Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 184 of 202
Found at i:56678531 original size:13 final size:13
Alignment explanation
Indices: 56678506--56678539 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
56678496 TCTGACTTGG
56678506 GTCACACGACCAA
1 GTCACACGACCAA
* *
56678519 GTTACACGGCCAA
1 GTCACACGACCAA
56678532 GTCACACG
1 GTCACACG
56678540 CCCGTGTGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.35, G:0.21, T:0.12
Consensus pattern (13 bp):
GTCACACGACCAA
Found at i:56679492 original size:21 final size:21
Alignment explanation
Indices: 56679468--56679537 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
56679458 CGAATACACC
*
56679468 AACAGAAGCTCGTAAGAATTG
1 AACAGAAGCTCGTAAGAACTG
*
56679489 AACAGAAGCTCGTAA-AAGCTA
1 AACAGAAGCTCGTAAGAA-CTG
*
56679510 AACAGAAGCTCAG-AAGAGCTG
1 AACAGAAGCTC-GTAAGAACTG
56679531 AACAGAA
1 AACAGAA
56679538 AGTAAAACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
20 2 0.05
21 38 0.90
22 2 0.05
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAACTG
Found at i:56682236 original size:12 final size:13
Alignment explanation
Indices: 56682209--56682239 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
56682199 TCATTTAATC
56682209 ATCAAGTTTTTCA
1 ATCAAGTTTTTCA
56682222 ATCAAGTTTTT-A
1 ATCAAGTTTTTCA
56682234 ATCAAG
1 ATCAAG
56682240 CTTTCATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (13 bp):
ATCAAGTTTTTCA
Found at i:56684467 original size:12 final size:13
Alignment explanation
Indices: 56684450--56684480 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
56684440 AAGATGAAAG
56684450 CTTGATT-AAAAA
1 CTTGATTGAAAAA
56684462 CTTGATTGAAAAA
1 CTTGATTGAAAAA
56684475 CTTGAT
1 CTTGAT
56684481 GATTAAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (13 bp):
CTTGATTGAAAAA
Found at i:56684971 original size:20 final size:22
Alignment explanation
Indices: 56684920--56684971 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 22
56684910 ATTCAAATTT
*
56684920 TAAAGGTAAAATCTTTAAAAGAA
1 TAAA-GTAAAATATTTAAAAGAA
56684943 TAATA-TAAAATATTT-AAA-AA
1 TAA-AGTAAAATATTTAAAAGAA
56684963 TAAAGTAAA
1 TAAAGTAAA
56684972 CTAAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 1 0.04
20 9 0.35
21 3 0.12
22 9 0.35
23 3 0.12
24 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (22 bp):
TAAAGTAAAATATTTAAAAGAA
Found at i:56685581 original size:2 final size:2
Alignment explanation
Indices: 56685574--56685610 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
56685564 CATTTATAAG
56685574 TA TA TA TA TA 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 TA TA T
56685611 TAAAATTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56686191 original size:33 final size:33
Alignment explanation
Indices: 56686146--56686216 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
56686136 TATTATGGGT
*
56686146 TTATAACGATTATCTTTCTATAACAATATACTA
1 TTATAACAATTATCTTTCTATAACAATATACTA
* * *
56686179 TTATAACAATTATTTTTCTGTAACAATGTACTA
1 TTATAACAATTATCTTTCTATAACAATATACTA
56686212 TTATA
1 TTATA
56686217 CGAGACTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (33 bp):
TTATAACAATTATCTTTCTATAACAATATACTA
Found at i:56690348 original size:2 final size:2
Alignment explanation
Indices: 56690341--56690366 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56690331 AACAATTTTC
56690341 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
56690367 GCTTTCCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56690775 original size:24 final size:24
Alignment explanation
Indices: 56690730--56690775 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
56690720 GAATAGTCGT
* *
56690730 ATATCGAGAAGTTCAAGTGAGCCA
1 ATATCGAGAAGCTCAAGAGAGCCA
*
56690754 ATATCGAGAAGCTCTAGAGAGC
1 ATATCGAGAAGCTCAAGAGAGC
56690776 TATTAATAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (24 bp):
ATATCGAGAAGCTCAAGAGAGCCA
Found at i:56692593 original size:15 final size:14
Alignment explanation
Indices: 56692575--56692608 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
56692565 ATTTATGTTT
*
56692575 TTTTTCTTCTTTTA
1 TTTTTCCTCTTTTA
56692589 CTTTTTCCTCTTTTA
1 -TTTTTCCTCTTTTA
56692604 TTTTT
1 TTTTT
56692609 GTCGATTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTCCTCTTTTA
Found at i:56693230 original size:9 final size:9
Alignment explanation
Indices: 56693216--56693243 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
56693206 TATAGTTTGA
56693216 TATTCGAAT
1 TATTCGAAT
56693225 TATTCGAAT
1 TATTCGAAT
56693234 TATTCGAAT
1 TATTCGAAT
56693243 T
1 T
56693244 CGAAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:56693313 original size:9 final size:9
Alignment explanation
Indices: 56693296--56693326 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
56693286 TCGAGTTGAT
56693296 TCGAATAAC
1 TCGAATAAC
*
56693305 TCGATTAAC
1 TCGAATAAC
56693314 TCGAATAAC
1 TCGAATAAC
56693323 TCGA
1 TCGA
56693327 TTTGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:56694052 original size:33 final size:33
Alignment explanation
Indices: 56694015--56694085 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
56694005 TGGTTTTTCC
56694015 CTTAAACGTTTTGATGTAGCCTCCAGACTTAAT
1 CTTAAACGTTTTGATGTAGCCTCCAGACTTAAT
56694048 CTTAAACGTTTTGATGTAGCCTCCAGACTTAAT
1 CTTAAACGTTTTGATGTAGCCTCCAGACTTAAT
56694081 CTTAA
1 CTTAA
56694086 TGTCTAAGCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (33 bp):
CTTAAACGTTTTGATGTAGCCTCCAGACTTAAT
Found at i:56695268 original size:13 final size:13
Alignment explanation
Indices: 56695250--56695277 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
56695240 GGCTGAGCCA
56695250 AGACTCCTCAATG
1 AGACTCCTCAATG
56695263 AGACTCCTCAATG
1 AGACTCCTCAATG
56695276 AG
1 AG
56695278 TTTCGAGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (13 bp):
AGACTCCTCAATG
Found at i:56698531 original size:10 final size:10
Alignment explanation
Indices: 56698483--56698560 Score: 60
Period size: 9 Copynumber: 8.2 Consensus size: 10
56698473 CATGTAGCAA
56698483 AAAAATTA-T
1 AAAAATTATT
*
56698492 AAAAA--ATA
1 AAAAATTATT
*
56698500 AAAAATTAAT
1 AAAAATTATT
*
56698510 AAAAGTTA-T
1 AAAAATTATT
56698519 AAAAATTATT
1 AAAAATTATT
*
56698529 -AAATTATATT
1 AAAAAT-TATT
56698539 AAAAA-TATT
1 AAAAATTATT
56698548 AAAAATTAATT
1 AAAAATT-ATT
56698559 AA
1 AA
56698561 TTTTTATACA
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
7 1 0.02
8 5 0.09
9 26 0.48
10 14 0.26
11 8 0.15
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (10 bp):
AAAAATTATT
Found at i:56698573 original size:29 final size:30
Alignment explanation
Indices: 56698518--56698611 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 30
56698508 ATAAAAGTTA
56698518 TAAAAATTATTAAATTATATTAAAAAT-AT
1 TAAAAATTATTAAATTATATTAAAAATCAT
* * *
56698547 TAAAAATTAATTAATTTTTA-TACAAATCAT
1 TAAAAATT-ATTAAATTATATTAAAAATCAT
* * * *
56698577 AAAAAATTGTAAAATTTTA-TAAAAATCAT
1 TAAAAATTATTAAATTATATTAAAAATCAT
*
56698606 AAAAAA
1 TAAAAA
56698612 AGTCATTTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 37 0.67
30 18 0.33
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (30 bp):
TAAAAATTATTAAATTATATTAAAAATCAT
Found at i:56698791 original size:21 final size:20
Alignment explanation
Indices: 56698767--56698809 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
56698757 AAAATGCTTC
56698767 TTTTAGTACGATAATTTATAT
1 TTTTAGTACGA-AATTTATAT
** *
56698788 TTTTTTTACGAATTTTATAT
1 TTTTAGTACGAAATTTATAT
56698808 TT
1 TT
56698810 CTTTAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTTAGTACGAAATTTATAT
Found at i:56698882 original size:11 final size:10
Alignment explanation
Indices: 56698855--56698881 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
56698845 AAATTTTATA
56698855 ATTTTTTACG
1 ATTTTTTACG
56698865 ATTTTTTACG
1 ATTTTTTACG
56698875 ATTTTTT
1 ATTTTTT
56698882 TGTAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.67
Consensus pattern (10 bp):
ATTTTTTACG
Found at i:56698910 original size:29 final size:28
Alignment explanation
Indices: 56698878--56698949 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
56698868 TTTTACGATT
*
56698878 TTTTTGTAATTTTAAATAAAATTTAAATA
1 TTTTTATAATTTTAAATAAAATTT-AATA
* * * *
56698907 TTTTTATATTTTTTACTGAAATTTAATA
1 TTTTTATAATTTTAAATAAAATTTAATA
56698935 TTTTTATAACTTTTA
1 TTTTTATAA-TTTTA
56698950 TTAATTTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
28 12 0.34
29 23 0.66
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (28 bp):
TTTTTATAATTTTAAATAAAATTTAATA
Found at i:56699242 original size:92 final size:91
Alignment explanation
Indices: 56699037--56699294 Score: 292
Period size: 91 Copynumber: 2.9 Consensus size: 91
56699027 TTAAGGACGT
* * * * *
56699037 TTCAAGTACCCAATTGAGTGC---AAAAAAAGGCAAGGGTTTAATTGCTTTTTTCGAAAAATTTT
1 TTCAAGTGCCCAATTGAGTGCAAAAAAAAAAAGCAAGGGCTTAATTGCTTTTTTTGAAAAAGTTT
* *
56699099 GAGGGCCTTTTTATGCATTTTGAAAG
66 AAGGGCCTTTTTATGCATTGTGAAAG
* * *
56699125 TTCAAGTGTCCAATTGAGTGCAAAAAAAAAAAACAAGGGCTTAATTGCTTTTTTTGAAAAAGCTT
1 TTCAAGTGCCCAATTGAGTGCAAAAAAAAAAAGCAAGGGCTTAATTGCTTTTTTTGAAAAAGTTT
**
56699190 AAGGGTTTTTTTGATGCATTGTGAAAG
66 AAGGGCCTTTTT-ATGCATTGTGAAAG
* * * * *
56699217 TTCAAGTGCCCAAGTT-TGTGTAAAAAAAAGAAAGTAGGGGCTTAATTGCTTTCTTTGAAAAAGT
1 TTCAAGTGCCCAA-TTGAGTGCAAAAAAAA-AAAGCAAGGGCTTAATTGCTTTTTTTGAAAAAGT
*
56699281 TTAAGAG-CTTTTTA
64 TTAAGGGCCTTTTTA
56699295 CACCCTTAAG
Statistics
Matches: 142, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
88 19 0.13
91 45 0.32
92 41 0.29
93 37 0.26
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (91 bp):
TTCAAGTGCCCAATTGAGTGCAAAAAAAAAAAGCAAGGGCTTAATTGCTTTTTTTGAAAAAGTTT
AAGGGCCTTTTTATGCATTGTGAAAG
Found at i:56699276 original size:93 final size:90
Alignment explanation
Indices: 56699037--56699294 Score: 274
Period size: 92 Copynumber: 2.9 Consensus size: 90
56699027 TTAAGGACGT
* ** * *
56699037 TTCAAGTACCCAATTGAGTGC---AAAAAAAGGCAAGGGTTTAATTGCTTTTTTCGAAAAATTTT
1 TTCAAGTGCCCAATTGAGTGCAAAAAAAAAAAACAAGGGCTTAATTGCTTTTTT-GAAAAAGTTT
* *
56699099 GAGGGCCTTTTTATGCATTTTGAAAG
65 AAGGGCCTTTTTATGCATTGTGAAAG
* *
56699125 TTCAAGTGTCCAATTGAGTGCAAAAAAAAAAAACAAGGGCTTAATTGCTTTTTTTGAAAAAGCTT
1 TTCAAGTGCCCAATTGAGTGCAAAAAAAAAAAACAAGGGCTTAATTGC-TTTTTTGAAAAAGTTT
**
56699190 AAGGGTTTTTTTGATGCATTGTGAAAG
65 AAGGGCCTTTTT-ATGCATTGTGAAAG
* * ** *
56699217 TTCAAGTGCCCAAGTT-TGTGTAAAAAAAAGAAAGTAGGGGCTTAATTGCTTTCTTTGAAAAAGT
1 TTCAAGTGCCCAA-TTGAGTGCAAAAAAAA-AAAACAAGGGCTTAATTGCTTT-TTTGAAAAAGT
*
56699281 TTAAGAG-CTTTTTA
63 TTAAGGGCCTTTTTA
56699295 CACCCTTAAG
Statistics
Matches: 142, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
88 19 0.13
91 39 0.27
92 50 0.35
93 34 0.24
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (90 bp):
TTCAAGTGCCCAATTGAGTGCAAAAAAAAAAAACAAGGGCTTAATTGCTTTTTTGAAAAAGTTTA
AGGGCCTTTTTATGCATTGTGAAAG
Found at i:56700070 original size:16 final size:16
Alignment explanation
Indices: 56700041--56700073 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56700031 TATATATTTC
56700041 AAAGTAAAGAAATGAG
1 AAAGTAAAGAAATGAG
56700057 AAAG-AAAGAGAATGAG
1 AAAGTAAAGA-AATGAG
56700073 A
1 A
56700074 GGGGTAGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (16 bp):
AAAGTAAAGAAATGAG
Found at i:56704214 original size:22 final size:23
Alignment explanation
Indices: 56704179--56704223 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
56704169 ACCACTATAA
56704179 AACACGAAAAAAATAAAACAGAG
1 AACACGAAAAAAATAAAACAGAG
56704202 AACACG-AAAAAATAAAACAGAG
1 AACACGAAAAAAATAAAACAGAG
56704224 TAAGCAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.69, C:0.13, G:0.13, T:0.04
Consensus pattern (23 bp):
AACACGAAAAAAATAAAACAGAG
Found at i:56706316 original size:14 final size:14
Alignment explanation
Indices: 56706297--56706335 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
56706287 TGGTACATTG
56706297 TATTTGTATATATA
1 TATTTGTATATATA
* *
56706311 TATTTGTAAATATT
1 TATTTGTATATATA
*
56706325 TATTCGTATAT
1 TATTTGTATAT
56706336 GCTGTAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (14 bp):
TATTTGTATATATA
Found at i:56709228 original size:39 final size:36
Alignment explanation
Indices: 56709103--56709280 Score: 123
Period size: 35 Copynumber: 5.0 Consensus size: 36
56709093 CGCGAAAGAG
* * *
56709103 TTTGCGCCCAGCGCTAGTCGGATAAACCGTC-AA-A
1 TTTGCGCCCAGCTCTAGTCGGATAAATCGACGAATA
* * * * * * * *
56709137 TGTGTGCCTATCACTAGTCAGATAAATTGACGGA-A
1 TTTGCGCCCAGCTCTAGTCGGATAAATCGACGAATA
*
56709172 GTTGCGCCCAG-TGCTAGTCGGATAAATCGACGAATAA
1 TTTGCGCCCAGCT-CTAGTCGGATAAATCGACGAAT-A
* * * * *
56709209 TTAGTGGGCCCAGCTCTAGTTGGGTAAACCAACG-ATA
1 TT--TGCGCCCAGCTCTAGTCGGATAAATCGACGAATA
*
56709246 TTTGCGCCCAGCACTAGTCGGATAAATCGACGAAT
1 TTTGCGCCCAGCTCTAGTCGGATAAATCGACGAAT
56709281 GTGTGCCCAG
Statistics
Matches: 105, Mismatches: 31, Indels: 14
0.70 0.21 0.09
Matches are distributed among these distances:
34 22 0.21
35 50 0.48
36 2 0.02
37 5 0.05
38 2 0.02
39 23 0.22
40 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.24
Consensus pattern (36 bp):
TTTGCGCCCAGCTCTAGTCGGATAAATCGACGAATA
Found at i:56710790 original size:20 final size:21
Alignment explanation
Indices: 56710767--56710811 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
56710757 AGAAAAATTC
56710767 AAGGAAATAA-AAAA-AAAGAA
1 AAGGAAA-AATAAAATAAAGAA
*
56710787 AAGGAAAAATAAAATAAGGAA
1 AAGGAAAAATAAAATAAAGAA
56710808 AAGG
1 AAGG
56710812 GAGAAGGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 2 0.09
20 11 0.50
21 9 0.41
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (21 bp):
AAGGAAAAATAAAATAAAGAA
Found at i:56716668 original size:29 final size:32
Alignment explanation
Indices: 56716601--56716674 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 32
56716591 GATTTTCTTT
*
56716601 TATG-TATTATTTACTTTTAAGCTGTTTTAGA
1 TATGTTATTATTTACTTTCAAGCTGTTTTAGA
* * *
56716632 TTTATTATTATTTA-TTTCAAG-T-TTTTATA
1 TATGTTATTATTTACTTTCAAGCTGTTTTAGA
56716661 TATGTTATTCATTT
1 TATGTTATT-ATTT
56716675 CGAATATATG
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
29 13 0.37
30 5 0.14
31 8 0.23
32 9 0.26
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (32 bp):
TATGTTATTATTTACTTTCAAGCTGTTTTAGA
Found at i:56720243 original size:18 final size:17
Alignment explanation
Indices: 56720212--56720247 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
56720202 ATGCTAATTA
56720212 AATTAATTGCTGAATAT
1 AATTAATTGCTGAATAT
*
56720229 AATTAGATTGTTGAATAT
1 AATTA-ATTGCTGAATAT
56720247 A
1 A
56720248 TATCAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.42, C:0.03, G:0.14, T:0.42
Consensus pattern (17 bp):
AATTAATTGCTGAATAT
Found at i:56721594 original size:22 final size:22
Alignment explanation
Indices: 56721569--56721616 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
56721559 TATCCAAACG
* *
56721569 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAACAAA
* *
56721591 ATAATATTAAAATAGTAACAAA
1 ATAACAATAAAATAGTAACAAA
56721613 ATAA
1 ATAA
56721617 GAAGAAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.23
Consensus pattern (22 bp):
ATAACAATAAAATAGTAACAAA
Found at i:56730819 original size:23 final size:23
Alignment explanation
Indices: 56730788--56730831 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
56730778 GCATCCTGAC
*
56730788 ATTATGGTGTAATTCATTCTGGT
1 ATTACGGTGTAATTCATTCTGGT
56730811 ATTACGGTGTAATTCATTCTG
1 ATTACGGTGTAATTCATTCTG
56730832 CAACACCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.45
Consensus pattern (23 bp):
ATTACGGTGTAATTCATTCTGGT
Found at i:56732628 original size:3 final size:3
Alignment explanation
Indices: 56732615--56732694 Score: 128
Period size: 3 Copynumber: 27.3 Consensus size: 3
56732605 TCTGGGTCTG
56732615 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
56732662 -TA ATA ATA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
56732695 ATAATAGCTT
Statistics
Matches: 74, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
2 4 0.05
3 70 0.95
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:56732789 original size:2 final size:2
Alignment explanation
Indices: 56732769--56732851 Score: 123
Period size: 2 Copynumber: 40.5 Consensus size: 2
56732759 TTTATCTATG
*
56732769 TA TA TC TA TA TA CTA -A TA TA TA GTA TA CTA TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA
56732811 TA TA TA TA TA TA TA 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 TA TA TA TA T
56732852 TGTATATTGA
Statistics
Matches: 75, Mismatches: 2, Indels: 8
0.88 0.02 0.09
Matches are distributed among these distances:
1 1 0.01
2 68 0.91
3 6 0.08
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:56736834 original size:21 final size:19
Alignment explanation
Indices: 56736808--56736924 Score: 68
Period size: 20 Copynumber: 6.1 Consensus size: 19
56736798 GCTCAGATTC
56736808 AATAAAAAAAGAGGAAAGAAA
1 AATAAAAAAAGA--AAAGAAA
*
56736829 AAT-AAAAAA-AACAGTAAA
1 AATAAAAAAAGAAAAG-AAA
**
56736847 AA-AACAAAAAGAAAAGATTC
1 AATAA-AAAAAGAAAAGA-AA
56736867 AATAAAAAAAGAGGAAAGAAA
1 AATAAAAAAAGA--AAAGAAA
*
56736888 AAT-AAAAAAG--CAGTAAA
1 AATAAAAAAAGAAAAG-AAA
*
56736905 AA-ACAAAAAGAAAAGAAA
1 AATAAAAAAAGAAAAGAAA
56736923 AA
1 AA
56736925 GAGAAAAATC
Statistics
Matches: 75, Mismatches: 9, Indels: 27
0.68 0.08 0.24
Matches are distributed among these distances:
16 2 0.03
17 14 0.19
18 11 0.15
19 9 0.12
20 26 0.35
21 8 0.11
22 5 0.07
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (19 bp):
AATAAAAAAAGAAAAGAAA
Found at i:56736839 original size:22 final size:21
Alignment explanation
Indices: 56736811--56736896 Score: 58
Period size: 22 Copynumber: 4.2 Consensus size: 21
56736801 CAGATTCAAT
56736811 AAAAAAAGAGGAAAGAAAAATA
1 AAAAAAAGA-GAAAGAAAAATA
* *
56736833 AAAAAAACAG---TAAAAA-A
1 AAAAAAAGAGAAAGAAAAATA
* **
56736850 ACAAAAAGA-AAAGATTCAAT-
1 AAAAAAAGAGAAAGA-AAAATA
56736870 AAAAAAAGAGGAAAGAAAAATA
1 AAAAAAAGA-GAAAGAAAAATA
56736892 AAAAA
1 AAAAA
56736897 GCAGTAAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 16
0.64 0.14 0.22
Matches are distributed among these distances:
17 8 0.17
18 5 0.11
19 1 0.02
20 10 0.22
21 4 0.09
22 18 0.39
ACGTcount: A:0.77, C:0.03, G:0.13, T:0.07
Consensus pattern (21 bp):
AAAAAAAGAGAAAGAAAAATA
Found at i:56736908 original size:57 final size:59
Alignment explanation
Indices: 56736802--56736920 Score: 215
Period size: 59 Copynumber: 2.1 Consensus size: 59
56736792 CTATGAGCTC
56736802 AGATTCAATAAAAAAAGAGGAAAGAAAAATAAAAAAAACAGTAAAAAAACAAAAAGAAA
1 AGATTCAATAAAAAAAGAGGAAAGAAAAATAAAAAAAACAGTAAAAAAACAAAAAGAAA
*
56736861 AGATTCAATAAAAAAAGAGGAAAGAAAAAT-AAAAAAGCAGT-AAAAAACAAAAAGAAA
1 AGATTCAATAAAAAAAGAGGAAAGAAAAATAAAAAAAACAGTAAAAAAACAAAAAGAAA
56736918 AGA
1 AGA
56736921 AAAAGAGAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
57 19 0.32
58 10 0.17
59 30 0.51
ACGTcount: A:0.73, C:0.05, G:0.13, T:0.08
Consensus pattern (59 bp):
AGATTCAATAAAAAAAGAGGAAAGAAAAATAAAAAAAACAGTAAAAAAACAAAAAGAAA
Found at i:56737872 original size:7 final size:7
Alignment explanation
Indices: 56737858--56737924 Score: 118
Period size: 7 Copynumber: 9.7 Consensus size: 7
56737848 TTGAGTCAAA
56737858 AAAAATG
1 AAAAATG
*
56737865 ACAAATG
1 AAAAATG
56737872 AAAAATG
1 AAAAATG
56737879 AAAAATG
1 AAAAATG
56737886 AAAAAT-
1 AAAAATG
56737892 AAAAATG
1 AAAAATG
56737899 AAAAATG
1 AAAAATG
56737906 AAAAATG
1 AAAAATG
56737913 AAAAATG
1 AAAAATG
56737920 AAAAA
1 AAAAA
56737925 GTAAAAGTGG
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
6 6 0.11
7 51 0.89
ACGTcount: A:0.73, C:0.01, G:0.12, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:56737896 original size:34 final size:35
Alignment explanation
Indices: 56737858--56737930 Score: 130
Period size: 34 Copynumber: 2.1 Consensus size: 35
56737848 TTGAGTCAAA
*
56737858 AAAAATGACAAATGAAAAATGAAAAATGAAAAA-T
1 AAAAATGAAAAATGAAAAATGAAAAATGAAAAAGT
56737892 AAAAATGAAAAATGAAAAATGAAAAATGAAAAAGT
1 AAAAATGAAAAATGAAAAATGAAAAATGAAAAAGT
56737927 AAAA
1 AAAA
56737931 GTGGAGAGGC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 32 0.86
35 5 0.14
ACGTcount: A:0.73, C:0.01, G:0.12, T:0.14
Consensus pattern (35 bp):
AAAAATGAAAAATGAAAAATGAAAAATGAAAAAGT
Found at i:56739287 original size:44 final size:44
Alignment explanation
Indices: 56739229--56739998 Score: 791
Period size: 44 Copynumber: 17.6 Consensus size: 44
56739219 AAGCTACCAG
* * **
56739229 TCCTATCTCTCTAAGCAGTAGTGGAGTAGGTTGAAGATGGTAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
* *
56739273 TCCTATCTCCCTAAGCAGTAGCGGAGCGGGTCAAAGATGGTAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
* * * *
56739317 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-CG-ACGAA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTA-G-A
* * * * * ** *****
56739361 TCTTATCTTCCTAAGCAGTAGTGAAGTAGATTTAAGCCACCAG-
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
*
56739404 TCCTATCTCCCTAAGTAGTAGTGGAGCAGGTCAAAGATGGTAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
*
56739448 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAAATGGTAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
56739492 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
* * * * * * *
56739536 TCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACGGCAAA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
* * * * * ** *****
56739580 TCTTATCTTCCTAAGCAGTAGTGAAGTAGATTTAAGCCACCAG-
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
**
56739623 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTTGAAGATGGTAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
* *
56739667 TCCTATCTCCCTAAGCAGTAGCGGAGCAGGTCGAAGATGGTAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
* *
56739711 TCCTATATCCCTAAGCAGTAGTGGAGTAGGTCAAAGATGGTAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
* *
56739755 TCCTATCTCCCTAAGCAGTAGCGGAGCAGGTCGAAGATGGTAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
*
56739799 TCCTATATCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
* * * * *
56739843 TCTTATCTCCCTAAGCAGTAGTGGAACAGATCGAAGACGGT-GAA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAG-A
* * * * ** *****
56739887 TCTTATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCAG-
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
* ** *
56739930 TCCTATCTCCCTAAGCAGTAGTGGGGCAGG-CAAAAGA-AATCGA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTC-AAAGATGGTAGA
*
56739973 TCTTATCTCCCTAAGCAGTAGTGGAG
1 TCCTATCTCCCTAAGCAGTAGTGGAG
56739999 TAGATCACAT
Statistics
Matches: 611, Mismatches: 105, Indels: 21
0.83 0.14 0.03
Matches are distributed among these distances:
42 3 0.00
43 117 0.19
44 488 0.80
45 2 0.00
46 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (44 bp):
TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
Found at i:56739455 original size:175 final size:175
Alignment explanation
Indices: 56739164--56740334 Score: 1033
Period size: 175 Copynumber: 6.8 Consensus size: 175
56739154 TATTAACGGC
* * * * *
56739164 GGAGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGCAGTAGTGAAGTAAATTTAAGCTACCAG
1 GGAGCAGATCGAAGACGACGAATCTTATCTTCCTAAGCAGTAGTGGAGTAGATTTAAGCCACAAG
* * ** *
56739229 TCCTATCTCTCTAAGCAGTAGTGGAGTAGGTTGAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
66 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATAGTAGATCCTATCTCCCTAAGCAGTAG
* *
56739294 CGGAGCGGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAGTAGT
131 TGGAGCAGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAGTAGT
* *
56739339 GGAGCAGATCGAAGACGACGAATCTTATCTTCCTAAGCAGTAGTGAAGTAGATTTAAGCCACCAG
1 GGAGCAGATCGAAGACGACGAATCTTATCTTCCTAAGCAGTAGTGGAGTAGATTTAAGCCACAAG
* *
56739404 TCCTATCTCCCTAAGTAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
66 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATAGTAGATCCTATCTCCCTAAGCAGTAG
* *
56739469 TGGAGCAGGTCAAAAATGGTAGATCCTATCTCCCTAAGCAGTAGT
131 TGGAGCAGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAGTAGT
* * * * * * ** **
56739514 GGAGCAGGTCAAAGATG--GTAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACGGC
1 GGAGCAGATCGAAGACGACG-A-ATCTTATCTTCCTAAGCAGTAGTGGAGTAGATTTAAG-CCAC
* * * * * * ** ** **
56739577 AAATCTTATCTTCCTAAGCAGTAGTGAAGTAGATTTAAGCCACCAG-TCCTATCTCCCTAAGCAG
63 AAGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATAGTAGATCCTATCTCCCTAAGCAG
** * *
56739641 TAGTGGAGCAGGTTGAAGATGGTAGATCCTATCTCCCTAAGCAGTAGC
128 TAGTGGAGCAGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAGTAGT
* * * * * * ** *****
56739689 GGAGCAGGTCGAAGATG--GTAGATCCTATATCCCTAAGCAGTAGTGGAGTAGGTCAAAGATGGT
1 GGAGCAGATCGAAGACGACG-A-ATCTTATCTTCCTAAGCAGTAGTGGAGTAGATTTAAGCCACA
* * * *
56739752 AGATCCTATCTCCCTAAGCAGTAGCGGAGCAGGTCGAAGATGGTAGATCCTATATCCCTAAGCAG
64 AG-TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATAGTAGATCCTATCTCCCTAAGCAG
56739817 TAGTGGAGCAGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAGTAGT
128 TAGTGGAGCAGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAGTAGT
* ** * * *
56739865 GGAACAGATCGAAGACGGTGAATCTTATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCAG
1 GGAGCAGATCGAAGACGACGAATCTTATCTTCCTAAGCAGTAGTGGAGTAGATTTAAGCCACAAG
* * * *
56739930 TCCTATCTCCCTAAGCAGTAGTGGGGCAGG-CAAAAGA-AATCGATCTTATCTCCCTAAGCAGTA
66 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTC-AAAGATAGTAGATCCTATCTCCCTAAGCAGTA
* * * ** *
56739993 GTGGAGTAGATC--ACAT-CAAG-TCTTATCTCCCTAACCAGTAGT
130 GTGGAGCAGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAGTAGT
* * *
56740035 GGAGCAGA-CGAAAGA-AACCG-ATCTTATC-TCCTTAAGCAGTAGTGGATTAGA--TCA--CAT
1 GGAGCAGATCG-AAGACGA-CGAATCTTATCTTCC-TAAGCAGTAGTGGAGTAGATTTAAGCCA-
* * * * *** *
56740092 CAAGTCTTATCTCCCTAAGTAGTAGTGGAGC-GGACGAAA-AAAACCGATCTTATCTCCCTAAGC
62 CAAGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTC-AAAGATAGTAGATCCTATCTCCCTAAGC
* * **
56740155 AGTAGTGGAGCA-GACGAAAGA---AACCTCTTATCTCCCTAAGCAGTAGT
126 AGTAGTGGAGCAGGTC-AAAGATGGTAGATCTTATCTCCCTAAGCAGTAGT
* * *
56740202 GGAGCAGA-CGAAAGA-AACCG-ATCTTATCTCCCTAAGCAGTAGTGGAGTAGA--TCA--CATC
1 GGAGCAGATCG-AAGACGA-CGAATCTTATCTTCCTAAGCAGTAGTGGAGTAGATTTAAGCCA-C
* * *** *
56740260 AAGTCTTATCTCCCTAAGCAGTAGTGGAGCA-GACGAAAGA-AACCGATCTTATCTCCCTAAGCA
63 AAGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTC-AAAGATAGTAGATCCTATCTCCCTAAGCA
*
56740323 GTAGTAGAGCAG
127 GTAGTGGAGCAG
56740335 ATCGCATCAA
Statistics
Matches: 848, Mismatches: 126, Indels: 51
0.83 0.12 0.05
Matches are distributed among these distances:
165 6 0.01
166 65 0.08
167 145 0.17
168 8 0.01
169 26 0.03
170 33 0.04
171 2 0.00
172 3 0.00
173 1 0.00
174 35 0.04
175 383 0.45
176 139 0.16
177 1 0.00
178 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (175 bp):
GGAGCAGATCGAAGACGACGAATCTTATCTTCCTAAGCAGTAGTGGAGTAGATTTAAGCCACAAG
TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATAGTAGATCCTATCTCCCTAAGCAGTAG
TGGAGCAGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAGTAGT
Found at i:56739608 original size:219 final size:219
Alignment explanation
Indices: 56739229--56740334 Score: 1015
Period size: 219 Copynumber: 5.1 Consensus size: 219
56739219 AAGCTACCAG
* * *
56739229 TCCTATCTCTCTAAGCAGTAGTGGAGTAGGTTGAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
* * * *
56739294 CGGAGCGGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACG
66 TGGAGCAGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCA
*
56739359 AATCTTATCTTCCTAAGCAGTAGTGAAGTAGATTTAAGCCACCAGTCCTATCTCCCTAAGTAGTA
131 AATCTTATCTTCCTAAGCAGTAGTGAAGTAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTA
*
56739424 GTGGAGCAGGTCAAAGATGGTAGA
196 GTGGAGCAGGTCGAAGATGGTAGA
* *
56739448 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAAATGGTAGATCCTATCTCCCTAAGCAGTAG
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
*
56739513 TGGAGCAGGTCAAAGATGGTAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACGGCA
66 TGGAGCAGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCA
56739578 AATCTTATCTTCCTAAGCAGTAGTGAAGTAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTA
131 AATCTTATCTTCCTAAGCAGTAGTGAAGTAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTA
*
56739643 GTGGAGCAGGTTGAAGATGGTAGA
196 GTGGAGCAGGTCGAAGATGGTAGA
* *
56739667 TCCTATCTCCCTAAGCAGTAGCGGAGCAGGTCGAAGATGGTAGATCCTATATCCCTAAGCAGTAG
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
* * * * * *
56739732 TGGAGTAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGCGGAGCAGGTCGAAGATGGTA
66 TGGAGCAGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCA
* * * * * * * ** ***** *
56739797 GATCCTATATCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAGT
131 AATCTTATCTTCCTAAGCAGTAGTGAAGTAGATTTAAGCCACCAG-TCCTATCTCCCTAAGCAGT
* * *
56739862 AGTGGAACAGATCGAAGACGGT-GAA
195 AGTGGAGCAGGTCGAAGATGGTAG-A
* * * * ** *****
56739887 TCTTATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCAG-TCCTATCTCCCTAAGCAGTAG
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
* ** * * **
56739951 TGGGGCAGG-CAAAAGA-AATCGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATC----ACATC
66 TGGAGCAGGTC-AAAGATGGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGC
* * * * * *** ** * *
56740010 AAGTCTTATCTCCCTAACCAGTAGTGGAGCAGACGAAAGAAACC-GATCTTATCTCCTTAAGCAG
130 AAATCTTATCTTCCTAAGCAGTAGTGAAGTAGATTTAAGCCACCAG-TCCTATCTCCCTAAGCAG
** * * **
56740074 TAGTGGATTAGATC--ACAT-CAAG-
194 TAGTGGAGCAGGTCGAAGATGGTAGA
* * * * ***** *
56740096 TCTTATCTCCCTAAGTAGTAGTGGAGC-GGACGAAAAAAACCGATCTTATCTCCCTAAGCAGTAG
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
* * ** **
56740160 TGGAGCA-GACGAAAGA---AACCTCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGA-AA
66 TGGAGCAGGTC-AAAGATGGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG-AAGACGG
** * * * * *
56740219 CCGATCTTATCTCCCTAAGCAGTAGTGGAGTAGA--TCA--CATCAAGTCTTATCTCCCTAAGCA
129 CAAATCTTATCTTCCTAAGCAGTAGTGAAGTAGATTTAAGCCA-CCAGTCCTATCTCCCTAAGCA
* **
56740280 GTAGTGGAGCA-GACGAA-A-GAAACCGA
193 GTAGTGGAGCAGGTCGAAGATGGTA--GA
* *
56740306 TCTTATCTCCCTAAGCAGTAGTAGAGCAG
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAG
56740335 ATCGCATCAA
Statistics
Matches: 741, Mismatches: 126, Indels: 48
0.81 0.14 0.05
Matches are distributed among these distances:
206 3 0.00
207 58 0.08
208 10 0.01
209 57 0.08
210 55 0.07
211 5 0.01
213 31 0.04
214 33 0.04
218 32 0.04
219 389 0.52
220 68 0.09
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (219 bp):
TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
TGGAGCAGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCA
AATCTTATCTTCCTAAGCAGTAGTGAAGTAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTA
GTGGAGCAGGTCGAAGATGGTAGA
Found at i:56739820 original size:307 final size:307
Alignment explanation
Indices: 56739404--56739959 Score: 995
Period size: 307 Copynumber: 1.8 Consensus size: 307
56739394 AAGCCACCAG
* *
56739404 TCCTATCTCCCTAAGTAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
1 TCCTATATCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
* *
56739469 TGGAGCAGGTCAAAAATGGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTA
66 CGGAGCAGGTCAAAAATGGTAGATCCTATATCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTA
* *
56739534 GATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCTAAGCAGT
131 GATCTTATCTCCCTAAGCAGTAGTGGAACAGATCGAAGACGGCAAATCTTATCTTCCTAAGCAGT
*
56739599 AGTGAAGTAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTTGAAGATGGT
196 AGTGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTTGAAGATGGT
56739664 AGATCCTATCTCCCTAAGCAGTAGCGGAGCAGGTCGAAGATGGTAGA
261 AGATCCTATCTCCCTAAGCAGTAGCGGAGCAGGTCGAAGATGGTAGA
*
56739711 TCCTATATCCCTAAGCAGTAGTGGAGTAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
1 TCCTATATCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
* *
56739776 CGGAGCAGGTCGAAGATGGTAGATCCTATATCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTA
66 CGGAGCAGGTCAAAAATGGTAGATCCTATATCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTA
**
56739841 GATCTTATCTCCCTAAGCAGTAGTGGAACAGATCGAAGACGGTGAATCTTATCTTCCTAAGCAGT
131 GATCTTATCTCCCTAAGCAGTAGTGGAACAGATCGAAGACGGCAAATCTTATCTTCCTAAGCAGT
*
56739906 AGTGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTAGTGGGGCAGG
196 AGTGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGCAGG
56739960 CAAAAGAAAT
Statistics
Matches: 236, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
307 236 1.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (307 bp):
TCCTATATCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
CGGAGCAGGTCAAAAATGGTAGATCCTATATCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTA
GATCTTATCTCCCTAAGCAGTAGTGGAACAGATCGAAGACGGCAAATCTTATCTTCCTAAGCAGT
AGTGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTTGAAGATGGT
AGATCCTATCTCCCTAAGCAGTAGCGGAGCAGGTCGAAGATGGTAGA
Found at i:56740218 original size:250 final size:253
Alignment explanation
Indices: 56739886--56740399 Score: 775
Period size: 250 Copynumber: 2.0 Consensus size: 253
56739876 AAGACGGTGA
* *** **
56739886 ATCTTATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGAAGCAGACGAAAGAAACCA-TCCTATCTCCCTAAGCAGTAG
* * *
56739951 TGGGGCAGGCAAAAGAAATCGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCACATCAAGTCT
65 TGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCACATCAAGTCT
* *
56740016 TATCTCCCTAACCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCCTTAAGCAGTAGTGGA
130 TATCTCCCTAACCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTAGA
** * **
56740081 TTAGATCACATCAAGTCTTATCTCCCT-AAG-TAGTAGTGGAGCGGACGAAAAAA-ACCG
195 GCAGATCACATCAAGTCTTATCTCCCTGAAGTTA-CAGTGGAGCGGACGAAAAAACAAAG
* *
56740138 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC-TCTTATCTCCCTAAGCAGTAGT
1 ATCTTATCTCCCTAAGCAGTAGTGAAGCAGACGAAAGAAACCATCCTATCTCCCTAAGCAGTAGT
*
56740202 GGAGCAGACGAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCACATCAAGTCTT
66 GGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCACATCAAGTCTT
*
56740267 ATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTAGAG
131 ATCTCCCTAACCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTAGAG
* **
56740332 CAGATCGCATCAAGTCTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAAACAAAG
196 CAGATCACATCAAGTCTTATCTCCCTGAAGTTACAGTGGAGCGGACGAAAAAACAAAG
56740390 ATCTTATCTC
1 ATCTTATCTC
56740400 TCTGAAGTTG
Statistics
Matches: 236, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
250 167 0.71
251 20 0.08
252 49 0.21
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.24
Consensus pattern (253 bp):
ATCTTATCTCCCTAAGCAGTAGTGAAGCAGACGAAAGAAACCATCCTATCTCCCTAAGCAGTAGT
GGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCACATCAAGTCTT
ATCTCCCTAACCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTAGAG
CAGATCACATCAAGTCTTATCTCCCTGAAGTTACAGTGGAGCGGACGAAAAAACAAAG
Found at i:56740333 original size:43 final size:43
Alignment explanation
Indices: 56739315--56740335 Score: 560
Period size: 44 Copynumber: 23.7 Consensus size: 43
56739305 AAAGATGGTA
*
56739315 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG-AAGACGA-C
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGA-AACC
* * * *** **
56739358 GAATCTTATCTTCCTAAGCAGTAGTGAAGTAGATTTAAGCCACC
1 G-ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
* * * ****
56739402 -AGTCCTATCTCCCTAAGTAGTAGTGGAGCAGGTC-AAAGATGGTA
1 GA-TCTTATCTCCCTAAGCAGTAGTGGAGCA-GACGAAAGA-AACC
* * ***
56739446 GATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTC-AAA-AATGGTA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCA-GACGAAAGAA--ACC
* * ****
56739490 GATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTC-AAAGATGGTA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCA-GACGAAAGA-AACC
* ** *
56739534 GATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCG-AAGACGGCA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGA-AACC
* * * * *** **
56739578 AATCTTATCTTCCTAAGCAGTAGTGAAGTAGATTTAAGCCACC
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
* ** **
56739621 -AGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTTGAAGATGGTA--
1 GA-TCTTATCTCCCTAAGCAGTAGTGGAGCA-GACGAA-A-GAAACC
* * * **
56739665 GATCCTATCTCCCTAAGCAGTAGCGGAGCAGGTCGAAGATGGTA--
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCA-GACGAA-A-GAAACC
* * * * ****
56739709 GATCCTATATCCCTAAGCAGTAGTGGAGTAGGTC-AAAGATGGTA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCA-GACGAAAGA-AACC
* * * **
56739753 GATCCTATCTCCCTAAGCAGTAGCGGAGCAGGTCGAAGATGGTA--
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCA-GACGAA-A-GAAACC
* * * ****
56739797 GATCCTATATCCCTAAGCAGTAGTGGAGCAGGTC-AAAGATGGTA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCA-GACGAAAGA-AACC
* ****
56739841 GATCTTATCTCCCTAAGCAGTAGTGGAACAGATCG-AAGACGGT
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACC
* * *** **
56739884 GAATCTTATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACC
1 G-ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
* * * * *
56739928 -AGTCCTATCTCCCTAAGCAGTAGTGGGGCAGGCAAAAGAAATC
1 GA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
* * **
56739971 GATCTTATCTCCCTAAGCAGTAGTGGAGTAGATC-ACATCAA--
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACC
*
56740012 G-TCTTATCTCCCTAACCAGTAGTGGAGCAGACGAAAGAAACC
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
* ** * **
56740054 GATCTTATCTCCTTAAGCAGTAGTGGATTAGATC-ACATCAA--
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACC
* * *
56740095 G-TCTTATCTCCCTAAGTAGTAGTGGAGCGGACGAAAAAAACC
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
56740137 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
56740180 --TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
* * **
56740221 GATCTTATCTCCCTAAGCAGTAGTGGAGTAGATC-ACATCAA--
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACC
56740262 G-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
*
56740304 GATCTTATCTCCCTAAGCAGTAGTAGAGCAGA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
56740336 TCGCATCAAG
Statistics
Matches: 794, Mismatches: 133, Indels: 102
0.77 0.13 0.10
Matches are distributed among these distances:
39 3 0.00
40 94 0.12
41 46 0.06
42 8 0.01
43 252 0.32
44 381 0.48
45 6 0.01
46 3 0.00
47 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (43 bp):
GATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
Found at i:56740372 original size:167 final size:164
Alignment explanation
Indices: 56739928--56740460 Score: 631
Period size: 167 Copynumber: 3.2 Consensus size: 164
56739918 TTAAGCCACC
* * * * *
56739928 AGTCCTATCTCCCTAAGCAGTAGTGGGGCAGGCAAAAGAAATCGATCTTATCTCCCTAAGCAGTA
1 AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCCCTAAGCAGTA
* *
56739993 GTGGAGTAGATCACATCAAGTCTTATCTCCCTAACCAGT-AGTGGAGCAGACGAAAGAAACCGAT
66 GTGGAGCAGATCGCATCAAGTCTTATCTCCCT-A--AGTAAGTGGAGCAGACGAAAGAAACCGAT
* *
56740057 CTTATCTCCTTAAGCAGTAGTGGATTAGATCACATCA
128 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCACATCA
* * *
56740094 AGTCTTATCTCCCTAAGTAGTAGTGGAGCGGACGAAAAAAACCGATCTTATCTCCCTAAGCAGTA
1 AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCCCTAAGCAGTA
* ** * *
56740159 GTGGAGCAGA-CGAAAGAAACCTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCGA
66 GTGGAGCAGATCG-CATCAA-GTCTTATCTCCCTAAGTA--AGTGGAGCAGACGAAAGAAACCGA
56740223 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCACATCA
127 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCACATCA
56740261 AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCCCTAAGCAGTA
1 AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCCCTAAGCAGTA
* * ** *
56740326 GTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA-AAACAAAG
66 GTGGAGCAGATCGCATCAAGTCTTATCTCCCT-AAG-TA-AGTGGAGCAGACGAAAGAAAC--CG
* ** * * * * *
56740390 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCC
126 ATCTTATCTCCCT-AAGCAGTAGTGGAGTAGATCACATCA
**
56740430 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCA
1 AGTCTTATCTCCCT-AAGCAGTAGTGGAGCA
56740461 AACTAAAAAC
Statistics
Matches: 314, Mismatches: 41, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
164 2 0.01
165 1 0.00
166 86 0.27
167 162 0.52
168 16 0.05
169 33 0.11
170 14 0.04
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.24
Consensus pattern (164 bp):
AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCCCTAAGCAGTA
GTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGTAAGTGGAGCAGACGAAAGAAACCGATCTT
ATCTCCCTAAGCAGTAGTGGAGTAGATCACATCA
Found at i:56740446 original size:41 final size:41
Alignment explanation
Indices: 56740306--56740460 Score: 141
Period size: 41 Copynumber: 3.7 Consensus size: 41
56740296 AAGAAACCGA
** *
56740306 TCTTATCTCCCT-AAGCAGTAGTAGAGCAGATCGCATCAAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGCATCAAG
* * * *** *
56740346 TCTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAAACAAAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-T-CGCATC-AAG
* *
56740390 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAG
1 -TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGCATCAAG
* *
56740432 TCTTATCTCCCTGAAGTTGTAGTGGAGCA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCA
56740461 AACTAAAAAC
Statistics
Matches: 88, Mismatches: 22, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
40 12 0.14
41 38 0.43
42 3 0.03
43 4 0.05
44 4 0.05
45 27 0.31
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (41 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGCATCAAG
Found at i:56740469 original size:86 final size:83
Alignment explanation
Indices: 56739843--56740460 Score: 566
Period size: 83 Copynumber: 7.3 Consensus size: 83
56739833 AGATGGTAGA
* **** * *
56739843 TCTTATCTCCCTAAGCAGTAGTGGAACAGATCG-AAGACGGTGAATCTTATCTTCCTAAGCAGTA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACAG-ATCTTATCTCCCTAAGCAGCA
* *
56739907 GT-GAAGCAGATTTAAGCCA-CCAG
64 GTAG-AGCAGA--T-CG-CATCAAG
* * * * *
56739930 TCCTATCTCCCTAAGCAGTAGTGGGGCAGGCAAAAGAAATC-GATCTTATCTCCCTAAGCAGTAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAA-CAGATCTTATCTCCCTAAGCAGCAG
* * *
56739994 TGGAGTAGATCACATCAAG
65 TAGAGCAGATCGCATCAAG
* * * *
56740013 TCTTATCTCCCTAACCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCCTTAAGCAGTAGT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACAGATCTTATCTCCCTAAGCAGCAGT
* ** *
56740078 GGATTAGATCACATCAAG
66 AGAGCAGATCGCATCAAG
* * * * *
56740096 TCTTATCTCCCTAAGTAGTAGTGGAGCGGACGAAAAAAACCGATCTTATCTCCCTAAGCAGTAGT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACAGATCTTATCTCCCTAAGCAGCAGT
* * ** *
56740161 GGAGCAGA-CGAAAGAAACC
66 AGAGCAGATCG-CATCAA-G
* *
56740180 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCCCTAAGCAGTAGT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACAGATCTTATCTCCCTAAGCAGCAGT
* * *
56740245 GGAGTAGATCACATCAAG
66 AGAGCAGATCGCATCAAG
* *
56740263 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCCCTAAGCAGTAGT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACAGATCTTATCTCCCTAAGCAGCAGT
56740328 AGAGCAGATCGCATCAAG
66 AGAGCAGATCGCATCAAG
* * * ** * **
56740346 TCTTATCTCCCTGAAGTTA-CAGTGGAGCGGATTAAA-AAACAAAGATCTTATCTCTCTGAAGTT
1 TCTTATCTCCCT-AAG-CAGTAGTGGAGCAGACGAAAGAAAC--AGATCTTATCTCCCT-AAGCA
*
56740409 GCAGTAGAGCAGATCGCATCCAG
61 GCAGTAGAGCAGATCGCATCAAG
**
56740432 TCTTATCTCCCTGAAGTTGTAGTGGAGCA
1 TCTTATCTCCCT-AAGCAGTAGTGGAGCA
56740461 AACTAAAAAC
Statistics
Matches: 459, Mismatches: 58, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
82 4 0.01
83 242 0.53
84 89 0.19
85 16 0.03
86 76 0.17
87 32 0.07
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (83 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACAGATCTTATCTCCCTAAGCAGCAGT
AGAGCAGATCGCATCAAG
Found at i:56741853 original size:3 final size:3
Alignment explanation
Indices: 56741845--56741897 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
56741835 GGGTCTGTTA
56741845 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
56741892 TAT TAT
1 TAT TAT
56741898 ATAATAGCTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:56741878 original size:26 final size:26
Alignment explanation
Indices: 56741842--56741899 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
56741832 TCTGGGTCTG
56741842 TTATATTATTATTATTATTATTATTA
1 TTATATTATTATTATTATTATTATTA
56741868 TTATATTATTATTATTATTATTATTA
1 TTATATTATTATTATTATTATTATTA
56741894 TTATAT
1 TTATAT
56741900 AATAGCTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTATATTATTATTATTATTATTATTA
Found at i:56742031 original size:2 final size:2
Alignment explanation
Indices: 56742008--56742071 Score: 94
Period size: 2 Copynumber: 32.0 Consensus size: 2
56741998 TTTCTTACGA
* *
56742008 AT AT AT GT AT AC AT AT -T CAT 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
56742050 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
56742072 TTTGTATATT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.02
2 54 0.96
3 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56744796 original size:3 final size:3
Alignment explanation
Indices: 56744788--56744876 Score: 69
Period size: 3 Copynumber: 30.0 Consensus size: 3
56744778 ATTAGCTTGC
*
56744788 TAT TAT TAT TAT TAT TAT TAT TACT CTAT TGT TAT TAT T-T TCAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TA-T -TAT TAT TAT TAT TAT T-AT TAT
* * * * *
56744834 TAT TA- TAT T-T TAC TAT TAT TCT TAG TAT TAT TCT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
56744877 AGATTACTAT
Statistics
Matches: 67, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
2 8 0.12
3 53 0.79
4 4 0.06
5 2 0.03
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:56747987 original size:36 final size:36
Alignment explanation
Indices: 56747946--56748017 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
56747936 ATTCATTAAA
56747946 GTAAATTTCACAAAAAATCAATACTTAACTAAAAGC
1 GTAAATTTCACAAAAAATCAATACTTAACTAAAAGC
56747982 GTAAATTTCACAAAAAATCAATACTTAACTAAAAGC
1 GTAAATTTCACAAAAAATCAATACTTAACTAAAAGC
56748018 ACAACAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.25
Consensus pattern (36 bp):
GTAAATTTCACAAAAAATCAATACTTAACTAAAAGC
Found at i:56751006 original size:18 final size:19
Alignment explanation
Indices: 56750983--56751027 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
56750973 CATAACAATA
*
56750983 ATAATAAAATTA-AATATT
1 ATAATAAAATTATAATATG
*
56751001 ATAATAATATTATAATATG
1 ATAATAAAATTATAATATG
56751020 A-AATAAAA
1 ATAATAAAA
56751028 AGTAAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
ATAATAAAATTATAATATG
Found at i:56755257 original size:105 final size:104
Alignment explanation
Indices: 56755096--56755300 Score: 227
Period size: 105 Copynumber: 2.0 Consensus size: 104
56755086 CACACATCCT
* * * * **
56755096 TGTCCTTGCCCGTGTAGTTCACATGGCCTAGGCACACGCTCATGTCCTTACCCGTGTGGTTTTAA
1 TGTCCTTCCCCGTGTAGCTCACACGGCCTAGGCACACGCTCATGTCCTCACCCGTGTGGTCCT-A
* *
56755161 AG-CATAAATAAGAGAGTTACATAGCCTAGACACACGGCCG
65 AGTCACAAA-AAGAGAGTTACACAGCCTAGACACACGGCCG
* * * *
56755201 TGTCCTTCCCCGTGT-GACTCACACGGCCTGGGCACACG-TCGATGTCCTCGCTCGTGTTGTCCT
1 TGTCCTTCCCCGTGTAG-CTCACACGGCCTAGGCACACGCTC-ATGTCCTCACCCGTGTGGTCCT
* *
56755264 AAGTCACAAACAGTGAGTTACACAGCCTAGACACACG
64 AAGTCACAAAAAGAGAGTTACACAGCCTAGACACACG
56755301 CCCATTTCCC
Statistics
Matches: 83, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
104 30 0.36
105 53 0.64
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.24
Consensus pattern (104 bp):
TGTCCTTCCCCGTGTAGCTCACACGGCCTAGGCACACGCTCATGTCCTCACCCGTGTGGTCCTAA
GTCACAAAAAGAGAGTTACACAGCCTAGACACACGGCCG
Found at i:56755961 original size:31 final size:33
Alignment explanation
Indices: 56755900--56755964 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 33
56755890 ACACAATCGA
*
56755900 AAAGGAGAAATCAAAGAAGTAAAAAGAAGAAAG
1 AAAGGAAAAATCAAAGAAGTAAAAAGAAGAAAG
56755933 AAAGGAAAAAT-AAA-AAG-AAAGAAGAAGAAAG
1 AAAGGAAAAATCAAAGAAGTAAA-AAGAAGAAAG
56755964 A
1 A
56755965 GTACAAAACG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 3 0.10
31 14 0.47
32 3 0.10
33 10 0.33
ACGTcount: A:0.71, C:0.02, G:0.23, T:0.05
Consensus pattern (33 bp):
AAAGGAAAAATCAAAGAAGTAAAAAGAAGAAAG
Found at i:56758239 original size:50 final size:50
Alignment explanation
Indices: 56758182--56758276 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
56758172 AGCGAGTCAA
* *
56758182 TATCGGGAAGCTCCGGAGAGCC-ATTAATCGGGAAGCTCATAAGAGCCAGT
1 TATCGGGAAGCTCCGAAGAGCCAATT-ATAGGGAAGCTCATAAGAGCCAGT
56758232 TATCGGGAAGCTCCGAAGAGCCAATTATAGGGAAGCTCATAAGAG
1 TATCGGGAAGCTCCGAAGAGCCAATTATAGGGAAGCTCATAAGAG
56758277 TCATAATGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
50 39 0.93
51 3 0.07
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.18
Consensus pattern (50 bp):
TATCGGGAAGCTCCGAAGAGCCAATTATAGGGAAGCTCATAAGAGCCAGT
Found at i:56758275 original size:25 final size:24
Alignment explanation
Indices: 56758182--56758350 Score: 128
Period size: 25 Copynumber: 6.9 Consensus size: 24
56758172 AGCGAGTCAA
***
56758182 TATCGGGAAGCTCCGGAGAGCCAT
1 TATCGGGAAGCTCATAAGAGCCAT
56758206 TAATCGGGAAGCTCATAAGAGCCAGT
1 T-ATCGGGAAGCTCATAAGAGCCA-T
**
56758232 TATCGGGAAGCTCCGAAGAGCCAAT
1 TATCGGGAAGCTCATAAGAGCC-AT
* *
56758257 TATAGGGAAGCTCATAAGAGTCAT
1 TATCGGGAAGCTCATAAGAGCCAT
* * * *
56758281 AAT-GAGAAGCTCACAAGAACCAT
1 TATCGGGAAGCTCATAAGAGCCAT
* * *
56758304 ATAAT-AGGAAGTTTCA-GAGAGCCAT
1 -T-ATCGGGAAG-CTCATAAGAGCCAT
56758329 ATATCGGGAAGCTCATAAGAGC
1 -TATCGGGAAGCTCATAAGAGC
56758351 TGCGGTGTGT
Statistics
Matches: 114, Mismatches: 23, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
23 16 0.14
24 10 0.09
25 82 0.72
26 6 0.05
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (24 bp):
TATCGGGAAGCTCATAAGAGCCAT
Found at i:56759645 original size:29 final size:29
Alignment explanation
Indices: 56759612--56759668 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
56759602 CATAATGAAG
*
56759612 ACCATGAAATAATGTAAAAATAAATTTTA
1 ACCATGAAATAATATAAAAATAAATTTTA
56759641 ACCATGAAATAATATAAAAATAAATTTT
1 ACCATGAAATAATATAAAAATAAATTTT
56759669 TCTTCCGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (29 bp):
ACCATGAAATAATATAAAAATAAATTTTA
Found at i:56761607 original size:244 final size:244
Alignment explanation
Indices: 56761152--56761705 Score: 665
Period size: 244 Copynumber: 2.3 Consensus size: 244
56761142 CAAAGGAAAG
*
56761152 CAAACTAACAA-AAATAAGAAA-ATGCT---AGGAGTTCTGAAATTTTAGAAATCATACATAC-G
1 CAAACTAACAAGAAA-AAGAAATATGCTAAAAGGAGTTCTGAAATTTTAGAAATCATACACACAG
** * * * *
56761211 AACATTTGTTGCCCTAATATAGATGTTAGTGATTAAAAGTATTTCATTACCTTTATTGATGATCA
65 -ACATTTGTAACCCTAATATAGATGCTAGTGATAAAAAATATTTCATCACCTTTATTGATGATCA
* * * *
56761276 TTTGCAATACATGTATCTCTAATTTCTCCATCACAAAAGTGAGGCATTAGTTGCCTTTAAGGCAT
129 TTTGCAATACATGTATCTCTAATTGCTCCATCACAAAACTAAGGCATTAGATGCCTTTAAGGCAT
* * *
56761341 GCAAAACATTAGTAGAGAAACAATGTAAAAACCAAACTAAGATTATGAGAT
194 ACAAAACATAAGTAGAGAAACAATGCAAAAACCAAACTAAGATTATGAGAT
* * *
56761392 CAAACTAACAAGAACAAGAAATATGCTAAAAGGAGTTCT-AGAATTTTAGACATCTTACACACAG
1 CAAACTAACAAGAAAAAGAAATATGCTAAAAGGAGTTCTGA-AATTTTAGAAATCATACACACAG
* * *
56761456 ACATTTGTAACCTTAATATATATGCTAGTGGTAAAAAATATTTCATCACCTTTATTGATGATC-T
65 ACATTTGTAACCCTAATATAGATGCTAGTGATAAAAAATATTTCATCACCTTTATTGATGATCAT
* * * * * ** * *
56761520 TTCTCGATACATGTATCTCTACTTGCTTCATCATAAAACTAATTCATTAGATGCTTTTAAGGTAT
130 TT-GCAATACATGTATCTCTAATTGCTCCATCACAAAACTAAGGCATTAGATGCCTTTAAGGCAT
* *
56761585 ACAAAGCATAAGTAGAGAAACAATGCAAAAAGCAAACTAAGATTATGAGAT
194 ACAAAACATAAGTAGAGAAACAATGCAAAAACCAAACTAAGATTATGAGAT
* * * * * *
56761636 TAGACTAACAAGAATAAAAAAAATATGCTAAAAGGAGTTCTGTAATTTTAGAAACCATACACGCA
1 CAAACTAACAAG-A-AAAAGAAATATGCTAAAAGGAGTTCTGAAATTTTAGAAATCATACACACA
56761701 GACAT
64 GACAT
56761706 AACAAGAATA
Statistics
Matches: 263, Mismatches: 40, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
240 17 0.06
241 7 0.03
243 4 0.02
244 186 0.71
245 2 0.01
246 47 0.18
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (244 bp):
CAAACTAACAAGAAAAAGAAATATGCTAAAAGGAGTTCTGAAATTTTAGAAATCATACACACAGA
CATTTGTAACCCTAATATAGATGCTAGTGATAAAAAATATTTCATCACCTTTATTGATGATCATT
TGCAATACATGTATCTCTAATTGCTCCATCACAAAACTAAGGCATTAGATGCCTTTAAGGCATAC
AAAACATAAGTAGAGAAACAATGCAAAAACCAAACTAAGATTATGAGAT
Found at i:56761767 original size:62 final size:63
Alignment explanation
Indices: 56761637--56761767 Score: 203
Period size: 62 Copynumber: 2.1 Consensus size: 63
56761627 TTATGAGATT
*
56761637 AGAC-TAACAAGAATAAAAAAAATATGCTAAAAGGAGTTCTGTAATTTTAGAAACCATACACGC
1 AGACATAACAAGAAT-AAAAAAATATGCTAAAAGGAGTTCTGTAATTTTAGAAACCATACACAC
* *
56761700 AGACATAACAAGAAT-AAGAAATATGCTAAAAGGAGTTCTGTAATTTTAGAAATCATACACAC
1 AGACATAACAAGAATAAAAAAATATGCTAAAAGGAGTTCTGTAATTTTAGAAACCATACACAC
*
56761762 GGACAT
1 AGACAT
56761768 TTCTTTCATC
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
62 49 0.78
63 4 0.06
64 10 0.16
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23
Consensus pattern (63 bp):
AGACATAACAAGAATAAAAAAATATGCTAAAAGGAGTTCTGTAATTTTAGAAACCATACACAC
Found at i:56765504 original size:18 final size:16
Alignment explanation
Indices: 56765464--56765498 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
56765454 TTTAAAAAAT
56765464 TATTTAATTTTTATTA
1 TATTTAATTTTTATTA
56765480 TATTTAATTTTT-TTA
1 TATTTAATTTTTATTA
56765495 TATT
1 TATT
56765499 CATTAAGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTAATTTTTATTA
Found at i:56766672 original size:27 final size:26
Alignment explanation
Indices: 56766642--56766707 Score: 60
Period size: 27 Copynumber: 2.5 Consensus size: 26
56766632 TTTTTTTCCT
56766642 TTTTACTTTTTCCAAGCCCCCAAAAC
1 TTTTACTTTTTCCAAGCCCCCAAAAC
** * *** *
56766668 ATTTTTGTTTTTGCTTTCCCCCAAATC
1 -TTTTACTTTTTCCAAGCCCCCAAAAC
56766695 TTTTACTTTTTCC
1 TTTTACTTTTTCC
56766708 CAAACCCCAA
Statistics
Matches: 29, Mismatches: 10, Indels: 1
0.73 0.25 0.03
Matches are distributed among these distances:
26 10 0.34
27 19 0.66
ACGTcount: A:0.18, C:0.29, G:0.05, T:0.48
Consensus pattern (26 bp):
TTTTACTTTTTCCAAGCCCCCAAAAC
Found at i:56768256 original size:16 final size:16
Alignment explanation
Indices: 56768235--56768284 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
56768225 TCAAAAACGA
56768235 ATACAGAACATATCAG
1 ATACAGAACATATCAG
*
56768251 ATACAG---TTA-CAG
1 ATACAGAACATATCAG
*
56768263 ATACAGAACATATTAG
1 ATACAGAACATATCAG
56768279 ATACAG
1 ATACAG
56768285 TTACAAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
15 2 0.07
16 14 0.52
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (16 bp):
ATACAGAACATATCAG
Found at i:56768297 original size:28 final size:28
Alignment explanation
Indices: 56768234--56768297 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
56768224 ATCAAAAACG
56768234 AATACAGAACATATCAGATACAGTTACA
1 AATACAGAACATATCAGATACAGTTACA
* *
56768262 GATACAGAACATATTAGATACAGTTACA
1 AATACAGAACATATCAGATACAGTTACA
*
56768290 AATTCAGA
1 AATACAGA
56768298 TACAAATGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.23
Consensus pattern (28 bp):
AATACAGAACATATCAGATACAGTTACA
Found at i:56769003 original size:63 final size:63
Alignment explanation
Indices: 56768900--56769043 Score: 191
Period size: 63 Copynumber: 2.3 Consensus size: 63
56768890 CTCAAATTCC
* * *
56768900 CAAAACAGTGAGTTACATGGCCTGGACACACGCCCATGTCTCTAGCCCGTGTGACCCT-AATT
1 CAAAACAGTGAGTTACACGGCCTGGACACACACCCATGTCTCTAGCCCGTGTAACCCTAAATT
*** * *
56768962 CACAAACAGTGAGTTACACGGCCTGGACACACACTTGTGTCTCTAGCCTGTGTAATCCTAAATT
1 CA-AAACAGTGAGTTACACGGCCTGGACACACACCCATGTCTCTAGCCCGTGTAACCCTAAATT
*
56769026 CAAAATAGTGAGTTACAC
1 CAAAACAGTGAGTTACAC
56769044 AGCTTGCCAC
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
62 2 0.03
63 63 0.89
64 6 0.08
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.24
Consensus pattern (63 bp):
CAAAACAGTGAGTTACACGGCCTGGACACACACCCATGTCTCTAGCCCGTGTAACCCTAAATT
Found at i:56771960 original size:19 final size:19
Alignment explanation
Indices: 56771936--56771982 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
56771926 GCTTAAAGGG
56771936 AAATTAGTATG-AAAATATA
1 AAATTAGTATGAAAAATA-A
* *
56771955 AAATTAAATGTGAAAAATAA
1 AAATT-AGTATGAAAAATAA
56771975 AAATTAGT
1 AAATTAGT
56771983 CTTGGTTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 7 0.30
20 10 0.43
21 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.30
Consensus pattern (19 bp):
AAATTAGTATGAAAAATAA
Found at i:56774526 original size:22 final size:22
Alignment explanation
Indices: 56774482--56774526 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
56774472 TGTCTTCAGG
* * * *
56774482 AATTATCAGCATTCTTTGGAAT
1 AATTACCACCATTCTTCGAAAT
56774504 AATTACCACCATTCTTCGAAAT
1 AATTACCACCATTCTTCGAAAT
56774526 A
1 A
56774527 TATTCACTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.36
Consensus pattern (22 bp):
AATTACCACCATTCTTCGAAAT
Found at i:56775933 original size:14 final size:13
Alignment explanation
Indices: 56775908--56775950 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
56775898 AATTGAAGAG
56775908 ATAAAAAGAAATAA
1 ATAAAAA-AAATAA
56775922 ATAAAGAAAAATAA
1 ATAAA-AAAAATAA
* *
56775936 ACAAACAAAATAA
1 ATAAAAAAAATAA
56775949 AT
1 AT
56775951 CAATAAACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 8 0.32
14 15 0.60
15 2 0.08
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.14
Consensus pattern (13 bp):
ATAAAAAAAATAA
Found at i:56785027 original size:2 final size:2
Alignment explanation
Indices: 56785014--56785055 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
56785004 TCACATCATC
56785014 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56785056 TAGTATAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56786820 original size:16 final size:17
Alignment explanation
Indices: 56786796--56786916 Score: 95
Period size: 16 Copynumber: 6.7 Consensus size: 17
56786786 CGAATATAAT
56786796 AAATATTTTT-ATTTTA
1 AAATATTTTTAATTTTA
*
56786812 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
* *
56786829 AAATACTTTTAAAATTCTTTTTT
1 AAATA-TTTT-TAA----TTTTA
56786852 AAAT-TTTTTAATTTTA
1 AAATATTTTTAATTTTA
*
56786868 AAATATTTTTAAAATACTTTT
1 AAATATTTTT--AAT--TTTA
56786889 AAAT-TTTTTAATTTTA
1 AAATATTTTTAATTTTA
56786905 AAATATTTTTAA
1 AAATATTTTTAA
56786917 AATTTTTGTT
Statistics
Matches: 84, Mismatches: 8, Indels: 25
0.72 0.07 0.21
Matches are distributed among these distances:
16 24 0.29
17 22 0.26
18 7 0.08
19 5 0.06
20 7 0.08
21 11 0.13
23 8 0.10
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:56786823 original size:11 final size:11
Alignment explanation
Indices: 56786824--56786923 Score: 57
Period size: 11 Copynumber: 10.3 Consensus size: 11
56786814 ATTTTTTTAA
*
56786824 TTTTAAAATAC
1 TTTTAAAATAT
*
56786835 TTTTAAAATTCT
1 TTTTAAAA-TAT
*
56786847 TTTTTAAAT-T
1 TTTTAAAATAT
56786857 TTTT---A-AT
1 TTTTAAAATAT
56786864 -TTTAAAATAT
1 TTTTAAAATAT
*
56786874 TTTTAAAATAC
1 TTTTAAAATAT
56786885 TTTT-AAAT-T
1 TTTTAAAATAT
56786894 TTTT---A-A-
1 TTTTAAAATAT
56786900 TTTTAAAATAT
1 TTTTAAAATAT
56786911 TTTTAAAAT-T
1 TTTTAAAATAT
56786921 TTT
1 TTT
56786924 GTTTTAATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 27
0.69 0.05 0.26
Matches are distributed among these distances:
6 7 0.10
7 3 0.04
9 6 0.08
10 16 0.23
11 31 0.44
12 8 0.11
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:56786866 original size:39 final size:39
Alignment explanation
Indices: 56786807--56786935 Score: 183
Period size: 39 Copynumber: 3.3 Consensus size: 39
56786797 AATATTTTTA
* *
56786807 TTTTAAAATTTTTTTAATTTTAAAATACTTTTAAAATTCT
1 TTTTTAAA-TTTTTTAATTTTAAAATATTTTTAAAATTCT
*
56786847 TTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATAC-
1 TTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATTCT
56786885 -TTTTAAATTTTTTAATTTTAAAATATTTTTAAAATT-T
1 TTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATTCT
*
56786922 TTGTTTTAATTTTT
1 TT-TTTAAATTTTT
56786936 AAAATAAATT
Statistics
Matches: 81, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
37 35 0.43
38 1 0.01
39 38 0.47
40 7 0.09
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (39 bp):
TTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATTCT
Found at i:56786898 original size:37 final size:38
Alignment explanation
Indices: 56786807--56786919 Score: 174
Period size: 37 Copynumber: 2.9 Consensus size: 38
56786797 AATATTTTTA
* * *
56786807 TTTTAAAATTTTTTTAATTTTAAAATACTTTTAAAATTC
1 TTTTTAAA-TTTTTTAATTTTAAAATATTTTTAAAATAC
56786846 TTTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATAC
1 -TTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATAC
56786885 -TTTTAAATTTTTTAATTTTAAAATATTTTTAAAAT
1 TTTTTAAATTTTTTAATTTTAAAATATTTTTAAAAT
56786920 TTTTGTTTTA
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
37 35 0.50
39 28 0.40
40 7 0.10
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (38 bp):
TTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:56786930 original size:25 final size:26
Alignment explanation
Indices: 56786807--56786923 Score: 93
Period size: 26 Copynumber: 4.5 Consensus size: 26
56786797 AATATTTTTA
56786807 TTTTAAAATTTTTTTAATTTTAAAATAC
1 TTTTAAAA--TTTTTAATTTTAAAATAC
*
56786835 TTTTAAAATTCTT--TTTT-AAAT--
1 TTTTAAAATTTTTAATTTTAAAATAC
* *
56786856 TTTT-TAATTTTAAAATATTTTTAAAATAC
1 TTTTAAAATTTT----TAATTTTAAAATAC
* *
56786885 TTTTAAATTTTTTAATTTTAAAATAT
1 TTTTAAAATTTTTAATTTTAAAATAC
56786911 TTTTAAAATTTTT
1 TTTTAAAATTTTT
56786924 GTTTTAATTT
Statistics
Matches: 71, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
20 5 0.07
21 4 0.06
23 4 0.06
24 5 0.07
26 32 0.45
27 4 0.06
28 8 0.11
29 4 0.06
30 5 0.07
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTTAAAATTTTTAATTTTAAAATAC
Found at i:56794868 original size:26 final size:26
Alignment explanation
Indices: 56794814--56794907 Score: 104
Period size: 26 Copynumber: 3.6 Consensus size: 26
56794804 TTATGAAATG
56794814 GCTCACACAAGCCTTC-GTATTTAGG-TT
1 GCTCACACAAG-CTTCAG-A-TTAGGATT
56794841 GCTCACACAAGCTTCAGATTAGGATT
1 GCTCACACAAGCTTCAGATTAGGATT
* * *
56794867 GCTCATACAAGCTT-AGTTTGATGATT
1 GCTCACACAAGCTTCAGATT-AGGATT
56794893 GCTCACACAAGCTTC
1 GCTCACACAAGCTTC
56794908 GGAATATCCA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
25 9 0.15
26 38 0.64
27 12 0.20
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (26 bp):
GCTCACACAAGCTTCAGATTAGGATT
Found at i:56806586 original size:56 final size:56
Alignment explanation
Indices: 56806520--56806628 Score: 191
Period size: 56 Copynumber: 1.9 Consensus size: 56
56806510 TTCACATTCC
56806520 ATTTATATAAACCATCATGTGAAGTTTAAACTAAATTAATATAAAAAAATATATAA
1 ATTTATATAAACCATCATGTGAAGTTTAAACTAAATTAATATAAAAAAATATATAA
* * *
56806576 ATTTATATAAACCATCATGTGAAGTTTAAAGTAAATTAATATATAATAATATA
1 ATTTATATAAACCATCATGTGAAGTTTAAACTAAATTAATATAAAAAAATATA
56806629 ATAATATAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.36
Consensus pattern (56 bp):
ATTTATATAAACCATCATGTGAAGTTTAAACTAAATTAATATAAAAAAATATATAA
Found at i:56806629 original size:8 final size:8
Alignment explanation
Indices: 56806612--56806648 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
56806602 TAAAGTAAAT
56806612 TAAT-ATA
1 TAATAATA
56806619 TAATAATA
1 TAATAATA
56806627 TAATAATA
1 TAATAATA
56806635 TAA-AATA
1 TAATAATA
56806642 TATATAA
1 TA-ATAA
56806649 CAAAGGAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 10 0.37
8 15 0.56
9 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TAATAATA
Found at i:56807616 original size:43 final size:43
Alignment explanation
Indices: 56807561--56807663 Score: 179
Period size: 43 Copynumber: 2.4 Consensus size: 43
56807551 GTTTTTTGCG
*
56807561 AAAAGCGCCGCTAAAGGTTGTGGTCTTTAGCGGCGTTTGCGAC
1 AAAAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGCGAC
56807604 AAAAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGCGAC
1 AAAAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGCGAC
* *
56807647 AGAAGTGCCGCTAAAGG
1 AAAAGCGCCGCTAAAGG
56807664 CCTAAAAAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.22
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGCGAC
Found at i:56809550 original size:17 final size:16
Alignment explanation
Indices: 56809523--56809557 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
56809513 TGAATGAATG
56809523 TTTTAATTTTATTCGT
1 TTTTAATTTTATTCGT
*
56809539 TTTTATATTTTATTTGT
1 TTTTA-ATTTTATTCGT
56809556 TT
1 TT
56809558 GGATGTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTAATTTTATTCGT
Found at i:56814316 original size:5 final size:5
Alignment explanation
Indices: 56814265--56814290 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
56814255 AGTAAATCCG
56814265 TTATA TTATA TTATA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA T
56814291 ATTTCATTTA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:56820727 original size:39 final size:41
Alignment explanation
Indices: 56820682--56820768 Score: 124
Period size: 39 Copynumber: 2.2 Consensus size: 41
56820672 AAAATTTATA
* * *
56820682 TTTAATACAATAAAATATTTATTATATTTAT-TTGTG-TTT
1 TTTAATACAATAAAACATTTATTATATTAATGTAGTGTTTT
*
56820721 TTTAATATAATAAAACATTTATTATATTAATGTAGTGTTTT
1 TTTAATACAATAAAACATTTATTATATTAATGTAGTGTTTT
56820762 TTTAATA
1 TTTAATA
56820769 TGAATACTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 28 0.67
40 4 0.10
41 10 0.24
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (41 bp):
TTTAATACAATAAAACATTTATTATATTAATGTAGTGTTTT
Found at i:56820814 original size:10 final size:10
Alignment explanation
Indices: 56820799--56820841 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
56820789 AGAAAACTTT
56820799 TATTTTAGTG
1 TATTTTAGTG
*
56820809 TATTTTAGCG
1 TATTTTAGTG
56820819 TATTTTTAGTG
1 TA-TTTTAGTG
*
56820830 CA-TTTAGTG
1 TATTTTAGTG
56820839 TAT
1 TAT
56820842 ATTTTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
9 8 0.30
10 11 0.41
11 8 0.30
ACGTcount: A:0.21, C:0.05, G:0.19, T:0.56
Consensus pattern (10 bp):
TATTTTAGTG
Found at i:56820846 original size:21 final size:22
Alignment explanation
Indices: 56820799--56820846 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
56820789 AGAAAACTTT
*
56820799 TATTTTAGTGTATTTTAGCGTA
1 TATTTTAGTGCATTTTAGCGTA
*
56820821 T-TTTTAGTGCA-TTTAGTGTA
1 TATTTTAGTGCATTTTAGCGTA
56820841 TATTTT
1 TATTTT
56820847 TTTTAAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 9 0.39
21 13 0.57
22 1 0.04
ACGTcount: A:0.21, C:0.04, G:0.17, T:0.58
Consensus pattern (22 bp):
TATTTTAGTGCATTTTAGCGTA
Found at i:56821274 original size:20 final size:18
Alignment explanation
Indices: 56821240--56821284 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
56821230 TAATTTTTTT
56821240 ATTAAT-ATAAGAACTAA
1 ATTAATAATAAGAACTAA
56821257 ATTAATAATAGAGAAACTAA
1 ATTAATAATA-AG-AACTAA
*
56821277 TTTAATAA
1 ATTAATAA
56821285 ATTACCTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 6 0.25
18 3 0.12
19 2 0.08
20 13 0.54
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (18 bp):
ATTAATAATAAGAACTAA
Found at i:56825509 original size:21 final size:21
Alignment explanation
Indices: 56825485--56825541 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 21
56825475 ATATAAGAAA
56825485 ATAAAAATATATAA-AATTATC
1 ATAAAAATATATAACAATT-TC
*
56825506 ATAAAAATAAATAACAATTTC
1 ATAAAAATATATAACAATTTC
56825527 ATAAATAATAATATA
1 ATAAA-AAT-ATATA
56825542 TCTTAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 20 0.65
22 7 0.23
23 4 0.13
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAAAAATATATAACAATTTC
Found at i:56836557 original size:11 final size:11
Alignment explanation
Indices: 56836530--56836568 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
56836520 CCCACAACTC
*
56836530 TCTTTATCTTCT
1 TCTTTCTCTT-T
56836542 TCTTTCTCTTT
1 TCTTTCTCTTT
*
56836553 TCTTTCCCTTT
1 TCTTTCTCTTT
56836564 TCTTT
1 TCTTT
56836569 TCATCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (11 bp):
TCTTTCTCTTT
Found at i:56839509 original size:20 final size:21
Alignment explanation
Indices: 56839484--56839525 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
56839474 TAAAAATTCT
*
56839484 TTAAAAA-TAATTTTAATCCC
1 TTAAAAATTAATTTCAATCCC
56839504 TTAAAAATTTAATTTCAATCCC
1 TTAAAAA-TTAATTTCAATCCC
56839526 ACACATGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAAAATTAATTTCAATCCC
Found at i:56841686 original size:98 final size:98
Alignment explanation
Indices: 56841512--56841708 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
56841502 GTACAATAAA
* *
56841512 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACATTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACATTAGGACACAATT
*
56841577 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
*
56841610 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACATTAGGACACAATT
*
56841675 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
56841708 A
1 A
56841709 TTATTTTTTT
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACATTAGGACACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:56842266 original size:2 final size:2
Alignment explanation
Indices: 56842261--56842295 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
56842251 TAAATATACG
* *
56842261 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56842296 GAGAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:56842935 original size:23 final size:22
Alignment explanation
Indices: 56842904--56842952 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
56842894 GATTAAAGGG
56842904 TATC-TCTAAGATTACAAAATCA
1 TATCTTCTAAGATTAC-AAATCA
* *
56842926 TATCTTCTAAGATTGCATATCA
1 TATCTTCTAAGATTACAAATCA
56842948 TATCT
1 TATCT
56842953 AAGATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (22 bp):
TATCTTCTAAGATTACAAATCA
Found at i:56842955 original size:19 final size:19
Alignment explanation
Indices: 56842931--56843043 Score: 172
Period size: 19 Copynumber: 5.8 Consensus size: 19
56842921 AATCATATCT
56842931 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
56842950 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
56842969 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
56842990 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
56843009 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
56843028 TCTAAGATTACATATC
1 TCTAAGATTGCATATC
56843044 CTCAAAAATT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
19 66 0.78
21 19 0.22
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:56842996 original size:40 final size:38
Alignment explanation
Indices: 56842908--56843043 Score: 182
Period size: 40 Copynumber: 3.4 Consensus size: 38
56842898 AAAGGGTATC
*
56842908 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATA
*
56842950 TCTAAGATTATATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGC--ATATCATA
* *
56842990 TCTAAGATTGCATATCATATCTAGGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
56843028 TCTAAGATTACATATC
1 TCTAAGATTACATATC
56843044 CTCAAAAATT
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
38 34 0.40
40 35 0.41
41 7 0.08
42 10 0.12
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:56843004 original size:59 final size:59
Alignment explanation
Indices: 56842908--56843042 Score: 191
Period size: 59 Copynumber: 2.3 Consensus size: 59
56842898 AAAGGGTATC
* *
56842908 TCTAAGATTACA-AAATCATATCTTCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTACATATATCATA---TCTAAGATTGCATATCATATCTAAGATTACATATCATA
* * *
56842969 TCTAAGATTGCATATATCATATCTAAGATTGCATATCATATCTAGGATTGCATATCATA
1 TCTAAGATTACATATATCATATCTAAGATTGCATATCATATCTAAGATTACATATCATA
56843028 TCTAAGATTACATAT
1 TCTAAGATTACATAT
56843043 CCTCAAAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
59 49 0.73
61 11 0.16
62 7 0.10
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.38
Consensus pattern (59 bp):
TCTAAGATTACATATATCATATCTAAGATTGCATATCATATCTAAGATTACATATCATA
Found at i:56849636 original size:23 final size:24
Alignment explanation
Indices: 56849593--56849637 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
56849583 CTGCGTTTAA
*
56849593 TTCACTACTCCCACTTTTCTTCCT
1 TTCACTACTCCCACTTGTCTTCCT
56849617 TTCACT-CTCCC-CTCTGTCTTC
1 TTCACTACTCCCACT-TGTCTTC
56849638 GAAAAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.11
23 11 0.58
24 6 0.32
ACGTcount: A:0.09, C:0.44, G:0.02, T:0.44
Consensus pattern (24 bp):
TTCACTACTCCCACTTGTCTTCCT
Found at i:56855234 original size:3 final size:3
Alignment explanation
Indices: 56855226--56855251 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
56855216 ATATATATAA
56855226 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
56855252 TGGTCAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:56856920 original size:2 final size:2
Alignment explanation
Indices: 56856913--56856962 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
56856903 CCAAGCATAC
56856913 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
56856955 AT AT AT AT
1 AT AT AT AT
56856963 TAGTATTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56857851 original size:42 final size:43
Alignment explanation
Indices: 56857804--56857904 Score: 125
Period size: 43 Copynumber: 2.4 Consensus size: 43
56857794 GCTCCCGGTA
*
56857804 TCGCACACTTAGTGCCC-GTTATTCAATATC-TCCATTTTAATT
1 TCGCACACTTAGTGCCCTGTTATTCAACATCAT-CATTTTAATT
* * *
56857846 TCGCACACTTAGTGCCCTTTTATTCAACCTCATCATTTTAGTT
1 TCGCACACTTAGTGCCCTGTTATTCAACATCATCATTTTAATT
* *
56857889 CCGCGCACTTAGTGCC
1 TCGCACACTTAGTGCC
56857905 GTTTATATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 17 0.33
43 33 0.65
44 1 0.02
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.38
Consensus pattern (43 bp):
TCGCACACTTAGTGCCCTGTTATTCAACATCATCATTTTAATT
Found at i:56860272 original size:12 final size:12
Alignment explanation
Indices: 56860255--56860281 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
56860245 GATTAGTCAA
56860255 TGGCTAATTTTG
1 TGGCTAATTTTG
56860267 TGGCTAATTTTG
1 TGGCTAATTTTG
56860279 TGG
1 TGG
56860282 GGCTGAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.07, G:0.30, T:0.48
Consensus pattern (12 bp):
TGGCTAATTTTG
Found at i:56871663 original size:20 final size:20
Alignment explanation
Indices: 56871634--56871680 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
56871624 TAATAGGTCG
*
56871634 ATTTTGTTAT-TTTTTAATAA
1 ATTTTTTTATATTTTT-ATAA
56871654 ATTTTTTTATATTTTTATAA
1 ATTTTTTTATATTTTTATAA
56871674 ATTTTTT
1 ATTTTTT
56871681 GCTTTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (20 bp):
ATTTTTTTATATTTTTATAA
Found at i:56883614 original size:34 final size:33
Alignment explanation
Indices: 56883575--56883683 Score: 141
Period size: 34 Copynumber: 3.3 Consensus size: 33
56883565 AGAAAATATA
*
56883575 AAAATAAAATATTTGAAATATTTTAATATATTTT
1 AAAATAAAATATTT-AAATATTTTAATATAATTT
**
56883609 AAAATAAAATATTT-AAT-TTCAAAATATAATTT
1 AAAATAAAATATTTAAATATT-TTAATATAATTT
56883641 AAAATAAAATATTCTAAATATTTTAATATAATTT
1 AAAATAAAATATT-TAAATATTTTAATATAATTT
*
56883675 AATATAAAA
1 AAAATAAAA
56883684 ATAATTATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
31 2 0.03
32 25 0.38
33 1 0.02
34 35 0.54
35 2 0.03
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (33 bp):
AAAATAAAATATTTAAATATTTTAATATAATTT
Found at i:56883622 original size:15 final size:15
Alignment explanation
Indices: 56883602--56883658 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
56883592 ATATTTTAAT
56883602 ATATTTTAAAATAAA
1 ATATTTTAAAATAAA
**
56883617 ATA-TTTAATTTCAAA
1 ATATTTTAAAAT-AAA
56883632 ATATAATTTAAAATAAA
1 ATAT--TTTAAAATAAA
*
56883649 ATATTCTAAA
1 ATATTTTAAA
56883659 TATTTTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 6 0.18
15 14 0.42
17 7 0.21
18 6 0.18
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATTTTAAAATAAA
Found at i:56883712 original size:21 final size:22
Alignment explanation
Indices: 56883686--56883755 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 22
56883676 ATATAAAAAT
56883686 AATTATATTA-AAAATTTATTA
1 AATTATATTATAAAATTTATTA
* **
56883707 AATTATA-TATTATTTTTATTA
1 AATTATATTATAAAATTTATTA
56883728 AATTATATTTAATAATAATTATATTA
1 AATTATA-TT-ATAA-AATT-TATTA
56883754 AA
1 AA
56883756 ATACGATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
20 2 0.05
21 22 0.59
23 1 0.03
24 3 0.08
25 2 0.05
26 7 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTATATTATAAAATTTATTA
Found at i:56883750 original size:58 final size:57
Alignment explanation
Indices: 56883683--56883818 Score: 184
Period size: 58 Copynumber: 2.4 Consensus size: 57
56883673 TTAATATAAA
56883683 AATAATTATATTAAAAATTTATTAAATTATATATTATTT-TTATTAAATTATATTTAAT
1 AATAATTATATT-AAAATTTATTAAATTATATATTATTTATTATTAAATTAT-TTTAAT
** * * *
56883741 AATAATTATATTAAAATACGATTAAATTATTTATTATTTATTTTTAATTTATTTTAAT
1 AATAATTATATTAAAAT-TTATTAAATTATATATTATTTATTATTAAATTATTTTAAT
*
56883799 AATAATTTTATTAAAATTTA
1 AATAATTATATTAAAATTTA
56883819 ATAACAATAT
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
57 6 0.09
58 52 0.76
59 10 0.15
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (57 bp):
AATAATTATATTAAAATTTATTAAATTATATATTATTTATTATTAAATTATTTTAAT
Found at i:56894487 original size:16 final size:15
Alignment explanation
Indices: 56894457--56894490 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
56894447 CAAATAACAT
*
56894457 AAATAAAATAATTAC
1 AAATAAAAAAATTAC
56894472 AAATAATAAAAATTAC
1 AAATAA-AAAAATTAC
56894488 AAA
1 AAA
56894491 AAGATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAAAAAAATTAC
Found at i:56894972 original size:21 final size:21
Alignment explanation
Indices: 56894946--56894987 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
56894936 CGGTCAAATG
56894946 ATTGGCTCAAAAAATTAGGGT
1 ATTGGCTCAAAAAATTAGGGT
56894967 ATTGGCTCAAAAAATTAGGGT
1 ATTGGCTCAAAAAATTAGGGT
56894988 GGTGTTGCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (21 bp):
ATTGGCTCAAAAAATTAGGGT
Found at i:56899827 original size:6 final size:6
Alignment explanation
Indices: 56899747--56899824 Score: 138
Period size: 6 Copynumber: 13.0 Consensus size: 6
56899737 CTATTTTAAT
56899747 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* *
56899795 TATACA TATACA TATACA CATACA CATACA
1 TATACA TATACA TATACA TATACA TATACA
56899825 CATTTATAAT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (6 bp):
TATACA
Found at i:56903749 original size:6 final size:6
Alignment explanation
Indices: 56903732--56903779 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
56903722 TCCTGACAAG
*
56903732 GAGAAA GGGAAA GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA GA-AAA
1 GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA
56903779 G
1 G
56903780 GATACAGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 4 0.10
6 36 0.90
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (6 bp):
GAGAAA
Found at i:56907366 original size:21 final size:20
Alignment explanation
Indices: 56907336--56907375 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
56907326 CATTTTGAAT
56907336 GGTTCCGAGGAAAATGGTGG
1 GGTTCCGAGGAAAATGGTGG
*
56907356 GGTTCACGAGGAAATTGGTG
1 GGTTC-CGAGGAAAATGGTG
56907376 ACAGTTACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.25, C:0.10, G:0.42, T:0.23
Consensus pattern (20 bp):
GGTTCCGAGGAAAATGGTGG
Found at i:56909654 original size:31 final size:29
Alignment explanation
Indices: 56909595--56909654 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
56909585 GCCATCTAAT
* * *
56909595 TATTACTAAATTTTTTTTGGTCATCCAAC
1 TATTACTAAATTTCTTTTGGTAACCCAAC
56909624 TATTACTAAATATCTCTTTTGGTAACCCAAC
1 TATTACTAAAT-T-TCTTTTGGTAACCCAAC
56909655 CATGAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 11 0.42
30 1 0.04
31 14 0.54
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (29 bp):
TATTACTAAATTTCTTTTGGTAACCCAAC
Found at i:56910195 original size:3 final size:3
Alignment explanation
Indices: 56910187--56910226 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
56910177 GCCTCCCATT
56910187 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
56910227 CTACAATGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:56922962 original size:12 final size:12
Alignment explanation
Indices: 56922933--56922987 Score: 60
Period size: 12 Copynumber: 4.5 Consensus size: 12
56922923 TTTATTTTAT
*
56922933 TTTATTTATTAT
1 TTTATTTATTAC
56922945 TATTATTCT-TTAC
1 T-TTATT-TATTAC
56922958 TTTATTTATTAC
1 TTTATTTATTAC
56922970 TTTATTTTATTA-
1 TTTA-TTTATTAC
56922982 TTTATT
1 TTTATT
56922988 ACTTATTTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
11 3 0.08
12 18 0.47
13 16 0.42
14 1 0.03
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTATTTATTAC
Found at i:56924009 original size:10 final size:10
Alignment explanation
Indices: 56923994--56924020 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
56923984 CCCTAAAGTA
56923994 AAAAAAAAAG
1 AAAAAAAAAG
56924004 AAAAAAAAAG
1 AAAAAAAAAG
56924014 AAAAAAA
1 AAAAAAA
56924021 TAATAATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:56924009 original size:11 final size:11
Alignment explanation
Indices: 56923988--56924020 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
56923978 GTATATCCCT
56923988 AAAGTAAAAAAA
1 AAAG-AAAAAAA
56924000 AAAG-AAAAAA
1 AAAGAAAAAAA
56924010 AAAGAAAAAAA
1 AAAGAAAAAAA
56924021 TAATAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 6 0.30
12 4 0.20
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:56926878 original size:103 final size:101
Alignment explanation
Indices: 56926689--56926882 Score: 244
Period size: 103 Copynumber: 1.9 Consensus size: 101
56926679 TTGACGGATA
* * * * * *
56926689 AGACCATGGTTGGACCATATAAATGTTTAAATGTAAGACCATAGCTGGGCTATGGTATTTTAATG
1 AGACCATGGTTGGACCATACAAATATATAAATGTAAGACCAGAGCTGGGCTATGGCATTCTAATG
* ***
56926754 AAAAGGCCATAACTGGGTTATGGCACCTTGAACGTC
66 AAAAGACCATAACTCACTTATGGCACCTTGAACGTC
* * *
56926790 AGACCATGGTTGGACCATGACAGTATATATATATGTAAGACCAGAGTTGGGCTATGGCATTCTAA
1 AGACCATGGTTGGACCAT-ACA-AATATATAAATGTAAGACCAGAGCTGGGCTATGGCATTCTAA
*
56926855 TGATAAGACCATAACTCACTTATGGCAC
64 TGAAAAGACCATAACTCACTTATGGCAC
56926883 TACAAATGTA
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
101 18 0.23
102 2 0.03
103 57 0.74
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (101 bp):
AGACCATGGTTGGACCATACAAATATATAAATGTAAGACCAGAGCTGGGCTATGGCATTCTAATG
AAAAGACCATAACTCACTTATGGCACCTTGAACGTC
Found at i:56926911 original size:103 final size:103
Alignment explanation
Indices: 56926719--56926911 Score: 219
Period size: 103 Copynumber: 1.9 Consensus size: 103
56926709 AAATGTTTAA
* * * * *** **
56926719 ATGTAAGACCATAGCTGGGCTATGGTATTTTAATGAAAAGGCCATAACTGGGTTATGGCACCTTG
1 ATGTAAGACCAGAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTCACTTATGGCACCTCA
* **
56926784 AACGTCAGACCATGGTTGGACCATGACAGTATATATAT
66 AACGTAAGACCATGGAAGGACCATGACAGTATATATAT
* *
56926822 ATGTAAGACCAGAGTTGGGCTATGGCATTCTAATGATAAGACCATAACTCACTTATGGCA-CTAC
1 ATGTAAGACCAGAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTCACTTATGGCACCT-C
*
56926886 AAATGTAAGACCATGGCAAGG-CCATG
65 AAACGTAAGACCATGG-AAGGACCATG
56926912 GCAATGCATG
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
102 2 0.03
103 69 0.95
104 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (103 bp):
ATGTAAGACCAGAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTCACTTATGGCACCTCA
AACGTAAGACCATGGAAGGACCATGACAGTATATATAT
Found at i:56930439 original size:24 final size:24
Alignment explanation
Indices: 56930412--56930458 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
56930402 ATTGAAATGG
56930412 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
56930436 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
56930459 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:56932328 original size:28 final size:29
Alignment explanation
Indices: 56932260--56932332 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 29
56932250 GGGACTATAG
* * *
56932260 TGCTCACACAAGCTGATAGTTATCACGGT
1 TGCTCACACAAGCTGACAATTATCACAGT
* *
56932289 TGCTCACACAAGCTGACAATTATGA-ATT
1 TGCTCACACAAGCTGACAATTATCACAGT
56932317 TGCTCACACAAGCTGA
1 TGCTCACACAAGCTGA
56932333 AGTCGTATTG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 17 0.44
29 22 0.56
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (29 bp):
TGCTCACACAAGCTGACAATTATCACAGT
Found at i:56943429 original size:41 final size:41
Alignment explanation
Indices: 56943368--56943468 Score: 157
Period size: 41 Copynumber: 2.4 Consensus size: 41
56943358 TTAATTTAAA
* * *
56943368 CAGATTCAACGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
*
56943410 CAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
56943451 CAGATCACCGGCACGTAG
1 CAGATCACCGGCACGTAG
56943469 NNNNNNNNNN
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
41 51 0.93
42 4 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (41 bp):
CAGATCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
Found at i:56946822 original size:16 final size:16
Alignment explanation
Indices: 56946801--56946845 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
56946791 TCGTCTCATA
56946801 TTCATTTCTCATATTT
1 TTCATTTCTCATATTT
*
56946817 TTCATTTC-AATATTT
1 TTCATTTCTCATATTT
56946832 TCTCA--TCTCATATT
1 T-TCATTTCTCATATT
56946846 CAGTTATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 2 0.08
15 12 0.48
16 11 0.44
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.58
Consensus pattern (16 bp):
TTCATTTCTCATATTT
Found at i:56946841 original size:43 final size:43
Alignment explanation
Indices: 56946787--56946872 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
56946777 TCATATTTCA
* * * *
56946787 TTTCTCGTCTCATATTCATTTCTCATATTTTTCATTTCAATAT
1 TTTCTCATCTCATATTCAGTTATCATATTTGTCATTTCAATAT
*
56946830 TTTCTCATCTCATATTCAGTTATCATCTTTGTCATTTCAATAT
1 TTTCTCATCTCATATTCAGTTATCATATTTGTCATTTCAATAT
56946873 CAATCACATA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.22, C:0.21, G:0.03, T:0.53
Consensus pattern (43 bp):
TTTCTCATCTCATATTCAGTTATCATATTTGTCATTTCAATAT
Found at i:56956228 original size:21 final size:21
Alignment explanation
Indices: 56956204--56956243 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
56956194 TAAAAATATA
56956204 ATAACAAT-AGTAATAATAAAG
1 ATAACAATGA-TAATAATAAAG
*
56956225 ATAAGAATGATAATAATAA
1 ATAACAATGATAATAATAA
56956244 CAGCGAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.25
Consensus pattern (21 bp):
ATAACAATGATAATAATAAAG
Done.