Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 13 of 240
Found at i:4797997 original size:36 final size:36
Alignment explanation
Indices: 4797925--4798000 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
4797915 TACCATCATC
* * *
4797925 ATCATCATCTGCAACAACAACATCAACATCATCACA
1 ATCATCATCTACAACAACAACACCAACATCAACACA
* *
4797961 ATCATCATCTACAACAGCAACACCATC-TCCAACACA
1 ATCATCATCTACAACAACAACACCAACAT-CAACACA
4797997 ATCA
1 ATCA
4798001 GCGGCTACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 1 0.03
36 33 0.97
ACGTcount: A:0.43, C:0.36, G:0.03, T:0.18
Consensus pattern (36 bp):
ATCATCATCTACAACAACAACACCAACATCAACACA
Found at i:4798214 original size:93 final size:93
Alignment explanation
Indices: 4798117--4798310 Score: 370
Period size: 93 Copynumber: 2.1 Consensus size: 93
4798107 CACCACCAGA
*
4798117 ACCAACACAATCAGCAACAACAGTAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
1 ACCAACACAATCAGCAACAACAGAAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
4798182 CACCATCATCGTCATCGTCGGTAGCAAC
66 CACCATCATCGTCATCGTCGGTAGCAAC
4798210 ACCAACACAATCAGCAACAACAGAAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
1 ACCAACACAATCAGCAACAACAGAAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
4798275 CACCATCATCGTCATCGTCGGTAGCAAC
66 CACCATCATCGTCATCGTCGGTAGCAAC
*
4798303 ACCGACAC
1 ACCAACAC
4798311 CGACACCAAC
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 99 1.00
ACGTcount: A:0.38, C:0.32, G:0.14, T:0.16
Consensus pattern (93 bp):
ACCAACACAATCAGCAACAACAGAAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
CACCATCATCGTCATCGTCGGTAGCAAC
Found at i:4798366 original size:87 final size:89
Alignment explanation
Indices: 4798117--4798381 Score: 236
Period size: 93 Copynumber: 2.9 Consensus size: 89
4798107 CACCACCAGA
* * * * * *
4798117 ACCAACACAATCAGCAACAACAGTAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
1 ACCAACAC-A-CAGCAACAACA-CA-AGCCAACACAATCATCATCACAAATAACAACTACGAGAG
4798182 CACCATCATCGTCATCGTCGGTAGCAAC
62 CACCATCATCGTCATCGTCGGTAGCAAC
* * * * *
4798210 ACCAACACAATCAGCAACAACAGAAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
1 ACCAACAC-A-CAGCAACAACACAA--GCCAACACAATCATCATCACAAATAACAACTACGAGAG
4798275 CACCATCATCGTCATCGTCGGTAGCAAC
62 CACCATCATCGTCATCGTCGGTAGCAAC
* * * *
4798303 ACCGACAC-C-GACACCAACACCA-CCAACACAATCATCATCAC-AATCAACAACTAC-AGCGAC
1 ACCAACACACAG-CAACAACACAAGCCAACACAATCATCATCACAAAT-AACAACTACGAGAG-C
*
4798363 ACCATTA-CGATCATCGTCG
63 ACCATCATCG-TCATCGTCG
4798382 CCATCCCCAG
Statistics
Matches: 154, Mismatches: 12, Indels: 18
0.84 0.07 0.10
Matches are distributed among these distances:
86 7 0.05
87 41 0.27
89 1 0.01
90 9 0.06
92 1 0.01
93 95 0.62
ACGTcount: A:0.38, C:0.34, G:0.12, T:0.15
Consensus pattern (89 bp):
ACCAACACACAGCAACAACACAAGCCAACACAATCATCATCACAAATAACAACTACGAGAGCACC
ATCATCGTCATCGTCGGTAGCAAC
Found at i:4801494 original size:60 final size:59
Alignment explanation
Indices: 4801381--4801510 Score: 154
Period size: 60 Copynumber: 2.2 Consensus size: 59
4801371 TTAATATAAC
* * * * * *
4801381 ATTTGGTACTTGAATTTGACACTTTTTTTTTTAATTTGGTACCTAAATTTTTTTTTATCTAA
1 ATTTGATACTTGAACTTGACAC-TATTTTTCTAATCTAGTACCTAAATTTTTTTTT-TC-AA
* *
4801443 TTTTGATACTTGAACTTGACAC-ATTTTTCTAATCTAGTACCTAAGTTTTTTTTTTCAA
1 ATTTGATACTTGAACTTGACACTATTTTTCTAATCTAGTACCTAAATTTTTTTTTTCAA
4801501 ATTTGATACT
1 ATTTGATACT
4801511 AAACTTGTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
58 11 0.19
59 2 0.03
60 27 0.46
62 19 0.32
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.53
Consensus pattern (59 bp):
ATTTGATACTTGAACTTGACACTATTTTTCTAATCTAGTACCTAAATTTTTTTTTTCAA
Found at i:4802138 original size:32 final size:32
Alignment explanation
Indices: 4802088--4802156 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
4802078 TTGGACTAAA
** * *
4802088 TAAGTTTAGATATTAAATT-AAGAAAAAATTGT
1 TAAGTTTAGATACCAAATTGAAAAAAAAAAT-T
4802120 TAAGTTTAGATACCAAATTGAAAAAAAAAATT
1 TAAGTTTAGATACCAAATTGAAAAAAAAAATT
4802152 TAAGT
1 TAAGT
4802157 ACCAAATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 23 0.72
33 9 0.28
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (32 bp):
TAAGTTTAGATACCAAATTGAAAAAAAAAATT
Found at i:4806971 original size:18 final size:19
Alignment explanation
Indices: 4806945--4806980 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4806935 TTGTTTCATA
4806945 CAAAATTACA-TTAAAAAT
1 CAAAATTACACTTAAAAAT
*
4806963 CAAATTTACACTTAAAAA
1 CAAAATTACACTTAAAAA
4806981 AAACTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (19 bp):
CAAAATTACACTTAAAAAT
Found at i:4807370 original size:6 final size:6
Alignment explanation
Indices: 4807359--4807390 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
4807349 CATTTTATAT
4807359 CAATCA CAATCA CAATCA CAATCA CAATCA CA
1 CAATCA CAATCA CAATCA CAATCA CAATCA CA
4807391 TTTTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (6 bp):
CAATCA
Found at i:4809503 original size:15 final size:15
Alignment explanation
Indices: 4809485--4809517 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4809475 TAATCTTTAA
4809485 AAATTA-TAAAAATAT
1 AAATTATTAAAAAT-T
4809500 AAATTATTAAAAATT
1 AAATTATTAAAAATT
4809515 AAA
1 AAA
4809518 ATTTCATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTATTAAAAATT
Found at i:4816113 original size:6 final size:6
Alignment explanation
Indices: 4816104--4816133 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
4816094 ACAAAACAAT
4816104 GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA
1 GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA
4816134 CGTGAAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (6 bp):
GAGAAA
Found at i:4816624 original size:23 final size:20
Alignment explanation
Indices: 4816586--4816628 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
4816576 TAAGTCGATA
4816586 ATAAAAATTTATATTAATTTT
1 ATAAAAATTTATATT-ATTTT
4816607 ATAAAATATATTATATTATTTT
1 ATAAAA-AT-TTATATTATTTT
4816629 GATCATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 7 0.35
23 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATAAAAATTTATATTATTTT
Found at i:4816642 original size:22 final size:20
Alignment explanation
Indices: 4816617--4816663 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
4816607 ATAAAATATA
4816617 TTATAT-TATTTTGATCATATTT
1 TTATATGTATTTTG-T-AT-TTT
4816639 TTAT-TGTATTTTGTATTTT
1 TTATATGTATTTTGTATTTT
4816658 TTATAT
1 TTATAT
4816664 AAAAAGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 7 0.30
20 3 0.13
21 2 0.09
22 11 0.48
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.68
Consensus pattern (20 bp):
TTATATGTATTTTGTATTTT
Found at i:4817270 original size:22 final size:22
Alignment explanation
Indices: 4817240--4817282 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4817230 TTATAGAAAA
*
4817240 TTATATTTTACAAATATTTTTT
1 TTATATTTTAAAAATATTTTTT
*
4817262 TTATTTTTTAAAAATATTTTT
1 TTATATTTTAAAAATATTTTT
4817283 ATATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATATTTTAAAAATATTTTTT
Found at i:4819353 original size:9 final size:9
Alignment explanation
Indices: 4819339--4819370 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
4819329 ATTATTTATT
4819339 AAAATAATA
1 AAAATAATA
4819348 AAAATAATA
1 AAAATAATA
4819357 AAAATAATA
1 AAAATAATA
4819366 AAAAT
1 AAAAT
4819371 TTAGACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAATAATA
Found at i:4820769 original size:18 final size:18
Alignment explanation
Indices: 4820742--4820778 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4820732 ATATTCTATT
*
4820742 AATTTAAACTTAAATTTA
1 AATTTAAACTCAAATTTA
*
4820760 AATTTCAACTCAAATTTA
1 AATTTAAACTCAAATTTA
4820778 A
1 A
4820779 TGTTAAAAAT
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:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTTAAACTCAAATTTA
Found at i:4845558 original size:2 final size:2
Alignment explanation
Indices: 4845553--4845585 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4845543 TTTTTTTTTT
*
4845553 TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
4845586 TGGGTTCTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4852426 original size:18 final size:17
Alignment explanation
Indices: 4852372--4852427 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
4852362 GGAGAAGCAG
4852372 AAGAGAATGGAAAATAA
1 AAGAGAATGGAAAATAA
* * *
4852389 AGAAAAAAAGGAAAAT-A
1 A-AGAGAATGGAAAATAA
4852406 AAGAGAATGGAAAATTAA
1 AAGAGAATGGAAAA-TAA
4852424 AAGA
1 AAGA
4852428 ACATAAAAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 10 0.33
17 4 0.13
18 16 0.53
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.11
Consensus pattern (17 bp):
AAGAGAATGGAAAATAA
Found at i:4853966 original size:27 final size:27
Alignment explanation
Indices: 4853936--4853987 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
4853926 GGCCAATCAC
4853936 ATTGGCGGCACCAAAGGCGCCAAAGAG
1 ATTGGCGGCACCAAAGGCGCCAAAGAG
* *
4853963 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAAAGGCGCCAAAG
4853988 GACTAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.25, G:0.33, T:0.12
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGCGCCAAAGAG
Found at i:4854548 original size:19 final size:19
Alignment explanation
Indices: 4854524--4854582 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
4854514 TCTAATTAAG
4854524 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
* * *
4854543 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTAATT
4854561 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
4854580 TAA
1 TAA
4854583 ATATTGGCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAACTCTATTTTAATT
Found at i:4862274 original size:11 final size:11
Alignment explanation
Indices: 4862258--4862283 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4862248 CTCTTATAGT
4862258 AAAATATTTTA
1 AAAATATTTTA
4862269 AAAATATTTTA
1 AAAATATTTTA
4862280 AAAA
1 AAAA
4862284 AACACATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATATTTTA
Found at i:4865694 original size:37 final size:37
Alignment explanation
Indices: 4865644--4865718 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
4865634 AAAAAATGAA
4865644 TGAAAAATTGACCTGATAAGTGGTGTCGAATTTATCG
1 TGAAAAATTGACCTGATAAGTGGTGTCGAATTTATCG
4865681 TGAAAAATTGACCTGATAAGTGGTGTCGAATTTATCG
1 TGAAAAATTGACCTGATAAGTGGTGTCGAATTTATCG
4865718 T
1 T
4865719 ACATGAAGCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (37 bp):
TGAAAAATTGACCTGATAAGTGGTGTCGAATTTATCG
Found at i:4870410 original size:22 final size:22
Alignment explanation
Indices: 4870376--4870424 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
4870366 TCTAAGCAAT
*
4870376 AATAATAAGAAAA-TAAAAACAA
1 AATAATAAAAAAAGTAAAAA-AA
*
4870398 AATATTAAAAAAAGTAAAAAAA
1 AATAATAAAAAAAGTAAAAAAA
4870420 AATAA
1 AATAA
4870425 ATACATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (22 bp):
AATAATAAAAAAAGTAAAAAAA
Found at i:4871044 original size:36 final size:38
Alignment explanation
Indices: 4871004--4871094 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 38
4870994 TTAATTAATT
4871004 TTTAAAAATT-TT-AAATATATAAAAAT-TATTTTA-AAA
1 TTTAAAAATTATTAAAAT-TATAAAAATAT-TTTTATAAA
*
4871040 TTT-AAAATTATTAAAATTATAAAAATATTTTTATAAT
1 TTTAAAAATTATTAAAATTATAAAAATATTTTTATAAA
4871077 TTTAAAAAGTTAATTAAA
1 TTTAAAAA-TT-ATTAAA
4871095 TTCTGAATGT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
35 6 0.13
36 19 0.40
37 10 0.21
38 4 0.09
39 2 0.04
40 6 0.13
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (38 bp):
TTTAAAAATTATTAAAATTATAAAAATATTTTTATAAA
Found at i:4871047 original size:28 final size:28
Alignment explanation
Indices: 4871003--4871059 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
4870993 TTTAATTAAT
*
4871003 TTTTAAAAATTTTAAATATATAAAAATTA
1 TTTTAAAAATTTAAAAT-TATAAAAATTA
*
4871032 TTTT-AAAATTTAAAATTATTAAAATTA
1 TTTTAAAAATTTAAAATTATAAAAATTA
4871059 T
1 T
4871060 AAAAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 11 0.42
28 11 0.42
29 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTTAAAAATTTAAAATTATAAAAATTA
Found at i:4871052 original size:21 final size:20
Alignment explanation
Indices: 4871011--4871070 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 20
4871001 ATTTTTAAAA
4871011 ATTTTAAATATATAAAAATT
1 ATTTTAAATATATAAAAATT
*
4871031 ATTTTAAA-AT-TTAAAATT
1 ATTTTAAATATATAAAAATT
*
4871049 A-TTAAAAT-TATAAAAA-T
1 ATTTTAAATATATAAAAATT
4871066 ATTTT
1 ATTTT
4871071 TATAATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 8 0.24
18 15 0.45
19 2 0.06
20 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTTAAATATATAAAAATT
Found at i:4871055 original size:16 final size:17
Alignment explanation
Indices: 4871006--4871068 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
4870996 AATTAATTTT
*
4871006 TAAAAAT-TTTAAATATA
1 TAAAAATATTAAAAT-TA
4871023 TAAAAATTATTTTAAAATT-
1 TAAAAA-TA--TTAAAATTA
*
4871042 TAAAATTATTAAAATTA
1 TAAAAATATTAAAATTA
4871059 TAAAAATATT
1 TAAAAATATT
4871069 TTTATAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
16 8 0.21
17 15 0.39
18 3 0.08
19 5 0.13
20 1 0.03
21 6 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAAATATTAAAATTA
Found at i:4871069 original size:27 final size:28
Alignment explanation
Indices: 4871000--4871069 Score: 67
Period size: 27 Copynumber: 2.6 Consensus size: 28
4870990 GTATTTAATT
*
4871000 AATTTTTAAAAAT-TTTAAATATATAAA
1 AATTATTAAAAATATTTAAATATATAAA
** *
4871027 AATTATTTTAAA-ATTTAAA-ATTATTAA
1 AATTATTAAAAATATTTAAATA-TATAAA
4871054 AATTA-TAAAAATATTT
1 AATTATTAAAAATATTT
4871070 TTATAATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
26 5 0.15
27 29 0.85
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
AATTATTAAAAATATTTAAATATATAAA
Found at i:4874707 original size:70 final size:70
Alignment explanation
Indices: 4874594--4874733 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
4874584 AATGTTATTT
4874594 GACGGGTTTTTTTACACTAATAAAAGAAATAATTATTAAAATAGAGTGGAAAGCAAATTATTTAC
1 GACGGGTTTTTTTACACTAATAAAAGAAATAATTATTAAAATAGAGTGGAAAGCAAATTATTTAC
4874659 GAGGA
66 GAGGA
4874664 GACGGGTTTTTTTACACTAATAAAAGAAATAATTATTAAAATAGAGTGGAAAGCAAATTATTTAC
1 GACGGGTTTTTTTACACTAATAAAAGAAATAATTATTAAAATAGAGTGGAAAGCAAATTATTTAC
4874729 GAGGA
66 GAGGA
4874734 TGAATAGTTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (70 bp):
GACGGGTTTTTTTACACTAATAAAAGAAATAATTATTAAAATAGAGTGGAAAGCAAATTATTTAC
GAGGA
Found at i:4875016 original size:25 final size:26
Alignment explanation
Indices: 4874986--4875043 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
4874976 AGCTGTTTTA
*
4874986 ATTTTATAAATT-T-AATTTTTTAAAT
1 ATTTTATAAATTATAAATTCTTT-AAT
4875011 ATTTTAT-AATTATAAATTCTTTAAT
1 ATTTTATAAATTATAAATTCTTTAAT
4875036 A-TTTATAA
1 ATTTTATAA
4875044 TAATGATCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 9 0.31
25 13 0.45
26 7 0.24
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTTATAAATTATAAATTCTTTAAT
Found at i:4875793 original size:76 final size:76
Alignment explanation
Indices: 4875702--4875857 Score: 312
Period size: 76 Copynumber: 2.1 Consensus size: 76
4875692 TTTTCCACCG
4875702 TATTTTTATAATTATTTATTTGTATTATTAACGTAAAAGACCCTTATTTGACACATCGGAGCATA
1 TATTTTTATAATTATTTATTTGTATTATTAACGTAAAAGACCCTTATTTGACACATCGGAGCATA
4875767 GATCTAAAATA
66 GATCTAAAATA
4875778 TATTTTTATAATTATTTATTTGTATTATTAACGTAAAAGACCCTTATTTGACACATCGGAGCATA
1 TATTTTTATAATTATTTATTTGTATTATTAACGTAAAAGACCCTTATTTGACACATCGGAGCATA
4875843 GATCTAAAATA
66 GATCTAAAATA
4875854 TATT
1 TATT
4875858 CATGGGGAGG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 80 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (76 bp):
TATTTTTATAATTATTTATTTGTATTATTAACGTAAAAGACCCTTATTTGACACATCGGAGCATA
GATCTAAAATA
Found at i:4880186 original size:3 final size:3
Alignment explanation
Indices: 4880178--4880218 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
4880168 AGCATATACG
4880178 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
4880219 CAGAAAACGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4886914 original size:25 final size:25
Alignment explanation
Indices: 4886886--4886933 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
4886876 TAAAGTAAGA
*
4886886 TTAATTATAAAAATATTTTTTAAAT
1 TTAATTATAAAAATATATTTTAAAT
4886911 TTAATTATAAAAATATATTTTAA
1 TTAATTATAAAAATATATTTTAA
4886934 TAAAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTAATTATAAAAATATATTTTAAAT
Found at i:4899193 original size:16 final size:17
Alignment explanation
Indices: 4899174--4899212 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
4899164 TATTTTTATT
4899174 AAATTATTA--TATAATA
1 AAATTATTAGTTAT-ATA
4899190 AAATTATTAGTTATATA
1 AAATTATTAGTTATATA
4899207 AAATTA
1 AAATTA
4899213 AATTTATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 9 0.43
18 3 0.14
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
AAATTATTAGTTATATA
Found at i:4903847 original size:51 final size:51
Alignment explanation
Indices: 4903783--4903885 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 51
4903773 GAAACTCTTT
* * *
4903783 CGGATCCGGTTTCTCGTCAAACGTATGATTATGAATTGG-GCTTGGTTAATC
1 CGGATCCGATTTCTCATCAAACGTATGATTATGAAATGGAG-TTGGTTAATC
*
4903834 CGGATCCGATTTCTCATCAAATGTATGATTATGAAATGGAGTTGGTTAATC
1 CGGATCCGATTTCTCATCAAACGTATGATTATGAAATGGAGTTGGTTAATC
4903885 C
1 C
4903886 AATGGGGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
51 46 0.98
52 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (51 bp):
CGGATCCGATTTCTCATCAAACGTATGATTATGAAATGGAGTTGGTTAATC
Found at i:4935532 original size:44 final size:44
Alignment explanation
Indices: 4935481--4935602 Score: 244
Period size: 44 Copynumber: 2.8 Consensus size: 44
4935471 TACATTGGAT
4935481 GATATTGTCTAATTGTTAATTAGAGTAAATATACTACACTGGGC
1 GATATTGTCTAATTGTTAATTAGAGTAAATATACTACACTGGGC
4935525 GATATTGTCTAATTGTTAATTAGAGTAAATATACTACACTGGGC
1 GATATTGTCTAATTGTTAATTAGAGTAAATATACTACACTGGGC
4935569 GATATTGTCTAATTGTTAATTAGAGTAAATATAC
1 GATATTGTCTAATTGTTAATTAGAGTAAATATAC
4935603 CCACTATTTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 78 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (44 bp):
GATATTGTCTAATTGTTAATTAGAGTAAATATACTACACTGGGC
Found at i:4947408 original size:24 final size:24
Alignment explanation
Indices: 4947380--4947426 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4947370 TGTTTCTTAT
4947380 ACAAAGAAAACA-AAAAGAAAATTA
1 ACAAA-AAAACACAAAAGAAAATTA
* *
4947404 ACAAAAAAGCACAAAAGATAATT
1 ACAAAAAAACACAAAAGAAAATT
4947427 TAATGTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.70, C:0.11, G:0.09, T:0.11
Consensus pattern (24 bp):
ACAAAAAAACACAAAAGAAAATTA
Found at i:4949192 original size:13 final size:13
Alignment explanation
Indices: 4949174--4949200 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4949164 CTCCGAAACA
4949174 TTTTTTTTTCTGT
1 TTTTTTTTTCTGT
4949187 TTTTTTTTTCTGT
1 TTTTTTTTTCTGT
4949200 T
1 T
4949201 ACAACCGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTCTGT
Found at i:4956160 original size:16 final size:16
Alignment explanation
Indices: 4956139--4956170 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4956129 GTTTTGTTGC
*
4956139 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
4956155 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
4956171 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:4956456 original size:51 final size:51
Alignment explanation
Indices: 4956398--4956588 Score: 260
Period size: 51 Copynumber: 3.8 Consensus size: 51
4956388 TCAGTTCACA
* * *
4956398 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACATG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
* ** * *
4956449 TAGTAGCCTGCACATAGTACTACACACGTGATCAAAACTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
* * *
4956500 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGGTACACG
4956550 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
4956589 TTCACTTTCA
Statistics
Matches: 120, Mismatches: 18, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
49 4 0.03
50 40 0.33
51 74 0.62
52 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
Found at i:4956578 original size:101 final size:102
Alignment explanation
Indices: 4956396--4956580 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
4956386 TATCAGTTCA
* *
4956396 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACATGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
4956461 CATAGTACTACACACGTGATCAAAACTATCCGGTACG
66 CATAGTACTACACACGTGATCAAAACTATCCGGTACG
* *
4956498 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCTGC
4956561 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
4956581 CCATCACTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
101 39 0.50
102 35 0.45
103 4 0.05
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCAAAACTATCCGGTACG
Found at i:4967751 original size:2 final size:2
Alignment explanation
Indices: 4967744--4967770 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4967734 GCATACTAAA
4967744 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
4967771 ATACATAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4978812 original size:16 final size:15
Alignment explanation
Indices: 4978778--4978824 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
4978768 AAATTATGGA
* *
4978778 TTTCTTTCTTCTTTC
1 TTTCTTTCTTTTTTT
4978793 TTTCTCTTCTTTTTTT
1 TTTCT-TTCTTTTTTT
4978809 TTTCTTT-TTTTTTT
1 TTTCTTTCTTTTTTT
4978823 TT
1 TT
4978825 AAGTTTTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 9 0.31
15 7 0.24
16 13 0.45
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTCTTTCTTTTTTT
Found at i:4978818 original size:13 final size:13
Alignment explanation
Indices: 4978782--4978824 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
4978772 TATGGATTTC
* *
4978782 TTTCTTCTTTCTT
1 TTTCTTTTTTTTT
*
4978795 TCTCTTCTTTTTTT
1 TTTCTT-TTTTTTT
4978809 TTTCTTTTTTTTT
1 TTTCTTTTTTTTT
4978822 TTT
1 TTT
4978825 AAGTTTTTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTCTTTTTTTTT
Found at i:5000974 original size:6 final size:6
Alignment explanation
Indices: 5000963--5001003 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
5000953 GAAAATTGGA
5000963 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAG
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAG
5001004 AAGTTGTGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:5001511 original size:2 final size:2
Alignment explanation
Indices: 5001504--5001543 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5001494 CTATTATCTT
5001504 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5001544 CCTCCCCTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5009814 original size:18 final size:17
Alignment explanation
Indices: 5009778--5009830 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
5009768 TATTTGATAT
5009778 ATTATTT-A-AAATT-A
1 ATTATTTGATAAATTAA
5009792 ATTATTTGATATAATTAA
1 ATTATTTGATA-AATTAA
5009810 ATTATTTGATAAATATAA
1 ATTATTTGATAAAT-TAA
5009828 ATT
1 ATT
5009831 TTAAATTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.21
15 1 0.03
16 1 0.03
17 7 0.21
18 18 0.53
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (17 bp):
ATTATTTGATAAATTAA
Found at i:5019493 original size:20 final size:20
Alignment explanation
Indices: 5019432--5019505 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 20
5019422 GTCACCATTT
5019432 AATTCATTTTAAAA-A-AAAA
1 AATT-ATTTTAAAATACAAAA
* *
5019451 AATATTTTTTAAAAT-CATTAA
1 AAT-TATTTTAAAATACA-AAA
5019472 AATTATTTTAAAATACAAAA
1 AATTATTTTAAAATACAAAA
5019492 AA-TATTTATAAAAT
1 AATTATTT-TAAAAT
5019506 TTTAAAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
19 16 0.36
20 22 0.49
21 7 0.16
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTATTTTAAAATACAAAA
Found at i:5019497 original size:19 final size:19
Alignment explanation
Indices: 5019437--5019505 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 19
5019427 CATTTAATTC
5019437 ATTTTAAAA-A-AAAAAAT
1 ATTTTAAAATACAAAAAAT
*
5019454 ATTTTTTAAAAT-CATTAAAATT
1 A--TTTTAAAATACA--AAAAAT
5019476 ATTTTAAAATACAAAAAAT
1 ATTTTAAAATACAAAAAAT
5019495 ATTTATAAAAT
1 ATTT-TAAAAT
5019506 TTTAAAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
17 1 0.02
19 17 0.40
20 16 0.38
21 2 0.05
22 6 0.14
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTTTAAAATACAAAAAAT
Found at i:5019512 original size:20 final size:19
Alignment explanation
Indices: 5019457--5019513 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
5019447 AAAAAATATT
*
5019457 TTTTAAAATCATTAAAATTA
1 TTTTAAAAT-ATTAAAAATA
**
5019477 TTTTAAAATACAAAAAATA
1 TTTTAAAATATTAAAAATA
*
5019496 TTTATAAAATTTTAAAAA
1 TTT-TAAAATATTAAAAA
5019514 ATTAATTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTTAAAATATTAAAAATA
Found at i:5021301 original size:29 final size:30
Alignment explanation
Indices: 5021266--5021335 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
5021256 AACGATAACG
*
5021266 TAAGTGACTAAAACGTAACAT-TTCAAACA
1 TAAGTGACTAAAACGTAACATGGTCAAACA
* *
5021295 TAAGTGACTAAAATGTAATATGGGTCAAACA
1 TAAGTGACTAAAACGTAACAT-GGTCAAACA
*
5021326 AAAGTGACTA
1 TAAGTGACTA
5021336 TTTTTTTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (30 bp):
TAAGTGACTAAAACGTAACATGGTCAAACA
Found at i:5021639 original size:8 final size:10
Alignment explanation
Indices: 5021617--5021649 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5021607 AACAAATATA
*
5021617 AAAAAATTAT
1 AAAAATTTAT
5021627 AAAAATTT-T
1 AAAAATTTAT
5021636 AAAAATTTAT
1 AAAAATTTAT
5021646 AAAA
1 AAAA
5021650 GAAGTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAAATTTAT
Found at i:5023201 original size:2 final size:2
Alignment explanation
Indices: 5023194--5023224 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5023184 GCTTCTAAAT
5023194 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5023225 TATAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5030253 original size:23 final size:24
Alignment explanation
Indices: 5030208--5030253 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
5030198 AGATGTATAC
**
5030208 AAAATAAATAAAAAATATTTTTAT
1 AAAATAAATAAAAAATAACTTTAT
*
5030232 AAAATAAAT-ATAAATAACTTTA
1 AAAATAAATAAAAAATAACTTTA
5030254 AATTTAACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAATAAATAAAAAATAACTTTAT
Found at i:5030860 original size:28 final size:31
Alignment explanation
Indices: 5030801--5030875 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 31
5030791 CCGATTAGTG
*
5030801 ATTTAATATAAATATAAATATATATAATTATT
1 ATTTAACAT-AATATAAATATATATAATTATT
*
5030833 ATTTAACAT-ATATAATTA-ATATAA-TATT
1 ATTTAACATAATATAAATATATATAATTATT
*
5030861 TTTTAACATAATATA
1 ATTTAACATAATATA
5030876 TTTAGGTCGG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 12 0.31
29 11 0.28
30 8 0.21
32 8 0.21
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (31 bp):
ATTTAACATAATATAAATATATATAATTATT
Found at i:5034217 original size:36 final size:36
Alignment explanation
Indices: 5034176--5034267 Score: 184
Period size: 36 Copynumber: 2.6 Consensus size: 36
5034166 ATATATATAT
5034176 ATTGAAAATAAAAATAAAAATAAAAAGAATATGTAA
1 ATTGAAAATAAAAATAAAAATAAAAAGAATATGTAA
5034212 ATTGAAAATAAAAATAAAAATAAAAAGAATATGTAA
1 ATTGAAAATAAAAATAAAAATAAAAAGAATATGTAA
5034248 ATTGAAAATAAAAATAAAAA
1 ATTGAAAATAAAAATAAAAA
5034268 AGAATATGTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (36 bp):
ATTGAAAATAAAAATAAAAATAAAAAGAATATGTAA
Found at i:5034222 original size:30 final size:30
Alignment explanation
Indices: 5034186--5034298 Score: 127
Period size: 36 Copynumber: 3.4 Consensus size: 30
5034176 ATTGAAAATA
5034186 AAAATAAAAATAAAAAGAATATGTAAATTG
1 AAAATAAAAATAAAAAGAATATGTAAATTG
5034216 AAAATAAAAATAAAAATAAAAAGAATATGTAAATTG
1 ------AAAATAAAAATAAAAAGAATATGTAAATTG
5034252 AAAATAAAAATAAAAAAGAATATGTAAAAAATTG
1 AAAATAAAAAT-AAAAAGAATATGT---AAATTG
*
5034286 AATATAAAAATAA
1 AAAATAAAAATAA
5034299 CAAATTTAGT
Statistics
Matches: 72, Mismatches: 1, Indels: 11
0.86 0.01 0.13
Matches are distributed among these distances:
30 11 0.15
31 13 0.18
33 2 0.03
34 16 0.22
36 30 0.42
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (30 bp):
AAAATAAAAATAAAAAGAATATGTAAATTG
Found at i:5034268 original size:7 final size:6
Alignment explanation
Indices: 5034180--5034237 Score: 55
Period size: 6 Copynumber: 9.7 Consensus size: 6
5034170 ATATATATTG
* * * * *
5034180 AAAATA AAAATA AAAATA AAAA-G AATATGT AAATTG AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAAT-A AAAATA AAAATA AAAATA
5034228 AAAATA AAAA
1 AAAATA AAAA
5034238 GAATATGTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
5 3 0.07
6 36 0.86
7 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:5034358 original size:20 final size:21
Alignment explanation
Indices: 5034314--5034359 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
5034304 TTAGTTAAAT
*
5034314 TTAAAAAAAAACTAAATATGT
1 TTAAAAAAAAACTAAATATGG
* *
5034335 TTAAAAATAAA-TAAATTTGG
1 TTAAAAAAAAACTAAATATGG
5034355 TTAAA
1 TTAAA
5034360 TTTTTACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (21 bp):
TTAAAAAAAAACTAAATATGG
Found at i:5034403 original size:16 final size:17
Alignment explanation
Indices: 5034367--5034414 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
5034357 AAATTTTTAC
5034367 AAAATTACAAGAAATTGT
1 AAAATTA-AAGAAATTGT
*
5034385 AAAATTAAA-AAATTTT
1 AAAATTAAAGAAATTGT
5034401 AAACATTAAAGAAA
1 AAA-ATTAAAGAAA
5034415 CAAAAATTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 9 0.33
17 8 0.30
18 10 0.37
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.27
Consensus pattern (17 bp):
AAAATTAAAGAAATTGT
Found at i:5034638 original size:14 final size:15
Alignment explanation
Indices: 5034619--5034651 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5034609 TTAACTTAAC
*
5034619 TTTTTATTTTC-ATT
1 TTTTTATGTTCAATT
5034633 TTTTTATGTTCAATT
1 TTTTTATGTTCAATT
5034648 TTTT
1 TTTT
5034652 GAATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTTATGTTCAATT
Found at i:5036616 original size:11 final size:10
Alignment explanation
Indices: 5036600--5036638 Score: 51
Period size: 11 Copynumber: 3.6 Consensus size: 10
5036590 AGATGTTTAG
5036600 TTATTTGTTTT
1 TTATTT-TTTT
5036611 TTATTTTATTT
1 TTATTTT-TTT
5036622 TTATTTTTGTT
1 TTATTTTT-TT
5036633 TTATTT
1 TTATTT
5036639 AATTTTTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.08
11 24 0.92
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (10 bp):
TTATTTTTTT
Found at i:5036625 original size:22 final size:22
Alignment explanation
Indices: 5036600--5036645 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5036590 AGATGTTTAG
*
5036600 TTATTTGTT-TTTTATTTTATTT
1 TTATTT-TTGTTTTATTTAATTT
5036622 TTATTTTTGTTTTATTTAATTT
1 TTATTTTTGTTTTATTTAATTT
5036644 TT
1 TT
5036646 CACAATAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.80
Consensus pattern (22 bp):
TTATTTTTGTTTTATTTAATTT
Found at i:5038287 original size:15 final size:16
Alignment explanation
Indices: 5038251--5038285 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5038241 TTAAAAAGTT
5038251 TTTTAAAATCTTAATA
1 TTTTAAAATCTTAATA
5038267 TTTTAAAAT-TTAATTA
1 TTTTAAAATCTTAA-TA
5038283 TTT
1 TTT
5038286 AAGGGAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTAAAATCTTAATA
Found at i:5038449 original size:28 final size:27
Alignment explanation
Indices: 5038397--5038452 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
5038387 TGAAGGGTTT
*
5038397 AAAAATAAATATAAATAATTTTTTTAA
1 AAAAATAAATATAAATAATATTTTTAA
* *
5038424 AAAAATAAATATTAATTATCATTTTTAA
1 AAAAATAAATATAAATAAT-ATTTTTAA
5038452 A
1 A
5038453 CATAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
AAAAATAAATATAAATAATATTTTTAA
Found at i:5042050 original size:2 final size:2
Alignment explanation
Indices: 5042043--5042124 Score: 55
Period size: 2 Copynumber: 42.0 Consensus size: 2
5042033 TATATTTAAT
* * * *
5042043 TA TA TA TA TA TA CA TA TA TA TT TA CA TA TA TA T- TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
5042084 T- TA TA TA TT TA -A CTA TCA TA TA TA TA CA TA TA GA T- TA TA TA
1 TA TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
5042125 ACGAAATGAG
Statistics
Matches: 60, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
1 4 0.07
2 53 0.88
3 3 0.05
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5043382 original size:18 final size:18
Alignment explanation
Indices: 5043359--5043395 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5043349 CCTATAATTA
5043359 TATTAATTATATTGTTTT
1 TATTAATTATATTGTTTT
5043377 TATTAATTATATTGTTTT
1 TATTAATTATATTGTTTT
5043395 T
1 T
5043396 TATTTTATTT
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:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TATTAATTATATTGTTTT
Found at i:5049579 original size:33 final size:33
Alignment explanation
Indices: 5049537--5049606 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
5049527 TCAGTAGTTT
5049537 CTTCAACACGATTTTAATGATAATCCAAAGTAA
1 CTTCAACACGATTTTAATGATAATCCAAAGTAA
5049570 CTTCAACACGATTTTAATGATAATCCAAAGTAA
1 CTTCAACACGATTTTAATGATAATCCAAAGTAA
5049603 CTTC
1 CTTC
5049607 TGTTGGTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (33 bp):
CTTCAACACGATTTTAATGATAATCCAAAGTAA
Found at i:5074808 original size:34 final size:35
Alignment explanation
Indices: 5074750--5074816 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
5074740 CAAACACCAG
* * *
5074750 AAAATATTTTCCTGTAAGTCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
5074785 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
5074817 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:5078102 original size:15 final size:16
Alignment explanation
Indices: 5078084--5078115 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5078074 TTAATTAATA
5078084 TAATTT-ATAATATTT
1 TAATTTAATAATATTT
5078099 TAATTTAATAATATTT
1 TAATTTAATAATATTT
5078115 T
1 T
5078116 TATAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTAATAATATTT
Found at i:5078106 original size:25 final size:26
Alignment explanation
Indices: 5078071--5078123 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
5078061 TATTATCTTA
5078071 ATTTTAATTAAT-ATA-ATTTATAAT
1 ATTTTAATTAATAATATATTTATAAT
*
5078095 ATTTTAATTTAATAATATTTTTATAAT
1 ATTTTAA-TTAATAATATATTTATAAT
5078122 AT
1 AT
5078124 AAATCAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 7 0.28
25 5 0.20
26 3 0.12
27 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTTAATTAATAATATATTTATAAT
Found at i:5081019 original size:27 final size:27
Alignment explanation
Indices: 5080985--5081079 Score: 115
Period size: 27 Copynumber: 3.6 Consensus size: 27
5080975 TCCTGCTGCC
*
5080985 GCTGAAGTTCCAACTGCCGTTGATGCT
1 GCTGAAGCTCCAACTGCCGTTGATGCT
* * *
5081012 GCTGAAGTTCCAACTG-C--TGCTGCC
1 GCTGAAGCTCCAACTGCCGTTGATGCT
* *
5081036 GCTGAAGCTCCAACAGACGTTGATGCT
1 GCTGAAGCTCCAACTGCCGTTGATGCT
5081063 GCTGAAGCTCCAACTGC
1 GCTGAAGCTCCAACTGC
5081080 TGCTGCCGCT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
24 19 0.33
25 1 0.02
26 1 0.02
27 36 0.63
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.24
Consensus pattern (27 bp):
GCTGAAGCTCCAACTGCCGTTGATGCT
Found at i:5081057 original size:51 final size:49
Alignment explanation
Indices: 5080977--5081232 Score: 273
Period size: 51 Copynumber: 5.1 Consensus size: 49
5080967 GACGAAGCTC
* * * * *
5080977 CTGCTGCCGCTGAAGTTCCAACTGCCGTTGATGCTGCTGAAGTTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG-CG-TGCTGCCGCTGAAGCTCCAACTG
* * * *
5081028 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG-CG-TGCTGCCGCTGAAGCTCCAACTG
* * *
5081079 CTGCTGCCGCTGATGCTCCAATTGC-TGCTGCCGCTGATGCTCCAATTG
1 CTGCTGCCGCTGATGCTCCAACTGCGTGCTGCCGCTGAAGCTCCAACTG
* *
5081127 CTGCTGCCGCTGATGCTCAAACTGC-TGCTGCCGCTGATGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTGCGTGCTGCCGCTGAAGCTCCAACTG
* * * *
5081175 CTGCTGCCGCTGATGCTCCAACTGATGCTGCTGCCGTTGTAGTTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG-CG-TGCTGCCGCTGAAGCTCCAACTG
*
5081226 CCGCTGC
1 CTGCTGC
5081233 TGTTCAACTT
Statistics
Matches: 181, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
48 87 0.48
50 1 0.01
51 93 0.51
ACGTcount: A:0.16, C:0.33, G:0.25, T:0.26
Consensus pattern (49 bp):
CTGCTGCCGCTGATGCTCCAACTGCGTGCTGCCGCTGAAGCTCCAACTG
Found at i:5081096 original size:24 final size:24
Alignment explanation
Indices: 5081081--5081205 Score: 214
Period size: 24 Copynumber: 5.2 Consensus size: 24
5081071 TCCAACTGCT
*
5081081 GCTGCCGCTGATGCTCCAATTGCT
1 GCTGCCGCTGATGCTCCAACTGCT
*
5081105 GCTGCCGCTGATGCTCCAATTGCT
1 GCTGCCGCTGATGCTCCAACTGCT
*
5081129 GCTGCCGCTGATGCTCAAACTGCT
1 GCTGCCGCTGATGCTCCAACTGCT
5081153 GCTGCCGCTGATGCTCCAACTGCT
1 GCTGCCGCTGATGCTCCAACTGCT
*
5081177 GCTGCCGCTGATGCTCCAACTGAT
1 GCTGCCGCTGATGCTCCAACTGCT
5081201 GCTGC
1 GCTGC
5081206 TGCCGTTGTA
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 97 1.00
ACGTcount: A:0.14, C:0.34, G:0.26, T:0.26
Consensus pattern (24 bp):
GCTGCCGCTGATGCTCCAACTGCT
Found at i:5081121 original size:48 final size:48
Alignment explanation
Indices: 5080977--5081205 Score: 269
Period size: 48 Copynumber: 4.6 Consensus size: 48
5080967 GACGAAGCTC
* * * * * *
5080977 CTGCTGCCGCTGAAGTTCCAACTGCCGTTGATGCTGCTGAAGTTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG-C--TGCTGCCGCTGATGCTCCAACTG
* * * * *
5081028 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG-C--TGCTGCCGCTGATGCTCCAACTG
* *
5081079 CTGCTGCCGCTGATGCTCCAATTGCTGCTGCCGCTGATGCTCCAATTG
1 CTGCTGCCGCTGATGCTCCAACTGCTGCTGCCGCTGATGCTCCAACTG
*
5081127 CTGCTGCCGCTGATGCTCAAACTGCTGCTGCCGCTGATGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTGCTGCTGCCGCTGATGCTCCAACTG
*
5081175 CTGCTGCCGCTGATGCTCCAACTGATGCTGC
1 CTGCTGCCGCTGATGCTCCAACTGCTGCTGC
5081206 TGCCGTTGTA
Statistics
Matches: 162, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
48 93 0.57
50 1 0.01
51 68 0.42
ACGTcount: A:0.16, C:0.33, G:0.25, T:0.26
Consensus pattern (48 bp):
CTGCTGCCGCTGATGCTCCAACTGCTGCTGCCGCTGATGCTCCAACTG
Found at i:5081153 original size:72 final size:72
Alignment explanation
Indices: 5080977--5081210 Score: 261
Period size: 72 Copynumber: 3.1 Consensus size: 72
5080967 GACGAAGCTC
* * * * * * *
5080977 CTGCTGCCGCTGAAGTTCCAACTGCCGTTGATGCTGCTGAAGTTCCAACTGCTGCTGCCGCTGAA
1 CTGCTGCCGCTGAAGCTCAAACTG-C--TGCTGCCGCTGATGCTCCAACTGCTGCTGCCGCTGAT
**
5081042 GCTCCAACAG
63 GCTCCAATTG
* * * *
5081052 ACGTTGATGCTGCTGAAGCTCCAACTGCTGCTGCCGCTGATGCTCCAATTGCTGCTGCCGCTGAT
1 -C--TGCTGCCGCTGAAGCTCAAACTGCTGCTGCCGCTGATGCTCCAACTGCTGCTGCCGCTGAT
5081117 GCTCCAATTG
63 GCTCCAATTG
*
5081127 CTGCTGCCGCTGATGCTCAAACTGCTGCTGCCGCTGATGCTCCAACTGCTGCTGCCGCTGATGCT
1 CTGCTGCCGCTGAAGCTCAAACTGCTGCTGCCGCTGATGCTCCAACTGCTGCTGCCGCTGATGCT
5081192 CCAACTGATG
66 CCAA-T--TG
5081202 CTGCTGCCG
1 CTGCTGCCG
5081211 TTGTAGTTCC
Statistics
Matches: 137, Mismatches: 16, Indels: 11
0.84 0.10 0.07
Matches are distributed among these distances:
72 63 0.46
73 1 0.01
74 1 0.01
75 50 0.36
76 1 0.01
77 1 0.01
78 20 0.15
ACGTcount: A:0.16, C:0.33, G:0.26, T:0.26
Consensus pattern (72 bp):
CTGCTGCCGCTGAAGCTCAAACTGCTGCTGCCGCTGATGCTCCAACTGCTGCTGCCGCTGATGCT
CCAATTG
Found at i:5081225 original size:27 final size:27
Alignment explanation
Indices: 5081026--5081210 Score: 193
Period size: 24 Copynumber: 7.4 Consensus size: 27
5081016 AAGTTCCAAC
* *
5081026 TGCTGCTGCCGCTGAAGCTCCAACAGA
1 TGCTGCTGCCGCTGATGCTCCAACTGA
* * * * *
5081053 CGTTGATGCTGCTGAAGCTCCAAC---
1 TGCTGCTGCCGCTGATGCTCCAACTGA
5081077 TGCTGCTGCCGCTGATGCTCCAA-T--
1 TGCTGCTGCCGCTGATGCTCCAACTGA
5081101 TGCTGCTGCCGCTGATGCTCCAA-T--
1 TGCTGCTGCCGCTGATGCTCCAACTGA
*
5081125 TGCTGCTGCCGCTGATGCTCAAAC---
1 TGCTGCTGCCGCTGATGCTCCAACTGA
5081149 TGCTGCTGCCGCTGATGCTCCAAC---
1 TGCTGCTGCCGCTGATGCTCCAACTGA
5081173 TGCTGCTGCCGCTGATGCTCCAACTGA
1 TGCTGCTGCCGCTGATGCTCCAACTGA
5081200 TGCTGCTGCCG
1 TGCTGCTGCCG
5081211 TTGTAGTTCC
Statistics
Matches: 142, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
24 111 0.78
27 31 0.22
ACGTcount: A:0.15, C:0.34, G:0.26, T:0.25
Consensus pattern (27 bp):
TGCTGCTGCCGCTGATGCTCCAACTGA
Found at i:5081231 original size:27 final size:27
Alignment explanation
Indices: 5080977--5081234 Score: 185
Period size: 24 Copynumber: 10.2 Consensus size: 27
5080967 GACGAAGCTC
* * *
5080977 CTGCTGCCGCTGAAGTTCCAACTGCCG
1 CTGCTGCCGCTGATGCTCCAACTGACG
* * * * *
5081004 TTGATGCTGCTGAAGTTCCAACT---G
1 CTGCTGCCGCTGATGCTCCAACTGACG
* *
5081028 CTGCTGCCGCTGAAGCTCCAACAGACG
1 CTGCTGCCGCTGATGCTCCAACTGACG
* * * *
5081055 TTGATGCTGCTGAAGCTCCAACT---G
1 CTGCTGCCGCTGATGCTCCAACTGACG
*
5081079 CTGCTGCCGCTGATGCTCCAA-T--TG
1 CTGCTGCCGCTGATGCTCCAACTGACG
*
5081103 CTGCTGCCGCTGATGCTCCAA-T--TG
1 CTGCTGCCGCTGATGCTCCAACTGACG
*
5081127 CTGCTGCCGCTGATGCTCAAACT---G
1 CTGCTGCCGCTGATGCTCCAACTGACG
5081151 CTGCTGCCGCTGATGCTCCAACT---G
1 CTGCTGCCGCTGATGCTCCAACTGACG
*
5081175 CTGCTGCCGCTGATGCTCCAACTGATG
1 CTGCTGCCGCTGATGCTCCAACTGACG
* * *
5081202 CTGCTGCCGTTG-TAGTTCCAACTGCCG
1 CTGCTGCCGCTGAT-GCTCCAACTGACG
5081229 CTGCTG
1 CTGCTG
5081235 TTCAACTTGA
Statistics
Matches: 200, Mismatches: 22, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
23 1 0.00
24 129 0.64
25 1 0.00
26 1 0.00
27 68 0.34
ACGTcount: A:0.16, C:0.33, G:0.26, T:0.26
Consensus pattern (27 bp):
CTGCTGCCGCTGATGCTCCAACTGACG
Found at i:5090634 original size:39 final size:39
Alignment explanation
Indices: 5090564--5090656 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
5090554 CATTTTTTAC
* * *
5090564 ATATCTA-TCCATATAAACATTTCGTACAATCACTTCAT
1 ATATCTATTTCATATAAACAATTCATACAATCACTTCAT
* * *
5090602 ATATCTATTTCATATAATCAATTCATATAATCATTTCAT
1 ATATCTATTTCATATAAACAATTCATACAATCACTTCAT
5090641 ATA-CTCATTT-ATATAA
1 ATATCT-ATTTCATATAA
5090657 CTATTTTGTA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 15 0.32
39 32 0.68
ACGTcount: A:0.39, C:0.18, G:0.01, T:0.42
Consensus pattern (39 bp):
ATATCTATTTCATATAAACAATTCATACAATCACTTCAT
Found at i:5090642 original size:26 final size:26
Alignment explanation
Indices: 5090573--5090656 Score: 91
Period size: 26 Copynumber: 3.3 Consensus size: 26
5090563 CATATCTATC
* * * *
5090573 CATATAAACATTTCGTACAATCACTT
1 CATATAATCATTTCATATAATCAATT
5090599 CATAT-ATCTATTTCATATAATCAATT
1 CATATAATC-ATTTCATATAATCAATT
*
5090625 CATATAATCATTTCATATACTC-ATT
1 CATATAATCATTTCATATAATCAATT
*
5090650 TATATAA
1 CATATAA
5090657 CTATTTTGTA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
25 11 0.22
26 36 0.72
27 3 0.06
ACGTcount: A:0.39, C:0.18, G:0.01, T:0.42
Consensus pattern (26 bp):
CATATAATCATTTCATATAATCAATT
Found at i:5090704 original size:26 final size:26
Alignment explanation
Indices: 5090670--5090741 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 26
5090660 TTTTGTATAC
*
5090670 CCATCTCATATTACAATTTCGTAG-AA
1 CCATTTCATATTACAATTTCG-AGTAA
* * * *
5090696 TCATTTCATATAACCATTTTGAGTAA
1 CCATTTCATATTACAATTTCGAGTAA
*
5090722 CCATTTCATTTTACACATTT
1 CCATTTCATATTACA-ATTT
5090742 AACATGTATT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
25 2 0.06
26 29 0.83
27 4 0.11
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.42
Consensus pattern (26 bp):
CCATTTCATATTACAATTTCGAGTAA
Found at i:5090713 original size:13 final size:13
Alignment explanation
Indices: 5090573--5090714 Score: 81
Period size: 13 Copynumber: 11.0 Consensus size: 13
5090563 CATATCTATC
*
5090573 CATATAAACATTT
1 CATATAACCATTT
* * * *
5090586 CGTACAATCACTT
1 CATATAACCATTT
* *
5090599 CATATATCTATTT
1 CATATAACCATTT
* *
5090612 CATATAATCAATT
1 CATATAACCATTT
*
5090625 CATATAATCATTT
1 CATATAACCATTT
5090638 CATAT-ACTCATTT
1 CATATAAC-CATTT
*
5090651 -ATATAACTATTT
1 CATATAACCATTT
** * *
5090663 TGTATACCCATCT
1 CATATAACCATTT
* *
5090676 CATATTACAATTT
1 CATATAACCATTT
* * *
5090689 CGTAGAATCATTT
1 CATATAACCATTT
5090702 CATATAACCATTT
1 CATATAACCATTT
5090715 TGAGTAACCA
Statistics
Matches: 91, Mismatches: 35, Indels: 6
0.69 0.27 0.05
Matches are distributed among these distances:
12 9 0.10
13 82 0.90
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (13 bp):
CATATAACCATTT
Found at i:5104332 original size:14 final size:14
Alignment explanation
Indices: 5104313--5104352 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5104303 TTGTTTGGCA
5104313 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
5104327 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
5104341 GGAAAATGTTTT
1 GTAAAATGTTTT
5104353 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:5104361 original size:20 final size:20
Alignment explanation
Indices: 5104336--5104375 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5104326 CGTAAAATGA
*
5104336 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
5104356 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
5104376 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:5104365 original size:34 final size:35
Alignment explanation
Indices: 5104321--5104387 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
5104311 CAGTAAAATG
*
5104321 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
5104355 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
5104388 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:5104391 original size:14 final size:15
Alignment explanation
Indices: 5104315--5104391 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
5104305 GTTTGGCAGT
* *
5104315 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
5104329 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
5104343 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
5104363 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
5104378 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
5104392 TGTTTGGTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:5104493 original size:14 final size:14
Alignment explanation
Indices: 5104474--5104501 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5104464 TTTTTACATA
5104474 TATTAATATATATT
1 TATTAATATATATT
5104488 TATTAATATATATT
1 TATTAATATATATT
5104502 AATAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTAATATATATT
Found at i:5105795 original size:35 final size:36
Alignment explanation
Indices: 5105749--5105817 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
5105739 ATTCAACCAT
5105749 TTCAATATCCAACAAGCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
5105784 TTCAATATCCAACAAGCTTAAAACATAATCAATA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATA
5105818 TCTAACAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.52, C:0.19, G:0.03, T:0.26
Consensus pattern (36 bp):
TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
Found at i:5105815 original size:27 final size:27
Alignment explanation
Indices: 5105785--5105853 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
5105775 AATAATAAAT
*
5105785 TCAATATCCAACAAGCTT-AAAACATAA
1 TCAATATCCAACAA-ATTCAAAACATAA
* *
5105812 TCAATATCTAACAAATTCAAGACATAA
1 TCAATATCCAACAAATTCAAAACATAA
*
5105839 TCAAAATCCAACAAA
1 TCAATATCCAACAAA
5105854 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
26 2 0.06
27 34 0.94
ACGTcount: A:0.54, C:0.22, G:0.03, T:0.22
Consensus pattern (27 bp):
TCAATATCCAACAAATTCAAAACATAA
Found at i:5107369 original size:15 final size:16
Alignment explanation
Indices: 5107349--5107381 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
5107339 AGTACCACTT
5107349 AAAATGAAAGCA-TGA
1 AAAATGAAAGCATTGA
5107364 AAAATGAAAGCATTGA
1 AAAATGAAAGCATTGA
5107380 AA
1 AA
5107382 GTTCAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.61, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
AAAATGAAAGCATTGA
Found at i:5109806 original size:25 final size:25
Alignment explanation
Indices: 5109767--5109818 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
5109757 AAAATGTCTG
5109767 CTGCTTAGAAGAGAACAGAAAATGT
1 CTGCTTAGAAGAGAACAGAAAATGT
**
5109792 CTGCTTAG-AGAAGAATGGAAAATGT
1 CTGCTTAGAAG-AGAACAGAAAATGT
5109817 CT
1 CT
5109819 TACCAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (25 bp):
CTGCTTAGAAGAGAACAGAAAATGT
Found at i:5120635 original size:3 final size:3
Alignment explanation
Indices: 5120627--5120651 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5120617 GAGGAGAGAG
5120627 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
5120652 AAAACGACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5121296 original size:23 final size:24
Alignment explanation
Indices: 5121251--5121296 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
5121241 AGATGTATAC
**
5121251 AAAATAAATAAAAAATATTTTTAT
1 AAAATAAATAAAAAATAACTTTAT
*
5121275 AAAATAAAT-ATAAATAACTTTA
1 AAAATAAATAAAAAATAACTTTA
5121297 AATTTAACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAATAAATAAAAAATAACTTTAT
Found at i:5121861 original size:10 final size:10
Alignment explanation
Indices: 5121840--5121890 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
5121830 TTAGTGATTT
5121840 AATATAATATA
1 AATAT-ATATA
5121851 AATATATATA
1 AATATATATA
* *
5121861 ATTATTATTTA
1 AATA-TATATA
*
5121872 AATATATATT
1 AATATATATA
5121882 AATATATAT
1 AATATATAT
5121891 TTTTTAACAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 21 0.62
11 13 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AATATATATA
Found at i:5125064 original size:5 final size:6
Alignment explanation
Indices: 5125050--5125106 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
5125040 ATATATATTG
* * * * *
5125050 AAAATA AAAATA AAAATA AAAA-G AATATGT AAATTG AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAAT-A AAAATA AAAATA AAAATA
5125098 AAAATA AAA
1 AAAATA AAA
5125107 GAATATGTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
5 3 0.07
6 35 0.85
7 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:5125083 original size:29 final size:30
Alignment explanation
Indices: 5125056--5125146 Score: 130
Period size: 35 Copynumber: 2.9 Consensus size: 30
5125046 ATTGAAAATA
5125056 AAAATAAAAATAAAAAGAATATGTAAATTG
1 AAAATAAAAATAAAAAGAATATGTAAATTG
5125086 AAAATAAAAATAAAAATAAAAGAATATGTAAATTG
1 AAAATAAAAAT----A-AAAAGAATATGTAAATTG
5125121 AAAAT-AAAATAAAAAGAATATGTAAA
1 AAAATAAAAATAAAAAGAATATGTAAA
5125147 AAATTGAATA
Statistics
Matches: 56, Mismatches: 0, Indels: 11
0.84 0.00 0.16
Matches are distributed among these distances:
29 15 0.27
30 12 0.21
34 6 0.11
35 23 0.41
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (30 bp):
AAAATAAAAATAAAAAGAATATGTAAATTG
Found at i:5125089 original size:18 final size:18
Alignment explanation
Indices: 5125068--5125124 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
5125058 AATAAAAATA
5125068 AAAAGAATATGTAAATTG
1 AAAAGAATATGTAAATTG
* * * *
5125086 AAAATAAAAAT-AAAAAT-
1 AAAA-GAATATGTAAATTG
5125103 AAAAGAATATGTAAATTG
1 AAAAGAATATGTAAATTG
5125121 AAAA
1 AAAA
5125125 TAAAATAAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
16 4 0.14
17 8 0.29
18 12 0.43
19 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.23
Consensus pattern (18 bp):
AAAAGAATATGTAAATTG
Found at i:5125114 original size:35 final size:36
Alignment explanation
Indices: 5125046--5125135 Score: 166
Period size: 35 Copynumber: 2.6 Consensus size: 36
5125036 ATATATATAT
5125046 ATTGAAAATAAAAATAAAAATAAAAAGAATATGTAA
1 ATTGAAAATAAAAATAAAAATAAAAAGAATATGTAA
5125082 ATTGAAAATAAAAATAAAAAT-AAAAGAATATGTAA
1 ATTGAAAATAAAAATAAAAATAAAAAGAATATGTAA
5125117 ATTGAAAAT-AAAATAAAAA
1 ATTGAAAATAAAAATAAAAA
5125136 GAATATGTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
34 10 0.19
35 23 0.43
36 21 0.39
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (36 bp):
ATTGAAAATAAAAATAAAAATAAAAAGAATATGTAA
Found at i:5125133 original size:16 final size:16
Alignment explanation
Indices: 5125114--5125164 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
5125104 AAAGAATATG
*
5125114 TAAATTGAAAATAAAA
1 TAAATTGAATATAAAA
** *
5125130 TAAAAAGAATATGTAAA
1 TAAATTGAATAT-AAAA
5125147 -AAATTGAATATAAAA
1 TAAATTGAATATAAAA
5125162 TAA
1 TAA
5125165 CAAATTTAGT
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (16 bp):
TAAATTGAATATAAAA
Found at i:5127474 original size:11 final size:10
Alignment explanation
Indices: 5127458--5127496 Score: 51
Period size: 11 Copynumber: 3.6 Consensus size: 10
5127448 AGATGTTTAG
5127458 TTATTTGTTTT
1 TTATTT-TTTT
5127469 TTATTTTATTT
1 TTATTTT-TTT
5127480 TTATTTTTGTT
1 TTATTTTT-TT
5127491 TTATTT
1 TTATTT
5127497 AATTTTTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.08
11 24 0.92
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (10 bp):
TTATTTTTTT
Found at i:5127483 original size:22 final size:22
Alignment explanation
Indices: 5127458--5127503 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5127448 AGATGTTTAG
*
5127458 TTATTTGTT-TTTTATTTTATTT
1 TTATTT-TTGTTTTATTTAATTT
5127480 TTATTTTTGTTTTATTTAATTT
1 TTATTTTTGTTTTATTTAATTT
5127502 TT
1 TT
5127504 CACAATAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.80
Consensus pattern (22 bp):
TTATTTTTGTTTTATTTAATTT
Found at i:5129149 original size:15 final size:16
Alignment explanation
Indices: 5129113--5129147 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5129103 TTAAAAAGTT
5129113 TTTTAAAATCTTAATA
1 TTTTAAAATCTTAATA
5129129 TTTTAAAAT-TTAATTA
1 TTTTAAAATCTTAA-TA
5129145 TTT
1 TTT
5129148 AAGGGAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTAAAATCTTAATA
Found at i:5129311 original size:28 final size:27
Alignment explanation
Indices: 5129259--5129314 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
5129249 TGAAGGGTTT
*
5129259 AAAAATAAATATAAATAATTTTTTTAA
1 AAAAATAAATATAAATAATATTTTTAA
* *
5129286 AAAAATAAATATTAATTATCATTTTTAA
1 AAAAATAAATATAAATAAT-ATTTTTAA
5129314 A
1 A
5129315 CATAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
AAAAATAAATATAAATAATATTTTTAA
Found at i:5132966 original size:12 final size:12
Alignment explanation
Indices: 5132936--5132966 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5132926 TTTAATTATC
*
5132936 ATATATATACAT
1 ATATATTTACAT
5132948 ATATATTTACAT
1 ATATATTTACAT
5132960 ATATATT
1 ATATATT
5132967 ATATGTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATATTTACAT
Found at i:5134291 original size:19 final size:19
Alignment explanation
Indices: 5134267--5134308 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
5134257 CCTATAATTA
5134267 TATTAATTATATTGTTTTT
1 TATTAATTATATTGTTTTT
5134286 TATTAATTATATTGTTTTT
1 TATTAATTATATTGTTTTT
5134305 TATT
1 TATT
5134309 TTATTTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
TATTAATTATATTGTTTTT
Found at i:5137254 original size:22 final size:22
Alignment explanation
Indices: 5137229--5137271 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5137219 TATCGAAATA
5137229 ATAACAATAAAATAATAGCAAT
1 ATAACAATAAAATAATAGCAAT
* * *
5137251 ATAATAGTAAAATGATAGCAA
1 ATAACAATAAAATAATAGCAA
5137272 AACAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.23
Consensus pattern (22 bp):
ATAACAATAAAATAATAGCAAT
Found at i:5140767 original size:33 final size:33
Alignment explanation
Indices: 5140725--5140794 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
5140715 TCAGTAGTTT
5140725 CTTCAACACGATTTTAATGATAATCCAAAGTAA
1 CTTCAACACGATTTTAATGATAATCCAAAGTAA
5140758 CTTCAACACGATTTTAATGATAATCCAAAGTAA
1 CTTCAACACGATTTTAATGATAATCCAAAGTAA
5140791 CTTC
1 CTTC
5140795 TGTTGGTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (33 bp):
CTTCAACACGATTTTAATGATAATCCAAAGTAA
Found at i:5143719 original size:16 final size:16
Alignment explanation
Indices: 5143699--5143751 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
5143689 TTGGTTCGCT
*
5143699 GTAATGGAATAGAGGT
1 GTAATGGAATAGAGGC
* *
5143715 GTAATAGAATAGATGC
1 GTAATGGAATAGAGGC
5143731 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
5143747 GTAAT
1 GTAAT
5143752 AGGTAATTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.40, C:0.04, G:0.32, T:0.25
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:5143815 original size:44 final size:46
Alignment explanation
Indices: 5143733--5143825 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
5143723 ATAGATGCGT
* *
5143733 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
5143779 AATGAAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
5143823 AAT
1 AAT
5143826 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 24 0.53
45 3 0.07
46 18 0.40
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.37
Consensus pattern (46 bp):
AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:5143821 original size:39 final size:44
Alignment explanation
Indices: 5143733--5143838 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 44
5143723 ATAGATGCGT
*
5143733 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--ATGG
*
5143779 AATGAAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
*
5143818 AATGGAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
5143839 CATAAGGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
39 18 0.33
40 2 0.04
43 1 0.02
44 13 0.24
45 3 0.05
46 18 0.33
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
Found at i:5144047 original size:56 final size:57
Alignment explanation
Indices: 5143929--5144049 Score: 131
Period size: 56 Copynumber: 2.1 Consensus size: 57
5143919 TTTTAATATG
* *
5143929 TTAA-TTAATATAAATAATAAATAATTTAATCATATTTTAACACAATTATTATTAAA
1 TTAATTTAATATAAATAATAAATAATTTAATAACATTTTAACACAATTATTATTAAA
* * * * * *
5143985 TATAATTTAATA-AAA-AATATATAATTTAATAACATTCTTAATATAATTTTTCTTATA
1 T-TAATTTAATATAAATAATAAATAATTTAATAACATT-TTAACACAATTATTATTAAA
5144042 TTAATTTA
1 TTAATTTA
5144050 CTTAAATTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
56 26 0.48
57 22 0.41
58 6 0.11
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (57 bp):
TTAATTTAATATAAATAATAAATAATTTAATAACATTTTAACACAATTATTATTAAA
Found at i:5145748 original size:68 final size:68
Alignment explanation
Indices: 5145630--5145770 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 68
5145620 AATATTATGT
5145630 ATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAACTCTCAATATCATAATTAGATAGCTAC
1 ATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAACTCTCAATATCATAATTAGATAGCTAC
5145695 AAA
66 AAA
* *
5145698 ATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAATTCTCGAA-ATCATAATTAGGTAGCTA
1 ATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAACTCTC-AATATCATAATTAGATAGCTA
5145762 CAAA
65 CAAA
5145766 ATCAT
1 ATCAT
5145771 ACATAAATTA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
68 68 0.97
69 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (68 bp):
ATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAACTCTCAATATCATAATTAGATAGCTAC
AAA
Found at i:5155534 original size:16 final size:16
Alignment explanation
Indices: 5155512--5155580 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
5155502 TTTGGTTCGC
5155512 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
5155528 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5155544 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
5155561 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5155577 TGTA
1 TGTA
5155581 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:5155558 original size:33 final size:32
Alignment explanation
Indices: 5155512--5155580 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
5155502 TTTGGTTCGC
5155512 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
5155544 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
5155577 TGTA
1 TGTA
5155581 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:5155645 original size:44 final size:45
Alignment explanation
Indices: 5155561--5155651 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
5155551 GGATTAGAGG
* * *
5155561 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
5155606 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
5155650 TG
1 TG
5155652 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:5155837 original size:18 final size:17
Alignment explanation
Indices: 5155816--5155850 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5155806 TTATTATTAA
*
5155816 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5155834 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5155851 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5156166 original size:120 final size:120
Alignment explanation
Indices: 5155799--5156540 Score: 1450
Period size: 120 Copynumber: 6.2 Consensus size: 120
5155789 ATCATATTTA
* *
5155799 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
*
5155864 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
5155919 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTT-AAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
5155983 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
5156038 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
5156103 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
5156158 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
5156223 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
5156278 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
5156343 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
5156398 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
5156463 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
5156518 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
5156541 AACTTGAAAA
Statistics
Matches: 618, Mismatches: 3, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
119 117 0.19
120 501 0.81
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:5158914 original size:23 final size:23
Alignment explanation
Indices: 5158886--5158969 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
5158876 AACATAAACA
*
5158886 AATCAACACAATTTCCAGCAGAC
1 AATCAAAACAATTTCCAGCAGAC
*
5158909 AATCAAAACAATTTCCAGCAGCC
1 AATCAAAACAATTTCCAGCAGAC
* *
5158932 AATCATACCAATTTCCAGCAGAC
1 AATCAAAACAATTTCCAGCAGAC
5158955 AATCAAAACAATTTC
1 AATCAAAACAATTTC
5158970 AGAACAAATC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.44, C:0.29, G:0.07, T:0.20
Consensus pattern (23 bp):
AATCAAAACAATTTCCAGCAGAC
Found at i:5158997 original size:22 final size:21
Alignment explanation
Indices: 5158955--5159000 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
5158945 TCCAGCAGAC
* *
5158955 AATCAAAACAATTTCAGAACA
1 AATCAAAACAATATCAAAACA
*
5158976 AATCAAGACCAATATCAAAACA
1 AATCAA-AACAATATCAAAACA
5158998 AAT
1 AAT
5159001 GCAACAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.59, C:0.20, G:0.04, T:0.17
Consensus pattern (21 bp):
AATCAAAACAATATCAAAACA
Found at i:5160880 original size:5 final size:5
Alignment explanation
Indices: 5160870--5160895 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5160860 AAAGAGAGTT
5160870 AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA A
5160896 AAGAGAGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:5164722 original size:20 final size:20
Alignment explanation
Indices: 5164697--5164736 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5164687 TGTTTATACA
5164697 TCATCTAACTTATATTTCAT
1 TCATCTAACTTATATTTCAT
*
5164717 TCATCTAATTTATATTTCAT
1 TCATCTAACTTATATTTCAT
5164737 GTAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (20 bp):
TCATCTAACTTATATTTCAT
Found at i:5166082 original size:16 final size:16
Alignment explanation
Indices: 5166049--5166082 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5166039 GTCTCGTGTT
* *
5166049 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
5166065 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
5166081 AA
1 AA
5166083 TACAAAGTGG
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:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Done.