Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold381
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: 1193157
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:475166 original size:13 final size:13
Alignment explanation
Indices: 475148--475173 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
475138 TACAGCAAGT
475148 ATGTATCGATACA
1 ATGTATCGATACA
475161 ATGTATCGATACA
1 ATGTATCGATACA
475174 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:477107 original size:22 final size:22
Alignment explanation
Indices: 477067--477108 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
477057 TTTAAAATAT
*
477067 TATTTTTATATTAATATTTATA
1 TATTTTTATAATAATATTTATA
477089 TATTTTTATAAATAA-ATTTA
1 TATTTTTAT-AATAATATTTA
477109 AATAAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTTATAATAATATTTATA
Found at i:477264 original size:6 final size:6
Alignment explanation
Indices: 477255--477288 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
477245 TTCTTTTCTT
477255 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
477289 TATTGTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:480241 original size:16 final size:16
Alignment explanation
Indices: 480222--480286 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
480212 AGTTTGATTC
480222 ATTTGAGATTTAAATT
1 ATTTGAGATTTAAATT
* *
480238 ATTTTAGATTTAAATC
1 ATTTGAGATTTAAATT
* *
480254 ATTTCAAATTTAAATAAT
1 ATTTGAGATTTAAAT--T
*
480272 TTTTGAG-TTTAAATT
1 ATTTGAGATTTAAATT
480287 CGTTTCAGGT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
15 1 0.03
16 27 0.69
17 7 0.18
18 4 0.10
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (16 bp):
ATTTGAGATTTAAATT
Found at i:480256 original size:32 final size:32
Alignment explanation
Indices: 480197--480285 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
480187 CTGATTAATT
* * * * *
480197 ATTTAAGTTATTTTGAGTTTGATTCATTTGAG
1 ATTTAAATTATTTTGAGTTTAAATCATTTCAA
480229 ATTTAAATTATTTT-AGATTTAAATCATTTCAA
1 ATTTAAATTATTTTGAG-TTTAAATCATTTCAA
*
480261 ATTTAAATAATTTTTGAGTTTAAAT
1 ATTTAAATTA-TTTTGAGTTTAAAT
480286 TCGTTTCAGG
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
31 2 0.04
32 33 0.69
33 11 0.23
34 2 0.04
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (32 bp):
ATTTAAATTATTTTGAGTTTAAATCATTTCAA
Found at i:483547 original size:23 final size:23
Alignment explanation
Indices: 483521--483567 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
483511 CTGTCTTTTT
483521 CCTTAAT-AACATTTATAAACATA
1 CCTTAATAAAC-TTTATAAACATA
483544 CCTTAATAAACTTTATAAACATA
1 CCTTAATAAACTTTATAAACATA
483567 C
1 C
483568 ATTTAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (23 bp):
CCTTAATAAACTTTATAAACATA
Found at i:487300 original size:28 final size:28
Alignment explanation
Indices: 487260--487323 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
487250 GACTCAGATA
*
487260 TGTGTTGGATATAAATATGATATGGATC
1 TGTGTTTGATATAAATATGATATGGATC
487288 TGTGTTTGATATAAATATGATATGGATC
1 TGTGTTTGATATAAATATGATATGGATC
487316 TGTGTTTG
1 TGTGTTTG
487324 TTACTTAGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.44
Consensus pattern (28 bp):
TGTGTTTGATATAAATATGATATGGATC
Found at i:491026 original size:32 final size:32
Alignment explanation
Indices: 490939--491027 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
490929 ACCCGAACCC
*
490939 AAAATAGCCCAAACCCGAGATAGCCTGAACTCG
1 AAAA-AGCCCAAACCCGAGAAAGCCTGAACTCG
* * **
490972 AGAAAGGCCAAACTTGAGAAAG-CTCGAACTCG
1 AAAAAGCCCAAACCCGAGAAAGCCT-GAACTCG
*
491004 AAAAAGCCCAAACCCGAAAAAGCC
1 AAAAAGCCCAAACCCGAGAAAGCC
491028 CAAGCCCGAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
31 2 0.05
32 38 0.86
33 4 0.09
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (32 bp):
AAAAAGCCCAAACCCGAGAAAGCCTGAACTCG
Found at i:491040 original size:17 final size:16
Alignment explanation
Indices: 490934--491054 Score: 75
Period size: 16 Copynumber: 7.6 Consensus size: 16
490924 AAATTACCCG
490934 AACCC-AAAATAGCCCA
1 AACCCGAAAA-AGCCCA
* * **
490950 AACCCGAGATAGCCTG
1 AACCCGAAAAAGCCCA
* * *
490966 AACTCGAGAAAGGCCA
1 AACCCGAAAAAGCCCA
** * * *
490982 AACTTGAGAAAGCTCG
1 AACCCGAAAAAGCCCA
*
490998 AACTCGAAAAAGCCCA
1 AACCCGAAAAAGCCCA
491014 AACCCGAAAAAGCCCA
1 AACCCGAAAAAGCCCA
* * *
491030 AGCCCGAAAAAACCCG
1 AACCCGAAAAAGCCCA
491046 AACCC-AAAA
1 AACCCGAAAA
491055 GACCTCGAAC
Statistics
Matches: 82, Mismatches: 22, Indels: 3
0.77 0.21 0.03
Matches are distributed among these distances:
15 4 0.05
16 76 0.93
17 2 0.02
ACGTcount: A:0.45, C:0.31, G:0.17, T:0.07
Consensus pattern (16 bp):
AACCCGAAAAAGCCCA
Found at i:491570 original size:16 final size:15
Alignment explanation
Indices: 491549--491578 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
491539 ATGTTACACT
491549 TAGAATAGCAATATAG
1 TAGAATAG-AATATAG
491565 TAGAATAGAATATA
1 TAGAATAGAATATA
491579 AAGTTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.27
Consensus pattern (15 bp):
TAGAATAGAATATAG
Found at i:492555 original size:16 final size:16
Alignment explanation
Indices: 492488--492561 Score: 94
Period size: 16 Copynumber: 4.6 Consensus size: 16
492478 AACCGACCCG
492488 AGCCTGAACCCGAATA
1 AGCCTGAACCCGAATA
* * *
492504 AGCTTAAACCCAAATA
1 AGCCTGAACCCGAATA
* *
492520 AGCTTGAACCCGAAAA
1 AGCCTGAACCCGAATA
492536 AGCCTGAACCCGAATA
1 AGCCTGAACCCGAATA
*
492552 AGCCAGAACC
1 AGCCTGAACC
492562 TGAAAAAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.42, C:0.30, G:0.16, T:0.12
Consensus pattern (16 bp):
AGCCTGAACCCGAATA
Found at i:492575 original size:48 final size:48
Alignment explanation
Indices: 492488--492586 Score: 112
Period size: 48 Copynumber: 2.1 Consensus size: 48
492478 AACCGACCCG
* ** *
492488 AGCCTGAACCCGAATAAGCTTAAACCCAAATAAGCTTGAACCCGAAAA
1 AGCCTGAACCCGAATAAGCTCAAACCCAAATAAAATTGAACCAGAAAA
* *
492536 AGCCTGAACCCGAATAAGC-CAGAACCTGAAA-AAAATTGAACTAGAAAA
1 AGCCTGAACCCGAATAAGCTCA-AACC-CAAATAAAATTGAACCAGAAAA
492584 AGC
1 AGC
492587 TCAAACTCGA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
47 1 0.02
48 39 0.91
49 3 0.07
ACGTcount: A:0.46, C:0.24, G:0.16, T:0.13
Consensus pattern (48 bp):
AGCCTGAACCCGAATAAGCTCAAACCCAAATAAAATTGAACCAGAAAA
Found at i:497334 original size:145 final size:146
Alignment explanation
Indices: 497175--497440 Score: 385
Period size: 145 Copynumber: 1.8 Consensus size: 146
497165 ATCATTTAAT
** *
497175 TCATATTAAATCAGTTTTCAAAAACTAATTCACTTTCAAGAGTTTTTGAA-TTTTTCCTTGAAAT
1 TCATATTAAATCAGTTTTCAAAAACTAATTCA-TTTCAAGAAATTTTGAATTTTTTCCTTAAAAT
*
497239 TTCTCTTTTTCT-GAAATACGAAGTTTTCTACT-TCGTAAATTTTTTCGGAGGGATTTTTTTATT
65 TTCTCTTTTTCTCGAAATACGAAGTTTTCTACTCT-ATAAATTTTTTCGGAGGGATTTTTTTATT
497302 TTTTGTTTATTATTTATA
129 TTTTGTTTATTATTTATA
* * * * *
497320 TCATATTAATTCAGTTTTCAAAAATTCATTCATTTCTATAAATTTTGAATTTTTTCCTTAAAATT
1 TCATATTAAATCAGTTTTCAAAAACTAATTCATTTCAAGAAATTTTGAATTTTTTCCTTAAAATT
* * *
497385 TTTCTTTTTTTCGAAATACGAAGTTTTCTACTCTATAAATTTTTTCGGGGGGATTT
66 TCTCTTTTTCTCGAAATACGAAGTTTTCTACTCTATAAATTTTTTCGGAGGGATTT
497441 CTCTTGTTTT
Statistics
Matches: 106, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
144 13 0.12
145 52 0.49
146 40 0.38
147 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (146 bp):
TCATATTAAATCAGTTTTCAAAAACTAATTCATTTCAAGAAATTTTGAATTTTTTCCTTAAAATT
TCTCTTTTTCTCGAAATACGAAGTTTTCTACTCTATAAATTTTTTCGGAGGGATTTTTTTATTTT
TTGTTTATTATTTATA
Found at i:498375 original size:13 final size:13
Alignment explanation
Indices: 498357--498400 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
498347 GCAAGCAAGC
498357 AAAAAAAGAGAGA
1 AAAAAAAGAGAGA
*
498370 AAAAAAAGAAAAAGA
1 AAAAAAAG--AGAGA
*
498385 AAAAAAAGCGAGA
1 AAAAAAAGAGAGA
498398 AAA
1 AAA
498401 TAGAAAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 14 0.54
15 12 0.46
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAGAGA
Found at i:500196 original size:155 final size:155
Alignment explanation
Indices: 499844--500183 Score: 396
Period size: 155 Copynumber: 2.2 Consensus size: 155
499834 CCGAGTACTT
* * * * ** * ***
499844 ATCTCTTAGGAGTATTTTCATAATTTTAT-AAAACTAATTTTTAGGTTGTCACCG-GATCTGCTT
1 ATCTCTTAGGGGTATTTTCATAATTTTTTAAAAAC-GAGTCCTAGGTTATCACCGAG-TCCATTT
* ** * * * *
499907 TTATGCCGAAGGTAGATATTTTGGATATGTTCATCTCATTTATTATCCTATTTAAATTCTTTAGG
64 TTATGCCAAAGGTAGATATTTAAGATAGGTTCATCTCATCTATTATCCTATTTAAATCCTTTACG
*
499972 GGTATCAAGTACTTTTACGTCAAAGGA
129 GATATCAAGTACTTTTACGTCAAAGGA
*
499999 ATCTCTTAGGGGTATTTTTATAATTTTTTAAAAACGAGTCCTAGGTTATCACCGAGTCCATTTTT
1 ATCTCTTAGGGGTATTTTCATAATTTTTTAAAAACGAGTCCTAGGTTATCACCGAGTCCATTTTT
* * * *
500064 ATGCTAAAGGTAGATATTTAAGATAGGTTCATCTCATCTATTATCTTTTTTAAGTCCTTTACGGA
66 ATGCCAAAGGTAGATATTTAAGATAGGTTCATCTCATCTATTATCCTATTTAAATCCTTTACGGA
* ** *
500129 TATCAGGTACTTTTACGTTGAAGGT
131 TATCAAGTACTTTTACGTCAAAGGA
*
500154 TTCTCTTAGGGGTATTTTCATAATTTTTTA
1 ATCTCTTAGGGGTATTTTCATAATTTTTTA
500184 GATATGAGTC
Statistics
Matches: 154, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
155 148 0.96
156 6 0.04
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.44
Consensus pattern (155 bp):
ATCTCTTAGGGGTATTTTCATAATTTTTTAAAAACGAGTCCTAGGTTATCACCGAGTCCATTTTT
ATGCCAAAGGTAGATATTTAAGATAGGTTCATCTCATCTATTATCCTATTTAAATCCTTTACGGA
TATCAAGTACTTTTACGTCAAAGGA
Found at i:500249 original size:155 final size:155
Alignment explanation
Indices: 499905--500251 Score: 383
Period size: 155 Copynumber: 2.2 Consensus size: 155
499895 CCGGATCTGC
* * * * * *
499905 TTTTATGCCGAAGGTAGATATTTTGGATATGTTCATCTCATTTATTATCCTATTTAAATTCTTTA
1 TTTTATGCCAAAAGTAGATAGTTAGGATATGTTCATCTCATCTATTATCCTATTTAAATCCTTTA
* * *
499970 GGGGTATCAAGTACTTTTACGTCAAAGGAATCTCTTAGGGGTATTTTTATAATTTTTTAAAAACG
66 CGGATATCAAGTACTTTTACGTCAAAGGAATCTCTTAGGGGTATTTTCATAATTTTTTAAAAACG
* * *
500035 AGTCCTAGGTTATCACCGAGTCCAT
131 AGTCCTAAGTTACCACAGAGTCCAT
* * * * * * * *
500060 TTTTATGCTAAAGGTAGATATTTAAGATAGGTTCATCTCATCTATTATCTTTTTTAAGTCCTTTA
1 TTTTATGCCAAAAGTAGATAGTTAGGATATGTTCATCTCATCTATTATCCTATTTAAATCCTTTA
* ** ** * * *
500125 CGGATATCAGGTACTTTTACGTTGAAGGTTTCTCTTAGGGGTATTTTCATAATTTTTTAGATATG
66 CGGATATCAAGTACTTTTACGTCAAAGGAATCTCTTAGGGGTATTTTCATAATTTTTTAAAAACG
* *
500190 AGTCCTAAGTTGCCACTAG-GTCCGCT
131 AGTCCTAAGTTACCAC-AGAGTCC-AT
*
500216 TTTT-TGCCAAAAGTGGATAGTTAGGATATGTTCATC
1 TTTTATGCCAAAAGTAGATAGTTAGGATATGTTCATC
500252 CTTTTTCAAA
Statistics
Matches: 158, Mismatches: 32, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
155 152 0.96
156 6 0.04
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (155 bp):
TTTTATGCCAAAAGTAGATAGTTAGGATATGTTCATCTCATCTATTATCCTATTTAAATCCTTTA
CGGATATCAAGTACTTTTACGTCAAAGGAATCTCTTAGGGGTATTTTCATAATTTTTTAAAAACG
AGTCCTAAGTTACCACAGAGTCCAT
Found at i:503446 original size:79 final size:77
Alignment explanation
Indices: 503265--503450 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 77
503255 ATATGTCCCG
* * * * *
503265 ATGAGAAATTTAATATTTTGGAGATAATAACGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTT
1 ATGAGAAA-TCAATA-TTTGGAAATAA-AACGGGATTAGAGTATCCCCTTGAAAATAACAGGGTT
**
503330 GGAGTATCCCCGGTT
63 GGAGTATCCCCAATT
* * * *
503345 GTGAAAAATCGATGATTGGGAAATAAAATCGGGATTAGAGTATCCCCTTGAAAATAACAGGGTTG
1 ATGAGAAATCAAT-ATTTGGAAATAAAA-CGGGATTAGAGTATCCCCTTGAAAATAACAGGGTTG
503410 GAGTATCCCCAATT
64 GAGTATCCCCAATT
503424 ATGAGAAATCAATATTCTGGAAATAAA
1 ATGAGAAATCAATATT-TGGAAATAAA
503451 GCCGGGGTTG
Statistics
Matches: 88, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
78 5 0.06
79 76 0.86
80 7 0.08
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (77 bp):
ATGAGAAATCAATATTTGGAAATAAAACGGGATTAGAGTATCCCCTTGAAAATAACAGGGTTGGA
GTATCCCCAATT
Found at i:503466 original size:79 final size:79
Alignment explanation
Indices: 503295--503471 Score: 223
Period size: 79 Copynumber: 2.2 Consensus size: 79
503285 GAGATAATAA
* * ** * *
503295 CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGA
1 CGGGGTTGAAGTATCCCCTTGAAAATAACAGGGTTGGAGTATCCCCAATTATGAAAAATCAATGA
*
503360 TTGGGAAATAAAAT
66 TTGGGAAATAAAAC
* *
503374 CGGGATT-AGAGTATCCCCTTGAAAATAACAGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-
1 CGGGGTTGA-AGTATCCCCTTGAAAATAACAGGGTTGGAGTATCCCCAATTATGAAAAATCAATG
* *
503437 ATTCTGGAAATAAAGC
65 ATT-GGGAAATAAAAC
503453 CGGGGTTGAAGTATCCCCT
1 CGGGGTTGAAGTATCCCCT
503472 CAGAGGTAAT
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
78 3 0.04
79 79 0.95
80 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (79 bp):
CGGGGTTGAAGTATCCCCTTGAAAATAACAGGGTTGGAGTATCCCCAATTATGAAAAATCAATGA
TTGGGAAATAAAAC
Found at i:503708 original size:51 final size:51
Alignment explanation
Indices: 503512--503731 Score: 210
Period size: 51 Copynumber: 4.3 Consensus size: 51
503502 GAAATAACGA
* * * * ** *
503512 GGTTGGAGTATCCTCGATTGTGA-AAGATTGGTGTTTTTAAAATAAAATCGG
1 GGTTAGAGTATCCCCGATTATGAGAA-ATTAGTGTTTTGGAAATAAAACCGG
* * *
503563 GGTTAGAGTATCCCCGATTA-AAGGAAATTTGGTGTTTTGAAAATAAAACCGG
1 GGTTAGAGTATCCCCGATTATGA-GAAA-TTAGTGTTTTGGAAATAAAACCGG
* * * **
503615 GGTTAGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAATTGG
1 GGTTAGAGTATCCCCGATTATGAGAAATTAGTGTTTTGGAAATAAAACCGG
* * * * *
503666 GGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGG
1 GGTTAGAGTATCCCCGATTATGAGAAATTAGTGTTTTGGAAATAAAACCGG
*
503717 GGTTGGAGTATCCCC
1 GGTTAGAGTATCCCC
503732 TCGGAGGTAA
Statistics
Matches: 141, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
50 1 0.01
51 93 0.66
52 46 0.33
53 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (51 bp):
GGTTAGAGTATCCCCGATTATGAGAAATTAGTGTTTTGGAAATAAAACCGG
Found at i:503907 original size:157 final size:158
Alignment explanation
Indices: 503615--503921 Score: 463
Period size: 157 Copynumber: 1.9 Consensus size: 158
503605 ATAAAACCGG
***
503615 GGTTAGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAATTGGGGTTGGAGTATCCC
1 GGTTAGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCAGGGTTGGAGTATCCC
* * * * **
503680 CGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAACGG
66 CGATTATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTGAAGTATCCCCTCGGAAATAACGG
503745 GGTTGGAGTATCCCCGATTAAATAACGA
131 GGTTGGAGTATCCCCGATTAAATAACGA
* * * *
503773 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGAAATAAAACCAGGGTTGGAGT-TCCC
1 GGTTAGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCAGGGTTGGAGTATCCC
* * *
503837 CGATTATGAAAAATTAATGTTTTAGAAATAAAACCGGGGTTGAAGTATCCCCTCGGAAATAATGG
66 CGATTATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTGAAGTATCCCCTCGGAAATAACGG
503902 GGTTGGAGTATCCCCGATTA
131 GGTTGGAGTATCCCCGATTA
503922 TGAAAATTTG
Statistics
Matches: 133, Mismatches: 16, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
157 80 0.60
158 53 0.40
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (158 bp):
GGTTAGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCAGGGTTGGAGTATCCC
CGATTATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTGAAGTATCCCCTCGGAAATAACGG
GGTTGGAGTATCCCCGATTAAATAACGA
Found at i:503955 original size:79 final size:79
Alignment explanation
Indices: 503823--504168 Score: 606
Period size: 79 Copynumber: 4.4 Consensus size: 79
503813 AATAAAACCA
* * *
503823 GGGTTGGAGT-TCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGGGGTTGAAGTATCC
1 GGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAACCGGGGTTGGAGTATCC
*
503887 CCTCGGAAATAATG
66 CCTCGGAAATAACG
* *
503901 GGGTTGGAGTATCCCCGATTATGAAAATTTGATGTTTTAGAGATAAAACTGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAACCGGGGTTGGAGTATCC
503966 CCTCGGAAATAACG
66 CCTCGGAAATAACG
503980 GGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAACCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAACCGGGGTTGGAGTATCC
504045 CCTCGGAAATAACG
66 CCTCGGAAATAACG
*
504059 GGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAATCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAACCGGGGTTGGAGTATCC
504124 CCTCGGAAATAACG
66 CCTCGGAAATAACG
*
504138 GGGTTGGAGTAT-CCCGATTGTGAAAAATTGA
1 GGGTTGGAGTATCCCCGATTATGAAAAATTGA
504169 GAAAATTAAA
Statistics
Matches: 257, Mismatches: 10, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
78 28 0.11
79 229 0.89
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAACCGGGGTTGGAGTATCC
CCTCGGAAATAACG
Found at i:505618 original size:35 final size:35
Alignment explanation
Indices: 505552--505706 Score: 264
Period size: 35 Copynumber: 4.5 Consensus size: 35
505542 TTCATTTTCG
*
505552 TCCATGCTTTCATTTTT-T-TT--ATGCCCATCAT
1 TCCATGCCTTCATTTTTATATTCCATGCCCATCAT
505583 TCCATGCCTTCATTTTTATATTCCATGCCCATCAT
1 TCCATGCCTTCATTTTTATATTCCATGCCCATCAT
*
505618 TCCATGCCTCCATTTTTATATTCCATGCCCATCAT
1 TCCATGCCTTCATTTTTATATTCCATGCCCATCAT
505653 TCCATGCCTTCATTTTTATATTCCATGCCCATCAT
1 TCCATGCCTTCATTTTTATATTCCATGCCCATCAT
505688 TCCATGCCTTCATTTTTAT
1 TCCATGCCTTCATTTTTAT
505707 TATTTTTTTT
Statistics
Matches: 117, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
31 16 0.14
32 1 0.01
33 2 0.02
35 98 0.84
ACGTcount: A:0.19, C:0.30, G:0.06, T:0.45
Consensus pattern (35 bp):
TCCATGCCTTCATTTTTATATTCCATGCCCATCAT
Found at i:505641 original size:21 final size:21
Alignment explanation
Indices: 505616--505681 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
505606 CATGCCCATC
505616 ATTCCATGCCTCCATTTTTAT
1 ATTCCATGCCTCCATTTTTAT
*
505637 ATTCCATG-C-CCA----T-C
1 ATTCCATGCCTCCATTTTTAT
*
505651 ATTCCATGCCTTCATTTTTAT
1 ATTCCATGCCTCCATTTTTAT
505672 ATTCCATGCC
1 ATTCCATGCC
505682 CATCATTCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
14 8 0.23
15 2 0.06
16 2 0.06
19 3 0.09
20 2 0.06
21 18 0.51
ACGTcount: A:0.20, C:0.32, G:0.06, T:0.42
Consensus pattern (21 bp):
ATTCCATGCCTCCATTTTTAT
Found at i:505733 original size:12 final size:13
Alignment explanation
Indices: 505713--505741 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
505703 TTATTATTTT
505713 TTTTGAATTTTAA
1 TTTTGAATTTTAA
505726 TTTT-AATTTTAA
1 TTTTGAATTTTAA
505738 TTTT
1 TTTT
505742 TGATTTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTGAATTTTAA
Found at i:509288 original size:21 final size:20
Alignment explanation
Indices: 509262--509311 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 20
509252 GATTGATACA
509262 TTGTATCGATACATTTACTGT
1 TTGTATC-ATACATTTACTGT
509283 TTG--T-AT-CATTTACTGT
1 TTGTATCATACATTTACTGT
509299 TTGTATCAATACA
1 TTGTATC-ATACA
509312 AATTATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
16 13 0.54
17 2 0.08
18 1 0.04
19 1 0.04
20 2 0.08
21 5 0.21
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (20 bp):
TTGTATCATACATTTACTGT
Found at i:509294 original size:16 final size:16
Alignment explanation
Indices: 509273--509306 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
509263 TGTATCGATA
509273 CATTTACTGTTTGTAT
1 CATTTACTGTTTGTAT
509289 CATTTACTGTTTGTAT
1 CATTTACTGTTTGTAT
509305 CA
1 CA
509307 ATACAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.15, G:0.12, T:0.53
Consensus pattern (16 bp):
CATTTACTGTTTGTAT
Found at i:511509 original size:418 final size:415
Alignment explanation
Indices: 510605--511438 Score: 1165
Period size: 426 Copynumber: 2.0 Consensus size: 415
510595 TAATTAAATT
* * * * * * * *
510605 ATTTAGATTTTTAGTTTAAAGACTAATTTATATTAAATGATATGAAATAGAAACTTCTCTAATAC
1 ATTTAGATTTTTAGTTTAAAGACTAATTTAAAATAGATAATATGAAACAGAAACTTTTTTAGTAC
* *
510670 TTGAACTGATAATTTGGATATAATATTAGAAGGGTTTACTTAACATGTATCTATAGACACTAGTA
66 TTGAACTGATAATTTGGATATAACATTAGAAGGGTCTACTTAACATGTATCTATAGACACTAGTA
* * *
510735 AAGATTATTTACTGAAAAATGTAATCAATGTCATTAGACACTGATTAAGATGATATATATTAAAA
131 AAGATTATTTAATGAAAAATGTAATCAATG--AGTAGACACTGATTAAGATGATATATATGAAAA
*
510800 TAAAAGTATAATTTATATGTTATTTTTTTTGAATTCTATAAAAGTAATATTATTAAATGAAAAAA
194 TAAAAGTATAATTTATATATTATTTTTTTTGAATTCTATAAAAGTAATATTATTAAATGAAAAAA
*
510865 AACTTTTTTAAAATGGTAAACCAAAGAATCCTTAAGCCTACAAGCATCTTTTCAGAGGACCCTTT
259 AACTTTTCTAAAATGGTAAACCAAAGAATCCTTAAGCCTACAAGCATCTTTTCAGAGGACCCTTT
*
510930 TTTAATTCCCATTTTTAAAAAATTATTTTTCATGTAATACATGGATTGTTATTAAGTATATTAGT
324 TTTAATTACCATTTTTAAAAAATTATTTTTCATGTAATAC---GATTG----T--GTATATTAGT
* *
510995 AGTGAATTTTTTTTAATTATATAATTTGGTTAAACT
380 AGTGAATTTTTTTTAATTATATAAGTTGGTTAAACA
* * *
511031 ATTTAGATTTTTAGTTTAAAGACTAATTTACATTAGATAATATGAAACAGAGACTTTTTTAGTAC
1 ATTTAGATTTTTAGTTTAAAGACTAATTTAAAATAGATAATATGAAACAGAAACTTTTTTAGTAC
* * **
511096 TTGGACTGATAATTTGGATATAACATTAGAAGGGTCTACTTAACATGTATCTATCGGTACTAGTA
66 TTGAACTGATAATTTGGATATAACATTAGAAGGGTCTACTTAACATGTATCTATAGACACTAGTA
* * *
511161 AAGATTATTTAATGAAAAATGT-ATTAA-G-GT-GATA-T-A-T-ATAT-ATATATATGAAAATA
131 AAGATTATTTAATGAAAAATGTAATCAATGAGTAGACACTGATTAAGATGATATATATGAAAATA
511217 AAAGTATAATTTATATATTA-TTTTTTTGAATTCTATAAAAGTAATATTATTAAATGAAAAAAAA
196 AAAGTATAATTTATATATTATTTTTTTTGAATTCTATAAAAGTAATATTATTAAATG---AAAAA
511281 AAACCTTTTCTAAAATGGTAAACCAAAGAATCCTTAAGCCTACAAGCATCTTTTCAGAGGACCCT
258 AAA-CTTTTCTAAAATGGTAAACCAAAGAATCCTTAAGCCTACAAGCATCTTTTCAGAGGACCCT
511346 TTTTTAATTACCATTTTTAAAAAATTATTTTTCATGTAATAC-A-TG-GTATATTAGTAGTGAA-
322 TTTTTAATTACCATTTTTAAAAAATTATTTTTCATGTAATACGATTGTGTATATTAGTAGTGAAT
* *
511407 TTTTTTTAATTCTATAAGTTGGTTAAAGA
387 TTTTTTTAATTATATAAGTTGGTTAAACA
511436 ATT
1 ATT
511439 GATAGTTGTC
Statistics
Matches: 377, Mismatches: 27, Indels: 29
0.87 0.06 0.07
Matches are distributed among these distances:
405 28 0.07
406 16 0.04
413 2 0.01
414 37 0.10
415 33 0.09
416 3 0.01
417 9 0.02
418 102 0.27
419 1 0.00
420 3 0.01
421 1 0.00
424 1 0.00
425 4 0.01
426 137 0.36
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (415 bp):
ATTTAGATTTTTAGTTTAAAGACTAATTTAAAATAGATAATATGAAACAGAAACTTTTTTAGTAC
TTGAACTGATAATTTGGATATAACATTAGAAGGGTCTACTTAACATGTATCTATAGACACTAGTA
AAGATTATTTAATGAAAAATGTAATCAATGAGTAGACACTGATTAAGATGATATATATGAAAATA
AAAGTATAATTTATATATTATTTTTTTTGAATTCTATAAAAGTAATATTATTAAATGAAAAAAAA
CTTTTCTAAAATGGTAAACCAAAGAATCCTTAAGCCTACAAGCATCTTTTCAGAGGACCCTTTTT
TAATTACCATTTTTAAAAAATTATTTTTCATGTAATACGATTGTGTATATTAGTAGTGAATTTTT
TTTAATTATATAAGTTGGTTAAACA
Found at i:513052 original size:18 final size:18
Alignment explanation
Indices: 513011--513052 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
513001 AATTTTTTTA
*
513011 AAATATTAAATAAATTATT
1 AAAT-TTAAATAAATAATT
513030 AAATTTAAATAAATAATT
1 AAATTTAAATAAATAATT
*
513048 TAATT
1 AAATT
513053 CTTAAATAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTTAAATAAATAATT
Found at i:513581 original size:2 final size:2
Alignment explanation
Indices: 513574--513613 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
513564 AGTGGACTTC
* * *
513574 AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
513614 CACTCTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:513705 original size:2 final size:2
Alignment explanation
Indices: 513698--513727 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
513688 TTTGAATTAC
513698 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
513728 GGAAATGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:520784 original size:16 final size:16
Alignment explanation
Indices: 520744--520813 Score: 72
Period size: 16 Copynumber: 4.4 Consensus size: 16
520734 AATGATCAGT
520744 ATTTAAAATGATTT-A
1 ATTTAAAATGATTTGA
* *
520759 AATAAAAATGATTTGA
1 ATTTAAAATGATTTGA
*
520775 ATTTAAAATGA-TTCA
1 ATTTAAAATGATTTGA
* *
520790 GATCTAAAATGATCTGA
1 -ATTTAAAATGATTTGA
520807 ATTTAAA
1 ATTTAAA
520814 TTAACTCAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
15 15 0.35
16 26 0.60
17 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (16 bp):
ATTTAAAATGATTTGA
Found at i:521038 original size:2 final size:2
Alignment explanation
Indices: 521031--521061 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
521021 AAAGTATAGA
521031 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
521062 TTGTGTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:521393 original size:17 final size:16
Alignment explanation
Indices: 521361--521400 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
521351 TAAATTTTGC
*
521361 TAAAATTATTATAAAT
1 TAAAATTATTAAAAAT
*
521377 TATAATTCATTAAAAAT
1 TAAAATT-ATTAAAAAT
521394 TAAAATT
1 TAAAATT
521401 TTCTTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAATTATTAAAAAT
Found at i:522866 original size:20 final size:20
Alignment explanation
Indices: 522798--522869 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
522788 ACTTTAACAA
522798 GTTGACTTTGA-ATGTTGATGG
1 GTTGACTTTGATA-GTTGAT-G
* **
522819 GTTGACTTTGAT-GATGGACA
1 GTTGACTTTGATAG-TTGATG
*
522839 GTTCACTTTGATAGTTGATG
1 GTTGACTTTGATAGTTGATG
522859 GTTGACTTTGA
1 GTTGACTTTGA
522870 CTTTGGCCAT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.21, C:0.08, G:0.29, T:0.42
Consensus pattern (20 bp):
GTTGACTTTGATAGTTGATG
Found at i:523213 original size:13 final size:14
Alignment explanation
Indices: 523187--523222 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
523177 TTTTAATTTT
523187 TTTTAAAAATATAA
1 TTTTAAAAATATAA
523201 TTTTAAAAA-ATAA
1 TTTTAAAAATATAA
523214 TTATTAAAA
1 TT-TTAAAA
523223 TAATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTTAAAAATATAA
Found at i:523243 original size:21 final size:22
Alignment explanation
Indices: 523217--523257 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
523207 AAAATAATTA
523217 TTAAAATAATTTTT-TTATTTT
1 TTAAAATAATTTTTATTATTTT
523238 TTAAAATAATTTTTATTATT
1 TTAAAATAATTTTTATTATT
523258 CAAAAAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTAAAATAATTTTTATTATTTT
Found at i:525383 original size:23 final size:24
Alignment explanation
Indices: 525326--525383 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
525316 ATATATAATT
*
525326 ATTAAAATTTTAATTTTGTCTTAC
1 ATTAATATTTTAATTTTGTCTTAC
* *
525350 ATTAGTA-TTTAATTTT-TTTTAC
1 ATTAATATTTTAATTTTGTCTTAC
525372 -TTATATATTTTA
1 ATTA-ATATTTTA
525384 GAAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 3 0.11
22 7 0.25
23 13 0.46
24 5 0.18
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.60
Consensus pattern (24 bp):
ATTAATATTTTAATTTTGTCTTAC
Found at i:525730 original size:2 final size:2
Alignment explanation
Indices: 525725--525752 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
525715 AAAAGAGATA
525725 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
525753 GATTTGCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:526220 original size:17 final size:19
Alignment explanation
Indices: 526181--526220 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
526171 TGATCATTAT
526181 TTAATAATTTTAATATCAA
1 TTAATAATTTTAATATCAA
*
526200 -TAAT-ATTTTATTAT-AA
1 TTAATAATTTTAATATCAA
526216 TTAAT
1 TTAAT
526221 TATGATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 2 0.11
17 13 0.68
18 4 0.21
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAATAATTTTAATATCAA
Found at i:526719 original size:19 final size:18
Alignment explanation
Indices: 526691--526740 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
526681 TTAAATATAA
526691 TAAAAATAT-ATATTTGAT
1 TAAAAATATAATATTT-AT
526709 TAAATAATATAATATTTAT
1 TAAA-AATATAATATTTAT
* *
526728 TATAAATCTAATA
1 TAAAAATATAATA
526741 AATTGATGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 12 0.43
19 10 0.36
20 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TAAAAATATAATATTTAT
Found at i:531424 original size:119 final size:119
Alignment explanation
Indices: 531290--531504 Score: 376
Period size: 119 Copynumber: 1.8 Consensus size: 119
531280 ATAATTGATT
531290 CTATTAATTAAAAGTATTTATTCCATAAACTAAAAACAATTAGTAACATAAAGTATATAGCAACA
1 CTATTAATTAAAAGTATTTATTCCATAAACTAAAAACAATTAGTAACATAAAGTATATAGCAACA
*
531355 TTATAAAGTTAAATTATTGATAATATATACAAAAAAATTAAATAATACATAGAA
66 TTATAAAGTTAAATTATTAATAATATATACAAAAAAATTAAATAATACATAGAA
* * * **
531409 CTATTAATTAAAAGTATTTGTTCCTTAAACTAAAAACAATTAGTAACATACAGTATATAGCAATT
1 CTATTAATTAAAAGTATTTATTCCATAAACTAAAAACAATTAGTAACATAAAGTATATAGCAACA
531474 TTATAAAGTTAAATTATTAATAATATATACA
66 TTATAAAGTTAAATTATTAATAATATATACA
531505 TATAATATGT
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
119 90 1.00
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (119 bp):
CTATTAATTAAAAGTATTTATTCCATAAACTAAAAACAATTAGTAACATAAAGTATATAGCAACA
TTATAAAGTTAAATTATTAATAATATATACAAAAAAATTAAATAATACATAGAA
Found at i:531584 original size:23 final size:22
Alignment explanation
Indices: 531558--531611 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
531548 TAAATAGGTG
531558 ATATAGTATATTATAATCATTTA
1 ATATAGTATATTATAAT-ATTTA
* *
531581 ATATGGTAGATTATAATATTTA
1 ATATAGTATATTATAATATTTA
*
531603 CTATAGTAT
1 ATATAGTAT
531612 TACATTATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (22 bp):
ATATAGTATATTATAATATTTA
Found at i:533107 original size:20 final size:20
Alignment explanation
Indices: 533093--533130 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
533083 AATACATTTT
533093 ACCATGTATCGATACAATCC
1 ACCATGTATCGATACAATCC
*
533113 ATCATGTATCGATACAAT
1 ACCATGTATCGATACAAT
533131 GTGAGTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.29
Consensus pattern (20 bp):
ACCATGTATCGATACAATCC
Found at i:533952 original size:16 final size:16
Alignment explanation
Indices: 533931--533961 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
533921 TGTATTACTC
*
533931 CCTCTTTTTGTAAAAT
1 CCTCTTTTTGGAAAAT
533947 CCTCTTTTTGGAAAA
1 CCTCTTTTTGGAAAA
533962 CAAATTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (16 bp):
CCTCTTTTTGGAAAAT
Found at i:542561 original size:17 final size:16
Alignment explanation
Indices: 542535--542570 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
542525 CATTAAAAAT
542535 TTTATTTTATAATTAA
1 TTTATTTTATAATTAA
*
542551 TTTATTATTATATTTAA
1 TTTATT-TTATAATTAA
542568 TTT
1 TTT
542571 GAAAAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATTTTATAATTAA
Found at i:543127 original size:17 final size:18
Alignment explanation
Indices: 543101--543161 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 18
543091 ACGGAGAGGA
*
543101 AAAGAAAAGAAAG-AGA-
1 AAAGGAAAGAAAGAAGAG
*
543117 AGAAGGGAAGAAAGAAGAG
1 A-AAGGAAAGAAAGAAGAG
*
543136 AAAGGAAAGAAAGACGA-
1 AAAGGAAAGAAAGAAGAG
543153 AAAGGAAAG
1 AAAGGAAAG
543162 GGAAAGTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
16 1 0.03
17 19 0.50
18 17 0.45
19 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.33, T:0.00
Consensus pattern (18 bp):
AAAGGAAAGAAAGAAGAG
Found at i:545567 original size:24 final size:23
Alignment explanation
Indices: 545523--545586 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
545513 TCTTAATTTG
* **
545523 TTCTTTTTTGTTTTTTATTTTTCT
1 TTCTTTTTT-TCTTTTCCTTTTCT
545547 TTCTTTTTTTCTTTTCCTTTTCT
1 TTCTTTTTTTCTTTTCCTTTTCT
* * *
545570 TCCCTTTCTTCTTTTCC
1 TTCTTTTTTTCTTTTCC
545587 CCTCGATCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 25 0.74
24 9 0.26
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (23 bp):
TTCTTTTTTTCTTTTCCTTTTCT
Found at i:546919 original size:2 final size:2
Alignment explanation
Indices: 546912--546938 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
546902 ATTTAATTTC
546912 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
546939 CACTTCGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:547835 original size:22 final size:21
Alignment explanation
Indices: 547798--547838 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
547788 AAGTTTTATT
547798 TAAATTTAATAATAAAATATA
1 TAAATTTAATAATAAAATATA
*
547819 TAAATATTAATATTAAAATA
1 TAAAT-TTAATAATAAAATA
547839 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATTTAATAATAAAATATA
Found at i:549324 original size:27 final size:27
Alignment explanation
Indices: 549278--549335 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
549268 GGAAAGATAT
* *
549278 ATTTTTAATTACTTGCATATTAATTCA
1 ATTTTTAATTACTTGCATATAAATTAA
* **
549305 ATTTTTAATTATTTTTATATAAATTAA
1 ATTTTTAATTACTTGCATATAAATTAA
549332 ATTT
1 ATTT
549336 GATAAATTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (27 bp):
ATTTTTAATTACTTGCATATAAATTAA
Found at i:549599 original size:20 final size:20
Alignment explanation
Indices: 549570--549607 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
549560 TAATTAAAAA
*
549570 AATTTAAATATTACATAAGT
1 AATTTAAATATTAAATAAGT
*
549590 AATTTTAATATTAAATAA
1 AATTTAAATATTAAATAA
549608 ATATTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
AATTTAAATATTAAATAAGT
Found at i:552369 original size:18 final size:18
Alignment explanation
Indices: 552336--552382 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
552326 TTTTAGTTAG
552336 ATTAAAGATTTT--TTTAC
1 ATTAAA-ATTTTAATTTAC
* *
552353 ATTTAAATTTTAATTTAT
1 ATTAAAATTTTAATTTAC
552371 ATTAAAATTTTA
1 ATTAAAATTTTA
552383 CGAATGCAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 5 0.20
17 5 0.20
18 15 0.60
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTAAAATTTTAATTTAC
Found at i:552619 original size:21 final size:22
Alignment explanation
Indices: 552593--552638 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
552583 CCTTTGATTC
*
552593 TTTTTTAATATTGA-AAAT-TA
1 TTTTTTTATATTGATAAATATA
*
552613 TTTTTTTATATTTATAAATATA
1 TTTTTTTATATTGATAAATATA
552635 TTTT
1 TTTT
552639 ATAAGTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.55
21 4 0.18
22 6 0.27
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTTTTATATTGATAAATATA
Found at i:552895 original size:15 final size:15
Alignment explanation
Indices: 552861--552901 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
552851 TACGTCACAT
552861 TTATTATAAT-AATG
1 TTATTATAATAAATG
*
552875 --AATATAATAAATG
1 TTATTATAATAAATG
552888 TTATTATAATAAAT
1 TTATTATAATAAAT
552902 TATAGTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
15 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (15 bp):
TTATTATAATAAATG
Found at i:554669 original size:29 final size:27
Alignment explanation
Indices: 554618--554677 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 27
554608 GCATTGAACA
* *
554618 TAAAAATTTTATTTTTTAAAATTATAT
1 TAAAAATTTTATATTTTAAAATTAAAT
554645 TAAAATATTTATATATTTTAAAATTAAAT
1 TAAAA-ATTT-TATATTTTAAAATTAAAT
554674 TAAA
1 TAAA
554678 TAAAAACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 5 0.17
28 4 0.14
29 20 0.69
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TAAAAATTTTATATTTTAAAATTAAAT
Found at i:555244 original size:19 final size:19
Alignment explanation
Indices: 555196--555264 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
555186 AATATGTAAT
*
555196 ATATATTATATATATTACAC
1 ATATA-TATATATATTACAA
*
555216 ATATACATATATATTACAA
1 ATATATATATATATTACAA
* * * *
555235 ATGTATATATACATT-TAT
1 ATATATATATATATTACAA
555253 ATATATATATAT
1 ATATATATATAT
555265 GTTTATATAT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
18 11 0.28
19 24 0.60
20 5 0.12
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.45
Consensus pattern (19 bp):
ATATATATATATATTACAA
Found at i:555350 original size:2 final size:2
Alignment explanation
Indices: 555194--555331 Score: 75
Period size: 2 Copynumber: 70.0 Consensus size: 2
555184 TCAATATGTA
* * * *
555194 AT AT AT AT -T AT AT AT AT -T AC AC AT AT AC AT AT AT AT -T AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
555233 AA AT GT AT AT AT AC AT TT AT AT AT AT AT AT AT GT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * ** * * * *
555275 AT TT AT GT CT GC AT AT GCT AT AT AT GT GT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
555318 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
555332 GTTTTAATTG
Statistics
Matches: 102, Mismatches: 30, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
1 3 0.03
2 98 0.96
3 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (2 bp):
AT
Found at i:555498 original size:21 final size:20
Alignment explanation
Indices: 555465--555515 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
555455 AATTAGTTGT
*
555465 ATAAAAAAATTTAAATATCAA
1 ATAAATAAATTT-AATATCAA
* *
555486 ATAAATAATTTTAATATTAA
1 ATAAATAAATTTAATATCAA
555506 ATATAATAAA
1 ATA-AATAAA
555516 AAAGATCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAATAAATTTAATATCAA
Found at i:555501 original size:20 final size:21
Alignment explanation
Indices: 555472--555514 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
555462 TGTATAAAAA
555472 AATTTAAATATCAAATA-AAT
1 AATTTAAATATCAAATATAAT
* *
555492 AATTTTAATATTAAATATAAT
1 AATTTAAATATCAAATATAAT
555513 AA
1 AA
555515 AAAAGATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTTAAATATCAAATATAAT
Found at i:557444 original size:16 final size:16
Alignment explanation
Indices: 557405--557454 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
557395 ATCAACTGAC
*
557405 TTATATATATATTATAT
1 TTATAT-TATAATATAT
557422 TAATATATTATAATATAT
1 T--TATATTATAATATAT
*
557440 TTATAATATAATATA
1 TTATATTATAATATA
557455 AAACTTGTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 13 0.45
17 1 0.03
18 10 0.34
19 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATATTATAATATAT
Found at i:561452 original size:16 final size:16
Alignment explanation
Indices: 561419--561457 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
561409 ACTTTTGATG
561419 TAAAATAAATAATAAA
1 TAAAATAAATAATAAA
*
561435 TATAATAAATAACT-AA
1 TAAAATAAATAA-TAAA
561451 TAAAATA
1 TAAAATA
561458 TGCATTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAAATAAATAATAAA
Found at i:564331 original size:6 final size:5
Alignment explanation
Indices: 564298--564336 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
564288 CATAAGGGAG
*
564298 AAGAA AATAA AAGAA AAGAA AAGAA AAGGAA AAGGAA AA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AA-GAA AA-GAA AA
564337 AGATAATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 20 0.65
6 11 0.35
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (5 bp):
AAGAA
Found at i:565024 original size:22 final size:22
Alignment explanation
Indices: 564994--565035 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
564984 ATTAAAAAAT
*
564994 TATTTTTAT-ATTAATATTTATA
1 TATTGTTATAATTAA-ATTTATA
565016 TATTGTTATAATTAAATTTA
1 TATTGTTATAATTAAATTTA
565036 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TATTGTTATAATTAAATTTATA
Found at i:565782 original size:2 final size:2
Alignment explanation
Indices: 565775--565808 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
565765 AAACTTAAGG
565775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
565809 CATTAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:566527 original size:18 final size:18
Alignment explanation
Indices: 566504--566544 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
566494 TGATTTTCAA
566504 TTATATAATATATAATTT
1 TTATATAATATATAATTT
* *
566522 TTATATATTATGTAATTT
1 TTATATAATATATAATTT
*
566540 GTATA
1 TTATA
566545 GTATAAAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TTATATAATATATAATTT
Found at i:571404 original size:20 final size:20
Alignment explanation
Indices: 571339--571407 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
571329 AACTAGTAAA
*
571339 ATAAAATTATAAATATTT-TT
1 ATAAAAATATAAAT-TTTATT
* *
571359 ATAAAATATGTAGAATTATATT
1 ATAAAA-ATATA-AATTTTATT
*
571381 ATAAAAATATAAATTTTATG
1 ATAAAAATATAAATTTTATT
571401 ATAAAAA
1 ATAAAAA
571408 AAATCTTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
20 20 0.50
21 9 0.22
22 11 0.28
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (20 bp):
ATAAAAATATAAATTTTATT
Found at i:572239 original size:4 final size:4
Alignment explanation
Indices: 572230--572256 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
572220 TAAACTTGTT
572230 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
572257 TGGTATAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:572905 original size:12 final size:13
Alignment explanation
Indices: 572888--572919 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
572878 ATTACAATCT
572888 TTAAAAT-AAAAA
1 TTAAAATAAAAAA
572900 TTAAAATAAAAAA
1 TTAAAATAAAAAA
572913 TTAAAAT
1 TTAAAAT
572920 TTTAAATGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TTAAAATAAAAAA
Found at i:572964 original size:2 final size:2
Alignment explanation
Indices: 572959--572989 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
572949 AAATAAAGTG
572959 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
572990 GTTAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:573317 original size:8 final size:8
Alignment explanation
Indices: 573304--573331 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
573294 TATTATTTAA
573304 AAAATATT
1 AAAATATT
573312 AAAATATT
1 AAAATATT
573320 AAAATATT
1 AAAATATT
573328 AAAA
1 AAAA
573332 AATATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
AAAATATT
Found at i:573362 original size:21 final size:21
Alignment explanation
Indices: 573333--573375 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
573323 ATATTAAAAA
* * *
573333 ATATTTTTTATATTTATATTT
1 ATATATTTTATAATTAAATTT
573354 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
573375 A
1 A
573376 AATAAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:573387 original size:25 final size:25
Alignment explanation
Indices: 573358--573418 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
573348 ATATTTATAT
573358 ATTTTATAATTAAATTTAAATAAAA
1 ATTTTATAATTAAATTTAAATAAAA
*
573383 ATTTTATAATT-AA-TTAAATAATA
1 ATTTTATAATTAAATTTAAATAAAA
573406 A-TTTA-AATTAAAT
1 ATTTTATAATTAAAT
573419 CAATTTAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.12
22 6 0.18
23 10 0.30
24 2 0.06
25 11 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTTTATAATTAAATTTAAATAAAA
Found at i:573403 original size:12 final size:12
Alignment explanation
Indices: 573370--573430 Score: 54
Period size: 12 Copynumber: 4.9 Consensus size: 12
573360 TTTATAATTA
*
573370 AATTTAAATAAA
1 AATTTAAATAAT
*
573382 AATTT-TATAATT
1 AATTTAAATAA-T
573394 AA-TTAAATAAT
1 AATTTAAATAAT
573405 AATTTAAATTAAAT
1 AATTTAAA-T-AAT
573419 CAATTTAAATAA
1 -AATTTAAATAA
573431 AAAAAATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
11 9 0.22
12 16 0.40
13 3 0.08
14 4 0.10
15 8 0.20
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
AATTTAAATAAT
Found at i:573925 original size:21 final size:21
Alignment explanation
Indices: 573901--573955 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
573891 CTAAAAAATT
573901 TTTAAAAAATTTAT-ATTAATA
1 TTTAAAAAATTTATAATTAA-A
* * *
573922 TTTATATATTTTATAATTAAA
1 TTTAAAAAATTTATAATTAAA
573943 TTTAAATAAATTT
1 TTTAAA-AAATTT
573956 TTTAATTATT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAAAAAATTTATAATTAAA
Found at i:574440 original size:18 final size:19
Alignment explanation
Indices: 574417--574459 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
574407 ATTATTTTAA
574417 ATTAAAATA-ATTTTAAAT
1 ATTAAAATACATTTTAAAT
* *
574435 ATTAAAATACATTTTTATT
1 ATTAAAATACATTTTAAAT
574454 ATTAAA
1 ATTAAA
574460 TAAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTAAAATACATTTTAAAT
Found at i:574479 original size:16 final size:16
Alignment explanation
Indices: 574458--574496 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
574448 TTTATTATTA
574458 AATAAATAA-TAAATAT
1 AATAAATAATTAAA-AT
574474 AATAAATAATTAAAAT
1 AATAAATAATTAAAAT
574490 AA-AAATA
1 AATAAATA
574497 TATATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.23
16 13 0.59
17 4 0.18
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AATAAATAATTAAAAT
Found at i:574523 original size:20 final size:20
Alignment explanation
Indices: 574489--574527 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
574479 ATAATTAAAA
574489 TAAAAATATATATTTTTAAC
1 TAAAAATATATATTTTTAAC
574509 TAAATAATATA-ATTTTTAA
1 TAAA-AATATATATTTTTAA
574528 TATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAAAATATATATTTTTAAC
Found at i:578395 original size:22 final size:22
Alignment explanation
Indices: 578359--578409 Score: 95
Period size: 21 Copynumber: 2.4 Consensus size: 22
578349 GGGGATGTCG
578359 ATTTTTTAGGGTTTTTA-TTTT
1 ATTTTTTAGGGTTTTTATTTTT
578380 ATTTTTTAGGGTTTTTATTTTT
1 ATTTTTTAGGGTTTTTATTTTT
578402 ATTTTTTA
1 ATTTTTTA
578410 TTCATGGTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.73
Consensus pattern (22 bp):
ATTTTTTAGGGTTTTTATTTTT
Found at i:578704 original size:13 final size:13
Alignment explanation
Indices: 578688--578720 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
578678 TTTTATATTT
578688 TTAAAAAATTAAA
1 TTAAAAAATTAAA
*
578701 TTAAAATATTAAA
1 TTAAAAAATTAAA
578714 TTAAAAA
1 TTAAAAA
578721 TAAATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TTAAAAAATTAAA
Found at i:578731 original size:17 final size:17
Alignment explanation
Indices: 578704--578736 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
578694 AATTAAATTA
578704 AAATATTAAATTAAAAAT
1 AAATATTAAA-TAAAAAT
578722 AAAT-TTAAATAAAAA
1 AAATATTAAATAAAAA
578737 ACTTTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATATTAAATAAAAAT
Found at i:578737 original size:17 final size:18
Alignment explanation
Indices: 578704--578737 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
578694 AATTAAATTA
*
578704 AAATATTAAATTAAAAAT
1 AAATATTAAATAAAAAAT
578722 AAAT-TTAAATAAAAAA
1 AAATATTAAATAAAAAA
578738 CTTTATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATATTAAATAAAAAAT
Found at i:581224 original size:24 final size:22
Alignment explanation
Indices: 581197--581243 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
581187 TTAAATTTAA
*
581197 ATTAATTTAAAATTTTATTTTACT
1 ATTAA-TTAAAATATT-TTTTACT
581221 ATTAATTAAAATATTTTTTACT
1 ATTAATTAAAATATTTTTTACT
581243 A
1 A
581244 ATATTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 9 0.41
24 5 0.23
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTAATTAAAATATTTTTTACT
Found at i:581294 original size:19 final size:19
Alignment explanation
Indices: 581270--581312 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
581260 TAAAATAAAA
* *
581270 ATAAAAATATTATTTTATT
1 ATAAAAATAATAATTTATT
581289 ATAAAAATAATAATTTATT
1 ATAAAAATAATAATTTATT
581308 -TAAAA
1 ATAAAA
581313 TTTTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAAAAATAATAATTTATT
Found at i:581479 original size:21 final size:21
Alignment explanation
Indices: 581441--581480 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
581431 AAATTATAAT
*
581441 TATTTTATATTAATATTTATA
1 TATTTTATACTAATATTTATA
581462 TATTTTATAACTAA-ATTTA
1 TATTTTAT-ACTAATATTTA
581481 ATTAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTATACTAATATTTATA
Found at i:587948 original size:41 final size:42
Alignment explanation
Indices: 587903--587981 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
587893 AAAAAAATTG
*
587903 AAAAACTTGA-TT-TTTTTTTACTTTTTTCAAAATTATTATCT
1 AAAAA-TTGATTTATTTTTTTACATTTTTCAAAATTATTATCT
*
587944 AAAAATTTATTTATTTTTTTACATTTTTCAAAATTATT
1 AAAAATTGATTTATTTTTTTACATTTTTCAAAATTATT
587982 TGGTAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 3 0.09
41 7 0.21
42 24 0.71
ACGTcount: A:0.34, C:0.08, G:0.01, T:0.57
Consensus pattern (42 bp):
AAAAATTGATTTATTTTTTTACATTTTTCAAAATTATTATCT
Found at i:589251 original size:20 final size:20
Alignment explanation
Indices: 589225--589299 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
589215 TTTTACCTAG
589225 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
589245 GTGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
589265 ATGTATCGATATATTCTGCA
1 ATGTATCGATACATTTTTCA
589285 ATGTATCGATACATT
1 ATGTATCGATACATT
589300 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:589290 original size:40 final size:39
Alignment explanation
Indices: 589225--589302 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
589215 TTTTACCTAG
* * *
589225 ATGTATCGATACATTTTTCAGTGTATCGATACATGTATGA
1 ATGTATCGATACATTCTGCAATGTATCGATACAT-TATGA
*
589265 ATGTATCGATATATTCTGCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTGCAATGTATCGATACATTATG
589303 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTGCAATGTATCGATACATTATGA
Found at i:592897 original size:15 final size:15
Alignment explanation
Indices: 592857--592902 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
592847 TTTTTTATAT
*
592857 AAAATTAAAAATCAA
1 AAAATTAAAAATTAA
592872 AAAATTAAAAATTAA
1 AAAATTAAAAATTAA
*
592887 AAAATAAAAAAATTAA
1 AAAAT-TAAAAATTAA
592903 TCAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 19 0.68
16 9 0.32
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAATTAAAAATTAA
Found at i:592908 original size:10 final size:9
Alignment explanation
Indices: 592863--592942 Score: 52
Period size: 8 Copynumber: 9.7 Consensus size: 9
592853 ATATAAAATT
592863 AAAA-ATCA
1 AAAATATCA
*
592871 AAAA-ATTA
1 AAAATATCA
*
592879 AAAAT-TAA
1 AAAATATCA
*
592887 AAAATA-AA
1 AAAATATCA
592895 AAAATTAATCA
1 AAAA-T-ATCA
592906 AAAATATCA
1 AAAATATCA
592915 AAAATAT--
1 AAAATATCA
592922 AAAATAT--
1 AAAATATCA
592929 AAAATAT-A
1 AAAATATCA
592937 AAAATA
1 AAAATA
592943 ATAATTAATT
Statistics
Matches: 63, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
7 14 0.22
8 30 0.48
9 12 0.19
10 2 0.03
11 5 0.08
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAATATCA
Found at i:592914 original size:9 final size:8
Alignment explanation
Indices: 592852--592942 Score: 68
Period size: 7 Copynumber: 11.2 Consensus size: 8
592842 TTAGTTTTTT
592852 TATATAAAA
1 TATA-AAAA
592861 T-TAAAAA
1 TATAAAAA
592868 TCA-AAAAA
1 T-ATAAAAA
592876 T-TAAAAA
1 TATAAAAA
592883 T-TAAAAAA
1 TAT-AAAAA
*
592891 TAAAAAAA
1 TATAAAAA
592899 TTAATCAAAAA
1 -T-AT-AAAAA
592910 TATCAAAAA
1 TAT-AAAAA
592919 TAT-AAAA
1 TATAAAAA
592926 TAT-AAAA
1 TATAAAAA
592933 TATAAAAA
1 TATAAAAA
592941 TA
1 TA
592943 ATAATTAATT
Statistics
Matches: 71, Mismatches: 2, Indels: 19
0.77 0.02 0.21
Matches are distributed among these distances:
7 26 0.37
8 25 0.35
9 13 0.18
10 2 0.03
11 5 0.07
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.25
Consensus pattern (8 bp):
TATAAAAA
Found at i:592939 original size:22 final size:23
Alignment explanation
Indices: 592853--592942 Score: 70
Period size: 22 Copynumber: 4.1 Consensus size: 23
592843 TAGTTTTTTT
592853 ATATAAAAT-TAAAA-ATCAAAA
1 ATATAAAATATAAAATATCAAAA
*
592874 A-ATTAAAA-ATTAAAAAAT-AAAA
1 ATA-TAAAATA-TAAAATATCAAAA
* *
592896 AAAT-TAATCA-AAAATATCAAAA
1 ATATAAAAT-ATAAAATATCAAAA
592918 ATATAAAATATAAAATAT-AAAA
1 ATATAAAATATAAAATATCAAAA
592940 ATA
1 ATA
592943 ATAATTAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
20 1 0.02
21 14 0.25
22 26 0.47
23 14 0.25
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.24
Consensus pattern (23 bp):
ATATAAAATATAAAATATCAAAA
Found at i:592946 original size:23 final size:23
Alignment explanation
Indices: 592853--592946 Score: 63
Period size: 23 Copynumber: 4.0 Consensus size: 23
592843 TAGTTTTTTT
592853 ATATAAAAT-TAAAAATCAA-AAA
1 ATATAAAATATAAAAAT-AATAAA
*
592875 AT-TAAAA-ATTAAAAAATAAAAAA
1 ATATAAAATA-T-AAAAATAATAAA
*
592898 ATTAATCAAAAATATCAAAA-ATATAAA
1 A-T-AT--AAAATATAAAAATA-ATAAA
592925 ATATAAAATATAAAAATAATAA
1 ATATAAAATATAAAAATAATAA
592947 TTAATTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 23
0.69 0.04 0.28
Matches are distributed among these distances:
21 5 0.09
22 5 0.09
23 25 0.44
24 2 0.04
25 2 0.04
26 3 0.05
27 9 0.16
28 5 0.09
29 1 0.02
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.24
Consensus pattern (23 bp):
ATATAAAATATAAAAATAATAAA
Found at i:593251 original size:88 final size:88
Alignment explanation
Indices: 593102--593264 Score: 281
Period size: 88 Copynumber: 1.9 Consensus size: 88
593092 AAAAAAAATC
* * * *
593102 CATGCATTTTATACTTTTATGTGAAGCTTAAGAAACATTTCATGCATTGCATTCATTTCATTGTA
1 CATGCATTTAATACTTTCATGTGAAACTTAAGAAACATTTCATGCATTACATTCATTTCATTGTA
593167 TTGCTTTCATGCCTTCATGCATA
66 TTGCTTTCATGCCTTCATGCATA
*
593190 CATGCATTTAATACTTTCATTTGAAACTTAAGAAACATTTCATGCATTACATTCATTTCATTGTA
1 CATGCATTTAATACTTTCATGTGAAACTTAAGAAACATTTCATGCATTACATTCATTTCATTGTA
593255 TTGCTTTCAT
66 TTGCTTTCAT
593265 ACATGCATTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (88 bp):
CATGCATTTAATACTTTCATGTGAAACTTAAGAAACATTTCATGCATTACATTCATTTCATTGTA
TTGCTTTCATGCCTTCATGCATA
Found at i:595053 original size:68 final size:69
Alignment explanation
Indices: 594937--595094 Score: 230
Period size: 68 Copynumber: 2.3 Consensus size: 69
594927 ATTCCTCTGA
*
594937 GGGGATACTCCAACCTCATTTTTAAACTCATCAAAATGTAAATATTA-TTTTTTCTAAATTATCA
1 GGGGATACTCCAACCCCATTTTTAAACTCATCAAAATGTAAATATTATTTTTTTC-AAATTATCA
*
595001 TTGTC
65 TTATC
* * * *
595006 -GGGATACTCCAACCCCATTTTTCAACTCATCAAAATTTAAGTCTTATTTTTTTCAAATTATCAT
1 GGGGATACTCCAACCCCATTTTTAAACTCATCAAAATGTAAATATTATTTTTTTCAAATTATCAT
595070 TATC
66 TATC
*
595074 GGGGATACTCCAACCCTATTT
1 GGGGATACTCCAACCCCATTT
595095 CTTTGAGTAG
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
68 54 0.68
69 26 0.32
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (69 bp):
GGGGATACTCCAACCCCATTTTTAAACTCATCAAAATGTAAATATTATTTTTTTCAAATTATCAT
TATC
Found at i:595989 original size:14 final size:14
Alignment explanation
Indices: 595970--595999 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
595960 GTCAAGCGCA
595970 CGTTACGACAGTAT
1 CGTTACGACAGTAT
595984 CGTTACGACAGTAT
1 CGTTACGACAGTAT
595998 CG
1 CG
596000 ATATAACAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (14 bp):
CGTTACGACAGTAT
Found at i:601673 original size:32 final size:32
Alignment explanation
Indices: 601636--601711 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
601626 CATTTCATAG
*
601636 TGTATCGATACATCTGGGCAAATTTGCCTGTA
1 TGTATCGATACATCTGGGCAAATTTGCCTGCA
601668 TGTATCGATACATCTGGGCAAATTTGCCTGCA
1 TGTATCGATACATCTGGGCAAATTTGCCTGCA
601700 TGTATCGATACA
1 TGTATCGATACA
601712 AAGATCAGTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATCTGGGCAAATTTGCCTGCA
Found at i:601738 original size:13 final size:13
Alignment explanation
Indices: 601720--601744 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
601710 CAAAGATCAG
601720 TGTATCGATACAA
1 TGTATCGATACAA
601733 TGTATCGATACA
1 TGTATCGATACA
601745 TTTGAGTAAT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:601807 original size:13 final size:13
Alignment explanation
Indices: 601789--601840 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
601779 AGCTTCGTAG
601789 CGATACATTGTAT
1 CGATACATTGTAT
601802 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
601821 CGATACATTGTAT
1 CGATACATTGTAT
601834 CGATACA
1 CGATACA
601841 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:601821 original size:19 final size:19
Alignment explanation
Indices: 601797--601861 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
601787 AGCGATACAT
601797 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
601816 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
601829 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
601848 TGTATCGATACAAA
1 TGTATCGATACAAA
601862 TTGTTGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 1 0.03
19 24 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:601830 original size:32 final size:32
Alignment explanation
Indices: 601789--601859 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
601779 AGCTTCGTAG
601789 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
601821 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
601853 CGATACA
1 CGATACA
601860 AATTGTTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:602695 original size:49 final size:49
Alignment explanation
Indices: 602624--603070 Score: 554
Period size: 49 Copynumber: 9.0 Consensus size: 49
602614 TTAGGAATGT
* * * *
602624 TAAAGATGCCAACATGCTGATTCAAGGCCAGTGATACTGGACTTAAAGA
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
* * * *
602673 TGAAGGTGCCAATATGGTGATTCAAGG-TAGCGACATTGGACTTAAAGATGA
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-GA
*
602724 TAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
* **
602773 CAAAGGTGCCTTTATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
* ** * * *
602822 CAAAGGTGCCTTTATGCTGATTCAAGGCTAGCGACATTGGAATTAAAGA
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
* * *
602871 CAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGG
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
* *
602920 TAAAGGTGCCAATATGCTGATTCAAGGTCAGCGATATTGGATTTAAAGA
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
* * * *
602969 TGAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGA
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
* * *
603018 TGAGAAAGGCGCCAATATGCTAATTCAAGGCCAGTGATATTGGACTTAGAAGA
1 T---AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGA
603071 AGATGCCACC
Statistics
Matches: 347, Mismatches: 43, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
48 12 0.03
49 250 0.72
50 2 0.01
51 28 0.08
52 51 0.15
53 4 0.01
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.24
Consensus pattern (49 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
Found at i:602861 original size:98 final size:98
Alignment explanation
Indices: 602531--603070 Score: 575
Period size: 98 Copynumber: 5.4 Consensus size: 98
602521 AGAAAAAGAA
* * * * * * * * *
602531 TGCCAATGTGCTGATTCACGGTCAGCGACATTAGATTTGAAGA-AGAA--TGCCAATGTGCTGAG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACA-AAGGTGCCAATATGCTGAT
* ** * * *
602593 ACAAGGCCAATGACATTGGGCTTAGGAATGTTAAAGA
65 TCAAGGCCAGCGACATTGGACTTA--AA-GATAAAGG
* * * ** *
602630 TGCCAACATGCTGATTCAAGGCCAGTGATACTGGACTTAAAGATGAAGGTGCCAATATGGTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTGCCAATATGCTGATT
*
602695 CAAGG-TAGCGACATTGGACTTAAAGATGATAAAGG
66 CAAGGCCAGCGACATTGGACTT-AA-A-GATAAAGG
* **
602730 CGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTGCCTTTATGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTGCCAATATGCTGATT
* *
602795 CAAGGCCAGCGATATTGGACTTAAAGACAAAGG
66 CAAGGCCAGCGACATTGGACTTAAAGATAAAGG
** * * *
602828 TGCCTTTATGCTGATTCAAGGCTAGCGACATTGGAATTAAAGACAAAGGTGCCAATATGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTGCCAATATGCTGATT
*
602893 CAAGGCCAGCGACATTGGACTTAAAGGTAAAGG
66 CAAGGCCAGCGACATTGGACTTAAAGATAAAGG
* * ** *
602926 TGCCAATATGCTGATTCAAGGTCAGCGATATTGGATTTAAAGATGAAGGTGCCAATGTGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTGCCAATATGCTGATT
*
602991 CAAGGCCAACGACATTGGACTTAAAGATGAGAAAGG
66 CAAGGCCAGCGACATTGGACTTAAAGAT---AAAGG
* * *
603027 CGCCAATATGCTAATTCAAGGCCAGTGATATTGGACTTAGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGA
603071 AGATGCCACC
Statistics
Matches: 371, Mismatches: 60, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
98 176 0.47
99 37 0.10
100 83 0.22
101 71 0.19
102 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (98 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTGCCAATATGCTGATT
CAAGGCCAGCGACATTGGACTTAAAGATAAAGG
Found at i:602925 original size:147 final size:150
Alignment explanation
Indices: 602625--603070 Score: 630
Period size: 147 Copynumber: 3.0 Consensus size: 150
602615 TAGGAATGTT
* * * * *
602625 AAAGATGCCAACATGCTGATTCAAGGCCAGTGATACTGGACTTAAAGATGAAGGTGCCAATATGG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATATGC
*
602690 TGATTCAAGG-TAGCGACATTGGACTTAAAGATGATAAAGGCGCCAATATGCTGATTCAAGGCCA
66 TGATTCAAGGCTAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCA
602754 GCGATATTGGACTTAAAGAC
131 GCGATATTGGACTTAAAGAC
** ** **
602774 AAAGGTGCCTTTATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTGCCTTTATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
602839 TGATTCAAGGCTAGCGACATTGGAATT-AA-A-GACAAAGGTGCCAATATGCTGATTCAAGGCCA
66 TGATTCAAGGCTAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCA
* **
602901 GCGACATTGGACTTAAAGGT
131 GCGATATTGGACTTAAAGAC
* * *
602921 AAAGGTGCCAATATGCTGATTCAAGGTCAGCGATATTGGATTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATATGC
* * * *
602986 TGATTCAAGGCCAACGACATTGGACTTAAAGATGAGAAAGGCGCCAATATGCTAATTCAAGGCCA
66 TGATTCAAGGCTAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCA
*
603051 GTGATATTGGACTTAGAAGA
131 GCGATATTGGACTTA-AAGA
603071 AGATGCCACC
Statistics
Matches: 257, Mismatches: 35, Indels: 8
0.86 0.12 0.03
Matches are distributed among these distances:
147 127 0.49
148 3 0.01
149 67 0.26
150 57 0.22
151 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.24
Consensus pattern (150 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCTAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCA
GCGATATTGGACTTAAAGAC
Found at i:603180 original size:29 final size:29
Alignment explanation
Indices: 603077--603181 Score: 99
Period size: 29 Copynumber: 3.6 Consensus size: 29
603067 AAGAAGATGC
603077 CACCAACTTGTGTAGGCTTTTGAAAGGGTTG
1 CACCAACTTGTG--GGCTTTTGAAAGGGTTG
* *
603108 CGCCAACTTGTGTGCTTTTG-AA-GGTTG
1 CACCAACTTGTGGGCTTTTGAAAGGGTTG
** * *
603135 CCACTGACTTGTAGGC-TTTGAAAGGGGTG
1 -CACCAACTTGTGGGCTTTTGAAAGGGTTG
603164 CTACCAACTTGTGGGCTT
1 C-ACCAACTTGTGGGCTT
603182 AAAAGGGTGC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
27 9 0.16
28 15 0.26
29 22 0.38
30 1 0.02
31 11 0.19
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (29 bp):
CACCAACTTGTGGGCTTTTGAAAGGGTTG
Found at i:603290 original size:36 final size:36
Alignment explanation
Indices: 603182--603340 Score: 152
Period size: 34 Copynumber: 4.6 Consensus size: 36
603172 TTGTGGGCTT
* * * *
603182 AAAAGGGTGCCACAGAATTGTGGAC-AT-AAAAGGA
1 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGGA
*
603216 AAAAGAGTGCCAC-GAAGTTGTGAGC-TT-AAAAGGA
1 AAAAGAGTGCCACAG-AGTTGTGGGCTTTAAAAAGGA
*
603250 AAAAGAGTGTCACAGAGTTGTGGGCTTTAAAAAGGA
1 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGGA
** **
603286 AAAAGAGCACCGTAGAGTTGTGGGCTTTAAAAA-GA
1 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGGA
*
603321 AGAAAG-GTGCCACGGAGTTG
1 A-AAAGAGTGCCACAGAGTTG
603341 CAGACTTTAA
Statistics
Matches: 103, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
33 1 0.01
34 48 0.47
35 15 0.15
36 39 0.38
ACGTcount: A:0.40, C:0.11, G:0.31, T:0.18
Consensus pattern (36 bp):
AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGGA
Found at i:603400 original size:30 final size:29
Alignment explanation
Indices: 603350--603813 Score: 479
Period size: 30 Copynumber: 16.1 Consensus size: 29
603340 GCAGACTTTA
* **
603350 AAAGGTTGCCGCTGGCTTGTGGGCTTTGG
1 AAAGGTTGCCACTGATTTGTGGGCTTTGG
603379 AAAATGG-TGCCACTGATTTGTGGGCTTT-G
1 -AAA-GGTTGCCACTGATTTGTGGGCTTTGG
*
603408 -AAGGTTGCCACTGATTTGTGGGCTTCGG
1 AAAGGTTGCCACTGATTTGTGGGCTTTGG
*
603436 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 -AAAGGTTGCCACTGATTTGTGGGCTTTGG
* *
603465 -AAGGTTGCCACTGATTTGTGGGCTTCGAA
1 AAAGGTTGCCACTGATTTGTGGGCTTTG-G
*
603494 AAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAGGTTGCCACTGATTTGTGGGCTTTGG
603522 -AAGGTTGCCACTGATTTGTGGGCTTT-G
1 AAAGGTTGCCACTGATTTGTGGGCTTTGG
* *
603549 -AAGGTTGCCACTGATTTGTGGGCTTCGAA
1 AAAGGTTGCCACTGATTTGTGGGCTTTG-G
* *
603578 AAATGG-TGCCATTGACTTGTGGGCTTTGG
1 AAA-GGTTGCCACTGATTTGTGGGCTTTGG
* * *
603607 AAAAGGGTGCCACTGACTTGTGGGCTTTTG
1 -AAAGGTTGCCACTGATTTGTGGGCTTTGG
*
603637 -AAGGTTGCCACTGACTTGTGGGCTTTGG
1 AAAGGTTGCCACTGATTTGTGGGCTTTGG
* * * *
603665 AAAAAGGGTGCCACTAACTTGTGGGCTTTTG
1 --AAAGGTTGCCACTGATTTGTGGGCTTTGG
*
603696 -AAGGTTGCCACTGACTTGTGGGCTTTGG
1 AAAGGTTGCCACTGATTTGTGGGCTTTGG
* * * *
603724 AAAAGGGTGCCACTAACTTGTGGGCTTTTG
1 -AAAGGTTGCCACTGATTTGTGGGCTTTGG
603754 -AAGGTTGCCACTGACTTT-TGGGCTTTGG
1 AAAGGTTGCCACTGA-TTTGTGGGCTTTGG
* * *
603782 AAAGGATGCCACTGACTTGTAGGCTTTGG
1 AAAGGTTGCCACTGATTTGTGGGCTTTGG
603811 AAA
1 AAA
603814 AGGTGAGGAA
Statistics
Matches: 373, Mismatches: 39, Indels: 45
0.82 0.09 0.10
Matches are distributed among these distances:
26 2 0.01
27 97 0.26
28 75 0.20
29 31 0.08
30 139 0.37
31 29 0.08
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.32
Consensus pattern (29 bp):
AAAGGTTGCCACTGATTTGTGGGCTTTGG
Found at i:603415 original size:57 final size:57
Alignment explanation
Indices: 603351--603809 Score: 622
Period size: 57 Copynumber: 8.0 Consensus size: 57
603341 CAGACTTTAA
* * * *
603351 AAGGTTGCCGCTGGCTTGTGGGCTTTGGAAAATGGTGCCACTGATTTGTGGGCTTTG
1 AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
603408 AAGGTTGCCACTGATTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGCTTTG
1 AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTG
* * * *
603465 AAGGTTGCCACTGATTTGTGGGCTTCGAAAAAGGGTGCCACTGATTTGTGGGCTTTG
1 AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTG
* * * *
603522 AAGGTTGCCACTGATTTGTGGGCTTT-G--AAGGTTGCCACTGATTTGTGGGCTTCG
1 AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTG
*
603576 AAAAATGG-TGCCATTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
1 ---AA-GGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGC-TTTG
*
603637 AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAAGGGTGCCACTAACTTGTGGGCTTTTG
1 AAGGTTGCCACTGACTTGTGGGCTTTGG-AAAAGGGTGCCACTGACTTGTGGGC-TTTG
*
603696 AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTAACTTGTGGGCTTTTG
1 AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGC-TTTG
* * *
603754 AAGGTTGCCACTGACTTTTGGGCTTTGG-AAAGGATGCCACTGACTTGTAGGCTTTG
1 AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTG
603810 GAAAAGGTGA
Statistics
Matches: 371, Mismatches: 21, Indels: 21
0.90 0.05 0.05
Matches are distributed among these distances:
54 25 0.07
56 4 0.01
57 177 0.48
58 84 0.23
59 57 0.15
60 21 0.06
61 3 0.01
ACGTcount: A:0.18, C:0.16, G:0.33, T:0.32
Consensus pattern (57 bp):
AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTG
Found at i:603816 original size:87 final size:85
Alignment explanation
Indices: 603350--603812 Score: 478
Period size: 87 Copynumber: 5.4 Consensus size: 85
603340 GCAGACTTTA
* * * *
603350 AAAGGTTGCCGCTGGCTTGTGGGCTTTGGAAAATGG-TGCCACTGATTTGTGGGCTTTG-AAGGT
1 AAAGGTTGCCACTGACTTGTGGGCTTTGG--AA-GGTTGCCACTGATTTGTGGGCTTCGAAAGGG
*
603413 TGCCACTGA-TTTGTGGGCTTCGG
63 TGCCACTGACTTT-TGGGCTTTGG
* *
603436 AAAAGGGTGCCACTGATTTGTGGGCTTT-GAAGGTTGCCACTGATTTGTGGGCTTCGAAAAAGGG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTGGAAGGTTGCCACTGATTTGTGGGCTTCG--AAAGGG
603500 TGCCACTGA-TTTGTGGGCTTT-G
63 TGCCACTGACTTT-TGGGCTTTGG
* *
603522 -AAGGTTGCCACTGATTTGTGGGCTTT-GAAGGTTGCCACTGATTTGTGGGCTTCGAAAAATGGT
1 AAAGGTTGCCACTGACTTGTGGGCTTTGGAAGGTTGCCACTGATTTGTGGGCTTCG--AAAGGGT
* *
603585 GCCATTGACTTGTGGGCTTTGG
64 GCCACTGACTTTTGGGCTTTGG
* * * *
603607 AAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAAGG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTGGAAGGTTGCCACTGATTTGTGGGC-TTCG--AAAGG
* * *
603672 GTGCCACTAACTTGTGGGCTTTTG
62 GTGCCACTGACTTTTGGGCTTTGG
* * * * *
603696 -AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTAACTTGTGGGCTTTTG-AAGGT
1 AAAGGTTGCCACTGACTTGTGGGCTTTGG--AAGGTTGCCACTGATTTGTGGGC-TTCGAAAGGG
603759 TGCCACTGACTTTTGGGCTTTGG
63 TGCCACTGACTTTTGGGCTTTGG
* *
603782 AAAGGATGCCACTGACTTGTAGGCTTTGGAA
1 AAAGGTTGCCACTGACTTGTGGGCTTTGGAA
603813 AAGGTGAGGA
Statistics
Matches: 333, Mismatches: 30, Indels: 28
0.85 0.08 0.07
Matches are distributed among these distances:
83 2 0.01
84 99 0.30
85 5 0.02
86 26 0.08
87 123 0.37
88 23 0.07
89 55 0.17
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.32
Consensus pattern (85 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTGGAAGGTTGCCACTGATTTGTGGGCTTCGAAAGGGTGC
CACTGACTTTTGGGCTTTGG
Found at i:605277 original size:6 final size:6
Alignment explanation
Indices: 605251--605311 Score: 61
Period size: 6 Copynumber: 9.7 Consensus size: 6
605241 ATCCGGACCC
* *
605251 TTTTTG TTGTTG TTGTTG TTTTTG TTTGTT- TTTTTG TTTTTTG TTTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTT-TTG TTTTTG -TTTTTG -TTTTTG
605301 TTTTTTG TTTT
1 -TTTTTG TTTT
605312 ATTTGTTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
5 2 0.04
6 26 0.52
7 22 0.44
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (6 bp):
TTTTTG
Found at i:605282 original size:9 final size:8
Alignment explanation
Indices: 605251--605323 Score: 71
Period size: 7 Copynumber: 8.9 Consensus size: 8
605241 ATCCGGACCC
605251 TTTTTGTTG
1 TTTTT-TTG
*
605260 TTGTTGTTG
1 TT-TTTTTG
605269 TTTTTGTTTG
1 -TTTT-TTTG
605279 TTTTTTTG
1 TTTTTTTG
605287 -TTTTTTG
1 TTTTTTTG
605294 -TTTTTTG
1 TTTTTTTG
605301 -TTTTTTG
1 TTTTTTTG
605308 TTTTATTTG
1 TTTT-TTTG
605317 TTTTTTT
1 TTTTTTT
605324 TTGTGGAGGA
Statistics
Matches: 57, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
7 21 0.37
8 10 0.18
9 19 0.33
10 7 0.12
ACGTcount: A:0.01, C:0.00, G:0.16, T:0.82
Consensus pattern (8 bp):
TTTTTTTG
Found at i:605323 original size:19 final size:19
Alignment explanation
Indices: 605270--605327 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
605260 TTGTTGTTGT
605270 TTTTGTTTGTTTTTTTGTT-
1 TTTTGTTTGTTTTTTT-TTG
605289 TTTTGTTT-TTTGTTTTTTG
1 TTTTGTTTGTTT-TTTTTTG
*
605308 TTTTATTTGTTTTTTTTTG
1 TTTTGTTTGTTTTTTTTTG
605327 T
1 T
605328 GGAGGACGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 5 0.14
19 27 0.77
20 3 0.09
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.84
Consensus pattern (19 bp):
TTTTGTTTGTTTTTTTTTG
Found at i:605325 original size:14 final size:13
Alignment explanation
Indices: 605269--605325 Score: 62
Period size: 15 Copynumber: 4.2 Consensus size: 13
605259 GTTGTTGTTG
*
605269 TTTTTG-TTTGTT
1 TTTTTGTTTTTTT
605281 TTTTTGTTTTTTGT
1 TTTTTGTTTTTT-T
605295 TTTTTGTTTTTTGTT
1 TTTTTG-TTTTT-TT
605310 TTATTTGTTTTTTT
1 TT-TTTGTTTTTTT
605324 TT
1 TT
605326 GTGGAGGACG
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
12 6 0.15
13 4 0.10
14 11 0.28
15 13 0.33
16 5 0.13
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (13 bp):
TTTTTGTTTTTTT
Found at i:619431 original size:52 final size:52
Alignment explanation
Indices: 619179--619411 Score: 378
Period size: 52 Copynumber: 4.5 Consensus size: 52
619169 CAAAATATGA
619179 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * * * *
619231 AAATTTGCCTGTATGTATCGATACACTATGA-AATGTATCGATACATCTCGGC
1 AAATTTGCCTGCATGTATCGATACA-TTTCATAGTGTATCGATACATCTGGGC
*
619283 AAATTTGCTTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
619335 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
619387 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
619412 AAGATCAGTG
Statistics
Matches: 164, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
51 3 0.02
52 158 0.96
53 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:619521 original size:19 final size:19
Alignment explanation
Indices: 619497--619548 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
619487 AACGATACAT
619497 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
619516 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
619535 TGTATCGATACAAA
1 TGTATCGATACAAA
619549 TCGTTGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:621719 original size:19 final size:19
Alignment explanation
Indices: 621695--621809 Score: 119
Period size: 19 Copynumber: 6.7 Consensus size: 19
621685 TATCGATACA
*
621695 TTGTATGGATACATAAGTG
1 TTGTATCGATACATAAGTG
621714 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
621733 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
621747 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
621765 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
621779 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
621797 TTGTATCGATACA
1 TTGTATCGATACA
621810 ATGTATCGCT
Statistics
Matches: 83, Mismatches: 1, Indels: 24
0.77 0.01 0.22
Matches are distributed among these distances:
13 22 0.27
15 4 0.05
17 4 0.05
19 53 0.64
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:621751 original size:32 final size:32
Alignment explanation
Indices: 621715--621817 Score: 197
Period size: 32 Copynumber: 3.2 Consensus size: 32
621705 ACATAAGTGT
*
621715 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
621747 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
621779 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
621811 TGTATCG
1 TGTATCG
621818 CTACGAAGCT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:621752 original size:13 final size:13
Alignment explanation
Indices: 621734--621790 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
621724 ACATAAGTGT
621734 TGTATCGATACAA
1 TGTATCGATACAA
621747 TGTATCGATACATAA
1 TGTATCGATAC--AA
621762 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
621779 TGTATCGATACA
1 TGTATCGATACA
621791 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:621862 original size:20 final size:20
Alignment explanation
Indices: 621837--621875 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
621827 TACTGCCAAG
621837 GAAATGTATCGATACATTAC
1 GAAATGTATCGATACATTAC
621857 GAAATGTATCGATACATTA
1 GAAATGTATCGATACATTA
621876 TATCGATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
GAAATGTATCGATACATTAC
Found at i:628695 original size:78 final size:79
Alignment explanation
Indices: 628404--628946 Score: 750
Period size: 79 Copynumber: 6.9 Consensus size: 79
628394 AAAATAAAAT
* * * * ** *
628404 CGGGGTTAGAGTATCCCCGATTATAAAAAAATTGATGCTTTAGAAGTAAGGGCCGGGGTTCGAGT
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAAATTGATGTTTTAGAAATAA-AACCGGGGTTGGAGT
* *
628469 TTCCCCAT-GAAAATAA
64 ATCCCC-TCGGAAATAA
* * * * * *
628485 CGGGGTTGAAGTATCCCTGATTGTGAGAAATTGATGTTTTAGAAATAAAACCGAGGTTAGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
* **
628550 CCACTCAAAAATAA
66 CCCCTCGGAAATAA
*
628564 CGGGGTTGGAGTATCCCCGATTATAAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
628629 CCCCTCGGAAATAA
66 CCCCTCGGAAATAA
* *
628643 CGGGGTTGGAGTAT-CCCGATTATGAAAAATTGAAGTTTTAGAAATAAAACCGGGATTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
**
628707 CCCCTTAGAAATAA
66 CCCCTCGGAAATAA
* * *
628721 CGGGGTTGAAGTATCCCCGATTATGAAAAATTGAAGTTTTAGAAATAAAATCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
628786 CCCCTCGGAAATAA
66 CCCCTCGGAAATAA
* * *
628800 CGGGGTTAGAGTAT-CCCGATTATGAAAAATTGAAGTTTTAGAAATAAAACTGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
628864 CCCCTTGGAAATAA
66 CCCCTCGGAAATAA
* *
628878 AGGGGTTGGGGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
628943 CCCC
66 CCCC
628947 GATTATGAGA
Statistics
Matches: 414, Mismatches: 45, Indels: 8
0.89 0.10 0.02
Matches are distributed among these distances:
78 145 0.35
79 229 0.55
80 20 0.05
81 20 0.05
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
CCCCTCGGAAATAA
Found at i:628721 original size:157 final size:156
Alignment explanation
Indices: 628404--628946 Score: 782
Period size: 157 Copynumber: 3.4 Consensus size: 156
628394 AAAATAAAAT
* * * ** *
628404 CGGGGTTAGAGTATCCCCGATTATAAAAAAATTGATGCTTTAGAAGTAAGGGCCGGGGTTCGAGT
1 CGGGGTTGGAGTATCCCCGATTAT-AAAAAATTGATGTTTTAGAAATAA-AACCGGGGTTGGAGT
* * * * * *
628469 TTCCCCAT-GAAAATAACGGGGTTGAAGTATCCCTGATTGTGAGAAATTGATGTTTTAGAAATAA
64 ATCCCC-TCGGAAATAACGGGGTTGGAGTATCCC-GATTATGAAAAATTGAAGTTTTAGAAATAA
* * * *
628533 AACCGAGGTTAGAGTATCCACTCAAAAATAA
127 AACCG-GGTTGGAGTATCCCCTTAGAAATAA
628564 CGGGGTTGGAGTATCCCCGATTATAAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATAAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
628629 CCCCTCGGAAATAACGGGGTTGGAGTATCCCGATTATGAAAAATTGAAGTTTTAGAAATAAAACC
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCGATTATGAAAAATTGAAGTTTTAGAAATAAAACC
628694 GGGATTGGAGTATCCCCTTAGAAATAA
131 GGG-TTGGAGTATCCCCTTAGAAATAA
* * * *
628721 CGGGGTTGAAGTATCCCCGATTATGAAAAATTGAAGTTTTAGAAATAAAATCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATAAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
628786 CCCCTCGGAAATAACGGGGTTAGAGTATCCCGATTATGAAAAATTGAAGTTTTAGAAATAAAACT
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCGATTATGAAAAATTGAAGTTTTAGAAATAAAAC-
* *
628851 GGGGTTGGAGTATCCCCTTGGAAATAA
130 CGGGTTGGAGTATCCCCTTAGAAATAA
* * *
628878 AGGGGTTGGGGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATAAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
628943 CCCC
66 CCCC
628947 GATTATGAGA
Statistics
Matches: 352, Mismatches: 28, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
156 2 0.01
157 262 0.74
158 43 0.12
159 22 0.06
160 23 0.07
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (156 bp):
CGGGGTTGGAGTATCCCCGATTATAAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
CCCCTCGGAAATAACGGGGTTGGAGTATCCCGATTATGAAAAATTGAAGTTTTAGAAATAAAACC
GGGTTGGAGTATCCCCTTAGAAATAA
Done.