Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 265 of 344
Found at i:88414047 original size:30 final size:32
Alignment explanation
Indices: 88413991--88414054 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 32
88413981 TAGTAATTAT
88413991 AAAATTGTACTTTAATTCTCTTAAAAATAATA
1 AAAATTGTACTTTAATTCTCTTAAAAATAATA
* * *
88414023 AAAATTTTA-TTTAA-TCTTTTAAAAATTATA
1 AAAATTGTACTTTAATTCTCTTAAAAATAATA
88414053 AA
1 AA
88414055 GATATAGTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 16 0.55
31 5 0.17
32 8 0.28
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (32 bp):
AAAATTGTACTTTAATTCTCTTAAAAATAATA
Found at i:88415630 original size:5 final size:5
Alignment explanation
Indices: 88415615--88415671 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
88415605 TGACAATAGA
88415615 AAAAT -AAAT AAAAT AAAAT AAAAT AAAATTT AAAGATT AAAA- AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA--T AAA-A-T AAAAT AAAAT
*
88415662 AAAAA AAAAT
1 AAAAT AAAAT
88415672 GCTTCTAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 8 0.18
5 26 0.58
6 1 0.02
7 9 0.20
8 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:88420182 original size:24 final size:22
Alignment explanation
Indices: 88420155--88420207 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 22
88420145 AAAATTTAAA
88420155 AATTAAATAAAATATTAAAACCCT
1 AATTAAATAAAAT-TT-AAACCCT
*
88420179 AATTTAATAAAATTTAAACCCT
1 AATTAAATAAAATTTAAACCCT
88420201 AATTAAA
1 AATTAAA
88420208 CAATTAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 13 0.48
23 2 0.07
24 12 0.44
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTAAATAAAATTTAAACCCT
Found at i:88420214 original size:42 final size:42
Alignment explanation
Indices: 88420127--88420222 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
88420117 TCCTAAAACC
* *
88420127 TTAAAACACTAATTAATAAAAATTTAAAAATTAAATAAAATA
1 TTAAAACCCTAATTAATAAAAATTTAAAAACTAAATAAAATA
** *
88420169 TTAAAACCCTAATTTAAT-AAAATTTAAACCCTAATTAAACA-A
1 TTAAAACCCTAA-TTAATAAAAATTTAAAAACTAAATAAA-ATA
88420211 TTAAAACCCTAA
1 TTAAAACCCTAA
88420223 AAAAATACAG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 41 0.87
43 6 0.13
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (42 bp):
TTAAAACCCTAATTAATAAAAATTTAAAAACTAAATAAAATA
Found at i:88423368 original size:15 final size:17
Alignment explanation
Indices: 88423330--88423369 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
88423320 CCATTATATG
88423330 TGATTAAATGATAAGTTA
1 TGATT-AATGATAAGTTA
88423348 TG-TTAATGA-AAG-TA
1 TGATTAATGATAAGTTA
88423362 TGATTAAT
1 TGATTAAT
88423370 TTAATTAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.19
15 8 0.38
16 5 0.24
17 2 0.10
18 2 0.10
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.40
Consensus pattern (17 bp):
TGATTAATGATAAGTTA
Found at i:88424541 original size:30 final size:30
Alignment explanation
Indices: 88424488--88424559 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
88424478 AGATGGGTAA
*
88424488 CCTAATATAA-GTAAGCTTCTGTGAGCAAC
1 CCTAATATAATGTAAGCTTCTGTGAGAAAC
* * * *
88424517 CTTGATATAATGTTAGCTTGTGTGAGAAAC
1 CCTAATATAATGTAAGCTTCTGTGAGAAAC
88424547 CCTAATATAATGT
1 CCTAATATAATGT
88424560 CAGCCTGCAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 8 0.23
30 27 0.77
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (30 bp):
CCTAATATAATGTAAGCTTCTGTGAGAAAC
Found at i:88431427 original size:15 final size:16
Alignment explanation
Indices: 88431403--88431432 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
88431393 AAACTTCATA
88431403 AAAAGAAAAAAGAAGC
1 AAAAGAAAAAAGAAGC
88431419 AAAAG-AAAAAGAAG
1 AAAAGAAAAAAGAAG
88431433 AACGTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAGAAGC
Found at i:88432662 original size:20 final size:21
Alignment explanation
Indices: 88432623--88432662 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
88432613 ATAACACAGC
88432623 TCTGAAGCATATCTTCCAAAA
1 TCTGAAGCATATCTTCCAAAA
* *
88432644 TCTGAATCAT-TCTTTCAAA
1 TCTGAAGCATATCTTCCAAA
88432663 CTGACCATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (21 bp):
TCTGAAGCATATCTTCCAAAA
Found at i:88434072 original size:735 final size:733
Alignment explanation
Indices: 88432615--88434078 Score: 1891
Period size: 735 Copynumber: 2.0 Consensus size: 733
88432605 AAAAGACAAT
* * *
88432615 AACACAGCTCTGAAGCATATCTTCCAAAATCTGAATCATTCTTTCAAACTGACCATTAGTCTATA
1 AACACAGCTCTGAAGCATATCTTCCAAAATCTGAATCACTCTTTCAAACTGACCATCAGTCTACA
* * * *
88432680 GATGAAATACCGTATTGAAATCAAATCAAGTATCTAGAGCCTCATGTAATTTCTTCCAGAAGTGA
66 GATGAAATACCGTACTGAAATCAAATCAAGTACCCAGAGCCTCATGTAATTTCTTCCAAAAGTGA
* *
88432745 GAAGTAAACCAAGGATCTCAATATGAGATAATCGATACCAAAACTCCATGGACCCTAACTACCTT
131 GAAGTAAACCAAGGATCTCAATATGAGATAATCAATACCAAAACTCCATAGACCCTAACTACCTT
* *
88432810 GGAAACATAAACTTTCGCCAATTTTTGTAAAGAGTAATCAATTCTGATCAGAATGAAGTGAGCAG
196 GGAAACATAAACTTTCACCAATTTTTGTAAAGAGTAATCAATTCTGATCAGAATGAAGTGAGCAA
*
88432875 ACTTAGTCAACTGATCCACAATAACCAAATAAAGTCCTTCTTAGTAGGTGTCAAGGGCAACTCAC
261 ACTTAGTCAACTGATCCACAATAACCAAATAAAGTCCTTCTTAGTAGGTGTCAAGGGAAACTCAC
* * * *
88432940 TAACGAAGTCCATAGTTACTCATTCCCATTTCCACAATTAAATCTTAACGGGTTGGAGAAAACCA
326 TAACAAAGTCCATAGTTACCCATTCCCATTTCCACAATGAAATCTTAACAGGTTGGAGAAAACCA
* * *
88433005 GAAGGAAGTTGATGCTTAGCCTTAACCTTCTGGCACATCAAACAATGGGACACAAAATTGGTTAC
391 GAAGGAAGTTGATGCTTAGCCTTAACCTTCTAGCACATCAAACAATGGGACACAAAATCGATTAC
* * * ** * * *
88433070 CTCACGTTTCAACCTATGCCACCAATACAACTTTTGAAGCTTATAGAACATCTTAATATCACCGA
456 CTCACGTTTCAACCTAGGCCACCAATAAAACTCTCAAAGCTGACAGAACATCTTAATACCACCGA
* * *
88433135 TATGCATAGCATAAGGGCTACTATGCACTTCCCACAGAATAGATTGCGTAAAATCCACATCACTA
521 GATGCATAGCATAAGGGCTACTATGCACTTCCCACAGAATAGATTACCTAAAATCCACATCACTA
* * * * * * *
88433200 GGCACAAAAATCTGACCTCAAAAACACAATATACCATTACGATTAAACCTAAAATCTGAAGTCTT
586 GGCACAAAAATCTAACCTCAAAAACACAAAATAACATCACGAGTAAACCAAAAATCTAAAGTCTT
* * * * *
88433265 ACCCTCATTAATTTGATGAATCCTATTAATCAAAGACTCATCTAAATGCTACTTATTTTTAATCT
651 ACCCTCATCAATCTGATGAATCCTACTAATCAAAGACTCATCCAAATGCTACTTATTCTTAATCT
88433330 CAGTTAACCAAGTTGAAG
716 CAGTTAACCAAGTTGAAG
* * * *
88433348 AACACAGCT-TCGAAGCATATCTTCTAAAATCTGAATCACTCTCTT-ATACTGACCATCAGTTTG
1 AACACAGCTCT-GAAGCATATCTTCCAAAATCTGAATCACTCT-TTCAAACTGACCATCAGTCTA
* * *
88433411 CGGATGAAATACCGTACTGAAATCCAATCGAGTACCCAGAGCCTCATGTAATTTCTTCCAAAAGT
64 CAGATGAAATACCGTACTGAAATCAAATCAAGTACCCAGAGCCTCATGTAATTTCTTCCAAAAGT
* * **** * * **
88433476 GAGAAGTAAACCAAGGATCTTAATCTGAGATAATCAATATTGGAACTCTATAGAGCCTAACT-GT
129 GAGAAGTAAACCAAGGATCTCAATATGAGATAATCAATACCAAAACTCCATAGACCCTAACTACC
* ** *
88433540 TTCGGAAACATAAAGTTTCACCAATTTTTGTAAAGAGTAATC-GGTCTTGA-CTGGAATGAAGTG
194 TT-GGAAACATAAACTTTCACCAATTTTTGTAAAGAGTAATCAATTC-TGATC-AGAATGAAGTG
* * *
88433603 AGCAAACTTAGTCAATTGATCCACAATAACCCAAATAGAGTGCTTCTTAGTAGGTGTCAAGGGAA
256 AGCAAACTTAGTCAACTGATCCACAATAA-CCAAATAAAGTCCTTCTTAGTAGGTGTCAAGGGAA
* * *
88433668 ACTCGCTAACAAAGTCCATAGTTACCCATTTCCTATTTCCACAATGGAATCTTAACAGGTTGGAG
320 ACTCACTAACAAAGTCCATAGTTACCCA-TTCCCATTTCCACAATGAAATCTTAACAGGTTGGAG
* * * * *
88433733 CAAACCAGAAGGAAGTTGGTGCTTAGCCTTAACCTTCTAGCACGTCAAATAATGGGACACAAAGT
384 AAAACCAGAAGGAAGTTGATGCTTAGCCTTAACCTTCTAGCACATCAAACAATGGGACACAAAAT
* * * * *
88433798 CGATTACCTCATGTTTCAACCTAGGCCACCAATAAAACTCTCAAAGGTGACGGTACATCTTATTA
449 CGATTACCTCACGTTTCAACCTAGGCCACCAATAAAACTCTCAAAGCTGACAGAACATCTTAATA
* * * * * *
88433863 CCGCC-AGGATGCATTGTATAAGGGCTACTATGCGCTTCTCACAGAATAGATTACCTCAAATCCA
514 CCACCGA-GATGCATAGCATAAGGGCTACTATGCACTTCCCACAGAATAGATTACCTAAAATCCA
* * * * * *
88433927 TATCACTAGGCACACAAATTTAACCTCAAAAACACAAAATAACATCACTAGTAGACCAAAAATTT
578 CATCACTAGGCACAAAAATCTAACCTCAAAAACACAAAATAACATCACGAGTAAACCAAAAATCT
* * * * * **
88433992 AAAGTCTTACTCTCATCAATCTGTTGAA-CCTGACTAATTAGAGACTTATCCAGAA-GCTGTTTA
643 AAAGTCTTACCCTCATCAATCTGATGAATCCT-ACTAATCAAAGACTCATCCA-AATGCTACTTA
*
88434055 TTCTTAATCTTAGTTAACCAAGTT
706 TTCTTAATCTCAGTTAACCAAGTT
88434079 AACTTAACTT
Statistics
Matches: 622, Mismatches: 99, Indels: 18
0.84 0.13 0.02
Matches are distributed among these distances:
732 6 0.01
733 238 0.38
734 63 0.10
735 313 0.50
736 2 0.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.28
Consensus pattern (733 bp):
AACACAGCTCTGAAGCATATCTTCCAAAATCTGAATCACTCTTTCAAACTGACCATCAGTCTACA
GATGAAATACCGTACTGAAATCAAATCAAGTACCCAGAGCCTCATGTAATTTCTTCCAAAAGTGA
GAAGTAAACCAAGGATCTCAATATGAGATAATCAATACCAAAACTCCATAGACCCTAACTACCTT
GGAAACATAAACTTTCACCAATTTTTGTAAAGAGTAATCAATTCTGATCAGAATGAAGTGAGCAA
ACTTAGTCAACTGATCCACAATAACCAAATAAAGTCCTTCTTAGTAGGTGTCAAGGGAAACTCAC
TAACAAAGTCCATAGTTACCCATTCCCATTTCCACAATGAAATCTTAACAGGTTGGAGAAAACCA
GAAGGAAGTTGATGCTTAGCCTTAACCTTCTAGCACATCAAACAATGGGACACAAAATCGATTAC
CTCACGTTTCAACCTAGGCCACCAATAAAACTCTCAAAGCTGACAGAACATCTTAATACCACCGA
GATGCATAGCATAAGGGCTACTATGCACTTCCCACAGAATAGATTACCTAAAATCCACATCACTA
GGCACAAAAATCTAACCTCAAAAACACAAAATAACATCACGAGTAAACCAAAAATCTAAAGTCTT
ACCCTCATCAATCTGATGAATCCTACTAATCAAAGACTCATCCAAATGCTACTTATTCTTAATCT
CAGTTAACCAAGTTGAAG
Found at i:88435769 original size:13 final size:13
Alignment explanation
Indices: 88435751--88435779 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
88435741 GGTTGTTTCT
88435751 TAAACTAATTAAC
1 TAAACTAATTAAC
88435764 TAAACTAATTAAC
1 TAAACTAATTAAC
88435777 TAA
1 TAA
88435780 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:88444094 original size:13 final size:13
Alignment explanation
Indices: 88444057--88444085 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
88444047 GGTTGTTTAT
88444057 TAAACTAATTAAC
1 TAAACTAATTAAC
88444070 TAAACTAATTAAC
1 TAAACTAATTAAC
88444083 TAA
1 TAA
88444086 TTAATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:88447894 original size:27 final size:26
Alignment explanation
Indices: 88447858--88447908 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
88447848 TCATATCAGA
*
88447858 ATTTTCATATTTTCAAAACGTATATC
1 ATTTTCATATTTTCAAAACATATATC
*
88447884 ATTTATCATATTTTCAGAACATATA
1 ATTT-TCATATTTTCAAAACATATA
88447909 ACATATTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.37, C:0.14, G:0.04, T:0.45
Consensus pattern (26 bp):
ATTTTCATATTTTCAAAACATATATC
Found at i:88451376 original size:57 final size:57
Alignment explanation
Indices: 88451301--88451414 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
88451291 AATATATGTT
* *
88451301 GTACTCTTTTTCCCTTAACCGAGGTTTTGTTCGCTAGGTTTCTTAGTAAGATTTTTA
1 GTACACTTTTTCCCTTAACCGAGGTTTTGTCCGCTAGGTTTCTTAGTAAGATTTTTA
*
88451358 GTACACTTTTTCCCTTAACCGAGGTTTTGTCCTCTAGGTTTCTTAGTAAGATTTTTA
1 GTACACTTTTTCCCTTAACCGAGGTTTTGTCCGCTAGGTTTCTTAGTAAGATTTTTA
88451415 ACGAGGCAGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.46
Consensus pattern (57 bp):
GTACACTTTTTCCCTTAACCGAGGTTTTGTCCGCTAGGTTTCTTAGTAAGATTTTTA
Found at i:88452749 original size:12 final size:12
Alignment explanation
Indices: 88452732--88452770 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
88452722 CGGCCAACTC
88452732 ATATTAATTTTT
1 ATATTAATTTTT
*
88452744 ATATTATTTTTT
1 ATATTAATTTTT
*
88452756 ATA-TAATTTTA
1 ATATTAATTTTT
88452767 ATAT
1 ATAT
88452771 ATATAATACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:88452921 original size:30 final size:30
Alignment explanation
Indices: 88452887--88452949 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
88452877 ACTTAACAAG
*
88452887 CAAATGCCTTTAGAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
*
88452917 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
88452947 CAA
1 CAA
88452950 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.27
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAACAAAATTAA
Found at i:88455914 original size:18 final size:17
Alignment explanation
Indices: 88455874--88455914 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
88455864 ATAATGAATA
*
88455874 ATAAATTTTATAAAATT
1 ATAAATTTTATAAAAAT
88455891 ATTAAATTTTAATAAAAAT
1 A-TAAATTTT-ATAAAAAT
88455910 ATAAA
1 ATAAA
88455915 AATTTAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 12 0.57
19 8 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAAATTTTATAAAAAT
Found at i:88455920 original size:19 final size:19
Alignment explanation
Indices: 88455871--88455920 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
88455861 ATTATAATGA
* *
88455871 ATAATAAATTTTATAAAATT
1 ATAA-AAATTTAATAAAAAT
* *
88455891 ATTAAATTTTAATAAAAAT
1 ATAAAAATTTAATAAAAAT
88455910 ATAAAAATTTA
1 ATAAAAATTTA
88455921 GAATTTTTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAAAAATTTAATAAAAAT
Found at i:88456227 original size:17 final size:17
Alignment explanation
Indices: 88456202--88456234 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
88456192 AATTTTTATA
*
88456202 ATATTTTTTATAATTTT
1 ATATATTTTATAATTTT
88456219 ATATATTTTATAATTT
1 ATATATTTTATAATTT
88456235 GTTACAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATATTTTATAATTTT
Found at i:88456243 original size:27 final size:29
Alignment explanation
Indices: 88456195--88456251 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
88456185 AGTTATAAAT
* *
88456195 TTTTATAATATTTTTTATAATTTTATATA
1 TTTTATAATATTTGTTACAATTTTATATA
*
88456224 TTTTAT-A-ATTTGTTACAATTTTTTATA
1 TTTTATAATATTTGTTACAATTTTATATA
88456251 T
1 T
88456252 AGTTTTTACG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.72
28 1 0.04
29 6 0.24
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (29 bp):
TTTTATAATATTTGTTACAATTTTATATA
Found at i:88456275 original size:18 final size:19
Alignment explanation
Indices: 88456224--88456285 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
88456214 ATTTTATATA
*
88456224 TTTTATAATTTGTTACAATT
1 TTTTAT-ATTTTTTACAATT
*
88456244 TTTTATATAGTTTTTACGA-T
1 TTTTATAT--TTTTTACAATT
88456264 TTTTATATTTTTT-CTAATT
1 TTTTATATTTTTTAC-AATT
88456283 TTT
1 TTT
88456286 AATACATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
17 1 0.03
18 6 0.17
19 6 0.17
20 15 0.43
21 7 0.20
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTTATATTTTTTACAATT
Found at i:88463030 original size:21 final size:21
Alignment explanation
Indices: 88463004--88463051 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
88462994 ATCACACAGC
88463004 TCTGAAGCACATCCTCCAGTA
1 TCTGAAGCACATCCTCCAGTA
88463025 TCTGAAGCACATCCTCCAGTA
1 TCTGAAGCACATCCTCCAGTA
88463046 TCTGAA
1 TCTGAA
88463052 TCACCCTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (21 bp):
TCTGAAGCACATCCTCCAGTA
Found at i:88464764 original size:7 final size:7
Alignment explanation
Indices: 88464752--88464782 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
88464742 ACTTTTCTAA
88464752 TCATCCC
1 TCATCCC
*
88464759 TCATCCA
1 TCATCCC
88464766 TCATCCC
1 TCATCCC
88464773 TCATCCC
1 TCATCCC
88464780 TCA
1 TCA
88464783 CTAATTCATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.19, C:0.52, G:0.00, T:0.29
Consensus pattern (7 bp):
TCATCCC
Found at i:88465237 original size:34 final size:34
Alignment explanation
Indices: 88465193--88465260 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
88465183 TTATTGCGTT
*
88465193 AGTTTTGCTAAAATCTATTTCATTCATATAGTTG
1 AGTTCTGCTAAAATCTATTTCATTCATATAGTTG
88465227 AGTTCTGCTAAAATCTATTTCATTCATATAGTTG
1 AGTTCTGCTAAAATCTATTTCATTCATATAGTTG
88465261 CATGTTAGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (34 bp):
AGTTCTGCTAAAATCTATTTCATTCATATAGTTG
Found at i:88468232 original size:28 final size:28
Alignment explanation
Indices: 88468169--88468321 Score: 229
Period size: 28 Copynumber: 5.5 Consensus size: 28
88468159 ATATTAAGTC
* *
88468169 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
88468196 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
88468224 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
88468252 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
* * *
88468280 CGCACACTTAGTGCTACGTAGTC-AATT
1 CGCACACTTAGTGCTACATAATCAAACT
88468307 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
88468322 GCACAATTTA
Statistics
Matches: 118, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 40 0.34
28 78 0.66
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:88468310 original size:83 final size:83
Alignment explanation
Indices: 88468169--88468321 Score: 236
Period size: 83 Copynumber: 1.8 Consensus size: 83
88468159 ATATTAAGTC
* *
88468169 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTATATAATCAAACTCGCACACTTA
1 CGCACACTCAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
88468234 GTGCTACATAGTCAAACT
66 GTGCTACATAGTCAAACT
* * * *
88468252 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACGTAGTC-AATTCGCACACTT
1 CGCACACTCAGTGCTACATAATC-AACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
88468316 AGTGCT
65 AGTGCT
88468322 GCACAATTTA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
83 39 0.62
84 24 0.38
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (83 bp):
CGCACACTCAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
GTGCTACATAGTCAAACT
Found at i:88471576 original size:46 final size:45
Alignment explanation
Indices: 88471416--88471632 Score: 158
Period size: 46 Copynumber: 4.7 Consensus size: 45
88471406 CTATCTGTGT
* * * *
88471416 CGATGCCATGTCCTAGACAGGTCTTACACTGACACATG--TCAA-GC
1 CGATG-CATGTCCCAGACATGTCTTACACTGGCTC-TGCCTCAATGC
* * *
88471460 CGATGCCATGTCCCAGACAGGTCTTACACTGGCT-TGCATATCTCGAGGC
1 CGATG-CATGTCCCAGACATGTCTTACACTGGCTCTGC----CTCAATGC
* *
88471509 CGATGTATGTCCCAGATATGTCTTACACTGGCTCTCGCCTCAATGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTCT-GCCTCAATGC
* ** * *
88471555 CGATGCATGTCCTAGACATGTCTTACGTTGGCTCT-CAT-AATGTGGT
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTCTGCCTCAA--T-GC
*
88471601 TGATGCATGTCCCAGACATGTCTTACACTGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGC
88471633 ACACATATCA
Statistics
Matches: 141, Mismatches: 20, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
42 2 0.01
43 2 0.01
44 33 0.23
45 1 0.01
46 65 0.46
48 28 0.20
49 8 0.06
50 2 0.01
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (45 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTCTGCCTCAATGC
Found at i:88471580 original size:94 final size:92
Alignment explanation
Indices: 88471365--88471632 Score: 222
Period size: 92 Copynumber: 2.9 Consensus size: 92
88471355 ATATATCGAG
* * * * * * ** * *
88471365 GCCGATGCCGTGTCTCAAACAGGTCTTACAGTGGCTCTAATCTATCTGTGTCGATGCCATGTCCT
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCAT-AATGAG-GCCGATG-CATGTCCC
* * *
88471430 AGACAGGTCTTACACTGACACAT-G--TCAA
63 AGACATGTCTTACACTGGCTC-TCGCCTCAA
* *
88471458 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCT-TGCATATCTCGAGGCCGATGTATGTCCC
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCT-CATA-AT-GAGGCCGATGCATGTCCC
*
88471522 AGATATGTCTTACACTGGCTCTCGCCTCAA
63 AGACATGTCTTACACTGGCTCTCGCCTCAA
* * ** * **
88471552 TGCCGATG-CATGTCCTAGACATGTCTTACGTTGGCTCTCATAATGTGGTTGATGCATGTCCCAG
1 -GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATAATGAGGCCGATGCATGTCCCAG
88471616 ACATGTCTTACACTGGC
65 ACATGTCTTACACTGGC
88471633 ACACATATCA
Statistics
Matches: 141, Mismatches: 26, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
91 1 0.01
92 57 0.40
93 42 0.30
94 33 0.23
95 8 0.06
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (92 bp):
GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATAATGAGGCCGATGCATGTCCCAGA
CATGTCTTACACTGGCTCTCGCCTCAA
Found at i:88478107 original size:21 final size:22
Alignment explanation
Indices: 88478066--88478107 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
88478056 CTTCATTCTA
*
88478066 CTATTTTTTATATCCCTCAAAG
1 CTATTTTTTATAACCCTCAAAG
88478088 CTATTTTCTTA-AACCC-CAAA
1 CTATTTT-TTATAACCCTCAAA
88478108 AATCCTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
22 11 0.61
23 3 0.17
ACGTcount: A:0.31, C:0.26, G:0.02, T:0.40
Consensus pattern (22 bp):
CTATTTTTTATAACCCTCAAAG
Found at i:88481852 original size:7 final size:7
Alignment explanation
Indices: 88481840--88481870 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
88481830 ACTTTTCTAA
88481840 TCATCCC
1 TCATCCC
88481847 TCATCCC
1 TCATCCC
*
88481854 TCATCCT
1 TCATCCC
88481861 TCATCCC
1 TCATCCC
88481868 TCA
1 TCA
88481871 GTTATCCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (7 bp):
TCATCCC
Found at i:88485301 original size:39 final size:39
Alignment explanation
Indices: 88485258--88485335 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
88485248 AAGAAAAAAG
*
88485258 AAAAAGAGAAAGACATATGGCCTAAGGGCTTTTAAGTTT
1 AAAAAGAGAAAGACACATGGCCTAAGGGCTTTTAAGTTT
88485297 AAAAAGAGAAAGACACATGGCCTAAGGGCTTTTAAGTTT
1 AAAAAGAGAAAGACACATGGCCTAAGGGCTTTTAAGTTT
88485336 CAAATTTCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (39 bp):
AAAAAGAGAAAGACACATGGCCTAAGGGCTTTTAAGTTT
Found at i:88490277 original size:17 final size:17
Alignment explanation
Indices: 88490251--88490284 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
88490241 CTTAGAGTTG
*
88490251 TTTTGTAAGTGTTACGA
1 TTTTGCAAGTGTTACGA
88490268 TTTTGCAAGTGTTACGA
1 TTTTGCAAGTGTTACGA
88490285 GAGAAACGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.44
Consensus pattern (17 bp):
TTTTGCAAGTGTTACGA
Found at i:88502331 original size:40 final size:40
Alignment explanation
Indices: 88502248--88502510 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
88502238 TTGAATGCTG
* * * * * *
88502248 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
88502288 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
88502328 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
88502368 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
88502408 TCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
88502448 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
88502487 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
88502511 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 34 0.17
40 157 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:88502530 original size:79 final size:80
Alignment explanation
Indices: 88502287--88502545 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
88502277 AAGTGAATAT
* * * * * *
88502287 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * * *
88502351 TCGTGCGAGTTA-TTAA
65 TCGAACAAG-GAGCTAA
* * *
88502367 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
88502432 CGTGCAAGTTGTTAA
66 CGAACAAGGAGCTAA
* * *
88502447 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* * *
88502511 TGAACGAGGAGCTAT
66 CGAACAAGGAGCTAA
*
88502526 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
88502546 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACAAGGAGCTAA
Found at i:88504912 original size:20 final size:20
Alignment explanation
Indices: 88504887--88504928 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
88504877 TTCAACAGAC
*
88504887 ATCGAAGAGATTTCGAGATG
1 ATCGAAGAGATATCGAGATG
88504907 ATCGAAGAGATATCGAGATG
1 ATCGAAGAGATATCGAGATG
88504927 AT
1 AT
88504929 GCGGGCCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.29, T:0.24
Consensus pattern (20 bp):
ATCGAAGAGATATCGAGATG
Found at i:88510310 original size:40 final size:40
Alignment explanation
Indices: 88510227--88510489 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
88510217 TTGAATGCTG
* * * * * *
88510227 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
88510267 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
88510307 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
88510347 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
88510387 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
88510427 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
88510466 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
88510490 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:88510509 original size:79 final size:80
Alignment explanation
Indices: 88510266--88510524 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
88510256 AAGTGAATAT
* * * * * *
88510266 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
88510330 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
88510346 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
88510411 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
88510426 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
88510490 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
88510505 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
88510525 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:88515336 original size:20 final size:20
Alignment explanation
Indices: 88515311--88515372 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
88515301 CAAAATATTT
*
88515311 ATATATATTAACTACTTAAA
1 ATATATATTAACTATTTAAA
* *
88515331 ATATATTTTAA-AATTTAAA
1 ATATATATTAACTATTTAAA
*
88515350 TTAATATATTAACTATTTAAA
1 AT-ATATATTAACTATTTAAA
88515371 AT
1 AT
88515373 TTAGATTTAC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
19 7 0.21
20 18 0.55
21 8 0.24
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATATATTAACTATTTAAA
Found at i:88519524 original size:31 final size:31
Alignment explanation
Indices: 88519467--88519525 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
88519457 TTCTTTAGGT
*
88519467 CCCTTAAAAGTTAAATAAAAAAAATTTTGGG
1 CCCTTAAAAGCTAAATAAAAAAAATTTTGGG
* *
88519498 CCCTTCAAAGCTAAA-AAATAATAATTTT
1 CCCTTAAAAGCTAAATAAA-AAAAATTTT
88519526 TGAACCTCTT
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:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (31 bp):
CCCTTAAAAGCTAAATAAAAAAAATTTTGGG
Found at i:88520000 original size:24 final size:23
Alignment explanation
Indices: 88519961--88520008 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
88519951 CATATAAGTA
*
88519961 TTTTAAAATTTGAA-TTTTAAAT
1 TTTTAAAAATTGAATTTTTAAAT
88519983 TTTTAAATAATTGAAATTTTTAAAT
1 TTTTAAA-AATTG-AATTTTTAAAT
88520008 T
1 T
88520009 AATTAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 2 0.09
25 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
TTTTAAAAATTGAATTTTTAAAT
Found at i:88520003 original size:18 final size:17
Alignment explanation
Indices: 88519977--88520017 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
88519967 AATTTGAATT
88519977 TTAAATTTTTAAA-TAA
1 TTAAATTTTTAAATTAA
88519993 TTGAAATTTTTAAATTAA
1 TT-AAATTTTTAAATTAA
88520011 TTAAATT
1 TTAAATT
88520018 GTAGTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.09
17 16 0.70
18 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TTAAATTTTTAAATTAA
Found at i:88522568 original size:13 final size:13
Alignment explanation
Indices: 88522552--88522577 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
88522542 TATTTTTAAT
88522552 AAATATTTACGAA
1 AAATATTTACGAA
88522565 AAATATTTACGAA
1 AAATATTTACGAA
88522578 GTTAGTTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
AAATATTTACGAA
Found at i:88523690 original size:16 final size:16
Alignment explanation
Indices: 88523671--88523704 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
88523661 AAATGAATAT
* *
88523671 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
88523687 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
88523703 AT
1 AT
88523705 TGGATATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:88530309 original size:11 final size:11
Alignment explanation
Indices: 88530293--88530317 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
88530283 ATATCTAGAA
88530293 TTCTCTTCATT
1 TTCTCTTCATT
88530304 TTCTCTTCATT
1 TTCTCTTCATT
88530315 TTC
1 TTC
88530318 ATCAACTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:88531599 original size:25 final size:25
Alignment explanation
Indices: 88531570--88531621 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
88531560 AAGAATAATT
**
88531570 TGAATATTTGATATTGCCTAATAAA
1 TGAATATCCGATATTGCCTAATAAA
* *
88531595 TGAATATCCGATATTGCTTAGTAAA
1 TGAATATCCGATATTGCCTAATAAA
88531620 TG
1 TG
88531622 TCAAGCCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (25 bp):
TGAATATCCGATATTGCCTAATAAA
Found at i:88534348 original size:39 final size:39
Alignment explanation
Indices: 88534305--88534385 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
88534295 GTGATAGTGT
88534305 GATGTTTCCTGAATTATGTGGATTTTGTTTTTTCACATG
1 GATGTTTCCTGAATTATGTGGATTTTGTTTTTTCACATG
88534344 GATGTTTCCTGAATTATGTGGATTTTGTTTTTTCACATG
1 GATGTTTCCTGAATTATGTGGATTTTGTTTTTTCACATG
88534383 GAT
1 GAT
88534386 AAAATATGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.19, C:0.10, G:0.21, T:0.51
Consensus pattern (39 bp):
GATGTTTCCTGAATTATGTGGATTTTGTTTTTTCACATG
Found at i:88535837 original size:25 final size:24
Alignment explanation
Indices: 88535809--88535863 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
88535799 AAAATTCAAG
* * *
88535809 GTTATGACTTTTCTATTAATTTGAT
1 GTTATGACATTT-TATGAATTTGAC
*
88535834 GTTACTGTCATTTTATGAATTTGAC
1 GTTA-TGACATTTTATGAATTTGAC
88535859 GTTAT
1 GTTAT
88535864 TCTGGGAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 18 0.72
26 6 0.24
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.53
Consensus pattern (24 bp):
GTTATGACATTTTATGAATTTGAC
Found at i:88541656 original size:25 final size:25
Alignment explanation
Indices: 88541628--88541686 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
88541618 TATAATTGCA
*
88541628 ATTTCATTTTTTATTTTTCTCGTTT
1 ATTTTATTTTTTATTTTTCTCGTTT
88541653 ATTTTATTTTTTATTTTTCTCGTTT
1 ATTTTATTTTTTATTTTTCTCGTTT
88541678 ATTTTATTT
1 ATTTTATTT
88541687 ATCATCATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (25 bp):
ATTTTATTTTTTATTTTTCTCGTTT
Found at i:88541657 original size:12 final size:13
Alignment explanation
Indices: 88541637--88541682 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
88541627 AATTTCATTT
88541637 TTTATTTTTCTCG
1 TTTATTTTTCTCG
*
88541650 TTTATTTTAT-T-T
1 TTTATTTT-TCTCG
88541662 TTTATTTTTCTCG
1 TTTATTTTTCTCG
88541675 TTTATTTT
1 TTTATTTT
88541683 ATTTATCATC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 1 0.04
12 9 0.32
13 17 0.61
14 1 0.04
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTATTTTTCTCG
Found at i:88542248 original size:5 final size:5
Alignment explanation
Indices: 88542240--88542267 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
88542230 GATTAAATTG
88542240 ATTTT ATTTT ATTTT ATTTT ATTTT ATT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATT
88542268 AAAAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:88549052 original size:37 final size:37
Alignment explanation
Indices: 88548997--88549111 Score: 194
Period size: 37 Copynumber: 3.1 Consensus size: 37
88548987 GAGAAAGTTA
* *
88548997 AAGGAAATAAAAACGCATTAGTGAATGAAAAATATAC
1 AAGGTAATAAAAAGGCATTAGTGAATGAAAAATATAC
88549034 AAGGTAATAAAAAGGCATTAGTGAATGAAAAATATAC
1 AAGGTAATAAAAAGGCATTAGTGAATGAAAAATATAC
*
88549071 AAGGTAATAAAGAGGCATTAGTGAATGAAAAAGTATAC
1 AAGGTAATAAAAAGGCATTAGTGAATGAAAAA-TATAC
88549109 AAG
1 AAG
88549112 CTGCATGATG
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
37 66 0.89
38 8 0.11
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (37 bp):
AAGGTAATAAAAAGGCATTAGTGAATGAAAAATATAC
Found at i:88550446 original size:25 final size:25
Alignment explanation
Indices: 88550417--88550465 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
88550407 AAAGAAGAAG
88550417 CGAATTTG-ACACTCACCAAAACAAA
1 CGAATTTGCA-ACTCACCAAAACAAA
*
88550442 CGAATTTGCAAGTCACCAAAACAA
1 CGAATTTGCAACTCACCAAAACAA
88550466 TGGAGACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.47, C:0.27, G:0.10, T:0.16
Consensus pattern (25 bp):
CGAATTTGCAACTCACCAAAACAAA
Found at i:88550937 original size:3 final size:3
Alignment explanation
Indices: 88550929--88550956 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
88550919 AATTTAGTAC
88550929 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
88550957 CAAGAATATA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:88574410 original size:25 final size:25
Alignment explanation
Indices: 88574356--88574504 Score: 138
Period size: 25 Copynumber: 6.0 Consensus size: 25
88574346 ACTATCTATG
* ** *
88574356 AAGCCTTTGTAGCGAACTCACTGTG
1 AAGCCTTTGTGGCGAACTCTTTGTA
* *
88574381 CAGCCTTTATGGCGAACTCTTTGTA
1 AAGCCTTTGTGGCGAACTCTTTGTA
* * *
88574406 AAGCCTTTATGGTGAACTCTCTGTA
1 AAGCCTTTGTGGCGAACTCTTTGTA
* * * *
88574431 AAGCCTCTGTGGCAAACTCTATGTG
1 AAGCCTTTGTGGCGAACTCTTTGTA
*
88574456 AAGCCTTTGTGGCGAACT-TTCTCTA
1 AAGCCTTTGTGGCGAACTCTT-TGTA
* *
88574481 AAACTTTTGTGGCGAACTCTTTGT
1 AAGCCTTTGTGGCGAACTCTTTGT
88574505 GAAACCTGTG
Statistics
Matches: 99, Mismatches: 23, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
24 1 0.01
25 96 0.97
26 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.34
Consensus pattern (25 bp):
AAGCCTTTGTGGCGAACTCTTTGTA
Found at i:88574410 original size:50 final size:50
Alignment explanation
Indices: 88574326--88574473 Score: 140
Period size: 50 Copynumber: 3.0 Consensus size: 50
88574316 ATGGCATATT
* *
88574326 CTGTGAAGCCT-TAATGGCAAACTATCTATG--AAGCCTTTGTAGCGAACTCA
1 CTGTAAAGCCTCT-ATGGCAAAC--TCTATGTAAAGCCTTTGTGGCGAACTCA
** * * * * * *
88574376 CTGTGCAGCCTTTATGGCGAACTCTTTGTAAAGCCTTTATGGTGAACTCT
1 CTGTAAAGCCTCTATGGCAAACTCTATGTAAAGCCTTTGTGGCGAACTCA
* *
88574426 CTGTAAAGCCTCTGTGGCAAACTCTATGTGAAGCCTTTGTGGCGAACT
1 CTGTAAAGCCTCTATGGCAAACTCTATGTAAAGCCTTTGTGGCGAACT
88574474 TTCTCTAAAA
Statistics
Matches: 79, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
48 5 0.06
50 73 0.92
51 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (50 bp):
CTGTAAAGCCTCTATGGCAAACTCTATGTAAAGCCTTTGTGGCGAACTCA
Found at i:88585055 original size:19 final size:19
Alignment explanation
Indices: 88584998--88585056 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
88584988 GAAAAAAATG
*
88584998 ATAAAAAATAATAAAATTT-
1 ATAAAAAATTAT-AAATTTA
* *
88585017 A-GAAAAATTATTAACTTTTA
1 ATAAAAAATTA-TAA-ATTTA
88585037 ATAAAAAATTATAAATTTA
1 ATAAAAAATTATAAATTTA
88585056 A
1 A
88585057 AAATTATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
18 9 0.29
19 10 0.32
20 4 0.13
21 8 0.26
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
ATAAAAAATTATAAATTTA
Found at i:88585287 original size:20 final size:20
Alignment explanation
Indices: 88585262--88585318 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
88585252 TACGAAAATT
88585262 TTTATAATTTTTTTACGAAA
1 TTTATAATTTTTTTACGAAA
* **
88585282 TTTAT-ATTTATTTAC-ATT
1 TTTATAATTTTTTTACGAAA
*
88585300 TTGTATAATTTTCTTACGA
1 TT-TATAATTTTTTTACGA
88585319 CTTTATAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 3 0.10
19 12 0.41
20 13 0.45
21 1 0.03
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTATAATTTTTTTACGAAA
Found at i:88587575 original size:18 final size:20
Alignment explanation
Indices: 88587554--88587590 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
88587544 GAAATAAAGG
88587554 ACATA-ATAGAAA-AAATAT
1 ACATATATAGAAATAAATAT
*
88587572 ACATATATATAAATAAATA
1 ACATATATAGAAATAAATA
88587591 AAAGAAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 6 0.38
20 5 0.31
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (20 bp):
ACATATATAGAAATAAATAT
Found at i:88598858 original size:2 final size:2
Alignment explanation
Indices: 88598851--88598876 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
88598841 GGTGAAATGG
88598851 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
88598877 GAGATAAGGA
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:88598980 original size:54 final size:54
Alignment explanation
Indices: 88598898--88599001 Score: 208
Period size: 54 Copynumber: 1.9 Consensus size: 54
88598888 TTCTAGTGTG
88598898 GACTAATTAAAATTATTGAATTTGTTATAATCTTGTAATGTTTTCGGAAATTTT
1 GACTAATTAAAATTATTGAATTTGTTATAATCTTGTAATGTTTTCGGAAATTTT
88598952 GACTAATTAAAATTATTGAATTTGTTATAATCTTGTAATGTTTTCGGAAA
1 GACTAATTAAAATTATTGAATTTGTTATAATCTTGTAATGTTTTCGGAAA
88599002 ATTATTAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (54 bp):
GACTAATTAAAATTATTGAATTTGTTATAATCTTGTAATGTTTTCGGAAATTTT
Found at i:88612346 original size:26 final size:26
Alignment explanation
Indices: 88612290--88612347 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
88612280 TTTTAATTAA
* *
88612290 GAAAATTACTTAAAAATAATATAGTT
1 GAAAATTAATTAAAAACAATATAGTT
* *
88612316 TAAAATTAATTAATAAACATTATA-TT
1 GAAAATTAATTAA-AAACAATATAGTT
88612342 GAAAAT
1 GAAAAT
88612348 AGGGGTGCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.36
Consensus pattern (26 bp):
GAAAATTAATTAAAAACAATATAGTT
Found at i:88616046 original size:28 final size:28
Alignment explanation
Indices: 88616010--88616251 Score: 147
Period size: 28 Copynumber: 8.6 Consensus size: 28
88616000 CTCAAGATTT
* *
88616010 GCCATAAAGGCTTTCCTTTTTTTAATTC
1 GCCACAAAGGCTTTCCTTTTTATAATTC
*
88616038 GCCACAAAGGCTATT-CTTTTTATGATTC
1 GCCACAAAGGCT-TTCCTTTTTATAATTC
* * *
88616066 ACCATAAAGGCTTTCCTTTCTATGAA-TC
1 GCCACAAAGGCTTTCCTTTTTAT-AATTC
** * *
88616094 ATCACAAAAGCTTTCCTTTTTATGATTC
1 GCCACAAAGGCTTTCCTTTTTATAATTC
88616122 GCCACAAAGGCTATT-CTTTTTATGAA-TC
1 GCCACAAAGGCT-TTCCTTTTTAT-AATTC
* * *
88616150 ACCATAAAGG-TTTATCTTTTTATGAA-TC
1 GCCACAAAGGCTTT-CCTTTTTAT-AATTC
* ** * * *
88616178 ACTTCAATGACTTCCCTTTTTATGAATT-
1 GCCACAAAGGCTTTCCTTTTTAT-AATTC
* * * *
88616206 GCCACAAAGTCTTTTCTTTTTATGACTC
1 GCCACAAAGGCTTTCCTTTTTATAATTC
* *
88616234 ACAACAAAGGCTTTCCTT
1 GCCACAAAGGCTTTCCTT
88616252 ATCTATAGTG
Statistics
Matches: 165, Mismatches: 38, Indels: 22
0.73 0.17 0.10
Matches are distributed among these distances:
26 2 0.01
27 6 0.04
28 148 0.90
29 9 0.05
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (28 bp):
GCCACAAAGGCTTTCCTTTTTATAATTC
Found at i:88616072 original size:56 final size:56
Alignment explanation
Indices: 88616011--88616251 Score: 229
Period size: 56 Copynumber: 4.3 Consensus size: 56
88616001 TCAAGATTTG
* * *
88616011 CCATAAAGGCTTTCCTTTTT-TTAATTCGCCACAAAGGCTATTCTTTTTATGATTCA
1 CCATAAAGGCTTTCCTTTTTATGAA-TCACCACAAAGGCTTTTCTTTTTATGATTCA
* * * * *
88616067 CCATAAAGGCTTTCCTTTCTATGAATCATCACAAAAGCTTTCCTTTTTATGATTCG
1 CCATAAAGGCTTTCCTTTTTATGAATCACCACAAAGGCTTTTCTTTTTATGATTCA
* * *
88616123 CCACAAAGGCTATT-CTTTTTATGAATCACCATAAAGG-TTTATCTTTTTATGAATCA
1 CCATAAAGGCT-TTCCTTTTTATGAATCACCACAAAGGCTTT-TCTTTTTATGATTCA
* * * * ** * *
88616179 -CTTCAATGACTTCCCTTTTTATGAATTGCCACAAAGTCTTTTCTTTTTATGACTCA
1 CCAT-AAAGGCTTTCCTTTTTATGAATCACCACAAAGGCTTTTCTTTTTATGATTCA
* *
88616235 CAACAAAGGCTTTCCTT
1 CCATAAAGGCTTTCCTT
88616252 ATCTATAGTG
Statistics
Matches: 146, Mismatches: 32, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
55 5 0.03
56 133 0.91
57 8 0.05
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (56 bp):
CCATAAAGGCTTTCCTTTTTATGAATCACCACAAAGGCTTTTCTTTTTATGATTCA
Found at i:88616114 original size:84 final size:83
Alignment explanation
Indices: 88616019--88616257 Score: 277
Period size: 84 Copynumber: 2.8 Consensus size: 83
88616009 TGCCATAAAG
*
88616019 GCTTTCCTTTTTTTAATTCGCCACAAAGGCTATTCTTTTTATGATTCACCATAAAGGCTTTCCTT
1 GCTTTCCTTTTTTTAATTCGCCACAAAGGCTATTCTTTTTATGAATCACCATAAAGGCTTTCCTT
88616084 TCTATGAATCA-TCACAAAA
66 TCTATGAATCACT-AC-AAA
* * *
88616103 GCTTTCCTTTTTATGATTCGCCACAAAGGCTATTCTTTTTATGAATCACCATAAAGG-TTTATCT
1 GCTTTCCTTTTTTTAATTCGCCACAAAGGCTATTCTTTTTATGAATCACCATAAAGGCTTT-CCT
* * *
88616167 TTTTATGAATCACTTCAAT
65 TTCTATGAATCACTACAAA
* * * * * * *
88616186 GACTTCCCTTTTTATGAATT-GCCACAAAGTCTTTTCTTTTTATGACTCACAACAAAGGCTTTCC
1 G-CTTTCCTTTTT-TTAATTCGCCACAAAGGCTATTCTTTTTATGAATCACCATAAAGGCTTTCC
88616250 TTATCTAT
64 TT-TCTAT
88616258 AGTGTTTTTC
Statistics
Matches: 131, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
83 6 0.05
84 114 0.87
85 11 0.08
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (83 bp):
GCTTTCCTTTTTTTAATTCGCCACAAAGGCTATTCTTTTTATGAATCACCATAAAGGCTTTCCTT
TCTATGAATCACTACAAA
Found at i:88622380 original size:18 final size:18
Alignment explanation
Indices: 88622353--88622389 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
88622343 TGGTTTTCTT
*
88622353 TAGCCGAACCACTCTTGC
1 TAGCCAAACCACTCTTGC
88622371 TAGCCAAACCACTCTTGC
1 TAGCCAAACCACTCTTGC
88622389 T
1 T
88622390 TTCTTCTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.38, G:0.14, T:0.24
Consensus pattern (18 bp):
TAGCCAAACCACTCTTGC
Found at i:88630263 original size:18 final size:18
Alignment explanation
Indices: 88630240--88630276 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
88630230 CAGTTTTCTT
88630240 TAGCCGAACCACTCTTGC
1 TAGCCGAACCACTCTTGC
88630258 TAGCCGAACCACTCTTGC
1 TAGCCGAACCACTCTTGC
88630276 T
1 T
88630277 TTCTTCTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (18 bp):
TAGCCGAACCACTCTTGC
Found at i:88638765 original size:23 final size:23
Alignment explanation
Indices: 88638735--88638782 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
88638725 GGTCACTTAC
*
88638735 TCATCTTTGAAATAATTCTATAT
1 TCATCTTTGAAATAATTCTACAT
88638758 TCATCTTTGAAATAATTCTACAT
1 TCATCTTTGAAATAATTCTACAT
88638781 TC
1 TC
88638783 TTTTAAGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (23 bp):
TCATCTTTGAAATAATTCTACAT
Found at i:88642151 original size:16 final size:18
Alignment explanation
Indices: 88642124--88642157 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
88642114 ACATTCTTTT
88642124 TTAAATTAATTTT-TCAA
1 TTAAATTAATTTTCTCAA
88642141 TTAAA-TAATTTTCTCAA
1 TTAAATTAATTTTCTCAA
88642158 CCCAATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAAATTAATTTTCTCAA
Found at i:88647322 original size:40 final size:40
Alignment explanation
Indices: 88647274--88647580 Score: 542
Period size: 40 Copynumber: 7.7 Consensus size: 40
88647264 ACAAACACAT
* *
88647274 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
88647314 TTGCCTTCGGGTCCTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
** *
88647354 TTGCCTTCGGGTCACAGCCCGGATATATCAACTCGCATAG
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
88647394 TTGCCTTCGGGTCTTAGCCCGGATACATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
88647434 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
88647474 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
88647514 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
88647554 TTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
88647581 ATCCAATGCT
Statistics
Matches: 254, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 254 1.00
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.29
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:88652320 original size:34 final size:34
Alignment explanation
Indices: 88652281--88652368 Score: 101
Period size: 33 Copynumber: 2.6 Consensus size: 34
88652271 TGTGGCCTGC
* *
88652281 CCGTGTGGGCCCACACGGTCC-AAATTAGCCTTGG
1 CCGTGTGGGACCACAAGG-CCTAAATTAGCCTTGG
*
88652315 CCGTGT-GGATCACAAGGCCTAAATTAGCCTTGG
1 CCGTGTGGGACCACAAGGCCTAAATTAGCCTTGG
* *
88652348 CCGTGT-GGATCACACGGCCTA
1 CCGTGTGGGACCACAAGGCCTA
88652369 GCCCAGAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
32 2 0.04
33 41 0.84
34 6 0.12
ACGTcount: A:0.20, C:0.30, G:0.28, T:0.22
Consensus pattern (34 bp):
CCGTGTGGGACCACAAGGCCTAAATTAGCCTTGG
Found at i:88652342 original size:33 final size:33
Alignment explanation
Indices: 88652302--88652368 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
88652292 CACACGGTCC
88652302 AAATTAGCCTTGGCCGTGTGGATCACAAGGCCT
1 AAATTAGCCTTGGCCGTGTGGATCACAAGGCCT
*
88652335 AAATTAGCCTTGGCCGTGTGGATCACACGGCCT
1 AAATTAGCCTTGGCCGTGTGGATCACAAGGCCT
88652368 A
1 A
88652369 GCCCAGAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (33 bp):
AAATTAGCCTTGGCCGTGTGGATCACAAGGCCT
Found at i:88659493 original size:11 final size:11
Alignment explanation
Indices: 88659477--88659536 Score: 86
Period size: 11 Copynumber: 5.5 Consensus size: 11
88659467 TTGTTTGACT
88659477 ATGATTCGACA
1 ATGATTCGACA
88659488 ATGATTCGACA
1 ATGATTCGACA
88659499 ATGATTCGACA
1 ATGATTCGACA
* *
88659510 GTGATTTGA-A
1 ATGATTCGACA
*
88659520 ATGATTCGACT
1 ATGATTCGACA
88659531 ATGATT
1 ATGATT
88659537 TGGTATTGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
10 8 0.19
11 35 0.81
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (11 bp):
ATGATTCGACA
Found at i:88659524 original size:21 final size:21
Alignment explanation
Indices: 88659470--88659538 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 21
88659460 CACAAACTTG
*
88659470 TTTGACTATGATTCGACAATGA
1 TTTGACAATGATTCGAC-ATGA
*
88659492 TTCGACAATGATTCGACAGTGA
1 TTTGACAATGATTCGACA-TGA
88659514 TTTGA-AATGATTCGACTATGA
1 TTTGACAATGATTCGAC-ATGA
88659535 TTTG
1 TTTG
88659539 GTATTGGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 19 0.45
22 23 0.55
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.36
Consensus pattern (21 bp):
TTTGACAATGATTCGACATGA
Found at i:88662076 original size:43 final size:42
Alignment explanation
Indices: 88662029--88662119 Score: 101
Period size: 43 Copynumber: 2.1 Consensus size: 42
88662019 TTTTGGACAT
* ** * * *
88662029 TGGCATCGTTATATGATTTCGTATAAGACCCTTTCTGGGATGA
1 TGGCATCGATATATGATAACATATAAGACCATATCTGGGAT-A
* *
88662072 TGGCATCGATATGTGATAACATGTAAGACCATATCTGGGATA
1 TGGCATCGATATATGATAACATATAAGACCATATCTGGGATA
88662114 TGGCAT
1 TGGCAT
88662120 TGTGCGAGCT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 7 0.17
43 33 0.82
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (42 bp):
TGGCATCGATATATGATAACATATAAGACCATATCTGGGATA
Found at i:88670112 original size:21 final size:21
Alignment explanation
Indices: 88670088--88670141 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
88670078 TGGTCATAGA
88670088 GAGAATTGAGGAGGG-ATATTG
1 GAGAATTGAGGAGGGAATA-TG
*
88670109 GAGAGA-TGAGGAGAGAATATG
1 GAGA-ATTGAGGAGGGAATATG
88670130 G-G-ATTGAGGAGG
1 GAGAATTGAGGAGG
88670142 TTGTTGTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 1 0.04
19 7 0.25
20 1 0.04
21 15 0.54
22 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.46, T:0.19
Consensus pattern (21 bp):
GAGAATTGAGGAGGGAATATG
Found at i:88670811 original size:26 final size:27
Alignment explanation
Indices: 88670700--88670995 Score: 216
Period size: 26 Copynumber: 11.5 Consensus size: 27
88670690 GTTATGACCA
** *
88670700 AAATACCTTCATAGGGTAAAATGATC-
1 AAATACCCCCATAGGGTAGAATGATCG
* *
88670726 AAATACCCCCCATA-AGTAGAA--ACCG
1 AAATA-CCCCCATAGGGTAGAATGATCG
** * * * *
88670751 AAATACCCTTA-AAGGAAGAATG-CCA
1 AAATACCCCCATAGGGTAGAATGATCG
*
88670776 AAATACCCCCGTA-GGTAGAATGATCG
1 AAATACCCCCATAGGGTAGAATGATCG
*
88670802 AAATAACCCCCATA-GG-AAAATGA-CTG
1 AAAT-ACCCCCATAGGGTAGAATGATC-G
* * *
88670828 AAATA-CCTCATAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAGAATGATCG
* *
88670854 AAATACCCTCATA-GGTAAAATGATCG
1 AAATACCCCCATAGGGTAGAATGATCG
*
88670880 AAATA-CCCCATAGGGTA-AA-AAT-G
1 AAATACCCCCATAGGGTAGAATGATCG
88670903 ---TACCCCCATAGGGTTAGAATGATCG
1 AAATACCCCCATAGGG-TAGAATGATCG
* **
88670928 AAATACCCCCATAGAGTAGAATGGCCG
1 AAATACCCCCATAGGGTAGAATGATCG
88670955 AAATACCCCCATAGGGTAGAATGATCG
1 AAATACCCCCATAGGGTAGAATGATCG
88670982 AAGATACCCCCATA
1 AA-ATACCCCCATA
88670996 TATGGTAAAT
Statistics
Matches: 218, Mismatches: 29, Indels: 44
0.75 0.10 0.15
Matches are distributed among these distances:
20 2 0.01
21 10 0.05
22 2 0.01
23 4 0.02
24 21 0.10
25 36 0.17
26 61 0.28
27 59 0.27
28 23 0.11
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.19
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAGAATGATCG
Found at i:88670964 original size:28 final size:27
Alignment explanation
Indices: 88670903--88670995 Score: 141
Period size: 27 Copynumber: 3.4 Consensus size: 27
88670893 GGTAAAAATG
88670903 TACCCCCATAGGGTTAGAATGATCGAAA
1 TACCCCCATAGGG-TAGAATGATCGAAA
* **
88670931 TACCCCCATAGAGTAGAATGGCCGAAA
1 TACCCCCATAGGGTAGAATGATCGAAA
88670958 TACCCCCATAGGGTAGAATGATCGAAGA
1 TACCCCCATAGGGTAGAATGATCGAA-A
88670986 TACCCCCATA
1 TACCCCCATA
88670996 TATGGTAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 35 0.60
28 23 0.40
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.18
Consensus pattern (27 bp):
TACCCCCATAGGGTAGAATGATCGAAA
Found at i:88678008 original size:14 final size:16
Alignment explanation
Indices: 88677991--88678033 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
88677981 ATAAATTTTA
88677991 TATTTATAT-TT-AAT
1 TATTTATATATTAAAT
88678005 TATTTAATATATTAAAT
1 TATTT-ATATATTAAAT
*
88678022 TATTAATATATT
1 TATTTATATATT
88678034 CATACTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 5 0.20
15 4 0.16
16 9 0.36
17 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTATATATTAAAT
Found at i:88678019 original size:16 final size:17
Alignment explanation
Indices: 88677995--88678033 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
88677985 ATTTTATATT
*
88677995 TATATTTAATTATTTAA
1 TATATTAAATTATTTAA
88678012 TATATTAAATTA-TTAA
1 TATATTAAATTATTTAA
88678028 TATATT
1 TATATT
88678034 CATACTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTAAATTATTTAA
Found at i:88678678 original size:161 final size:163
Alignment explanation
Indices: 88678394--88678699 Score: 437
Period size: 162 Copynumber: 1.9 Consensus size: 163
88678384 CTCCAACTCT
* * * **
88678394 CTCTCAATTCTCTCTTTATCTCACTCATTCTCTCAGTTCATCTTATTTTTTATTAAACATTTCTT
1 CTCTCAATTCTCTCTTAATCTCACTAATTCTCTCAATTCATCACATTTTTTATTAAACATTTCTT
**
88678459 AAGGTTTTTTTTAATTAATTTTTGTATTATGATTTTTATTCATATTTATTGAAATTCTTAATGG-
66 AAGGTTTTTTTTAATTAATTTTTGTATTACAATTTTTATTCATATTTATTGAAATTCTTAATGGA
88678523 AAATTCTCTTATTCGCTTCTCTCTCTCAATTTA
131 AAATTCTCTTATTCGCTTCTCTCTCTCAATTTA
88678556 CTCTC-ATT-TCTCTTAATTCTCACTTAATTCTCTCAATTCACTCACATTTTTTATTAAA-ATTG
1 CTCTCAATTCTCTCTTAA-TCTCAC-TAATTCTCTCAATTCA-TCACATTTTTTATTAAACATT-
* *
88678618 TTTTAA-GTTTTTTTTAATTAA-TTTT-TATTACAATTTTTATTCGTATTTTATTGAAATTCTTA
62 TCTTAAGGTTTTTTTTAATTAATTTTTGTATTACAATTTTTATTCATA-TTTATTGAAATTCTTA
88678680 ATGGAAAATTCTCTTATTCG
126 ATGGAAAATTCTCTTATTCG
88678700 TTTATATGGA
Statistics
Matches: 129, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
160 24 0.19
161 33 0.26
162 52 0.40
163 20 0.16
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.54
Consensus pattern (163 bp):
CTCTCAATTCTCTCTTAATCTCACTAATTCTCTCAATTCATCACATTTTTTATTAAACATTTCTT
AAGGTTTTTTTTAATTAATTTTTGTATTACAATTTTTATTCATATTTATTGAAATTCTTAATGGA
AAATTCTCTTATTCGCTTCTCTCTCTCAATTTA
Found at i:88695748 original size:18 final size:18
Alignment explanation
Indices: 88695715--88695771 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
88695705 TTTACACAAG
88695715 TAATTTTAATATTTCAAAA
1 TAATTTTAA-ATTTCAAAA
88695734 TAATTTTAAATTTCAAAA
1 TAATTTTAAATTTCAAAA
88695752 T-ATTTATAAAATTTCAAAA
1 TAATTT-T-AAATTTCAAAA
88695771 T
1 T
88695772 TTATATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.11
18 11 0.31
19 21 0.58
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATTTTAAATTTCAAAA
Found at i:88695814 original size:21 final size:22
Alignment explanation
Indices: 88695782--88695827 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
88695772 TTATATTTTT
88695782 AAAAAATATAAA-AAT-TATAA
1 AAAAAATATAAAGAATATATAA
*
88695802 AAAAAATCCTAAAGAATATATAA
1 AAAAAAT-ATAAAGAATATATAA
88695825 AAA
1 AAA
88695828 GTTAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 3 0.14
23 8 0.36
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (22 bp):
AAAAAATATAAAGAATATATAA
Found at i:88695866 original size:12 final size:11
Alignment explanation
Indices: 88695838--88695872 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
88695828 GTTAAAAATT
*
88695838 AAAACCGTAAA
1 AAAACCTTAAA
88695849 AAAACCTTAAA
1 AAAACCTTAAA
88695860 CAAAACCTTAAA
1 -AAAACCTTAAA
88695872 A
1 A
88695873 CTCTAAACCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.63, C:0.20, G:0.03, T:0.14
Consensus pattern (11 bp):
AAAACCTTAAA
Found at i:88699497 original size:13 final size:13
Alignment explanation
Indices: 88699479--88699538 Score: 70
Period size: 13 Copynumber: 4.7 Consensus size: 13
88699469 TTTTCATTGT
88699479 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
88699492 TTTTGAAAAGTG-
1 TTTTGAAAAGTGC
* *
88699504 TTGTGGAAAAATGC
1 TT-TTGAAAAGTGC
*
88699518 TTTTGAGAAGTGC
1 TTTTGAAAAGTGC
88699531 -TTTGAAAA
1 TTTTGAAAA
88699539 AATTTAAGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
12 9 0.23
13 28 0.72
14 2 0.05
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:88703209 original size:46 final size:46
Alignment explanation
Indices: 88703038--88703209 Score: 238
Period size: 46 Copynumber: 3.7 Consensus size: 46
88703028 TGCCATAATG
* * * *
88703038 TCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTA
* *** *
88703084 TCTTTCAACCATAGTCTTGTTCATTTCATATCACGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
*
88703130 TCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
88703176 TCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TCTTTCAACCATGGTCTTACACATTTCATATCAG
88703210 AGAGCATACT
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 4 0.04
46 109 0.96
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.40
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
Found at i:88704073 original size:33 final size:34
Alignment explanation
Indices: 88704036--88704100 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
88704026 ATCTTGAACT
* *
88704036 AAAATAAT-AATTTCATTCAATTTTGTAATTTAA
1 AAAATAATCAATTTCATACAATTTGGTAATTTAA
*
88704069 AAAATAATCCATTTCATACAATTTGGTAATTT
1 AAAATAATCAATTTCATACAATTTGGTAATTT
88704101 CTGACATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 8 0.29
34 20 0.71
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (34 bp):
AAAATAATCAATTTCATACAATTTGGTAATTTAA
Found at i:88704398 original size:77 final size:77
Alignment explanation
Indices: 88704271--88704416 Score: 292
Period size: 77 Copynumber: 1.9 Consensus size: 77
88704261 AACATTATCT
88704271 ATTATCTCCTTGTACAGAATTCGAATGATGTTCATATTTGTTTCTGTTGAAAATAGACTCATTCA
1 ATTATCTCCTTGTACAGAATTCGAATGATGTTCATATTTGTTTCTGTTGAAAATAGACTCATTCA
88704336 AGATAAAAATTA
66 AGATAAAAATTA
88704348 ATTATCTCCTTGTACAGAATTCGAATGATGTTCATATTTGTTTCTGTTGAAAATAGACTCATTCA
1 ATTATCTCCTTGTACAGAATTCGAATGATGTTCATATTTGTTTCTGTTGAAAATAGACTCATTCA
88704413 AGAT
66 AGAT
88704417 TCTAAACATA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 69 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (77 bp):
ATTATCTCCTTGTACAGAATTCGAATGATGTTCATATTTGTTTCTGTTGAAAATAGACTCATTCA
AGATAAAAATTA
Found at i:88705906 original size:24 final size:26
Alignment explanation
Indices: 88705878--88705930 Score: 76
Period size: 24 Copynumber: 2.1 Consensus size: 26
88705868 TAAAATTAGT
88705878 AAATTGA-CCCACAACAAAT-TT-TAA
1 AAATTGATCCCACAA-AAATATTATAA
88705902 AAATTGATCCCACAAAAATATTATAA
1 AAATTGATCCCACAAAAATATTATAA
88705928 AAA
1 AAA
88705931 AAACTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 11 0.42
25 9 0.35
26 6 0.23
ACGTcount: A:0.55, C:0.17, G:0.04, T:0.25
Consensus pattern (26 bp):
AAATTGATCCCACAAAAATATTATAA
Found at i:88707143 original size:30 final size:30
Alignment explanation
Indices: 88707086--88707143 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
88707076 TATGAAAAAT
* *
88707086 TAAATATTAAATTTTTAGTATAGAATTTGG
1 TAAATATTAAATTTATAGTATAAAATTTGG
*
88707116 TAAATA-TAAATTTATATTATATAAATTT
1 TAAATATTAAATTTATAGTATA-AAATTT
88707144 TTGGTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (30 bp):
TAAATATTAAATTTATAGTATAAAATTTGG
Found at i:88707153 original size:20 final size:21
Alignment explanation
Indices: 88707128--88707167 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
88707118 AATATAAATT
88707128 TATATTA-TATAAATT-TTTGG
1 TATATTAGTA-AAATTATTTGG
88707148 TATATTAGTAAAATTATTTG
1 TATATTAGTAAAATTATTTG
88707168 ATAACAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (21 bp):
TATATTAGTAAAATTATTTGG
Found at i:88708153 original size:22 final size:23
Alignment explanation
Indices: 88708116--88708158 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
88708106 AGAAAATTAG
* *
88708116 TTAAATTTTAATTCTA-TTATAT
1 TTAAATTTGAAATCTAGTTATAT
88708138 TTAAATTTGAAATCTAGTTAT
1 TTAAATTTGAAATCTAGTTAT
88708159 TATACTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (23 bp):
TTAAATTTGAAATCTAGTTATAT
Found at i:88709576 original size:13 final size:13
Alignment explanation
Indices: 88709558--88709585 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
88709548 TTTATTCCAC
88709558 TGGAATCTTGATT
1 TGGAATCTTGATT
88709571 TGGAATCTTGATT
1 TGGAATCTTGATT
88709584 TG
1 TG
88709586 TTATGTCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.46
Consensus pattern (13 bp):
TGGAATCTTGATT
Found at i:88711577 original size:40 final size:40
Alignment explanation
Indices: 88711537--88711689 Score: 233
Period size: 39 Copynumber: 3.9 Consensus size: 40
88711527 GATTCCACTC
* *
88711537 CCCCCATGCTACTTTG-TTTTATTATTAATTAAAACTACT
1 CCCCCATACTATTTTGTTTTTATTATTAATTAAAACTACT
88711576 CCCCCATACTATTTTG-TTTTATTATTAATTAAAACTA-T
1 CCCCCATACTATTTTGTTTTTATTATTAATTAAAACTACT
* *
88711614 TCCCCATACTATTTTGTTTTTATTATTAATTAAAA-TCATT
1 CCCCCATACTATTTTGTTTTTATTATTAATTAAAACT-ACT
88711654 CCCCCATACTATTTTGTTTTTATTATTAATTAAAAC
1 CCCCCATACTATTTTGTTTTTATTATTAATTAAAAC
88711690 CATACTTTAT
Statistics
Matches: 106, Mismatches: 4, Indels: 6
0.91 0.03 0.05
Matches are distributed among these distances:
38 17 0.16
39 54 0.51
40 35 0.33
ACGTcount: A:0.30, C:0.19, G:0.03, T:0.48
Consensus pattern (40 bp):
CCCCCATACTATTTTGTTTTTATTATTAATTAAAACTACT
Found at i:88712344 original size:22 final size:23
Alignment explanation
Indices: 88712296--88712361 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 23
88712286 AACCCCCTCT
88712296 AATACAATCTG-TTCTCTCCCCAA
1 AATACAATC-GATTCTCTCCCCAA
*
88712319 AATACAATCGATTCT-TCCTCAA
1 AATACAATCGATTCTCTCCCCAA
* * *
88712341 AATACCATCGATCCCCTCCCC
1 AATACAATCGATTCTCTCCCC
88712362 CCTTTACAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 19 0.53
23 17 0.47
ACGTcount: A:0.30, C:0.38, G:0.05, T:0.27
Consensus pattern (23 bp):
AATACAATCGATTCTCTCCCCAA
Found at i:88712871 original size:44 final size:44
Alignment explanation
Indices: 88712817--88713152 Score: 240
Period size: 44 Copynumber: 7.6 Consensus size: 44
88712807 TTCTTCGATC
* *
88712817 TGTTCCCTATAAACACAGGGATGCCAAAGCTGCTATCTTCAACT
1 TGTTCCCTATAAGCACAGGGATGCCAAATCTGCTATCTTCAACT
* * * *
88712861 TGTTCCCTATAAACACAGGGATGCC--ATGCTGAAATAT-TTGATC-
1 TGTTCCCTATAAGCACAGGGATGCCAAAT-CTG--CTATCTTCAACT
* * * * * *
88712904 TGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGA-T
1 TG-TTCCCTATAAGCACAGGGATGCCAAATCTGCTATCTTCAACT
* * *
88712948 CTGTTCCCTATAAGCACAGGGATGCCAAATTTGCTGTTTTTCAACT
1 -TGTTCCCTATAAGCACAGGGATGCCAAATCTGCT-ATCTTCAACT
** *
88712994 TGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTCGA-T
1 TGTTCCCTATAAGCACAGGGATGCCAAAT-CTGCTATCTTCAACT
** * * * ** * *
88713036 CTGCTTTACTGTGAGCACAGGAATGTTAGATCTGCTATCTTCGA-T
1 -TG-TTCCCTATAAGCACAGGGATGCCAAATCTGCTATCTTCAACT
* * *
88713081 CTGTTCCCTATAAGCACAGGGATGCCAAATCTGTTGTTTTTCAACT
1 -TGTTCCCTATAAGCACAGGGATGCCAAATCTGCT-ATCTTCAACT
88713127 TGTTCCCTATAAGCACAGGGATGCCA
1 TGTTCCCTATAAGCACAGGGATGCCA
88713153 TGCTGAAATC
Statistics
Matches: 225, Mismatches: 49, Indels: 35
0.73 0.16 0.11
Matches are distributed among these distances:
42 2 0.01
43 17 0.08
44 116 0.52
45 84 0.37
46 6 0.03
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (44 bp):
TGTTCCCTATAAGCACAGGGATGCCAAATCTGCTATCTTCAACT
Found at i:88713047 original size:133 final size:133
Alignment explanation
Indices: 88712808--88713208 Score: 637
Period size: 133 Copynumber: 3.0 Consensus size: 133
88712798 AGTTTTGAGT
* * * *
88712808 TCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAAGCTGCT-ATCTTCAACTTGTTCCCTATA
1 TCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTTCAACTTGTTCCCTATA
* * *
88712872 AACACAGGGATGCCATGCTGAAATATTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTG
66 AGCACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTG
88712937 CTA
131 CTA
*
88712940 TCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAAATTTGCTGTTTTTCAACTTGTTCCCTATA
1 TCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTTCAACTTGTTCCCTATA
* * *
88713005 AGCACAGGGATGCCATGCTGAAATCTTCGATCTGCTTTACTGTGAGCACAGGAATGTTAGATCTG
66 AGCACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTG
88713070 CTA
131 CTA
*
88713073 TCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAAATCTGTTGTTTTTCAACTTGTTCCCTATA
1 TCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTTCAACTTGTTCCCTATA
* * *
88713138 AGCACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAA-CTCAGGAA-GGCGATATCT
66 AGCACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTC-AGATCT
88713201 GCTA
130 GCTA
88713205 TCTT
1 TCTT
88713209 TGATATGCCC
Statistics
Matches: 248, Mismatches: 19, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
131 1 0.00
132 60 0.24
133 187 0.75
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (133 bp):
TCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTTCAACTTGTTCCCTATA
AGCACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTG
CTA
Found at i:88713164 original size:88 final size:87
Alignment explanation
Indices: 88712808--88713171 Score: 294
Period size: 88 Copynumber: 4.1 Consensus size: 87
88712798 AGTTTTGAGT
* *
88712808 TCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAAGCTGCTATCTTCAA-CTTGTTCCCTATA
1 TCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTATCTTCAATC-TGTTCCCTATA
*
88712872 AACACAGGGATGCCATGCTGAAA
65 AGCACAGGGATGCCATGCTGAAA
* * * * * * * *
88712895 TATTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATCTGTTCCCTATA
1 TCTTCGATCTG-TTCCCTATAAGCACAGGGATGCCAAATCTGCTATCTTCAATCTGTTCCCTATA
*
88712960 AGCACAGGGATGCCAAATTTGCTG--T
65 AGCACAGGGATGCC--A--TGCTGAAA
* * ** * ** *
88712985 TTTTC-AACTTGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTCGATCTGCTTTACTG
1 TCTTCGATC-TGTTCCCTATAAGCACAGGGATGCCAAAT-CTGCTATCTTCAATCTG-TTCCCTA
* * ** **
88713047 TGAGCACAGGAATGTTA-GATCTGCTA
63 TAAGCACAGGGATGCCATG--CTGAAA
* * *
88713073 TCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAAATCTGTTGTTTTTCAA-CTTGTTCCCTAT
1 TCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAAATCTGCT-ATCTTCAATC-TGTTCCCTAT
88713137 AAGCACAGGGATGCCATGCTGAAA
64 AAGCACAGGGATGCCATGCTGAAA
88713161 TCTTCGATCTG
1 TCTTCGATCTG
88713172 CTTCACTGTA
Statistics
Matches: 213, Mismatches: 45, Indels: 37
0.72 0.15 0.13
Matches are distributed among these distances:
84 1 0.00
86 3 0.01
87 12 0.06
88 115 0.54
89 61 0.29
90 16 0.08
92 5 0.02
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (87 bp):
TCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTATCTTCAATCTGTTCCCTATAA
GCACAGGGATGCCATGCTGAAA
Found at i:88713631 original size:205 final size:203
Alignment explanation
Indices: 88713250--88714029 Score: 1215
Period size: 205 Copynumber: 3.8 Consensus size: 203
88713240 AAATCTATTT
* * * * * * *
88713250 CTTCGATTTGTTCCCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTTAACGTAAGCAC
1 CTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAATCAC
* * * * *
88713315 GTGAAAACCAAATCAACTATG-ATTCGATTTGCTCCTTGTAAGCATAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
* * *
88713379 GGATCCGCTTCAGCATAAACATCCGAAGGTGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
131 GGATCTGCTTCAG--TAAACATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
88713444 AGATGCCAAA
194 AGATGCCAAA
* *
88713454 CTTCGATTTGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTC-TCGTAATCA
1 CTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGC-TTCATCGTAATCA
88713518 CGTGAAAGCCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCT
65 CGTGAAAGCCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCT
88713583 TGGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTG
130 TGGATCTGCTTCAGT-AAA-CATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTG
88713648 AAGATGCCAAA
193 AAGATGCCAAA
* * *
88713659 CTTCGATTCATTCTCTGACGATACAGAGACGATAAATCATCTTAGATTTGCTTCATCGTAATCAC
1 CTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAATCAC
*
88713724 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
* * *
88713789 GGATCTGCTTTAGTGAAATCATCTGAAGGTGAGATCTGCTATGCGTCTGCTCTCCATCAAAGTGA
131 GGATCTGCTTCAGT-AAA-CATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
88713854 AGATGCCAAA
194 AGATGCCAAA
88713864 CTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAATCAC
1 CTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAATCAC
*
88713929 GTGAAAGCCAAATCAGCTATGTCTTCGATTT-TCTCCTTGTAAACACAAGGATGCCAAACCATCT
66 GTGAAAGCCAAATCAACTATGTCTTCGATTTGT-TCCTTGTAAACACAAGGATGCCAAACCATCT
* *
88713993 TGGATCTACTTCAGTATAACATCTGAAGGCCAGATCT
130 TGGATCTGCTTCAGTA-AACATCTGAAGGCGAGATCT
88714030 ATTATGCTGC
Statistics
Matches: 540, Mismatches: 29, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
203 1 0.00
204 99 0.18
205 440 0.81
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (203 bp):
CTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAATCAC
GTGAAAGCCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
GGATCTGCTTCAGTAAACATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGAAG
ATGCCAAA
Found at i:88722039 original size:15 final size:14
Alignment explanation
Indices: 88721997--88722046 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
88721987 ATAACTTTGA
*
88721997 ATGCAAATGATGTG
1 ATGCAAATGATGAG
88722011 ATG-AAATGTTATGAG
1 ATGCAAATG--ATGAG
88722026 ATGCAAATGCATGA-
1 ATGCAAATG-ATGAG
88722040 ATGCAAA
1 ATGCAAA
88722047 AAGAATATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.32
15 11 0.35
16 5 0.16
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (14 bp):
ATGCAAATGATGAG
Found at i:88725950 original size:27 final size:26
Alignment explanation
Indices: 88725877--88726034 Score: 97
Period size: 26 Copynumber: 6.0 Consensus size: 26
88725867 GAAAAAAGTC
*
88725877 TAAAATAAATAATATATAT-ATAATAT
1 TAAAATAAAAAATATATATAATAAT-T
* * * *
88725903 TAAAGTGAATAATATACATAATAATT
1 TAAAATAAAAAATATATATAATAATT
*
88725929 TAAAATACAAAAATGTATATAA-AAGTT
1 TAAAATA-AAAAATATATATAATAA-TT
* * *
88725956 TCAAAATAAACAATATGTATAATAGTT
1 T-AAAATAAAAAATATATATAATAATT
* * * * *
88725983 TAAAAGAAATAACATATGTAA-AATA
1 TAAAATAAAAAATATATATAATAATT
* *
88726008 AAATAATATAAAATATATGATAATAAT
1 TAA-AATAAAAAATATAT-ATAATAAT
88726035 AATGGTAATA
Statistics
Matches: 99, Mismatches: 25, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
25 4 0.04
26 49 0.49
27 36 0.36
28 10 0.10
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (26 bp):
TAAAATAAAAAATATATATAATAATT
Found at i:88726070 original size:20 final size:20
Alignment explanation
Indices: 88726047--88726095 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
88726037 TGGTAATAAT
88726047 AATATAAATAAATACAAAA-A
1 AATATAAATAAA-ACAAAACA
* *
88726067 AATATACAATATAACAAAACC
1 AATATA-AATAAAACAAAACA
88726088 AATATAAA
1 AATATAAA
88726096 GTTACCTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.20
Consensus pattern (20 bp):
AATATAAATAAAACAAAACA
Found at i:88727196 original size:20 final size:21
Alignment explanation
Indices: 88727155--88727196 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
88727145 CTTCGAGAAG
*
88727155 AGAAAAAAAAGAAAATACAAA
1 AGAAAAAAAAGAAAATAAAAA
*
88727176 AGAAAAAAAA-TAAATAAAAA
1 AGAAAAAAAAGAAAATAAAAA
88727196 A
1 A
88727197 TCAAAAGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.83, C:0.02, G:0.07, T:0.07
Consensus pattern (21 bp):
AGAAAAAAAAGAAAATAAAAA
Found at i:88729710 original size:15 final size:15
Alignment explanation
Indices: 88729676--88729718 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
88729666 GGTTCACAAG
**
88729676 TAGGGTTCACACATA
1 TAGGGTTCACATGTA
*
88729691 CAGGGTTCACATGTA
1 TAGGGTTCACATGTA
*
88729706 TAGGGTTCGCATG
1 TAGGGTTCACATG
88729719 CTAATTCATG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (15 bp):
TAGGGTTCACATGTA
Found at i:88731751 original size:21 final size:21
Alignment explanation
Indices: 88731721--88731764 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
88731711 TTTTCTAAAG
* *
88731721 GTATGTATTGGATTGAATTGA
1 GTATGAATTGGATTAAATTGA
*
88731742 GTATGAATTGTATTAAATTGA
1 GTATGAATTGGATTAAATTGA
88731763 GT
1 GT
88731765 TAAATTCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.43
Consensus pattern (21 bp):
GTATGAATTGGATTAAATTGA
Found at i:88732129 original size:25 final size:25
Alignment explanation
Indices: 88732101--88732327 Score: 168
Period size: 25 Copynumber: 9.2 Consensus size: 25
88732091 CTTCCGAGTG
88732101 TCCCGATAATTGGCTCTCATGAGCT
1 TCCCGATAATTGGCTCTCATGAGCT
* *
88732126 TCCCG-TTATATGGCTCTCACGAGCT
1 TCCCGATAAT-TGGCTCTCATGAGCT
* * *
88732151 TCCTGATTAA-TGGCT-TCTTGAGAT
1 TCCCGA-TAATTGGCTCTCATGAGCT
* * *
88732175 TTCCGTTTA-TGGCTCGT-ATGAGCT
1 TCCCGATAATTGGCTC-TCATGAGCT
*
88732199 TCTCGATAATTGGCTCTCCA-GAGCT
1 TCCCGATAATTGGCTCT-CATGAGCT
* *
88732224 TTCCAATAATTGGCTCTCCA-GAGCT
1 TCCCGATAATTGGCTCT-CATGAGCT
*
88732249 TTCCGATAATTGGCTCTCATGAGCT
1 TCCCGATAATTGGCTCTCATGAGCT
** **
88732274 TCTTGATTAA-TGGCTCTCCGGAGC-
1 TCCCGA-TAATTGGCTCTCATGAGCT
*
88732298 TCCTCGAT-ATTGGCTCGCATGAGCT
1 TCC-CGATAATTGGCTCTCATGAGCT
88732323 TCCCG
1 TCCCG
88732328 TTTATGACTT
Statistics
Matches: 158, Mismatches: 31, Indels: 27
0.73 0.14 0.12
Matches are distributed among these distances:
23 8 0.05
24 41 0.26
25 103 0.65
26 4 0.03
27 2 0.01
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.34
Consensus pattern (25 bp):
TCCCGATAATTGGCTCTCATGAGCT
Found at i:88733833 original size:39 final size:39
Alignment explanation
Indices: 88733790--88734006 Score: 317
Period size: 39 Copynumber: 5.5 Consensus size: 39
88733780 CTTCGGAACT
* * ** * * *
88733790 TTAAGCCCGGATATATTTCCAGCACGTAACTTGCGAACC
1 TTAAGTCCGGATATAATTCCAGCATATAGCCTGCGGACC
*
88733829 TTAAGTCTGGATTATAATTCCAGCATATAGCCTGCGGACC
1 TTAAGTCCGGA-TATAATTCCAGCATATAGCCTGCGGACC
* *
88733869 TTAAGTCCGAATATATTTCCAGCATATAGCCTGCGGACC
1 TTAAGTCCGGATATAATTCCAGCATATAGCCTGCGGACC
*
88733908 TTAAGTCCGGATATAATTCCAGTATATAGCCTGCGGACC
1 TTAAGTCCGGATATAATTCCAGCATATAGCCTGCGGACC
*
88733947 TTAAGTCCGGATATATTTCCAGCATATAGCCTGCGGACC
1 TTAAGTCCGGATATAATTCCAGCATATAGCCTGCGGACC
88733986 TTAAGTCCGGATATAATTCCA
1 TTAAGTCCGGATATAATTCCA
88734007 AATATCATAT
Statistics
Matches: 160, Mismatches: 17, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
39 129 0.81
40 31 0.19
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (39 bp):
TTAAGTCCGGATATAATTCCAGCATATAGCCTGCGGACC
Found at i:88738970 original size:17 final size:18
Alignment explanation
Indices: 88738938--88739052 Score: 146
Period size: 17 Copynumber: 6.5 Consensus size: 18
88738928 AACCATATCT
*
88738938 TCTAAGATTGTATATCATA
1 TCTAAGATTG-CTATCATA
*
88738957 TTTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
* *
88738974 TCTAAAATTGCAATCATA
1 TCTAAGATTGCTATCATA
88738992 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
88739009 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
*
88739027 TTTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
88739044 TCTAAGATT
1 TCTAAGATT
88739053 ACATATCATT
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
17 45 0.54
18 30 0.36
19 9 0.11
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.41
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:88739049 original size:35 final size:36
Alignment explanation
Indices: 88738938--88739061 Score: 198
Period size: 35 Copynumber: 3.5 Consensus size: 36
88738928 AACCATATCT
*
88738938 TCTAAGATTGTATATCATATTTAAGATTGTATCATA
1 TCTAAGATTGCATATCATATTTAAGATTGTATCATA
* *
88738974 TCTAAAATTGCA-ATCATATCTAAGATTGTATCATA
1 TCTAAGATTGCATATCATATTTAAGATTGTATCATA
88739009 TCTAAGATTGCA-ATCATATTTAAGATTGTATCATA
1 TCTAAGATTGCATATCATATTTAAGATTGTATCATA
*
88739044 TCTAAGATTACATATCAT
1 TCTAAGATTGCATATCAT
88739062 TGAAGATTAT
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
35 66 0.81
36 15 0.19
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (36 bp):
TCTAAGATTGCATATCATATTTAAGATTGTATCATA
Found at i:88739069 original size:52 final size:52
Alignment explanation
Indices: 88738938--88739052 Score: 151
Period size: 52 Copynumber: 2.2 Consensus size: 52
88738928 AACCATATCT
* *
88738938 TCTAAGATTGTATATCATATTTAAGATTGTATCATATCTAAAATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGAATCATATCTAAAATTGCAATCATA
* * *
88738992 TCTAAGATTGTATCATATCTAAGATTGCAATCATATTTAAGATTG-TATCATA
1 TCTAAGATTGTATCATATCTAAGATTG-AATCATATCTAAAATTGCAATCATA
88739044 TCTAAGATT
1 TCTAAGATT
88739053 ACATATCATT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
52 31 0.56
53 14 0.25
54 10 0.18
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.41
Consensus pattern (52 bp):
TCTAAGATTGTATCATATCTAAGATTGAATCATATCTAAAATTGCAATCATA
Found at i:88749541 original size:3 final size:3
Alignment explanation
Indices: 88749535--88749571 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
88749525 TGCTGCCATG
88749535 GAA GAA G-A GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
88749572 GGGCGGCGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:88749829 original size:11 final size:11
Alignment explanation
Indices: 88749813--88749842 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
88749803 ATTATTGTTG
*
88749813 ATTTAATTGGA
1 ATTTAATTGAA
88749824 ATTTAATTGAA
1 ATTTAATTGAA
88749835 ATTTAATT
1 ATTTAATT
88749843 TTTAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (11 bp):
ATTTAATTGAA
Found at i:88750372 original size:27 final size:27
Alignment explanation
Indices: 88750333--88750396 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
88750323 TGCCAGCAGC
88750333 ACCCTCAACCGGTGCGGCCTATGGGGT
1 ACCCTCAACCGGTGCGGCCTATGGGGT
* *
88750360 ACCCTCCATCGGTGCGGCCTATGGGGT
1 ACCCTCAACCGGTGCGGCCTATGGGGT
88750387 ACCCTCAACC
1 ACCCTCAACC
88750397 TATATTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.16, C:0.38, G:0.28, T:0.19
Consensus pattern (27 bp):
ACCCTCAACCGGTGCGGCCTATGGGGT
Found at i:88750746 original size:25 final size:24
Alignment explanation
Indices: 88750710--88750756 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
88750700 TATCATTTAT
*
88750710 TTTCTTTTTTAAAA-AAAGAATTCA
1 TTTCTTTCTTAAAATAAA-AATTCA
88750734 TTTCATTTCTTAAAATAAAAATT
1 TTTC-TTTCTTAAAATAAAAATT
88750757 TCCAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 4 0.20
25 13 0.65
26 3 0.15
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTCTTTCTTAAAATAAAAATTCA
Found at i:88762977 original size:19 final size:18
Alignment explanation
Indices: 88762927--88762978 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
88762917 ATACCTCTAA
* *
88762927 AATAATAACAAAATTAAC
1 AATAAAAACAGAATTAAC
*
88762945 AATAAAAAGAAGAATTATAC
1 AATAAAAA-CAGAATTA-AC
*
88762965 AATAACAACAGAAT
1 AATAAAAACAGAAT
88762979 AGTAGTAACA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 7 0.26
19 11 0.41
20 9 0.33
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.19
Consensus pattern (18 bp):
AATAAAAACAGAATTAAC
Found at i:88769128 original size:14 final size:15
Alignment explanation
Indices: 88769104--88769132 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
88769094 ATATTTAATT
88769104 TTCATATAATATAAA
1 TTCATATAATATAAA
88769119 TTCA-ATAATATAAA
1 TTCATATAATATAAA
88769133 AAAAATTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
TTCATATAATATAAA
Found at i:88770200 original size:14 final size:14
Alignment explanation
Indices: 88770181--88770214 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
88770171 TATAAATATT
88770181 TATAAATTTTAAAA
1 TATAAATTTTAAAA
88770195 TATAAATTTTAAAA
1 TATAAATTTTAAAA
*
88770209 AATAAA
1 TATAAA
88770215 AATATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TATAAATTTTAAAA
Found at i:88770217 original size:16 final size:17
Alignment explanation
Indices: 88770191--88770228 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
88770181 TATAAATTTT
*
88770191 AAAATATAAAT-TTTAA
1 AAAATAAAAATATTTAA
*
88770207 AAAATAAAAATATTTAT
1 AAAATAAAAATATTTAA
88770224 AAAAT
1 AAAAT
88770229 TAAAGGGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATAAAAATATTTAA
Found at i:88776826 original size:21 final size:21
Alignment explanation
Indices: 88776800--88776840 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
88776790 AGACGAGCGA
* *
88776800 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
88776821 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
88776841 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:88786123 original size:14 final size:14
Alignment explanation
Indices: 88786089--88786140 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
88786079 AAGCTTAAAT
*
88786089 TTTAGTTAATTAAAG
1 TTTAATTAATT-AAG
*
88786104 TTTAATTAATTAAT
1 TTTAATTAATTAAG
88786118 TTTAATTAATTAAG
1 TTTAATTAATTAAG
88786132 TTTAATTAA
1 TTTAATTAA
88786141 AAGTATATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
14 24 0.71
15 10 0.29
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
TTTAATTAATTAAG
Found at i:88788305 original size:12 final size:12
Alignment explanation
Indices: 88788288--88788312 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
88788278 CATGTGGGTC
88788288 TTTTTGGCCAAT
1 TTTTTGGCCAAT
88788300 TTTTTGGCCAAT
1 TTTTTGGCCAAT
88788312 T
1 T
88788313 AAGGGCCATT
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:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (12 bp):
TTTTTGGCCAAT
Found at i:88788866 original size:5 final size:5
Alignment explanation
Indices: 88788856--88788931 Score: 55
Period size: 5 Copynumber: 15.2 Consensus size: 5
88788846 GGGGTAGAAC
* * * * * * *
88788856 ATGAT ATGAT ATGTT ATGCT GTGAT TTGAT ATGAC ATGAT ATAAT TTGAT
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT
* *
88788906 -TCGAT ATGGT ATGAT ATGAT AAGAT A
1 AT-GAT ATGAT ATGAT ATGAT ATGAT A
88788932 CATTATACGA
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
4 1 0.02
5 53 0.96
6 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (5 bp):
ATGAT
Done.