Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007751.1 Hibiscus syriacus cultivar Beakdansim tig00110017_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1434969
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 5 of 6
Found at i:1020827 original size:29 final size:29
Alignment explanation
Indices: 1020767--1020835 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 29
1020757 ATCCCGTTGT
* ** * *
1020767 ATATGAAAATAAAGTCTTTATTCCGTTGC
1 ATATGAAAATAAAGTCCTTACCCCATTAC
*
1020796 ATATGAAAATAAGGTCCTTACCCCATTAC
1 ATATGAAAATAAAGTCCTTACCCCATTAC
*
1020825 ATATGAGAATA
1 ATATGAAAATA
1020836 GGATTTTATT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (29 bp):
ATATGAAAATAAAGTCCTTACCCCATTAC
Found at i:1021581 original size:22 final size:22
Alignment explanation
Indices: 1021550--1021593 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1021540 CACCCCTATG
1021550 GTAGGAGAGCAGTGATACAGGC
1 GTAGGAGAGCAGTGATACAGGC
* * *
1021572 GTAGGGGAGCGGTGATGCAGGC
1 GTAGGAGAGCAGTGATACAGGC
1021594 CGGGGTAGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.14, G:0.48, T:0.14
Consensus pattern (22 bp):
GTAGGAGAGCAGTGATACAGGC
Found at i:1038681 original size:277 final size:277
Alignment explanation
Indices: 1038170--1038701 Score: 798
Period size: 277 Copynumber: 1.9 Consensus size: 277
1038160 ATAGTTAAAG
* *
1038170 AAATTATCTTTTCTGAACCCATGAATGCAATGATCAGTACAAAACATAAAATTAACTAGAACCAA
1 AAATTATCTATTCTGAACCCATGAATGCAATGATCAGTACAAAACACAAAATTAACTAGAACCAA
* * *
1038235 GAACTAATTTCCTGCATACACCTCCACCAACAAATTAAGCTTCAACACATCTATATTAATTGGTC
66 GAACTAATTCCCTGCATACACCTCCACCAACAAATTAAGATTCAACACATCTATATTAATTGATC
*
1038300 ATATATGCTCAAGGGGTAAAAACACTTGAACATTAAAACAAAAGCTGCACCACAGAAGCAAACAC
131 ATATATGCTCAAGGGGCAAAAACACTTGAACATTAAAACAAAAGCTGCACCACAGAAGCAAACAC
** * *
1038365 CAAGAAAAGTGCTAAGATGAACATATACAACAATTCCTTATGAAAGCTTTTCTAAACTTTTTTTC
196 CAAGAAAAGTGAGAAGATGAACACATACAACAATTCCTTATGAAAGATTTTCTAAACTTTTTTTC
1038430 ACCATTTTGAGTCAACA
261 ACCATTTTGAGTCAACA
* * *
1038447 AAATTATCATATTCTGAACCCATGAATGCAGTGATCAGTACGAGACACAAAATTAACTAGAACCA
1 AAATTATC-TATTCTGAACCCATGAATGCAATGATCAGTACAAAACACAAAATTAACTAGAACCA
* *** * *
1038512 AGAACTAATTCCCTGCATACACTTCCACCAGTGAA-TAGGATTCAACACATCTATATTATTTGAT
65 AGAACTAATTCCCTGCATACACCTCCACCAACAAATTAAGATTCAACACATCTATATTAATTGAT
* *
1038576 CATATATGCTCAAGGGGCAAAAACACTTGAATATTTAAACAAAAGCTGCACCACAGAAGCAAA-A
130 CATATATGCTCAAGGGGCAAAAACACTTGAACATTAAAACAAAAGCTGCACCACAGAAGCAAACA
* * * * *
1038640 GCCCAGAAAAGTGAGAAGATGCAGACATACGACATTTCCTTATGAAAGATTTTCTAAACTTT
195 -CCAAGAAAAGTGAGAAGATGAACACATACAACAATTCCTTATGAAAGATTTTCTAAACTTT
1038702 AAAATATTTT
Statistics
Matches: 227, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
276 1 0.00
277 145 0.64
278 81 0.36
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.26
Consensus pattern (277 bp):
AAATTATCTATTCTGAACCCATGAATGCAATGATCAGTACAAAACACAAAATTAACTAGAACCAA
GAACTAATTCCCTGCATACACCTCCACCAACAAATTAAGATTCAACACATCTATATTAATTGATC
ATATATGCTCAAGGGGCAAAAACACTTGAACATTAAAACAAAAGCTGCACCACAGAAGCAAACAC
CAAGAAAAGTGAGAAGATGAACACATACAACAATTCCTTATGAAAGATTTTCTAAACTTTTTTTC
ACCATTTTGAGTCAACA
Found at i:1045433 original size:65 final size:65
Alignment explanation
Indices: 1045329--1045594 Score: 372
Period size: 65 Copynumber: 4.1 Consensus size: 65
1045319 GATCTTTGTA
* * * * * *
1045329 GTATTCAATTATCATTCCACCTCACGCACCACAAAGGTACATGAGTCATATGACTAATATGTACT
1 GTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
* *
1045394 GTATTTAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGTGATGTGTATT
1 GTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
* * * * *
1045459 GTATTCAATTATCACTCCACCCCATGCACCACATAGATACATGAGTCGTATTAGTGATTTGTATT
1 GTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
* ** *
1045524 GTATTCAATTATCATTCCACCTTATGCACCACAAAGGTACATGAGTCATATGAATGATATGTATT
1 GTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
1045589 -TATTCA
1 GTATTCA
1045595 CTCTACATCT
Statistics
Matches: 178, Mismatches: 23, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
64 6 0.03
65 172 0.97
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (65 bp):
GTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
Found at i:1049442 original size:33 final size:35
Alignment explanation
Indices: 1049373--1049451 Score: 126
Period size: 36 Copynumber: 2.3 Consensus size: 35
1049363 AGAAGCATTC
1049373 GGCTCTTCAAGAGGCCCCCATGGATACTACCTCCAT
1 GGCTCTTCAAGAGGCCCCCATGGA-ACTACCTCCAT
1049409 GGCTCTTCAAGAGGCCCCCATGG-A-TACCTCCAT
1 GGCTCTTCAAGAGGCCCCCATGGAACTACCTCCAT
*
1049442 GTCTCTTCAA
1 GGCTCTTCAA
1049452 TAATGGCAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
33 18 0.43
34 1 0.02
36 23 0.55
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (35 bp):
GGCTCTTCAAGAGGCCCCCATGGAACTACCTCCAT
Found at i:1050808 original size:32 final size:31
Alignment explanation
Indices: 1050720--1050809 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 31
1050710 AAAAAGTAAT
* *
1050720 AATTTAATGATTATTTTATGAAAATTATATAA
1 AATTTAATGATTATTTTAT-AATATTTTATAA
* ** * *
1050752 AATTTAGTGAGCATTTCATTATATTTTGATAA
1 AATTTAATGATTATTTTATAATATTTT-ATAA
1050784 AATTTAATGATTATTTTATAATATTT
1 AATTTAATGATTATTTTATAATATTT
1050810 AAAAAAATAA
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
31 5 0.11
32 40 0.89
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (31 bp):
AATTTAATGATTATTTTATAATATTTTATAA
Found at i:1053642 original size:77 final size:77
Alignment explanation
Indices: 1053513--1053672 Score: 275
Period size: 77 Copynumber: 2.1 Consensus size: 77
1053503 TGCGCAAGCA
* * *
1053513 GTGCTTCGGGTCACAAGTGTTGCTCGTGAAGGCCACGTAATCTGTTCTTAACAGTGAGTTTCTAT
1 GTGCTCCGGGTCACAAGTGTTGCTCGTGAAGGCCACGTAATCGGTTCCTAACAGTGAGTTTCTAT
*
1053578 ATAAAACCTTAC
66 ATAAAACCATAC
*
1053590 GTGCTCCGGGTCACACGTGTTGCTCGTGAAGGCCACGTAATCGGTTCCTAACAGTGAGTTTCTAT
1 GTGCTCCGGGTCACAAGTGTTGCTCGTGAAGGCCACGTAATCGGTTCCTAACAGTGAGTTTCTAT
1053655 ATAAAACCATAC
66 ATAAAACCATAC
1053667 GTGCTC
1 GTGCTC
1053673 GTATCAAGTA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (77 bp):
GTGCTCCGGGTCACAAGTGTTGCTCGTGAAGGCCACGTAATCGGTTCCTAACAGTGAGTTTCTAT
ATAAAACCATAC
Found at i:1064033 original size:32 final size:33
Alignment explanation
Indices: 1063995--1064062 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 33
1063985 TAACTTAAGA
*
1063995 GGGGCAA-AGTATAATTAA-TCATA-AAATATGAG
1 GGGGCAAGA-TATAATTAACCCATAGAAA-ATGAG
1064027 GGGGCAAGATATAATTAACCCATAGAAAATGAG
1 GGGGCAAGATATAATTAACCCATAGAAAATGAG
1064060 GGG
1 GGG
1064063 TTAAAATCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
32 16 0.50
33 13 0.41
34 3 0.09
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (33 bp):
GGGGCAAGATATAATTAACCCATAGAAAATGAG
Found at i:1073722 original size:175 final size:176
Alignment explanation
Indices: 1073402--1073752 Score: 679
Period size: 175 Copynumber: 2.0 Consensus size: 176
1073392 TTGGTTGCAT
1073402 CGCACTCCGTAAATTTCAATTACTTATATAACTGATGCATTTTCTTTATATTTTTATTGATAATT
1 CGCACTCCGTAAATTTCAATTACTTATATAACTGATGCATTTTCTTTATATTTTTATTGATAATT
1073467 TTATTTGTATCTCTTGAAATCTTTGGGTAAAGTACACAATGATCTATAACTATAGGCACTACTTT
66 TTATTTGTATCTCTTGAAATCTTTGGGTAAAGTACACAATGATCTATAACTATAGGCACTACTTT
1073532 ATTGAGTTTTTCAACTATTAAAAGTTACAAAATGGTCTTCTGATTA
131 ATTGAGTTTTTCAACTATTAAAAGTTACAAAATGGTCTTCTGATTA
1073578 CGCACTCCGTAAATTTCAATTACTTATATAACTGATGCA-TTTCTTTATATTTTTATTGATAATT
1 CGCACTCCGTAAATTTCAATTACTTATATAACTGATGCATTTTCTTTATATTTTTATTGATAATT
1073642 TTATTTTGTATCTCTTGAAATCTTTGGGTAAAGTACA-AATGATCTATAACTATAGGCACTACTT
66 TTA-TTTGTATCTCTTGAAATCTTTGGGTAAAGTACACAATGATCTATAACTATAGGCACTACTT
1073706 TATTGAGTTTTTCAACTATTAAAAGTTACAAAATGGTCTTCTGATTA
130 TATTGAGTTTTTCAACTATTAAAAGTTACAAAATGGTCTTCTGATTA
1073753 TAGGACGTTA
Statistics
Matches: 174, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
175 102 0.59
176 72 0.41
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (176 bp):
CGCACTCCGTAAATTTCAATTACTTATATAACTGATGCATTTTCTTTATATTTTTATTGATAATT
TTATTTGTATCTCTTGAAATCTTTGGGTAAAGTACACAATGATCTATAACTATAGGCACTACTTT
ATTGAGTTTTTCAACTATTAAAAGTTACAAAATGGTCTTCTGATTA
Found at i:1075164 original size:21 final size:20
Alignment explanation
Indices: 1075121--1075164 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1075111 TTTTATTTTA
*
1075121 TAATTATATATTATTTAAAT
1 TAATTATAAATTATTTAAAT
* *
1075141 TAATTATAAACTTTTTTGAAT
1 TAATTATAAA-TTATTTAAAT
1075162 TAA
1 TAA
1075165 AAAACATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATTATAAATTATTTAAAT
Found at i:1093351 original size:16 final size:16
Alignment explanation
Indices: 1093310--1093351 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1093300 ACAAAATAAC
**
1093310 AAAAAAAAATATAAAT
1 AAAAAAAAGGATAAAT
1093326 AAAAAAAAGGATAAAT
1 AAAAAAAAGGATAAAT
*
1093342 AAAAATAAGG
1 AAAAAAAAGG
1093352 CCAAACAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (16 bp):
AAAAAAAAGGATAAAT
Found at i:1093642 original size:31 final size:31
Alignment explanation
Indices: 1093540--1093642 Score: 81
Period size: 31 Copynumber: 3.3 Consensus size: 31
1093530 AAACTACATA
* *
1093540 TTTAGCACATAAACTATTAATTTTG-TTCTG-T
1 TTTAGTACCTAAACT-TTAATTTTGTTTC-GAT
* *
1093571 TTTTGTACCTAAACTTTTTAATTTT-TTTCGAA
1 TTTAGTACCTAAAC--TTTAATTTTGTTTCGAT
*
1093603 ATTA-TACCTAAACTTTAATTTTTGTTTC-AT
1 TTTAGTACCTAAACTTTAA-TTTTGTTTCGAT
1093633 TTTAGTACCT
1 TTTAGTACCT
1093643 CTTCGTTAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
29 5 0.09
30 8 0.14
31 30 0.53
32 13 0.23
33 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (31 bp):
TTTAGTACCTAAACTTTAATTTTGTTTCGAT
Found at i:1102574 original size:20 final size:17
Alignment explanation
Indices: 1102520--1102559 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1102510 GAAGAATCTT
*
1102520 ATATAAGTATAGAAACG
1 ATATGAGTATAGAAACG
1102537 ATATGAGTATAGAAACG
1 ATATGAGTATAGAAACG
1102554 ATATGA
1 ATATGA
1102560 TCAGTAGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (17 bp):
ATATGAGTATAGAAACG
Found at i:1106432 original size:2 final size:2
Alignment explanation
Indices: 1106425--1106473 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
1106415 ATTATATCAC
1106425 AT 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 AT
1106467 AGT AT AT
1 A-T AT AT
1106474 GAGTATAAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1106478 original size:8 final size:7
Alignment explanation
Indices: 1106426--1106480 Score: 59
Period size: 6 Copynumber: 8.6 Consensus size: 7
1106416 TTATATCACA
1106426 TATATA-
1 TATATAG
1106432 TATATA-
1 TATATAG
1106438 TATATA-
1 TATATAG
1106444 TATATA-
1 TATATAG
1106450 TATATA-
1 TATATAG
1106456 TATATA-
1 TATATAG
1106462 TATATAG
1 TATATAG
1106469 TATATGAG
1 TATAT-AG
1106477 TATA
1 TATA
1106481 AACGCCATTC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
6 36 0.77
7 5 0.11
8 6 0.13
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (7 bp):
TATATAG
Found at i:1109211 original size:46 final size:46
Alignment explanation
Indices: 1109154--1109254 Score: 179
Period size: 46 Copynumber: 2.2 Consensus size: 46
1109144 AATACTTTAA
1109154 GTTTAATTTTTTGTTTCATTTTAGTATCCGTCATTAAAAGCTTTAGC
1 GTTTAA-TTTTTGTTTCATTTTAGTATCCGTCATTAAAAGCTTTAGC
1109201 GTTTAATTTTTGTTTCATTTTAGTATCCGTCATTAAAAGCTTTAGC
1 GTTTAATTTTTGTTTCATTTTAGTATCCGTCATTAAAAGCTTTAGC
1109247 -TTT-ATTTT
1 GTTTAATTTT
1109255 ATTTTAATAC
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
44 5 0.09
45 3 0.06
46 40 0.74
47 6 0.11
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (46 bp):
GTTTAATTTTTGTTTCATTTTAGTATCCGTCATTAAAAGCTTTAGC
Found at i:1111013 original size:12 final size:12
Alignment explanation
Indices: 1110996--1111020 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1110986 ACCCCTAAAT
1110996 GTAACAATGGCA
1 GTAACAATGGCA
1111008 GTAACAATGGCA
1 GTAACAATGGCA
1111020 G
1 G
1111021 GATAGGATGA
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:0.40, C:0.16, G:0.28, T:0.16
Consensus pattern (12 bp):
GTAACAATGGCA
Found at i:1112204 original size:18 final size:18
Alignment explanation
Indices: 1112177--1112213 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1112167 ATGAAAAAAC
*
1112177 ATAAACGAACTAACATAA
1 ATAAACGAACAAACATAA
*
1112195 ATAAATGAACAAACATAA
1 ATAAACGAACAAACATAA
1112213 A
1 A
1112214 CGAATGTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.65, C:0.14, G:0.05, T:0.16
Consensus pattern (18 bp):
ATAAACGAACAAACATAA
Found at i:1113739 original size:17 final size:17
Alignment explanation
Indices: 1113717--1113750 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1113707 CCTTAGTGGA
1113717 AACATTTAAAAAATAAT
1 AACATTTAAAAAATAAT
* *
1113734 AACATTTTAAAATTAAT
1 AACATTTAAAAAATAAT
1113751 CAAGAGGGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
AACATTTAAAAAATAAT
Found at i:1114797 original size:22 final size:19
Alignment explanation
Indices: 1114772--1114811 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 19
1114762 GATATAGATC
1114772 TTTAATTATAACATTTTATATA
1 TTTAATT-TAA-A-TTTATATA
1114794 TTTAATTTAAATTTATAT
1 TTTAATTTAAATTTATAT
1114812 CATGTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 3 0.17
22 7 0.39
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAATTTAAATTTATATA
Found at i:1114859 original size:30 final size:27
Alignment explanation
Indices: 1114825--1114954 Score: 116
Period size: 30 Copynumber: 4.9 Consensus size: 27
1114815 GTTTTAAAAC
1114825 ATATATTTTATTTTCTATCTAACTTATTAA
1 ATATATTTTATTTT-TAT-TAACTTA-TAA
1114855 ATATATTTTATTTTTATT---TTA-AA
1 ATATATTTTATTTTTATTAACTTATAA
*
1114878 ATATATTTTATTCTTATATTAACTTTAAAA
1 ATATATTTTATT-TT-TATTAAC-TTATAA
*
1114908 ATATATTTTATTTTTATTACCTTA-AA
1 ATATATTTTATTTTTATTAACTTATAA
*
1114934 A-A-A-TTT-TTGTTATTAACTTAT
1 ATATATTTTATTTTTATTAACTTAT
1114955 CTTCAAATGA
Statistics
Matches: 89, Mismatches: 3, Indels: 23
0.77 0.03 0.20
Matches are distributed among these distances:
22 12 0.13
23 17 0.19
24 3 0.03
25 8 0.09
26 3 0.03
27 3 0.03
28 7 0.08
29 8 0.09
30 28 0.31
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (27 bp):
ATATATTTTATTTTTATTAACTTATAA
Found at i:1114887 original size:53 final size:55
Alignment explanation
Indices: 1114816--1114925 Score: 156
Period size: 53 Copynumber: 2.0 Consensus size: 55
1114806 TTATATCATG
* *
1114816 TTTTAAAACATATATTTTATT-TTCTATCTAAC-TTATTAAATATATTTTATTTTTA
1 TTTTAAAACATATATTTTATTCTTATAT-TAACTTTA-AAAATATATTTTATTTTTA
1114871 TTTT-AAA-ATATATTTTATTCTTATATTAACTTTAAAAATATATTTTATTTTTA
1 TTTTAAAACATATATTTTATTCTTATATTAACTTTAAAAATATATTTTATTTTTA
1114924 TT
1 TT
1114926 ACCTTAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
53 36 0.71
54 11 0.22
55 4 0.08
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (55 bp):
TTTTAAAACATATATTTTATTCTTATATTAACTTTAAAAATATATTTTATTTTTA
Found at i:1115288 original size:21 final size:19
Alignment explanation
Indices: 1115235--1115303 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 19
1115225 TGGAGAAAAC
1115235 TAAATTTAATGAA-TTAAG
1 TAAATTTAATGAATTTAAG
*
1115253 TAAATTATAAATGAATTTAGGAT
1 TAAATT-T-AATGAATTTA--AG
*
1115276 TAAATTTAATGAATTTAAT
1 TAAATTTAATGAATTTAAG
*
1115295 TAAAATTAA
1 TAAATTTAA
1115304 GATTAAATTG
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
18 6 0.14
19 11 0.25
20 6 0.14
21 13 0.30
22 1 0.02
23 7 0.16
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
TAAATTTAATGAATTTAAG
Found at i:1116430 original size:16 final size:15
Alignment explanation
Indices: 1116409--1116439 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1116399 TTTAATTTGG
1116409 GTTTAAAATTGATTAA
1 GTTTAAAATT-ATTAA
1116425 GTTTAAAATTATTAA
1 GTTTAAAATTATTAA
1116440 TGGGATTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (15 bp):
GTTTAAAATTATTAA
Found at i:1117046 original size:2 final size:2
Alignment explanation
Indices: 1117039--1117086 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1117029 ATAATATTGG
1117039 AT 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 AT
1117081 AT AT AT
1 AT AT AT
1117087 TCCATGATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1117512 original size:12 final size:12
Alignment explanation
Indices: 1117472--1117504 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1117462 AGCGGAGTTT
*
1117472 TGATTTTTTTAA
1 TGATTTTTTAAA
1117484 TGATTTTTTAAA
1 TGATTTTTTAAA
1117496 TGATTTTTT
1 TGATTTTTT
1117505 CATTGATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (12 bp):
TGATTTTTTAAA
Found at i:1118183 original size:21 final size:21
Alignment explanation
Indices: 1118132--1118184 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1118122 ATTATTACTA
1118132 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
1118153 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1118174 TCGCAATGCGA
1 TCGCAATGCGA
1118185 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1118204 original size:41 final size:42
Alignment explanation
Indices: 1118159--1118247 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 42
1118149 AATTTCGCGT
* * * *
1118159 TGCGATTTTCCCAATTCGCAATGCGAA-TAAGTAAATCGCAA
1 TGCGATTTTACAAAATCGCAATGCGAATTAAGAAAATCGCAA
* * **
1118200 TGCGAATTTAGAAAATCGCAATGCGAATTTGGAAAATCGCAA
1 TGCGATTTTACAAAATCGCAATGCGAATTAAGAAAATCGCAA
1118242 TGCGAT
1 TGCGAT
1118248 ACTGACTATC
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
41 22 0.58
42 16 0.42
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (42 bp):
TGCGATTTTACAAAATCGCAATGCGAATTAAGAAAATCGCAA
Found at i:1118217 original size:21 final size:21
Alignment explanation
Indices: 1118174--1118246 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
1118164 TTTTCCCAAT
* *
1118174 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTAGAAAA
1118194 TCGCAATGCGAATTTAGAAAA
1 TCGCAATGCGAATTTAGAAAA
*
1118215 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
1118236 TCGCAATGCGA
1 TCGCAATGCGA
1118247 TACTGACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 12 0.24
21 37 0.76
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTAGAAAA
Found at i:1118260 original size:20 final size:20
Alignment explanation
Indices: 1118235--1118329 Score: 111
Period size: 20 Copynumber: 4.7 Consensus size: 20
1118225 AATTTGGAAA
*
1118235 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1118255 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
1118276 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1118296 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1118316 ATCGCAACGAGATA
1 ATCGCAACGCGATA
1118330 ATACAGAATC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.03
20 43 0.69
21 15 0.24
22 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1119097 original size:24 final size:24
Alignment explanation
Indices: 1119070--1119123 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1119060 GTATTCGAAA
*
1119070 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1119094 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1119118 TTTGAT
1 TTTGAT
1119124 GATATTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1121661 original size:19 final size:17
Alignment explanation
Indices: 1121626--1121776 Score: 86
Period size: 19 Copynumber: 8.8 Consensus size: 17
1121616 ATTAATGTCT
1121626 ATCGCAATGCGGAAATGA
1 ATCGCAATGC-GAAATGA
1121644 CTATCGCAATGCGAAATGAAA
1 --ATCGCAATGCGAAATG--A
*
1121665 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
1121679 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
1121698 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
1121712 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
**
1121731 ATCGCAA--CG-AGGGA
1 ATCGCAATGCGAAATGA
*
1121745 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
1121764 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1121777 TTTAGTTTCG
Statistics
Matches: 105, Mismatches: 9, Indels: 35
0.70 0.06 0.23
Matches are distributed among these distances:
14 24 0.23
16 14 0.13
17 14 0.13
19 42 0.40
20 10 0.10
21 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.13
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:1121683 original size:14 final size:14
Alignment explanation
Indices: 1121664--1121751 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
1121654 GCGAAATGAA
1121664 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1121678 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1121697 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1121711 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1121730 AATCGCAACGAGGG
1 AATCGCAACGAGAG
1121744 AATCGCAA
1 AATCGCAA
1121752 AGCGAAATGA
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 27 0.46
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.34
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1121688 original size:33 final size:33
Alignment explanation
Indices: 1121646--1121772 Score: 236
Period size: 33 Copynumber: 3.8 Consensus size: 33
1121636 GGAAATGACT
1121646 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1121679 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1121712 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1121745 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1121773 CGAATTTAGT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 92 1.00
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1121807 original size:19 final size:19
Alignment explanation
Indices: 1121772--1121834 Score: 101
Period size: 19 Copynumber: 3.3 Consensus size: 19
1121762 AAATCGCAAC
*
1121772 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
1121791 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
1121810 GCGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
1121829 GCGATT
1 GCGATT
1121835 CTCTCGTTGC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
19 41 0.98
20 1 0.02
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.44
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:1121844 original size:14 final size:14
Alignment explanation
Indices: 1121825--1121881 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1121815 TTTCATTTCG
1121825 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1121839 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
1121856 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
1121872 CGTTGCGATT
1 CGTTGCGATT
1121882 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1121848 original size:33 final size:33
Alignment explanation
Indices: 1121806--1121899 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
1121796 TTTAGTTTCG
*
1121806 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1121839 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1121872 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1121900 AGTCATTTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1121865 original size:19 final size:19
Alignment explanation
Indices: 1121782--1121899 Score: 114
Period size: 19 Copynumber: 6.7 Consensus size: 19
1121772 GCGAATTTAG
1121782 TTTCGCGTTGCGATTTT-A
1 TTTCGCGTTGCGATTTTCA
1121800 GTTTCGCGTTGCGATTTTCA
1 -TTTCGCGTTGCGATTTTCA
1121820 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
1121836 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
1121853 TTTCGCATTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
1121869 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
1121886 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1121900 AGTCATTTTT
Statistics
Matches: 81, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
14 19 0.23
16 6 0.07
17 6 0.07
19 49 0.60
20 1 0.01
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.46
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:1122025 original size:14 final size:14
Alignment explanation
Indices: 1122006--1122042 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1121996 CATCAATTAA
1122006 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1122020 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1122034 ACAAATCAA
1 ACAAATCAA
1122043 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1123477 original size:42 final size:42
Alignment explanation
Indices: 1123431--1123510 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
1123421 TGATGACAGT
* * *
1123431 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
1123473 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
1123511 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:1123981 original size:17 final size:17
Alignment explanation
Indices: 1123959--1123991 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1123949 ATACTAACTT
1123959 CACAGTGTTAA-AGAATA
1 CACAGT-TTAACAGAATA
1123976 CACAGTTTAACAGAAT
1 CACAGTTTAACAGAAT
1123992 TGGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.24
Consensus pattern (17 bp):
CACAGTTTAACAGAATA
Found at i:1124056 original size:94 final size:94
Alignment explanation
Indices: 1123895--1124199 Score: 494
Period size: 94 Copynumber: 3.3 Consensus size: 94
1123885 GAATAGTTTC
*
1123895 AATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
*
1123960 ACAGTGTTAAAGAATACACAGTTTAACAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
1123989 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1124054 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
* * *
1124083 AATTGACAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAAGACAACTACTAACTT
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTT
*
1124147 CACAGTGTT----AATAAACAGTTTAGCAG
65 CACAGTGTTAAAGAATACACAGTTTAGCAG
* *
1124173 TATTGGCAGCAACCGAATAAATTTACT
1 AATTGGCAGCAACCGAACAAATTTACT
1124200 AAGCAATCTA
Statistics
Matches: 201, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
90 40 0.20
93 19 0.09
94 142 0.71
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.21
Consensus pattern (94 bp):
AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
ACAGTGTTAAAGAATACACAGTTTAGCAG
Found at i:1125906 original size:20 final size:21
Alignment explanation
Indices: 1125879--1125943 Score: 100
Period size: 20 Copynumber: 3.2 Consensus size: 21
1125869 TCTTTTGGTT
1125879 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
*
1125900 G-AATGAAAATCGCAACGCG-
1 GAAATGAAAATCGCAACGAGA
1125919 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1125940 -AAAT
1 GAAAT
1125944 CGCAATGCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.03
20 38 0.95
21 1 0.03
ACGTcount: A:0.51, C:0.15, G:0.23, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:1125974 original size:19 final size:19
Alignment explanation
Indices: 1125949--1126052 Score: 110
Period size: 19 Copynumber: 5.7 Consensus size: 19
1125939 AAAATCGCAA
**
1125949 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
1125968 TGTGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
1125987 TGCGA--TT-A--TCTCGT
1 TGCGATTTTCATTTCGCGT
1126001 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
**
1126020 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTT-CGCGT
1126040 TGCGATTTTCATT
1 TGCGATTTTCATT
1126053 CTCGAAACTA
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 37 0.54
20 16 0.23
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:1126052 original size:39 final size:33
Alignment explanation
Indices: 1125962--1126052 Score: 110
Period size: 33 Copynumber: 2.6 Consensus size: 33
1125952 GATTTTGGTT
*
1125962 TCGCGTTGTGATTTTCATTTCGCGTTGCGATTA
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTA
*
1125995 TCTCGTTGCGATTTTCATTTCGCGTTGCGATAGTCA
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGAT--T-A
1126031 TTTCCGCGTTGCGATTTTCATT
1 --T-CGCGTTGCGATTTTCATT
1126053 CTCGAAACTA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
33 29 0.59
35 1 0.02
36 1 0.02
38 1 0.02
39 17 0.35
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (33 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTA
Found at i:1126621 original size:20 final size:20
Alignment explanation
Indices: 1126594--1126789 Score: 139
Period size: 20 Copynumber: 9.7 Consensus size: 20
1126584 CGATAGTCAG
1126594 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
1126614 ATTTGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
1126634 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
1126655 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
1126675 ATTCGCATTGCGAATTATGAA
1 ATTCGCATTGCGATTTACG-T
* ** *
1126696 AATCGCAACGCGA-ATACGT
1 ATTCGCATTGCGATTTACGT
* *
1126715 AAATCGCATTGCGATTT-TGT
1 -ATTCGCATTGCGATTTACGT
* *
1126735 ATTATCGCGTTGCGATAGT-CAGT
1 A-T-TCGCATTGCGAT-TTAC-GT
*
1126758 A-TCGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACGT
1126777 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1126790 ATTGGGAAAA
Statistics
Matches: 135, Mismatches: 31, Indels: 20
0.73 0.17 0.11
Matches are distributed among these distances:
19 4 0.03
20 88 0.65
21 39 0.29
22 1 0.01
23 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1126644 original size:41 final size:40
Alignment explanation
Indices: 1126594--1126687 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
1126584 CGATAGTCAG
* * *
1126594 ATTCGCATTGCGATTTACGTATTTGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
1126634 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
1126675 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1126688 ATTATGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:1126748 original size:102 final size:101
Alignment explanation
Indices: 1126618--1126871 Score: 257
Period size: 102 Copynumber: 2.5 Consensus size: 101
1126608 TTACGTATTT
* * *
1126618 GCATTGCGATTTTCCTAAT-TCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGTATTCGCA
1 GCATTGCGATTTT-GTATTATCGCGTTGCGA-TTA-TTAATCGCGTTGCGATTTACGTATTCGCA
* *
1126682 TTGCGAATTATGAAAATCGCAACGCG-AATACGTAAATC
63 TTGCGAATTAGGAAAATCGCAACGCGAAATACGAAAATC
* * *
1126720 GCATTGCGATTTTGTATTATCGCGTTGCGA-TAGTCAGTATCGCATTGCGATTTACTTATTCGCA
1 GCATTGCGATTTTGTATTATCGCGTTGCGATTA-TTA--ATCGCGTTGCGATTTACGTATTCGCA
* * **
1126784 TTGCGAATTGGGAAAATCGCAATGCGAAATTGGAAAATC
63 TTGCGAATTAGGAAAATCGCAACGCGAAATACGAAAATC
* * *
1126823 GCATTGCGA--TAGTAATAATCGCGTTGCGATAGTAATAATCGCGTTGCGA
1 GCATTGCGATTTTGT-ATTATCGCGTTGCGAT--TATTAATCGCGTTGCGA
1126872 ATCTAGAAAC
Statistics
Matches: 126, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
100 4 0.03
101 6 0.05
102 95 0.75
103 18 0.14
104 1 0.01
105 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (101 bp):
GCATTGCGATTTTGTATTATCGCGTTGCGATTATTAATCGCGTTGCGATTTACGTATTCGCATTG
CGAATTAGGAAAATCGCAACGCGAAATACGAAAATC
Found at i:1126809 original size:21 final size:20
Alignment explanation
Indices: 1126779--1126831 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 20
1126769 ATTTACTTAT
1126779 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
*
1126800 TCGCAATGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
1126821 TCGCATTGCGA
1 TCGCATTGCGA
1126832 TAGTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.03
21 24 0.83
22 4 0.14
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:1126844 original size:20 final size:20
Alignment explanation
Indices: 1126819--1126871 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1126809 GAAATTGGAA
*
1126819 AATCGCATTGCGATAGTAAT
1 AATCGCGTTGCGATAGTAAT
1126839 AATCGCGTTGCGATAGTAAT
1 AATCGCGTTGCGATAGTAAT
1126859 AATCGCGTTGCGA
1 AATCGCGTTGCGA
1126872 ATCTAGAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTAAT
Found at i:1127684 original size:30 final size:31
Alignment explanation
Indices: 1127628--1127693 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 31
1127618 ATGGCTGAGA
*
1127628 GACTAAAATCGAATGGATCAATAATGTTAGG
1 GACTAAAATCGAACGGATCAATAATGTTAGG
**
1127659 GACTAAAA-CGAACGGATTGATAATGTTAGG
1 GACTAAAATCGAACGGATCAATAATGTTAGG
1127689 GACTA
1 GACTA
1127694 TTTCCCCTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 24 0.75
31 8 0.25
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (31 bp):
GACTAAAATCGAACGGATCAATAATGTTAGG
Found at i:1130460 original size:21 final size:21
Alignment explanation
Indices: 1130430--1130469 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1130420 TTCTCATTCG
* *
1130430 TTGTTTGGCGAAATCGAAACA
1 TTGTTGGGCGAAACCGAAACA
1130451 TTGTTGGGCGAAACCGAAA
1 TTGTTGGGCGAAACCGAAA
1130470 TGACTCCGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.25
Consensus pattern (21 bp):
TTGTTGGGCGAAACCGAAACA
Found at i:1133040 original size:2 final size:2
Alignment explanation
Indices: 1133033--1133060 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1133023 TAATATGTTA
1133033 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
1133061 TTCAATTAAA
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:1142292 original size:22 final size:23
Alignment explanation
Indices: 1142240--1142294 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
1142230 GATAAAAAAC
1142240 GTGTCATAAAAATAGAAAACACAT
1 GTGT-ATAAAAATAGAAAACACAT
* * *
1142264 GT-CATAAAGATAGAAAA-ATAT
1 GTGTATAAAAATAGAAAACACAT
1142285 GTGTATAAAA
1 GTGTATAAAA
1142295 GCATAACTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
21 5 0.20
22 18 0.72
24 2 0.08
ACGTcount: A:0.55, C:0.07, G:0.15, T:0.24
Consensus pattern (23 bp):
GTGTATAAAAATAGAAAACACAT
Found at i:1143476 original size:92 final size:92
Alignment explanation
Indices: 1143375--1143560 Score: 336
Period size: 92 Copynumber: 2.0 Consensus size: 92
1143365 AACTAAATGT
*
1143375 TAGGTATGATTTTGAAAAAATTGAAAGTTTAGATACTAAAACAAACCAAAATTAATAGCTTAGAT
1 TAGGTATGATTTTGAAAAAACTGAAAGTTTAGATACTAAAACAAACCAAAATTAATAGCTTAGAT
*
1143440 ACTAAATAAGTAGTTTACCCTAAATAA
66 ACTAAATAAGTAGTTTACCCTAAACAA
1143467 TAGGTATGATTTTGAAAAAACTGAAAGTTTAGATACTAAAACAAACCAAAATTAATAGCTTAGAT
1 TAGGTATGATTTTGAAAAAACTGAAAGTTTAGATACTAAAACAAACCAAAATTAATAGCTTAGAT
* *
1143532 ATTAAATACGTAGTTTACCCTAAACAA
66 ACTAAATAAGTAGTTTACCCTAAACAA
1143559 TA
1 TA
1143561 AAGTCAACTA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (92 bp):
TAGGTATGATTTTGAAAAAACTGAAAGTTTAGATACTAAAACAAACCAAAATTAATAGCTTAGAT
ACTAAATAAGTAGTTTACCCTAAACAA
Found at i:1143799 original size:64 final size:65
Alignment explanation
Indices: 1143716--1143836 Score: 183
Period size: 64 Copynumber: 1.9 Consensus size: 65
1143706 ATAATCCTCA
1143716 ATTTAAAAAATAAATAAATATTTAGCTTGAAAAACTCTTATTATTCAATT-AATTTTGATATCTG
1 ATTTAAAAAATAAATAAATATTTAGCTTGAAAAACTCTTATTATTCAATTAAATTTTGATATCTG
* * **
1143780 ATTTTAAAAA-AAATCAAATATTTTGCTTGAAAATGTCTTATTATTCAATTAAATTTT
1 ATTTAAAAAATAAAT-AAATATTTAGCTTGAAAAACTCTTATTATTCAATTAAATTTT
1143837 TTATTAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
63 4 0.08
64 41 0.80
65 6 0.12
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (65 bp):
ATTTAAAAAATAAATAAATATTTAGCTTGAAAAACTCTTATTATTCAATTAAATTTTGATATCTG
Found at i:1143833 original size:20 final size:20
Alignment explanation
Indices: 1143810--1143867 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
1143800 TTTTGCTTGA
1143810 AAATGTCTTATTATTCAATT
1 AAATGTCTTATTATTCAATT
*
1143830 AAAT-T-TT-TTATT-AATAA
1 AAATGTCTTATTATTCAAT-T
*
1143847 AAAAGTCTTATTATTCAATT
1 AAATGTCTTATTATTCAATT
1143867 A
1 A
1143868 TATTTTTAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
16 3 0.10
17 8 0.27
18 3 0.10
19 3 0.10
20 10 0.33
21 3 0.10
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.48
Consensus pattern (20 bp):
AAATGTCTTATTATTCAATT
Found at i:1144416 original size:6 final size:6
Alignment explanation
Indices: 1144405--1144429 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1144395 TGAATAATTA
1144405 TAGGGT TAGGGT TAGGGT TAGGGT T
1 TAGGGT TAGGGT TAGGGT TAGGGT T
1144430 GAGTGGCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.36
Consensus pattern (6 bp):
TAGGGT
Found at i:1145087 original size:30 final size:29
Alignment explanation
Indices: 1145053--1145122 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
1145043 TATTAATATA
*
1145053 TAATTAAAATAAATTAAAAATTAGAGTGAT
1 TAATTAAAATAAATTAAAAATTA-AGTAAT
* * *
1145083 TAATTAAGAGTAAATTGAAAGTTAAGTAAT
1 TAATTAA-AATAAATTAAAAATTAAGTAAT
1145113 TAAATTAAAA
1 T-AATTAAAA
1145123 AAACAAACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (29 bp):
TAATTAAAATAAATTAAAAATTAAGTAAT
Found at i:1147987 original size:4 final size:4
Alignment explanation
Indices: 1147967--1148003 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
1147957 TAAGTAAAGC
* *
1147967 ACAT ACAT GCAT GCAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1148004 TTATTGGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1153828 original size:64 final size:64
Alignment explanation
Indices: 1153755--1153874 Score: 197
Period size: 64 Copynumber: 1.9 Consensus size: 64
1153745 ATCAAGTACC
*
1153755 AATTTTATAACTTTTAGTAATCAATGAAA-TCAACAAAATAATATCTATAATAAAAATATAATTA
1 AATTTTATAACTTTTAATAATCAAT-AAACTCAACAAAATAATATCTATAATAAAAATATAATTA
* *
1153819 AATTTTATAATTTTTAATAATCAATAAACTCAACAACATAATATCTATAATAAAAA
1 AATTTTATAACTTTTAATAATCAATAAACTCAACAAAATAATATCTATAATAAAAA
1153875 ATTATTTCAA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
63 3 0.06
64 49 0.94
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (64 bp):
AATTTTATAACTTTTAATAATCAATAAACTCAACAAAATAATATCTATAATAAAAATATAATTA
Found at i:1157811 original size:60 final size:59
Alignment explanation
Indices: 1157694--1157811 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 59
1157684 TTTGGATGAA
* * *
1157694 TTTGGGGATGAAATTGAAAGATCTAAAAGCTTAGGACCAATTTAGGATGAGATTCATAG
1 TTTGGGGATGAAATTGAAAGATCTAAAAGCTTAGGACCAATTTAGAACGAGAGTCATAG
* * *
1157753 TTTGGGGATGAAATTTGAATG-T-TAAAAAGTTTTAGGACTAATTTAGAACGAGAGTCATA
1 TTTGGGGATGAAA-TTGAAAGATCT-AAAAG-CTTAGGACCAATTTAGAACGAGAGTCATA
1157812 TTTTAAGGAC
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
58 1 0.02
59 19 0.38
60 30 0.60
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (59 bp):
TTTGGGGATGAAATTGAAAGATCTAAAAGCTTAGGACCAATTTAGAACGAGAGTCATAG
Found at i:1158496 original size:45 final size:47
Alignment explanation
Indices: 1158404--1158496 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 47
1158394 CAGGTTTAGT
1158404 GAATCCAAATTGAACTTGAAAAAATGAAAAAAAAAACTGAGGATGAGC
1 GAATCCAAATTGAACTTGAAAAAAT-AAAAAAAAAACTGAGGATGAGC
1158452 GAATCCAAATTGAACTTGAAAAAAT-AAAAAAAAA-TGAGGATGAGC
1 GAATCCAAATTGAACTTGAAAAAATAAAAAAAAAACTGAGGATGAGC
1158497 TACTTGATCG
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
45 11 0.24
46 9 0.20
48 25 0.56
ACGTcount: A:0.55, C:0.10, G:0.18, T:0.17
Consensus pattern (47 bp):
GAATCCAAATTGAACTTGAAAAAATAAAAAAAAAACTGAGGATGAGC
Found at i:1158638 original size:26 final size:25
Alignment explanation
Indices: 1158608--1158679 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 25
1158598 TCATAGGGAA
1158608 TATTTTTTTAATTTAATTATAATTT
1 TATTTTTTTAATTTAATTATAATTT
**
1158633 TGATTTTTTTTGTTTCAA-TATAATTT
1 T-ATTTTTTTAATTT-AATTATAATTT
***
1158659 TAAAATTTTAATTTAATTATA
1 TATTTTTTTAATTTAATTATA
1158680 TTATTTTAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
24 2 0.05
25 13 0.35
26 20 0.54
27 2 0.05
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (25 bp):
TATTTTTTTAATTTAATTATAATTT
Found at i:1159646 original size:24 final size:24
Alignment explanation
Indices: 1159600--1159646 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1159590 ACATCAGCAT
**
1159600 ATTATTTAAATTAATTTTTATTAA
1 ATTATTTAAATTAATTTAGATTAA
1159624 ATTATTTATAATTAA-TTAGATTA
1 ATTATTTA-AATTAATTTAGATTA
1159647 TGACACATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTATTTAAATTAATTTAGATTAA
Found at i:1164854 original size:4 final size:4
Alignment explanation
Indices: 1164845--1164875 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1164835 AAGTAATCGA
*
1164845 ATAC ATAC ATAC ATAC ATAC ACAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1164876 GATAGATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAC
Found at i:1170246 original size:14 final size:14
Alignment explanation
Indices: 1170227--1170278 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1170217 AAACCTTAAG
1170227 TTAGGGTTTGAGGT
1 TTAGGGTTTGAGGT
1170241 TTAGGGTTTAGAGG-
1 TTAGGGTTT-GAGGT
*
1170255 TTATGGGGTT-ATGGT
1 TTA-GGGTTTGA-GGT
1170270 TTAGGGTTT
1 TTAGGGTTT
1170279 AATTTTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 1 0.03
14 19 0.59
15 12 0.38
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.44
Consensus pattern (14 bp):
TTAGGGTTTGAGGT
Found at i:1172799 original size:34 final size:36
Alignment explanation
Indices: 1172765--1172832 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
1172755 ATCCAATTAT
1172765 TTTTAAA-AAATTATAAA-AAA-TAATAATATTTTA
1 TTTTAAATAAATTATAAATAAATTAATAATATTTTA
*
1172798 TTTTAAATAATTTATAAATTAAATTAATAATATTT
1 TTTTAAATAAATTATAAA-TAAATTAATAATATTT
1172833 AACGGTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 7 0.23
34 9 0.30
36 3 0.10
37 11 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (36 bp):
TTTTAAATAAATTATAAATAAATTAATAATATTTTA
Found at i:1177935 original size:8 final size:8
Alignment explanation
Indices: 1177922--1177946 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1177912 GTGGTAACAA
1177922 AGGGAGTG
1 AGGGAGTG
1177930 AGGGAGTG
1 AGGGAGTG
1177938 AGGGAGTG
1 AGGGAGTG
1177946 A
1 A
1177947 CTACAGTGTT
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:0.28, C:0.00, G:0.60, T:0.12
Consensus pattern (8 bp):
AGGGAGTG
Found at i:1195096 original size:21 final size:21
Alignment explanation
Indices: 1195045--1195102 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1195035 AACCACTATA
*
1195045 GACTGTCACGTTAATATAGTG
1 GACTGTCACGTCAATATAGTG
* * *
1195066 GATTGCCACGTCAGTATAG-G
1 GACTGTCACGTCAATATAGTG
1195086 GCACTGTCACGTCAATA
1 G-ACTGTCACGTCAATA
1195103 CCGTAACGGT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (21 bp):
GACTGTCACGTCAATATAGTG
Found at i:1209394 original size:29 final size:32
Alignment explanation
Indices: 1209357--1209415 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
1209347 ACATTAATTT
*
1209357 ATATCATGT-AT-TATTTT-TTATTATTTTTG
1 ATATCATGTGATATATTTTATTAGTATTTTTG
*
1209386 ATATGATGTGATATATTTTATTAGTATTTT
1 ATATCATGTGATATATTTTATTAGTATTTT
1209416 AGTGTCACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.32
30 2 0.08
31 6 0.24
32 9 0.36
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (32 bp):
ATATCATGTGATATATTTTATTAGTATTTTTG
Found at i:1217868 original size:3 final size:3
Alignment explanation
Indices: 1217857--1217893 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
1217847 AAATTATTAA
1217857 AAT AA- AAT AAT AAT AGA- AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AA
1217894 ATAAATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 3 0.10
3 27 0.87
4 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1217878 original size:12 final size:11
Alignment explanation
Indices: 1217857--1217898 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 11
1217847 AAATTATTAA
1217857 AATAAAATAAT
1 AATAAAATAAT
1217868 AATAGAAATAAT
1 AATA-AAATAAT
1217880 AATAATAATAAT
1 AATAA-AATAAT
1217892 AAATAAA
1 -AATAAA
1217899 TAAATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.18
12 18 0.64
13 5 0.18
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:1218007 original size:43 final size:42
Alignment explanation
Indices: 1217932--1218012 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
1217922 AAACTATATA
* *
1217932 ATATAAATTTTTAAAAATGCTTCTTTAAAAACTATATATTAT
1 ATATAAATTTTCAAAAAAGCTTCTTTAAAAACTATATATTAT
* * *
1217974 ATATAAATTTTCAAAAAAGTTTTTTTTTAAAACTATATA
1 ATATAAATTTTCAAAAAAG-CTTCTTTAAAAACTATATA
1218013 ATTTTTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
42 17 0.52
43 16 0.48
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (42 bp):
ATATAAATTTTCAAAAAAGCTTCTTTAAAAACTATATATTAT
Found at i:1218053 original size:30 final size:28
Alignment explanation
Indices: 1217996--1218071 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 28
1217986 AAAAAAGTTT
* **
1217996 TTTTTTAAAACTATATAATTTTTAAAAA
1 TTTTTTAAAAATATATAATTTCCAAAAA
1218024 CGTTTTTTAAAAATATATAATTTCCAAAAA
1 --TTTTTTAAAAATATATAATTTCCAAAAA
*
1218054 TGTTTTAAAAATTATATA
1 TTTTTTAAAAA-TATATA
1218072 TTATATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
28 10 0.24
29 6 0.15
30 25 0.61
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (28 bp):
TTTTTTAAAAATATATAATTTCCAAAAA
Found at i:1218100 original size:40 final size:39
Alignment explanation
Indices: 1218036--1218189 Score: 208
Period size: 39 Copynumber: 4.0 Consensus size: 39
1218026 TTTTTTAAAA
* *
1218036 ATATATAATTTCCAAAAATG-TTTTAAAAATTATATATT
1 ATATATAATTTTCAAAAATGTTTTTAAAAACTATATATT
1218074 ATATATAAGTTTTCAAAAATGTTTTTAAAAACTATATATT
1 ATATATAA-TTTTCAAAAATGTTTTTAAAAACTATATATT
1218114 ATATA-AATTTTCAAAAAATGTTTTTAAAAACTATATATT
1 ATATATAATTTTC-AAAAATGTTTTTAAAAACTATATATT
* * * *
1218153 ATATA-AGTTTTC-AAAATGATTTTAAAAAGTATGTATT
1 ATATATAATTTTCAAAAATGTTTTTAAAAACTATATATT
1218190 TTCAAAAACC
Statistics
Matches: 107, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
37 22 0.21
38 13 0.12
39 50 0.47
40 22 0.21
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (39 bp):
ATATATAATTTTCAAAAATGTTTTTAAAAACTATATATT
Found at i:1225320 original size:21 final size:22
Alignment explanation
Indices: 1225285--1225325 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1225275 TATCTTCCAT
*
1225285 AAACCTTCAAATTCCCTAAATC
1 AAACCTTCAAATTCCATAAATC
*
1225307 AAACCTT-TAATTCCATAAA
1 AAACCTTCAAATTCCATAAA
1225326 ACCCAAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (22 bp):
AAACCTTCAAATTCCATAAATC
Found at i:1234851 original size:20 final size:19
Alignment explanation
Indices: 1234798--1234851 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
1234788 AATTTTTAAA
*
1234798 AAAATAAAATTTAAATACT
1 AAAATATAATTTAAATACT
*
1234817 AAAATATATAGTTTAGATACT
1 AAAATATA-A-TTTAAATACT
1234838 AAACATATAATTTA
1 AAA-ATATAATTTA
1234852 TTAAACTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 7 0.23
20 5 0.17
21 13 0.43
22 5 0.17
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (19 bp):
AAAATATAATTTAAATACT
Found at i:1241102 original size:335 final size:334
Alignment explanation
Indices: 1240495--1242002 Score: 2175
Period size: 335 Copynumber: 4.5 Consensus size: 334
1240485 CGAACACGAT
* * * * * *
1240495 AAAAATCCAGGTGGAACATAGCT-TTCAAACTCAACAAAACCTCTTGTTACAACAAACAAGGTAG
1 AAAAATCAAGGTGGAACATAGCTGTT-GATCCCAACAAAACCTCTTGTTACAACAAGCAAGGTGG
* * * * *
1240559 GATTCCGAGAGAATGTATACAAAGGAACATCAACAAGAGCTAAACGATGCGAC---T-AGTA---
65 GATTCTGAGAGAATGTACACAAAAGAAAATCAACAAGGGCTAAACGATGCGACTAGTGAGTAGTG
* *
1240617 AGATCAACCATCAACCA-TCATAAAAACAACATTTCAAGCATACCCTAACATTTTCCTACTATTC
130 AGATCGACCATCAA-CAGTCATAAAAACAACATTTCAAGCATACCCTAACATTTTCCTACTAATC
* * * *
1240681 CCCAAAACCACGGATGGTCCGAGAGGGGCTAACAAGGCAGTCTCCCCTCTCAAAATTTCGATTTC
194 CCCAAAACCAGGGATGGTCCGAGAGGGGCTAACGAGGCAGTCTCCCCTCTCAAAATTTTGAATTC
* * *
1240746 TCATATAATTTGGACAATGTTTTGTATTTTCTATAT-ATAAACTGTTTTCAACCCTAAAATTTTG
259 TCATATAATTTGGATAATGTTTTGAATTTTCTAT-TGATAAACTGTTTTCAACCCTAAAATTCTG
1240810 ATACTAAAGCATG
323 ATA-TAAAGCATG
1240823 AAAAATCAAGGTGGAACATAGCTGTTGATCCCAACAAAACCTCTTGTTACAACAAGCAAGGTGGG
1 AAAAATCAAGGTGGAACATAGCTGTTGATCCCAACAAAACCTCTTGTTACAACAAGCAAGGTGGG
* * * *
1240888 ATTATGCGAGAATGTACACAAAAGAAAATCAACATGGGCTAAACAATGCGACTAGTGAGTAGTGA
66 ATTCTGAGAGAATGTACACAAAAGAAAATCAACAAGGGCTAAACGATGCGACTAGTGAGTAGTGA
1240953 GATCGACCATCAACAGTCATAAAAACAACATTTCAAGCATACCCTAACATTTTCCTACTAATCCC
131 GATCGACCATCAACAGTCATAAAAACAACATTTCAAGCATACCCTAACATTTTCCTACTAATCCC
* *
1241018 CAAAACCATGGATGGTCCGAGAGGGGCTAACGAGGCAGTCTCCCCTCTCAAAATTTTGGATTCTC
196 CAAAACCAGGGATGGTCCGAGAGGGGCTAACGAGGCAGTCTCCCCTCTCAAAATTTTGAATTCTC
** *
1241083 ATATAATTTGGATAATGTTTTGAATTTTCTATTGATAAACTGTTTTTGACCCTAAAATTATGATA
261 ATATAATTTGGATAATGTTTTGAATTTTCTATTGATAAACTGTTTTCAACCCTAAAATTCTGATA
1241148 GTAAAGCATG
326 -TAAAGCATG
* * * *
1241158 AAAAATCAAGGCGGAACATAGCTGTTGATCCCAACAAAACCTCTTGTTACAAGAAGCAAGGTAGA
1 AAAAATCAAGGTGGAACATAGCTGTTGATCCCAACAAAACCTCTTGTTACAACAAGCAAGGTGGG
* *
1241223 ATTCTGAGAGAATATACACAAAAGAAAATCAACAAGGGCTAAATGATGCGACTAGTGAGTAGTGA
66 ATTCTGAGAGAATGTACACAAAAGAAAATCAACAAGGGCTAAACGATGCGACTAGTGAGTAGTGA
*
1241288 GATCGACCATCAACAGTCATAAAAACGACATTTTCAAGCATACCCTAACATTTTCCTACTAA-CC
131 GATCGACCATCAACAGTCATAAAAACAACA-TTTCAAGCATACCCTAACATTTTCCTACTAATCC
* * *
1241352 CCAAAACCAGGGATGGCCCAAGAGGGGCTAACGAGGCGGTCTCCCCTCTCAAAATTTTGAATTCT
195 CCAAAACCAGGGATGGTCCGAGAGGGGCTAACGAGGCAGTCTCCCCTCTCAAAATTTTGAATTCT
*
1241417 CATATAATTTGGATAATGTTTTGAATTTTCTATTGATAAACTGTTTTCAACCCCAAAATTCTGAT
260 CATATAATTTGGATAATGTTTTGAATTTTCTATTGATAAACTGTTTTCAACCCTAAAATTCTGAT
1241482 GATAAAGCATG
325 -ATAAAGCATG
*
1241493 AAAAATCAAGGTGGAACATAGCAGTTGATCCCAACAAAACCTCTTGTTACAACAAGCAAGGTGGG
1 AAAAATCAAGGTGGAACATAGCTGTTGATCCCAACAAAACCTCTTGTTACAACAAGCAAGGTGGG
* * *
1241558 ATTCT---TGAATGTACACAAAAGAAAATCAACAAGGGCTAAACGATGCGACCAGTGACTAGTGA
66 ATTCTGAGAGAATGTACACAAAAGAAAATCAACAAGGGCTAAACGATGCGACTAGTGAGTAGTGA
* * *
1241620 AATCGACCATCAACAATCATAAAAA-AACATTTCAAGCATACCCTAACATTTTCCTACTAAACCC
131 GATCGACCATCAACAGTCATAAAAACAACATTTCAAGCATACCCTAACATTTTCCTACTAATCCC
* * * * *
1241684 CGAAACCAGGGATGGTCCGAGAGGGACTAAGGAGGCAGTTTCCCCTCTCAAAATATTGAATTCTC
196 CAAAACCAGGGATGGTCCGAGAGGGGCTAACGAGGCAGTCTCCCCTCTCAAAATTTTGAATTCTC
* * *
1241749 ATATAATTTGGATAATGTTTTGTATTTTCTATCGATAAACTGTTTTCGACCCTAAAATTCTGATA
261 ATATAATTTGGATAATGTTTTGAATTTTCTATTGATAAACTGTTTTCAACCCTAAAATTCTGAT-
1241814 ATAAAGCATG
325 ATAAAGCATG
*
1241824 AAAAATCAAGGTGGAACATAACTGTTGATCCCAACAAAACCTCTTGTTACAACAAGCATGACAAA
1 AAAAATCAAGGTGGAACATAGCTGTTGATCCCAACAAAACCTCTTGTTACAAC-A--A-G-----
* *
1241889 TCAAGGTGGGATTCTGAGAGAATGTACACAAAAGAAAAATCAACAAGGGCTAAACGATGCAACTG
57 -CAAGGTGGGATTCTGAGAGAATGTACACAAAAG-AAAATCAACAAGGGCTAAACGATGCGACTA
* ***
1241954 GTGAGTAGGGAGATCGACCATCAACAGTCAT-ACCCCAACATTTCAAGCA
120 GTGAGTAGTGAGATCGACCATCAACAGTCATAAAAACAACATTTCAAGCA
1242003 GTCTCCCCTC
Statistics
Matches: 1065, Mismatches: 87, Indels: 39
0.89 0.07 0.03
Matches are distributed among these distances:
328 99 0.09
329 2 0.00
330 31 0.03
331 185 0.17
332 80 0.08
334 4 0.00
335 535 0.50
336 32 0.03
341 14 0.01
344 16 0.02
345 67 0.06
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (334 bp):
AAAAATCAAGGTGGAACATAGCTGTTGATCCCAACAAAACCTCTTGTTACAACAAGCAAGGTGGG
ATTCTGAGAGAATGTACACAAAAGAAAATCAACAAGGGCTAAACGATGCGACTAGTGAGTAGTGA
GATCGACCATCAACAGTCATAAAAACAACATTTCAAGCATACCCTAACATTTTCCTACTAATCCC
CAAAACCAGGGATGGTCCGAGAGGGGCTAACGAGGCAGTCTCCCCTCTCAAAATTTTGAATTCTC
ATATAATTTGGATAATGTTTTGAATTTTCTATTGATAAACTGTTTTCAACCCTAAAATTCTGATA
TAAAGCATG
Found at i:1244675 original size:20 final size:20
Alignment explanation
Indices: 1244652--1244690 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1244642 TTAAAATAAT
*
1244652 AATAATTTACAATTAATTTA
1 AATAATATACAATTAATTTA
*
1244672 AATAATATATAATTAATTT
1 AATAATATACAATTAATTT
1244691 GATTCAAACA
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:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAATATACAATTAATTTA
Found at i:1251887 original size:59 final size:60
Alignment explanation
Indices: 1251818--1251947 Score: 145
Period size: 61 Copynumber: 2.2 Consensus size: 60
1251808 TAAAGTACAT
* **
1251818 AAATCGTCATT-GACTATAGGGTACTATTTTATTAAGTCTATCGAATATTAAAAGTTATA
1 AAATTGTCATTAGACTATAGAATACTATTTTATTAAGTCTATCGAATATTAAAAGTTATA
** * * * * *
1251877 AAATTGTCATTTAGACTATAGAATGTTGTTTTGTTAAGTCTCTCTACTATTAAAAGTTATA
1 AAATTGTCA-TTAGACTATAGAATACTATTTTATTAAGTCTATCGAATATTAAAAGTTATA
*
1251938 AAATTATCAT
1 AAATTGTCAT
1251948 ATTACTATTC
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 8 0.14
60 3 0.05
61 47 0.81
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (60 bp):
AAATTGTCATTAGACTATAGAATACTATTTTATTAAGTCTATCGAATATTAAAAGTTATA
Found at i:1264435 original size:23 final size:20
Alignment explanation
Indices: 1264382--1264440 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
1264372 TTTAAAGTTC
*
1264382 ATTTATTAATTATATATAGT
1 ATTTATTAATTATAAATAGT
* *
1264402 AATGATTAATTATAAATAGGTTT
1 ATTTATTAATTATAAATA-G--T
1264425 ATTTATTAATTATAAA
1 ATTTATTAATTATAAA
1264441 ATTTATTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 15 0.48
21 1 0.03
23 15 0.48
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
ATTTATTAATTATAAATAGT
Found at i:1267867 original size:2 final size:2
Alignment explanation
Indices: 1267860--1267890 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1267850 TTTATATCAG
*
1267860 GA GA GA GA GA GA GA GA GA GA GA GA CA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1267891 GAATAGTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1269151 original size:21 final size:21
Alignment explanation
Indices: 1269112--1269151 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1269102 TAGTAGGATT
* **
1269112 AATATTTTTTTTTTTTTCATA
1 AATATGTTTTTTTAATTCATA
1269133 AATATGTTTTTTTAATTCA
1 AATATGTTTTTTTAATTCA
1269152 GAGACATATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.65
Consensus pattern (21 bp):
AATATGTTTTTTTAATTCATA
Found at i:1270545 original size:59 final size:59
Alignment explanation
Indices: 1270384--1270560 Score: 203
Period size: 60 Copynumber: 3.0 Consensus size: 59
1270374 TTTGGATGAA
* * * *
1270384 GATGAAATTGGAA-GATCTAAAAGTTTAGGGACTAATCTAGAATGAGATTCATAGTTTGGG
1 GATGAAATTGGAATG-T-TAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTGAG
** * * *
1270444 GATGAAATTAAAATATTCAAAAGTTTAAGTACTAATTTAGAATTAGAGTCATAGTTTGAG
1 GATGAAATTGGAATGTT-AAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTGAG
* * * *
1270504 GCTGAAATTGGAATGTTTAAAGTTTAAGGACTAATTTAGAATGAGGGTCATAATTTG
1 GATGAAATTGGAATGTTAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTG
1270561 GGGACATATG
Statistics
Matches: 97, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
59 36 0.37
60 61 0.63
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (59 bp):
GATGAAATTGGAATGTTAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTGAG
Found at i:1270857 original size:28 final size:28
Alignment explanation
Indices: 1270824--1270917 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
1270814 TTGAATAGTC
*
1270824 TAGGTACCTATTTTGACATAAAATACTT
1 TAGGTACATATTTTGACATAAAATACTT
* *
1270852 TAGGTACATGTTTTGATTATAAATATAACTT
1 TAGGTACATATTTTGA-CATAAA-AT-ACTT
** ** **
1270883 TATATATTTATTTTGACCGAAAATACTT
1 TAGGTACATATTTTGACATAAAATACTT
1270911 TAGGTAC
1 TAGGTAC
1270918 TTAAATGTAA
Statistics
Matches: 49, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
28 22 0.45
29 7 0.14
30 5 0.10
31 15 0.31
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.43
Consensus pattern (28 bp):
TAGGTACATATTTTGACATAAAATACTT
Found at i:1274878 original size:55 final size:54
Alignment explanation
Indices: 1274769--1274878 Score: 123
Period size: 55 Copynumber: 2.0 Consensus size: 54
1274759 AAATAGTTTA
* * * * * *
1274769 AGGATGAAATTAAAATGTTCAAAAGTTTAAGGACTATTTTAAAATGAGACTTAT
1 AGGATGAAAATAAAATATTCAAAAATTTAAGGAATAATTTAAAATGACACTTAT
* *
1274823 AGGATGAAAATATAAATATTCAAAAATTTAA-GAATAAATTTAAAATTACAGTTAT
1 AGGATGAAAATA-AAATATTCAAAAATTTAAGGAAT-AATTTAAAATGACACTTAT
1274878 A
1 A
1274879 ATTTGGAGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
54 14 0.30
55 32 0.70
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.33
Consensus pattern (54 bp):
AGGATGAAAATAAAATATTCAAAAATTTAAGGAATAATTTAAAATGACACTTAT
Found at i:1277252 original size:165 final size:164
Alignment explanation
Indices: 1276929--1277258 Score: 626
Period size: 165 Copynumber: 2.0 Consensus size: 164
1276919 ATAGAAGAAT
1276929 GTCGTTGTTGCAGTACAGATTTCCAATCATTGTTGCCATTAACTTATACAGCGTTCGAACTTTCG
1 GTCGTTGTTGCAGTACAGATTTCCAATCATTGTTGCCATTAACTTATACAGCGTTCGAACTTTCG
*
1276994 AACAATGATGATGTTCAAATGATGGTTTGAAGCTTAAAGTAATTATTCAGACGCCGCTATTGCGA
66 AACAATGATGATGTTCAAATGATGGTTTGAAGCTTAAAGTAATTATTCAGACGCCGCTATTGAGA
1277059 TGTATGCACATTTTGTTCAAGAGCGTGTTGTTCG
131 TGTATGCACATTTTGTTCAAGAGCGTGTTGTTCG
1277093 GTCGTTGTTGCAGTACAGATTTCCAACATCATTGTTGCCATTAACTTATACAGCGTTCGAACTTT
1 GTCGTTGTTGCAGTACAGATTTCC-A-ATCATTGTTGCCATTAACTTATACAGCGTTCGAACTTT
1277158 CGAACAATGATGATGTTCAAATGATGG-TTGAAGCTTAAAGTAATTATTCAGACGCCGCTATTGA
64 CGAACAATGATGATGTTCAAATGATGGTTTGAAGCTTAAAGTAATTATTCAGACGCCGCTATTGA
1277222 GATGTATGCACATTTTGTTCAAGAGCGTGTTGTTCG
129 GATGTATGCACATTTTGTTCAAGAGCGTGTTGTTCG
1277258 G
1 G
1277259 GGTCAATCTT
Statistics
Matches: 163, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
164 24 0.15
165 74 0.45
166 65 0.40
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (164 bp):
GTCGTTGTTGCAGTACAGATTTCCAATCATTGTTGCCATTAACTTATACAGCGTTCGAACTTTCG
AACAATGATGATGTTCAAATGATGGTTTGAAGCTTAAAGTAATTATTCAGACGCCGCTATTGAGA
TGTATGCACATTTTGTTCAAGAGCGTGTTGTTCG
Found at i:1280002 original size:26 final size:24
Alignment explanation
Indices: 1279973--1280044 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
1279963 AAAATCTAAC
1279973 AAATTTAACAAAATAAAGTAAGTATT
1 AAATTTAACAAAATAAAGTAA--ATT
1279999 AAA-TTAGA-AATAATAAA--AAATT
1 AAATTTA-ACAA-AATAAAGTAAATT
*
1280021 ACAATTAAACAAAATAAAGTAAAT
1 A-AATTTAACAAAATAAAGTAAAT
1280045 AAAAATATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 15
0.70 0.02 0.28
Matches are distributed among these distances:
22 4 0.11
23 9 0.24
24 6 0.16
25 9 0.24
26 10 0.26
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (24 bp):
AAATTTAACAAAATAAAGTAAATT
Found at i:1282026 original size:106 final size:108
Alignment explanation
Indices: 1281831--1282148 Score: 395
Period size: 110 Copynumber: 3.0 Consensus size: 108
1281821 GGTCATTCTC
1281831 CTAAAAATAAATAATTACAAAAAATT-A-TCTTAATCTA-ATATAA-GCATTAAATAAATCAACT
1 CTAAAAATAAATAATTACAAAAAATTAATTCTTAATCTATA-ATAATGCATTAAATAAATCAACT
* *
1281892 AATTACTA--AATAATTTAAATTAAATAAAATGTTAAAATGTCA
65 AATTATTACTAATAATTTAAATTAATTAAAATGTTAAAATGTCA
1281934 -TAAAAATAAATAATTAC-AAAAATTAATTCTTAATCTATAATAATGCATTAAATAAATCAACTA
1 CTAAAAATAAATAATTACAAAAAATTAATTCTTAATCTATAATAATGCATTAAATAAATCAACTA
1281997 ATTATTACTAATAATTTAAATTAATTAAAATGTTAAAATGTCA
66 ATTATTACTAATAATTTAAATTAATTAAAATGTTAAAATGTCA
* ** ** * * * * *
1282040 CTGTATCAGCAA-AGTGT-CGAGATATTTAATTCTTAATCTAATAATCATGCATTAAATAAATCA
1 CT-AAAAATAAATAAT-TAC-AAAAAATTAATTCTTAATCT-ATAATAATGCATTAAATAAATCA
*
1282103 ACTAATTATTACTAATAATTTAAATTAAATTAAAACGTTAAAATGT
62 ACTAATTATTACTAATAATTTAAATT-AATTAAAATGTTAAAATGT
1282149 TACCGTATCA
Statistics
Matches: 189, Mismatches: 13, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
101 7 0.04
102 18 0.10
103 14 0.07
104 26 0.14
106 33 0.17
107 4 0.02
108 5 0.03
109 16 0.08
110 48 0.25
111 18 0.10
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.36
Consensus pattern (108 bp):
CTAAAAATAAATAATTACAAAAAATTAATTCTTAATCTATAATAATGCATTAAATAAATCAACTA
ATTATTACTAATAATTTAAATTAATTAAAATGTTAAAATGTCA
Found at i:1282111 original size:110 final size:109
Alignment explanation
Indices: 1281858--1282187 Score: 426
Period size: 111 Copynumber: 3.1 Consensus size: 109
1281848 CAAAAAATTA
* * *
1281858 TCTTAATCTAAT-ATAAGCATTAAATAAATCAACTAATTACTA--AATAATTTAAATTAAATAAA
1 TCTTAATCTAATAATATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAATTAAA
* ** ** * *
1281920 ATGTTAAAATGTCA-T-AAAAATAAATAAT-TAC-A-AAAATTAAT
66 ATGTTAAAATGTCACTGTATCAGCAA-AATGT-CGAGATATTTAAT
1281961 TCTTAATCT-ATAATAATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAATTAA
1 TCTTAATCTAATAAT-ATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAATTAA
*
1282025 AATGTTAAAATGTCACTGTATCAGCAAAGTGTCGAGATATTTAAT
65 AATGTTAAAATGTCACTGTATCAGCAAAATGTCGAGATATTTAAT
1282070 TCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAATTA
1 TCTTAATCTAATAAT-ATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATT-AATTA
* * *
1282135 AAACGTTAAAATGTTACCGTATCAGCAAAATGTCGAGATATTTAAT
64 AAATGTTAAAATGTCACTGTATCAGCAAAATGTCGAGATATTTAAT
1282181 TCTTAAT
1 TCTTAAT
1282188 ATTTTAAATT
Statistics
Matches: 200, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
102 2 0.01
103 11 0.05
104 26 0.13
106 33 0.17
107 4 0.02
108 6 0.03
109 16 0.08
110 48 0.24
111 54 0.27
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (109 bp):
TCTTAATCTAATAATATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAATTAAA
ATGTTAAAATGTCACTGTATCAGCAAAATGTCGAGATATTTAAT
Found at i:1286165 original size:15 final size:15
Alignment explanation
Indices: 1286143--1286180 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1286133 CAAAAGCGTT
1286143 TGTT-GAACTCTTGG
1 TGTTCGAACTCTTGG
1286157 TGTTCGAACTCTTGG
1 TGTTCGAACTCTTGG
1286172 TGTTCGAAC
1 TGTTCGAAC
1286181 CCGGGACTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.39
Consensus pattern (15 bp):
TGTTCGAACTCTTGG
Found at i:1286692 original size:6 final size:6
Alignment explanation
Indices: 1286681--1286708 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1286671 TAAAAAATAA
1286681 ACAAAC ACAAAC ACAAAC ACAAAC ACAA
1 ACAAAC ACAAAC ACAAAC ACAAAC ACAA
1286709 TCTTATTCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (6 bp):
ACAAAC
Found at i:1288815 original size:116 final size:115
Alignment explanation
Indices: 1288644--1288866 Score: 362
Period size: 116 Copynumber: 1.9 Consensus size: 115
1288634 CGTATCCACG
*
1288644 TACACATATTTATGATTAATTTGATTCAGCATTGAAATTCCCCCTGCACCAAGTTGAAGTATAGA
1 TACACATATTTATGATTAATTTGATTCAGCATTGAAATCCCCCCTGCACCAAGTTGAAGTATAG-
1288709 ATAAAACATTTAAAAG-TG-AAAA-CCCTATTATCATTTGGATCACCTAATT
65 ATAAAACATTT-AAAGTTGAAAAATCCCTATTATCATTTGGATCACCTAATT
1288758 TACACATATTTATTGATTAATTTGATTCAGCAATTGAAATCCCCCCTGCACCAAGTTGAAGTATA
1 TACACATATTTA-TGATTAATTTGATTCAGC-ATTGAAATCCCCCCTGCACCAAGTTGAAGTATA
1288823 GATAAAACATTTAAAGTTGAAAAATTTCCCTATTATCATTTGGA
64 GATAAAACATTTAAAGTTGAAAAA--TCCCTATTATCATTTGGA
1288867 ACCTCATCGT
Statistics
Matches: 101, Mismatches: 1, Indels: 9
0.91 0.01 0.08
Matches are distributed among these distances:
114 16 0.16
115 31 0.31
116 37 0.37
119 17 0.17
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (115 bp):
TACACATATTTATGATTAATTTGATTCAGCATTGAAATCCCCCCTGCACCAAGTTGAAGTATAGA
TAAAACATTTAAAGTTGAAAAATCCCTATTATCATTTGGATCACCTAATT
Found at i:1289223 original size:40 final size:42
Alignment explanation
Indices: 1289136--1289223 Score: 126
Period size: 40 Copynumber: 2.1 Consensus size: 42
1289126 GCAACATTTG
*
1289136 TGCATGATAGAGACATGGATGGCAGTGCATGATACCCATAGA
1 TGCATGATAGAGAAATGGATGGCAGTGCATGATACCCATAGA
* * *
1289178 TGCATGATGGAGAAATGGATGG-A-TGGATGGTACCCATAGA
1 TGCATGATAGAGAAATGGATGGCAGTGCATGATACCCATAGA
1289218 TGCATG
1 TGCATG
1289224 TGCTCTCATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 21 0.50
41 1 0.02
42 20 0.48
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.23
Consensus pattern (42 bp):
TGCATGATAGAGAAATGGATGGCAGTGCATGATACCCATAGA
Found at i:1290035 original size:60 final size:60
Alignment explanation
Indices: 1289901--1290055 Score: 170
Period size: 60 Copynumber: 2.6 Consensus size: 60
1289891 TATTGGTCCT
* * * * *
1289901 AAACTTTTAAATACTCTAATTTCATCCCTAAACCATGACTATCATTCTAAACTAATCCCC
1 AAACTTTTAAACATTCCAATTTCATCCCCAAACTATGACTATCATTCTAAACTAATCCCC
* * * **
1289961 AAACTTTTAAACATTTCAATTTCATCCCCAAACTATGAC-ATTCATTCTATATTGGTCCCC
1 AAACTTTTAAACATTCCAATTTCATCCCCAAACTATGACTA-TCATTCTAAACTAATCCCC
* * *
1290021 AAACTTTTGAACATTCCAATTCCAT-CTCAAACTAT
1 AAACTTTTAAACATTCCAATTTCATCCCCAAACTAT
1290056 ATGTATATAC
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
59 10 0.12
60 70 0.88
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (60 bp):
AAACTTTTAAACATTCCAATTTCATCCCCAAACTATGACTATCATTCTAAACTAATCCCC
Found at i:1290317 original size:60 final size:56
Alignment explanation
Indices: 1290173--1290352 Score: 155
Period size: 60 Copynumber: 3.1 Consensus size: 56
1290163 TATTTGGTGA
* * * **
1290173 AATTCAGGATGAAATGAGAATATTC-AAACTTTAGAAACCAATTTAAAAGTGTCAT
1 AATTTAGGATGAAATTAGAATATTCAAAACTTTAAAAACCAATTTAAAAAAGTCAT
* * * * *
1290228 AGTTTAGGGATGAAATTAGAATGTCCAAAATTTTAAAAACTAATTTAGAATGAAAGTCAT
1 AATTTA-GGATGAAATTAGAATATTCAAAACTTTAAAAACCAATTTA-AA--AAAGTCAT
** ** *
1290288 AATTTAGGAATGAAATTAGAATATTCAAAAAATTAAGGACCAATTTAAAATAGAGTTAT
1 AATTTAGG-ATGAAATTAGAATATTCAAAACTTTAAAAACCAATTTAAAA-A-AGTCAT
1290347 AATTTA
1 AATTTA
1290353 AAAACATATG
Statistics
Matches: 98, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
55 4 0.04
56 16 0.16
57 18 0.18
58 3 0.03
59 15 0.15
60 42 0.43
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.31
Consensus pattern (56 bp):
AATTTAGGATGAAATTAGAATATTCAAAACTTTAAAAACCAATTTAAAAAAGTCAT
Found at i:1297913 original size:10 final size:10
Alignment explanation
Indices: 1297898--1297931 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1297888 GTTTTTATCC
1297898 ATTTGTTTTT
1 ATTTGTTTTT
1297908 ATTTGTTTTT
1 ATTTGTTTTT
*
1297918 ATTTTATTTTT
1 A-TTTGTTTTT
1297929 ATT
1 ATT
1297932 ATTAATCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (10 bp):
ATTTGTTTTT
Found at i:1297949 original size:16 final size:16
Alignment explanation
Indices: 1297921--1297973 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
1297911 TGTTTTTATT
*
1297921 TTATTTTTATTATTAA
1 TTATTATTATTATTAA
*
1297937 TCTATTA-TATTATTTA
1 T-TATTATTATTATTAA
1297953 TTATTATTATTATT-A
1 TTATTATTATTATTAA
1297968 TTATTA
1 TTATTA
1297974 ATAAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
15 12 0.36
16 17 0.52
17 4 0.12
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTATTATTATTAA
Found at i:1297985 original size:38 final size:37
Alignment explanation
Indices: 1297916--1297988 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 37
1297906 TTATTTGTTT
* ** **
1297916 TTATTTTATTTTTATTATTAATCTATTATATTATTTA
1 TTATTTTATTATTATTATTAATAAAAAATATTATTTA
1297953 TTATTATTATTATTATTATTAATAAAAAATATTATT
1 TTATT-TTATTATTATTATTAATAAAAAATATTATT
1297989 ACATTTCAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 5 0.17
38 25 0.83
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (37 bp):
TTATTTTATTATTATTATTAATAAAAAATATTATTTA
Found at i:1297989 original size:3 final size:3
Alignment explanation
Indices: 1297916--1297973 Score: 66
Period size: 3 Copynumber: 19.0 Consensus size: 3
1297906 TTATTTGTTT
*
1297916 TTA TT- TTA TTT TTA TTA TTAA TCTA TTA -TA TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A T-TA TTA TTA TTA -TTA TTA TTA TTA
1297962 TTA TTA TTA TTA
1 TTA TTA TTA TTA
1297974 ATAAAAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 4 0.08
3 36 0.75
4 7 0.15
5 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1300948 original size:2 final size:2
Alignment explanation
Indices: 1300939--1300970 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1300929 ATATACTTAT
1300939 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1300971 TTTGTATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1310593 original size:19 final size:19
Alignment explanation
Indices: 1310533--1310593 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
1310523 TCAAATGAAG
*
1310533 ATTGCATCAACA-TTCATGC
1 ATTGCAT-AACAGATCATGC
*
1310552 ATT-CAT-A-AGAACAT-C
1 ATTGCATAACAGATCATGC
1310567 ATTTGCATAACAGATCATGC
1 A-TTGCATAACAGATCATGC
1310587 ATTGCAT
1 ATTGCAT
1310594 TGATACATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
15 3 0.09
16 6 0.18
17 3 0.09
18 4 0.12
19 15 0.45
20 2 0.06
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.31
Consensus pattern (19 bp):
ATTGCATAACAGATCATGC
Found at i:1311527 original size:124 final size:124
Alignment explanation
Indices: 1311181--1311621 Score: 733
Period size: 123 Copynumber: 3.6 Consensus size: 124
1311171 CAATGGATCG
* * * *
1311181 ACATTTTCAGAGAAAGTTCATAATAAGAAGAACTTATCTGAAG-AGGAAGAAAAAGTTCATAATG
1 ACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * *
1311245 AGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCGCAGAAGGAGATAAATCATCACCA
66 AGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCA
* *
1311304 ACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAATG-AGAAGAAGTTCATAATG
1 ACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1311368 AGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCA
66 AGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCA
*
1311427 ACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1 ACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
1311492 AGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGGTAGATCAACATCA
66 AGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCA
** *
1311551 ATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATG
1 ACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1311616 AGAAGA
66 AGAAGA
1311622 ATTTGTTTAA
Statistics
Matches: 301, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
123 156 0.52
124 145 0.48
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (124 bp):
ACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
AGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCA
Found at i:1311985 original size:16 final size:16
Alignment explanation
Indices: 1311957--1312038 Score: 80
Period size: 16 Copynumber: 5.1 Consensus size: 16
1311947 GTTTTTATTT
*
1311957 TTATTTTTATTATTAA
1 TTATTATTATTATTAA
1311973 TCTATTA-TATTATT-A
1 T-TATTATTATTATTAA
*
1311988 TTA-TATTTATTATAATAT
1 TTATTA-TTATTAT--TAA
*
1312006 TTATTATTATTATTTA
1 TTATTATTATTATTAA
1312022 TTATTATTATTATTAA
1 TTATTATTATTATTAA
1312038 T
1 T
1312039 AAAAAATATT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
13 2 0.04
14 2 0.04
15 8 0.15
16 25 0.46
17 5 0.09
18 10 0.19
19 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTATTATTATTAA
Found at i:1311985 original size:25 final size:24
Alignment explanation
Indices: 1311957--1312036 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 24
1311947 GTTTTTATTT
* *
1311957 TTATTTTTATTATTAATCTATTATA
1 TTATTATTATTATTTAT-TATTATA
*
1311982 TTATTATTA-TATTTATTATAATA
1 TTATTATTATTATTTATTATTATA
1312005 TTTATTATTATTATTTATTATTATTA
1 -TTATTATTATTATTTATTATTA-TA
1312031 TTATTA
1 TTATTA
1312037 ATAAAAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.12
24 15 0.31
25 25 0.52
26 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATTATTATTATTTATTATTATA
Found at i:1312052 original size:3 final size:3
Alignment explanation
Indices: 1311951--1312036 Score: 79
Period size: 3 Copynumber: 28.0 Consensus size: 3
1311941 CCATTTGTTT
* *
1311951 TTA TTT TTA TTT TTA TTA TTAA TCTA TTA -TA TTA TTA TTA -TA TTTA
1 TTA TTA TTA TTA TTA TTA TT-A T-TA TTA TTA TTA TTA TTA TTA -TTA
*
1311997 TTA -TA ATA TTTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
1312037 ATAAAAAATA
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
2 6 0.09
3 52 0.74
4 11 0.16
5 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1321886 original size:17 final size:17
Alignment explanation
Indices: 1321864--1321916 Score: 106
Period size: 17 Copynumber: 3.1 Consensus size: 17
1321854 CTGTGAGAAA
1321864 CAACTAATGCAGCAGGG
1 CAACTAATGCAGCAGGG
1321881 CAACTAATGCAGCAGGG
1 CAACTAATGCAGCAGGG
1321898 CAACTAATGCAGCAGGG
1 CAACTAATGCAGCAGGG
1321915 CA
1 CA
1321917 TACCATGTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.36, C:0.25, G:0.28, T:0.11
Consensus pattern (17 bp):
CAACTAATGCAGCAGGG
Found at i:1325968 original size:51 final size:51
Alignment explanation
Indices: 1325873--1325973 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 51
1325863 CCCATCATCA
* *
1325873 TCGTCGTTGTCATTATCATTCTTCTTTTTTTGATATCTCAATTTCTTATCG
1 TCGTCGTTGTCATCATCATTCTTCTTTTTTTGATATCTCAATTTCCTATCG
* * **
1325924 TCGTCGTTGTCGTCATCATTTTTCTTTTTTCT-ATATCTTGATTTCCTATC
1 TCGTCGTTGTCATCATCATTCTTCTTTTTT-TGATATCTCAATTTCCTATC
1325974 ATCATCATCA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.10, T:0.55
Consensus pattern (51 bp):
TCGTCGTTGTCATCATCATTCTTCTTTTTTTGATATCTCAATTTCCTATCG
Found at i:1327894 original size:51 final size:51
Alignment explanation
Indices: 1327818--1327919 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
1327808 ATAAGTCGTA
1327818 TTTTTATTGATTTAGGATTCAGGATTTAAGGCTTGGTTTCCATGAGTAATG
1 TTTTTATTGATTTAGGATTCAGGATTTAAGGCTTGGTTTCCATGAGTAATG
1327869 TTTTTATTGATTTAGGATTCAGGATTTAAGGCTTGGTTTCCATGAGTAATG
1 TTTTTATTGATTTAGGATTCAGGATTTAAGGCTTGGTTTCCATGAGTAATG
1327920 CTTGTATCTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.45
Consensus pattern (51 bp):
TTTTTATTGATTTAGGATTCAGGATTTAAGGCTTGGTTTCCATGAGTAATG
Found at i:1334044 original size:63 final size:63
Alignment explanation
Indices: 1333958--1334109 Score: 245
Period size: 63 Copynumber: 2.4 Consensus size: 63
1333948 GCGATTTTCT
*
1333958 AAATTCGTGTTACGATAGTCCAAGTTCGTTACGATAGTCAAAGTTCGCGTTGCGATTTATTCC
1 AAATTCGTGTTGCGATAGTCCAAGTTCGTTACGATAGTCAAAGTTCGCGTTGCGATTTATTCC
* * *
1334021 AAATTCGTGTTGCGATAGTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGTGATTTATTCC
1 AAATTCGTGTTGCGATAGTCCAAGTTCGTTACGATAGTCAAAGTTCGCGTTGCGATTTATTCC
*
1334084 AAGTTC--GTTGCGATAGTCCAAGTTCG
1 AAATTCGTGTTGCGATAGTCCAAGTTCG
1334110 CGTTGCGATT
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
61 20 0.24
63 64 0.76
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (63 bp):
AAATTCGTGTTGCGATAGTCCAAGTTCGTTACGATAGTCAAAGTTCGCGTTGCGATTTATTCC
Found at i:1334107 original size:105 final size:104
Alignment explanation
Indices: 1333976--1334177 Score: 343
Period size: 105 Copynumber: 1.9 Consensus size: 104
1333966 GTTACGATAG
1333976 TCCAAGTTCGTTACGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTGTTGCGATAGTC
1 TCCAAGTTCGTTACGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATT--TGTTGCGATAGTC
1334041 CAAGTT-CGTTGCGATAGTCCAAGTTCGCGTTGTGATTTAT
64 CAAGTTCCGTTGCGATAGTCCAAGTTCGCGTTGTGATTTAT
* *
1334081 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTTGTTGCGATAGTCCA
1 TCCAAGTTCGTTACGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTTGTTGCGATAGTCCA
*
1334146 AGTTCGCGTTGCGATAGTCGAAGTTCGCGTTG
66 AGTTC-CGTTGCGATAGTCCAAGTTCGCGTTG
1334178 CGAATCTGGA
Statistics
Matches: 92, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
103 19 0.21
105 73 0.79
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (104 bp):
TCCAAGTTCGTTACGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTTGTTGCGATAGTCCA
AGTTCCGTTGCGATAGTCCAAGTTCGCGTTGTGATTTAT
Found at i:1334173 original size:21 final size:21
Alignment explanation
Indices: 1333961--1334180 Score: 213
Period size: 21 Copynumber: 10.6 Consensus size: 21
1333951 ATTTTCTAAA
* *
1333961 TTCGTGTTACGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1333982 TT--CGTTACGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1334001 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
1334024 TTCGTGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
1334045 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1334064 TTCGCGTTGTGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
1334087 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1334106 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
1334129 TT--TGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
1334148 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
1334169 TTCGCGTTGCGA
1 TTCGCGTTGCGA
1334181 ATCTGGAAAC
Statistics
Matches: 164, Mismatches: 21, Indels: 28
0.77 0.10 0.13
Matches are distributed among these distances:
19 54 0.33
21 74 0.45
23 36 0.22
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:1334200 original size:20 final size:20
Alignment explanation
Indices: 1334175--1334241 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
1334165 GAAGTTCGCG
1334175 TTGCGAATCTGGAAACTGAT
1 TTGCGAATCTGGAAACTGAT
** **
1334195 TTGCGATAGTC--GAAGTTCGCG
1 TTGCGA-A-TCTGGAAACT-GAT
1334216 TTGCGAATCTGGAAACTGAT
1 TTGCGAATCTGGAAACTGAT
1334236 TTGCGA
1 TTGCGA
1334242 TACCGGAGAT
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
19 2 0.06
20 18 0.53
21 12 0.35
22 2 0.06
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (20 bp):
TTGCGAATCTGGAAACTGAT
Found at i:1334202 original size:41 final size:41
Alignment explanation
Indices: 1334154--1334263 Score: 186
Period size: 41 Copynumber: 2.7 Consensus size: 41
1334144 CAAGTTCGCG
1334154 TTGCGATAGTCGAAGTTCGCGTTGCGAATCTGGAAACTGAT
1 TTGCGATAGTCGAAGTTCGCGTTGCGAATCTGGAAACTGAT
1334195 TTGCGATAGTCGAAGTTCGCGTTGCGAATCTGGAAACTGAT
1 TTGCGATAGTCGAAGTTCGCGTTGCGAATCTGGAAACTGAT
* * *
1334236 TTGCGATA-CCGGAGATCGCGTTGCGAAT
1 TTGCGATAGTCGAAGTTCGCGTTGCGAAT
1334264 TATCGATCGC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
40 17 0.26
41 49 0.74
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (41 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGAATCTGGAAACTGAT
Found at i:1340929 original size:19 final size:20
Alignment explanation
Indices: 1340888--1340929 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
1340878 CTAAACTTTC
* *
1340888 AATTTTTTAAAACTTAATGTT
1 AATTTTTT-AAACTGAATATT
1340909 AATTTTTT-AACTGAATATT
1 AATTTTTTAAACTGAATATT
1340928 AA
1 AA
1340930 AACGAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 11 0.58
21 8 0.42
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (20 bp):
AATTTTTTAAACTGAATATT
Found at i:1345693 original size:18 final size:19
Alignment explanation
Indices: 1345670--1345711 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1345660 TGAGGGTCGA
*
1345670 GGTTGATGAT-GAGGGATT
1 GGTTGAAGATGGAGGGATT
*
1345688 GGTTGAAGATGGTGGGATT
1 GGTTGAAGATGGAGGGATT
1345707 -GTTGA
1 GGTTGA
1345712 CCAGAAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.33
Consensus pattern (19 bp):
GGTTGAAGATGGAGGGATT
Found at i:1350094 original size:46 final size:47
Alignment explanation
Indices: 1349996--1350095 Score: 166
Period size: 47 Copynumber: 2.1 Consensus size: 47
1349986 TTAGTTGTTC
* *
1349996 CCATGCCTTTTGAACCAAATGCCAATGTTTGGGGTACCCTTTAGGGA
1 CCATGTCTTTTGAACCAAATGCCAACGTTTGGGGTACCCTTTAGGGA
1350043 CCATGTCTTTTGAACCAAATGCCAACGTTT-GGGTACCCTTTAGGGA
1 CCATGTCTTTTGAACCAAATGCCAACGTTTGGGGTACCCTTTAGGGA
*
1350089 GCATGTC
1 CCATGTC
1350096 CGATGCATGG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
46 22 0.44
47 28 0.56
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (47 bp):
CCATGTCTTTTGAACCAAATGCCAACGTTTGGGGTACCCTTTAGGGA
Found at i:1358435 original size:32 final size:32
Alignment explanation
Indices: 1358392--1358463 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
1358382 GTTCATTTAT
* *
1358392 ATTCATTCGTTTATGTTCATTTACGTTTGGTA
1 ATTCATTCGTTTATGTTCATTTACGCTAGGTA
* *
1358424 ATTCGTTCGTTTATGTTCGTTTACGCTAGGTA
1 ATTCATTCGTTTATGTTCATTTACGCTAGGTA
*
1358456 ATCCATTC
1 ATTCATTC
1358464 ATCAATGTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.49
Consensus pattern (32 bp):
ATTCATTCGTTTATGTTCATTTACGCTAGGTA
Found at i:1359988 original size:108 final size:112
Alignment explanation
Indices: 1359707--1360119 Score: 563
Period size: 114 Copynumber: 3.7 Consensus size: 112
1359697 GGGTAAGATC
* * *
1359707 TGCCATTTTTCAGGAATTGGGTATTTGTTTATGCTCTTTGGTATCTAAATATTTGAATTGAAATG
1 TGCCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGGTATCTAAAGATTTGAATTGAAATG
*
1359772 AAGTTTCATGATAACCGGGTGAGTTGAACTTGAGCTCTTTAAGATGATT
66 AAGTTCCATGATAACC-GGTGA-TTGAACTTGAGCTCTTTAAGATGATT
* * *
1359821 TGTCATTTTTCAGGAATTTAGGTATTTGTTAACGATCTTTGGTATCTAAAGATTTG-ATAT-AAA
1 TGCCATTTTTCAGGAA-TTGGGTATTTGTTTACGATCTTTGGTATCTAAAGATTTGAAT-TGAAA
* *
1359884 TTGAAGTTCCATCATAACC-G-GA-TG-ACTTGAGCTCTTTGAGATGATT
64 -TGAAGTTCCATGATAACCGGTGATTGAACTTGAGCTCTTTAAGATGATT
* *
1359930 TGCCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGTTATCTAAAGATTTG-ATATAAAAT
1 TGCCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGGTATCTAAAGATTTGAAT-TGAAAT
1359994 GAAGTTCCATGATAACCGGATGACTTGAACTTGAGCTCTTTAAGATGATT
65 GAAGTTCCATGATAACCGG-TGA-TTGAACTTGAGCTCTTTAAGATGATT
* * * *
1360044 TGCCATTTTTCAGGAATTGGGTA-TTGTTTATGATTTTTGGTATCTGAACATTTGAATTGAAATG
1 TGCCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGGTATCTAAAGATTTGAATTGAAATG
1360108 AAGTTCCATGAT
66 AAGTTCCATGAT
1360120 TCCATTTTTC
Statistics
Matches: 267, Mismatches: 21, Indels: 23
0.86 0.07 0.07
Matches are distributed among these distances:
108 57 0.21
109 40 0.15
110 2 0.01
111 2 0.01
112 2 0.01
113 47 0.18
114 66 0.25
115 51 0.19
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (112 bp):
TGCCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGGTATCTAAAGATTTGAATTGAAATG
AAGTTCCATGATAACCGGTGATTGAACTTGAGCTCTTTAAGATGATT
Done.