTTTTCTTCATTTTCTTTTTC
1 TTTCAATTTCTTTTTCAATCTCTTTTTCTTTTGCAATTTTCTTTTCTTCATTTTCTTTTAC
* ** *
36939110 TCTC-A---CTTTTTTGATTTCTTTTTCTTTTGCAA-TTTC-TTT-TTC-TTTT-TGTTTAC
1 TTTCAATTTCTTTTTCAATCTCTTTTTCTTTTGCAATTTTCTTTTCTTCATTTTCT-TTTAC
36939163 TTTCAATTTCTTTTTCAATCTCTTT
1 TTTCAATTTCTTTTTCAATCTCTTT
36939188 CTCCTTTTCT
Statistics
Matches: 61, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
52 1 0.02
53 11 0.18
54 4 0.07
55 3 0.05
56 4 0.07
57 34 0.56
60 1 0.02
61 3 0.05
ACGTcount: A:0.12, C:0.17, G:0.02, T:0.68
Consensus pattern (61 bp):
TTTCAATTTCTTTTTCAATCTCTTTTTCTTTTGCAATTTTCTTTTCTTCATTTTCTTTTAC
Found at i:36949961 original size:20 final size:20
Alignment explanation
Indices: 36949938--36949984 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
36949928 GGGTTAAAAT
*
36949938 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
36949958 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
36949978 TGAGCTG
1 TGAGCTG
36949985 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:36953226 original size:22 final size:24
Alignment explanation
Indices: 36953200--36953243 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
36953190 CTTGGACCAA
36953200 GATTTTCAAGA-T-TTGAAATCTT
1 GATTTTCAAGATTCTTGAAATCTT
*
36953222 GATTTTCATGATTCTTGAAATC
1 GATTTTCAAGATTCTTGAAATC
36953244 ACTCCAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 1 0.05
24 8 0.42
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (24 bp):
GATTTTCAAGATTCTTGAAATCTT
Found at i:36953671 original size:29 final size:29
Alignment explanation
Indices: 36953637--36953709 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
36953627 TTAGATATTA
* *
36953637 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
36953666 TTAAATATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
36953695 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
36953710 ACTAATACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:36956256 original size:11 final size:11
Alignment explanation
Indices: 36956225--36956258 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
36956215 GCATAAAGAC
36956225 GTTCACACCAT
1 GTTCACACCAT
*
36956236 GTTCA-GCCAT
1 GTTCACACCAT
36956246 GTTCACACCAT
1 GTTCACACCAT
36956257 GT
1 GT
36956259 GGCTCTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (11 bp):
GTTCACACCAT
Found at i:36958250 original size:6 final size:6
Alignment explanation
Indices: 36958241--36958269 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
36958231 AAAAAGAAAA
36958241 TGAGAG TGAGAG TGAGAG TGAGAG TGAGA
1 TGAGAG TGAGAG TGAGAG TGAGAG TGAGA
36958270 AAAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.48, T:0.17
Consensus pattern (6 bp):
TGAGAG
Found at i:36968535 original size:21 final size:21
Alignment explanation
Indices: 36968509--36968571 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
36968499 TTGGTATTTG
36968509 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
**
36968530 GGAATTGGTATAAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
36968551 GGTATTTGGTACGAAATGGTA
1 GG-AATTGGTACGAAATGGTA
36968572 ATGGTTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 21 0.58
22 15 0.42
ACGTcount: A:0.33, C:0.03, G:0.32, T:0.32
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:36970473 original size:14 final size:14
Alignment explanation
Indices: 36970443--36970472 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
36970433 CAATTTTTCA
36970443 TTCACTTTTTCTTT
1 TTCACTTTTTCTTT
36970457 TTCATCTTTTTCTTT
1 TTCA-CTTTTTCTTT
36970472 T
1 T
36970473 CTCGCTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (14 bp):
TTCACTTTTTCTTT
Found at i:36970531 original size:20 final size:20
Alignment explanation
Indices: 36970482--36970535 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
36970472 TCTCGCTCTC
* *
36970482 TTTTCATTTTCATTTTTTGAA
1 TTTTC-TTTTCTTTTTTTCAA
*
36970503 TTTTC-TTTCTTTTTTTCAT
1 TTTTCTTTTCTTTTTTTCAA
36970522 TTTTCTTTTCTTTT
1 TTTTCTTTTCTTTT
36970536 GTATTTTCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 16 0.55
20 8 0.28
21 5 0.17
ACGTcount: A:0.09, C:0.13, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTTTCAA
Found at i:36972753 original size:16 final size:16
Alignment explanation
Indices: 36972732--36972769 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
36972722 CCGTATGCAA
36972732 TTTTTTTCTTTC-AAT
1 TTTTTTTCTTTCGAAT
36972747 TTTTTTTCTTTCGAAT
1 TTTTTTTCTTTCGAAT
36972763 TTTTTTT
1 TTTTTTT
36972770 TCAAACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTTTTCTTTCGAAT
Found at i:36974558 original size:22 final size:22
Alignment explanation
Indices: 36974530--36974573 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
36974520 TTTTGAACCA
36974530 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
36974552 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
36974574 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:36976473 original size:40 final size:41
Alignment explanation
Indices: 36976429--36976512 Score: 125
Period size: 40 Copynumber: 2.1 Consensus size: 41
36976419 TAAATAAAAG
36976429 AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTA-AT
1 AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTATAT
* * * *
36976469 AAAGTCCAGCAACTCATTTATTAAGTAAGATGAGTTTATAT
1 AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTATAT
36976510 AAA
1 AAA
36976513 TTGCAAGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 34 0.87
41 5 0.13
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (41 bp):
AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTATAT
Found at i:36980523 original size:18 final size:18
Alignment explanation
Indices: 36980502--36980541 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
36980492 GATTGAGAGT
* * *
36980502 GAAAAGGAATGTGAAACA
1 GAAAAGAAAAGTGAAAAA
36980520 GAAAAGAAAAGTGAAAAA
1 GAAAAGAAAAGTGAAAAA
36980538 GAAA
1 GAAA
36980542 TTGAAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (18 bp):
GAAAAGAAAAGTGAAAAA
Found at i:36995574 original size:92 final size:93
Alignment explanation
Indices: 36995417--36995605 Score: 371
Period size: 92 Copynumber: 2.0 Consensus size: 93
36995407 CAACCCCCGT
36995417 ATCAGCGTTCATGCACAATCCTTAATGCATTCATACGTTGAAGGTAGTCATTCATGCACCCGCAC
1 ATCAGCGTTCATGCACAATCCTTAATGCATTCATACGTTGAAGGTAGTCATTCATGCACCCGCAC
36995482 ATACATTGAACCAGCCCATTCATGAA-C
66 ATACATTGAACCAGCCCATTCATGAACC
36995509 ATCAGCGTTCATGCACAATCCTTAATGCATTCATACGTTGAAGGTAGTCATTCATGCACCCGCAC
1 ATCAGCGTTCATGCACAATCCTTAATGCATTCATACGTTGAAGGTAGTCATTCATGCACCCGCAC
36995574 ATACATTGAACCAGCCCATTCATGAACC
66 ATACATTGAACCAGCCCATTCATGAACC
36995602 ATCA
1 ATCA
36995606 TTGATTGTGT
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
92 91 0.95
93 5 0.05
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.26
Consensus pattern (93 bp):
ATCAGCGTTCATGCACAATCCTTAATGCATTCATACGTTGAAGGTAGTCATTCATGCACCCGCAC
ATACATTGAACCAGCCCATTCATGAACC
Found at i:37002253 original size:22 final size:22
Alignment explanation
Indices: 37002223--37002266 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
37002213 TTTGGTATTT
37002223 GGGAATTGGTACAAAATGGTAA
1 GGGAATTGGTACAAAATGGTAA
* *
37002245 GGGATTTGGTGCAAAATGGTAA
1 GGGAATTGGTACAAAATGGTAA
37002267 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.34, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACAAAATGGTAA
Found at i:37008711 original size:29 final size:29
Alignment explanation
Indices: 37008674--37008746 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 29
37008664 TTAGATATTA
37008674 TTAAATATGTCCTAATTAGTT-AAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAA-GTGTT
*
37008703 TTAATTATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
37008732 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
37008747 ACTAATACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
29 39 0.95
30 2 0.05
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:37011296 original size:46 final size:46
Alignment explanation
Indices: 37011224--37011317 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
37011214 CAAAGAAAAG
37011224 ACCTCGACCCACTATCAAGAAAGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAAAGATAGGAACCTTGGTATATGATGA
* *
37011270 ACCTCGACCCAGTATCAATG-ATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAA-GAAAGATAGGAACCTTGGTATATGATGA
37011316 AC
1 AC
37011318 GCCAGACTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.23
Consensus pattern (46 bp):
ACCTCGACCCACTATCAAGAAAGATAGGAACCTTGGTATATGATGA
Found at i:37015454 original size:20 final size:20
Alignment explanation
Indices: 37015429--37015471 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
37015419 AAAAGAAAAG
37015429 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
37015449 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
37015469 AAA
1 AAA
37015472 ACAAGAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:37027777 original size:21 final size:21
Alignment explanation
Indices: 37027753--37027793 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
37027743 AATGGAAACT
37027753 AATTTTTTTCAAATTTTTTTG
1 AATTTTTTTCAAATTTTTTTG
* *
37027774 AATTTTTTTCGAGTTTTTTT
1 AATTTTTTTCAAATTTTTTT
37027794 TCGAGAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (21 bp):
AATTTTTTTCAAATTTTTTTG
Found at i:37027782 original size:10 final size:11
Alignment explanation
Indices: 37027753--37027793 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
37027743 AATGGAAACT
*
37027753 AATTTTTTTCA
1 AATTTTTTTCG
37027764 AATTTTTTT-G
1 AATTTTTTTCG
37027774 AATTTTTTTCG
1 AATTTTTTTCG
*
37027785 AGTTTTTTT
1 AATTTTTTT
37027794 TCGAGAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (11 bp):
AATTTTTTTCG
Found at i:37028164 original size:46 final size:46
Alignment explanation
Indices: 37028111--37028203 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
37028101 CAAAGAAAAG
37028111 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAGGAACCTTGGTATATGATGA
*
37028157 ACCTCGACCCAGTATCAATGATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
37028203 A
1 A
37028204 TGCCAGACTA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
Found at i:37044464 original size:27 final size:28
Alignment explanation
Indices: 37044434--37044487 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
37044424 AGTATGTTTT
*
37044434 ATTTTAATGCATGTTATTAATG-TGTCA
1 ATTTTAATACATGTTATTAATGATGTCA
* *
37044461 ATTTTATTACATGTTTTTAATGATGTC
1 ATTTTAATACATGTTATTAATGATGTC
37044488 CAAGTCCAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (28 bp):
ATTTTAATACATGTTATTAATGATGTCA
Found at i:37045796 original size:12 final size:12
Alignment explanation
Indices: 37045781--37045822 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
37045771 GTAAGTAGAT
37045781 TTGTAAAAAAAA
1 TTGTAAAAAAAA
*
37045793 TTGTTAAAAAAA
1 TTGTAAAAAAAA
*
37045805 TCGTACAAAAAAA
1 TTGTA-AAAAAAA
37045818 TTGTA
1 TTGTA
37045823 TTTATTTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.29
Consensus pattern (12 bp):
TTGTAAAAAAAA
Found at i:37049020 original size:29 final size:29
Alignment explanation
Indices: 37048979--37049051 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
37048969 TTAGATATTA
* *
37048979 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
* *
37049008 TTAATTATTTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
37049037 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
37049052 ACTAATACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.48
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:37050271 original size:9 final size:10
Alignment explanation
Indices: 37050254--37050278 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
37050244 ATTTCTCTTC
37050254 TCTTTTTTTT
1 TCTTTTTTTT
37050264 TCTTTTTTTT
1 TCTTTTTTTT
37050274 TCTTT
1 TCTTT
37050279 GGAAGCAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:37055116 original size:20 final size:20
Alignment explanation
Indices: 37055091--37055157 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
37055081 AGCTCGTTTC
37055091 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
37055111 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* * *
37055131 CAGCTCATTCGAGTTCAATT
1 CAGCTCACTCGAGCTCAAGT
37055151 CAGCTCA
1 CAGCTCA
37055158 ACCTCAACCC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:37057296 original size:39 final size:38
Alignment explanation
Indices: 37057229--37057361 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
37057219 ACCAGAATGG
*
37057229 CACCCAGTGCCTCATCGG-ATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGTATAG-CCGAAG-AATAGTTGA
* * *
37057268 CACCCAGTGTCTCATCGGTAAAGCCGAAGAA-AGTTGG
1 CACCCAGTGCCTCATCGGTATAGCCGAAGAATAGTTGA
* * * * *
37057305 TACCCAGTACCTCATCGAATCTATCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCG-GTATAGCCGAAG-AATAGT--TGA
*
37057346 CACCCAGTGTCTCATC
1 CACCCAGTGCCTCATC
37057362 AACTCGAGGT
Statistics
Matches: 73, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
37 19 0.26
38 10 0.14
39 25 0.34
40 4 0.05
41 15 0.21
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGTATAGCCGAAGAATAGTTGA
Found at i:37057516 original size:24 final size:25
Alignment explanation
Indices: 37057466--37057536 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 25
37057456 CATATAATCC
**
37057466 CAATTCAATCACAATTTCTCACACTTT
1 CAATTCAATCA-TTTTTC-CACACTTT
37057493 CAATTCAATCATTTTTCCAC-CTTT
1 CAATTCAATCATTTTTCCACACTTT
* *
37057517 CAA-TCAATAATTATTCCACA
1 CAATTCAATCATTTTTCCACA
37057537 ATTAACACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
23 14 0.36
24 7 0.18
25 3 0.08
26 4 0.10
27 11 0.28
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (25 bp):
CAATTCAATCATTTTTCCACACTTT
Found at i:37057697 original size:12 final size:12
Alignment explanation
Indices: 37057680--37057725 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
37057670 CCACTCATCT
*
37057680 TAATAATAATAA
1 TAATAATACTAA
*
37057692 TAATAATACTAT
1 TAATAATACTAA
*
37057704 TACTAATACTAA
1 TAATAATACTAA
*
37057716 TATTAATACT
1 TAATAATACT
37057726 TACCTCACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (12 bp):
TAATAATACTAA
Found at i:37058917 original size:21 final size:21
Alignment explanation
Indices: 37058893--37058935 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
37058883 AATAATAACT
37058893 AATAACTAATAATAAATAATA
1 AATAACTAATAATAAATAATA
* * * *
37058914 AATATCTTATACTAATTAATA
1 AATAACTAATAATAAATAATA
37058935 A
1 A
37058936 GCAAATTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAACTAATAATAAATAATA
Found at i:37059067 original size:25 final size:23
Alignment explanation
Indices: 37059023--37059083 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
37059013 ATTTTGATTT
*
37059023 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
37059047 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
37059071 ATATAAATTATAT
1 AT-TTAATTATAT
37059084 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:37059086 original size:35 final size:35
Alignment explanation
Indices: 37059031--37059110 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
37059021 TTATTTAATA
* *
37059031 ATATAATAT-CATTATAATTTAATTATCATAAATT
1 ATATAATATAAATTATAATTTAAATATCATAAATT
*
37059065 CATATAATATAAATTAT-ATTTAAATATCATTAATT
1 -ATATAATATAAATTATAATTTAAATATCATAAATT
37059100 ATATAAT-TAAA
1 ATATAATATAAA
37059111 CAAATAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
33 4 0.10
34 7 0.17
35 25 0.61
36 5 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (35 bp):
ATATAATATAAATTATAATTTAAATATCATAAATT
Found at i:37063579 original size:21 final size:21
Alignment explanation
Indices: 37063537--37063579 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
37063527 TTCAATACGC
*
37063537 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
37063558 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
37063579 A
1 A
37063580 ATTTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:37065090 original size:6 final size:6
Alignment explanation
Indices: 37065079--37065121 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
37065069 CCACTCATCT
* * * *
37065079 TAATAA TAATAA TAATAC TATTAC TAATAC TAATAT TAATAC T
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC T
37065122 TACCTCACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (6 bp):
TAATAC
Found at i:37067991 original size:25 final size:23
Alignment explanation
Indices: 37067947--37068007 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
37067937 ATTTTGATTT
*
37067947 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
37067971 ATTTAATTATCATAA-ACTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
37067995 ATATAAATTATAT
1 AT-TTAATTATAT
37068008 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:37068010 original size:35 final size:35
Alignment explanation
Indices: 37067955--37068034 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
37067945 TTATTTAATA
* *
37067955 ATATAATAT-CATTATAATTTAATTATCATAAACTC
1 ATATAATATAAATTATAATTTAAATATCATAAA-TC
* *
37067990 ATATAATATAAATTAT-ATTTAAATATCATTAATT
1 ATATAATATAAATTATAATTTAAATATCATAAATC
37068024 ATATAAT-TAAA
1 ATATAATATAAA
37068035 CAAATAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
33 4 0.10
34 8 0.20
35 23 0.57
36 5 0.12
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (35 bp):
ATATAATATAAATTATAATTTAAATATCATAAATC
Found at i:37086840 original size:11 final size:11
Alignment explanation
Indices: 37086824--37086864 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
37086814 CGTATGCAAT
37086824 ATTTTTTTTCA
1 ATTTTTTTTCA
37086835 ATTTTTTTTCA
1 ATTTTTTTTCA
37086846 ATTTTTTTT--
1 ATTTTTTTTCA
37086855 ATTTTTTTTC
1 ATTTTTTTTC
37086865 GAAAACTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.31
11 20 0.69
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (11 bp):
ATTTTTTTTCA
Found at i:37086841 original size:13 final size:12
Alignment explanation
Indices: 37086820--37086854 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
37086810 AGACCGTATG
37086820 CAATATTTTTTTT
1 CAAT-TTTTTTTT
37086833 CAA-TTTTTTTT
1 CAATTTTTTTTT
37086844 CAATTTTTTTT
1 CAATTTTTTTT
37086855 ATTTTTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.52
12 7 0.33
13 3 0.14
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:37086852 original size:20 final size:20
Alignment explanation
Indices: 37086827--37086864 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
37086817 ATGCAATATT
37086827 TTTTTTCAATTTTTTTTCAA
1 TTTTTTCAATTTTTTTTCAA
**
37086847 TTTTTTTTATTTTTTTTC
1 TTTTTTCAATTTTTTTTC
37086865 GAAAACTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTCAATTTTTTTTCAA
Found at i:37089168 original size:21 final size:21
Alignment explanation
Indices: 37089144--37089187 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
37089134 TTCGACTAAG
37089144 AAAGAAAGAAAACAAATATTA
1 AAAGAAAGAAAACAAATATTA
37089165 AAAGAAAGAAAACAAATATTA
1 AAAGAAAGAAAACAAATATTA
37089186 AA
1 AA
37089188 GGTATGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.14
Consensus pattern (21 bp):
AAAGAAAGAAAACAAATATTA
Found at i:37091421 original size:27 final size:28
Alignment explanation
Indices: 37091384--37091448 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
37091374 TGTTTTTTTA
* *
37091384 CTTTCACTTTCTTTTTC-TTTTTCATTT
1 CTTTCAATTTCTTTTTCATTGTTCATTT
*
37091411 CTTTCAATTTCTTTTTCATTGTTCGTTT
1 CTTTCAATTTCTTTTTCATTGTTCATTT
*
37091439 CTCTCAATTT
1 CTTTCAATTT
37091449 TTCCACAGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 16 0.48
28 17 0.52
ACGTcount: A:0.11, C:0.22, G:0.03, T:0.65
Consensus pattern (28 bp):
CTTTCAATTTCTTTTTCATTGTTCATTT
Found at i:37093651 original size:11 final size:11
Alignment explanation
Indices: 37093620--37093651 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
37093610 TTTTCAATTT
37093620 TTTTTCTTTTGA
1 TTTTT-TTTTGA
37093632 TTTTTTTTTGA
1 TTTTTTTTTGA
37093643 TTTTTTTTT
1 TTTTTTTTT
37093652 CAAATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:37093651 original size:16 final size:16
Alignment explanation
Indices: 37093598--37093639 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
37093588 AGACCGTATA
37093598 CAATTTTTTTTCTTTT
1 CAATTTTTTTTCTTTT
37093614 CAATTTTTTTTCTTTT
1 CAATTTTTTTTCTTTT
*
37093630 -GATTTTTTTT
1 CAATTTTTTTT
37093640 TGATTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 9 0.36
16 16 0.64
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (16 bp):
CAATTTTTTTTCTTTT
Found at i:37093671 original size:15 final size:13
Alignment explanation
Indices: 37093642--37093668 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
37093632 TTTTTTTTTG
37093642 ATTTTTTTTTCAA
1 ATTTTTTTTTCAA
37093655 ATTTTTTTTTCAA
1 ATTTTTTTTTCAA
37093668 A
1 A
37093669 AATCTACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTTTTTTTCAA
Found at i:37095941 original size:27 final size:28
Alignment explanation
Indices: 37095897--37095950 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 28
37095887 GCTGGACTTG
*
37095897 GACATCATTAAAAACATGTAATAAAATT
1 GACATCATTAAAAACATGCAATAAAATT
* * *
37095925 GACA-CATTAATAGCATGCATTAAAAT
1 GACATCATTAAAAACATGCAATAAAAT
37095951 AAAACACATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.28
Consensus pattern (28 bp):
GACATCATTAAAAACATGCAATAAAATT
Found at i:37098700 original size:14 final size:14
Alignment explanation
Indices: 37098681--37098709 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
37098671 TGCATCTCCC
37098681 CATGCATGAATCTA
1 CATGCATGAATCTA
37098695 CATGCATGAATCTA
1 CATGCATGAATCTA
37098709 C
1 C
37098710 CCAATGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (14 bp):
CATGCATGAATCTA
Found at i:37100995 original size:12 final size:12
Alignment explanation
Indices: 37100962--37101006 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
37100952 TTTTCACTCG
37100962 ATTTC-TTTTCA
1 ATTTCTTTTTCA
* *
37100973 AGTTCTCTTTCA
1 ATTTCTTTTTCA
37100985 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
37100997 ATCTCTTTTT
1 ATTTCTTTTT
37101007 ATTTTTCACT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 4 0.14
12 24 0.86
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:37101010 original size:22 final size:22
Alignment explanation
Indices: 37100962--37101004 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
37100952 TTTTCACTCG
37100962 ATTTCTTTTCAAGTTCTCTTTCA
1 ATTTCTTTTCAAG-TCTCTTTCA
37100985 ATTTCTTTTTCAA-TCTCTTT
1 ATTTC-TTTTCAAGTCTCTTT
37101005 TTATTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 5 0.26
24 7 0.37
ACGTcount: A:0.16, C:0.21, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTCTTTTCAAGTCTCTTTCA
Found at i:37104640 original size:22 final size:22
Alignment explanation
Indices: 37104588--37104652 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
37104578 TATTTGGGAA
* * *
37104588 TTGGTATGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
37104610 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
37104632 TTGGTACGAAAATGGAAATGG
1 TTGGTACG-AAATGGTAATGG
37104653 TTCAAAAAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:37104826 original size:359 final size:356
Alignment explanation
Indices: 37104350--37105064 Score: 1189
Period size: 359 Copynumber: 2.0 Consensus size: 356
37104340 TCTAAGGCTG
37104350 TGATACGATCTCGGTTTAGTAGTTGAGCCCGAGTCGTTTAGTTCCCGATCGTAAACGAAGAAGTA
1 TGATACGATCTCGGTTTAGTAGTTGAGCCCGAGTCGTTTAGTTCCCGATCGTAAACGAAGAAGTA
*
37104415 GATTAGACGAGAAGAAGTTAGAAAATATTTGTGTTCAAAGAAGTAAGATAAGTTCGTGCAAAGTT
66 GATTAGACGAGAAGAAGTTAGAAAATATTTGTGTACAAAGAAGTAAGATAAGTTCGTGCAAAGTT
* *
37104480 GGATGTGGATTTGGTTTAAGTCGAAATGGTATGAATAGAATGGACGAGTTCGGTTTAGGATAATT
131 GGATGTGGATTTGGTTTAAGTCGAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAAGATAATT
* * * *
37104545 AAGAAATGGTCTTTGGTTTTGGATACGTTTTGGTATTTGGGAATTGGTATGAAACGGTAAGGGAT
196 AAGAAATGGTATTTGGTTTTGG-TACATTTTGGTATTTGGGAATTGGTACGAAACGGT-AGGGAA
*
37104610 TTGAAACGAAATGGTAATGG-ATTTGGTACGAAAATGGAAATGGTTCAAAAAGGCCAAGAGTGAA
259 TTGAAACGAAATGGT-ATGGTATTTGGTACG-AAATGGAAATGGTTCAAAAAGGCCAAGAATGAA
37104674 CCAACACTAAAGAAAAGTGTCGACCCGAAACTTAT
322 CCAACACTAAAGAAAAGTGTCGACCCGAAACTTAT
* *
37104709 TGATACGATCTCGGTTTAGTAGTTGAGTCCGAGTCGTTTGGTTCCCGATCGTAAACGAAGAAGTA
1 TGATACGATCTCGGTTTAGTAGTTGAGCCCGAGTCGTTTAGTTCCCGATCGTAAACGAAGAAGTA
* * *
37104774 GATTAGACGAGAAGGAGTTAGAATATATTTGTGTACAAAGAAGTAAGATAAGTTTGTGCAAAGTT
66 GATTAGACGAGAAGAAGTTAGAAAATATTTGTGTACAAAGAAGTAAGATAAGTTCGTGCAAAGTT
37104839 GGATGTGGATTTGGTTTAAGTCGAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAAGATAATT
131 GGATGTGGATTTGGTTTAAGTCGAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAAGATAATT
* *
37104904 AAGAAATGGTATTTGGTTTTGGTACATTTTGGTATTTGGGAATTGGTACGAAATGGTATGGAATT
196 AAGAAATGGTATTTGGTTTTGGTACATTTTGGTATTTGGGAATTGGTACGAAACGGTAGGGAATT
** * * * * *
37104969 GGTATGAAATGGTATGGTATTTGGTACGAATTGGTAATGGTTCAAAGAGGTCAAGAATGAACCAA
261 GAAACGAAATGGTATGGTATTTGGTACGAAATGGAAATGGTTCAAAAAGGCCAAGAATGAACCAA
37105034 CACTAAAGAAAAGTGTCGACCCGAAACTTAT
326 CACTAAAGAAAAGTGTCGACCCGAAACTTAT
37105065 AGGACCTAAA
Statistics
Matches: 333, Mismatches: 22, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
356 67 0.20
357 26 0.08
358 32 0.10
359 208 0.62
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.30
Consensus pattern (356 bp):
TGATACGATCTCGGTTTAGTAGTTGAGCCCGAGTCGTTTAGTTCCCGATCGTAAACGAAGAAGTA
GATTAGACGAGAAGAAGTTAGAAAATATTTGTGTACAAAGAAGTAAGATAAGTTCGTGCAAAGTT
GGATGTGGATTTGGTTTAAGTCGAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAAGATAATT
AAGAAATGGTATTTGGTTTTGGTACATTTTGGTATTTGGGAATTGGTACGAAACGGTAGGGAATT
GAAACGAAATGGTATGGTATTTGGTACGAAATGGAAATGGTTCAAAAAGGCCAAGAATGAACCAA
CACTAAAGAAAAGTGTCGACCCGAAACTTAT
Found at i:37104968 original size:21 final size:21
Alignment explanation
Indices: 37104942--37105004 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
37104932 TTGGTATTTG
37104942 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
37104963 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
37104984 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
37105005 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:37108190 original size:22 final size:21
Alignment explanation
Indices: 37108158--37108199 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
37108148 TTGGTATTTA
37108158 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
37108179 GGAATTTGGTACGAATTGGTA
1 GGAA-TTGGTACGAAATGGTA
37108200 ATGGTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.31
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:37111902 original size:20 final size:19
Alignment explanation
Indices: 37111879--37111943 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
37111869 AAGCTCAAAC
37111879 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
37111899 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
37111919 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
37111939 GAGCT
1 GAGCT
37111944 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:37114193 original size:30 final size:30
Alignment explanation
Indices: 37114159--37114217 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
37114149 ACTTTAATAC
* *
37114159 GAGCT-GAATTAACTTCCATTTCAGCTCAAT
1 GAGCTCGAATTAAC-TCAACTTCAGCTCAAT
*
37114189 GAGCTCGAATTAGCTCAACTTCAGCTCAA
1 GAGCTCGAATTAACTCAACTTCAGCTCAA
37114218 ACATTTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (30 bp):
GAGCTCGAATTAACTCAACTTCAGCTCAAT
Found at i:37114546 original size:31 final size:32
Alignment explanation
Indices: 37114490--37114556 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 32
37114480 TCATTTATAT
*
37114490 AGGTTGGCCGAATGTGTGGGATCA-TTTAACA
1 AGGTTAGCCGAATGTGTGGGATCATTTTAACA
*
37114521 AGGTTAGCCGAAT-T-TGGAGATTCATTTTAGCA
1 AGGTTAGCCGAATGTGTGG-GA-TCATTTTAACA
37114553 AGGT
1 AGGT
37114557 GCATGCATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 3 0.10
30 3 0.10
31 15 0.48
32 10 0.32
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.31
Consensus pattern (32 bp):
AGGTTAGCCGAATGTGTGGGATCATTTTAACA
Found at i:37115374 original size:22 final size:22
Alignment explanation
Indices: 37115346--37115387 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
37115336 CCTTTTTGAA
37115346 CCATTACCATTTCGTACCAAAT
1 CCATTACCATTTCGTACCAAAT
37115368 CCATTACCATTTCGTACCAA
1 CCATTACCATTTCGTACCAA
37115388 TTCCCAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:37125259 original size:10 final size:10
Alignment explanation
Indices: 37125246--37125301 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
37125236 AAAGCTAAAT
37125246 TGAGCTCCAA
1 TGAGCTCCAA
*
37125256 TGAGCT-GAA
1 TGAGCTCCAA
37125265 TTGAGCTCCAA
1 -TGAGCTCCAA
*
37125276 TGAGCT-GAA
1 TGAGCTCCAA
*
37125285 TTGAGCTCAAA
1 -TGAGCTCCAA
37125296 TGAGCT
1 TGAGCT
37125302 GATTGGAGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 4 0.11
10 30 0.79
11 4 0.11
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (10 bp):
TGAGCTCCAA
Found at i:37125266 original size:20 final size:20
Alignment explanation
Indices: 37125238--37125303 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
37125228 GCTCAAAGAA
*
37125238 AGCTAAATTGAGCTCCAATG
1 AGCTGAATTGAGCTCCAATG
37125258 AGCTGAATTGAGCTCCAATG
1 AGCTGAATTGAGCTCCAATG
*
37125278 AGCTGAATTGAGCTCAAATG
1 AGCTGAATTGAGCTCCAATG
37125298 AGCTGA
1 AGCTGA
37125304 TTGGAGCTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (20 bp):
AGCTGAATTGAGCTCCAATG
Found at i:37125310 original size:20 final size:20
Alignment explanation
Indices: 37125238--37125321 Score: 107
Period size: 20 Copynumber: 4.2 Consensus size: 20
37125228 GCTCAAAGAA
* *
37125238 AGCTAAATTGAGCTCCAATG
1 AGCTGAATTGAGCTCAAATG
*
37125258 AGCTGAATTGAGCTCCAATG
1 AGCTGAATTGAGCTCAAATG
37125278 AGCTGAATTGAGCTCAAATG
1 AGCTGAATTGAGCTCAAATG
* *
37125298 AGCTG-ATTGGAGCTGAAACG
1 AGCTGAATT-GAGCTCAAATG
37125318 AGCT
1 AGCT
37125322 AAAGGGGCTG
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
19 3 0.05
20 56 0.95
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (20 bp):
AGCTGAATTGAGCTCAAATG
Found at i:37127434 original size:18 final size:18
Alignment explanation
Indices: 37127413--37127447 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
37127403 TTTTTATTTT
37127413 TCAATTT-TTTTCTCAATC
1 TCAATTTATTTT-TCAATC
37127431 TCAATTTATTTTTCAAT
1 TCAATTTATTTTTCAAT
37127448 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTATTTTTCAATC
Found at i:37127504 original size:24 final size:24
Alignment explanation
Indices: 37127447--37127507 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
37127437 TATTTTTCAA
37127447 TTTTCTTTTCTTCGATTTCTTTTTCT
1 TTTTC-TTT-TTCGATTTCTTTTTCT
* **
37127473 CTCACTTTTTCGATTTCTTTTTCT
1 TTTTCTTTTTCGATTTCTTTTTCT
37127497 TTTTCTTTTTC
1 TTTTCTTTTTC
37127508 ACATGCTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
24 24 0.83
25 3 0.10
26 2 0.07
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.70
Consensus pattern (24 bp):
TTTTCTTTTTCGATTTCTTTTTCT
Found at i:37128424 original size:13 final size:13
Alignment explanation
Indices: 37128408--37128442 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
37128398 TTTTTACTTC
37128408 GTTCTTTTTTTTT
1 GTTCTTTTTTTTT
*
37128421 GTTC-TTATTTTT
1 GTTCTTTTTTTTT
37128433 GTTCTTTTTT
1 GTTCTTTTTT
37128443 GTTTCGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.03, C:0.09, G:0.09, T:0.80
Consensus pattern (13 bp):
GTTCTTTTTTTTT
Found at i:37128463 original size:23 final size:22
Alignment explanation
Indices: 37128411--37128464 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
37128401 TTACTTCGTT
* * *
37128411 CTTTTTTTTTGTTCTTATTTTT
1 CTTTTTTTTTGTTCGTAATTTC
* *
37128433 GTTCTTTTTTGTTTCGTAATTTC
1 CTTTTTTTTTG-TTCGTAATTTC
37128456 CTTTTTTTT
1 CTTTTTTTT
37128465 CAATTACAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.06, C:0.11, G:0.07, T:0.76
Consensus pattern (22 bp):
CTTTTTTTTTGTTCGTAATTTC
Found at i:37131807 original size:27 final size:28
Alignment explanation
Indices: 37131772--37131825 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
37131762 GCTGGACTTG
*
37131772 GACATCATTAAAAACATGTAATAAAATT
1 GACATCATTAAAAACATGCAATAAAATT
* *
37131800 GACA-CATTAATAACATGCATTAAAAT
1 GACATCATTAAAAACATGCAATAAAAT
37131826 AAAACTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (28 bp):
GACATCATTAAAAACATGCAATAAAATT
Found at i:37135393 original size:28 final size:28
Alignment explanation
Indices: 37135360--37135442 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 28
37135350 ATCGGCAGTA
*
37135360 GCTAGGACATAATAAAAACATGTTTTAG
1 GCTAGGACATAATAAAAACATGTATTAG
* * *
37135388 TCTAGGACA-AATTAATAATATGTATTAG
1 GCTAGGACATAA-TAAAAACATGTATTAG
* * *
37135416 GCTATGACATATTAAAAACTTGTATTA
1 GCTAGGACATAATAAAAACATGTATTA
37135443 AAATAAGACA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
27 2 0.05
28 40 0.93
29 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (28 bp):
GCTAGGACATAATAAAAACATGTATTAG
Found at i:37135452 original size:28 final size:29
Alignment explanation
Indices: 37135421--37135482 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
37135411 ATTAGGCTAT
* *
37135421 GACATATTAAAAACTT-GTATTAAAATAA
1 GACATATTAAAAACTTAATAATAAAATAA
* * *
37135449 GACACATTAAACACTTAATAATAAAATCA
1 GACATATTAAAAACTTAATAATAAAATAA
37135478 GACAT
1 GACAT
37135483 TTTTTTTATT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.27
Consensus pattern (29 bp):
GACATATTAAAAACTTAATAATAAAATAA
Found at i:37135829 original size:34 final size:34
Alignment explanation
Indices: 37135791--37135887 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 34
37135781 TAAAGTCATG
37135791 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
1 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
* *
37135825 CATTA---AA--TT-AAGTCATGTT-AGTTT--A-
1 CATTATGTAACTTTCATGTTA-GTTAAGTTTGCAT
37135850 -ATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
1 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
37135883 CATTA
1 CATTA
37135888 AATTAAGTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 24
0.63 0.05 0.32
Matches are distributed among these distances:
24 4 0.09
26 1 0.02
27 2 0.04
28 9 0.19
29 10 0.21
30 9 0.19
31 2 0.04
32 1 0.02
34 9 0.19
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.46
Consensus pattern (34 bp):
CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
Found at i:37135841 original size:33 final size:33
Alignment explanation
Indices: 37135804--37135899 Score: 102
Period size: 33 Copynumber: 3.2 Consensus size: 33
37135794 TATGTAACTT
37135804 TCATGTTAGTTAAGTTTGCATCATTAAATTAAG
1 TCATGTTAGTTAAGTTTGCATCATTAAATTAAG
* *
37135837 TCATGTTAGTTTAA--TT--AT--GTAACTT---
1 TCATGTTAG-TTAAGTTTGCATCATTAAATTAAG
37135862 TCATGTTAGTTAAGTTTGCATCATTAAATTAAG
1 TCATGTTAGTTAAGTTTGCATCATTAAATTAAG
37135895 TCATG
1 TCATG
37135900 CATTAACTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 20
0.67 0.05 0.27
Matches are distributed among these distances:
24 4 0.08
25 9 0.18
26 2 0.04
28 7 0.14
30 7 0.14
32 2 0.04
33 14 0.29
34 4 0.08
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (33 bp):
TCATGTTAGTTAAGTTTGCATCATTAAATTAAG
Found at i:37137637 original size:11 final size:11
Alignment explanation
Indices: 37137618--37137661 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
37137608 TAGTAGTTTC
37137618 TTCAAAAAAAA
1 TTCAAAAAAAA
37137629 -TCGAAAAAAAA
1 TTC-AAAAAAAA
37137640 TTCAAAAAAAA
1 TTCAAAAAAAA
37137651 TTCAAAAAAAA
1 TTCAAAAAAAA
37137662 AAATTGGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 2 0.06
11 27 0.87
12 2 0.06
ACGTcount: A:0.73, C:0.09, G:0.02, T:0.16
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:37137701 original size:32 final size:32
Alignment explanation
Indices: 37137660--37137723 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
37137650 ATTCAAAAAA
37137660 AAAAATTGGTTTCCATTCAAACTCAAGAGATT
1 AAAAATTGGTTTCCATTCAAACTCAAGAGATT
37137692 AAAAATTGGTTTCCATTCAAACTCAAGAGATT
1 AAAAATTGGTTTCCATTCAAACTCAAGAGATT
37137724 GGATATCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (32 bp):
AAAAATTGGTTTCCATTCAAACTCAAGAGATT
Found at i:37137759 original size:17 final size:16
Alignment explanation
Indices: 37137735--37137777 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
37137725 GATATCAAGT
37137735 TGAAAAAAAAATTTCG
1 TGAAAAAAAAATTTCG
37137751 TGAAAAAAAAATTTCG
1 TGAAAAAAAAATTTCG
37137767 TGAAAAAAAAA
1 TGAAAAAAAAA
37137778 GAAGAAGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.21
Consensus pattern (16 bp):
TGAAAAAAAAATTTCG
Found at i:37144563 original size:19 final size:20
Alignment explanation
Indices: 37144519--37144564 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
37144509 CCAGCTCAAA
*
37144519 TTTAGCTCAATGAGCTCGTT
1 TTTAGCTCAATAAGCTCGTT
**
37144539 CCTAGCTCAA-AAGCTCGTT
1 TTTAGCTCAATAAGCTCGTT
37144558 TTTAGCT
1 TTTAGCT
37144565 TACTTTGTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (20 bp):
TTTAGCTCAATAAGCTCGTT
Found at i:37150867 original size:18 final size:18
Alignment explanation
Indices: 37150844--37150910 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
37150834 CATGTTGTAA
37150844 TGAAAAAGA-AAAAGAGAT
1 TGAAAAAGAGAAAAGA-AT
*
37150862 TGAAAAAGAGGAAAAAAAT
1 TGAAAAAGA-GAAAAGAAT
*
37150881 TGAAAGAGAGAAAAGAA-
1 TGAAAAAGAGAAAAGAAT
*
37150898 TCAAAAA-AGAAAA
1 TGAAAAAGAGAAAA
37150911 CAAAAAAGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
16 6 0.14
17 5 0.12
18 16 0.38
19 10 0.24
20 5 0.12
ACGTcount: A:0.69, C:0.01, G:0.21, T:0.09
Consensus pattern (18 bp):
TGAAAAAGAGAAAAGAAT
Found at i:37151443 original size:37 final size:37
Alignment explanation
Indices: 37151402--37151475 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
37151392 TCAGACTTAG
37151402 TTGAAAATCAGACCAAATTGTCAAAGTGGCCCAATTT
1 TTGAAAATCAGACCAAATTGTCAAAGTGGCCCAATTT
*
37151439 TTGAAAATCAGGCCAAATTGTCAAAGTGGCCCAATTT
1 TTGAAAATCAGACCAAATTGTCAAAGTGGCCCAATTT
37151476 GTTAAGTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (37 bp):
TTGAAAATCAGACCAAATTGTCAAAGTGGCCCAATTT
Found at i:37151474 original size:17 final size:17
Alignment explanation
Indices: 37151417--37151474 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
37151407 AATCAGACCA
37151417 AATTGTCAAAGTGGCCC
1 AATTGTCAAAGTGGCCC
* * * *
37151434 AATTTTTGAAAATCAGGCCA
1 AA-TTGTCAAAGT--GGCCC
37151454 AATTGTCAAAGTGGCCC
1 AATTGTCAAAGTGGCCC
37151471 AATT
1 AATT
37151475 TGTTAAGTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
17 10 0.33
18 7 0.23
19 7 0.23
20 6 0.20
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (17 bp):
AATTGTCAAAGTGGCCC
Found at i:37151477 original size:18 final size:18
Alignment explanation
Indices: 37151414--37151477 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
37151404 GAAAATCAGA
37151414 CCAAATTGTCAAAGTGGC
1 CCAAATTGTCAAAGTGGC
* * * *
37151432 CCAATTTTTGAAAATCAGG-
1 CCAAATTGTCAAAGT--GGC
37151451 CCAAATTGTCAAAGTGGC
1 CCAAATTGTCAAAGTGGC
*
37151469 CCAATTTGT
1 CCAAATTGT
37151478 TAAGTTTTAA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 2 0.06
18 19 0.56
19 11 0.32
20 2 0.06
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (18 bp):
CCAAATTGTCAAAGTGGC
Found at i:37153558 original size:15 final size:16
Alignment explanation
Indices: 37153540--37153569 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
37153530 AAGAAAGAAA
37153540 AAAAATT-AAAAAAAT
1 AAAAATTGAAAAAAAT
37153555 AAAAATTGAAAAAAA
1 AAAAATTGAAAAAAA
37153570 AGAGGATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAAATTGAAAAAAAT
Found at i:37155461 original size:12 final size:12
Alignment explanation
Indices: 37155444--37155470 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
37155434 GTCGTCAAGC
37155444 CAAGGTGAGTAT
1 CAAGGTGAGTAT
37155456 CAAGGTGAGTAT
1 CAAGGTGAGTAT
37155468 CAA
1 CAA
37155471 ATTGAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.22
Consensus pattern (12 bp):
CAAGGTGAGTAT
Found at i:37165123 original size:19 final size:18
Alignment explanation
Indices: 37165087--37165126 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
37165077 TTTCCACTCG
*
37165087 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
37165105 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
37165124 TTT
1 TTT
37165127 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:37166188 original size:13 final size:12
Alignment explanation
Indices: 37166170--37166217 Score: 78
Period size: 12 Copynumber: 3.8 Consensus size: 12
37166160 CTAGCTCTCT
37166170 TTTTTTTTCACAA
1 TTTTTTTTCA-AA
37166183 TTTTTTTTTCAAA
1 -TTTTTTTTCAAA
37166196 TTTTTTTTCAAA
1 TTTTTTTTCAAA
37166208 TTTTTTTTCA
1 TTTTTTTTCA
37166218 CAACTTGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 22 0.65
13 2 0.06
14 10 0.29
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:37166302 original size:12 final size:12
Alignment explanation
Indices: 37166258--37166302 Score: 58
Period size: 11 Copynumber: 3.9 Consensus size: 12
37166248 TGAAAACTAG
37166258 TTTTTTTCGA-T
1 TTTTTTTCGAGT
*
37166269 TTTTTTT-GAAT
1 TTTTTTTCGAGT
*
37166280 TTCTTTTCGAGT
1 TTTTTTTCGAGT
37166292 TTTTTTTCGAG
1 TTTTTTTCGAG
37166303 AAACTACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 2 0.07
11 14 0.48
12 13 0.45
ACGTcount: A:0.11, C:0.09, G:0.13, T:0.67
Consensus pattern (12 bp):
TTTTTTTCGAGT
Found at i:37168886 original size:19 final size:20
Alignment explanation
Indices: 37168849--37168886 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
37168839 TGAAAGCAAT
*
37168849 GCCCAATAAGAAAATTCCAA
1 GCCCAATAAGAAAAGTCCAA
*
37168869 GCCCAATCA-AAAAGTCCA
1 GCCCAATAAGAAAAGTCCA
37168887 CCCATACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.47, C:0.29, G:0.11, T:0.13
Consensus pattern (20 bp):
GCCCAATAAGAAAAGTCCAA
Found at i:37173049 original size:27 final size:27
Alignment explanation
Indices: 37173016--37173071 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
37173006 ACATAAGGCC
* *
37173016 ATAACAGTCATTTTATCTCCTAGGGGT
1 ATAACAGTCATTTTACCTCATAGGGGT
*
37173043 ATAACAGTCATTTTACCTTATAGGGGT
1 ATAACAGTCATTTTACCTCATAGGGGT
37173070 AT
1 AT
37173072 TTTGATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (27 bp):
ATAACAGTCATTTTACCTCATAGGGGT
Found at i:37173080 original size:27 final size:27
Alignment explanation
Indices: 37173050--37173365 Score: 304
Period size: 27 Copynumber: 11.7 Consensus size: 27
37173040 GGTATAACAG
*
37173050 TCATTTTACCTTATAGGGGTATTTTGA
1 TCATTTTACCCTATAGGGGTATTTTGA
* *
37173077 TCATTTTACCCTATAGGGGTATTTCGG
1 TCATTTTACCCTATAGGGGTATTTTGA
* ** *
37173104 TCATTCTACCCTATAAAGGTA-TTTCA
1 TCATTTTACCCTATAGGGGTATTTTGA
* * *
37173130 GTCATTTTACCCTATGGGGGTCTTTTGG
1 -TCATTTTACCCTATAGGGGTATTTTGA
*
37173158 TCATTTTACCCTAT-GAGGGTATTTTGG
1 TCATTTTACCCTATAG-GGGTATTTTGA
* *
37173185 TCATTTTACCTTAT-GAGGGTATTTTGG
1 TCATTTTACCCTATAG-GGGTATTTTGA
* *
37173212 TCATTTTACCCAAT-GAGGGTATTTTGG
1 TCATTTTACCCTATAG-GGGTATTTTGA
* * *
37173239 TCACTTTACCCTATGGGGGTA-TTTCA
1 TCATTTTACCCTATAGGGGTATTTTGA
* *
37173265 GTCATTTTACCCTATGGGGGTATTTCGA
1 -TCATTTTACCCTATAGGGGTATTTTGA
* *
37173293 TCATTTTACCCTATAAGGGTATTTCGA
1 TCATTTTACCCTATAGGGGTATTTTGA
* *
37173320 TCATTTTACCATATGGGGGTATTTT-A
1 TCATTTTACCCTATAGGGGTATTTTGA
*
37173346 GTCATTTTACTCTAT-GGGGT
1 -TCATTTTACCCTATAGGGGT
37173366 TCTCAGTGCA
Statistics
Matches: 247, Mismatches: 35, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
26 12 0.05
27 228 0.92
28 7 0.03
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (27 bp):
TCATTTTACCCTATAGGGGTATTTTGA
Found at i:37173094 original size:54 final size:53
Alignment explanation
Indices: 37173049--37173365 Score: 336
Period size: 54 Copynumber: 5.9 Consensus size: 53
37173039 GGGTATAACA
*
37173049 GTCATTTTACCTTATAGGGGTATTTTGATCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTTGATCATTTTACCCTATAGGGGTATTTCG
* ** * * * *
37173103 GTCATTCTACCCTATAAAGGTA-TTTCAGTCATTTTACCCTATGGGGGTCTTTTG
1 GTCATTTTACCCTAT-GGGGTATTTTGA-TCATTTTACCCTATAGGGGTATTTCG
* * *
37173157 GTCATTTTACCCTATGAGGGTATTTTGGTCATTTTACCTTAT-GAGGGTATTTTG
1 GTCATTTTACCCTATG-GGGTATTTTGATCATTTTACCCTATAG-GGGTATTTCG
* * * * *
37173211 GTCATTTTACCCAATGAGGGTATTTTGGTCACTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATG-GGGTATTTTGATCATTTTACCCTATAGGGGTATTTCG
* *
37173265 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAAGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTTGATCATTTTACCCTATAGGGGTATTTCG
* * *
37173319 ATCATTTTACCATATGGGGGTATTTT-AGTCATTTTACTCTAT-GGGGT
1 GTCATTTTACCCTAT-GGGGTATTTTGA-TCATTTTACCCTATAGGGGT
37173366 TCTCAGTGCA
Statistics
Matches: 224, Mismatches: 32, Indels: 15
0.83 0.12 0.06
Matches are distributed among these distances:
53 10 0.04
54 209 0.93
55 5 0.02
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (53 bp):
GTCATTTTACCCTATGGGGTATTTTGATCATTTTACCCTATAGGGGTATTTCG
Found at i:37173162 original size:81 final size:81
Alignment explanation
Indices: 37173022--37173365 Score: 381
Period size: 81 Copynumber: 4.3 Consensus size: 81
37173012 GGCCATAACA
** * *
37173022 GTCATTTTATCTCCTA-G-GGGTATAACAGTCATTTTACCTTATAGGGGTATTTTGATCATTTTA
1 GTCATTTTA-C-CCTATGAGGGTATTTCAGTCATTTTACCCTATAAGGGTATTTTGATCATTTTA
*
37173085 CCCTATAGGGGTATTTCG
64 CCCTATGGGGGTATTTCG
* * * ** * *
37173103 GTCATTCTACCCTATAAAGGTATTTCAGTCATTTTACCCTATGGGGGTCTTTTGGTCATTTTACC
1 GTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATAAGGGTATTTTGATCATTTTACC
* *
37173168 CTATGAGGGTATTTTG
66 CTATGGGGGTATTTCG
* ** * * * *
37173184 GTCATTTTACCTTATGAGGGTATTTTGGTCATTTTACCCAATGAGGGTATTTTGGTCACTTTACC
1 GTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATAAGGGTATTTTGATCATTTTACC
*
37173249 CTATGGGGGTATTTCA
66 CTATGGGGGTATTTCG
* *
37173265 GTCATTTTACCCTATGGGGGTATTTC-GATCATTTTACCCTATAAGGGTATTTCGATCATTTTAC
1 GTCATTTTACCCTATGAGGGTATTTCAG-TCATTTTACCCTATAAGGGTATTTTGATCATTTTAC
* **
37173329 CATATGGGGGTATTTTA
65 CCTATGGGGGTATTTCG
*
37173346 GTCATTTTACTCTATG-GGGT
1 GTCATTTTACCCTATGAGGGT
37173366 TCTCAGTGCA
Statistics
Matches: 224, Mismatches: 36, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
79 4 0.02
80 6 0.03
81 214 0.96
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.42
Consensus pattern (81 bp):
GTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATAAGGGTATTTTGATCATTTTACC
CTATGGGGGTATTTCG
Found at i:37173623 original size:19 final size:19
Alignment explanation
Indices: 37173588--37173625 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
37173578 GTGTGAGGCC
*
37173588 CACGAGCCCATTGAGCCCA
1 CACGAGCCCATTCAGCCCA
37173607 CACG-GCCCATTACAGCCCA
1 CACGAGCCCATT-CAGCCCA
37173626 AGCCCATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.26, C:0.45, G:0.18, T:0.11
Consensus pattern (19 bp):
CACGAGCCCATTCAGCCCA
Found at i:37191328 original size:17 final size:16
Alignment explanation
Indices: 37191281--37191328 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
37191271 AATGCTCGTG
37191281 AAAAAGAAAAGAA-AA
1 AAAAAGAAAAGAACAA
* *
37191296 GAAAAGAAAAATAACAA
1 AAAAAG-AAAAGAACAA
37191313 AAAAAGAAGAAGAACA
1 AAAAAGAA-AAGAACA
37191329 TATGTACTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 5 0.19
16 8 0.31
17 13 0.50
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAGAACAA
Found at i:37199839 original size:20 final size:20
Alignment explanation
Indices: 37199816--37199879 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
37199806 CACATACGTG
37199816 CCCTTGTTTGTACTTCGGTA
1 CCCTTGTTTGTACTTCGGTA
* * * ** *
37199836 CCCTTGAATTGCACATATGTG
1 CCCTTG-TTTGTACTTCGGTA
*
37199857 CCCTTGTTTGTACTTCGATA
1 CCCTTGTTTGTACTTCGGTA
37199877 CCC
1 CCC
37199880 CTGAATTGCA
Statistics
Matches: 30, Mismatches: 13, Indels: 2
0.67 0.29 0.04
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.16, C:0.28, G:0.17, T:0.39
Consensus pattern (20 bp):
CCCTTGTTTGTACTTCGGTA
Found at i:37199860 original size:41 final size:41
Alignment explanation
Indices: 37199803--37199909 Score: 178
Period size: 41 Copynumber: 2.6 Consensus size: 41
37199793 TAATGATGAT
* * *
37199803 TTGCACATACGTGCCCTTGTTTGTACTTCGGTACCCTTGAA
1 TTGCACATATGTGCCCTTGTTTGTACTTCGATACCCCTGAA
37199844 TTGCACATATGTGCCCTTGTTTGTACTTCGATACCCCTGAA
1 TTGCACATATGTGCCCTTGTTTGTACTTCGATACCCCTGAA
*
37199885 TTGCACATATGTGCCCCTGTTTGTA
1 TTGCACATATGTGCCCTTGTTTGTA
37199910 ATTTGGTGCT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.37
Consensus pattern (41 bp):
TTGCACATATGTGCCCTTGTTTGTACTTCGATACCCCTGAA
Found at i:37199862 original size:21 final size:21
Alignment explanation
Indices: 37199836--37199900 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
37199826 TACTTCGGTA
37199836 CCCTTGAATTGCACATATGTG
1 CCCTTGAATTGCACATATGTG
* * *
37199857 CCCTTG-TTTGTAC-T-TCGATA
1 CCCTTGAATTGCACATAT-G-TG
*
37199877 CCCCTGAATTGCACATATGTG
1 CCCTTGAATTGCACATATGTG
37199898 CCC
1 CCC
37199901 CTGTTTGTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 10
0.65 0.14 0.20
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 11 0.34
21 15 0.47
22 2 0.06
23 1 0.03
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (21 bp):
CCCTTGAATTGCACATATGTG
Found at i:37200929 original size:28 final size:28
Alignment explanation
Indices: 37200897--37200976 Score: 142
Period size: 28 Copynumber: 2.9 Consensus size: 28
37200887 AACAGTATAG
*
37200897 TGTGGGCCTTAGCCCAATATAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
*
37200925 TGTGGGCCTTAGCCTAATACAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
37200953 TGTGGGCCTTAGCCCAATACAGTA
1 TGTGGGCCTTAGCCCAATACAGTA
37200977 TCGATACAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAGTAACAA
Found at i:37201454 original size:81 final size:81
Alignment explanation
Indices: 37201342--37201563 Score: 345
Period size: 81 Copynumber: 2.7 Consensus size: 81
37201332 GGTATAACAG
* * * * * * *
37201342 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGGTAGTTCGGTCATTTTACCT
1 TCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTGTAGGGGTAATTCGATCATTTTACCC
*
37201407 TGTGGGGGTAATTCGG
66 TGTGGGGGTAATTCGC
*
37201423 TTATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTGTAGGGGTAATTCGATCATTTTACCC
1 TCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTGTAGGGGTAATTCGATCATTTTACCC
37201488 TGTGGGGGTAATTCGC
66 TGTGGGGGTAATTCGC
* *
37201504 TCATTTTACCCTGTAGGGGTAATTCGATCATTTTTCCCTGTAGGGGTAATTCGATCATTT
1 TCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTGTAGGGGTAATTCGATCATTT
37201564 ATTGACCTCT
Statistics
Matches: 129, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 129 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (81 bp):
TCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTGTAGGGGTAATTCGATCATTTTACCC
TGTGGGGGTAATTCGC
Found at i:37201552 original size:27 final size:27
Alignment explanation
Indices: 37201342--37201563 Score: 309
Period size: 27 Copynumber: 8.2 Consensus size: 27
37201332 GGTATAACAG
* * * *
37201342 TCATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTGTAGGGGTAATTCGA
* * *
37201369 TCATTTTACCCTATAGGGGTAGTTCGG
1 TCATTTTACCCTGTAGGGGTAATTCGA
* * *
37201396 TCATTTTACCTTGTGGGGGTAATTCGG
1 TCATTTTACCCTGTAGGGGTAATTCGA
* *
37201423 TTATTTTACCCTGTGGGGGTAATTCGA
1 TCATTTTACCCTGTAGGGGTAATTCGA
37201450 TCATTTTACCCTGTAGGGGTAATTCGA
1 TCATTTTACCCTGTAGGGGTAATTCGA
* *
37201477 TCATTTTACCCTGTGGGGGTAATTCGC
1 TCATTTTACCCTGTAGGGGTAATTCGA
37201504 TCATTTTACCCTGTAGGGGTAATTCGA
1 TCATTTTACCCTGTAGGGGTAATTCGA
*
37201531 TCATTTTTCCCTGTAGGGGTAATTCGA
1 TCATTTTACCCTGTAGGGGTAATTCGA
37201558 TCATTT
1 TCATTT
37201564 ATTGACCTCT
Statistics
Matches: 179, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 179 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (27 bp):
TCATTTTACCCTGTAGGGGTAATTCGA
Found at i:37202264 original size:24 final size:25
Alignment explanation
Indices: 37202228--37202276 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
37202218 CCTAAATCCC
*
37202228 AATATTCTCTCCTCAAATCTCTCTA
1 AATATCCTCTCCTCAAATCTCTCTA
*
37202253 AATATCCT-TCCTCAATTCTCTCTA
1 AATATCCTCTCCTCAAATCTCTCTA
37202277 TGACCAGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATCCTCTCCTCAAATCTCTCTA
Found at i:37207625 original size:32 final size:31
Alignment explanation
Indices: 37207571--37207647 Score: 109
Period size: 32 Copynumber: 2.5 Consensus size: 31
37207561 CAGCTACTGT
* * **
37207571 TGTTCACACCAATGGACCGTCCAATTCCTGG
1 TGTTCACACCAAAGGACCGTCCAAGTCCAAG
37207602 TGTTCACACCTAAAGGACCGTCCAAGTCCAAG
1 TGTTCACACC-AAAGGACCGTCCAAGTCCAAG
37207634 TGTTCACACCAAAG
1 TGTTCACACCAAAG
37207648 ACTCTTCAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 14 0.34
32 27 0.66
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (31 bp):
TGTTCACACCAAAGGACCGTCCAAGTCCAAG
Found at i:37216014 original size:21 final size:22
Alignment explanation
Indices: 37215990--37216074 Score: 56
Period size: 21 Copynumber: 4.0 Consensus size: 22
37215980 GAAAAAGGAG
37215990 AAGAGA-AAAATAAAAGTGAAA
1 AAGAGACAAAATAAAAGTGAAA
*
37216011 AAGA-AGAAAATGAAAA-TGAAA
1 AAGAGACAAAAT-AAAAGTGAAA
*
37216032 AAG-G-CAAAA-AGGAAAGCGAAA
1 AAGAGACAAAATA--AAAGTGAAA
* *
37216053 GAGAAACAAAATAAAATGTGAA
1 AAGAGACAAAATAAAA-GTGAA
37216075 TGAAGTGAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
18 1 0.02
20 8 0.16
21 23 0.47
22 7 0.14
23 9 0.18
24 1 0.02
ACGTcount: A:0.67, C:0.04, G:0.21, T:0.08
Consensus pattern (22 bp):
AAGAGACAAAATAAAAGTGAAA
Found at i:37220642 original size:36 final size:36
Alignment explanation
Indices: 37220590--37220660 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
37220580 GTTGAATGTG
37220590 TTTGTGCCTCAATTGGTCATGTTGTTAATTAAAATA
1 TTTGTGCCTCAATTGGTCATGTTGTTAATTAAAATA
*
37220626 TTTGTGCCTCAGTTGGTCATGTTGTTAATTAAAAT
1 TTTGTGCCTCAATTGGTCATGTTGTTAATTAAAAT
37220661 CAAGATGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.45
Consensus pattern (36 bp):
TTTGTGCCTCAATTGGTCATGTTGTTAATTAAAATA
Found at i:37221199 original size:14 final size:14
Alignment explanation
Indices: 37221180--37221207 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
37221170 TCAATTTTGC
37221180 ATCTAGTTAAATTA
1 ATCTAGTTAAATTA
37221194 ATCTAGTTAAATTA
1 ATCTAGTTAAATTA
37221208 TCATCACTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
ATCTAGTTAAATTA
Found at i:37221527 original size:23 final size:23
Alignment explanation
Indices: 37221497--37221541 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
37221487 TTGTGACACG
37221497 ACCCCCTACTGTAC-CCCATCTAT
1 ACCCCCTACTGTACACCC-TCTAT
37221520 ACCCCCTACTGTACACCCTCTA
1 ACCCCCTACTGTACACCCTCTA
37221542 GGACCTCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.22, C:0.49, G:0.04, T:0.24
Consensus pattern (23 bp):
ACCCCCTACTGTACACCCTCTAT
Found at i:37224882 original size:27 final size:28
Alignment explanation
Indices: 37224823--37224876 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
37224813 AATATAACTA
*
37224823 AAATTAAATATGTTAATAATTTAAGTGC
1 AAATTAAATATGTTAATAATTAAAGTGC
* *
37224851 AAATTAATTATTTTAA-AATTAAAGTG
1 AAATTAAATATGTTAATAATTAAAGTG
37224877 TGAATTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (28 bp):
AAATTAAATATGTTAATAATTAAAGTGC
Found at i:37231030 original size:194 final size:194
Alignment explanation
Indices: 37230694--37231078 Score: 680
Period size: 194 Copynumber: 2.0 Consensus size: 194
37230684 TATTCCAAGG
37230694 TGGAAGATGACTCTTTTTCAAGAGGGAAATCAACAAGGGAAATGGACAAGAAAAAGGGAAAAACA
1 TGGAAGATGACTCTTTTTCAAGAGGGAAATCAACAAGGGAAATGGACAAGAAAAAGGGAAAAACA
* *
37230759 AAGGAGAGAAAGTGAGTGAAAGAGAGAGAGATGTGTAAGAATGAAGGTGTGTTGAGTTAATAGGT
66 AAGGAGAGAAAGTGAGTGAAAGAGAGAGAGATGTATAAGAATGAAGGTGTGTTGAATTAATAGGT
*
37230824 GAAAGAGGGTATTTATAGGTTGGAGTGGCTACTAAAAATAGCAAATAATTAACAGCCACACACT
131 GAAAGAGGGTATTTATAGGTTGGAGTGGCTACTAAAAATAGCAAATAATTAACAACCACACACT
* *
37230888 TGGAAGCTGACTCTTTTTCAAGAGGGAAATCGACAAGGGAAATGGACAAGAAAAAGGGAAAAACA
1 TGGAAGATGACTCTTTTTCAAGAGGGAAATCAACAAGGGAAATGGACAAGAAAAAGGGAAAAACA
**
37230953 AAGGAGAGAAAGTGAGTGAAAGAGAGAGAGATGTATGGGAATGAAGGTGTGTTGAATTAATAGGT
66 AAGGAGAGAAAGTGAGTGAAAGAGAGAGAGATGTATAAGAATGAAGGTGTGTTGAATTAATAGGT
* * *
37231018 GAAGGAGGGTATTTATAGGTTGGATTGGCTACTAAAAATAGCAAATAATTAGCAACCACAC
131 GAAAGAGGGTATTTATAGGTTGGAGTGGCTACTAAAAATAGCAAATAATTAACAACCACAC
37231079 TCCTCTCTTA
Statistics
Matches: 181, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
194 181 1.00
ACGTcount: A:0.42, C:0.08, G:0.29, T:0.20
Consensus pattern (194 bp):
TGGAAGATGACTCTTTTTCAAGAGGGAAATCAACAAGGGAAATGGACAAGAAAAAGGGAAAAACA
AAGGAGAGAAAGTGAGTGAAAGAGAGAGAGATGTATAAGAATGAAGGTGTGTTGAATTAATAGGT
GAAAGAGGGTATTTATAGGTTGGAGTGGCTACTAAAAATAGCAAATAATTAACAACCACACACT
Found at i:37235034 original size:19 final size:18
Alignment explanation
Indices: 37234998--37235037 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
37234988 TTTCCACTCG
*
37234998 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
37235016 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
37235035 TTT
1 TTT
37235038 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:37236117 original size:12 final size:12
Alignment explanation
Indices: 37236099--37236155 Score: 71
Period size: 13 Copynumber: 4.6 Consensus size: 12
37236089 CTAGCTCTCT
37236099 TTTTTTTTCACAA
1 TTTTTTTTCA-AA
37236112 TTTTTTTTTCAAA
1 -TTTTTTTTCAAA
37236125 TTTTTTTTTCAAA
1 -TTTTTTTTCAAA
*
37236138 TTTTTTTTC-GA
1 TTTTTTTTCAAA
37236149 TTTTTTT
1 TTTTTTT
37236156 GAATTTTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
11 8 0.19
12 9 0.21
13 15 0.36
14 10 0.24
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.72
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:37236154 original size:13 final size:12
Alignment explanation
Indices: 37236098--37236155 Score: 71
Period size: 12 Copynumber: 4.6 Consensus size: 12
37236088 ACTAGCTCTC
37236098 TTTTTTTTTCACAA
1 TTTTTTTTT--CAA
37236112 TTTTTTTTTCAAA
1 TTTTTTTTTC-AA
37236125 TTTTTTTTTCAA
1 TTTTTTTTTCAA
* *
37236137 ATTTTTTTTCGA
1 TTTTTTTTTCAA
37236149 TTTTTTT
1 TTTTTTT
37236156 GAATTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
12 19 0.47
13 12 0.30
14 9 0.22
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:37236165 original size:13 final size:13
Alignment explanation
Indices: 37236098--37236145 Score: 87
Period size: 13 Copynumber: 3.6 Consensus size: 13
37236088 ACTAGCTCTC
37236098 TTTTTTTTTCACAA
1 TTTTTTTTTCA-AA
37236112 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
37236125 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
37236138 TTTTTTTT
1 TTTTTTTT
37236146 CGATTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 23 0.68
14 11 0.32
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Done.