Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015254.1 Kokia drynarioides strain JFW-HI SEQ_130299, 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: 1276691
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 890 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:1074476 original size:26 final size:26
Alignment explanation
Indices: 1074447--1074507 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
1074437 GTACAATGGT
1074447 GGAAA-GGAGAAATGGG-AAGGGAAAGG
1 GGAAATGG-GAAA-GGGAAAGGGAAAGG
*
1074473 GGAAATGGGGAAGGGAAAGGGAAAGG
1 GGAAATGGGAAAGGGAAAGGGAAAGG
1074499 GGAAATGGG
1 GGAAATGGG
1074508 GAAGAGGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 3 0.09
26 27 0.84
27 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.52, T:0.05
Consensus pattern (26 bp):
GGAAATGGGAAAGGGAAAGGGAAAGG
Found at i:1074492 original size:6 final size:6
Alignment explanation
Indices: 1074447--1074499 Score: 54
Period size: 6 Copynumber: 8.3 Consensus size: 6
1074437 GTACAATGGT
*
1074447 GGAAAG GAGAAATG GG-AAG GGAAAGG GGAAATG GGGAAG GGAAAG GGAAAG
1 GGAAAG G-GAAA-G GGAAAG GGAAA-G GGAAA-G GGAAAG GGAAAG GGAAAG
1074498 GG
1 GG
1074500 GAAATGGGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 3 0.08
6 19 0.47
7 16 0.40
8 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.53, T:0.04
Consensus pattern (6 bp):
GGAAAG
Found at i:1080450 original size:11 final size:11
Alignment explanation
Indices: 1080431--1080486 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
1080421 TCATGTCAAC
*
1080431 AAATGATTTTA
1 AAATTATTTTA
*
1080442 AAATTATTTTT
1 AAATTATTTTA
1080453 AAA-TA---TA
1 AAATTATTTTA
1080460 AAATTA--TTA
1 AAATTATTTTA
1080469 AAATTATTTTA
1 AAATTATTTTA
1080480 AAATTAT
1 AAATTAT
1080487 AATCATCATC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
7 4 0.11
8 2 0.05
9 8 0.21
10 2 0.05
11 22 0.58
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:1081261 original size:27 final size:29
Alignment explanation
Indices: 1081231--1081307 Score: 95
Period size: 27 Copynumber: 2.7 Consensus size: 29
1081221 ATTGAAAATT
*
1081231 AAAATTATTTAATAATTTTATA-TTTGAA
1 AAAATTATTTAATAATTTTATATTTTAAA
* *
1081259 AAAA-TATTTAAAAAATTTATATTTTAAA
1 AAAATTATTTAATAATTTTATATTTTAAA
*
1081287 AAAATAATTTTAATAATTTTA
1 AAAATTA-TTTAATAATTTTA
1081308 AAATCATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 15 0.38
28 13 0.32
29 1 0.03
30 11 0.28
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
AAAATTATTTAATAATTTTATATTTTAAA
Found at i:1081282 original size:15 final size:15
Alignment explanation
Indices: 1081236--1081289 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 15
1081226 AAATTAAAAT
* *
1081236 TATTTAATAATTTTA
1 TATTTAAAAAATTTA
*
1081251 TATTTGAAAAA---A
1 TATTTAAAAAATTTA
1081263 TATTTAAAAAATTTA
1 TATTTAAAAAATTTA
1081278 TATTTTAAAAAA
1 TA-TTTAAAAAA
1081290 ATAATTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
12 11 0.35
15 11 0.35
16 9 0.29
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
TATTTAAAAAATTTA
Found at i:1082424 original size:143 final size:143
Alignment explanation
Indices: 1082148--1082429 Score: 370
Period size: 143 Copynumber: 2.0 Consensus size: 143
1082138 AAGCTCTGAT
* * ** *
1082148 TTTATTAGACGTATTCATTATTTTTTGACGAATATAGGACTTTGGGATTTGAAACATATTTTTAG
1 TTTATTAGACGTATTCATCATTTTTAGACGAATATAGGACTTTGAAATTTGAAACATATTCTTAG
* * * * *
1082213 TGACTACAATAAAATTGCTAATTGCATGACCAGAATGACTTTTGATACAAACCATAGCCTAAATG
66 GGACTACAATAAAATTACTAATTGCATGACCAGAATGACTTTTGATACAAACCATAACATAAAGG
1082278 TGTTTAAAATGAC
131 TGTTTAAAATGAC
* *
1082291 TTTATTAGACGTATTCATCATATTTTAG-CGTATATAGGACTTTGAAATTTGCAACATATTCTTA
1 TTTATTAGACGTATTCATCAT-TTTTAGACGAATATAGGACTTTGAAATTTGAAACATATTCTTA
* *** * *
1082355 GGGACTACAATAAAATTACTGATTGCATGGTTA-AATTGACTTTTGATACGAATCATAACATAAA
65 GGGACTACAATAAAATTACTAATTGCATGACCAGAA-TGACTTTTGATACAAACCATAACATAAA
1082419 GGTGTTTAAAA
129 GGTGTTTAAAA
1082430 AGATTCCAAA
Statistics
Matches: 119, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
142 2 0.02
143 112 0.94
144 5 0.04
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (143 bp):
TTTATTAGACGTATTCATCATTTTTAGACGAATATAGGACTTTGAAATTTGAAACATATTCTTAG
GGACTACAATAAAATTACTAATTGCATGACCAGAATGACTTTTGATACAAACCATAACATAAAGG
TGTTTAAAATGAC
Found at i:1085207 original size:57 final size:57
Alignment explanation
Indices: 1085090--1085208 Score: 150
Period size: 57 Copynumber: 2.1 Consensus size: 57
1085080 GTGTTATCTT
** * *
1085090 AATGTAATTTATAACTGTTGTCATAATGTCTCTTAATGTGAATATTTATGCTATCCA
1 AATGTAATTTATAACTACTGTCATAATGTCTCTTAATGTCAATATTTATGCTATCAA
** * *
1085147 AATGTAATTTATAGTTACTGTCATAATGTCTCTTAATG-CACATATTTATGTTGTCAA
1 AATGTAATTTATAACTACTGTCATAATGTCTCTTAATGTCA-ATATTTATGCTATCAA
1085204 AATGT
1 AATGT
1085209 GAATAATGCT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
56 1 0.02
57 52 0.98
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.44
Consensus pattern (57 bp):
AATGTAATTTATAACTACTGTCATAATGTCTCTTAATGTCAATATTTATGCTATCAA
Found at i:1110742 original size:52 final size:52
Alignment explanation
Indices: 1110656--1110945 Score: 345
Period size: 52 Copynumber: 5.6 Consensus size: 52
1110646 CTTTCTCTCC
** * * * * *
1110656 ATTCATATACTCGTGATTACACATAGCCAACGGACCTCATAATTCAT-AAGG
1 ATTCATATACTCACGATGACACAGAGTCATCGGACCTCTTAATTCATAAAGG
* *
1110707 AATTCATATACTCACGATGACACAGAGTCATCGGACCTCTTAA-TCGGTAAAGT
1 -ATTCATATACTCACGATGACACAGAGTCATCGGACCTCTTAATTC-ATAAAGG
*
1110760 ATTCATATACTCACGATGACACAGAGTCATCGGACCTCTTAATCCATAAAGG
1 ATTCATATACTCACGATGACACAGAGTCATCGGACCTCTTAATTCATAAAGG
* * * * *
1110812 ATTCATATACTCACAATGACACAAAGTCATCAGACCACTTAATCCATAAAGG
1 ATTCATATACTCACGATGACACAGAGTCATCGGACCTCTTAATTCATAAAGG
* * * *
1110864 ATTCATATACTCACAATGACATAGAGTCATCGAACCTCTTAA-TCTGTAAAGG
1 ATTCATATACTCACGATGACACAGAGTCATCGGACCTCTTAATTC-ATAAAGG
*
1110916 ATTC-TATACTCACGATGACATAGAGTCATC
1 ATTCATATACTCACGATGACACAGAGTCATC
1110946 AAACCTTTTA
Statistics
Matches: 210, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
51 28 0.13
52 178 0.85
53 4 0.02
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACAGAGTCATCGGACCTCTTAATTCATAAAGG
Found at i:1121993 original size:119 final size:119
Alignment explanation
Indices: 1121782--1122023 Score: 484
Period size: 119 Copynumber: 2.0 Consensus size: 119
1121772 TAAAGGATTT
1121782 CATTGAAATCCCCATAGACAAGTCAAGGGGTTTGACTATCATTAGCTAGTCTTCGTAATAATTCC
1 CATTGAAATCCCCATAGACAAGTCAAGGGGTTTGACTATCATTAGCTAGTCTTCGTAATAATTCC
1121847 CAAGCTTCCTCCTTAGTATTTGGTGTCAGGCTATCATAAAAACCTGTAAATCGC
66 CAAGCTTCCTCCTTAGTATTTGGTGTCAGGCTATCATAAAAACCTGTAAATCGC
1121901 CATTGAAATCCCCATAGACAAGTCAAGGGGTTTGACTATCATTAGCTAGTCTTCGTAATAATTCC
1 CATTGAAATCCCCATAGACAAGTCAAGGGGTTTGACTATCATTAGCTAGTCTTCGTAATAATTCC
1121966 CAAGCTTCCTCCTTAGTATTTGGTGTCAGGCTATCATAAAAACCTGTAAATCGC
66 CAAGCTTCCTCCTTAGTATTTGGTGTCAGGCTATCATAAAAACCTGTAAATCGC
1122020 CATT
1 CATT
1122024 TGATGTCAGT
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 123 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (119 bp):
CATTGAAATCCCCATAGACAAGTCAAGGGGTTTGACTATCATTAGCTAGTCTTCGTAATAATTCC
CAAGCTTCCTCCTTAGTATTTGGTGTCAGGCTATCATAAAAACCTGTAAATCGC
Found at i:1124195 original size:6 final size:6
Alignment explanation
Indices: 1124184--1124210 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1124174 TAAATATTAA
1124184 AATGTT AATGTT AATGTT AATGTT AAT
1 AATGTT AATGTT AATGTT AATGTT AAT
1124211 TTTATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (6 bp):
AATGTT
Found at i:1124736 original size:3 final size:3
Alignment explanation
Indices: 1124728--1124765 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1124718 CAGACTTCTT
1124728 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1124766 TATTTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1126431 original size:97 final size:97
Alignment explanation
Indices: 1126258--1126436 Score: 279
Period size: 97 Copynumber: 1.8 Consensus size: 97
1126248 TGAAAAATGG
* * * *
1126258 TATTCGATTATCCCGGTTTGGAGAAAAATCGCGCTTAGTAAGTTAAGGAACAAATTTTCAAAACC
1 TATTCGATTATCCCGATTTGAAGAAAAATCACGCCTAGTAAGTTAAGGAACAAATTTTCAAAACC
*
1126323 CAAGATGAAGGAATATTTCCTTGATTTAAGGA
66 CAAGATAAAGGAATATTTCCTTGATTTAAGGA
* *
1126355 TATTCGATTATCCTGATTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTCAAAACC
1 TATTCGATTATCCCGATTTGAAGAAAAATCACGCCTAGTAAGTTAAGGAACAAATTTTCAAAACC
1126420 CGAA-ATAAAGGAATATT
66 C-AAGATAAAGGAATATT
1126437 GCCTCAATTT
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
97 72 0.97
98 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (97 bp):
TATTCGATTATCCCGATTTGAAGAAAAATCACGCCTAGTAAGTTAAGGAACAAATTTTCAAAACC
CAAGATAAAGGAATATTTCCTTGATTTAAGGA
Found at i:1126949 original size:30 final size:30
Alignment explanation
Indices: 1126857--1127067 Score: 202
Period size: 29 Copynumber: 7.2 Consensus size: 30
1126847 TCCCAAGGGA
*
1126857 AAAATGATAATTTTGG--AAGTTTAGGGGTA
1 AAAATG-TAATTTTGGAAAAGTTTAGGGGTC
* *
1126886 AAAATGTAATGTTT-GAGAAG-TTAGGGGTA
1 AAAATGTAAT-TTTGGAAAAGTTTAGGGGTC
*
1126915 AAAATGTAATTTTGGAAAAGTTTAGGAGTC
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTC
1126945 AAAATGTAATTTTGGAAAAGGTTT-GGGGTC
1 AAAATGTAATTTTGGAAAA-GTTTAGGGGTC
* * * *
1126975 AAAGTGTAATTTTAGAAAA-TTTATGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTC
** * * * *
1127004 AAAAAATATTTTTGG-AAACTTTAAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTC
* *
1127033 AAAATGTAATTTTAGAAAAGTTTAGGTGTC
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTC
1127063 AAAAT
1 AAAAT
1127068 ATGATTTTTG
Statistics
Matches: 151, Mismatches: 22, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
28 14 0.09
29 67 0.44
30 66 0.44
31 4 0.03
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGGTC
Found at i:1126951 original size:59 final size:58
Alignment explanation
Indices: 1126856--1127067 Score: 182
Period size: 59 Copynumber: 3.6 Consensus size: 58
1126846 TTCCCAAGGG
* *
1126856 AAAAATGATAATTTT-G-GAAGTTTAGGGGTAAAAATGTAATGTTTGAGAA-GTTAGGGGT
1 AAAAATG-TAATTTTAGAAAAGTTTA-GGGTCAAAATGTAAT-TTTGAGAACGTTAGGGGT
* * * *
1126914 AAAAATGTAATTTTGGAAAAGTTTAGGAGTCAAAATGTAATTTTGGAAAAGGTTTGGGGT
1 AAAAATGTAATTTTAGAAAAGTTTAGG-GTCAAAATGTAATTTT-GAGAACGTTAGGGGT
* * * ** * * *
1126974 CAAAGTGTAATTTTAGAAAA-TTTATGGGTTAAAAAATATTTTTG-GAAACTTTAAGGGT
1 AAAAATGTAATTTTAGAAAAGTTTA-GGGTCAAAATGTAATTTTGAG-AACGTTAGGGGT
*
1127032 TAAAATGTAATTTTAGAAAAGTTTAGGTGTCAAAAT
1 AAAAATGTAATTTTAGAAAAGTTTAGG-GTCAAAAT
1127068 ATGATTTTTG
Statistics
Matches: 125, Mismatches: 20, Indels: 17
0.77 0.12 0.10
Matches are distributed among these distances:
57 7 0.06
58 42 0.34
59 49 0.39
60 27 0.22
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.35
Consensus pattern (58 bp):
AAAAATGTAATTTTAGAAAAGTTTAGGGTCAAAATGTAATTTTGAGAACGTTAGGGGT
Found at i:1127050 original size:29 final size:29
Alignment explanation
Indices: 1126759--1127067 Score: 185
Period size: 30 Copynumber: 10.6 Consensus size: 29
1126749 AGTTTCAGAG
* *
1126759 AGTTT-GGGGTTAAAACGTAATTTTGGAA
1 AGTTTAGGGGTAAAAATGTAATTTTGGAA
* * *
1126787 AGTTT-GAGGTCGAAAATGTGACTTTTGGAA
1 AGTTTAGGGGT-AAAAATGT-AATTTTGGAA
*
1126817 A-TTT-GGGAGCAAAAATGGTAACTTTT-G-A
1 AGTTTAGGG-GTAAAAAT-GTAA-TTTTGGAA
* *
1126845 A-TTCCCAAGGG-AAAAATGATAATTTTGG-A
1 AGTT--TAGGGGTAAAAATG-TAATTTTGGAA
1126874 AGTTTAGGGGTAAAAATGTAATGTTT-GAGA
1 AGTTTAGGGGTAAAAATGTAAT-TTTGGA-A
1126904 AG-TTAGGGGTAAAAATGTAATTTTGGAAA
1 AGTTTAGGGGTAAAAATGTAATTTTGG-AA
* *
1126933 AGTTTAGGAGTCAAAATGTAATTTTGGAAA
1 AGTTTAGGGGTAAAAATGTAATTTTGG-AA
* * *
1126963 AGGTTT-GGGGTCAAAGTGTAATTTTAGAA
1 A-GTTTAGGGGTAAAAATGTAATTTTGGAA
* * * *
1126992 AATTTATGGGTTAAAAA-ATATTTTTGGAA
1 AGTTTA-GGGGTAAAAATGTAATTTTGGAA
* * * *
1127021 ACTTTAAGGGTTAAAATGTAATTTTAGAAA
1 AGTTTAGGGGTAAAAATGTAATTTT-GGAA
* *
1127051 AGTTTAGGTGTCAAAAT
1 AGTTTAGGGGTAAAAAT
1127068 ATGATTTTTG
Statistics
Matches: 223, Mismatches: 35, Indels: 44
0.74 0.12 0.15
Matches are distributed among these distances:
28 40 0.18
29 86 0.39
30 91 0.41
31 6 0.03
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (29 bp):
AGTTTAGGGGTAAAAATGTAATTTTGGAA
Found at i:1128813 original size:17 final size:17
Alignment explanation
Indices: 1128792--1128835 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1128782 AATTTTTAAT
1128792 TAAATTTAAATTTAAAAC
1 TAAATTTAAATTT-AAAC
*
1128810 -AAATTTAAATTTATAC
1 TAAATTTAAATTTAAAC
1128826 TAAATTTAAA
1 TAAATTTAAA
1128836 CTCAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAC
Found at i:1129248 original size:33 final size:33
Alignment explanation
Indices: 1129186--1129248 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
1129176 AGTACATAAA
* *
1129186 TATTTTTTTTATGTGAATTTATTATATTAACAG
1 TATTTTTTTAATGTGAATTTAATATATTAACAG
1129219 TATTTTTTGTAATGT-AATATTAATA-ATTAA
1 TATTTTTT-TAATGTGAAT-TTAATATATTAA
1129249 TTATATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
33 16 0.62
34 10 0.38
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (33 bp):
TATTTTTTTAATGTGAATTTAATATATTAACAG
Found at i:1131902 original size:22 final size:22
Alignment explanation
Indices: 1131877--1131927 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1131867 GGTTCATTCC
* * *
1131877 AATTTTAAGTGTTATGTCATAT
1 AATTTCAAGTGTTATGTAAAAT
1131899 AATTTCAAGTGTTATGTAAAAT
1 AATTTCAAGTGTTATGTAAAAT
1131921 AATTTCA
1 AATTTCA
1131928 CTAAATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (22 bp):
AATTTCAAGTGTTATGTAAAAT
Found at i:1135752 original size:18 final size:18
Alignment explanation
Indices: 1135726--1135761 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1135716 CCACCAAAAA
1135726 TAAAATATACATTTAAAT
1 TAAAATATACATTTAAAT
* *
1135744 TAAATTATATATTTAAAT
1 TAAAATATACATTTAAAT
1135762 ATTAAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATATACATTTAAAT
Found at i:1135847 original size:107 final size:105
Alignment explanation
Indices: 1135699--1135938 Score: 331
Period size: 107 Copynumber: 2.3 Consensus size: 105
1135689 GAATTGGTGG
* * *
1135699 CGCCATTTAGAATGGCTCCACCAAAAAT-AAAATATACATTTAAATTAAATTATATATTTAAATA
1 CGCCATTTAAAATGACTCCACCAAAAATAAAAATATACATTTAAATTAAACTATATATTTAAATA
* **
1135763 TTAAATAATAAATAATAAAAA-ACAAAAAATTAATCGGGTGA
66 TTAAATAATAAATAA-AAAAATA-AAAAAATAAATCAAGTGA
* * *
1135804 CGTCATTTAATATGACTCCACCAAAAATAAAAAATATATATTTAAATTAAACTATATATTTAAAT
1 CGCCATTTAAAATGACTCCACCAAAAAT-AAAAATATACATTTAAATTAAACTATATATTTAAAT
* * *
1135869 ATTATATAATAAATAAAAAAATAAAAAAATAAATTAAGTGG
65 ATTAAATAATAAATAAAAAAATAAAAAAATAAATCAAGTGA
1135910 CGCCATTTAAAATGACTCCACCAAAAATA
1 CGCCATTTAAAATGACTCCACCAAAAATA
1135939 TTTAAATTTT
Statistics
Matches: 118, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
105 25 0.21
106 44 0.37
107 49 0.42
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (105 bp):
CGCCATTTAAAATGACTCCACCAAAAATAAAAATATACATTTAAATTAAACTATATATTTAAATA
TTAAATAATAAATAAAAAAATAAAAAAATAAATCAAGTGA
Found at i:1137755 original size:16 final size:17
Alignment explanation
Indices: 1137718--1137755 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1137708 AGTTTATAAT
1137718 ATTT-TATATTATGTCA
1 ATTTATATATTATGTCA
1137734 ATTTTATATATTATGT-A
1 A-TTTATATATTATGTCA
1137751 ATTTA
1 ATTTA
1137756 GAATACATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 5 0.25
18 10 0.50
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (17 bp):
ATTTATATATTATGTCA
Found at i:1141129 original size:20 final size:20
Alignment explanation
Indices: 1141082--1141135 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
1141072 ATTTTGAAGT
* *
1141082 GTTAAAATGATTTTGACTTA
1 GTTAAAATCATTTTGACATA
* *
1141102 GTTCAAATTATTTTGACAT-
1 GTTAAAATCATTTTGACATA
1141121 GTTTAAAATCATTTT
1 G-TTAAAATCATTTT
1141136 AACTCAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.48
Consensus pattern (20 bp):
GTTAAAATCATTTTGACATA
Found at i:1141878 original size:14 final size:14
Alignment explanation
Indices: 1141859--1141885 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1141849 TGTTACCTTC
1141859 CCCCTTCCCTTTCT
1 CCCCTTCCCTTTCT
1141873 CCCCTTCCCTTTC
1 CCCCTTCCCTTTC
1141886 CCTTTTCACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (14 bp):
CCCCTTCCCTTTCT
Found at i:1142618 original size:10 final size:11
Alignment explanation
Indices: 1142588--1142623 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1142578 TTATATTTAA
1142588 AAAATAATTTT
1 AAAATAATTTT
*
1142599 AAATTAATTTT
1 AAAATAATTTT
*
1142610 AAAATATTTTT
1 AAAATAATTTT
1142621 AAA
1 AAA
1142624 TAAAAAAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:1147697 original size:17 final size:18
Alignment explanation
Indices: 1147670--1147703 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1147660 ATCGATGTGA
1147670 AATTATTAAATATATTCC
1 AATTATTAAATATATTCC
1147688 AATT-TTAAATATATTC
1 AATTATTAAATATATTC
1147704 AATCTGTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTATTAAATATATTCC
Found at i:1150308 original size:24 final size:24
Alignment explanation
Indices: 1150281--1150340 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
1150271 AATAATCTTC
*
1150281 CAATTAAACTTTGTTTATTTGTTT
1 CAATTAAACTCTGTTTATTTGTTT
1150305 CAATTAAACTCTGTTTATTTGTTT
1 CAATTAAACTCTGTTTATTTGTTT
*
1150329 CAATCAAACTCT
1 CAATTAAACTCT
1150341 TATGAGTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (24 bp):
CAATTAAACTCTGTTTATTTGTTT
Found at i:1150495 original size:15 final size:16
Alignment explanation
Indices: 1150469--1150498 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1150459 TTAGTGTTTA
1150469 CGTTTTGAGGGTTTTT
1 CGTTTTGAGGGTTTTT
1150485 CGTTTTG-GGGTTTT
1 CGTTTTGAGGGTTTT
1150499 AGTTTTTATT
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:0.03, C:0.07, G:0.33, T:0.57
Consensus pattern (16 bp):
CGTTTTGAGGGTTTTT
Found at i:1150902 original size:22 final size:23
Alignment explanation
Indices: 1150861--1150903 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1150851 TCGTAACAAT
*
1150861 ACTTTTATATATTTTATATTTCA
1 ACTTTTATACATTTTATATTTCA
*
1150884 ACTTTT-TACATTTTTTATTT
1 ACTTTTATACATTTTATATTT
1150904 TTTAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (23 bp):
ACTTTTATACATTTTATATTTCA
Found at i:1158084 original size:28 final size:28
Alignment explanation
Indices: 1158053--1158107 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
1158043 TATAAGAAAT
* *
1158053 TATTAATAATATTATTTAAATTATAATA
1 TATTAATAATAATATTTAAACTATAATA
* *
1158081 TATTGATATTAATATTTAAACTATAAT
1 TATTAATAATAATATTTAAACTATAAT
1158108 GAATTTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
TATTAATAATAATATTTAAACTATAATA
Found at i:1158227 original size:21 final size:21
Alignment explanation
Indices: 1158203--1158242 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1158193 TTTTAAAAAT
*
1158203 ATTTAGTAATTAATTTTTTTA
1 ATTTAGTAATAAATTTTTTTA
* *
1158224 ATTTATTGATAAATTTTTT
1 ATTTAGTAATAAATTTTTT
1158243 AAAAGAATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
ATTTAGTAATAAATTTTTTTA
Found at i:1177197 original size:26 final size:26
Alignment explanation
Indices: 1177132--1177199 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
1177122 GAGTCATTCT
* * *
1177132 AGAAGTTTAGCTCATACGAGCCCAGAC
1 AGAA-TTTAGCTCTTACGAGCACAAAC
*
1177159 AGAATTTAGCTCTTACTAGCACAAAC
1 AGAATTTAGCTCTTACGAGCACAAAC
1177185 AGAATTTAGCTCTTA
1 AGAATTTAGCTCTTA
1177200 TAGAGCTAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 33 0.89
27 4 0.11
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.26
Consensus pattern (26 bp):
AGAATTTAGCTCTTACGAGCACAAAC
Found at i:1185087 original size:24 final size:24
Alignment explanation
Indices: 1185055--1185268 Score: 232
Period size: 24 Copynumber: 8.9 Consensus size: 24
1185045 GTTCAGTACA
* * *
1185055 TTTATGCTCATCAGCTAAGATACG
1 TTTACGCTCGTCAGCTAATATACG
** *
1185079 TTTACGCTCACCAGCTAATATGCG
1 TTTACGCTCGTCAGCTAATATACG
* * *
1185103 TTTATGCTCGCCAGCTAATATATG
1 TTTACGCTCGTCAGCTAATATACG
**
1185127 TTTACGCTCGTCAGCTAATATGTG
1 TTTACGCTCGTCAGCTAATATACG
* *
1185151 TTTACGCTCGCCAGCTAATATACA
1 TTTACGCTCGTCAGCTAATATACG
*
1185175 TTTACGCTCGTCAGCTTATATACG
1 TTTACGCTCGTCAGCTAATATACG
**
1185199 TTTACGCTCGTCAGCTAATATAAT
1 TTTACGCTCGTCAGCTAATATACG
* * *
1185223 TTTACGCTCATCAACTAATATATG
1 TTTACGCTCGTCAGCTAATATACG
*
1185247 TTTACGCTC-ACTAGCTAATATA
1 TTTACGCTCGTC-AGCTAATATA
1185269 AGAAACATTG
Statistics
Matches: 162, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
23 1 0.01
24 161 0.99
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (24 bp):
TTTACGCTCGTCAGCTAATATACG
Found at i:1185184 original size:72 final size:72
Alignment explanation
Indices: 1185055--1185268 Score: 259
Period size: 72 Copynumber: 3.0 Consensus size: 72
1185045 GTTCAGTACA
* * * * * *
1185055 TTTATGCTCATCAGCTAAGATACGTTTACGCTCACCAGCTAATATGCGTTTATGCTCGCCAGCTA
1 TTTACGCTCGTCAGCTAATATATGTTTACGCTCACCAGCTAATATACGTTTACGCTCGCCAGCTA
*
1185120 ATATATG
66 ATATACG
* * * * *
1185127 TTTACGCTCGTCAGCTAATATGTGTTTACGCTCGCCAGCTAATATACATTTACGCTCGTCAGCTT
1 TTTACGCTCGTCAGCTAATATATGTTTACGCTCACCAGCTAATATACGTTTACGCTCGCCAGCTA
1185192 ATATACG
66 ATATACG
* * * * *
1185199 TTTACGCTCGTCAGCTAATATAAT-TTTACGCTCATCAACTAATATATGTTTACGCTCACTAGCT
1 TTTACGCTCGTCAGCTAATAT-ATGTTTACGCTCACCAGCTAATATACGTTTACGCTCGCCAGCT
1185263 AATATA
65 AATATA
1185269 AGAAACATTG
Statistics
Matches: 119, Mismatches: 22, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
72 118 0.99
73 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (72 bp):
TTTACGCTCGTCAGCTAATATATGTTTACGCTCACCAGCTAATATACGTTTACGCTCGCCAGCTA
ATATACG
Found at i:1191082 original size:20 final size:20
Alignment explanation
Indices: 1191043--1191082 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1191033 TCAATAACTT
*
1191043 AATTAAAATAAAGTTTATTA
1 AATTAAAATAAAGTTAATTA
* *
1191063 AATTAAAGTAAGGTTAATTA
1 AATTAAAATAAAGTTAATTA
1191083 TGTTAATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (20 bp):
AATTAAAATAAAGTTAATTA
Found at i:1193508 original size:35 final size:34
Alignment explanation
Indices: 1193469--1193578 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 34
1193459 CCAAACTCAT
**
1193469 TTTAAATTTATTTTAAGA-TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTAATTT-AAA
* *
1193504 TTTAAATTTATTTTAAATTTAAATTTAATTTGAG
1 TTTAAATTTATTTTAAATTTAAATTTAATTTAAA
*
1193538 TTTAAATTTATTTTCAAATTTAAAATT-ATTATAAA
1 TTTAAATTTATTTT-AAATTTAAATTTAATT-TAAA
1193573 TTTAAA
1 TTTAAA
1193579 ATAAAAAAGT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
34 19 0.29
35 46 0.71
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTAAA
Found at i:1193512 original size:6 final size:6
Alignment explanation
Indices: 1193501--1193578 Score: 58
Period size: 6 Copynumber: 13.5 Consensus size: 6
1193491 ATTTGTTTTA
* * *
1193501 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT GAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
1193547 -ATTTT CAAATTT AAAATT --ATTAT AAATTT AAA
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAA
1193579 ATAAAAAAGT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
4 2 0.04
5 14 0.25
6 33 0.59
7 7 0.12
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:1193531 original size:23 final size:23
Alignment explanation
Indices: 1193501--1193547 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1193491 ATTTGTTTTA
*
1193501 AAATTTAAATTT-ATTTTAAATTT
1 AAATTT-AATTTGAGTTTAAATTT
1193524 AAATTTAATTTGAGTTTAAATTT
1 AAATTTAATTTGAGTTTAAATTT
1193547 A
1 A
1193548 TTTTCAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
AAATTTAATTTGAGTTTAAATTT
Found at i:1193543 original size:52 final size:52
Alignment explanation
Indices: 1193469--1193578 Score: 157
Period size: 52 Copynumber: 2.1 Consensus size: 52
1193459 CCAAACTCAT
* * * *
1193469 TTTAAATTTATTTTAAGATTAAATTTGTTTTAAAATTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
* * *
1193521 TTTAAATTTAATTTGAGTTTAAATTTATTTTCAAATTTAAAATTATTATAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
1193573 TTTAAA
1 TTTAAA
1193579 ATAAAAAAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (52 bp):
TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
Found at i:1193556 original size:12 final size:11
Alignment explanation
Indices: 1193504--1193559 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
1193494 TGTTTTAAAA
1193504 TTTAAATTTAT
1 TTTAAATTTAT
*
1193515 TTTAAATTTAAA
1 TTTAAATTT-AT
*
1193527 TTT-AATTTGAG
1 TTTAAATTT-AT
1193538 TTTAAATTTAT
1 TTTAAATTTAT
1193549 TTTCAAATTTA
1 TTT-AAATTTA
1193560 AAATTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
11 22 0.58
12 16 0.42
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:1193580 original size:17 final size:17
Alignment explanation
Indices: 1193469--1193578 Score: 132
Period size: 17 Copynumber: 6.4 Consensus size: 17
1193459 CCAAACTCAT
1193469 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
1193487 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
1193504 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
1193521 TTTAAATTTAATTTGAG
1 TTTAAATTTATTTTAAA
1193538 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
1193556 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
1193573 TTTAAA
1 TTTAAA
1193579 ATAAAAAAGT
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
17 52 0.66
18 27 0.34
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:1194318 original size:18 final size:18
Alignment explanation
Indices: 1194295--1194343 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1194285 TAATAACTAT
* **
1194295 TAATAATAACAACAGTAA
1 TAATAATAATAACAACAA
*
1194313 TAATAATAGTAACAACAA
1 TAATAATAATAACAACAA
1194331 TAATAAATAATAA
1 TAAT-AATAATAA
1194344 TTAATATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.63, C:0.08, G:0.04, T:0.24
Consensus pattern (18 bp):
TAATAATAATAACAACAA
Found at i:1194325 original size:21 final size:22
Alignment explanation
Indices: 1194295--1194344 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
1194285 TAATAACTAT
*
1194295 TAATAATAACAACAGTAAT-AA
1 TAATAATAACAACAATAATAAA
*
1194316 TAATAGTAACAACAATAATAAA
1 TAATAATAACAACAATAATAAA
1194338 TAATAAT
1 TAATAAT
1194345 TAATATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (22 bp):
TAATAATAACAACAATAATAAA
Found at i:1195015 original size:29 final size:28
Alignment explanation
Indices: 1194983--1195344 Score: 225
Period size: 29 Copynumber: 12.4 Consensus size: 28
1194973 CCAAAATTAT
* *
1194983 ATTTTTGACCCTAAACTTTTAAAAATCCC
1 ATTTTT-ACCCTAAACTTTCAAAAATTCC
* *
1195012 ATTTTAACCCTAAAACTTTCAAAAATTAC
1 ATTTTTACCCT-AAACTTTCAAAAATTCC
1195041 ATTTTATACCCCTAAACTTTCAAAAATTCC
1 ATTTT-TA-CCCTAAACTTTCAAAAATTCC
* * * *
1195071 ATTTTAACCTCAAAACTTCCAAAAATTAC
1 ATTTTTACC-CTAAACTTTCAAAAATTCC
* * *
1195100 ATTTTTACCCCCAAACTTCCAAAAATTTCA
1 ATTTTTA-CCCTAAACTTTCAAAAA-TTCC
* * * *
1195130 ATTTTGACCCCAAAACTTTCAAAATTTAC
1 ATTTTTA-CCCTAAACTTTCAAAAATTCC
*
1195159 A-TTTTAACCTATGAAC-TTCTAAAAATTCC
1 ATTTTTACCCTA--AACTTTC-AAAAATTCC
* * *
1195188 ATTTTTAACCCCCAAAACTTCCAAAAATTAC
1 ATTTTT-A--CCCTAAACTTTCAAAAATTCC
* * *
1195219 ATTTTAACCCTTGAAC-TTCCAAAATTCC
1 ATTTTTACCC-TAAACTTTCAAAAATTCC
* * *
1195247 ATTTTTGACCTCGATACTTTCGAAAATTACC
1 ATTTTT-ACC-CTAAACTTTCAAAAATT-CC
*
1195278 A-TTTTACCTTCT-AAC-TTCCAAAATTCC
1 ATTTTTACC--CTAAACTTTCAAAAATTCC
*
1195305 ATTTTTGACCTCGAAACTTTCAAAAATTACC
1 ATTTTT-ACC-CTAAACTTTCAAAAATT-CC
1195336 A-TTTTACCC
1 ATTTTTACCC
1195345 CTGGATGTCC
Statistics
Matches: 263, Mismatches: 45, Indels: 51
0.73 0.13 0.14
Matches are distributed among these distances:
27 6 0.02
28 47 0.18
29 97 0.37
30 81 0.31
31 27 0.10
32 2 0.01
33 3 0.01
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.36
Consensus pattern (28 bp):
ATTTTTACCCTAAACTTTCAAAAATTCC
Found at i:1195154 original size:58 final size:59
Alignment explanation
Indices: 1194966--1195398 Score: 364
Period size: 58 Copynumber: 7.4 Consensus size: 59
1194956 GAGGCCCCTG
* * * ** * * *
1194966 AACTTCTCCAAAATTATATTTTTGA-CCCTAAACTTTTAAAAA-TCCCATTTTAACCCTAA
1 AACTT-TCAAAAATTACATTTTT-ACCCCTGAACTTCCAAAAATTCCAATTTTGACCCCAA
* * * *
1195025 AACTTTCAAAAATTACATTTTATACCCCTAAACTTTCAAAAATTCC-ATTTTAACCTCAA
1 AACTTTCAAAAATTACATTTT-TACCCCTGAACTTCCAAAAATTCCAATTTTGACCCCAA
* ** *
1195084 AACTTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTTCAATTTTGACCCCAA
1 AACTTTCAAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCAATTTTGACCCCAA
* * ** * * *
1195143 AACTTTCAAAATTTACATTTTAACCTATGAACTTCTAAAAATTCCATTTTTAACCCCCAA
1 AACTTTCAAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCAATTTTGA-CCCCAA
* * * * * *
1195203 AACTTCCAAAAATTACATTTTAACCCTTGAACTTCC-AAAATTCCATTTTTGACCTCGA
1 AACTTTCAAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCAATTTTGACCCCAA
* * * * * *
1195261 TACTTTCGAAAATTACCA-TTTTACCTTCT-AACTTCC-AAAATTCCATTTTTGACCTCGA
1 AACTTTCAAAAATTA-CATTTTTACC-CCTGAACTTCCAAAAATTCCAATTTTGACCCCAA
* * *
1195319 AACTTTCAAAAATTACCA-TTTTACCCCTGGA-TGTCCAAAAACT-CTATTTTGACCCCAA
1 AACTTTCAAAAATTA-CATTTTTACCCCTGAACT-TCCAAAAATTCCAATTTTGACCCCAA
*
1195377 AACTTTTAAAAATTACCATTTT
1 AACTTTCAAAAATTA-CATTTT
1195399 AGCCCCGAAT
Statistics
Matches: 317, Mismatches: 46, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
57 3 0.01
58 142 0.45
59 132 0.42
60 40 0.13
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (59 bp):
AACTTTCAAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCAATTTTGACCCCAA
Found at i:1204692 original size:120 final size:120
Alignment explanation
Indices: 1204527--1204789 Score: 463
Period size: 120 Copynumber: 2.2 Consensus size: 120
1204517 ATGCGGTCAT
* *
1204527 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCACACCCACGCTCAATATGAGCAAATTTTCGA
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAATATGAGCAAATCTTCGA
*
1204592 ACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGTAATAAAATGATTAG
66 ACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGATTAG
* *
1204647 CTTCCTGATGAGATACTGAGAAGAAGATCAAATCAAACCCACGCTCAATATGAGTAAATCTTCGA
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAATATGAGCAAATCTTCGA
* *
1204712 ACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAG
66 ACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGATTAG
1204767 CTTCCTGATGAGATACTGAGAAG
1 CTTCCTGATGAGATACTGAGAAG
1204790 TGGACTAAAT
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 136 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (120 bp):
CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAATATGAGCAAATCTTCGA
ACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGATTAG
Found at i:1205198 original size:207 final size:204
Alignment explanation
Indices: 1204647--1205285 Score: 831
Period size: 200 Copynumber: 3.1 Consensus size: 204
1204637 AAATGATTAG
* * *
1204647 CTTCCTGATGAGATACTGAGAAGAAGATCAAATCAAACCCACGCTCAATATGAGTAAATCTTCGA
1 CTTCCTGATGAGATACTGAGAAGAAGA-C-AATCAAACCCACGCTCGATGTGAGCAAATCTTCGA
* *
1204712 ACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGATG
64 ACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATG
* * *
1204777 AGATACTGAGAAGTGGACTAAATTCGTCTTCCTGATTAGATACAGAGAAGCGGATTGAAATAAGT
129 AGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCGGATTGAAACAAGT
*
1204842 GAGGCGATCAT
194 GATGCGATCAT
* * * * *
1204853 CTTCTTGATGAGATAC--AG-AGAAGTA-TATC--ACTCGACGCTCGATGCGAGCAAATCTTTGA
1 CTTCCTGATGAGATACTGAGAAGAAG-ACAATCAAAC-CCACGCTCGATGTGAGCAAATCTTCGA
**
1204912 ACGTCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATG
64 ACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATG
* * * *
1204977 AGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGGAACAAGT
129 AGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCGGATTGAAACAAGT
*
1205042 GATACGATCAT
194 GATGCGATCAT
* **
1205053 CTTCCTAATGAGATACTGAGAAGAAGACCGAATCAAACCCACGCTCGATGTGAGCAAAAATTCGA
1 CTTCCTGATGAGATACTGAGAAGAAGA-C-AATCAAACCCACGCTCGATGTGAGCAAATCTTCGA
* * * *
1205118 ACCCCCAGCTTCTTGATGAGATACTGAGAAGCAAGTCAAAGCAATAAAGTGGTTAGCTTCCTGAT
64 A-CCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGAT
* * * * * * * **
1205183 GAGATACGGAGAAGTGAACCAAATCCGTCTTCTTGATAAAACACAGAGAAGTGGATCAAAACAAG
128 GAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCGGATTGAAACAAG
*
1205248 TGATGCGGTCAT
193 TGATGCGATCAT
1205260 CTTCCTGATGAGATACTGAGAAGAAG
1 CTTCCTGATGAGATACTGAGAAGAAG
1205286 GCCAAGTCAA
Statistics
Matches: 372, Mismatches: 50, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
199 2 0.01
200 164 0.44
201 3 0.01
202 3 0.01
203 10 0.03
204 3 0.01
205 3 0.01
206 38 0.10
207 146 0.39
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (204 bp):
CTTCCTGATGAGATACTGAGAAGAAGACAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAAC
CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAG
ATACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCGGATTGAAACAAGTGA
TGCGATCAT
Found at i:1205647 original size:17 final size:18
Alignment explanation
Indices: 1205624--1205716 Score: 93
Period size: 17 Copynumber: 5.3 Consensus size: 18
1205614 CCAAACTCAT
* *
1205624 TTTAAATTCATTTTAAGA
1 TTTAAATTTATTTTAAAA
*
1205642 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAAA
*
1205659 TTTAAATTTA-TTTCAAA
1 TTTAAATTTATTTTAAAA
* * *
1205676 TTTAAATTTACTTT-GAG
1 TTTAAATTTATTTTAAAA
*
1205693 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAAA
1205711 TTTAAA
1 TTTAAA
1205717 ATAAATAAAG
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
17 44 0.71
18 18 0.29
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:1206470 original size:21 final size:22
Alignment explanation
Indices: 1206440--1206489 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
1206430 TAATAACTAT
1206440 TAATAATAACAACAGTAAT-AA
1 TAATAATAACAACAGTAATAAA
*
1206461 TAATAGTAACAACAGTAATAAA
1 TAATAATAACAACAGTAATAAA
1206483 TAATAAT
1 TAATAAT
1206490 TAATATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.60, C:0.08, G:0.06, T:0.26
Consensus pattern (22 bp):
TAATAATAACAACAGTAATAAA
Found at i:1207264 original size:40 final size:40
Alignment explanation
Indices: 1207198--1207411 Score: 163
Period size: 39 Copynumber: 5.4 Consensus size: 40
1207188 ATAGCTTTAG
* * * *
1207198 GGGTAAGATATTAGATTGT-TTCAATCTGTCTCATGGTCA
1 GGGTAAGAGATTGGATGGTCTTCAATCTGCCTCATGGTCA
* *
1207237 GGGTAAGAGATCGGATGGTCTTCAATCTGCCCTC-TGGTTA
1 GGGTAAGAGATTGGATGGTCTTCAATCTG-CCTCATGGTCA
* * **
1207277 GGGTAAAAGATTGGAT--TACTTCAAT-TAGCCCCATAATCA
1 GGGTAAGAGATTGGATGGT-CTTCAATCT-GCCTCATGGTCA
* * * * *
1207316 GGGTAAGGGATCGGATGGTCTTCAATTTGCCCTC-TAGTTA
1 GGGTAAGAGATTGGATGGTCTTCAATCTG-CCTCATGGTCA
* * * * *
1207356 GGGTAAAAGATTGCATTG-CTTCAATCTACCCCATGGTCA
1 GGGTAAGAGATTGGATGGTCTTCAATCTGCCTCATGGTCA
1207395 GGGTAAGAGATTGGATG
1 GGGTAAGAGATTGGATG
1207412 ATGCCTTTCA
Statistics
Matches: 134, Mismatches: 31, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
38 8 0.06
39 65 0.49
40 53 0.40
41 8 0.06
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (40 bp):
GGGTAAGAGATTGGATGGTCTTCAATCTGCCTCATGGTCA
Found at i:1207318 original size:79 final size:79
Alignment explanation
Indices: 1207234--1207411 Score: 268
Period size: 79 Copynumber: 2.3 Consensus size: 79
1207224 TGTCTCATGG
* *
1207234 TCAGGGTAAGAGATCGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATTACTTC
1 TCAGGGTAAGAGATCGGATGGTCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGCATTACTTC
1207299 AAT-TAGCCCCATAA
66 AATCTA-CCCCATAA
* * *
1207313 TCAGGGTAAGGGATCGGATGGTCTTCAATTTGCCCTCTAGTTAGGGTAAAAGATTGCATTGCTTC
1 TCAGGGTAAGAGATCGGATGGTCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGCATTACTTC
**
1207378 AATCTACCCCATGG
66 AATCTACCCCATAA
*
1207392 TCAGGGTAAGAGATTGGATG
1 TCAGGGTAAGAGATCGGATG
1207412 ATGCCTTTCA
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
79 87 0.98
80 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (79 bp):
TCAGGGTAAGAGATCGGATGGTCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGCATTACTTC
AATCTACCCCATAA
Found at i:1207441 original size:42 final size:41
Alignment explanation
Indices: 1207217--1207726 Score: 255
Period size: 42 Copynumber: 12.8 Consensus size: 41
1207207 ATTAGATTGT
* * * * * *
1207217 TTCAATCTGTCTCATGGTCAGGGTAAGAGATCGGATGGT-C
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGC
* ** * *
1207257 TTCAATCTGCCCTC-TGGTTAGGGTAAAAGATTGGAT--TAC
1 TTCAATCTGCCC-CATGATCGGGGTAAGAGATTGGATGATGC
* * * * *
1207296 TTCAAT-TAGCCCCATAATCAGGGTAAGGGATCGGATGGT-C
1 TTCAATCT-GCCCCATGATCGGGGTAAGAGATTGGATGATGC
* ** * *
1207336 TTCAATTTGCCCTC-T-AGTTAGGGTAAAAGATTGCAT--TGC
1 TTCAATCTGCCC-CATGA-TCGGGGTAAGAGATTGGATGATGC
* * *
1207375 TTCAATCTACCCCATGGTCAGGGTAAGAGATTGGATGATGCC
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATG-C
* ** * *
1207417 TTTC-ATCTGCCCCATGATCGGGGTAAAAGATTAAATGGT-T
1 -TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGC
* * *** * * * *
1207457 TTTAATCTACCCTC-TGATTAAGGAAAAAG-TTTGATGATATC
1 TTCAATCTGCCC-CATGATCGGGGTAAGAGATTGGATGAT-GC
* * *
1207498 TTCAATTTGCCCCGTGATCGGGGTAAAAGATTGGATGATGCC
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATG-C
*
1207540 TTTC-ATCTGCCCCATGATCGGTGTAAGAGATTGG--G-TGC
1 -TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGC
* * *
1207578 TTCAATCTGCCCTATGATTGAGGTAAGAGA-T---TG--G-
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGC
* *
1207612 -TCAATCTGCCCCATTG-TCGGGGTAAGAGATTGGAAGATATC
1 TTCAATCTGCCCCA-TGATCGGGGTAAGAGATTGGATGAT-GC
* *
1207653 TTCAATCTGCCCTATGATCGGGGTAAGAGATTGGATGATGTA
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATG-C
* *
1207695 TTCAATTTGCCCCATGATCGGGGTAAAAGATT
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATT
1207727 AGACGGTGAT
Statistics
Matches: 363, Mismatches: 69, Indels: 74
0.72 0.14 0.15
Matches are distributed among these distances:
33 23 0.06
34 3 0.01
35 1 0.00
36 1 0.00
37 5 0.01
38 28 0.08
39 66 0.18
40 75 0.21
41 29 0.08
42 126 0.35
43 6 0.02
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (41 bp):
TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGC
Found at i:1207621 original size:33 final size:33
Alignment explanation
Indices: 1207579--1207644 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1207569 ATTGGGTGCT
* *
1207579 TCAATCTGCCCTA-TGATTGAGGTAAGAGATTGG
1 TCAATCTGCCCCATTG-TCGAGGTAAGAGATTGG
*
1207612 TCAATCTGCCCCATTGTCGGGGTAAGAGATTGG
1 TCAATCTGCCCCATTGTCGAGGTAAGAGATTGG
1207645 AAGATATCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (33 bp):
TCAATCTGCCCCATTGTCGAGGTAAGAGATTGG
Found at i:1207678 original size:75 final size:71
Alignment explanation
Indices: 1207544--1207686 Score: 198
Period size: 75 Copynumber: 2.0 Consensus size: 71
1207534 GATGCCTTTC
* *
1207544 ATCTGCCCCATGATCGGTGTAAGAGATTGGGTGCTTCAATCTGCCCTATGATTGAGGTAAGAGAT
1 ATCTGCCCCATGATCGGGGTAAGAGATTGGGTGCTTCAATCTGCCCTATGATCGAGGTAAGAGAT
1207609 TGGTCA
66 TGGTCA
* *
1207615 ATCTGCCCCATTG-TCGGGGTAAGAGATTGGAAGATATCTTCAATCTGCCCTATGATCGGGGTAA
1 ATCTGCCCCA-TGATCGGGGTAAGAGATTGG--G-T-GCTTCAATCTGCCCTATGATCGAGGTAA
1207679 GAGATTGG
61 GAGATTGG
1207687 ATGATGTATT
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
71 26 0.41
72 2 0.03
73 1 0.02
74 1 0.02
75 33 0.52
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (71 bp):
ATCTGCCCCATGATCGGGGTAAGAGATTGGGTGCTTCAATCTGCCCTATGATCGAGGTAAGAGAT
TGGTCA
Found at i:1207949 original size:95 final size:96
Alignment explanation
Indices: 1207836--1208055 Score: 266
Period size: 96 Copynumber: 2.3 Consensus size: 96
1207826 ATCTAGTGCT
* * *
1207836 TCACTCCACTCCACTGTAACCTCAAGGACGTTGAACTCT-TCCACCTATTTTGACCTATTTCTCT
1 TCACTCCACTCCATTGTAACCTCAAGGACGTTGAACTCTATCCA-CTATTTTGACCCACTTCTCT
* * *
1207900 GTACCTCACCAGGAAGATA-GGATTCGAAGTC
65 ATACCACACCAAGAAGATAGGGATTCGAAGTC
* * * * * *
1207931 TCACTCCAATCCATTGTAACCTCAGGGACGTTGAGCTCTACTTCATTATTTTGACCCACTTCTTT
1 TCACTCCACTCCATTGTAACCTCAAGGACGTTGAACTCTA-TCCACTATTTTGACCCACTTCTCT
* *
1207996 ATACCACACCAAGAAGATAGGGTTTTGAAGTC
65 ATACCACACCAAGAAGATAGGGATTCGAAGTC
*
1208028 TCACTCTACTCCATTGTAACCTC-AGGAC
1 TCACTCCACTCCATTGTAACCTCAAGGAC
1208056 ATTAAGCTCT
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
95 35 0.33
96 36 0.34
97 34 0.32
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (96 bp):
TCACTCCACTCCATTGTAACCTCAAGGACGTTGAACTCTATCCACTATTTTGACCCACTTCTCTA
TACCACACCAAGAAGATAGGGATTCGAAGTC
Found at i:1208048 original size:97 final size:95
Alignment explanation
Indices: 1207836--1208053 Score: 267
Period size: 97 Copynumber: 2.3 Consensus size: 95
1207826 ATCTAGTGCT
* * * * *
1207836 TCACTCCACTCCACTGTAACCTCAAGGACGTTGAACTCTTCCACCTATTTTGACCTATTTCTCTG
1 TCACTCCACTCCATTGTAACCTCAGGGACGTTGAACTCTTCCACCTATTTTGACCCACTTCTCTA
* *
1207901 TACCTCACCAGGAAGATAGGATTCGAAGTC
66 TACCACACCAAGAAGATAGGATTCGAAGTC
* * * * *
1207931 TCACTCCAATCCATTGTAACCTCAGGGACGTTGAGCTCTACTTCA-TTATTTTGACCCACTTCTT
1 TCACTCCACTCCATTGTAACCTCAGGGACGTTGAACTCT--TCCACCTATTTTGACCCACTTCTC
* *
1207995 TATACCACACCAAGAAGATAGGGTTTTGAAGTC
64 TATACCACACCAAGAAGATA-GGATTCGAAGTC
*
1208028 TCACTCTACTCCATTGTAACCTCAGG
1 TCACTCCACTCCATTGTAACCTCAGG
1208054 ACATTAAGCT
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
95 35 0.34
96 32 0.31
97 37 0.36
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.31
Consensus pattern (95 bp):
TCACTCCACTCCATTGTAACCTCAGGGACGTTGAACTCTTCCACCTATTTTGACCCACTTCTCTA
TACCACACCAAGAAGATAGGATTCGAAGTC
Found at i:1208087 original size:97 final size:96
Alignment explanation
Indices: 1207881--1208087 Score: 238
Period size: 96 Copynumber: 2.1 Consensus size: 96
1207871 CTCTTCCACC
* * * * * *
1207881 TATTTTGACCTATTTCTCTGTACCTCACCAGGAAGATAGGATTCGAAGTCTCACTCCAATCCATT
1 TATTTTGACCCACTTCTTTATACCACACCAAGAAGATAGGATTCGAAGTCTCACTCCAATCCATT
* * *
1207946 GTAACCTCAGGGACGTTGAGCTCTACTTCAT
66 GTAACCTCAGGGACATTAAGCTCTAATTCAT
* * * *
1207977 TATTTTGACCCACTTCTTTATACCACACCAAGAAGATAGGGTTTTGAAGTCTCACTCTACTCCAT
1 TATTTTGACCCACTTCTTTATACCACACCAAGAAGATA-GGATTCGAAGTCTCACTCCAATCCAT
1208042 TGTAACCTCA-GGACATTAAGCTCTTAATT-AT
65 TGTAACCTCAGGGACATTAAGCTC-TAATTCAT
* *
1208073 TTTTTTCGATCCACT
1 TATTTT-GACCCACT
1208088 GCAACTGGGA
Statistics
Matches: 93, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
96 50 0.54
97 43 0.46
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (96 bp):
TATTTTGACCCACTTCTTTATACCACACCAAGAAGATAGGATTCGAAGTCTCACTCCAATCCATT
GTAACCTCAGGGACATTAAGCTCTAATTCAT
Found at i:1208378 original size:49 final size:49
Alignment explanation
Indices: 1208315--1208490 Score: 163
Period size: 49 Copynumber: 3.6 Consensus size: 49
1208305 TGTTGTGGCC
* * *
1208315 TCAATCTTTCCCTTCACATCTCTAGGGTACAAGGTTCGTCGTTGCTGCT
1 TCAACCTTTCCCTTCACATCTCTAGGGTACAAGGTTCGCCGTTGCAGCT
* * * ** * *
1208364 TCAACCTTTTCCTTCATAACTCTAGGGTACAAAATTCACCGTCGCAGCT
1 TCAACCTTTCCCTTCACATCTCTAGGGTACAAGGTTCGCCGTTGCAGCT
* * * * * * * *
1208413 TCTATCTTTCCCATCACGTCCCTAAGGTACAAGGTTCGCCATTGCGGCT
1 TCAACCTTTCCCTTCACATCTCTAGGGTACAAGGTTCGCCGTTGCAGCT
* * *
1208462 TCTACCTTTCTCTTCATATCTCTAGGGTA
1 TCAACCTTTCCCTTCACATCTCTAGGGTA
1208491 TCAGATTTGT
Statistics
Matches: 95, Mismatches: 32, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
49 95 1.00
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.35
Consensus pattern (49 bp):
TCAACCTTTCCCTTCACATCTCTAGGGTACAAGGTTCGCCGTTGCAGCT
Found at i:1209407 original size:6 final size:6
Alignment explanation
Indices: 1209398--1209455 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 6
1209388 TCGACCTCCC
* *
1209398 CTTTTT CTTTTT C-TTTT C-TTTT -TTTTT CCTTTT CTTTCT CTTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C-TTTTT
1209444 CCTTTTT -TTTTT
1 -CTTTTT CTTTTT
1209456 AATTTTTTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
5 18 0.41
6 16 0.36
7 9 0.20
8 1 0.02
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:1209416 original size:11 final size:11
Alignment explanation
Indices: 1209400--1209442 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
1209390 GACCTCCCCT
1209400 TTTTCTTTTTC
1 TTTTCTTTTTC
1209411 TTTTCTTTTT-
1 TTTTCTTTTTC
*
1209421 TTTTCCTTTTC
1 TTTTCTTTTTC
1209432 TTTCTCTTTTT
1 TTT-TCTTTTT
1209443 TCCTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 9 0.32
11 13 0.46
12 6 0.21
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:1209449 original size:27 final size:27
Alignment explanation
Indices: 1209400--1209451 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1209390 GACCTCCCCT
* *
1209400 TTTTCTTTTTCTTTTCTTTTTTTTTCC
1 TTTTCTTTCTCTTTTCTTCTTTTTTCC
1209427 TTTTCTTTCTCTTTT-TTCCTTTTTT
1 TTTTCTTTCTCTTTTCTT-CTTTTTT
1209452 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (27 bp):
TTTTCTTTCTCTTTTCTTCTTTTTTCC
Found at i:1209452 original size:11 final size:10
Alignment explanation
Indices: 1209399--1209472 Score: 69
Period size: 10 Copynumber: 7.3 Consensus size: 10
1209389 CGACCTCCCC
1209399 TTTTTCTTTT
1 TTTTTCTTTT
1209409 TCTTTTCTTTT
1 T-TTTTCTTTT
*
1209420 TTTTTCCTTT
1 TTTTTCTTTT
* *
1209430 TCTTTCTCTT
1 TTTTTCTTTT
*
1209440 TTTTCCTTTT
1 TTTTTCTTTT
*
1209450 TTTTT-TAATT
1 TTTTTCT-TTT
*
1209460 TTTTTGTTTT
1 TTTTTCTTTT
1209470 TTT
1 TTT
1209473 GTTTTTTTGG
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
9 1 0.02
10 39 0.76
11 11 0.22
ACGTcount: A:0.03, C:0.14, G:0.01, T:0.82
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:1209480 original size:11 final size:11
Alignment explanation
Indices: 1209399--1209480 Score: 60
Period size: 11 Copynumber: 7.2 Consensus size: 11
1209389 CGACCTCCCC
1209399 TTTTTCTTTTT
1 TTTTTCTTTTT
*
1209410 CTTTTCTTTTT
1 TTTTTCTTTTT
* *
1209421 TTTTCCTTTTC
1 TTTTTCTTTTT
*
1209432 TTTCTCTTTTT
1 TTTTTCTTTTT
1209443 TCCTTTT-TTTTT
1 T--TTTTCTTTTT
1209455 TAATTTT-TTTGTT
1 T--TTTTCTTT-TT
*
1209468 TTTTTGTTTTT
1 TTTTTCTTTTT
1209479 TT
1 TT
1209481 GGTGAAATTT
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
11 35 0.61
12 16 0.28
13 6 0.11
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:1214157 original size:29 final size:29
Alignment explanation
Indices: 1213994--1214232 Score: 171
Period size: 30 Copynumber: 8.1 Consensus size: 29
1213984 ATAAAAATCT
*
1213994 GGTCAAAATTAAATTTTTGAAAACTTTAGG
1 GGTCAAATTTAAATTTTTGAAAA-TTTAGG
* ** *
1214024 GGTTAAATCAAAAATTTTTGAAAGTTTA-G
1 GGTCAAAT-TTAAATTTTTGAAAATTTAGG
* **
1214053 GGTCAAATTGGATTTTTTTAGAAAATTTAGG
1 GGTCAAATT-TAAATTTTT-GAAAATTTAGG
* * *
1214084 GGTCAAATTGAAATTTTTAGAAAGTTTAGT
1 GGTCAAATTTAAATTTTT-GAAAATTTAGG
*
1214114 GGTCAAATTTGAATTTTTGGAAAATTT-GG
1 GGTCAAATTTAAATTTTT-GAAAATTTAGG
* * **
1214143 GGTCAAATTCAAATTTTT-AGAATTTAAA
1 GGTCAAATTTAAATTTTTGAAAATTTAGG
* * *
1214171 AGTTAAATTTGAATTTTTAGAAAATTT-GG
1 GGTCAAATTTAAATTTTT-GAAAATTTAGG
* * * *
1214200 GGTTAAATTTAGATTTTTGGAAAAATTAAG
1 GGTCAAATTTAAATTTTT-GAAAATTTAGG
1214230 GGT
1 GGT
1214233 TAAAAATAAT
Statistics
Matches: 163, Mismatches: 38, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
27 6 0.04
28 14 0.09
29 53 0.33
30 68 0.42
31 22 0.13
ACGTcount: A:0.37, C:0.03, G:0.19, T:0.40
Consensus pattern (29 bp):
GGTCAAATTTAAATTTTTGAAAATTTAGG
Found at i:1214198 original size:57 final size:59
Alignment explanation
Indices: 1213995--1214222 Score: 207
Period size: 57 Copynumber: 3.9 Consensus size: 59
1213985 TAAAAATCTG
* * * **
1213995 GTCAAAATTAAATTTTT-GAAAACTTTAGGGGTTAAA-TCAAAAATTTTT-GAAAGTTT-AGG
1 GTCAAATTTGAATTTTTAGAAAA-TTT-GGGGTCAAATTC--AAATTTTTAGAAAGTTTAAAA
* * * ***
1214054 GTCAAATTGGATTTTTTTAGAAAATTTAGGGGTCAAATTGAAATTTTTAGAAAGTTTAGTG
1 GTCAAATTTGA-ATTTTTAGAAAATTT-GGGGTCAAATTCAAATTTTTAGAAAGTTTAAAA
*
1214115 GTCAAATTTGAATTTTTGGAAAATTTGGGGTCAAATTCAAATTTTTAG-AA-TTTAAAA
1 GTCAAATTTGAATTTTTAGAAAATTTGGGGTCAAATTCAAATTTTTAGAAAGTTTAAAA
* * * * *
1214172 GTTAAATTTGAATTTTTAGAAAATTTGGGGTTAAATTTAGATTTTTGGAAA
1 GTCAAATTTGAATTTTTAGAAAATTTGGGGTCAAATTCAAATTTTTAGAAA
1214223 AATTAAGGGT
Statistics
Matches: 142, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
57 46 0.32
58 4 0.03
59 37 0.26
60 38 0.27
61 17 0.12
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (59 bp):
GTCAAATTTGAATTTTTAGAAAATTTGGGGTCAAATTCAAATTTTTAGAAAGTTTAAAA
Found at i:1215227 original size:7 final size:7
Alignment explanation
Indices: 1215215--1215253 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
1215205 CAAGGTTTAT
1215215 TTTATTA
1 TTTATTA
1215222 TTTATTA
1 TTTATTA
1215229 TTTATTA
1 TTTATTA
1215236 TTTATTA
1 TTTATTA
1215243 TTT-TTA
1 TTTATTA
1215249 TTTAT
1 TTTAT
1215254 AAAATAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTATTA
Found at i:1215268 original size:13 final size:12
Alignment explanation
Indices: 1215254--1215295 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
1215244 TTTTATTTAT
1215254 AAAAT-AAATAA
1 AAAATAAAATAA
1215265 ATAAATAAAATAA
1 A-AAATAAAATAA
*
1215278 GAAATAAAAATAA
1 AAAAT-AAAATAA
1215291 AAAAT
1 AAAAT
1215296 GATTTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 1 0.04
12 8 0.31
13 17 0.65
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:1220742 original size:21 final size:21
Alignment explanation
Indices: 1220718--1220824 Score: 126
Period size: 21 Copynumber: 5.6 Consensus size: 21
1220708 AATTTATTAA
1220718 AATATCGTAATAATAATAAAT
1 AATATCGTAATAATAATAAAT
*
1220739 AATATCG---TAAT-AT-AGT
1 AATATCGTAATAATAATAAAT
1220755 AATATCGTAATAATAATAAAT
1 AATATCGTAATAATAATAAAT
*
1220776 AATATCG---TAAT-AT-AGT
1 AATATCGTAATAATAATAAAT
1220792 AATATCGTAATAATAATAAAT
1 AATATCGTAATAATAATAAAT
1220813 AATATCGTAATA
1 AATATCGTAATA
1220825 TAGTAATATC
Statistics
Matches: 72, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
16 18 0.25
17 4 0.06
18 8 0.11
19 8 0.11
20 4 0.06
21 30 0.42
ACGTcount: A:0.52, C:0.06, G:0.07, T:0.35
Consensus pattern (21 bp):
AATATCGTAATAATAATAAAT
Found at i:1220751 original size:8 final size:8
Alignment explanation
Indices: 1220738--1220840 Score: 83
Period size: 8 Copynumber: 13.6 Consensus size: 8
1220728 TAATAATAAA
1220738 TAATATCG
1 TAATATCG
*
1220746 TAATATAG
1 TAATATCG
1220754 TAATATCG
1 TAATATCG
*
1220762 TAATA--A
1 TAATATCG
**
1220768 TAATA-AA
1 TAATATCG
1220775 TAATATCG
1 TAATATCG
*
1220783 TAATATAG
1 TAATATCG
1220791 TAATATCG
1 TAATATCG
*
1220799 TAATA--A
1 TAATATCG
**
1220805 TAATA-AA
1 TAATATCG
1220812 TAATATCG
1 TAATATCG
*
1220820 TAATATAG
1 TAATATCG
1220828 TAATATCG
1 TAATATCG
1220836 TAATA
1 TAATA
1220841 GCCCTCAAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
6 10 0.13
7 12 0.15
8 57 0.72
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.36
Consensus pattern (8 bp):
TAATATCG
Found at i:1220756 original size:29 final size:29
Alignment explanation
Indices: 1220719--1220832 Score: 88
Period size: 29 Copynumber: 3.7 Consensus size: 29
1220709 ATTTATTAAA
**
1220719 ATATCGTAATA-A-TAATAAATAATATCGTA
1 ATATCGTAATATAGTAAT-AATAATA-AATA
* *
1220748 ATATAGTAATATCGTAATAATAATAAATA
1 ATATCGTAATATAGTAATAATAATAAATA
1220777 ATATCGTAATATAGTAATATCGTAATAATAATAAATA
1 ATATCGT---A-A-T-ATA--GTAATAATAATAAATA
1220814 ATATCGTAATATAGTAATA
1 ATATCGTAATATAGTAATA
1220833 TCGTAATAGC
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
29 24 0.35
30 7 0.10
31 7 0.10
32 2 0.03
33 2 0.03
34 2 0.03
35 2 0.03
37 23 0.33
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (29 bp):
ATATCGTAATATAGTAATAATAATAAATA
Found at i:1220759 original size:16 final size:16
Alignment explanation
Indices: 1220738--1220840 Score: 101
Period size: 16 Copynumber: 6.8 Consensus size: 16
1220728 TAATAATAAA
1220738 TAATATCGTAATATAG
1 TAATATCGTAATATAG
1220754 TAATATCGTAATA-A-
1 TAATATCGTAATATAG
** *
1220768 TAATA-AATAATATCG
1 TAATATCGTAATATAG
* *
1220783 TAATATAGTAATATCG
1 TAATATCGTAATATAG
* *
1220799 TAATA--ATAATA-AA
1 TAATATCGTAATATAG
1220812 TAATATCGTAATATAG
1 TAATATCGTAATATAG
1220828 TAATATCGTAATA
1 TAATATCGTAATA
1220841 GCCCTCAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
13 10 0.14
14 10 0.14
15 11 0.15
16 41 0.57
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.36
Consensus pattern (16 bp):
TAATATCGTAATATAG
Found at i:1220765 original size:37 final size:37
Alignment explanation
Indices: 1220718--1220840 Score: 246
Period size: 37 Copynumber: 3.3 Consensus size: 37
1220708 AATTTATTAA
1220718 AATATCGTAATAATAATAAATAATATCGTAATATAGT
1 AATATCGTAATAATAATAAATAATATCGTAATATAGT
1220755 AATATCGTAATAATAATAAATAATATCGTAATATAGT
1 AATATCGTAATAATAATAAATAATATCGTAATATAGT
1220792 AATATCGTAATAATAATAAATAATATCGTAATATAGT
1 AATATCGTAATAATAATAAATAATATCGTAATATAGT
1220829 AATATCGTAATA
1 AATATCGTAATA
1220841 GCCCTCAAAA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 86 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (37 bp):
AATATCGTAATAATAATAAATAATATCGTAATATAGT
Found at i:1223938 original size:39 final size:39
Alignment explanation
Indices: 1223884--1223964 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
1223874 TAAATACTAG
*
1223884 GTTTCAAATATACAAATAGTAGATAGACTTGGATTATAT
1 GTTTCAAATATACAAATAGTACATAGACTTGGATTATAT
*
1223923 GTTTCAAATATACAAATATTACATAGACTTGGATTATAT
1 GTTTCAAATATACAAATAGTACATAGACTTGGATTATAT
1223962 GTT
1 GTT
1223965 GATATTCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38
Consensus pattern (39 bp):
GTTTCAAATATACAAATAGTACATAGACTTGGATTATAT
Found at i:1226705 original size:16 final size:17
Alignment explanation
Indices: 1226675--1226715 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1226665 CATTGAAATT
1226675 GAATA-AGTTTATAATA
1 GAATAGAGTTTATAATA
*
1226691 GAATAGAGTTT-TAATG
1 GAATAGAGTTTATAATA
1226707 GAATAGAGT
1 GAATAGAGT
1226716 AGTAATGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (17 bp):
GAATAGAGTTTATAATA
Found at i:1226721 original size:16 final size:16
Alignment explanation
Indices: 1226686--1226737 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1226676 AATAAGTTTA
* *
1226686 TAATAGAATAGAGTTT
1 TAATGGAATAGAGTTG
*
1226702 TAATGGAATAGAGTAG
1 TAATGGAATAGAGTTG
* *
1226718 TAATGAAATAAAGTTG
1 TAATGGAATAGAGTTG
1226734 TAAT
1 TAAT
1226738 CAGTAATTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.33
Consensus pattern (16 bp):
TAATGGAATAGAGTTG
Found at i:1226944 original size:35 final size:35
Alignment explanation
Indices: 1226905--1226972 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
1226895 GTTATTAAAT
*
1226905 ATAATTTAATAAAAATGATAATAAATAATTTAATC
1 ATAATTTAATAAAAATAATAATAAATAATTTAATC
*
1226940 ATAATTTAATAAAAATAATAATATATAATTTAA
1 ATAATTTAATAAAAATAATAATAAATAATTTAA
1226973 CAACATCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (35 bp):
ATAATTTAATAAAAATAATAATAAATAATTTAATC
Found at i:1230796 original size:30 final size:32
Alignment explanation
Indices: 1230726--1230798 Score: 96
Period size: 30 Copynumber: 2.3 Consensus size: 32
1230716 TTTTTAAATT
1230726 AATAATAAAAAATTAACTTTAATCCCTTCAAA
1 AATAATAAAAAATTAACTTTAATCCCTTCAAA
* * *
1230758 AATAATAAAAAATTTA-TTTAAT-CTTTTAAA
1 AATAATAAAAAATTAACTTTAATCCCTTCAAA
*
1230788 AATTATAAAAA
1 AATAATAAAAA
1230799 TATAGACTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 16 0.43
31 6 0.16
32 15 0.41
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (32 bp):
AATAATAAAAAATTAACTTTAATCCCTTCAAA
Found at i:1234728 original size:20 final size:20
Alignment explanation
Indices: 1234702--1234741 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1234692 AATTTAGAGA
*
1234702 TTTTTTTTTTACTTCTTTTTC
1 TTTTTTCTTT-CTTCTTTTTC
1234723 TTTTTTCTTTCTTCTTTTT
1 TTTTTTCTTTCTTCTTTTT
1234742 TCAATGTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTCTTTCTTCTTTTTC
Found at i:1234737 original size:14 final size:13
Alignment explanation
Indices: 1234714--1234743 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1234704 TTTTTTTTAC
1234714 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
1234727 TTCTTTCTTCTTTT
1 TTCTTT-TTCTTTT
1234741 TTC
1 TTC
1234744 AATGTGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTCTTTTTCTTTT
Found at i:1234968 original size:22 final size:21
Alignment explanation
Indices: 1234922--1234968 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
1234912 CGAGTTTCCT
** *
1234922 AAAATAATTAAAAAAGGAAAC
1 AAAATAATTAAAAAAAAAAAA
1234943 AAAATAACTTAAAAAAAAAAAA
1 AAAATAA-TTAAAAAAAAAAAA
1234965 AAAA
1 AAAA
1234969 CCAATGGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.13
Consensus pattern (21 bp):
AAAATAATTAAAAAAAAAAAA
Found at i:1236471 original size:39 final size:39
Alignment explanation
Indices: 1236417--1236497 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
1236407 TACCGTCTGG
*
1236417 AAAGCCCATCAAAAGAGAGCCCAGAATGAAGCAGCACAA
1 AAAGCCCATCAAAAGAGAGCCCAAAATGAAGCAGCACAA
* * *
1236456 AAAGCCTATCAAAAGATAGCCCAAAATGAAGCAGTACAA
1 AAAGCCCATCAAAAGAGAGCCCAAAATGAAGCAGCACAA
1236495 AAA
1 AAA
1236498 TTTCAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.52, C:0.22, G:0.17, T:0.09
Consensus pattern (39 bp):
AAAGCCCATCAAAAGAGAGCCCAAAATGAAGCAGCACAA
Found at i:1236913 original size:61 final size:61
Alignment explanation
Indices: 1236839--1237012 Score: 154
Period size: 61 Copynumber: 2.9 Consensus size: 61
1236829 TATTTTAGTT
* * * ** **
1236839 TTTACACATTTTATCAATTTAATTTTAAATTTAAAAATTTTAATAAATTTAACTTTCAATG
1 TTTACAAAATTTATCAATTTAGTTTTAAATTTAAAAATTTTAATAAATTTAACCCTCAACA
* * ** * *
1236900 TTTACAAAATTTATCATTTTAGTTTT-AGTTCTAAAAAAATCAATAAATTTGACCCTCAACA
1 TTTACAAAATTTATCAATTTAGTTTTAAATT-TAAAAATTTTAATAAATTTAACCCTCAACA
* * * * *
1236961 TTTACAAAATTTATTAATTTAGTCTCAACTTT-AAAATTTTAAAAATATTTAA
1 TTTACAAAATTTATCAATTTAGTTTTAAATTTAAAAATTTTAATAA-ATTTAA
1237013 AAAAAAAAAA
Statistics
Matches: 87, Mismatches: 23, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
60 12 0.14
61 72 0.83
62 3 0.03
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (61 bp):
TTTACAAAATTTATCAATTTAGTTTTAAATTTAAAAATTTTAATAAATTTAACCCTCAACA
Found at i:1250840 original size:22 final size:23
Alignment explanation
Indices: 1250798--1250840 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1250788 TTGCTGTTAA
*
1250798 AACAAAATTTCGTTAATAATTTT
1 AACAAAATTTAGTTAATAATTTT
*
1250821 AACAAATTTTAGTTAA-AATT
1 AACAAAATTTAGTTAATAATT
1250841 GAAATGTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (23 bp):
AACAAAATTTAGTTAATAATTTT
Found at i:1254618 original size:17 final size:17
Alignment explanation
Indices: 1254596--1254634 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1254586 AGGTGGAGAA
* *
1254596 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
1254613 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
1254630 CTTGT
1 CTTGT
1254635 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:1258960 original size:19 final size:19
Alignment explanation
Indices: 1258916--1258966 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
1258906 ATTTTAATAA
1258916 AAATATAAAAATGTAAACTT
1 AAAT-TAAAAATGTAAACTT
**
1258936 TTATTAAAAATCGTAAA-TT
1 AAATTAAAAAT-GTAAACTT
1258955 AAATTATAAAAT
1 AAATTA-AAAAT
1258967 ATATAGAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (19 bp):
AAATTAAAAATGTAAACTT
Found at i:1259050 original size:10 final size:9
Alignment explanation
Indices: 1258955--1259063 Score: 68
Period size: 9 Copynumber: 11.8 Consensus size: 9
1258945 ATCGTAAATT
1258955 AAATTAT-A
1 AAATTATAA
*
1258963 AAATATATAG
1 AAAT-TATAA
*
1258973 AAATATAAAA
1 AAAT-TATAA
1258983 AAATTAT-A
1 AAATTATAA
1258991 AAATT-TAA
1 AAATTATAA
*
1258999 TAAATTCGTAAAA
1 -AAA-T--TATAA
1259012 AAATTATAA
1 AAATTATAA
1259021 AAATGTA-AA
1 AAAT-TATAA
1259030 GAAA-TAT-A
1 -AAATTATAA
1259038 AAATTCATAA
1 AAATT-ATAA
1259048 AAATTATAA
1 AAATTATAA
1259057 AAATTAT
1 AAATTAT
1259064 TGTACCGATA
Statistics
Matches: 81, Mismatches: 6, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
7 4 0.05
8 15 0.19
9 31 0.38
10 24 0.30
11 1 0.01
12 4 0.05
13 2 0.02
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (9 bp):
AAATTATAA
Found at i:1262279 original size:17 final size:17
Alignment explanation
Indices: 1262257--1262290 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1262247 AAGGGACCTA
1262257 ATAATTAAAAAATTAAT
1 ATAATTAAAAAATTAAT
* *
1262274 ATAATTATAAATTTAAT
1 ATAATTAAAAAATTAAT
1262291 TCTTAATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATTAAAAAATTAAT
Found at i:1264254 original size:7 final size:7
Alignment explanation
Indices: 1264244--1264276 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1264234 GTTATATTTA
1264244 TTATTAT
1 TTATTAT
1264251 TTATTAT
1 TTATTAT
1264258 TTATTAT
1 TTATTAT
*
1264265 ATATTA-
1 TTATTAT
1264271 TTATTA
1 TTATTA
1264277 AACACACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TTATTAT
Found at i:1264261 original size:14 final size:13
Alignment explanation
Indices: 1264235--1264276 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
1264225 TAATTTTAAG
1264235 TTATAT-TTATTA
1 TTATATATTATTA
*
1264247 TTATTTATTATTTA
1 TTATATATTA-TTA
1264261 TTATATATTATTA
1 TTATATATTATTA
1264274 TTA
1 TTA
1264277 AACACACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 5 0.19
13 9 0.35
14 12 0.46
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATATATTATTA
Found at i:1268346 original size:2 final size:2
Alignment explanation
Indices: 1268339--1268365 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1268329 ATAGATGCCT
1268339 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1268366 GTGGAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.