Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold198
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: 3915534
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 240068 characters in sequence are not A, C, G, or T
File 8 of 13
Found at i:2043240 original size:14 final size:15
Alignment explanation
Indices: 2043216--2043250 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2043206 TTTTGGTTTG
2043216 TTATATGGACTGTTA
1 TTATATGGACTGTTA
*
2043231 TTAT-TGGACTTTTA
1 TTATATGGACTGTTA
2043245 TTATAT
1 TTATAT
2043251 ATATATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (15 bp):
TTATATGGACTGTTA
Found at i:2047027 original size:268 final size:268
Alignment explanation
Indices: 2046550--2047075 Score: 946
Period size: 268 Copynumber: 2.0 Consensus size: 268
2046540 GGCCTATTTA
2046550 TAGGCATGGCCGGCCACCCTTGTTAGACACATTACAATACATTAAAATTTTAGATTTTTGTTGAG
1 TAGGCATGGCCGGCCACCCTTGTTAGACACATTACAATACATTAAAATTTTAGATTTTTGTTGAG
2046615 TAAAAATTCTCTTAGAGTTTTCTCCAAGAATTCTCTCTTGAGTTTCTTTAGAAGTAGTTTTAACA
66 TAAAAATTCTCTTAGAGTTTTCTCCAAGAATTCTCTCTTGAGTTTCTTTAGAAGTAGTTTTAACA
*
2046680 ATCTTTTTCATTGTGGGAGCCATCTTCAACCTTCTTCTTGCCGTGTTTTTACATTGGAGGAAAGA
131 ATCTTTTTCATTGTGGGAGCCATCTTCAACCTTCTTCTTGCCGTGTTCTTACATTGGAGGAAAGA
* * *
2046745 TTAGGGCCGTTTGAAGGGAGTTGTGAAATCTTTCTTGATTTCAAGGCTTCTTAGGACTTTATCCA
196 TTAGAGCCGTTTGAAGGGAGTTGTGAAATATTTCTCGATTTCAAGGCTTCTTAGGACTTTATCCA
2046810 TCTTTTTT
261 TCTTTTTT
2046818 TAGGCATGGCCGGCCACCCTTGTTAGACACATTACAATACATTAAAATTTTAGATTTTTGTTGAG
1 TAGGCATGGCCGGCCACCCTTGTTAGACACATTACAATACATTAAAATTTTAGATTTTTGTTGAG
2046883 TAAAAATTCTCTTAGAGTTTTCTCCAAGAATTCTCTCTTGAGTTTCTTTAGAAGTAGTTTTAACA
66 TAAAAATTCTCTTAGAGTTTTCTCCAAGAATTCTCTCTTGAGTTTCTTTAGAAGTAGTTTTAACA
* * * **
2046948 ATCTTTTTCATTGTGGGAGCCATCTTTAGCCTTCTTCTTGCCATTGTTCTT-CATTGGAGGGGAG
131 ATCTTTTTCATTGTGGGAGCCATCTTCAACCTTCTTCTTGCC-GTGTTCTTACATTGGAGGAAAG
*
2047012 GTTAGAGCCGTTTGAAGGGAGTTGTGAAATATTTCTCGATTTCAAGGCTTCTTAGGACTTTATC
195 ATTAGAGCCGTTTGAAGGGAGTTGTGAAATATTTCTCGATTTCAAGGCTTCTTAGGACTTTATC
2047076 TTTATTTTCT
Statistics
Matches: 247, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
268 241 0.98
269 6 0.02
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (268 bp):
TAGGCATGGCCGGCCACCCTTGTTAGACACATTACAATACATTAAAATTTTAGATTTTTGTTGAG
TAAAAATTCTCTTAGAGTTTTCTCCAAGAATTCTCTCTTGAGTTTCTTTAGAAGTAGTTTTAACA
ATCTTTTTCATTGTGGGAGCCATCTTCAACCTTCTTCTTGCCGTGTTCTTACATTGGAGGAAAGA
TTAGAGCCGTTTGAAGGGAGTTGTGAAATATTTCTCGATTTCAAGGCTTCTTAGGACTTTATCCA
TCTTTTTT
Found at i:2052986 original size:17 final size:17
Alignment explanation
Indices: 2052953--2052990 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2052943 CAAGTCCACA
*
2052953 ACCAATTTACTTAGCAT
1 ACCAATTTACATAGCAT
2052970 ACCAATTTACCAT-GCAT
1 ACCAATTTA-CATAGCAT
2052987 ACCA
1 ACCA
2052991 TCCATTAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.37, C:0.29, G:0.05, T:0.29
Consensus pattern (17 bp):
ACCAATTTACATAGCAT
Found at i:2054791 original size:15 final size:15
Alignment explanation
Indices: 2054748--2054795 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2054738 TAGGGTTGTA
*
2054748 GTAAATAAAATATAT
1 GTAAGTAAAATATAT
*
2054763 ATAAGTAAATAATATAT
1 GTAAGT-AA-AATATAT
*
2054780 GTATGTAAAATATAT
1 GTAAGTAAAATATAT
2054795 G
1 G
2054796 CGATGTTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 12 0.44
16 4 0.15
17 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.35
Consensus pattern (15 bp):
GTAAGTAAAATATAT
Found at i:2055547 original size:16 final size:17
Alignment explanation
Indices: 2055514--2055553 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
2055504 TGCTTGGGAA
2055514 ATTATTTTGGACTTTGG
1 ATTATTTTGGACTTTGG
*
2055531 ATTATTTT-GATTTTGG
1 ATTATTTTGGACTTTGG
2055547 ATT-TTTT
1 ATTATTTT
2055554 TACATGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 10 0.45
17 8 0.36
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.62
Consensus pattern (17 bp):
ATTATTTTGGACTTTGG
Found at i:2056251 original size:16 final size:16
Alignment explanation
Indices: 2056230--2056261 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2056220 ATATATTGTG
*
2056230 AAACTCTAGATTCTGA
1 AAACTCTAGATACTGA
2056246 AAACTCTAGATACTGA
1 AAACTCTAGATACTGA
2056262 TACAATAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (16 bp):
AAACTCTAGATACTGA
Found at i:2059874 original size:22 final size:22
Alignment explanation
Indices: 2059846--2059890 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2059836 ATTATGATGA
2059846 TTGATATG-ATGAGATTGATATT
1 TTGATATGTATGAGATT-ATATT
*
2059868 TTGATATGTATGTGATTATATT
1 TTGATATGTATGAGATTATATT
2059890 T
1 T
2059891 GTGTTGATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (22 bp):
TTGATATGTATGAGATTATATT
Found at i:2061045 original size:15 final size:15
Alignment explanation
Indices: 2061025--2061053 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2061015 TATGCATACA
2061025 AAATATAAAAGACAG
1 AAATATAAAAGACAG
2061040 AAATATAAAAGACA
1 AAATATAAAAGACA
2061054 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.07, G:0.10, T:0.14
Consensus pattern (15 bp):
AAATATAAAAGACAG
Found at i:2077188 original size:51 final size:50
Alignment explanation
Indices: 2077060--2077247 Score: 209
Period size: 51 Copynumber: 3.7 Consensus size: 50
2077050 TACCATTCGA
* **
2077060 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAACTTTCCGG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGATCAAACCCTCCGG
* *
2077110 TTCACGTAGTAGCCTACACATAGTACTACACACGTGA-CTAAATCCCTCTGG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGATC-AAA-CCCTCCGG
* * * * * *
2077161 TACACATAGTAGCCTGCACATAGTACTACACATGTGATCATTA-TCTACCGA
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGATCA-AACCCT-CCGG
* *
2077212 TACACGTAGTAGCCTACACTTATTACTACACACGTG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTG
2077248 TCCACAAACA
Statistics
Matches: 115, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.01
50 40 0.35
51 72 0.63
52 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (50 bp):
TACACGTAGTAGCCTACACATAGTACTACACACGTGATCAAACCCTCCGG
Found at i:2078790 original size:24 final size:24
Alignment explanation
Indices: 2078766--2078812 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
2078756 AAACTCCTTC
2078766 TAAAGAAAACTCAAGAAAGAATTCT
1 TAAAGAAAACTCAA-AAAGAATTCT
** *
2078791 TGGAGAAAACTCAAAGAGAATT
1 TAAAGAAAACTCAAAAAGAATT
2078813 TTTCACTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (24 bp):
TAAAGAAAACTCAAAAAGAATTCT
Found at i:2096287 original size:12 final size:12
Alignment explanation
Indices: 2096270--2096340 Score: 56
Period size: 12 Copynumber: 5.9 Consensus size: 12
2096260 TCACTCTCAT
2096270 TTTCTTTTTCAA
1 TTTCTTTTTCAA
2096282 TTTCTTGTTTTC--
1 TTTC-T-TTTTCAA
* * *
2096294 TTTCATGTTCAT
1 TTTCTTTTTCAA
2096306 TTTCTTTTTCAA
1 TTTCTTTTTCAA
***
2096318 TTTCTTTTTGTT
1 TTTCTTTTTCAA
2096330 TTTCTTTTTCA
1 TTTCTTTTTCA
2096341 CATGCTGTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
10 4 0.09
12 35 0.78
13 1 0.02
14 5 0.11
ACGTcount: A:0.10, C:0.15, G:0.04, T:0.70
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:2097384 original size:13 final size:12
Alignment explanation
Indices: 2097352--2097383 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
2097342 AACGCAACCA
2097352 TTTTTTTTGAAC
1 TTTTTTTTGAAC
2097364 TTTTTTTTGAAC
1 TTTTTTTTGAAC
2097376 TTTTTTTT
1 TTTTTTTT
2097384 TCAATTCACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.75
Consensus pattern (12 bp):
TTTTTTTTGAAC
Found at i:2098604 original size:20 final size:20
Alignment explanation
Indices: 2098579--2098623 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
2098569 TAAATTCACA
2098579 TAATTAAAAC-AAGACAC-AAT
1 TAATT-AAACTAAGAC-CTAAT
2098599 TAATTAAACTAAGACCTAAT
1 TAATTAAACTAAGACCTAAT
2098619 TAATT
1 TAATT
2098624 CTGTTAGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.29
Consensus pattern (20 bp):
TAATTAAACTAAGACCTAAT
Found at i:2100317 original size:18 final size:19
Alignment explanation
Indices: 2100294--2100332 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2100284 CTTGGCCCAT
* *
2100294 TACAGTATC-GATATTCAG
1 TACAGTAACTGATATACAG
2100312 TACAGTAACTGATATACAG
1 TACAGTAACTGATATACAG
2100331 TA
1 TA
2100333 TCAAATCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (19 bp):
TACAGTAACTGATATACAG
Found at i:2100385 original size:23 final size:23
Alignment explanation
Indices: 2100355--2100410 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
2100345 CAGCCAGCCT
*
2100355 CTACACTCCAACTCTGTCCAACC
1 CTACACTCCAACTCCGTCCAACC
2100378 CTACACTCCAACTCCGTCCAACC
1 CTACACTCCAACTCCGTCCAACC
2100401 CTACACTCCA
1 CTACACTCCA
2100411 TGTGGGGATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.27, C:0.50, G:0.04, T:0.20
Consensus pattern (23 bp):
CTACACTCCAACTCCGTCCAACC
Found at i:2106129 original size:173 final size:172
Alignment explanation
Indices: 2105840--2106184 Score: 654
Period size: 173 Copynumber: 2.0 Consensus size: 172
2105830 TATAAACTCA
2105840 TCAGTATTAGCAAGATGAATTGTCTTAATTGCATGATCTGAAATTAATTATTTAAACAAATAATC
1 TCAGTATTAGCAAGATGAATTGTCTTAATTGCATGATCTGAAATTAATTATTTAAACAAATAATC
**
2105905 CTGCAAATGACAGGTTGCAAGTTGGTAACACATATGTGATTATTTTGTAGATGTATCTACCAAAA
66 CTGCAAACAACAGGTTGCAAGTTGGTAACACATATGTGATTATTTTGTAGATGTATCTACCAAAA
2105970 TCATATAATATCAAAATCATCCACATTTTGGATGAATGAGCCC
131 TCATATAATATC-AAATCATCCACATTTTGGATGAATGAGCCC
2106013 TCAGTATTAGCAAGATGAATTGTCTTAATTGCATGATCTGAAATTAATTATTTAAACAAATAATC
1 TCAGTATTAGCAAGATGAATTGTCTTAATTGCATGATCTGAAATTAATTATTTAAACAAATAATC
*
2106078 TTGCAAACAACAGGTTGCAAGTTGGTAACACATATGTGATTATTTTGTAGATGTATCTACCAAAA
66 CTGCAAACAACAGGTTGCAAGTTGGTAACACATATGTGATTATTTTGTAGATGTATCTACCAAAA
2106143 TCATATAATATCAAATCATCCACATTTTGGATGAATGAGCCC
131 TCATATAATATCAAATCATCCACATTTTGGATGAATGAGCCC
2106185 ATATTCATTT
Statistics
Matches: 169, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
172 30 0.18
173 139 0.82
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (172 bp):
TCAGTATTAGCAAGATGAATTGTCTTAATTGCATGATCTGAAATTAATTATTTAAACAAATAATC
CTGCAAACAACAGGTTGCAAGTTGGTAACACATATGTGATTATTTTGTAGATGTATCTACCAAAA
TCATATAATATCAAATCATCCACATTTTGGATGAATGAGCCC
Found at i:2107657 original size:15 final size:16
Alignment explanation
Indices: 2107627--2107660 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
2107617 AGCATATTTA
2107627 ATAAAAATAATTTAATC
1 ATAAAAAT-ATTTAATC
2107644 ATAAAAAT-TTTAATC
1 ATAAAAATATTTAATC
2107659 AT
1 AT
2107661 CCAAATATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAAAATATTTAATC
Found at i:2117133 original size:31 final size:31
Alignment explanation
Indices: 2117094--2117174 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
2117084 GTATATGTTT
* *
2117094 TATACATTGTCGAATTTGATTTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
2117125 TATGCATTGCCGAATTTGATTTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
2117156 TATACATTGCCGAATTTGA
1 TATACATTGCCGAATTTGA
2117175 ATTGCCGAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.44
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTTGTATATAGA
Found at i:2117180 original size:14 final size:14
Alignment explanation
Indices: 2117161--2117192 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2117151 ATAGATATAC
2117161 ATTGCCGAATTTGA
1 ATTGCCGAATTTGA
2117175 ATTGCCGAATTTGA
1 ATTGCCGAATTTGA
2117189 ATTG
1 ATTG
2117193 TTTATAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (14 bp):
ATTGCCGAATTTGA
Found at i:2117194 original size:45 final size:45
Alignment explanation
Indices: 2117130--2117223 Score: 179
Period size: 45 Copynumber: 2.1 Consensus size: 45
2117120 ATAGATATGC
*
2117130 ATTGCCGAATTTGATTTGTTTATAGATATACATTGCCGAATTTGA
1 ATTGCCGAATTTGAATTGTTTATAGATATACATTGCCGAATTTGA
2117175 ATTGCCGAATTTGAATTGTTTATAGATATACATTGCCGAATTTGA
1 ATTGCCGAATTTGAATTGTTTATAGATATACATTGCCGAATTTGA
2117220 ATTG
1 ATTG
2117224 TTTATAGATA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (45 bp):
ATTGCCGAATTTGAATTGTTTATAGATATACATTGCCGAATTTGA
Found at i:2117210 original size:31 final size:31
Alignment explanation
Indices: 2117175--2117593 Score: 540
Period size: 31 Copynumber: 13.6 Consensus size: 31
2117165 CCGAATTTGA
* *
2117175 ATTGCCGAATTTGAATTGTTTATAGATATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
* *
2117206 ATTGCCGAATTTGAATTGTTTATAGATATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
* *
2117237 ATTGCCGAATTTGAATTGTTTATAGATATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
2117268 ATTGCCGAA-TTGATTTGTATATAGATATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
* * * *
2117298 ACTGTCGAATTTGATTTGTATATGGTTATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
* * *
2117329 ATTACCGAATTTGATTTGCATATGGATATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
2117360 ATTGCCGAA-TTGATTTGTATATAGATATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
2117390 ATTGCCGAATTTGATTTGTATATAGATATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
* *
2117421 ATTGCCAAATTTGATTTGTATATAGATAAAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
* * *
2117452 ATTGCCGAATTTTATTTGTATATGGTTATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
* * * * *
2117483 ATTGCCAAATTTGTTTTTTATATGGATATTC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
* *
2117514 ATTGCCG-AGTTGATTTTTATATAGATATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
* * *
2117544 ATTGTCGAATTTGATTTGTATATGGATATATAT
1 ATTGCCGAATTTGATTTGTATAT--AGATATAC
2117577 ATTGCCGAA-TTGATTTG
1 ATTGCCGAATTTGATTTG
2117594 AGCATTGGAT
Statistics
Matches: 345, Mismatches: 38, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
30 79 0.23
31 244 0.71
32 8 0.02
33 14 0.04
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (31 bp):
ATTGCCGAATTTGATTTGTATATAGATATAC
Found at i:2117230 original size:76 final size:76
Alignment explanation
Indices: 2117099--2117254 Score: 276
Period size: 76 Copynumber: 2.1 Consensus size: 76
2117089 TGTTTTATAC
* * * *
2117099 ATTGTCGAATTTGATTTGTTTATAGATATGCATTGCCGAATTTGATTTGTTTATAGATATACATT
1 ATTGCCGAATTTGAATTGTTTATAGATATACATTGCCGAATTTGAATTGTTTATAGATATACATT
2117164 GCCGAATTTGA
66 GCCGAATTTGA
2117175 ATTGCCGAATTTGAATTGTTTATAGATATACATTGCCGAATTTGAATTGTTTATAGATATACATT
1 ATTGCCGAATTTGAATTGTTTATAGATATACATTGCCGAATTTGAATTGTTTATAGATATACATT
2117240 GCCGAATTTGA
66 GCCGAATTTGA
2117251 ATTG
1 ATTG
2117255 TTTATAGATA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (76 bp):
ATTGCCGAATTTGAATTGTTTATAGATATACATTGCCGAATTTGAATTGTTTATAGATATACATT
GCCGAATTTGA
Found at i:2117337 original size:92 final size:93
Alignment explanation
Indices: 2117175--2117593 Score: 522
Period size: 92 Copynumber: 4.5 Consensus size: 93
2117165 CCGAATTTGA
* * * *
2117175 ATTGCCGAATTTGAATTGTTTATAGATATACATTGCCGAATTTGAATTGTTTATAGATATACATT
1 ATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATATACATT
*
2117240 GCCGAATTTGAATTGTTTATAGATATAC
66 GCCGAATTTGAATTGTATATAGATATAC
* * * *
2117268 ATTGCCGAA-TTGATTTGTATATAGATATACACTGTCGAATTTGATTTGTATATGGTTATACATT
1 ATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATATACATT
* * * *
2117332 ACCGAATTTGATTTGCATATGGATATAC
66 GCCGAATTTGAATTGTATATAGATATAC
2117360 ATTGCCGAA-TTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATATACATT
1 ATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATATACATT
* * *
2117424 GCCAAATTTGATTTGTATATAGATAAAC
66 GCCGAATTTGAATTGTATATAGATATAC
* * * * * * * *
2117452 ATTGCCGAATTTTATTTGTATATGGTTATACATTGCCAAATTTGTTTTTTATATGGATATTCATT
1 ATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATATACATT
* * *
2117517 GCCG-AGTTGATTTTTATATAGATATAC
66 GCCGAATTTGAATTGTATATAGATATAC
* * *
2117544 ATTGTCGAATTTGATTTGTATATGGATATATATATTGCCGAA-TTGATTTG
1 ATTGCCGAATTTGATTTGTATAT--AGATATACATTGCCGAATTTGATTTG
2117594 AGCATTGGAT
Statistics
Matches: 280, Mismatches: 43, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
92 203 0.73
93 65 0.23
94 12 0.04
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (93 bp):
ATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATATACATT
GCCGAATTTGAATTGTATATAGATATAC
Found at i:2117404 original size:123 final size:123
Alignment explanation
Indices: 2117175--2117593 Score: 554
Period size: 123 Copynumber: 3.4 Consensus size: 123
2117165 CCGAATTTGA
* * * * * *
2117175 ATTGCCGAATTTGAATTGTTTATAGATATACATTGCCGAATTTGAATTGTTTATAGATATACATT
1 ATTGTCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATACATT
* *
2117240 GCCGAATTTGAATTGTTTATAGATATACATTGCCGAATTGATTTGTATATAGATATAC
66 GCCGAATTTGATTTGTATATAGATATACATTGCCGAATTGATTTGTATATAGATATAC
* * * * *
2117298 ACTGTCGAATTTGATTTGTATATGGTTATACATTACCGAATTTGATTTGCATATGGATATACATT
1 ATTGTCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATACATT
2117363 GCCGAA-TTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATATAC
66 GCCGAATTTGATTTGTATATAGATATACATTGCCGAA-TTGATTTGTATATAGATATAC
* * * * *
2117421 ATTGCCAAATTTGATTTGTATATAGATAAACATTGCCGAATTTTATTTGTATATGGTTATACATT
1 ATTGTCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATACATT
* * * * * * *
2117486 GCCAAATTTGTTTTTTATATGGATATTCATTGCCGAGTTGATTTTTATATAGATATAC
66 GCCGAATTTGATTTGTATATAGATATACATTGCCGAATTGATTTGTATATAGATATAC
* *
2117544 ATTGTCGAATTTGATTTGTATATGGATATATATATTGCCGAA-TTGATTTG
1 ATTGTCGAATTTGATTTGTATAT--AGATATACATTGCCGAATTTGATTTG
2117594 AGCATTGGAT
Statistics
Matches: 256, Mismatches: 36, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
122 28 0.11
123 182 0.71
124 32 0.12
125 14 0.05
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (123 bp):
ATTGTCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATACATT
GCCGAATTTGATTTGTATATAGATATACATTGCCGAATTGATTTGTATATAGATATAC
Found at i:2122833 original size:13 final size:12
Alignment explanation
Indices: 2122813--2122859 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
2122803 TAAAACATCT
2122813 TTTCTTTTTCTC
1 TTTCTTTTTCTC
*
2122825 TTTCATTTT-TC
1 TTTCTTTTTCTC
** *
2122836 TTTCACTTTCTT
1 TTTCTTTTTCTC
2122848 TTTCTTTTTCTC
1 TTTCTTTTTCTC
2122860 CGCTCTTGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTCTTTTTCTC
Found at i:2122844 original size:17 final size:16
Alignment explanation
Indices: 2122819--2122854 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2122809 ATCTTTTCTT
*
2122819 TTTCTCTTTCATTTTTC
1 TTTCACTTTC-TTTTTC
2122836 TTTCACTTTCTTTTTC
1 TTTCACTTTCTTTTTC
2122852 TTT
1 TTT
2122855 TTCTCCGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTCACTTTCTTTTTC
Found at i:2126929 original size:27 final size:27
Alignment explanation
Indices: 2126869--2126987 Score: 170
Period size: 27 Copynumber: 4.4 Consensus size: 27
2126859 CTCCAAAATA
2126869 TTATAAAATGACTATTATGCCCTCATATG
1 TTATAAAATGACTATTATGCCC-C-TATG
* *
2126898 --GTAAAAGGACTATTATGCCCCTATG
1 TTATAAAATGACTATTATGCCCCTATG
**
2126923 TTATAAAATGACGGTTATGCCCCTATG
1 TTATAAAATGACTATTATGCCCCTATG
2126950 TTATAAAATGACTATTATGCCCCTATG
1 TTATAAAATGACTATTATGCCCCTATG
2126977 TTATAAAATGA
1 TTATAAAATGA
2126988 ATGTATACTT
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
25 4 0.05
26 1 0.01
27 75 0.94
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (27 bp):
TTATAAAATGACTATTATGCCCCTATG
Found at i:2127308 original size:34 final size:31
Alignment explanation
Indices: 2127270--2127344 Score: 96
Period size: 34 Copynumber: 2.3 Consensus size: 31
2127260 TATTACTGTC
*
2127270 ACTGTAATGGGCTAGGGCCCACACTAATACTGA
1 ACTGTAATGGGCTAAGGCCCA-ACTAA-ACTGA
*
2127303 TACTGTAATGGGCTAAGGCCCAACTGAACTGA
1 -ACTGTAATGGGCTAAGGCCCAACTAAACTGA
2127335 ACTGTTAATG
1 ACTG-TAATG
2127345 AATTGGGCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 4 0.11
32 10 0.26
33 4 0.11
34 20 0.53
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (31 bp):
ACTGTAATGGGCTAAGGCCCAACTAAACTGA
Found at i:2133577 original size:15 final size:15
Alignment explanation
Indices: 2133538--2133567 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2133528 TATACATGTA
*
2133538 AAATATAAAAGACAT
1 AAATACAAAAGACAT
2133553 AAATACAAAAGACAT
1 AAATACAAAAGACAT
2133568 GATAGCAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:2146029 original size:124 final size:124
Alignment explanation
Indices: 2145786--2146217 Score: 625
Period size: 124 Copynumber: 3.5 Consensus size: 124
2145776 AAAATCAAAG
* * * * * * *
2145786 CAGGATGATTTATCAGAAGGATTTTTTAAGTCGCACCCACGTGTACGCGCTTTTGCTACAGTAGG
1 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCACCCACGTGGACGCGCTTTTGCTACAGTAGG
* * * * * *
2145851 TCCT-GAAAAATAATTCTGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC-AA
66 TCCTGGAAAAATAATTTTGACTTGACGTTTCTGAGCAAACAATAT-AAAATCGCTTCTAA
* *
2145909 GCAGGATGCTTTATGAGAAGAATTTTTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAGTAG
1 -CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCACCCACGTGGACGCGCTTTTGCTACAGTAG
2145974 GTCCTGGAAAAATAATTTTGACTTGACGTTTCTGAGCAAACAATATAAAATCGCTTCTAA
65 GTCCTGGAAAAATAATTTTGACTTGACGTTTCTGAGCAAACAATATAAAATCGCTTCTAA
* * * * *
2146034 CAGGATGCTTTGTGAGAGGAATTTGTGAAATCGCGCCCTCGAGGACGCGCTTTTGCTACAGTAGG
1 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCACCCACGTGGACGCGCTTTTGCTACAGTAGG
2146099 TCCTGGAAAAATAATTTTGACTTGACGTTTCTGAGCAAACAATATAAAATCGCTTCTAA
66 TCCTGGAAAAATAATTTTGACTTGACGTTTCTGAGCAAACAATATAAAATCGCTTCTAA
* * *
2146158 CAGGATGCTTTGTGAGAGGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACA
1 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCACCCACGTGGACGCGCTTTTGCTACA
2146218 ATAGCATGTT
Statistics
Matches: 286, Mismatches: 20, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
124 249 0.87
125 37 0.13
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (124 bp):
CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCACCCACGTGGACGCGCTTTTGCTACAGTAGG
TCCTGGAAAAATAATTTTGACTTGACGTTTCTGAGCAAACAATATAAAATCGCTTCTAA
Found at i:2148281 original size:644 final size:644
Alignment explanation
Indices: 2147044--2148298 Score: 2366
Period size: 644 Copynumber: 1.9 Consensus size: 644
2147034 AGAAGTTGGC
2147044 TTATTTTCTGAACCAAGGCCTATTCCAACAGAACCTAAAGATGCTAAAAAGAGTTCAAATGAAGA
1 TTATTTTCTGAACCAAGGCCTATTCCAACAGAACCTAAAGATGCTAAAAAGAGTTCAAATGAAGA
2147109 AGAAAATCCACGATTCAGAGCATACTCACCTCCAGCCCACATGCATAATGTCGATCTGTCTGCAG
66 AGAAAATCCACGATTCAGAGCATACTCACCTCCAGCCCACATGCATAATGTCGATCTGTCTGCAG
2147174 ATGATGCGTTAGACTTCCAGATCTACCACACCGGTTGCGTGATCGTACAAGTTCAGGGCTAGAGT
131 ATGATGCGTTAGACTTCCAGATCTACCACACCGGTTGCGTGATCGTACAAGTTCAGGGCTAGAGT
2147239 TGGGTGAATTTGAAGTTGGTAGTCAGTTTACCAACAATGATAGTTTTATTAGTGCTTTGAAACAA
196 TGGGTGAATTTGAAGTTGGTAGTCAGTTTACCAACAATGATAGTTTTATTAGTGCTTTGAAACAA
2147304 TATAGCATCAAAAACTGCGTTAACTACCACATCGTTAAATCCAAATCTGATAAGTTTGAGGCGAA
261 TATAGCATCAAAAACTGCGTTAACTACCACATCGTTAAATCCAAATCTGATAAGTTTGAGGCGAA
2147369 GTGTGTGGTGCAAGACGGCACATGTTCATGGAAAATCTACGCCTCGTTAAGGAAAAGGACAGGGT
326 GTGTGTGGTGCAAGACGGCACATGTTCATGGAAAATCTACGCCTCGTTAAGGAAAAGGACAGGGT
2147434 TGTGGGAGATTAAAAAGTACAAAGGTCCACATACATGTGCTGCAGGTATAGTATTGACGGTTTCT
391 TGTGGGAGATTAAAAAGTACAAAGGTCCACATACATGTGCTGCAGGTATAGTATTGACGGTTTCT
* *
2147499 GAATAATACTTTTATTATGCAATGTTGCATTATTTAATATACTCCATTTGTAGGTGTTTCACAAG
456 GAATAATACTTTTATTATGCAATGTTACATTATTTAATATACTCCATTTATAGGTGTTTCACAAG
*
2147564 ATCATCCCAAAATGGATTCAGCTATGTTAGCTAGCTTGATACTGCCCACGATAAAAGTAGATCCT
521 ATCATCCCAAAATGGATTCAGCTATGTTAGCTAGCTTGATACTGCCCACGATAAAAGTAGATCCC
*
2147629 AGGACTTCAGTGCCGGCGATAATTGCTAATCTCCCGAGCCACCTGGGGTATACGTCCAG
586 AAGACTTCAGTGCCGGCGATAATTGCTAATCTCCCGAGCCACCTGGGGTATACGTCCAG
2147688 TTATTTTCTGAACCAAGGCCTATTCCAACAGAACCTAAAGATGCTAAAAAGAGTTCAAATGAAGA
1 TTATTTTCTGAACCAAGGCCTATTCCAACAGAACCTAAAGATGCTAAAAAGAGTTCAAATGAAGA
2147753 AGAAAATCCACGATTCAGAGCATACTCACCTCCAGCCCACATGCATAATGTCGATCTGTCTGCAG
66 AGAAAATCCACGATTCAGAGCATACTCACCTCCAGCCCACATGCATAATGTCGATCTGTCTGCAG
2147818 ATGATGCGTTAGACTTCCAGATCTACCACACCGGTTGCGTGATCGTACAAGTTCAGGGCTAGAGT
131 ATGATGCGTTAGACTTCCAGATCTACCACACCGGTTGCGTGATCGTACAAGTTCAGGGCTAGAGT
2147883 TGGGTGAATTTGAAGTTGGTAGTCAGTTTACCAACAATGATAGTTTTATTAGTGCTTTGAAACAA
196 TGGGTGAATTTGAAGTTGGTAGTCAGTTTACCAACAATGATAGTTTTATTAGTGCTTTGAAACAA
2147948 TATAGCATCAAAAACTGCGTTAACTACCACATCGTTAAATCCAAATCTGATAAGTTTGAGGCGAA
261 TATAGCATCAAAAACTGCGTTAACTACCACATCGTTAAATCCAAATCTGATAAGTTTGAGGCGAA
2148013 GTGTGTGGTGCAAGACGGCACATGTTCATGGAAAATCTACGCCTCGTTAAGGAAAAGGACAGGGT
326 GTGTGTGGTGCAAGACGGCACATGTTCATGGAAAATCTACGCCTCGTTAAGGAAAAGGACAGGGT
2148078 TGTGGGAGATTAAAAAGTACAAAGGTCCACATACATGTGCTGCAGGTATAGTATTGACGGTTTCT
391 TGTGGGAGATTAAAAAGTACAAAGGTCCACATACATGTGCTGCAGGTATAGTATTGACGGTTTCT
* * * *** *
2148143 GAGTAATACTTTTATTATGTAATGTTACATTATTTAATGTACTTTGTTTATAGTTGTTTCACAAG
456 GAATAATACTTTTATTATGCAATGTTACATTATTTAATATACTCCATTTATAGGTGTTTCACAAG
* * *
2148208 ATCTTCCCAAGATGGATTCAGCTATGTTAGCTAGCTTGATACTGCCCACGGTAAAAGTAGATCCC
521 ATCATCCCAAAATGGATTCAGCTATGTTAGCTAGCTTGATACTGCCCACGATAAAAGTAGATCCC
* *
2148273 AAGACTTCAGTGCCGGTGTTAATTGC
586 AAGACTTCAGTGCCGGCGATAATTGC
2148299 CAATATCCGT
Statistics
Matches: 595, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
644 595 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (644 bp):
TTATTTTCTGAACCAAGGCCTATTCCAACAGAACCTAAAGATGCTAAAAAGAGTTCAAATGAAGA
AGAAAATCCACGATTCAGAGCATACTCACCTCCAGCCCACATGCATAATGTCGATCTGTCTGCAG
ATGATGCGTTAGACTTCCAGATCTACCACACCGGTTGCGTGATCGTACAAGTTCAGGGCTAGAGT
TGGGTGAATTTGAAGTTGGTAGTCAGTTTACCAACAATGATAGTTTTATTAGTGCTTTGAAACAA
TATAGCATCAAAAACTGCGTTAACTACCACATCGTTAAATCCAAATCTGATAAGTTTGAGGCGAA
GTGTGTGGTGCAAGACGGCACATGTTCATGGAAAATCTACGCCTCGTTAAGGAAAAGGACAGGGT
TGTGGGAGATTAAAAAGTACAAAGGTCCACATACATGTGCTGCAGGTATAGTATTGACGGTTTCT
GAATAATACTTTTATTATGCAATGTTACATTATTTAATATACTCCATTTATAGGTGTTTCACAAG
ATCATCCCAAAATGGATTCAGCTATGTTAGCTAGCTTGATACTGCCCACGATAAAAGTAGATCCC
AAGACTTCAGTGCCGGCGATAATTGCTAATCTCCCGAGCCACCTGGGGTATACGTCCAG
Found at i:2149999 original size:22 final size:22
Alignment explanation
Indices: 2149974--2150112 Score: 110
Period size: 22 Copynumber: 6.2 Consensus size: 22
2149964 AATGTTAATT
2149974 GTTAAGGGGTTAGGGTTTTTAA
1 GTTAAGGGGTTAGGGTTTTTAA
* *
2149996 GTTAAGGGTTAAGGTTATGGTTTTTAG
1 GTTAA-GG----GGTTAGGGTTTTTAA
*
2150023 GTTAAGGTGTTAGGG---TTAA
1 GTTAAGGGGTTAGGGTTTTTAA
*
2150042 GGGTT-A-GGGTTAGGGTTTTTAG
1 --GTTAAGGGGTTAGGGTTTTTAA
* *
2150064 GTTAAGGGTTTAGGGTTTTTAG
1 GTTAAGGGGTTAGGGTTTTTAA
2150086 GTTAAGGGGTTAGGGTTTGTTAA
1 GTTAAGGGGTTAGGGTTT-TTAA
2150109 -TTAA
1 GTTAA
2150113 ATTTTTAATA
Statistics
Matches: 94, Mismatches: 10, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
19 11 0.12
20 4 0.04
21 4 0.04
22 50 0.53
23 5 0.05
26 2 0.02
27 18 0.19
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.42
Consensus pattern (22 bp):
GTTAAGGGGTTAGGGTTTTTAA
Found at i:2150019 original size:27 final size:28
Alignment explanation
Indices: 2149981--2150046 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
2149971 ATTGTTAAGG
2149981 GGTTAGGGTTTTTAAGTTAAGG-GTTAA
1 GGTTAGGGTTTTTAAGTTAAGGTGTTAA
* * *
2150008 GGTTATGGTTTTTAGGTTAAGGTGTTAG
1 GGTTAGGGTTTTTAAGTTAAGGTGTTAA
2150036 GGTTAAGGGTT
1 GGTT-AGGGTT
2150047 AGGGTTAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 20 0.61
28 8 0.24
29 5 0.15
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.42
Consensus pattern (28 bp):
GGTTAGGGTTTTTAAGTTAAGGTGTTAA
Found at i:2150026 original size:41 final size:42
Alignment explanation
Indices: 2149981--2150074 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 42
2149971 ATTGTTAAGG
*
2149981 GGTTAGGGTTTTTA-AGTTAAGGGTTAAGGTTATGGTTTTTA
1 GGTTAGGGTTTTTAGAGTTAAGGGTTAAGGTTAGGGTTTTTA
* * * *
2150022 GGTTAAGG-TGTTAGGGTTAAGGGTTAGGGTTAGGGTTTTTA
1 GGTTAGGGTTTTTAGAGTTAAGGGTTAAGGTTAGGGTTTTTA
2150063 GGTTAAGGGTTT
1 GGTT-AGGGTTT
2150075 AGGGTTTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
40 4 0.09
41 35 0.81
42 3 0.07
43 1 0.02
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (42 bp):
GGTTAGGGTTTTTAGAGTTAAGGGTTAAGGTTAGGGTTTTTA
Found at i:2150052 original size:27 final size:28
Alignment explanation
Indices: 2150018--2150080 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
2150008 GGTTATGGTT
2150018 TTTA-GGTTAAGG-TGTTAGGGTTAAGGG
1 TTTAGGGTTAAGGTTGTTA-GGTTAAGGG
* *
2150045 -TTAGGGTTAGGGTTTTTAGGTTAAGGG
1 TTTAGGGTTAAGGTTGTTAGGTTAAGGG
2150072 TTTAGGGTT
1 TTTAGGGTT
2150081 TTTAGGTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 3 0.10
27 16 0.52
28 12 0.39
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.41
Consensus pattern (28 bp):
TTTAGGGTTAAGGTTGTTAGGTTAAGGG
Found at i:2150077 original size:41 final size:41
Alignment explanation
Indices: 2149996--2150080 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
2149986 GGGTTTTTAA
*
2149996 GTTAAGGGTTAAGGTTATGGTTTTTAGGTTAAGGTGTTAGG
1 GTTAAGGGTTAAGGTTAGGGTTTTTAGGTTAAGGTGTTAGG
*
2150037 GTTAAGGGTTAGGGTTAGGGTTTTTAGGTTAAGG-GTTTAGG
1 GTTAAGGGTTAAGGTTAGGGTTTTTAGGTTAAGGTG-TTAGG
2150078 GTT
1 GTT
2150081 TTTAGGTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 1 0.02
41 40 0.98
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (41 bp):
GTTAAGGGTTAAGGTTAGGGTTTTTAGGTTAAGGTGTTAGG
Found at i:2150345 original size:21 final size:21
Alignment explanation
Indices: 2150306--2150346 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2150296 TTTGTCTAGC
*
2150306 TTCCGGCGGCGGTTGTGGTTA
1 TTCCGGCGGCGGTTCTGGTTA
2150327 TTCCGGCGG-GGATTCTGGTT
1 TTCCGGCGGCGG-TTCTGGTT
2150347 CTTTCGGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.05, C:0.20, G:0.41, T:0.34
Consensus pattern (21 bp):
TTCCGGCGGCGGTTCTGGTTA
Found at i:2151352 original size:20 final size:20
Alignment explanation
Indices: 2151315--2151352 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2151305 TTTATTTTTA
*
2151315 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
2151335 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
2151353 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:2152284 original size:10 final size:10
Alignment explanation
Indices: 2152245--2152282 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
2152235 ATTTTTACGG
2152245 TTTAAAAAAA
1 TTTAAAAAAA
2152255 TTTAAAAAAA
1 TTTAAAAAAA
2152265 -TTAAAAAATA
1 TTTAAAAAA-A
2152275 TTTAAAAA
1 TTTAAAAA
2152283 TAGGGATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 8 0.31
10 11 0.42
11 7 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TTTAAAAAAA
Found at i:2152353 original size:11 final size:12
Alignment explanation
Indices: 2152339--2152384 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
2152329 TTAAATATGG
2152339 ATTTGAGA-GAA
1 ATTTGAGAGGAA
2152350 ATTTG-GAAGGAA
1 ATTTGAG-AGGAA
*
2152362 TTTTGAGAGGAA
1 ATTTGAGAGGAA
2152374 ATTTGAGAGGA
1 ATTTGAGAGGA
2152385 TTAGTTTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 1 0.03
11 6 0.20
12 22 0.73
13 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.28
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:2152361 original size:51 final size:53
Alignment explanation
Indices: 2152280--2152381 Score: 129
Period size: 51 Copynumber: 2.0 Consensus size: 53
2152270 AAATATTTAA
2152280 AAATAGGGATTTAAGAGAAATTTAAGAGGAA-CTTGAGA-GAAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAAGAGGAATCTTGAGAGGAAAATTGAGATT
* * * * *
2152331 AAATATGGATTTGAGAGAAATTT-GGAAGGAATTTTGAGAGGAAATTTGAGA
1 AAATAGGGATTTAAGAGAAATTTAAG-AGGAATCTTGAGAGGAAAATTGAGA
2152382 GGATTAGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
50 1 0.02
51 26 0.60
52 6 0.14
53 10 0.23
ACGTcount: A:0.44, C:0.01, G:0.27, T:0.27
Consensus pattern (53 bp):
AAATAGGGATTTAAGAGAAATTTAAGAGGAATCTTGAGAGGAAAATTGAGATT
Found at i:2157144 original size:2 final size:2
Alignment explanation
Indices: 2157137--2157166 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2157127 TCAAGAAATC
2157137 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2157167 AGGTCTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2159589 original size:291 final size:292
Alignment explanation
Indices: 2159054--2159638 Score: 1154
Period size: 291 Copynumber: 2.0 Consensus size: 292
2159044 TAATGTGAAC
2159054 TCTAGTTTTAAATATTAATTAATTTAAGTTTAAATAAATTAATAAAGTTTCTCAAAAAAAATAAA
1 TCTAGTTTT-AATATTAATTAATTTAAGTTTAAATAAATTAATAAAGTTTCTCAAAAAAAATAAA
2159119 ACAATAAAATTAAATATTTAGATAATATAACTTTAAAGAATTTTAAAAATATTTACATTGTTAAT
65 ACAATAAAATTAAATATTTAGATAATATAACTTTAAAGAATTTTAAAAATATTTACATTGTTAAT
2159184 TTGATGTTTAGACATATATAGATGTGGGTCAAGAATTGGTTAGACTGAAATTAACCATTAAATGT
130 TTGATGTTTAGACATATATAGATGTGGGTCAAGAATTGGTTAGACTGAAATTAACCATTAAATGT
2159249 TGACATTAAGACATTGTCTATTTTCTAAACCAACCTATATCTTTTCAAGTTCATCTTTATTACTT
195 TGACATTAAGACATTGTCTATTTTCTAAACCAACCTATATCTTTTCAAGTTCATCTTTATTACTT
2159314 CAAATTTTCTTGAAATATCGACTTTTTGGATTT
260 CAAATTTTCTTGAAATATCGACTTTTTGGATTT
2159347 TCTAGTTTT-ATATTAATTAATTTAAGTTTAAATAAATTAATAAAGTTTCTCAAAAAAAATAAAA
1 TCTAGTTTTAATATTAATTAATTTAAGTTTAAATAAATTAATAAAGTTTCTCAAAAAAAATAAAA
2159411 CAATAAAATTAAATATTTAGATAATATAACTTTAAAGAATTTTAAAAATATTTACATTGTTAATT
66 CAATAAAATTAAATATTTAGATAATATAACTTTAAAGAATTTTAAAAATATTTACATTGTTAATT
2159476 TGATGTTTAGACATATATAGATGTGGGTCAAGAATTGGTTAGACTGAAATTAACCATTAAATGTT
131 TGATGTTTAGACATATATAGATGTGGGTCAAGAATTGGTTAGACTGAAATTAACCATTAAATGTT
2159541 GACATTAAGACATTGTCTATTTTCTAAACCAACCTATATCTTTTCAAGTTCATCTTTATTACTTC
196 GACATTAAGACATTGTCTATTTTCTAAACCAACCTATATCTTTTCAAGTTCATCTTTATTACTTC
2159606 AAATTTTCTTGAAATATCGACTTTTTGGATTT
261 AAATTTTCTTGAAATATCGACTTTTTGGATTT
2159638 T
1 T
2159639 TCTAACAACA
Statistics
Matches: 292, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
291 283 0.97
293 9 0.03
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.41
Consensus pattern (292 bp):
TCTAGTTTTAATATTAATTAATTTAAGTTTAAATAAATTAATAAAGTTTCTCAAAAAAAATAAAA
CAATAAAATTAAATATTTAGATAATATAACTTTAAAGAATTTTAAAAATATTTACATTGTTAATT
TGATGTTTAGACATATATAGATGTGGGTCAAGAATTGGTTAGACTGAAATTAACCATTAAATGTT
GACATTAAGACATTGTCTATTTTCTAAACCAACCTATATCTTTTCAAGTTCATCTTTATTACTTC
AAATTTTCTTGAAATATCGACTTTTTGGATTT
Found at i:2174668 original size:39 final size:38
Alignment explanation
Indices: 2174601--2174679 Score: 104
Period size: 39 Copynumber: 2.1 Consensus size: 38
2174591 ATGAACTTAT
* * * *
2174601 GCAATGTTTTTTCTTCGTGCAATTTGAGAAAGAAGAAG
1 GCAATGTTTTTTCTTCATACAATGTGAGAAAGAAAAAG
*
2174639 GCAATGTTTTTTTCTTCATATAATGTGAGAAAGAAAAAG
1 GCAATG-TTTTTTCTTCATACAATGTGAGAAAGAAAAAG
2174678 GC
1 GC
2174680 TACTATCTGC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
38 6 0.17
39 29 0.83
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (38 bp):
GCAATGTTTTTTCTTCATACAATGTGAGAAAGAAAAAG
Found at i:2178721 original size:23 final size:23
Alignment explanation
Indices: 2178695--2178783 Score: 99
Period size: 23 Copynumber: 3.8 Consensus size: 23
2178685 TACCATCTGG
2178695 ACACAACCAAATATACCCTCCAA
1 ACACAACCAAATATACCCTCCAA
* * *
2178718 ACACAACCATATATATAACCTTCGA
1 ACACAACCA-A-ATATACCCTCCAA
* *
2178743 ACAAAACCAAGTATACCCTCCAA
1 ACACAACCAAATATACCCTCCAA
*
2178766 ACACAACC-ACTATACCCT
1 ACACAACCAAATATACCCT
2178784 TCAACCAAGT
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
22 9 0.17
23 25 0.46
24 2 0.04
25 18 0.33
ACGTcount: A:0.45, C:0.36, G:0.02, T:0.17
Consensus pattern (23 bp):
ACACAACCAAATATACCCTCCAA
Found at i:2179020 original size:6 final size:6
Alignment explanation
Indices: 2179006--2179175 Score: 288
Period size: 6 Copynumber: 28.2 Consensus size: 6
2178996 ATAATAAAAT
*
2179006 AAAATA AAAACA AAAACA AAAACA AAAACAA AAAACA AAAACA AAAACA
1 AAAACA AAAACA AAAACA AAAACA AAAAC-A AAAACA AAAACA AAAACA
2179055 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
*
2179103 AAAAAA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
*
2179151 AAAGCA AAATA-A AAAACA AAAACA A
1 AAAACA AAA-ACA AAAACA AAAACA A
2179176 TAATAAATGA
Statistics
Matches: 156, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
5 1 0.01
6 149 0.96
7 6 0.04
ACGTcount: A:0.84, C:0.15, G:0.01, T:0.01
Consensus pattern (6 bp):
AAAACA
Found at i:2179021 original size:1 final size:1
Alignment explanation
Indices: 2179001--2179172 Score: 92
Period size: 1 Copynumber: 172.0 Consensus size: 1
2178991 AGTGCATAAT
* * * * * * * * * * *
2179001 AAAATAAAATAAAAACAAAAACAAAAACAAAAACAAAAAACAAAAACAAAAACAAAAACAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * *
2179066 AAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAAAAAAAACAAAAACAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * ** * *
2179131 CAAAAACAAAAACAAAAACAAAAGCAAAATAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2179173 CAATAATAAA
Statistics
Matches: 116, Mismatches: 55, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 116 1.00
ACGTcount: A:0.84, C:0.14, G:0.01, T:0.02
Consensus pattern (1 bp):
A
Found at i:2190701 original size:51 final size:50
Alignment explanation
Indices: 2190525--2190846 Score: 314
Period size: 51 Copynumber: 6.4 Consensus size: 50
2190515 TCATTCGATA
* * *
2190525 CACGTAGTAGCCTTTACATAGTACTACACACGTGATCAAG-TTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAGCTTTT-CGGTT
* * *
2190575 CACGCAGTAGCCTTCACATAGTACTACTCATGTGATCAAG-TTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAGCTTTT-CGGTT
*
2190625 CACGTAATAGCCTTCACATAGTACTACACATGTGACCAAAGCTTTTCGGTAT
1 CACGTAGTAGCCTTCACATAGTACTACACATGTGACC-AAGCTTTTCGGT-T
* * * * *
2190677 -ACATAGTAGCCTTCACTTAGTACTACACATGTAACC-ATCATTTATCGATT
1 CACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAGC-TTT-TCGGTT
* * ** *
2190727 CACGTAGTAGCCTTCACACAATACTACACACATGACCAAAGCTTCTC-GTT
1 CACGTAGTAGCCTTCACATAGTACTACACATGTGACC-AAGCTTTTCGGTT
* * * * *
2190777 ACACATTGTAGCCTTCACTTAGTACTACACATGTGACC-ATCATTTATCGATT
1 -CACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAGC-TTT-TCGGTT
2190829 CACGTAGTAGCCTTCACA
1 CACGTAGTAGCCTTCACA
2190847 CANNNNNNNN
Statistics
Matches: 223, Mismatches: 37, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
49 4 0.02
50 87 0.39
51 121 0.54
52 9 0.04
53 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAGCTTTTCGGTT
Found at i:2190755 original size:102 final size:102
Alignment explanation
Indices: 2190519--2190848 Score: 407
Period size: 102 Copynumber: 3.3 Consensus size: 102
2190509 ACTTTATCAT
* * * * **
2190519 TCGATACACGTAGTAGCCTTTACATAGTACTACACACGTGATC-AAG-TTTTACGGT-TCACGCA
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CGGTAT-ACATA
* * * ***
2190581 GTAGCCTTCACATAGTACTACTCATGTGATCAAGTTTTA
64 GTAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * * *
2190620 -CGGTTCACGTAATAGCCTTCACATAGTACTACACATGTGACCAAAGCTTTTCGGTATACATAGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTATACATAGT
*
2190684 AGCCTTCACTTAGTACTACACATGTAACCATCATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * * * * *
2190721 TCGATTCACGTAGTAGCCTTCACACAATACTACACACATGACCAAAGCTTCTCGTTACACATTGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTATACATAGT
2190786 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
2190823 TCGATTCACGTAGTAGCCTTCACACA
1 TCGATTCACGTAGTAGCCTTCACACA
2190849 NNNNNNNNNN
Statistics
Matches: 199, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
100 36 0.18
101 42 0.21
102 121 0.61
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (102 bp):
TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTATACATAGT
AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
Found at i:2196921 original size:21 final size:18
Alignment explanation
Indices: 2196894--2196945 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 18
2196884 TACTGTTGAG
2196894 AAGGAAGTTGCTGCTGCATA
1 AAGGAAGTTGCTGCTG-A-A
*
2196914 AGAGGAAGTTGTTGCTGAA
1 A-AGGAAGTTGCTGCTGAA
*
2196933 AAAGAAGTTGCTG
1 AAGGAAGTTGCTG
2196946 AAGATGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 10 0.36
19 2 0.07
20 2 0.07
21 14 0.50
ACGTcount: A:0.33, C:0.10, G:0.33, T:0.25
Consensus pattern (18 bp):
AAGGAAGTTGCTGCTGAA
Found at i:2200720 original size:42 final size:42
Alignment explanation
Indices: 2200663--2201082 Score: 716
Period size: 42 Copynumber: 9.9 Consensus size: 42
2200653 ATTTACAAAC
2200663 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
2200705 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
2200747 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
2200789 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
2200831 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
2200873 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG-AA
* ** *
2200916 AAAACGCCACGCCGCTAAAGAACATGTTCTTTAGTAGCGCTTTGAA
1 AAAA----ACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* *
2200962 AAAAACGCCTCTAAAGACCATGTTCTTTAGTGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
2201004 AAAAACGCCGCTAAAGACAATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
2201046 AAAAACGCCGCTAAAGA-TATGTTCTTTAGCGGCGCTT
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT
2201083 TTATACAAAA
Statistics
Matches: 361, Mismatches: 12, Indels: 11
0.94 0.03 0.03
Matches are distributed among these distances:
41 19 0.05
42 298 0.83
43 6 0.02
46 6 0.02
47 32 0.09
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:2201446 original size:21 final size:21
Alignment explanation
Indices: 2201400--2201446 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2201390 TTTTAGCCTG
*
2201400 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
2201421 TTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
2201442 CTCTG
1 CTCTG
2201447 TTTTAAGTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.45, G:0.19, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:2207740 original size:9 final size:9
Alignment explanation
Indices: 2207728--2208078 Score: 187
Period size: 9 Copynumber: 39.8 Consensus size: 9
2207718 ATTAAGTCAA
2207728 TTATGTAAG
1 TTATGTAAG
*
2207737 TTATGTACG
1 TTATGTAAG
2207746 TGTA--TAAG
1 T-TATGTAAG
2207754 TTATGTAAG
1 TTATGTAAG
2207763 TTATGT-A-
1 TTATGTAAG
*
2207770 TTAAGTAAG
1 TTATGTAAG
2207779 TTATGTAAG
1 TTATGTAAG
**
2207788 TTATCAAAG
1 TTATGTAAG
* *
2207797 TAATGTATG
1 TTATGTAAG
2207806 TTATGTAAG
1 TTATGTAAG
2207815 TT-T-TAAG
1 TTATGTAAG
*
2207822 TTAT-TATG
1 TTATGTAAG
2207830 TATTATGTAAG
1 --TTATGTAAG
2207841 TTATGTAAG
1 TTATGTAAG
*
2207850 CTATGTAAG
1 TTATGTAAG
2207859 TTGAATGT-A-
1 TT--ATGTAAG
2207868 TTATGTAAG
1 TTATGTAAG
*
2207877 TTAT-TATG
1 TTATGTAAG
2207885 TATTATGTAAG
1 --TTATGTAAG
2207896 -T-TGTAAG
1 TTATGTAAG
2207903 TTAAATGT-A-
1 TT--ATGTAAG
2207912 TTATGTAAG
1 TTATGTAAG
2207921 -T-TGTAAG
1 TTATGTAAG
*
2207928 TTAT-TATG
1 TTATGTAAG
2207936 TATTATGTAAG
1 --TTATGTAAG
*
2207947 TTATTTAAG
1 TTATGTAAG
**
2207956 TTACCTAAG
1 TTATGTAAG
2207965 TTAAATGT-A-
1 TT--ATGTAAG
2207974 TTATGTAAG
1 TTATGTAAG
*
2207983 TTATTTAAG
1 TTATGTAAG
**
2207992 TTACCTAAG
1 TTATGTAAG
2208001 TTAAATGT-A-
1 TT--ATGTAAG
2208010 TTATGTAAG
1 TTATGTAAG
*
2208019 TTGTATG-AAT
1 -T-TATGTAAG
2208029 TTATGT-A-
1 TTATGTAAG
2208036 TTATGTAAG
1 TTATGTAAG
2208045 TTATGTAAG
1 TTATGTAAG
2208054 TTAAATGT-A-
1 TT--ATGTAAG
*
2208063 TTATGTAGG
1 TTATGTAAG
2208072 TTATGTA
1 TTATGTA
2208079 NNNNNNNNNN
Statistics
Matches: 266, Mismatches: 32, Indels: 88
0.69 0.08 0.23
Matches are distributed among these distances:
7 51 0.19
8 31 0.12
9 134 0.50
10 22 0.08
11 28 0.11
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:2207778 original size:42 final size:42
Alignment explanation
Indices: 2207727--2207812 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
2207717 TATTAAGTCA
* * *
2207727 ATTATGTAAGTTATGTACGTGTAT-AAGTTATGTAAGTTATGT
1 ATTAAGTAAGTTATGTAAGT-TATAAAGTAATGTAAGTTATGT
*
2207769 ATTAAGTAAGTTATGTAAGTTATCAAAGTAATGTATGTTATGT
1 ATTAAGTAAGTTATGTAAGTTAT-AAAGTAATGTAAGTTATGT
2207812 A
1 A
2207813 AGTTTTAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 3 0.08
42 18 0.47
43 17 0.45
ACGTcount: A:0.35, C:0.02, G:0.20, T:0.43
Consensus pattern (42 bp):
ATTAAGTAAGTTATGTAAGTTATAAAGTAATGTAAGTTATGT
Found at i:2207834 original size:62 final size:62
Alignment explanation
Indices: 2207750--2207893 Score: 172
Period size: 62 Copynumber: 2.3 Consensus size: 62
2207740 TGTACGTGTA
*
2207750 TAAGTTATGTAAG--TTATGTATTAAGTAAGTTATGTAAGTTATCAAAG-T-AATGTATGTTATG
1 TAAGTTAT-TAAGTATTATGTATTAAGTAAGTTATGTAAGCTATCAAAGTTGAATGTA--TTATG
* **
2207811 TAAGTT-TTAAGTTATTATGTATTATGTAAGTTATGTAAGCTATGTAAGTTGAATGTATTATG
1 TAAGTTATTAAG-TATTATGTATTAAGTAAGTTATGTAAGCTATCAAAGTTGAATGTATTATG
*
2207873 TAAGTTATTATGTATTATGTA
1 TAAGTTATTAAGTATTATGTA
2207894 AGTTGTAAGT
Statistics
Matches: 72, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
59 4 0.06
60 1 0.01
61 6 0.08
62 50 0.69
63 5 0.07
64 6 0.08
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (62 bp):
TAAGTTATTAAGTATTATGTATTAAGTAAGTTATGTAAGCTATCAAAGTTGAATGTATTATG
Found at i:2207855 original size:44 final size:42
Alignment explanation
Indices: 2207807--2207922 Score: 111
Period size: 37 Copynumber: 2.9 Consensus size: 42
2207797 TAATGTATGT
2207807 TATGTAAGTTTTAAGTTATTATGTATTATGTAAGTTATGTAAGC
1 TATGTAAGTTTTAAGTTATTATGTATTATGTAAGTTATGT-A-C
* * *
2207851 TATGTAAG-TTGAA-TGTATTATGTA--A-GTTA-TTATGTAT
1 TATGTAAGTTTTAAGT-TATTATGTATTATGTAAGTTATGTAC
* *
2207888 TATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTT
1 TATGTAAGTTTTAAGTTATTATGTATTATGTAAGTT
2207923 GTAAGTTATT
Statistics
Matches: 58, Mismatches: 7, Indels: 17
0.71 0.09 0.21
Matches are distributed among these distances:
37 13 0.22
38 6 0.10
39 8 0.14
40 6 0.10
41 3 0.05
42 1 0.02
43 13 0.22
44 8 0.14
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (42 bp):
TATGTAAGTTTTAAGTTATTATGTATTATGTAAGTTATGTAC
Found at i:2207873 original size:36 final size:36
Alignment explanation
Indices: 2207727--2208020 Score: 217
Period size: 36 Copynumber: 8.3 Consensus size: 36
2207717 TATTAAGTCA
*
2207727 ATTATGTAAGTTATGTACGTGTA--TAAGTT--ATGT
1 ATTATGTAAGTTATGTAAGT-TATGTAAGTTAAATGT
* *
2207760 AAGTTATGT-A-TTAAGTAAGTTATGTAAGTTATCAAAGT
1 -A-TTATGTAAGTTATGTAAGTTATGTAAGTTA--AATGT
* *
2207798 A--ATGTATGTTATGTAAGTT-T-TAAGTTATTATGT
1 ATTATGTAAGTTATGTAAGTTATGTAAGTTA-AATGT
* *
2207831 ATTATGTAAGTTATGTAAGCTATGTAAGTTGAATGT
1 ATTATGTAAGTTATGTAAGTTATGTAAGTTAAATGT
* *
2207867 ATTATGTAAGTTAT-TATGTATTATGTAAGTTGTAA-GT
1 ATTATGTAAGTTATGTAAG--TTATGTAAGTT-AAATGT
* *
2207904 -TAAATGT-A-TTATGTAAG-T-TGTAAGTTATTATGT
1 AT-TATGTAAGTTATGTAAGTTATGTAAGTTA-AATGT
* **
2207937 ATTATGTAAGTTATTTAAGTTACCTAAGTTAAATGT
1 ATTATGTAAGTTATGTAAGTTATGTAAGTTAAATGT
* **
2207973 ATTATGTAAGTTATTTAAGTTACCTAAGTTAAATGT
1 ATTATGTAAGTTATGTAAGTTATGTAAGTTAAATGT
2208009 ATTATGTAAGTT
1 ATTATGTAAGTT
2208021 GTATGAATTT
Statistics
Matches: 211, Mismatches: 24, Indels: 48
0.75 0.08 0.17
Matches are distributed among these distances:
32 11 0.05
33 19 0.09
34 21 0.10
35 38 0.18
36 87 0.41
37 30 0.14
38 5 0.02
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (36 bp):
ATTATGTAAGTTATGTAAGTTATGTAAGTTAAATGT
Found at i:2207879 original size:55 final size:54
Alignment explanation
Indices: 2207712--2207987 Score: 216
Period size: 55 Copynumber: 5.0 Consensus size: 54
2207702 TGATATATAT
* * *
2207712 TTATGTATTAAGTCAA-TTATGTAAGTTATGTACGTGT-AT-AAGTTATGTAAGTTA
1 TTATGTATTATGT-AAGTTATGTAAGTTATGTAAGT-TAATGTA-TTATGTAAGTTA
** * *
2207766 TGTATTAAGTAAGTTATGTAAGTTATCAAAGTAATGTATGTT-ATGTAAGTT-T-TAAGTTA
1 T-TA-T--GT-A-TTATGTAAGTTATGTAAGTTATGTAAGTTAATGT-A-TTATGTAAGTTA
*
2207825 TTATGTATTATGTAAGTTATGTAAGCTATGTAAGTTGAATGTATTATGTAAGTTA
1 TTATGTATTATGTAAGTTATGTAAGTTATGTAAGTT-AATGTATTATGTAAGTTA
*
2207880 TTATGTATTATGTAAG-T-TGTAAGTTAAATGT-A-TT-ATGTAAGT-TGTAAGTTA
1 TTATGTATTATGTAAGTTATGTAAGTT--ATGTAAGTTAATGT-ATTATGTAAGTTA
* **
2207931 TTATGTATTATGTAAGTTATTTAAGTTACCTAAGTTAAATGTATTATGTAAGTTA
1 TTATGTATTATGTAAGTTATGTAAGTTATGTAAGTT-AATGTATTATGTAAGTTA
2207986 TT
1 TT
2207988 TAAGTTACCT
Statistics
Matches: 182, Mismatches: 17, Indels: 45
0.75 0.07 0.18
Matches are distributed among these distances:
51 31 0.17
52 4 0.02
53 44 0.24
54 8 0.04
55 50 0.27
56 1 0.01
57 1 0.01
58 4 0.02
59 14 0.08
60 21 0.12
61 4 0.02
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (54 bp):
TTATGTATTATGTAAGTTATGTAAGTTATGTAAGTTAATGTATTATGTAAGTTA
Found at i:2207933 original size:44 final size:46
Alignment explanation
Indices: 2207841--2208075 Score: 153
Period size: 44 Copynumber: 4.9 Consensus size: 46
2207831 ATTATGTAAG
* *
2207841 TTATGTAAGCTATGTAAGTTGAATGTATTATGTAAGTTATTATGTA
1 TTATGTAAGCTATGTAAGTTAAATGTATTATGTAAGTTATAATGTA
*
2207887 TTATGTAAG-T-TGTAAGTTAAATGTATTATGTAAGTTGTAA-GTTA
1 TTATGTAAGCTATGTAAGTTAAATGTATTATGTAAGTTATAATG-TA
* * **
2207931 TTATGT-A-TTATGTAAGTT--ATTTAAGTTACCTAAGTTA-AATGTA
1 TTATGTAAGCTATGTAAGTTAAATGT-A-TTATGTAAGTTATAATGTA
*
2207974 TTATGTAAGTTATTTAAGTTACCTAAGTTAAATGTATTATGTAAGTTGTATGAATTTATGTA
1 TTATGTAAGCTA--T--G-----TAAGTTAAATGTATTATGTAAG-T-TAT--A---ATGTA
* *
2208036 TTATGTAAGTTATGTAAGTTAAATGTATTATGTAGGTTAT
1 TTATGTAAGCTATGTAAGTTAAATGTATTATGTAAGTTAT
2208076 GTANNNNNNN
Statistics
Matches: 151, Mismatches: 11, Indels: 49
0.72 0.05 0.23
Matches are distributed among these distances:
42 3 0.02
43 14 0.09
44 54 0.36
45 4 0.03
46 9 0.06
47 1 0.01
49 1 0.01
51 3 0.02
52 1 0.01
53 21 0.14
54 13 0.09
55 2 0.01
56 5 0.03
58 1 0.01
59 1 0.01
60 1 0.01
62 17 0.11
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (46 bp):
TTATGTAAGCTATGTAAGTTAAATGTATTATGTAAGTTATAATGTA
Found at i:2208076 original size:62 final size:61
Alignment explanation
Indices: 2207878--2208078 Score: 182
Period size: 62 Copynumber: 3.3 Consensus size: 61
2207868 TTATGTAAGT
* **
2207878 TATTATGTATTATGTAAGTTGTA-AGTTAAATGTATTATGTAAG-T-TGTAAGTTATTATG
1 TATTATGTATTATGTAAGTTGTATAATTAAATGTATTATGTAAGTTATGTAAGTTACAATG
* *** *
2207936 TATTATGTAAGTTATTTAAGTTACCTAAGTTAAATGTATTATGTAAGTTATTTAAGTTACCTAA-
1 TATTATGT-A-TTATGTAAGTTGTATAA-TTAAATGTATTATGTAAGTTATGTAAGTTA-C-AAT
2208000 G
61 G
* *
2208001 T-TAAATGTATTATGTAAGTTGTATGAATT-TATGTATTATGTAAGTTATGTAAGTTA-AATG
1 TAT-TATGTATTATGTAAGTTGTAT-AATTAAATGTATTATGTAAGTTATGTAAGTTACAATG
2208061 TATTATGTAGGTTATGTA
1 TATTATGTA--TTATGTA
2208079 NNNNNNNNNN
Statistics
Matches: 113, Mismatches: 16, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
58 8 0.07
59 3 0.03
60 17 0.15
61 2 0.02
62 50 0.44
63 14 0.12
64 12 0.11
65 6 0.05
66 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (61 bp):
TATTATGTATTATGTAAGTTGTATAATTAAATGTATTATGTAAGTTATGTAAGTTACAATG
Found at i:2209141 original size:31 final size:32
Alignment explanation
Indices: 2209074--2209158 Score: 120
Period size: 31 Copynumber: 2.7 Consensus size: 32
2209064 GAGCTATTTC
* *
2209074 CCAT-TTAGCAGCAGAAATCAATAGAAGCAGTA
1 CCATCTTAGCAGCAAAAACCAATAGAAG-AGTA
2209106 CCATCTTAGCAGCAAAAACCAATAGAAG-GTA
1 CCATCTTAGCAGCAAAAACCAATAGAAGAGTA
*
2209137 CCATCTTAGCTGCAAAAACCAA
1 CCATCTTAGCAGCAAAAACCAA
2209159 CTAAAATCCA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
31 24 0.49
32 4 0.08
33 21 0.43
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.18
Consensus pattern (32 bp):
CCATCTTAGCAGCAAAAACCAATAGAAGAGTA
Found at i:2209882 original size:20 final size:20
Alignment explanation
Indices: 2209857--2209956 Score: 182
Period size: 20 Copynumber: 5.0 Consensus size: 20
2209847 AAGAGATGAA
2209857 GAAAGGATGAGGGGAAATCG
1 GAAAGGATGAGGGGAAATCG
*
2209877 GAAAGGATGAGGGGAAATCA
1 GAAAGGATGAGGGGAAATCG
2209897 GAAAGGATGAGGGGAAATCG
1 GAAAGGATGAGGGGAAATCG
*
2209917 GAAAGGATGAGGGGAAATCA
1 GAAAGGATGAGGGGAAATCG
2209937 GAAAGGATGAGGGGAAATCG
1 GAAAGGATGAGGGGAAATCG
2209957 CAGAAAGACT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.42, C:0.05, G:0.43, T:0.10
Consensus pattern (20 bp):
GAAAGGATGAGGGGAAATCG
Found at i:2209901 original size:40 final size:40
Alignment explanation
Indices: 2209856--2209956 Score: 202
Period size: 40 Copynumber: 2.5 Consensus size: 40
2209846 TAAGAGATGA
2209856 AGAAAGGATGAGGGGAAATCGGAAAGGATGAGGGGAAATC
1 AGAAAGGATGAGGGGAAATCGGAAAGGATGAGGGGAAATC
2209896 AGAAAGGATGAGGGGAAATCGGAAAGGATGAGGGGAAATC
1 AGAAAGGATGAGGGGAAATCGGAAAGGATGAGGGGAAATC
2209936 AGAAAGGATGAGGGGAAATCG
1 AGAAAGGATGAGGGGAAATCG
2209957 CAGAAAGACT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.43, C:0.05, G:0.43, T:0.10
Consensus pattern (40 bp):
AGAAAGGATGAGGGGAAATCGGAAAGGATGAGGGGAAATC
Found at i:2212441 original size:113 final size:114
Alignment explanation
Indices: 2212252--2212463 Score: 266
Period size: 113 Copynumber: 1.9 Consensus size: 114
2212242 CGTTTCTCTC
* * * *
2212252 AAAACGCCGCTATATCCCAATATTTTGCGGCGTTTTTTAATAAGCGCCACTAACTCTAATCCAAC
1 AAAACGCCGCTATATACCAATATTTAGCGGCGTTTTTTAATAAACGCCACTAACTCTAATACAAC
* *
2212317 TCAATACCAAACGGTGCGTTTTGGTTAAGATATTGGCGGCGCTTTTTGT
66 TCAAAACCAAACGCTGCGTTTTGGTTAAGATATTGGCGGCGCTTTTTGT
* * * ** * *
2212366 AAAACGCCGCTA-ATACCATTCTTTAGCGGTGTTTTTTCGTAAACGCCACTAA-TACTAATATAC
1 AAAACGCCGCTATATACCAATATTTAGCGGCGTTTTTTAATAAACGCCACTAACT-CTAATACAA
* *
2212429 CTCAAAATCAAACGCTGCGTTTTGGTTAAGGTATT
65 CTCAAAACCAAACGCTGCGTTTTGGTTAAGATATT
2212464 TTGCAGCGCT
Statistics
Matches: 82, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
112 1 0.01
113 69 0.84
114 12 0.15
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (114 bp):
AAAACGCCGCTATATACCAATATTTAGCGGCGTTTTTTAATAAACGCCACTAACTCTAATACAAC
TCAAAACCAAACGCTGCGTTTTGGTTAAGATATTGGCGGCGCTTTTTGT
Found at i:2215533 original size:16 final size:15
Alignment explanation
Indices: 2215512--2215541 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2215502 GGCAATCATC
2215512 ACATTAAAATGTTAAG
1 ACATTAAAAT-TTAAG
2215528 ACATTAAAATTTAA
1 ACATTAAAATTTAA
2215542 TTGCTTTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (15 bp):
ACATTAAAATTTAAG
Found at i:2216675 original size:27 final size:27
Alignment explanation
Indices: 2216592--2216677 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
2216582 TTTTATGAAA
*
2216592 AATAAACTTAAATCCTACCTTTTTATT
1 AATAAACTTAAATCCTACCTTTTAATT
* ** *
2216619 AAT-AAC-TACAA--GTATTTTATTAATAA
1 AATAAACTTA-AATCCTACCTT-TTAAT-T
2216645 AATAAACTTAAATCCTACCTTTTAATT
1 AATAAACTTAAATCCTACCTTTTAATT
2216672 AATAAA
1 AATAAA
2216678 AATTATAGTT
Statistics
Matches: 43, Mismatches: 9, Indels: 14
0.65 0.14 0.21
Matches are distributed among these distances:
24 4 0.09
25 6 0.14
26 8 0.19
27 14 0.33
28 7 0.16
29 4 0.09
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.40
Consensus pattern (27 bp):
AATAAACTTAAATCCTACCTTTTAATT
Found at i:2216695 original size:127 final size:129
Alignment explanation
Indices: 2216540--2216796 Score: 500
Period size: 127 Copynumber: 2.0 Consensus size: 129
2216530 ATAAAAAACT
2216540 ATTAATAAAATAATTATAGTTATAATTATTTTATATTAATATTTTTATGAAAAATAAACTTAAAT
1 ATTAATAAAATAATTATAGTTATAATTATTTTATATTAATATTTTTATGAAAAATAAACTTAAAT
2216605 CCTACCTTTTTATTAATAACTACAAGTATTTTATTAATAAAATAAACTTAAATCCTACCTTTTA
66 CCTACCTTTTTATTAATAACTACAAGTATTTTATTAATAAAATAAACTTAAATCCTACCTTTTA
2216669 ATTAAT-AAA-AATTATAGTTATAATTATTTTATATTAATATTTTTATGAAAAATAAACTTAAAT
1 ATTAATAAAATAATTATAGTTATAATTATTTTATATTAATATTTTTATGAAAAATAAACTTAAAT
2216732 CCTACCTTTTTATTAATAACTACAAGTATTTTATTAATAAAATAAACTTAAATCCTACCTTTTA
66 CCTACCTTTTTATTAATAACTACAAGTATTTTATTAATAAAATAAACTTAAATCCTACCTTTTA
2216796 A
1 A
2216797 ACATATAAAA
Statistics
Matches: 128, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
127 119 0.93
128 3 0.02
129 6 0.05
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (129 bp):
ATTAATAAAATAATTATAGTTATAATTATTTTATATTAATATTTTTATGAAAAATAAACTTAAAT
CCTACCTTTTTATTAATAACTACAAGTATTTTATTAATAAAATAAACTTAAATCCTACCTTTTA
Found at i:2224922 original size:27 final size:27
Alignment explanation
Indices: 2224879--2225028 Score: 86
Period size: 27 Copynumber: 5.6 Consensus size: 27
2224869 ACTGATGACC
* * *
2224879 CTAGCTCGCAAGACCTACTGGTAAACA
1 CTAGCTCGCCAGGCCTACTGGCAAACA
* * *
2224906 CTAGCTCGCCTGGCCTATTGGCGAACA
1 CTAGCTCGCCAGGCCTACTGGCAAACA
* * *
2224933 CTAGCTCGTCAGGCCTA-TTGCGAACA
1 CTAGCTCGCCAGGCCTACTGGCAAACA
* ** * * *
2224959 CCAATTCGCTAGGCCTACTAGCGAACA
1 CTAGCTCGCCAGGCCTACTGGCAAACA
* ** * *
2224986 CCAATTTGCCAGGCCTACTGGCGAACA
1 CTAGCTCGCCAGGCCTACTGGCAAACA
* * *
2225013 CCAGCTTGCCAAGCCT
1 CTAGCTCGCCAGGCCT
2225029 CAAACTCCTA
Statistics
Matches: 101, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
26 20 0.20
27 81 0.80
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.20
Consensus pattern (27 bp):
CTAGCTCGCCAGGCCTACTGGCAAACA
Found at i:2226916 original size:18 final size:18
Alignment explanation
Indices: 2226895--2226930 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2226885 TAGTTACTTA
*
2226895 AGTTTAAACATCATTAAT
1 AGTTCAAACATCATTAAT
*
2226913 AGTTCGAACATCATTAAT
1 AGTTCAAACATCATTAAT
2226931 TTTTGTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (18 bp):
AGTTCAAACATCATTAAT
Found at i:2240263 original size:12 final size:12
Alignment explanation
Indices: 2240248--2240298 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
2240238 GAAAAAGGAA
2240248 GAAAAGAAAGAG
1 GAAAAGAAAGAG
*
2240260 GAAAAGAAAGAA
1 GAAAAGAAAGAG
*
2240272 GAGAAA-AACGAG
1 GA-AAAGAAAGAG
*
2240284 GAGAAGAAAGAG
1 GAAAAGAAAGAG
2240296 GAA
1 GAA
2240299 GTCAAGGAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 2 0.06
12 26 0.84
13 3 0.10
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (12 bp):
GAAAAGAAAGAG
Found at i:2240264 original size:21 final size:21
Alignment explanation
Indices: 2240229--2240277 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2240219 TAGGACCTGC
*
2240229 AAAAG-AAGAGAAAAAGGAAG
1 AAAAGAAAGAGAAAAAGAAAG
*
2240249 AAAAGAAAGAGGAAAAGAAAG
1 AAAAGAAAGAGAAAAAGAAAG
*
2240270 AAGAGAAA
1 AAAAGAAA
2240278 AACGAGGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (21 bp):
AAAAGAAAGAGAAAAAGAAAG
Found at i:2240272 original size:24 final size:24
Alignment explanation
Indices: 2240245--2240294 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2240235 AGAGAAAAAG
2240245 GAAGA-AAAGAAAGAGGAAAAGAAA
1 GAAGAGAAA-AAAGAGGAAAAGAAA
* *
2240269 GAAGAGAAAAACGAGGAGAAGAAA
1 GAAGAGAAAAAAGAGGAAAAGAAA
2240293 GA
1 GA
2240295 GGAAGTCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (24 bp):
GAAGAGAAAAAAGAGGAAAAGAAA
Found at i:2240272 original size:36 final size:36
Alignment explanation
Indices: 2240230--2240298 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
2240220 AGGACCTGCA
*
2240230 AAAGAAGAGAAAAAGGAAGAAAAGAAAGAGGAAAAG
1 AAAGAAGAGAAAAACGAAGAAAAGAAAGAGGAAAAG
* *
2240266 AAAGAAGAGAAAAACGAGGAGAAGAAAGAGGAA
1 AAAGAAGAGAAAAACGAAGAAAAGAAAGAGGAA
2240299 GTCAAGGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.67, C:0.01, G:0.32, T:0.00
Consensus pattern (36 bp):
AAAGAAGAGAAAAACGAAGAAAAGAAAGAGGAAAAG
Found at i:2240309 original size:36 final size:36
Alignment explanation
Indices: 2240230--2240316 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
2240220 AGGACCTGCA
* *
2240230 AAAGAAGAGAAAAAGGAAGAAAAGAAAGAGGAAAAG
1 AAAGAAGAGAAAAACGAAGAAAAGAAAGAGGAAAAC
* * **
2240266 AAAGAAGAGAAAAACGAGGAGAAGAAAGAGGAAGTC
1 AAAGAAGAGAAAAACGAAGAAAAGAAAGAGGAAAAC
*
2240302 AAGGAAGAGCAAAAA
1 AAAGAAGAG-AAAAA
2240317 TAATGGAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 38 0.88
37 5 0.12
ACGTcount: A:0.64, C:0.03, G:0.31, T:0.01
Consensus pattern (36 bp):
AAAGAAGAGAAAAACGAAGAAAAGAAAGAGGAAAAC
Found at i:2240871 original size:26 final size:26
Alignment explanation
Indices: 2240825--2240874 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2240815 AAATTTCGGT
*
2240825 TTAATTATCAATTCAATCGATTCATA
1 TTAATTATCAATTCAACCGATTCATA
*
2240851 TTAATTCTCAA-TCTAACCGATTCA
1 TTAATTATCAATTC-AACCGATTCA
2240875 AAGTCAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (26 bp):
TTAATTATCAATTCAACCGATTCATA
Found at i:2241126 original size:28 final size:28
Alignment explanation
Indices: 2241068--2241127 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
2241058 GGGATTTACG
* * * * *
2241068 TTATATATAACACCTTCACGTTTTTTTT
1 TTATATATAAAACCTTCACATCTTCTAT
*
2241096 TTATATATAAAACCTTCATATCTTCTAT
1 TTATATATAAAACCTTCACATCTTCTAT
2241124 TTAT
1 TTAT
2241128 TAATTTTTTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.17, G:0.02, T:0.52
Consensus pattern (28 bp):
TTATATATAAAACCTTCACATCTTCTAT
Found at i:2242640 original size:378 final size:379
Alignment explanation
Indices: 2241936--2242695 Score: 1513
Period size: 378 Copynumber: 2.0 Consensus size: 379
2241926 CTTAATTGGA
2241936 AAAAGACTAAAAAAATCAAAATTAAAAAAAAAATTATTATAAAGGAATTTATGTATTTCAATAAT
1 AAAAGACTAAAAAAATCAAAATTAAAAAAAAAATTATTATAAAGGAATTTATGTATTTCAATAAT
2242001 TTTATAATATATTTTTTAAATTAAATAGCTTAAATTACAACCTTACGAGTGTGTTTGAATGAATA
66 TTTATAATATATTTTTTAAATTAAATAGCTTAAATTACAACCTTACGAGTGTGTTTGAATGAATA
2242066 ATTTTGAATTTTATCAATTCAAAATACTAGCTAGTTTATTTGTTTTGTTTGAATAAATAATTGTT
131 ATTTTGAATTTTATCAATTCAAAATACTAGCTAGTTTATTTGTTTTGTTTGAATAAATAATTGTT
2242131 TTAAGAAAAATTAGGTTAATGAAATTTTGAAAACTAAAAAAATTCTAAAACAAAAATATTTTTTT
196 TTAAGAAAAATTAGGTTAATGAAATTTTGAAAACTAAAAAAATTCTAAAACAAAAATATTTTTTT
2242196 TTGTCGAAATTAAGGTGTTCACCGCCAGGAGGTGTGACTAAACCTCTTGCTGCAAATGCTCTTCA
261 TTGTCGAAATTAAGGTGTTCACCGCCAGGAGGTGTGACTAAACCTCTTGCTGCAAATGCTCTTCA
2242261 AAGAGGTAAACTGGCCAAGCAACACCCAAAAATACTAGTATTTTTGTAAATATG
326 AAGAGGTAAACTGGCCAAGCAACACCCAAAAATACTAGTATTTTTGTAAATATG
2242315 AAAAGACT-AAAAAATCAAAATTAAAAAAAAAATTATTATAAAGGAATTTATGTATTTCAATAAT
1 AAAAGACTAAAAAAATCAAAATTAAAAAAAAAATTATTATAAAGGAATTTATGTATTTCAATAAT
2242379 TTTATAATATATTTTTTAAATTAAATAGCTTAAATTACAACCTTACGAGTGTGTTTGAATGAATA
66 TTTATAATATATTTTTTAAATTAAATAGCTTAAATTACAACCTTACGAGTGTGTTTGAATGAATA
2242444 ATTTTGAATTTTATCAATTCAAAATACTAGCTAGTTTATTTGTTTTGTTTGAATAAATAATTGTT
131 ATTTTGAATTTTATCAATTCAAAATACTAGCTAGTTTATTTGTTTTGTTTGAATAAATAATTGTT
2242509 TTAAGAAAAATTAGGTTAATGAAATTTTGAAAACTAAAAAAATTCTAAAACAAAAATATTTTTTT
196 TTAAGAAAAATTAGGTTAATGAAATTTTGAAAACTAAAAAAATTCTAAAACAAAAATATTTTTTT
2242574 TTGTCGAAATTAAGGTGTTCACCGCCAGGAGGTGTGACTAAACCTCTTGCTGCAAATGCTCTTCA
261 TTGTCGAAATTAAGGTGTTCACCGCCAGGAGGTGTGACTAAACCTCTTGCTGCAAATGCTCTTCA
2242639 AAGAGGTAAACTGGCCAAGCAACACCCAAAAATACTAGTATTTTTGTAAATATG
326 AAGAGGTAAACTGGCCAAGCAACACCCAAAAATACTAGTATTTTTGTAAATATG
2242693 AAA
1 AAA
2242696 CATAAACTAT
Statistics
Matches: 381, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
378 373 0.98
379 8 0.02
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (379 bp):
AAAAGACTAAAAAAATCAAAATTAAAAAAAAAATTATTATAAAGGAATTTATGTATTTCAATAAT
TTTATAATATATTTTTTAAATTAAATAGCTTAAATTACAACCTTACGAGTGTGTTTGAATGAATA
ATTTTGAATTTTATCAATTCAAAATACTAGCTAGTTTATTTGTTTTGTTTGAATAAATAATTGTT
TTAAGAAAAATTAGGTTAATGAAATTTTGAAAACTAAAAAAATTCTAAAACAAAAATATTTTTTT
TTGTCGAAATTAAGGTGTTCACCGCCAGGAGGTGTGACTAAACCTCTTGCTGCAAATGCTCTTCA
AAGAGGTAAACTGGCCAAGCAACACCCAAAAATACTAGTATTTTTGTAAATATG
Found at i:2243429 original size:13 final size:13
Alignment explanation
Indices: 2243411--2243435 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2243401 TAGTTATTTG
2243411 TTTTCTTTCTTTC
1 TTTTCTTTCTTTC
2243424 TTTTCTTTCTTT
1 TTTTCTTTCTTT
2243436 TATTTATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTTCTTTC
Found at i:2244508 original size:21 final size:21
Alignment explanation
Indices: 2244460--2244507 Score: 82
Period size: 19 Copynumber: 2.4 Consensus size: 21
2244450 AAAAATACAT
2244460 TATTTTTTAAATTATTATCAA
1 TATTTTTTAAATTATTATCAA
2244481 TATTTTTTAAA-T-TTATCAA
1 TATTTTTTAAATTATTATCAA
2244500 TATTTTTT
1 TATTTTTT
2244508 TAAAAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 15 0.56
20 1 0.04
21 11 0.41
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTTTAAATTATTATCAA
Found at i:2275261 original size:34 final size:33
Alignment explanation
Indices: 2275218--2275281 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 33
2275208 ACAGTTCAAT
*
2275218 TCAGTTGGACCTTAGCGCATTACACTATCAGTA
1 TCAGTTGGACCTTAGCCCATTACACTATCAGTA
*
2275251 TCAGTGTGGACCTTAGCCCATTACAGTATCA
1 TCAGT-TGGACCTTAGCCCATTACACTATCA
2275282 ACTCAGACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 5 0.18
34 23 0.82
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (33 bp):
TCAGTTGGACCTTAGCCCATTACACTATCAGTA
Found at i:2275864 original size:19 final size:20
Alignment explanation
Indices: 2275840--2275877 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2275830 CACAAGCCTA
2275840 TTTGGCCC-ACACGGCCCAT
1 TTTGGCCCAACACGGCCCAT
*
2275859 TTTGGCCCAACATGGCCCA
1 TTTGGCCCAACACGGCCCA
2275878 AAGCGGCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.18, C:0.39, G:0.21, T:0.21
Consensus pattern (20 bp):
TTTGGCCCAACACGGCCCAT
Found at i:2283971 original size:18 final size:17
Alignment explanation
Indices: 2283944--2283977 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2283934 ATCATTTCAT
2283944 ATTTCATTTCCCATCTC
1 ATTTCATTTCCCATCTC
*
2283961 ATTTCCATTTCTCATCT
1 ATTT-CATTTCCCATCT
2283978 TGTCATCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTCATTTCCCATCTC
Found at i:2285085 original size:6 final size:6
Alignment explanation
Indices: 2285076--2285100 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2285066 TATTATGACT
2285076 ATTATA ATTATA ATTATA ATTATA A
1 ATTATA ATTATA ATTATA ATTATA A
2285101 AATGTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTATA
Found at i:2295474 original size:29 final size:28
Alignment explanation
Indices: 2295434--2295488 Score: 101
Period size: 29 Copynumber: 1.9 Consensus size: 28
2295424 TTAATTATGA
2295434 TTTGAAAATTTTCTATTATAATATTTTT
1 TTTGAAAATTTTCTATTATAATATTTTT
2295462 TTTGAATAATTTTCTATTATAATATTT
1 TTTGAA-AATTTTCTATTATAATATTT
2295489 GAGTTGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (28 bp):
TTTGAAAATTTTCTATTATAATATTTTT
Found at i:2295485 original size:16 final size:16
Alignment explanation
Indices: 2295440--2295485 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
2295430 ATGATTTGAA
2295440 AATTTTCTATTATAAT
1 AATTTTCTATTATAAT
2295456 -ATTTT-T-TT-TGAAT
1 AATTTTCTATTAT-AAT
2295469 AATTTTCTATTATAAT
1 AATTTTCTATTATAAT
2295485 A
1 A
2295486 TTTGAGTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
12 1 0.04
13 5 0.20
14 6 0.24
15 6 0.24
16 6 0.24
17 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (16 bp):
AATTTTCTATTATAAT
Found at i:2295495 original size:29 final size:28
Alignment explanation
Indices: 2295435--2295495 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
2295425 TAATTATGAT
***
2295435 TTGAAAATTTTCTATTATAATATTTTTT
1 TTGAAAATTTTCTATTATAATATTTGAG
2295463 TTGAATAATTTTCTATTATAATATTTGAG
1 TTGAA-AATTTTCTATTATAATATTTGAG
2295492 TTGA
1 TTGA
2295496 TAAGTTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (28 bp):
TTGAAAATTTTCTATTATAATATTTGAG
Found at i:2297597 original size:50 final size:50
Alignment explanation
Indices: 2297522--2297769 Score: 234
Period size: 50 Copynumber: 4.9 Consensus size: 50
2297512 CATTTCGGTA
* * *
2297522 AAGAGGTCCCCTGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGAT
* * *
2297572 AAGAGGTCCCATGTAAGACCGTGTCTGGGACATGACATTGGCATCATTGAGACT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--TGAGA-T
*
2297626 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGATAT
1 A--AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGAT
* ** * * * *
2297678 GAGAACTCCCATGTAAGACCATATCTGGGATATTGCATTGG-A---AGTAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAG-AT
** *
2297725 AAGAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AAG--AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
2297770 TGTTATTATC
Statistics
Matches: 163, Mismatches: 25, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
46 1 0.01
47 4 0.02
49 33 0.20
50 73 0.45
51 1 0.01
52 1 0.01
53 8 0.05
54 2 0.01
55 1 0.01
56 39 0.24
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGAT
Found at i:2297717 original size:106 final size:101
Alignment explanation
Indices: 2297521--2297769 Score: 281
Period size: 106 Copynumber: 2.4 Consensus size: 101
2297511 ACATTTCGGT
* * **
2297521 AAAGAGGTCCCCTGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATAAGAGGTCCCATGT
1 AAAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATAAGAACTCCCATGT
* * * *
2297586 AAGACCGTGTCTGGGACATGACATTGGCA-TCATTGAG
66 AAGACCATATCTGGGACATGACATTGGAAGT-A-TAAG
* * *
2297623 ACTATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGATATGAGAACTCCC
1 A--A--AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATAAGAACTCCC
*
2297688 ATGTAAGACCATATCTGGGATATTG-CATTGGAAGTATAAG
62 ATGTAAGACCATATCTGGGACA-TGACATTGGAAGTATAAG
* *
2297728 AAACA--TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AAAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
2297770 TGTTATTATC
Statistics
Matches: 127, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
99 36 0.28
101 2 0.02
102 1 0.01
103 1 0.01
104 1 0.01
105 4 0.03
106 79 0.62
107 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (101 bp):
AAAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATAAGAACTCCCATGT
AAGACCATATCTGGGACATGACATTGGAAGTATAAG
Found at i:2307558 original size:55 final size:55
Alignment explanation
Indices: 2307498--2307609 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
2307488 ACAAGTTAGT
2307498 TGATAAATGGTTAAATGTGCACATGTTTAGGTATCTTTGATGTTTGTGATTGAGG
1 TGATAAATGGTTAAATGTGCACATGTTTAGGTATCTTTGATGTTTGTGATTGAGG
*
2307553 TGATAAATGGTTAAATGTGTACATGTTTAGGTATCTTTGATGTTTGTGATTGAGG
1 TGATAAATGGTTAAATGTGCACATGTTTAGGTATCTTTGATGTTTGTGATTGAGG
2307608 TG
1 TG
2307610 TCTATATGAC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.25, C:0.04, G:0.28, T:0.43
Consensus pattern (55 bp):
TGATAAATGGTTAAATGTGCACATGTTTAGGTATCTTTGATGTTTGTGATTGAGG
Found at i:2308601 original size:24 final size:24
Alignment explanation
Indices: 2308572--2308625 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
2308562 AATAGTAGAA
* *
2308572 AATAATTTATCAGCTAATAATAGT
1 AATAATTAATCAACTAATAATAGT
* * *
2308596 AATAATTAATTAATTAATAATGGT
1 AATAATTAATCAACTAATAATAGT
2308620 AATAAT
1 AATAAT
2308626 AAAATAATTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (24 bp):
AATAATTAATCAACTAATAATAGT
Found at i:2308633 original size:24 final size:24
Alignment explanation
Indices: 2308586--2308634 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2308576 ATTTATCAGC
* *
2308586 TAATAATAGTAATAATTAATTAAT
1 TAATAATAGTAATAATAAAATAAT
*
2308610 TAATAATGGTAATAATAAAATAAT
1 TAATAATAGTAATAATAAAATAAT
2308634 T
1 T
2308635 GGATTATTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (24 bp):
TAATAATAGTAATAATAAAATAAT
Found at i:2310210 original size:20 final size:22
Alignment explanation
Indices: 2310162--2310214 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
2310152 ATACACATAT
*
2310162 TATATTATATGCGTGGGTCTTAC
1 TATA-TATATGCATGGGTCTTAC
*
2310185 TATATATATGCATGGGTCTTAT
1 TATATATATGCATGGGTCTTAC
2310207 TATATATA
1 TATATATA
2310215 ATATATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.45
Consensus pattern (22 bp):
TATATATATGCATGGGTCTTAC
Found at i:2310559 original size:18 final size:18
Alignment explanation
Indices: 2310538--2310593 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
2310528 TCTGTTAACT
2310538 TGGTGAATTATATTATTA
1 TGGTGAATTATATTATTA
*
2310556 TGGTGAAATATATTAATT-
1 TGGTGAATTATATT-ATTA
* * *
2310574 TGGTGATTTGTATTAATA
1 TGGTGAATTATATTATTA
2310592 TG
1 TG
2310594 ACGAATTGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 2 0.06
18 26 0.84
19 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (18 bp):
TGGTGAATTATATTATTA
Found at i:2311330 original size:12 final size:13
Alignment explanation
Indices: 2311310--2311350 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
2311300 AATAAAATGG
*
2311310 TTTCTAATAT-CC
1 TTTCAAATATACC
2311322 TTTCAAATATAGCC
1 TTTCAAATATA-CC
2311336 TTTCAAA-ATACC
1 TTTCAAATATACC
2311348 TTT
1 TTT
2311351 TTGCATCCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 14 0.54
13 3 0.12
14 9 0.35
ACGTcount: A:0.32, C:0.22, G:0.02, T:0.44
Consensus pattern (13 bp):
TTTCAAATATACC
Found at i:2337293 original size:50 final size:50
Alignment explanation
Indices: 2337182--2337419 Score: 210
Period size: 50 Copynumber: 4.7 Consensus size: 50
2337172 ATTTGGGTAA
* * *
2337182 AGAGATCCCA-GTAAGACCATGTCTGGGACATGGCATTGGCATCATTGGGATTGTG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAGA---TG
*
2337237 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
2337287 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * * * *
2337337 AGAACTCCCATGTAAGACCATATTTGGGATATGGCATTGCCAAC-ACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** * *
2337386 AAACATCTCATGTAAGACCATGCCTGGGACATGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGG
2337420 GTTTGGCATG
Statistics
Matches: 153, Mismatches: 29, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
49 29 0.19
50 81 0.53
53 3 0.02
55 10 0.07
56 30 0.20
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:2347920 original size:56 final size:50
Alignment explanation
Indices: 2347834--2348081 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
2347824 ATTTGGGTAA
*
2347834 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCTTCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG---CACTGAG---ATG
* * *
2347890 AGAGGTCCCATGTAGGACCATGTCTGGGACATGGCGTTGACACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
* *
2347940 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
** *
2347990 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCA-TGGACACCT-ATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG-CA-CTGAGATG
** * * *
2348040 AGAACTCCCATGTAAGACCATATTTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
2348082 GTACAAGAAA
Statistics
Matches: 170, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
49 3 0.02
50 120 0.71
51 4 0.02
53 6 0.04
56 37 0.22
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
Found at i:2353795 original size:50 final size:50
Alignment explanation
Indices: 2353684--2353930 Score: 289
Period size: 50 Copynumber: 4.8 Consensus size: 50
2353674 ATTTGGGTAA
* *
2353684 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* *
2353740 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*** *
2353790 AGAGGTCCCATGTAAGACCATGTCCCAGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
2353840 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATAGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
2353890 AGAACTCCC-TGTAAGACCATATCTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
2353931 ATACAAGAAA
Statistics
Matches: 170, Mismatches: 21, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
49 29 0.17
50 98 0.58
53 3 0.02
55 1 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:2353952 original size:49 final size:49
Alignment explanation
Indices: 2353850--2353969 Score: 136
Period size: 49 Copynumber: 2.4 Consensus size: 49
2353840 AGAGGTCCCC
* * * *
2353850 TGTAAGACCATGTCTGGGACATGGCATAGGCACCTATATGAGAACTCCC
1 TGTAAGACCATGTCTGGGACATGGCATAGGCACATACAAGAGAACTCCA
* * *
2353899 TGTAAGACCATATCTGGGATATGGCATTGGCA-ATACAAGA-AACATCTCA
1 TGTAAGACCATGTCTGGGACATGGCATAGGCACATACAAGAGAAC-TC-CA
*
2353948 TGTAAGACTATGTCTGGGACAT
1 TGTAAGACCATGTCTGGGACAT
2353970 AGTTGATACG
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
47 3 0.05
48 7 0.12
49 49 0.83
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (49 bp):
TGTAAGACCATGTCTGGGACATGGCATAGGCACATACAAGAGAACTCCA
Found at i:2360290 original size:51 final size:50
Alignment explanation
Indices: 2360125--2360301 Score: 203
Period size: 51 Copynumber: 3.5 Consensus size: 50
2360115 ATTGAAAATG
* *
2360125 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGGT
* * * *
2360176 A-GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
* ** * * * *
2360225 TTCGACCACTTGTGTAGTACTATGTGTAGGCTACTACGTGTATCAGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
2360276 AATGGTCACATGTGTAGTACTATGTG
1 -ATGGTCACATGTGTAGTACTATGTG
2360302 AACCGAACAT
Statistics
Matches: 102, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
49 3 0.03
50 39 0.38
51 59 0.58
52 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
Found at i:2368058 original size:15 final size:15
Alignment explanation
Indices: 2368038--2368069 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2368028 CATTTCACTA
*
2368038 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
2368053 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
2368068 TT
1 TT
2368070 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:2369359 original size:13 final size:13
Alignment explanation
Indices: 2369341--2369365 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2369331 CCCAATATGT
2369341 AATTGAACTTGAA
1 AATTGAACTTGAA
2369354 AATTGAACTTGA
1 AATTGAACTTGA
2369366 GATCGTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
AATTGAACTTGAA
Found at i:2369742 original size:17 final size:17
Alignment explanation
Indices: 2369720--2369793 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 17
2369710 ATTTTAATAG
2369720 TTTAATATTAAATTTAA
1 TTTAATATTAAATTTAA
2369737 TTTAATACTT--ATCTTAA
1 TTTAATA-TTAAAT-TTAA
** *
2369754 --TAATATTTTA-TGAA
1 TTTAATATTAAATTTAA
*
2369768 TTTAATATTAAATCTAA
1 TTTAATATTAAATTTAA
2369785 TTTAATATT
1 TTTAATATT
2369794 TATATTGTAG
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
14 5 0.11
15 5 0.11
16 11 0.24
17 22 0.49
18 2 0.04
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (17 bp):
TTTAATATTAAATTTAA
Found at i:2369761 original size:48 final size:48
Alignment explanation
Indices: 2369703--2369796 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
2369693 ATTCCAGAAA
* * *
2369703 TAATATTATTTTAAT-AGTTTAATATTAAATTTAATTTAATACTTATCT
1 TAATAATATTTT-ATGAATTTAATATTAAATCTAATTTAATACTTATCT
*
2369751 TAATAATATTTTATGAATTTAATATTAAATCTAATTTAATATTTAT
1 TAATAATATTTTATGAATTTAATATTAAATCTAATTTAATACTTAT
2369797 ATTGTAGATA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 2 0.05
48 39 0.95
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.53
Consensus pattern (48 bp):
TAATAATATTTTATGAATTTAATATTAAATCTAATTTAATACTTATCT
Found at i:2369867 original size:28 final size:29
Alignment explanation
Indices: 2369824--2369882 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
2369814 TATTATTTTA
* *
2369824 ATAAGATTTAATATTAAATTTAATCTAAT
1 ATAAGATTAAATATTAAATTAAATCTAAT
* *
2369853 ATAAGA-TAAATATTAGATTAAATTTAAT
1 ATAAGATTAAATATTAAATTAAATCTAAT
2369881 AT
1 AT
2369883 TAAAGTGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (29 bp):
ATAAGATTAAATATTAAATTAAATCTAAT
Found at i:2379220 original size:37 final size:36
Alignment explanation
Indices: 2379169--2379244 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
2379159 ATTCCAAAAA
*
2379169 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATATTATCTTAATAGTATT-ATATT-AATTTAATAT
*
2379205 TAATACTTATCTTAATAGTATTTTATTAATTTAATAT
1 TAATA-TTATCTTAATAGTATTATATTAATTTAATAT
2379242 TAA
1 TAA
2379245 AGTAATTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 13 0.37
37 20 0.57
38 2 0.06
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (36 bp):
TAATATTATCTTAATAGTATTATATTAATTTAATAT
Found at i:2384536 original size:61 final size:63
Alignment explanation
Indices: 2384420--2384540 Score: 158
Period size: 61 Copynumber: 2.0 Consensus size: 63
2384410 GTTTTCTCCA
* * * * **
2384420 AAATGAAAATGAAAATGGAGAAAATGGAATCTTTTGAAAATGAATATGGTTTTCTCAAAATGG
1 AAATGAAAATGAAAATGGAGAAAATGGAATCATTTAAAAATGAACAAGGAATTCTCAAAATGG
2384483 AAATGAAAATGAAAAT-GAG-AAAT-GAATTCATTTAAAAATGAACAAGGAATTCTCAAAA
1 AAATGAAAATGAAAATGGAGAAAATGGAA-TCATTTAAAAATGAACAAGGAATTCTCAAAA
2384541 ATGATCGAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
60 3 0.06
61 29 0.57
62 3 0.06
63 16 0.31
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (63 bp):
AAATGAAAATGAAAATGGAGAAAATGGAATCATTTAAAAATGAACAAGGAATTCTCAAAATGG
Found at i:2388001 original size:20 final size:20
Alignment explanation
Indices: 2387952--2388009 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
2387942 GAACTTTTAT
*
2387952 TAATTTTTTTAATTTTTAAA
1 TAATTTTTTAAATTTTTAAA
** *
2387972 TAATACTTTAAAATTTTAAA
1 TAATTTTTTAAATTTTTAAA
*
2387992 TTATTTTTTAAATTTTTA
1 TAATTTTTTAAATTTTTA
2388010 TTAGTATTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TAATTTTTTAAATTTTTAAA
Found at i:2388019 original size:21 final size:20
Alignment explanation
Indices: 2387993--2388043 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 20
2387983 AATTTTAAAT
2387993 TATTTTTTAA-ATTTTTATTA
1 TATTTTTTAAGATTTTTA-TA
2388013 GTATTTTTTATAAGATTTTTATA
1 -TA-TTTTT-TAAGATTTTTATA
2388036 TATTTTTT
1 TATTTTTT
2388044 TTGAAGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 1 0.04
21 7 0.26
22 7 0.26
23 5 0.19
24 7 0.26
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (20 bp):
TATTTTTTAAGATTTTTATA
Found at i:2388039 original size:22 final size:22
Alignment explanation
Indices: 2387995--2388044 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
2387985 TTTTAAATTA
2387995 TTTTTTAAATTTTTATTAGTAT
1 TTTTTTAAATTTTTATTAGTAT
2388017 TTTTTATAAGATTTTTA-TA-TAT
1 TTTTT-TAA-ATTTTTATTAGTAT
2388039 TTTTTT
1 TTTTTT
2388045 TGAAGTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 1 0.04
22 13 0.50
23 5 0.19
24 7 0.27
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTTTTAAATTTTTATTAGTAT
Found at i:2388939 original size:50 final size:50
Alignment explanation
Indices: 2388864--2388964 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
2388854 ATTCTATGAG
2388864 AAAGAAAACTAGAATATAATTACATTATAAGGTTTAAGACCCTAACTGAC
1 AAAGAAAACTAGAATATAATTACATTATAAGGTTTAAGACCCTAACTGAC
2388914 AAAGAAAACTAGAATATAATTACATTATAAGGTTTAAGACCCTAACTGAC
1 AAAGAAAACTAGAATATAATTACATTATAAGGTTTAAGACCCTAACTGAC
2388964 A
1 A
2388965 TAGACACTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.26
Consensus pattern (50 bp):
AAAGAAAACTAGAATATAATTACATTATAAGGTTTAAGACCCTAACTGAC
Found at i:2390460 original size:13 final size:13
Alignment explanation
Indices: 2390442--2390466 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2390432 AAAATTATGT
2390442 TATTTTAATTTAA
1 TATTTTAATTTAA
2390455 TATTTTAATTTA
1 TATTTTAATTTA
2390467 TTAAATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTTAATTTAA
Found at i:2390673 original size:21 final size:22
Alignment explanation
Indices: 2390634--2390674 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2390624 TTTGAATGTT
2390634 TGAGTTTAACTTATTTTTTAAA
1 TGAGTTTAACTTATTTTTTAAA
*
2390656 TGAGTTTAA-TTTTTTTTTA
1 TGAGTTTAACTTATTTTTTA
2390675 TCTAAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (22 bp):
TGAGTTTAACTTATTTTTTAAA
Found at i:2395322 original size:23 final size:23
Alignment explanation
Indices: 2395303--2395356 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
2395293 ACCAAAAATT
2395303 TATTTTAAAAA-TAAAAAAAAAG
1 TATTTTAAAAATTAAAAAAAAAG
*
2395325 TATTTTAAAAATTAAAAATAAAAA
1 TATTTTAAAAATTAAAAA-AAAAG
2395349 TATATTTA
1 TAT-TTTA
2395357 TTGTATTCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 11 0.39
23 6 0.21
24 7 0.25
25 4 0.14
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
TATTTTAAAAATTAAAAAAAAAG
Found at i:2395328 original size:22 final size:24
Alignment explanation
Indices: 2395308--2395356 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2395298 AAATTTATTT
*
2395308 TAAAAA-TAAAAA-AAAAGTATTT
1 TAAAAATTAAAAATAAAAATATTT
2395330 TAAAAATTAAAAATAAAAATATATT
1 TAAAAATTAAAAATAAAAATAT-TT
2395355 TA
1 TA
2395357 TTGTATTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 6 0.26
24 7 0.30
25 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (24 bp):
TAAAAATTAAAAATAAAAATATTT
Found at i:2397726 original size:168 final size:169
Alignment explanation
Indices: 2397423--2397786 Score: 522
Period size: 168 Copynumber: 2.2 Consensus size: 169
2397413 TGGTCTTGAA
*
2397423 TGATTTTAGGAAACACG-TTTGTTTAAATTAAGACTTCAATTTTACAGCTTGATAAATTAGACTT
1 TGATTTTAGGAAACA-GATTTGTTTAAATTAAGACTTCAATTTTACAGCATGATAAATTAGACTT
2397487 TGTGATGACATGCAATTTGAATGCTTGCTTGTCCTTGATTTATATGGTTTTCCAATCACACAAAG
65 TGTGATGACATGCAA-TTGAATGCTTGCTTGTCCTTGATTTATATGGTTTTCCAATCACACAAAG
2397552 GAATATAAGTAAATAGTAATGAAACCTTGGATCTT-AAATTT
129 GAATATAAGTAAATAGTAATGAAACCTTGG-TCTTAAAATTT
* *
2397593 TGATTCTAGGAAACAGATTTGTTTAAA-TAAGACTTCAATTTTACAGCATGATAAATTAGATTTT
1 TGATTTTAGGAAACAGATTTGTTTAAATTAAGACTTCAATTTTACAGCATGATAAATTAGACTTT
* * * ** *
2397657 GTGATGACATTCACA-TGAATGCTTTCTTGTCCTTTATTTATATGGTTTTCCAATTTCACAATGG
66 GTGATGACATGCA-ATTGAATGCTTGCTTGTCCTTGATTTATATGGTTTTCCAATCACACAAAGG
** * *
2397721 AATATACTTAAATGGTAATGAAACCTTTGTCTTAAAATTT
130 AATATAAGTAAATAGTAATGAAACCTTGGTCTTAAAATTT
* *
2397761 T-ATTTTAGGAAACTGATTTGCTTAAA
1 TGATTTTAGGAAACAGATTTGTTTAAA
2397787 ATTATATCTT
Statistics
Matches: 175, Mismatches: 16, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
167 26 0.15
168 76 0.43
169 48 0.27
170 25 0.14
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (169 bp):
TGATTTTAGGAAACAGATTTGTTTAAATTAAGACTTCAATTTTACAGCATGATAAATTAGACTTT
GTGATGACATGCAATTGAATGCTTGCTTGTCCTTGATTTATATGGTTTTCCAATCACACAAAGGA
ATATAAGTAAATAGTAATGAAACCTTGGTCTTAAAATTT
Found at i:2405556 original size:18 final size:18
Alignment explanation
Indices: 2405533--2405568 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2405523 ACTTAGACAG
2405533 GAAAATCAGTTAATGCAT
1 GAAAATCAGTTAATGCAT
2405551 GAAAATCAGTTAATGCAT
1 GAAAATCAGTTAATGCAT
2405569 CTTTGTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (18 bp):
GAAAATCAGTTAATGCAT
Found at i:2406613 original size:20 final size:20
Alignment explanation
Indices: 2406575--2406613 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2406565 AATATTATAA
** *
2406575 ATAAATAAATTTTATTAATC
1 ATAAATAAATAATAATAATC
2406595 ATAAATAAATAATAATAAT
1 ATAAATAAATAATAATAAT
2406614 TAAGTAAGAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAATAAATAATAATAATC
Found at i:2406615 original size:24 final size:24
Alignment explanation
Indices: 2406571--2406616 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2406561 CTTTAATATT
* *
2406571 ATAAATAAATAAATTTTATTAATC
1 ATAAATAAATAAATATAATTAATC
2406595 ATAAATAAAT-AATAATAATTAA
1 ATAAATAAATAAAT-ATAATTAA
2406617 GTAAGACTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
ATAAATAAATAAATATAATTAATC
Found at i:2408711 original size:7 final size:7
Alignment explanation
Indices: 2408699--2408726 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2408689 GCCCTGGCCC
2408699 TATTTAT
1 TATTTAT
2408706 TATTTAT
1 TATTTAT
2408713 TATTTAT
1 TATTTAT
2408720 TATTTAT
1 TATTTAT
2408727 GTCTTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TATTTAT
Found at i:2416605 original size:70 final size:70
Alignment explanation
Indices: 2416459--2416624 Score: 156
Period size: 70 Copynumber: 2.4 Consensus size: 70
2416449 GCAAGGAAAG
* * *
2416459 CTTTTGTAACTTCAACATGGTGAGAAGATGACCTATTTCAAACTTTGCAACATCAACATGGTGGG
1 CTTTTGCAACTTCAACATGGTGAGAAGATGACCCATTTCAAACTTTGCAACATCAACACGGTGGG
*
2416524 AAGCA
66 AAGAA
* * * * * * *
2416529 CCTTTGCAACTTCAACATTGTGAGAGGA-GAGCCCA-TTCTGAACTTTGTATCATCAATACGGTG
1 CTTTTGCAACTTCAACATGGTGAGAAGATGA-CCCATTTC-AAACTTTGCAACATCAACACGGTG
2416592 GGAAGAA
64 GGAAGAA
* * * * *
2416599 GTTTTGCACCTTTAGCATGGCGAGAA
1 CTTTTGCAACTTCAACATGGTGAGAA
2416625 ACTTCAACAT
Statistics
Matches: 75, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
69 5 0.07
70 70 0.93
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (70 bp):
CTTTTGCAACTTCAACATGGTGAGAAGATGACCCATTTCAAACTTTGCAACATCAACACGGTGGG
AAGAA
Done.