Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 20 of 226
Found at i:9115240 original size:84 final size:83
Alignment explanation
Indices: 9115141--9115306 Score: 296
Period size: 84 Copynumber: 2.0 Consensus size: 83
9115131 GGACAGCTTT
9115141 TATACACCAAATTGGACAGCATTTTTACACCAAAATTGGACAGCATATAGACACCAAATTGGGCA
1 TATACACCAAATTGGACAGCATTTTTACACCAAAATTGGACAGCATATAGACACCAAATTGGGCA
9115206 GCATATATATACCCAAATA
66 GCATATATATA-CCAAATA
* * *
9115225 TATATACCAAATTGGACAGCATTTTTACACTAAAATTGGATAGCATATAGACACCAAATTGGGCA
1 TATACACCAAATTGGACAGCATTTTTACACCAAAATTGGACAGCATATAGACACCAAATTGGGCA
9115290 GCATATATATACCAAAT
66 GCATATATATACCAAAT
9115307 TGGACAGCAT
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
83 6 0.08
84 73 0.92
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (83 bp):
TATACACCAAATTGGACAGCATTTTTACACCAAAATTGGACAGCATATAGACACCAAATTGGGCA
GCATATATATACCAAATA
Found at i:9115292 original size:23 final size:23
Alignment explanation
Indices: 9115222--9115358 Score: 148
Period size: 23 Copynumber: 5.9 Consensus size: 23
9115212 ATATACCCAA
*
9115222 ATATATATACCAAATTGGACAGC
1 ATATATACACCAAATTGGACAGC
* * * *
9115245 ATTTTTACACTAAAATTGGATAGC
1 ATATATACAC-CAAATTGGACAGC
* *
9115269 ATATAGACACCAAATTGGGCAGC
1 ATATATACACCAAATTGGACAGC
*
9115292 ATATATATACCAAATTGGACAGC
1 ATATATACACCAAATTGGACAGC
* *
9115315 ATTTTTACACCCAAATTGGACAGC
1 ATATATACA-CCAAATTGGACAGC
* *
9115339 ATATAGACACCGAATTGGAC
1 ATATATACACCAAATTGGAC
9115359 TTGAATCGAA
Statistics
Matches: 91, Mismatches: 21, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
23 53 0.58
24 38 0.42
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.26
Consensus pattern (23 bp):
ATATATACACCAAATTGGACAGC
Found at i:9115340 original size:70 final size:70
Alignment explanation
Indices: 9115222--9115356 Score: 234
Period size: 70 Copynumber: 1.9 Consensus size: 70
9115212 ATATACCCAA
* *
9115222 ATATATATACCAAATTGGACAGCATTTTTACACTAAAATTGGATAGCATATAGACACCAAATTGG
1 ATATATATACCAAATTGGACAGCATTTTTACACCAAAATTGGACAGCATATAGACACCAAATTGG
9115287 GCAGC
66 GCAGC
* *
9115292 ATATATATACCAAATTGGACAGCATTTTTACACCCAAATTGGACAGCATATAGACACCGAATTGG
1 ATATATATACCAAATTGGACAGCATTTTTACACCAAAATTGGACAGCATATAGACACCAAATTGG
9115357 ACTTGAATCG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (70 bp):
ATATATATACCAAATTGGACAGCATTTTTACACCAAAATTGGACAGCATATAGACACCAAATTGG
GCAGC
Found at i:9116176 original size:41 final size:40
Alignment explanation
Indices: 9116118--9116216 Score: 126
Period size: 41 Copynumber: 2.5 Consensus size: 40
9116108 ATTGATCTTA
* * *
9116118 ATTTCGCACACTTAGTGCCCGTTATTTAACATCATTATTT
1 ATTTCGCACACTTAGTGCCCATTATTCAACATCATCATTT
* *
9116158 AGTTTCGCACACTTAGTGCTCATTATTCAACCTCATCATTT
1 A-TTTCGCACACTTAGTGCCCATTATTCAACATCATCATTT
* *
9116199 AATTCGTACACTTAGTGC
1 ATTTCGCACACTTAGTGC
9116217 TAATCATTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 16 0.31
41 35 0.69
ACGTcount: A:0.25, C:0.24, G:0.11, T:0.39
Consensus pattern (40 bp):
ATTTCGCACACTTAGTGCCCATTATTCAACATCATCATTT
Found at i:9118601 original size:25 final size:25
Alignment explanation
Indices: 9118567--9118615 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
9118557 AATGACTTGA
9118567 CCGGCTAAGCTTCAGCTTTCTTTTT
1 CCGGCTAAGCTTCAGCTTTCTTTTT
9118592 CCGGCTAAGCTTCAGCTTTCTTTT
1 CCGGCTAAGCTTCAGCTTTCTTTT
9118616 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.12, C:0.29, G:0.16, T:0.43
Consensus pattern (25 bp):
CCGGCTAAGCTTCAGCTTTCTTTTT
Found at i:9128996 original size:12 final size:12
Alignment explanation
Indices: 9128979--9129003 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9128969 CTTTAAGTAA
9128979 CGATTCGACTAT
1 CGATTCGACTAT
9128991 CGATTCGACTAT
1 CGATTCGACTAT
9129003 C
1 C
9129004 ATTGAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (12 bp):
CGATTCGACTAT
Found at i:9132844 original size:23 final size:23
Alignment explanation
Indices: 9132817--9132915 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
9132807 AGTGTTATTG
*
9132817 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
9132840 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
9132863 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
9132886 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
9132909 ATCAGTG
1 ATCAGTG
9132916 TTGCACTTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:9137839 original size:38 final size:39
Alignment explanation
Indices: 9137747--9137855 Score: 202
Period size: 39 Copynumber: 2.8 Consensus size: 39
9137737 AAATTATCCA
9137747 ACCCAACCCAATAAAACTAAAACTAAAGTCTACCCAATT
1 ACCCAACCCAATAAAACTAAAACTAAAGTCTACCCAATT
9137786 ACCCAACCCAATAAAACTAAAACTAAAGTCTACCCAATT
1 ACCCAACCCAATAAAACTAAAACTAAAGTCTACCCAATT
*
9137825 A-CCAACCCAATAAAAATAAAACTAAAGTCTA
1 ACCCAACCCAATAAAACTAAAACTAAAGTCTA
9137856 ACTCTTAAGT
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
38 29 0.42
39 40 0.58
ACGTcount: A:0.51, C:0.28, G:0.03, T:0.17
Consensus pattern (39 bp):
ACCCAACCCAATAAAACTAAAACTAAAGTCTACCCAATT
Found at i:9138029 original size:37 final size:37
Alignment explanation
Indices: 9137983--9138057 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
9137973 TGTTAATTTC
*
9137983 AAGAATTATGCAAT-GCTTTTGATTATATAGTGATTCA
1 AAGAATTATGCAATAG-TTTTAATTATATAGTGATTCA
* * *
9138020 AAGACTTATGTAATAGTTTTAATTATGTAGTGATTCA
1 AAGAATTATGCAATAGTTTTAATTATATAGTGATTCA
9138057 A
1 A
9138058 TTCGGGTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 32 0.97
38 1 0.03
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (37 bp):
AAGAATTATGCAATAGTTTTAATTATATAGTGATTCA
Found at i:9138091 original size:9 final size:9
Alignment explanation
Indices: 9138056--9138089 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
9138046 GTAGTGATTC
9138056 AATTCGGGT
1 AATTCGGGT
*
9138065 AATTTGGGT
1 AATTCGGGT
*
9138074 AATTCGGTT
1 AATTCGGGT
9138083 AATTCGG
1 AATTCGG
9138090 TTCATTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.09, G:0.29, T:0.38
Consensus pattern (9 bp):
AATTCGGGT
Found at i:9139316 original size:22 final size:23
Alignment explanation
Indices: 9139260--9139317 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
9139250 CGGCCCGTTT
* * *
9139260 TTAATTAAAATTAAAATTATTTTT
1 TTAA-TAAAATTAAAACTATATTG
9139284 TTAATAAAATTAAAACTA-ATTG
1 TTAATAAAATTAAAACTATATTG
*
9139306 TTAGTAAAATTA
1 TTAATAAAATTA
9139318 TCAAATTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 13 0.43
23 13 0.43
24 4 0.13
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (23 bp):
TTAATAAAATTAAAACTATATTG
Found at i:9139376 original size:66 final size:67
Alignment explanation
Indices: 9139285--9139448 Score: 244
Period size: 68 Copynumber: 2.4 Consensus size: 67
9139275 ATTATTTTTT
9139285 TAATAAAAT-TAAAACTAATTG-TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAAT
1 TAATAAAATCTAAAA-T--TTGATTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAAT
9139347 TGTTG
63 TGTTG
*
9139352 TAATAAAATCTAAAATTTGATTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTG
1 TAATAAAATCTAAAATTTGATTAGTAAAATTATCAAATTATTAATTG-ATTAATTGTATTAATTG
9139417 TTG
65 TTG
* *
9139420 TAACAAAATCTAACATTTGATTAGTAAAA
1 TAATAAAATCTAAAATTTGATTAGTAAAA
9139449 CAAACTTGAT
Statistics
Matches: 89, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
65 3 0.03
66 26 0.29
67 10 0.11
68 50 0.56
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (67 bp):
TAATAAAATCTAAAATTTGATTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGT
TG
Found at i:9139402 original size:9 final size:9
Alignment explanation
Indices: 9139390--9139417 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
9139380 TTTATCAAAT
9139390 TATTAATTG
1 TATTAATTG
9139399 TATTAATTG
1 TATTAATTG
9139408 TATTAATTG
1 TATTAATTG
9139417 T
1 T
9139418 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:9139554 original size:22 final size:24
Alignment explanation
Indices: 9139514--9139557 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
9139504 AAATAAACTT
9139514 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
9139538 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
9139558 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:9141234 original size:83 final size:85
Alignment explanation
Indices: 9141095--9141292 Score: 328
Period size: 83 Copynumber: 2.3 Consensus size: 85
9141085 TTGTGGCTTT
* *
9141095 GAACTTGTAATATTGTGTTTCTCATCCTTCCTTGTTTGGTTGCTCATAAAATTGAGGG-A-AAAT
1 GAACTTGTAACATTGTGTTTCTCATTCTTCCTTGTTTGGTTGCTCATAAAATTGAGGGAATAAAT
*
9141158 GGGTATTTAACTACTTGATA
66 GAGTATTTAACTACTTGATA
9141178 GAACTTGTAACATTGTGTTTCTCATTCTTCCTTGTTTGGTTGCTCATAAAATTGAGGGAAATTAA
1 GAACTTGTAACATTGTGTTTCTCATTCTTCCTTGTTTGGTTGCTCATAAAATTGAGGG-AA-TAA
*
9141243 ATGAGTATTTAACTACTTGATG
64 ATGAGTATTTAACTACTTGATA
9141265 GAACTTGTAACATTGTGTTTCTCATTCT
1 GAACTTGTAACATTGTGTTTCTCATTCT
9141293 AGTCTAGTCA
Statistics
Matches: 107, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
83 56 0.52
85 1 0.01
87 50 0.47
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (85 bp):
GAACTTGTAACATTGTGTTTCTCATTCTTCCTTGTTTGGTTGCTCATAAAATTGAGGGAATAAAT
GAGTATTTAACTACTTGATA
Found at i:9141708 original size:18 final size:17
Alignment explanation
Indices: 9141682--9141717 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
9141672 TTTGGTTATA
9141682 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
9141700 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
9141717 T
1 T
9141718 CATTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Found at i:9142420 original size:14 final size:14
Alignment explanation
Indices: 9142401--9142434 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
9142391 CAAAAACACA
9142401 TTCTTTTCTTTTCT
1 TTCTTTTCTTTTCT
*
9142415 TTCTTTTTTTTTCT
1 TTCTTTTCTTTTCT
9142429 TT-TTTT
1 TTCTTTT
9142435 GGGTGATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTCTTTTCTTTTCT
Found at i:9144927 original size:15 final size:15
Alignment explanation
Indices: 9144907--9144973 Score: 77
Period size: 15 Copynumber: 4.6 Consensus size: 15
9144897 TTATGTTTTA
*
9144907 TATATATTATTTTAT
1 TATATATTATATTAT
*
9144922 TATATAATATATTAT
1 TATATATTATATTAT
*
9144937 AATATATTA-ATTA-
1 TATATATTATATTAT
9144950 TAT-TGATTATATTAT
1 TATAT-ATTATATTAT
9144965 TATATATTA
1 TATATATTA
9144974 AATAAACCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
12 1 0.02
13 6 0.14
14 8 0.19
15 27 0.63
16 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (15 bp):
TATATATTATATTAT
Found at i:9144939 original size:10 final size:10
Alignment explanation
Indices: 9144924--9144977 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
9144914 TATTTTATTA
9144924 TATAATATAT
1 TATAATATAT
9144934 TATAATATAT
1 TATAATATAT
*
9144944 TA-ATTATAT
1 TATAATATAT
9144953 TGAT--TATAT
1 T-ATAATATAT
*
9144962 TATTATATAT
1 TATAATATAT
9144972 TA-AATA
1 TATAATA
9144978 AACCAAATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 2 0.05
9 16 0.42
10 20 0.53
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (10 bp):
TATAATATAT
Found at i:9144968 original size:17 final size:16
Alignment explanation
Indices: 9144904--9144973 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 16
9144894 TTTTTATGTT
*
9144904 TTATATATATTATTTTA
1 TTATAT-TATTATATTA
*
9144921 TTATA-TAATATATTA
1 TTATATTATTATATTA
9144936 TAATATATTAATTATATTGA
1 T--TATATT-ATTATATT-A
9144956 TTATATTATTATA-TA
1 TTATATTATTATATTA
9144971 TTA
1 TTA
9144974 AATAAACCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
15 13 0.29
16 1 0.02
17 15 0.33
18 7 0.16
19 7 0.16
20 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (16 bp):
TTATATTATTATATTA
Found at i:9146399 original size:2 final size:2
Alignment explanation
Indices: 9146394--9146433 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9146384 TAAAAAAAAA
9146394 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9146434 GAATTTAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9148501 original size:16 final size:16
Alignment explanation
Indices: 9148480--9148515 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
9148470 TGAATTACTG
* *
9148480 ATTACAGTTTTATTCC
1 ATTACAGTTCTATTCA
9148496 ATTACAGTTCTATTCA
1 ATTACAGTTCTATTCA
9148512 ATTA
1 ATTA
9148516 TAGTGAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (16 bp):
ATTACAGTTCTATTCA
Found at i:9156713 original size:27 final size:27
Alignment explanation
Indices: 9156675--9156750 Score: 116
Period size: 27 Copynumber: 2.8 Consensus size: 27
9156665 TTTGGTTAAA
*
9156675 AATTAACCGAATTAACCAAATTACCCG
1 AATTACCCGAATTAACCAAATTACCCG
*
9156702 AATTACCCGAATTAACCAAATTATCCG
1 AATTACCCGAATTAACCAAATTACCCG
* *
9156729 AATTACTCGAATTACCCAAATT
1 AATTACCCGAATTAACCAAATT
9156751 GAATCCCTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (27 bp):
AATTACCCGAATTAACCAAATTACCCG
Found at i:9156743 original size:9 final size:9
Alignment explanation
Indices: 9156675--9156750 Score: 80
Period size: 9 Copynumber: 8.4 Consensus size: 9
9156665 TTTGGTTAAA
*
9156675 AATTAACCG
1 AATTACCCG
* *
9156684 AATTAACCA
1 AATTACCCG
9156693 AATTACCCG
1 AATTACCCG
9156702 AATTACCCG
1 AATTACCCG
* *
9156711 AATTAACCA
1 AATTACCCG
*
9156720 AATTATCCG
1 AATTACCCG
*
9156729 AATTACTCG
1 AATTACCCG
*
9156738 AATTACCCA
1 AATTACCCG
9156747 AATT
1 AATT
9156751 GAATCCCTAC
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 56 1.00
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (9 bp):
AATTACCCG
Found at i:9157130 original size:2 final size:2
Alignment explanation
Indices: 9157123--9157148 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9157113 TTGCTTTTTG
9157123 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
9157149 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9157903 original size:29 final size:29
Alignment explanation
Indices: 9157864--9157919 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
9157854 ATTGAATTAA
9157864 TTTTAAATTTTGGGTTTATA-TAATTTTT
1 TTTTAAATTTTGGGTTTATATTAATTTTT
9157892 TTTTAAAGTTTTGGGTTTATATTAATTT
1 TTTTAAA-TTTTGGGTTTATATTAATTT
9157920 GTATTTGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 7 0.27
29 13 0.50
30 6 0.23
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (29 bp):
TTTTAAATTTTGGGTTTATATTAATTTTT
Found at i:9164376 original size:21 final size:20
Alignment explanation
Indices: 9164352--9164398 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
9164342 AAATTAAATT
9164352 TTAAAATTTGAAATATAAAAA
1 TTAAAATTTGAAA-ATAAAAA
*
9164373 TTAAAAATTTTAAAATAAAAA
1 TT-AAAATTTGAAAATAAAAA
9164394 -TAAAA
1 TTAAAA
9164399 AAGAGGGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.17
20 1 0.04
21 9 0.38
22 10 0.42
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
TTAAAATTTGAAAATAAAAA
Found at i:9164399 original size:21 final size:22
Alignment explanation
Indices: 9164354--9164400 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
9164344 ATTAAATTTT
*
9164354 AAAATTTGAAATATAAAAATTA
1 AAAATTTGAAATATAAAAATAA
*
9164376 AAAATTTTAAA-ATAAAAATAA
1 AAAATTTGAAATATAAAAATAA
9164397 AAAA
1 AAAA
9164401 GAGGGAAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAATTTGAAATATAAAAATAA
Found at i:9170830 original size:24 final size:24
Alignment explanation
Indices: 9170792--9170862 Score: 124
Period size: 24 Copynumber: 2.9 Consensus size: 24
9170782 CCGGTGCTCT
9170792 CTGTTAAAGTGCTATTCGGAGCTTC
1 CTGTT-AAGTGCTATTCGGAGCTTC
9170817 CTGTTAAGTGCTATTCGGAGCTTC
1 CTGTTAAGTGCTATTCGGAGCTTC
*
9170841 CTGTTAAGTGCTCTTCGGAGCT
1 CTGTTAAGTGCTATTCGGAGCT
9170863 ACCCAATATA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
24 40 0.89
25 5 0.11
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (24 bp):
CTGTTAAGTGCTATTCGGAGCTTC
Found at i:9179643 original size:25 final size:25
Alignment explanation
Indices: 9179594--9179644 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
9179584 TCTTCCAAGT
* **
9179594 TGAATAATGAGAAGCTCATGCGAGC
1 TGAATAACGAGAAGCTCATAAGAGC
*
9179619 TGAATAACGGGAAGCTCATAAGAGC
1 TGAATAACGAGAAGCTCATAAGAGC
9179644 T
1 T
9179645 ATGGTGTGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (25 bp):
TGAATAACGAGAAGCTCATAAGAGC
Found at i:9192060 original size:10 final size:10
Alignment explanation
Indices: 9192045--9192069 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9192035 AATGTTACAA
9192045 ATATAAATAT
1 ATATAAATAT
9192055 ATATAAATAT
1 ATATAAATAT
9192065 ATATA
1 ATATA
9192070 TTTACCGCTA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATAAATAT
Found at i:9207825 original size:47 final size:47
Alignment explanation
Indices: 9207756--9207849 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
9207746 GCCCTCCTAA
9207756 TTTCTGAGAATACCAAGCTGAAATGTTATCGTATGGCCAGAACATGT
1 TTTCTGAGAATACCAAGCTGAAATGTTATCGTATGGCCAGAACATGT
9207803 TTTCTGAGAATACCAAGCTGAAATGTTATCGTATGGCCAGAACATGT
1 TTTCTGAGAATACCAAGCTGAAATGTTATCGTATGGCCAGAACATGT
9207850 AAAACCGGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (47 bp):
TTTCTGAGAATACCAAGCTGAAATGTTATCGTATGGCCAGAACATGT
Found at i:9239400 original size:3 final size:3
Alignment explanation
Indices: 9239392--9239449 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
9239382 TAGGTTCAAC
9239392 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9239440 ATA ATA ATA A
1 ATA ATA ATA A
9239450 AGAAAAGGGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:9248197 original size:9 final size:9
Alignment explanation
Indices: 9248183--9248208 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
9248173 GCTCAAGCAA
9248183 GCTTAATTG
1 GCTTAATTG
9248192 GCTTAATTG
1 GCTTAATTG
9248201 GCTTAATT
1 GCTTAATT
9248209 AGGTATGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (9 bp):
GCTTAATTG
Found at i:9249053 original size:24 final size:25
Alignment explanation
Indices: 9249002--9249059 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
9248992 TAGACATCTC
* * *
9249002 GAGCTTCCTGTTATATGGTTCTTGT
1 GAGCTTCCCGTTATATGGCTCTTCT
*
9249027 GAGCTTCCCGTTA-ATTGCTCTTCT
1 GAGCTTCCCGTTATATGGCTCTTCT
9249051 GAGCATTCC
1 GAGC-TTCC
9249060 GATTGGTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.41
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCTTCT
Found at i:9249156 original size:26 final size:26
Alignment explanation
Indices: 9249127--9249200 Score: 112
Period size: 26 Copynumber: 2.8 Consensus size: 26
9249117 ATGGCTCTTC
* *
9249127 GTGATCTTCCCGATTAAAGGCTATTT
1 GTGAGCTTCCTGATTAAAGGCTATTT
*
9249153 GTGAGCTTCCTGATTAAAGGCTCTTT
1 GTGAGCTTCCTGATTAAAGGCTATTT
*
9249179 GTGAGCTTCCTGATTAATGGCT
1 GTGAGCTTCCTGATTAAAGGCT
9249201 TTCCGGAGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (26 bp):
GTGAGCTTCCTGATTAAAGGCTATTT
Found at i:9249283 original size:25 final size:25
Alignment explanation
Indices: 9249117--9249283 Score: 80
Period size: 26 Copynumber: 6.6 Consensus size: 25
9249107 GAGCTGTTAT
* * *
9249117 ATGGCTCTTCGTGATCTTCCCGATTA
1 ATGGCTTTTCG-GAGCTTCCTGATTA
*
9249143 AAGGCTATTT-GTGAGCTTCCTGATTA
1 ATGGCT-TTTCG-GAGCTTCCTGATTA
*
9249169 AAGGCTCTTT-GTGAGCTTCCTGATTA
1 ATGGCT-TTTCG-GAGCTTCCTGATTA
*
9249195 ATGGCTTTCCGGAGCTT-CTCGA-T-
1 ATGGCTTTTCGGAGCTTCCT-GATTA
* * *
9249218 ATGGCTCACTT--GAACTTCCCGA-TA
1 ATGGCT--TTTCGGAGCTTCCTGATTA
* * **
9249242 TATGGCTATCCCAAGCTTCCTGATTA
1 -ATGGCTTTTCGGAGCTTCCTGATTA
9249268 ATGGCTTTTCGGAGCT
1 ATGGCTTTTCGGAGCT
9249284 ACCCGTTATT
Statistics
Matches: 110, Mismatches: 20, Indels: 23
0.72 0.13 0.15
Matches are distributed among these distances:
23 15 0.14
24 4 0.04
25 37 0.34
26 52 0.47
27 2 0.02
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (25 bp):
ATGGCTTTTCGGAGCTTCCTGATTA
Found at i:9257020 original size:15 final size:16
Alignment explanation
Indices: 9256987--9257020 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
9256977 TACTATAGGG
*
9256987 TATTAAAATAAATAAA
1 TATTAAAATAAACAAA
9257003 TATTAAAA-AAACAAA
1 TATTAAAATAAACAAA
9257018 TAT
1 TAT
9257021 CAATTTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
TATTAAAATAAACAAA
Found at i:9272199 original size:31 final size:30
Alignment explanation
Indices: 9272148--9272211 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
9272138 ACTGAGTTTA
* * *
9272148 TATTATTTTTGTTTATAAAAATATAGTTAT
1 TATTATTTTTGTATATAAAAATAAAATTAT
*
9272178 TATTTTTTATTGTATATAAAAATAAAATTAT
1 TATTATTT-TTGTATATAAAAATAAAATTAT
9272209 TAT
1 TAT
9272212 AAGCGATAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (30 bp):
TATTATTTTTGTATATAAAAATAAAATTAT
Found at i:9273808 original size:17 final size:17
Alignment explanation
Indices: 9273782--9273820 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
9273772 TGTTTGATTA
* *
9273782 TATTTCTGTTTTTTATT
1 TATTTATGTTTTGTATT
9273799 TATTTATGTTTTGTATT
1 TATTTATGTTTTGTATT
*
9273816 GATTT
1 TATTT
9273821 GATTTTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.03, G:0.10, T:0.72
Consensus pattern (17 bp):
TATTTATGTTTTGTATT
Found at i:9276393 original size:3 final size:3
Alignment explanation
Indices: 9276385--9276412 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
9276375 GACCCTTTCG
9276385 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9276413 TTGATTATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:9277843 original size:15 final size:16
Alignment explanation
Indices: 9277798--9277845 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 16
9277788 ATTTTATCTA
9277798 ATAATAATTAAAATATT
1 ATAATAA-TAAAATATT
9277815 ATAAATAA-ATAAATATT
1 AT-AATAATA-AAATATT
9277832 -TAATAATAAAATAT
1 ATAATAATAAAATAT
9277846 GTGATCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
17 9 0.32
18 5 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAATAATAAAATATT
Found at i:9278621 original size:21 final size:22
Alignment explanation
Indices: 9278597--9278648 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
9278587 TGGCTAGTAC
*
9278597 AAATAACAA-AAACAATAGC-AA
1 AAATAACAACAAA-AACAGCAAA
9278618 AAATAACAACAAAAACAGCAGAA
1 AAATAACAACAAAAACAGCA-AA
9278641 AAATAACA
1 AAATAACA
9278649 GCACCAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 14 0.52
22 3 0.11
23 10 0.37
ACGTcount: A:0.71, C:0.15, G:0.06, T:0.08
Consensus pattern (22 bp):
AAATAACAACAAAAACAGCAAA
Found at i:9278642 original size:23 final size:24
Alignment explanation
Indices: 9278601--9278648 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
9278591 TAGTACAAAT
*
9278601 AACAAAAACAATAGCAAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
*
9278625 AACAAAAACAGCAG-AAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
9278648 A
1 A
9278649 GCACCAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.71, C:0.17, G:0.06, T:0.06
Consensus pattern (24 bp):
AACAAAAACAACAGCAAAAATAAC
Found at i:9280096 original size:13 final size:14
Alignment explanation
Indices: 9280065--9280102 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
9280055 TCATTATATT
*
9280065 TTAACAAAATCAAAG
1 TTAA-AAAATTAAAG
9280080 TTAAAAAATTAAA-
1 TTAAAAAATTAAAG
9280093 TTAAAAAATT
1 TTAAAAAATT
9280103 TATCTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (14 bp):
TTAAAAAATTAAAG
Found at i:9285834 original size:46 final size:46
Alignment explanation
Indices: 9285767--9285905 Score: 224
Period size: 46 Copynumber: 3.0 Consensus size: 46
9285757 CATGGCAAAA
* *
9285767 TGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATATTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
* *
9285813 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAGCCATACTGATT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
* *
9285859 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
9285905 T
1 T
9285906 ATAGCATTGT
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.30
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
Found at i:9286307 original size:33 final size:33
Alignment explanation
Indices: 9286270--9286392 Score: 131
Period size: 33 Copynumber: 3.7 Consensus size: 33
9286260 ACATTTGTAG
** *
9286270 TGCCATAACCCAGTTATGGTCTTATTATCAGAA
1 TGCCATAACCCAACTATGGTCTTATCATCAGAA
* * ** *
9286303 TGCCATAGCCCAGCTATGGTCTTA-CATTTGTAG
1 TGCCATAACCCAACTATGGTCTTATCATCAG-AA
*
9286336 TGCCATAACCCAATTATGGTCTTATCATCAGAA
1 TGCCATAACCCAACTATGGTCTTATCATCAGAA
* *
9286369 TGTCATAGCCCAACTATGGTCTTA
1 TGCCATAACCCAACTATGGTCTTA
9286393 CTAGCCCAAC
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
32 3 0.04
33 66 0.90
34 4 0.05
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Consensus pattern (33 bp):
TGCCATAACCCAACTATGGTCTTATCATCAGAA
Found at i:9286358 original size:66 final size:66
Alignment explanation
Indices: 9286252--9286393 Score: 248
Period size: 66 Copynumber: 2.2 Consensus size: 66
9286242 TGGCCCTGCC
* * *
9286252 ATGGTCTTACATTTGTAGTGCCATAACCCAGTTATGGTCTTATTATCAGAATGCCATAGCCCAGC
1 ATGGTCTTACATTTGTAGTGCCATAACCCAATTATGGTCTTATCATCAGAATGCCATAGCCCAAC
9286317 T
66 T
*
9286318 ATGGTCTTACATTTGTAGTGCCATAACCCAATTATGGTCTTATCATCAGAATGTCATAGCCCAAC
1 ATGGTCTTACATTTGTAGTGCCATAACCCAATTATGGTCTTATCATCAGAATGCCATAGCCCAAC
9286383 T
66 T
9286384 ATGGTCTTAC
1 ATGGTCTTAC
9286394 TAGCCCAACT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 72 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.34
Consensus pattern (66 bp):
ATGGTCTTACATTTGTAGTGCCATAACCCAATTATGGTCTTATCATCAGAATGCCATAGCCCAAC
T
Found at i:9286399 original size:20 final size:20
Alignment explanation
Indices: 9286374--9286413 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
9286364 CAGAATGTCA
9286374 TAGCCCAACTATGGTCTTAC
1 TAGCCCAACTATGGTCTTAC
9286394 TAGCCCAACTATGGTCTTAC
1 TAGCCCAACTATGGTCTTAC
9286414 ATTTAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (20 bp):
TAGCCCAACTATGGTCTTAC
Found at i:9309659 original size:31 final size:31
Alignment explanation
Indices: 9309616--9309675 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
9309606 CGTAATATAA
*
9309616 AATTGCACATAAAACCATAATTCATGTATGC
1 AATTACACATAAAACCATAATTCATGTATGC
*
9309647 AATTACACATAAAATCATAATTCATGTAT
1 AATTACACATAAAACCATAATTCATGTAT
9309676 AGATTTAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.32
Consensus pattern (31 bp):
AATTACACATAAAACCATAATTCATGTATGC
Found at i:9311942 original size:22 final size:22
Alignment explanation
Indices: 9311914--9311982 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
9311904 CACTAATGAA
9311914 CAGAGAGCACAGATGTGCTAAT
1 CAGAGAGCACAGATGTGCTAAT
*
9311936 CGGAGAGCACTA-ATGTGCTAATAAT
1 CAGAGAGCAC-AGATGTGC---TAAT
*
9311961 CAGAGAGCACTGATGTGCTAAT
1 CAGAGAGCACAGATGTGCTAAT
9311983 AATCAGAGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
22 19 0.49
23 1 0.03
25 19 0.49
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (22 bp):
CAGAGAGCACAGATGTGCTAAT
Found at i:9311966 original size:25 final size:25
Alignment explanation
Indices: 9311932--9311993 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
9311922 ACAGATGTGC
*
9311932 TAATCGGAGAGCACTAATGTGCTAA
1 TAATCAGAGAGCACTAATGTGCTAA
*
9311957 TAATCAGAGAGCACTGATGTGCTAA
1 TAATCAGAGAGCACTAATGTGCTAA
9311982 TAATCAGAGAGC
1 TAATCAGAGAGC
9311994 GTGCTAAGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (25 bp):
TAATCAGAGAGCACTAATGTGCTAA
Found at i:9319818 original size:30 final size:30
Alignment explanation
Indices: 9319775--9319834 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
9319765 ATTTAATACA
* *
9319775 TGAACTTTAATTTGGTACAATTATATATAT
1 TGAAATTTAATTTGATACAATTATATATAT
* **
9319805 TGAAATTTGATTTGATGTAATTATATATAT
1 TGAAATTTAATTTGATACAATTATATATAT
9319835 ATATAATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.48
Consensus pattern (30 bp):
TGAAATTTAATTTGATACAATTATATATAT
Found at i:9319940 original size:23 final size:23
Alignment explanation
Indices: 9319895--9319941 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
9319885 TATATACATT
9319895 TTAAAAATATATATCGATTTTTATG
1 TTAAAAATATATA-C-ATTTTTATG
9319920 TTAAAAATATATA-ATTATTTAT
1 TTAAAAATATATACATT-TTTAT
9319942 ATTGTAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 3 0.14
23 5 0.24
25 13 0.62
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
TTAAAAATATATACATTTTTATG
Found at i:9322882 original size:124 final size:124
Alignment explanation
Indices: 9322739--9323018 Score: 339
Period size: 124 Copynumber: 2.3 Consensus size: 124
9322729 TTTTTTCGAG
** ** ** * *
9322739 TTGACGTTTCTGATTAAATAGTGGGAAATCGCTTCTACTAGGATGCTATTTAAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTGTAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTG
*** *
9322804 AAATAGTGGCCTCGTAGACGCGATTTCGCTACAG-TGGTCATGT-GAGAAATAATTTTTT
66 AAATAGCACCCTCGTAGACGCGATTTCACTACAGTTGGTCATGTAG-GAAATAATTTTTT
* * * *
9322862 TTGACGTTTTCTGAGGAAATAGTATAAAATTGCTGATACCAGGATGCTATATGAGAAGAAATTGT
1 TTGACG-TTTCTGAGCAAATAGTGTAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGT
* * * *
9322927 GAAATCGCACCCTCGTGGACGTGATTTCACTACAGTTGGTCATGTAGGAAATATTTTTTT
65 GAAATAGCACCCTCGTAGACGCGATTTCACTACAGTTGGTCATGTAGGAAATAATTTTTT
*
9322987 TTGACGTTTCTGAGCAAATAGTGTCAAATCGC
1 TTGACGTTTCTGAGCAAATAGTGTAAAATCGC
9323019 GCCCTCGTGG
Statistics
Matches: 131, Mismatches: 23, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
123 6 0.05
124 97 0.74
125 27 0.21
126 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTGTAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTG
AAATAGCACCCTCGTAGACGCGATTTCACTACAGTTGGTCATGTAGGAAATAATTTTTT
Found at i:9325011 original size:28 final size:29
Alignment explanation
Indices: 9324979--9325034 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
9324969 TGAAAATATT
9324979 AAAAATTTTAAAATTAT-TTAAAAAAATA
1 AAAAATTTTAAAATTATCTTAAAAAAATA
*
9325007 AAAAATTTTAAAATTTTCTTAAAAAAAT
1 AAAAATTTTAAAATTATCTTAAAAAAAT
9325035 GAAATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAAATTTTAAAATTATCTTAAAAAAATA
Found at i:9325106 original size:22 final size:22
Alignment explanation
Indices: 9325076--9325117 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9325066 ATTTGGAGAT
*
9325076 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
9325098 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
9325118 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:9325138 original size:52 final size:51
Alignment explanation
Indices: 9325067--9325169 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
9325057 TTAATATGGA
* * *
9325067 TTTGGAGATTTTTTGAAGGAAATTGAGAG-GATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTT-GAAGGGAA-TTGAGAG
*
9325118 TTTGAGAGAATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
9325170 AAATTTTGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.33
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
Found at i:9325144 original size:22 final size:23
Alignment explanation
Indices: 9325119--9325210 Score: 111
Period size: 22 Copynumber: 4.2 Consensus size: 23
9325109 ATTTGAGAGT
9325119 TTGAGAG-AATTTTGGAAGGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
9325141 TTGATAGAAATTTT-GAAGGGAA
1 TTGAGAGAAATTTTGGAAGGAAA
*
9325163 TTGAGAGAAATTTTGAAAGG-AA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
9325185 TTGAGAG-AATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
9325207 TTGA
1 TTGA
9325211 TATTGAATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
21 9 0.15
22 41 0.68
23 10 0.17
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (23 bp):
TTGAGAGAAATTTTGGAAGGAAA
Found at i:9325168 original size:44 final size:44
Alignment explanation
Indices: 9325119--9325210 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
9325109 ATTTGAGAGT
* * * *
9325119 TTGAGAG-AATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAA
1 TTGAGAGAAATTTTGAAAGG-AATTGAGAGAAATTTTGAAAGAAA
*
9325163 TTGAGAGAAATTTTGAAAGGAATTGAGAGAATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
9325207 TTGA
1 TTGA
9325211 TATTGAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 31 0.74
45 11 0.26
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (44 bp):
TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
Found at i:9325962 original size:38 final size:39
Alignment explanation
Indices: 9325911--9326023 Score: 169
Period size: 38 Copynumber: 2.9 Consensus size: 39
9325901 TCACTATTTT
*
9325911 GTATGAGTCATAAAAATAAGCTTGTTTGTTATGTAAAA-
1 GTATGAGTCATAAAAATAAGTTTGTTTGTTATGTAAAAG
* *
9325949 GTATGAGTTATAAAAGTAAGTTTGTTTGTTATG-AAAAG
1 GTATGAGTCATAAAAATAAGTTTGTTTGTTATGTAAAAG
9325987 GTATGAGTCA-AAAAAGTAAGTTTGTTTGTTATGTAAA
1 GTATGAGTCATAAAAA-TAAGTTTGTTTGTTATGTAAA
9326024 TGAGATTCTT
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
37 8 0.12
38 56 0.84
39 3 0.04
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (39 bp):
GTATGAGTCATAAAAATAAGTTTGTTTGTTATGTAAAAG
Found at i:9330266 original size:20 final size:20
Alignment explanation
Indices: 9330241--9330280 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9330231 CATTTCATTT
*
9330241 ATGCAATTGCTTTATCCATA
1 ATGCAATTACTTTATCCATA
*
9330261 ATGCAATTACTTTATGCATA
1 ATGCAATTACTTTATCCATA
9330281 CCATATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (20 bp):
ATGCAATTACTTTATCCATA
Found at i:9330505 original size:37 final size:40
Alignment explanation
Indices: 9330448--9330556 Score: 116
Period size: 37 Copynumber: 2.8 Consensus size: 40
9330438 TCGGATAATT
* *
9330448 CGAAGTAATAAATTGACACCCAGTGTCTCATC-AGTTAAAC
1 CGAAG-AATAAATTGGCACCCAGTGTCTCATCTAATTAAAC
* * * * *
9330488 TG-A-AATAAATTGGCACCCAGAGCCTTATCTAATTAATC
1 CGAAGAATAAATTGGCACCCAGTGTCTCATCTAATTAAAC
9330526 CGAAGTAATAAATTGGCACCCAGTGTCTCAT
1 CGAAG-AATAAATTGGCACCCAGTGTCTCAT
9330557 TGACTCGAAG
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
37 22 0.41
38 7 0.13
39 2 0.04
40 1 0.02
41 22 0.41
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (40 bp):
CGAAGAATAAATTGGCACCCAGTGTCTCATCTAATTAAAC
Found at i:9330761 original size:24 final size:24
Alignment explanation
Indices: 9330716--9330762 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
9330706 TATATATACC
9330716 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
9330740 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
9330763 CCATTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:9331442 original size:17 final size:17
Alignment explanation
Indices: 9331422--9331485 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
9331412 AATTTTTCTC
*
9331422 CTTTCTTTCTTTTTTTT
1 CTTTCTTTCTTTTCTTT
* *
9331439 CTTTTATTTC-TTTCCTT
1 C-TTTCTTTCTTTTCTTT
* *
9331456 CTTTGTTTCGTTTCTTT
1 CTTTCTTTCTTTTCTTT
9331473 CTCTTC-TTCTTTT
1 CT-TTCTTTCTTTT
9331486 TCTATTTCCA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
16 7 0.19
17 21 0.57
18 9 0.24
ACGTcount: A:0.02, C:0.22, G:0.03, T:0.73
Consensus pattern (17 bp):
CTTTCTTTCTTTTCTTT
Found at i:9331555 original size:35 final size:36
Alignment explanation
Indices: 9331506--9331606 Score: 109
Period size: 35 Copynumber: 2.8 Consensus size: 36
9331496 TTTCTTTTAC
* *
9331506 TTTATCATTATAATATAATAATATATATACT-TA-ACT
1 TTTAACATT-TAATATTATAATATATATACTATATA-T
* *
9331542 TTTAACTTTTAATATTATAATAT-TATAATATATAT
1 TTTAACATTTAATATTATAATATATATACTATATAT
*
9331577 TTTAACATTAAATATTTATAATATATATAC
1 TTTAACATTTAATA-TTATAATATATATAC
9331607 ACTTATGTCG
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
34 5 0.09
35 28 0.52
36 17 0.31
37 4 0.07
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.50
Consensus pattern (36 bp):
TTTAACATTTAATATTATAATATATATACTATATAT
Found at i:9331579 original size:28 final size:28
Alignment explanation
Indices: 9331548--9331604 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
9331538 AACTTTTAAC
*
9331548 TTTTAATATTATAATA-TTATAATATATA
1 TTTTAACATTA-AATATTTATAATATATA
9331576 TTTTAACATTAAATATTTATAATATATA
1 TTTTAACATTAAATATTTATAATATATA
9331604 T
1 T
9331605 ACACTTATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTTAACATTAAATATTTATAATATATA
Found at i:9331586 original size:20 final size:19
Alignment explanation
Indices: 9331553--9331591 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
9331543 TTAACTTTTA
*
9331553 ATATTATAATATTATAATAT
1 ATATTATAACATTA-AATAT
*
9331573 ATATTTTAACATTAAATAT
1 ATATTATAACATTAAATAT
9331592 TTATAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTATAACATTAAATAT
Found at i:9334404 original size:25 final size:25
Alignment explanation
Indices: 9334334--9334414 Score: 135
Period size: 25 Copynumber: 3.2 Consensus size: 25
9334324 ACTTTAGCGC
***
9334334 GCTCTCTGATTATTAGCACGCCAGT
1 GCTCTCTGATTATTAGCACGTTGGT
9334359 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
9334384 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
9334409 GCTCTC
1 GCTCTC
9334415 CGTTTAGCAC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.37
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTGGT
Found at i:9334424 original size:22 final size:24
Alignment explanation
Indices: 9334334--9334424 Score: 87
Period size: 25 Copynumber: 3.8 Consensus size: 24
9334324 ACTTTAGCGC
* ***
9334334 GCTCTCTGATTATTAGCACGCCAGT
1 GCTCTCCGA-TATTAGCACGTTGGT
*
9334359 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCCGA-TATTAGCACGTTGGT
*
9334384 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCCGA-TATTAGCACGTTGGT
9334409 GCTCTCCG-T-TTAGCAC
1 GCTCTCCGATATTAGCAC
9334425 ATCTGCGCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
22 7 0.11
23 1 0.02
25 54 0.87
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.36
Consensus pattern (24 bp):
GCTCTCCGATATTAGCACGTTGGT
Found at i:9335493 original size:51 final size:51
Alignment explanation
Indices: 9335417--9335517 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
9335407 CGTGTAGCAA
* * *
9335417 CAACATTATTCAGTCCATCTGATGTTGCAAAATCACCAGCATATTCATCAG
1 CAACATTATCCACTCCATCTAATGTTGCAAAATCACCAGCATATTCATCAG
*
9335468 CAACATTATCCACTCTATCTAATGTTGCAAAATCACCAGCATATTCATCA
1 CAACATTATCCACTCCATCTAATGTTGCAAAATCACCAGCATATTCATCA
9335518 ACAATAACTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.35, C:0.27, G:0.09, T:0.30
Consensus pattern (51 bp):
CAACATTATCCACTCCATCTAATGTTGCAAAATCACCAGCATATTCATCAG
Found at i:9335725 original size:33 final size:33
Alignment explanation
Indices: 9335688--9335762 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
9335678 CCTTTTCTAG
* * *
9335688 ATCACCTTCACCATCAGA-TTCTACCCCTTCATC
1 ATCACCCTCACCATCA-ACTTCCACCCCTTCAAC
*
9335721 ATCACCCTCCCCATCAACTTCCACCCCTTCAAC
1 ATCACCCTCACCATCAACTTCCACCCCTTCAAC
*
9335754 ATCGCCCTC
1 ATCACCCTC
9335763 CCTAGTAGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
32 1 0.03
33 35 0.97
ACGTcount: A:0.23, C:0.49, G:0.03, T:0.25
Consensus pattern (33 bp):
ATCACCCTCACCATCAACTTCCACCCCTTCAAC
Found at i:9336560 original size:117 final size:117
Alignment explanation
Indices: 9336351--9336561 Score: 359
Period size: 117 Copynumber: 1.8 Consensus size: 117
9336341 GGTAACAGAA
* * * *
9336351 ATCAACATCATCGGGACCACTGTCGCATCACAAATTGACAAAACAAACCCTACATTGTGGCACTG
1 ATCAACAACATCGGGACCACTATCGCATCAAAAATCGACAAAACAAACCCTACATTGTGGCACTG
*
9336416 AAATTGCAATAATAAATAACAATTAACCATCTACAATTTTTACAACAGTTTT
66 AAATTGCAATAATAAATAACAAATAACCATCTACAATTTTTACAACAGTTTT
9336468 ATCAACAACATCGGGACCACTATCGCATCAAAAATCGACAAAACAAACCCTACATTGTGGCACTG
1 ATCAACAACATCGGGACCACTATCGCATCAAAAATCGACAAAACAAACCCTACATTGTGGCACTG
* *
9336533 AAATTGCAATAATAAATCATAAATAACCA
66 AAATTGCAATAATAAATAACAAATAACCA
9336562 ACAAATCAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 87 1.00
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.23
Consensus pattern (117 bp):
ATCAACAACATCGGGACCACTATCGCATCAAAAATCGACAAAACAAACCCTACATTGTGGCACTG
AAATTGCAATAATAAATAACAAATAACCATCTACAATTTTTACAACAGTTTT
Found at i:9336788 original size:17 final size:16
Alignment explanation
Indices: 9336748--9336792 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
9336738 GAATGCTAAT
9336748 GATTTAGGGATTTAAA
1 GATTTAGGGATTTAAA
*
9336764 GATTTAGGGATTTGAA
1 GATTTAGGGATTTAAA
9336780 GATTTTAGGGATT
1 GA-TTTAGGGATT
9336793 CAATAAAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (16 bp):
GATTTAGGGATTTAAA
Found at i:9337433 original size:18 final size:18
Alignment explanation
Indices: 9337402--9337453 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
9337392 CAAAAATTAT
*
9337402 ATAATTATATATTTTGTA
1 ATAATTTTATATTTTGTA
9337420 AT-ATTTTAATATTTTGTA
1 ATAATTTT-ATATTTTGTA
9337438 ATAAATTTTATATTTT
1 AT-AATTTTATATTTT
9337454 TTGAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.13
18 14 0.47
19 7 0.23
20 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (18 bp):
ATAATTTTATATTTTGTA
Found at i:9343106 original size:50 final size:49
Alignment explanation
Indices: 9343003--9343125 Score: 131
Period size: 50 Copynumber: 2.5 Consensus size: 49
9342993 GAGATCCCAT
* * *
9343003 GTAAGACCATGTCTGGGACAAGGCGTTAGCACCGAGATGAGCGGTCATTC
1 GTAAGACCATGTCTGGGACATGGCATGAGCACCGAGATGAGCGGTCA-TC
* * **
9343053 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTTTCA-C
1 GTAAGACCATGTCTGGGACATGGCATGAGCACCGAGATGAG--CGGTCATC
* *
9343103 GTAAGACCATATCTGGGATATGG
1 GTAAGACCATGTCTGGGACATGG
9343126 TATTGACAGT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
50 58 0.94
52 4 0.06
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGGCATGAGCACCGAGATGAGCGGTCATC
Found at i:9343434 original size:20 final size:20
Alignment explanation
Indices: 9343396--9343434 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9343386 TAAGCAAGCA
*
9343396 AGTAAGTAAACAAGTAAGTG
1 AGTAAGTAAACAAGAAAGTG
*
9343416 AGTAAGTAAAGAAGAAAGT
1 AGTAAGTAAACAAGAAAGT
9343435 AAAGATCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.26, T:0.18
Consensus pattern (20 bp):
AGTAAGTAAACAAGAAAGTG
Found at i:9354892 original size:6 final size:7
Alignment explanation
Indices: 9354877--9354902 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
9354867 TTACTCGGTC
9354877 TTTTCTT
1 TTTTCTT
9354884 TTTTCTT
1 TTTTCTT
9354891 TTTTCTT
1 TTTTCTT
9354898 TTTTC
1 TTTTC
9354903 CAACAATTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTCTT
Found at i:9365835 original size:23 final size:23
Alignment explanation
Indices: 9365809--9365923 Score: 68
Period size: 23 Copynumber: 4.8 Consensus size: 23
9365799 TTTTTAATTA
*
9365809 AATTAGGTTAGCTTAGGGATTTC
1 AATTAAGTTAGCTTAGGGATTTC
* * *
9365832 AATTAAGTTAGGTTAGGGTTTTTAATTA
1 AATTAAGTTAGCTTAGGG-----ATTTC
* * *
9365860 AATTAAGTTAGGTTAGGGTTTTT
1 AATTAAGTTAGCTTAGGGATTTC
* * * *
9365883 AATTAAATTAGGTTAGGGTTTTT
1 AATTAAGTTAGCTTAGGGATTTC
* *
9365906 AATTAAATTAGGTTAGGG
1 AATTAAGTTAGCTTAGGG
9365924 TTAGGGTTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
23 58 0.73
28 21 0.27
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.43
Consensus pattern (23 bp):
AATTAAGTTAGCTTAGGGATTTC
Found at i:9365836 original size:28 final size:28
Alignment explanation
Indices: 9365773--9366196 Score: 582
Period size: 28 Copynumber: 15.4 Consensus size: 28
9365763 AATTATTACA
* *
9365773 TTAATTCAAA-TAGGTTAGGGTTGGGGTTT
1 TTAATT-AAATTAAGTTA-GGTTAGGGTTT
* *
9365802 TTAATTAAATTAGGTTAGCTTAGGG---
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
* *
9365827 --ATTTCAATTAAGTTAGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
9365853 TTAATTAAATTAAGTTAGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
9365881 TTAATT--A--AA-TTAGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
*
9365904 TTAATTAAATTAGGTTAGGGTTAGGGTTT
1 TTAATTAAATTAAGTTA-GGTTAGGGTTT
9365933 TTAATTAAATTAAGTTAGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
9365961 TTAATTAAATTAAGTTAGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
*
9365989 TTAATTAAATTAAGTTAAGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
* *
9366017 TTAATTACATTAAGTTAGGTTATGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
*
9366045 TTAATTAAATTAGGTTAGGGTTAGGGTTT
1 TTAATTAAATTAAGTTA-GGTTAGGGTTT
* *
9366074 TTAATTAAATTAAATTGGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
9366102 TTAATTAAATTAAGTTAGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
9366130 TTAATTAAATTAAGTTAGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
* *
9366158 TTAATTAAATTAGGTTAGGGTTAAGGTTT
1 TTAATTAAATTAAGTTA-GGTTAGGGTTT
*
9366187 TTAATCAAAT
1 TTAATTAAAT
9366197 AATGTCAAAA
Statistics
Matches: 356, Mismatches: 25, Indels: 28
0.87 0.06 0.07
Matches are distributed among these distances:
23 39 0.11
24 2 0.01
25 1 0.00
26 1 0.00
27 1 0.00
28 229 0.64
29 83 0.23
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (28 bp):
TTAATTAAATTAAGTTAGGTTAGGGTTT
Found at i:9365916 original size:18 final size:21
Alignment explanation
Indices: 9365871--9365925 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 21
9365861 ATTAAGTTAG
9365871 GTTAGGGTTTTTAATTAAATTA
1 GTTAGGGTTTTTAATTAAA-TA
9365893 GGTTAGGGTTTTTAATTAAATTA
1 -GTTAGGGTTTTTAATTAAA-TA
9365916 GGTTAGGGTT
1 -GTTAGGGTT
9365926 AGGGTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.47
Consensus pattern (21 bp):
GTTAGGGTTTTTAATTAAATA
Found at i:9366022 original size:113 final size:112
Alignment explanation
Indices: 9365796--9366196 Score: 581
Period size: 113 Copynumber: 3.7 Consensus size: 112
9365786 GTTAGGGTTG
* * * *
9365796 GGGTTTTTAATTAAATTAGGTTAGCTTAGGG-----ATTTCAATTAAGTTA-GGTTAGGGTTTTT
1 GGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTTT
9365855 AATTAAATTAAGTTAGGTTAGGGTTTTTAATTAAATT-AG---GTTA
66 AATTAAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGTTA
*
9365898 GGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTA-GGTTAGGGTTTT
1 GGGTTTTTAATTAAATTAAGTTA-GGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTT
9365962 TAATTAAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAAGTTA
65 TAATTAAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTT-AGTTA
* * *
9366011 GGGTTTTTAATTACATTAAGTTAGGTTATGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTT
1 GGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTTT
* *
9366076 AATTAAATTAAATTGGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTA
66 AATTAAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTA-GTTA
* *
9366124 GGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTTT
1 GGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTTT
*
9366189 AATCAAAT
66 AATTAAAT
9366197 AATGTCAAAA
Statistics
Matches: 273, Mismatches: 13, Indels: 15
0.91 0.04 0.05
Matches are distributed among these distances:
102 23 0.08
103 7 0.03
108 63 0.23
109 2 0.01
112 27 0.10
113 151 0.55
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (112 bp):
GGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTTT
AATTAAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGTTA
Found at i:9366065 original size:141 final size:140
Alignment explanation
Indices: 9365773--9366196 Score: 634
Period size: 141 Copynumber: 3.1 Consensus size: 140
9365763 AATTATTACA
* * * * *
9365773 TTAATTCAAA-TAGGTTAGGGTTGGGGTTTTTAATTAAATTAGGTTAGCTTAGGG-----ATTTC
1 TTAATT-AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTTAATTA
9365832 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTTAATT-A--AA-TTA
65 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTTAATTAATTAAGTTA
*
9365893 GGTTAGGGTTT
130 GGTTAAGGTTT
9365904 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTTAATTAA
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTTAATTAA
*
9365969 ATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAAGTTAGGGTTTTTAATTACATTAAGTTA
66 ATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTTAATTA-ATTAAGTTA
*
9366034 GGTTATGGTTT
130 GGTTAAGGTTT
* *
9366045 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTGGGTTAGGGTTTTTAATTAA
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTTAATTAA
*
9366110 ATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTA
66 ATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTTAATT-AATTAAGTTA
9366175 GGGTTAAGGTTT
130 -GGTTAAGGTTT
*
9366187 TTAATCAAAT
1 TTAATTAAAT
9366197 AATGTCAAAA
Statistics
Matches: 267, Mismatches: 13, Indels: 15
0.91 0.04 0.05
Matches are distributed among these distances:
130 3 0.01
131 47 0.18
136 57 0.21
138 1 0.00
140 2 0.01
141 137 0.51
142 20 0.07
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (140 bp):
TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTTAATTAA
ATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTTAATTAATTAAGTTAG
GTTAAGGTTT
Found at i:9377009 original size:8 final size:8
Alignment explanation
Indices: 9376996--9377020 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9376986 ATATATACTA
9376996 AATAAAAT
1 AATAAAAT
9377004 AATAAAAT
1 AATAAAAT
9377012 AATAAAAT
1 AATAAAAT
9377020 A
1 A
9377021 TCATTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:9395101 original size:3 final size:3
Alignment explanation
Indices: 9395095--9395121 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9395085 AAAATGTATG
9395095 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
9395122 CCACCTCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:9416878 original size:46 final size:46
Alignment explanation
Indices: 9416825--9416914 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
9416815 ATAAGAAATA
9416825 GCAAAACCACGTCGTTTTGATAAATATTTACCCATTAAGTTAAAAG
1 GCAAAACCACGTCGTTTTGATAAATATTTACCCATTAAGTTAAAAG
*
9416871 GCAAAACCACGTCGTTTTGATAAATGTTTACCCATTAAGTTAAA
1 GCAAAACCACGTCGTTTTGATAAATATTTACCCATTAAGTTAAA
9416915 TTATCTTCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (46 bp):
GCAAAACCACGTCGTTTTGATAAATATTTACCCATTAAGTTAAAAG
Found at i:9417250 original size:30 final size:31
Alignment explanation
Indices: 9417209--9417273 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
9417199 TTAAATAAAT
*
9417209 AAATGATAAAATTATAG-TTTGTT-CTTTCAA
1 AAATAATAAAATT-TAGATTTGTTCCTTTCAA
* *
9417239 AAATAATAAAATTTTGATTTGTTCCTTTTAA
1 AAATAATAAAATTTAGATTTGTTCCTTTCAA
9417270 AAAT
1 AAAT
9417274 TTAAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 2 0.07
30 18 0.60
31 10 0.33
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.45
Consensus pattern (31 bp):
AAATAATAAAATTTAGATTTGTTCCTTTCAA
Found at i:9417479 original size:10 final size:10
Alignment explanation
Indices: 9417466--9417499 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
9417456 ATTATTAATT
9417466 TTTTCTATTA
1 TTTTCTATTA
9417476 TTTTCTATTA
1 TTTTCTATTA
* *
9417486 TTTTATGTTA
1 TTTTCTATTA
9417496 TTTT
1 TTTT
9417500 TTAAATGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (10 bp):
TTTTCTATTA
Found at i:9425169 original size:2 final size:2
Alignment explanation
Indices: 9425164--9425189 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9425154 AAACAAATTG
9425164 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
9425190 TTTATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9425302 original size:20 final size:22
Alignment explanation
Indices: 9425255--9425303 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
9425245 CTCAAAATTC
*
9425255 AATAATATTCTAGAAAAAAATT
1 AATAATATTCTAGAAAAAAAGT
9425277 CAATAATATTCTAG-AAAAAAGT
1 -AATAATATTCTAGAAAAAAAGT
9425299 -ATAAT
1 AATAAT
9425304 TTATATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 5 0.20
22 7 0.28
23 13 0.52
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (22 bp):
AATAATATTCTAGAAAAAAAGT
Found at i:9425309 original size:24 final size:23
Alignment explanation
Indices: 9425248--9425296 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
9425238 CAAGTTCCTC
9425248 AAAATTCAATAATATTCTAGAAA
1 AAAATTCAATAATATTCTAGAAA
9425271 AAAATTCAATAATATTCTAGAAA
1 AAAATTCAATAATATTCTAGAAA
9425294 AAA
1 AAA
9425297 GTATAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.59, C:0.08, G:0.04, T:0.29
Consensus pattern (23 bp):
AAAATTCAATAATATTCTAGAAA
Found at i:9433517 original size:23 final size:24
Alignment explanation
Indices: 9433481--9433525 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
9433471 CAAAAGAAAA
9433481 ACAAAACTGTTTTAAAAAAAATTG
1 ACAAAACTGTTTTAAAAAAAATTG
*
9433505 ACAAAATTG-TTTAAAAAAAAT
1 ACAAAACTGTTTTAAAAAAAAT
9433526 AACTGACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.29
Consensus pattern (24 bp):
ACAAAACTGTTTTAAAAAAAATTG
Found at i:9434250 original size:27 final size:27
Alignment explanation
Indices: 9434153--9434247 Score: 120
Period size: 27 Copynumber: 3.5 Consensus size: 27
9434143 CCTATGGGGA
** * *
9434153 AGGCGTGATTGGTGCTGCCTCTTTCCT
1 AGGCGTGACCGGTGCAGCCTCTTCCCT
*
9434180 AGGCGTGACCGGTGCAGCCCCTTCCCT
1 AGGCGTGACCGGTGCAGCCTCTTCCCT
9434207 AGGCGTGACCGGTGTC-GCCTCTTCCCT
1 AGGCGTGACCGGTG-CAGCCTCTTCCCT
*
9434234 AGGCGTGACTGGTG
1 AGGCGTGACCGGTG
9434248 TCGTGCTATC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 59 0.98
28 1 0.02
ACGTcount: A:0.09, C:0.32, G:0.33, T:0.26
Consensus pattern (27 bp):
AGGCGTGACCGGTGCAGCCTCTTCCCT
Found at i:9434308 original size:21 final size:20
Alignment explanation
Indices: 9434268--9434313 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
9434258 CCATCACCTG
*
9434268 TTTTTCATTAGTTTTATTTT
1 TTTTTCATCAGTTTTATTTT
* *
9434288 TTTTTCATCAGCTTTGTTTT
1 TTTTTCATCAGTTTTATTTT
9434308 TGTTTT
1 T-TTTT
9434314 AGTGTCAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.11, C:0.09, G:0.09, T:0.72
Consensus pattern (20 bp):
TTTTTCATCAGTTTTATTTT
Found at i:9439650 original size:38 final size:39
Alignment explanation
Indices: 9439598--9439814 Score: 125
Period size: 45 Copynumber: 5.2 Consensus size: 39
9439588 ATTTGTCGGC
*
9439598 TTACTGATTAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATTAGGCACTTTATGTGCCGAATACTGTTACTG
* * *
9439636 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATTAGGCACTTTATGTGCCGAATACTGTTACTG
* **
9439675 TTACTG-TTACCGACTCGGCACTTTGTGTGTTGAATACTGTTACTG
1 TTACTGATT----A---GGCACTTTATGTGCCGAATACTGTTACTG
* *
9439720 TTACTG-TTACCGACTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATT----A---GGCACTTTATGTGCCGAATACTGTTACTG
* * * *
9439765 TTACTGTATCGATTCGGCACTTTGTGTGTCGAATACTGTTACCG
1 TTAC----T-GATTAGGCACTTTATGTGCCGAATACTGTTACTG
9439809 TTACTG
1 TTACTG
9439815 TTACAGATTC
Statistics
Matches: 156, Mismatches: 9, Indels: 27
0.81 0.05 0.14
Matches are distributed among these distances:
38 16 0.10
39 27 0.17
40 1 0.01
44 32 0.21
45 76 0.49
49 1 0.01
50 1 0.01
51 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.39
Consensus pattern (39 bp):
TTACTGATTAGGCACTTTATGTGCCGAATACTGTTACTG
Found at i:9439693 original size:45 final size:45
Alignment explanation
Indices: 9439625--9439863 Score: 372
Period size: 45 Copynumber: 5.3 Consensus size: 45
9439615 ATGTGCCGAC
*
9439625 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* *
9439670 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
*
9439715 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
*
9439760 TACTGTTACTG-TATCGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* * * *
9439804 TACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* *
9439849 TACTGCTACCGTTAC
1 TACTGTTACTGTTAC
9439864 TAATTACTGT
Statistics
Matches: 179, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
44 41 0.23
45 138 0.77
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (45 bp):
TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:9439830 original size:89 final size:90
Alignment explanation
Indices: 9439629--9439863 Score: 364
Period size: 89 Copynumber: 2.6 Consensus size: 90
9439619 GCCGACTACT
*
9439629 GTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGACTCGGC
1 GTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGACTCGGC
* *
9439694 ACTTTGTGTGTTGAATACTGTTACT
66 ACTTTGTGTGTCGAATACTGTTACC
* * * *
9439719 GTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTG-TATCGATTCGGC
1 GTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGACTCGGC
9439783 ACTTTGTGTGTCGAATACTGTTACC
66 ACTTTGTGTGTCGAATACTGTTACC
* * * *
9439808 GTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATACTGTTACTGCTACCGTTAC
1 GTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTAC
9439864 TAATTACTGT
Statistics
Matches: 131, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
89 79 0.60
90 52 0.40
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.40
Consensus pattern (90 bp):
GTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGACTCGGC
ACTTTGTGTGTCGAATACTGTTACC
Found at i:9445616 original size:45 final size:45
Alignment explanation
Indices: 9445552--9445694 Score: 189
Period size: 45 Copynumber: 3.2 Consensus size: 45
9445542 AGTATACAGT
* * *
9445552 AATCAGTAACGGTAGCAGTAACAGTATTCGACACACAAAGTGCCG
1 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
*
9445597 AGTCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
* * * * *
9445642 AATCGATAACAGTAACAGTAACAGTAGTCGGCACA-TAAGTGCCT
1 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
*
9445686 AATCAGTAA
1 AATCGGTAA
9445695 GCCGGCAAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
44 14 0.16
45 72 0.84
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (45 bp):
AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
Found at i:9448168 original size:18 final size:18
Alignment explanation
Indices: 9448145--9448182 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
9448135 CATTAGTTTA
9448145 TTTT-AATAGTTTTATTTT
1 TTTTAAATAGTTTT-TTTT
9448163 TTTTAAATAGTTTTTTTT
1 TTTTAAATAGTTTTTTTT
9448181 TT
1 TT
9448183 GTCAGAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (18 bp):
TTTTAAATAGTTTTTTTT
Found at i:9453483 original size:24 final size:24
Alignment explanation
Indices: 9453428--9453484 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
9453418 TCAATCCCCA
* * * *
9453428 CCACCACCACCTCCACCATTAGTG
1 CCACCACCACCACCACCATCAATC
**
9453452 CCTTCACCACCACCACCATCAATC
1 CCACCACCACCACCACCATCAATC
9453476 CCACCACCA
1 CCACCACCA
9453485 TCGCTAATCC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.54, G:0.04, T:0.14
Consensus pattern (24 bp):
CCACCACCACCACCACCATCAATC
Found at i:9453507 original size:18 final size:18
Alignment explanation
Indices: 9453458--9453508 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
9453448 AGTGCCTTCA
*
9453458 CCACCACCACC-ATCAATC
1 CCACCACCACCGCT-AATC
*
9453476 CCACCACCATCGCTAATC
1 CCACCACCACCGCTAATC
9453494 CCACCACCACCGCTA
1 CCACCACCACCGCTA
9453509 GTTTTTTCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 28 0.97
19 1 0.03
ACGTcount: A:0.29, C:0.55, G:0.04, T:0.12
Consensus pattern (18 bp):
CCACCACCACCGCTAATC
Found at i:9465157 original size:12 final size:11
Alignment explanation
Indices: 9465140--9465169 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
9465130 ATGTTAAAAT
9465140 TTTAATTTTATA
1 TTTAATTTTA-A
9465152 TTTAATTTTAA
1 TTTAATTTTAA
9465163 TTTAATT
1 TTTAATT
9465170 ATATTCATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTAATTTTAA
Found at i:9469771 original size:2 final size:2
Alignment explanation
Indices: 9469764--9469790 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9469754 AAATAAATAA
9469764 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9469791 ATCCAACCTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9472750 original size:51 final size:52
Alignment explanation
Indices: 9472679--9472781 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 52
9472669 AAAAGCAAGA
9472679 TAATTTTTATATATAGATTTTATCGTTAAAGCC-TTTTTTTTCATTTATAAT
1 TAATTTTTATATATAGATTTTATCGTTAAAGCCTTTTTTTTTCATTTATAAT
9472730 TAATTTTTATATATAGATTTTATCGTTAAAGCCTTTTTTTTTCATTTATAAT
1 TAATTTTTATATATAGATTTTATCGTTAAAGCCTTTTTTTTTCATTTATAAT
9472782 ATCGTAAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 33 0.65
52 18 0.35
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (52 bp):
TAATTTTTATATATAGATTTTATCGTTAAAGCCTTTTTTTTTCATTTATAAT
Found at i:9472793 original size:51 final size:51
Alignment explanation
Indices: 9472687--9472793 Score: 155
Period size: 51 Copynumber: 2.1 Consensus size: 51
9472677 GATAATTTTT
* **
9472687 ATATATAGATTTTATCGTTAAAGCCTTTTTTTTCATTTATAATTAATTTTT
1 ATATATAGATTTTATCGTTAAAGCCTTTTTTTTCATTTATAATTAATGTAA
9472738 ATATATAGATTTTATCGTTAAAGCCTTTTTTTTTCATTTATAA-T-ATCGTAA
1 ATATATAGATTTTATCGTTAAAGCC-TTTTTTTTCATTTATAATTAAT-GTAA
9472789 ATATA
1 ATATA
9472794 ACCTATCAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
50 2 0.04
51 32 0.63
52 17 0.33
ACGTcount: A:0.32, C:0.08, G:0.07, T:0.53
Consensus pattern (51 bp):
ATATATAGATTTTATCGTTAAAGCCTTTTTTTTCATTTATAATTAATGTAA
Found at i:9476642 original size:127 final size:127
Alignment explanation
Indices: 9476411--9476670 Score: 511
Period size: 127 Copynumber: 2.0 Consensus size: 127
9476401 AGCAGCAGAC
9476411 AATACTTACCTTTCAATTTTCACATACGTTTACACGCACCAAAGACCAAACCCATCGTTACTCGT
1 AATA-TTACCTTTCAATTTTCACATACGTTTACACGCACCAAAGACCAAACCCATCGTTACTCGT
9476476 TTTCCCTCCAATCTTCTTGGACTTCATTTACTTTCATTGAAAAATTAAGAGCAACATAACTCT
65 TTTCCCTCCAATCTTCTTGGACTTCATTTACTTTCATTGAAAAATTAAGAGCAACATAACTCT
9476539 AATATTACCTTTCAATTTTCACATACGTTTACACGCACCAAAGACCAAACCCATCGTTACTCGTT
1 AATATTACCTTTCAATTTTCACATACGTTTACACGCACCAAAGACCAAACCCATCGTTACTCGTT
9476604 TTCCCTCCAATCTTCTTGGACTTCATTTACTTTCATTGAAAAATTAAGAGCAACATAACTCT
66 TTCCCTCCAATCTTCTTGGACTTCATTTACTTTCATTGAAAAATTAAGAGCAACATAACTCT
9476666 AATAT
1 AATAT
9476671 AAGATTATAT
Statistics
Matches: 132, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
127 128 0.97
128 4 0.03
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.34
Consensus pattern (127 bp):
AATATTACCTTTCAATTTTCACATACGTTTACACGCACCAAAGACCAAACCCATCGTTACTCGTT
TTCCCTCCAATCTTCTTGGACTTCATTTACTTTCATTGAAAAATTAAGAGCAACATAACTCT
Found at i:9482703 original size:31 final size:32
Alignment explanation
Indices: 9482668--9482743 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
9482658 AGATAGACGT
* *
9482668 AAAAA-AAATTTACATTAATAAGTGATATGTG
1 AAAAATAAATTTACATTAATAAGTGAAAAGTG
*
9482699 AAAAATAAA-TTAAATTAATAAGTGAAAAGTG
1 AAAAATAAATTTACATTAATAAGTGAAAAGTG
*
9482730 AAAAATATATTTAC
1 AAAAATAAATTTAC
9482744 TTTTTTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
31 32 0.84
32 6 0.16
ACGTcount: A:0.57, C:0.03, G:0.11, T:0.30
Consensus pattern (32 bp):
AAAAATAAATTTACATTAATAAGTGAAAAGTG
Found at i:9482971 original size:5 final size:5
Alignment explanation
Indices: 9482961--9482985 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9482951 TTAGTAATTT
9482961 ACTAC ACTAC ACTAC ACTAC ACTAC
1 ACTAC ACTAC ACTAC ACTAC ACTAC
9482986 TCCGCACTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
ACTAC
Found at i:9483937 original size:21 final size:21
Alignment explanation
Indices: 9483902--9483941 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9483892 AATGTAGTAT
9483902 ACAAATTAAACATGAATCTGAA
1 ACAAATTAAACATG-ATCTGAA
*
9483924 ACAAA-TAAATATGATCTG
1 ACAAATTAAACATGATCTG
9483942 TTTATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.25
Consensus pattern (21 bp):
ACAAATTAAACATGATCTGAA
Found at i:9485113 original size:19 final size:19
Alignment explanation
Indices: 9485089--9485128 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
9485079 TTAAAAACAT
*
9485089 ATAATTTTTAT-AGTTTTTA
1 ATAATTTTAATGA-TTTTTA
9485108 ATAATTTTAATGATTTTTA
1 ATAATTTTAATGATTTTTA
9485127 AT
1 AT
9485129 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
ATAATTTTAATGATTTTTA
Found at i:9492769 original size:3 final size:3
Alignment explanation
Indices: 9492761--9492790 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
9492751 TTCTCTCTTT
9492761 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9492791 GCCAGGGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:9507770 original size:24 final size:24
Alignment explanation
Indices: 9507743--9507794 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
9507733 TCAGATTATG
* *
9507743 CAGCAGAAGCATCAA-CTAATGCAA
1 CAGCAGAAGCAGCAAGC-AAAGCAA
*
9507767 CAGCAGCAGCAGCAAGCAAAGCAA
1 CAGCAGAAGCAGCAAGCAAAGCAA
9507791 CAGC
1 CAGC
9507795 TGCCCACTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.44, C:0.29, G:0.21, T:0.06
Consensus pattern (24 bp):
CAGCAGAAGCAGCAAGCAAAGCAA
Found at i:9511948 original size:20 final size:20
Alignment explanation
Indices: 9511909--9511947 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
9511899 ATGTGCTATA
* *
9511909 AAAATATTTTTTATTATTTT
1 AAAATATTTATAATTATTTT
9511929 AAAATATTTATAATT-TTTT
1 AAAATATTTATAATTATTTT
9511948 TTTGAAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AAAATATTTATAATTATTTT
Found at i:9513975 original size:3 final size:3
Alignment explanation
Indices: 9513967--9513995 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
9513957 TATATAAATA
9513967 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
9513996 TAGGCCTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:9516538 original size:31 final size:31
Alignment explanation
Indices: 9516481--9516539 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
9516471 CAAAAAAATA
* **
9516481 AAATATAAAGATTAAATTTTAAATTTAATCG
1 AAATATAAAAATTAAATGCTAAATTTAATCG
9516512 AAATATAAAAATTAAA-GCTAATATTTAA
1 AAATATAAAAATTAAATGCTAA-ATTTAA
9516540 CCTTTCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 21 0.88
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (31 bp):
AAATATAAAAATTAAATGCTAAATTTAATCG
Found at i:9516699 original size:17 final size:18
Alignment explanation
Indices: 9516674--9516708 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
9516664 TTCGTAGTAG
9516674 TATAATTTAT-TTTTATT
1 TATAATTTATATTTTATT
*
9516691 TATATTTTATATTTTATT
1 TATAATTTATATTTTATT
9516709 GAAATGATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TATAATTTATATTTTATT
Found at i:9526902 original size:2 final size:2
Alignment explanation
Indices: 9526895--9526922 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9526885 GAATTGGTAG
9526895 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9526923 TATTGAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9527155 original size:41 final size:37
Alignment explanation
Indices: 9527108--9527213 Score: 122
Period size: 37 Copynumber: 2.8 Consensus size: 37
9527098 TTCGACTTCG
*
9527108 AGTCGATGAGACACTGGGTGTTAATTCACTACTTCGGATTA
1 AGTCGATGAGACACTGGGTGTCAATT---TACTTCGG-TTA
* * * *
9527149 ATTCGATGAGGCACTGGGTGCCAATTTACTTCGGTTT
1 AGTCGATGAGACACTGGGTGTCAATTTACTTCGGTTA
*
9527186 AGCCGATGAGACACTGGGTGTCAATTTA
1 AGTCGATGAGACACTGGGTGTCAATTTA
9527214 TTTCTTCAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 26 0.46
38 8 0.14
41 22 0.39
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (37 bp):
AGTCGATGAGACACTGGGTGTCAATTTACTTCGGTTA
Found at i:9532446 original size:21 final size:19
Alignment explanation
Indices: 9532404--9532446 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
9532394 AACTTAATAA
*
9532404 TAATTAAAAAGATATGAGT
1 TAATTAAAAAGATATGAAT
*
9532423 TAATGTAAAAAGATTTAGAAT
1 TAAT-TAAAAAGATAT-GAAT
9532444 TAA
1 TAA
9532447 GAATTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 10 0.50
21 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (19 bp):
TAATTAAAAAGATATGAAT
Found at i:9534395 original size:21 final size:21
Alignment explanation
Indices: 9534369--9534413 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
9534359 GGTCGATGAT
* * *
9534369 AAAAAGTAAATATAAATTGTA
1 AAAAAGAAAAAATAAATTATA
*
9534390 AAAAAGAAAAAATATATTATA
1 AAAAAGAAAAAATAAATTATA
9534411 AAA
1 AAA
9534414 CTTTAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (21 bp):
AAAAAGAAAAAATAAATTATA
Done.