Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020750.1 Corchorus olitorius cultivar O-4 contig20783, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1071 original size:39 final size:40
Alignment explanation
Indices: 1017--1097 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
1007 CTACCTAAGA
* *
1017 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGCATTTCAGTTATTATATATATTAC
* *
1056 ATTTAATTGATGTAAGCATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGCATTTCAGTTATTATATATATTAC
1096 AT
1 AT
1098 AGGAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (40 bp):
ATTTAATTAATGTAAGCATTTCAGTTATTATATATATTAC
Found at i:1263 original size:103 final size:103
Alignment explanation
Indices: 1156--1363 Score: 380
Period size: 103 Copynumber: 2.0 Consensus size: 103
1146 ATTTTAATAT
* * *
1156 AATAATATATTTAATTTAGTTGATAAATGAAATTATATATTAAACCTTAAAAGTTTTATTTGATA
1 AATAATATATTTAATTTAATTGATAAATGAAATTACATATTAAACCTTAAAAGTTTAATTTGATA
1221 AATACATGTTTACCCTTTAAATGAATACTAAACTTTTA
66 AATACATGTTTACCCTTTAAATGAATACTAAACTTTTA
*
1259 AATAATATATTTAATTTAATTGATAAATGAAATTACATATTGAACCTTAAAAGTTTAATTTGATA
1 AATAATATATTTAATTTAATTGATAAATGAAATTACATATTAAACCTTAAAAGTTTAATTTGATA
1324 AATACATGTTTACCCTTTAAATGAATACTAAACTTTTA
66 AATACATGTTTACCCTTTAAATGAATACTAAACTTTTA
1362 AA
1 AA
1364 ATTAAAAAGG
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (103 bp):
AATAATATATTTAATTTAATTGATAAATGAAATTACATATTAAACCTTAAAAGTTTAATTTGATA
AATACATGTTTACCCTTTAAATGAATACTAAACTTTTA
Found at i:10165 original size:78 final size:78
Alignment explanation
Indices: 10033--10190 Score: 253
Period size: 78 Copynumber: 2.0 Consensus size: 78
10023 AGAGGATACG
* * *
10033 ATTCATAACATCCTCTGGCAACTCGGAAATTCGATCTGTTGCACTCGGTGAAGCATAAGCAGGCT
1 ATTCATAACATCCTCGGGCAACTCGGAAATTCGATCTGTTGCACTCGGTAAAGCATAAGAAGGCT
10098 CTAATCTCATATT
66 CTAATCTCATATT
* * * *
10111 ATTCATAATATCCTCGGGCAATTCGTAAATTCGATCTGTTGCACTCGGTAAAGCATAAGAAGGGT
1 ATTCATAACATCCTCGGGCAACTCGGAAATTCGATCTGTTGCACTCGGTAAAGCATAAGAAGGCT
10176 CTAATCTCATATT
66 CTAATCTCATATT
10189 AT
1 AT
10191 CCATGGCTGT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (78 bp):
ATTCATAACATCCTCGGGCAACTCGGAAATTCGATCTGTTGCACTCGGTAAAGCATAAGAAGGCT
CTAATCTCATATT
Found at i:10205 original size:21 final size:20
Alignment explanation
Indices: 10181--10245 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
10171 AGGGTCTAAT
*
10181 CTCATATTATCCATGGCTGTG
1 CTCATATTA-CCATGGCTGCG
*
10202 CTCATATTACCCATGTCTGCG
1 CTCATATTA-CCATGGCTGCG
*
10223 CTAATATTACCTATGGCTGCG
1 CTCATATTACC-ATGGCTGCG
10244 CT
1 CT
10246 ATTGCACTCG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 2 0.05
21 36 0.95
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (20 bp):
CTCATATTACCATGGCTGCG
Found at i:10584 original size:16 final size:16
Alignment explanation
Indices: 10563--10602 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
10553 GAGCATTAAA
10563 AAAAAAAATAGTTCAT
1 AAAAAAAATAGTTCAT
*
10579 AAAAAAACTAGTTCAT
1 AAAAAAAATAGTTCAT
10595 AAAAAAAA
1 AAAAAAAA
10603 AAACTAGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (16 bp):
AAAAAAAATAGTTCAT
Found at i:10585 original size:20 final size:19
Alignment explanation
Indices: 10559--10612 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 19
10549 ATTAGAGCAT
*
10559 TAAAAAAAAAAATAGTTCA
1 TAAAAAAAAAACTAGTTCA
10578 T---AAAAAAACTAGTTCA
1 TAAAAAAAAAACTAGTTCA
10594 TAAAAAAAAAAACTAGTTC
1 T-AAAAAAAAAACTAGTTC
10613 TCCATTAGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 15 0.50
19 1 0.03
20 14 0.47
ACGTcount: A:0.63, C:0.09, G:0.06, T:0.22
Consensus pattern (19 bp):
TAAAAAAAAAACTAGTTCA
Found at i:21402 original size:24 final size:24
Alignment explanation
Indices: 21374--21421 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
21364 ATTTATTATC
21374 CAATGAGTTGATAATTCTGTTTTT
1 CAATGAGTTGATAATTCTGTTTTT
21398 CAATGAGTTGATAATTCTGTTTTT
1 CAATGAGTTGATAATTCTGTTTTT
21422 GGTCTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (24 bp):
CAATGAGTTGATAATTCTGTTTTT
Found at i:25790 original size:105 final size:106
Alignment explanation
Indices: 25530--25794 Score: 401
Period size: 107 Copynumber: 2.5 Consensus size: 106
25520 AAGTTTAGTC
* *
25530 TTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAAT
1 TTAAATTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAAT
*
25595 TAATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAA
66 TAATAA-TTATTATTATAGGGTTTTAGAAATAAAATACAAAA
* *
25637 CT-AATTCCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAA
1 TTAAATT-CACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAA
* *
25701 TTAATAA-TATTATTATAGGGTTTTAGAAATAAAATATATAA
65 TTAATAATTATTATTATAGGGTTTTAGAAATAAAATACAAAA
**
25742 TTAAATTCACTAAGTTTAG-CCCAAATTAAAATTAAAATTTTTATTTTAAGGGT
1 TTAAATTCACTAAGTTTAGCCCCAAATTAAAATT-TTATTTTTATTTTAAGGGT
25795 TAGAAAAATT
Statistics
Matches: 145, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
104 14 0.10
105 61 0.42
106 7 0.05
107 63 0.43
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.42
Consensus pattern (106 bp):
TTAAATTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAAT
TAATAATTATTATTATAGGGTTTTAGAAATAAAATACAAAA
Found at i:26315 original size:114 final size:114
Alignment explanation
Indices: 26139--26365 Score: 400
Period size: 114 Copynumber: 2.0 Consensus size: 114
26129 CAATTTTTTT
*
26139 CCGAATTAATTTATATTTAAATCGAAATAAGATTCAAATAATCGTAAAAACAAATCCTTAAATCC
1 CCGAATTAATTTATATTTAAATCGAAATAAGATTCAAATAATCGTAAAAACAAATCCATAAATCC
* *
26204 ATTGTGGCTGATATTTGGTTAGATTAATATAGATATTTCAATGAGTTTC
66 ATTGTGGCAGATATTTGGTTAAATTAATATAGATATTTCAATGAGTTTC
* * *
26253 CCGAATTAATTTCTATTTAAATCGAAATAAGATTCAGATGATCGTAAAAACAAATCCATAAATCC
1 CCGAATTAATTTATATTTAAATCGAAATAAGATTCAAATAATCGTAAAAACAAATCCATAAATCC
26318 ATTGTGGCAGATATTTGGTTAAATTAATATAGATATTTCAATGAGTTT
66 ATTGTGGCAGATATTTGGTTAAATTAATATAGATATTTCAATGAGTTT
26366 TGGCACCAAA
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 107 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (114 bp):
CCGAATTAATTTATATTTAAATCGAAATAAGATTCAAATAATCGTAAAAACAAATCCATAAATCC
ATTGTGGCAGATATTTGGTTAAATTAATATAGATATTTCAATGAGTTTC
Found at i:27405 original size:666 final size:664
Alignment explanation
Indices: 26256--28091 Score: 2759
Period size: 666 Copynumber: 2.8 Consensus size: 664
26246 GAGTTTCCCG
* * *
26256 AATTAATTTCTATTTAAATCGAAATAAGATTCAGATGATCGTAAAAACAAATCCATAAATCCATT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATT
* * * * *
26321 GTGGCAGATATTT-GGTTAAATTAATATAGATATTTCAATGAGTTTTGGCACCAAAAATCTTGCA
66 GTGGCTGAGATTTGGGAT-GATTAATATAGATATTTCAATGAGTTTTGGCACCAAAAATCATGCA
* * * *
26385 AAACTGAATCGGGGCATCGAAACGCGTTTTTAGGCAAAAA-C-----------CACGATTTCGGT
130 AAACTGAACCGGGGCCTCGAAACGCGTTTTTAGCCAAAAACCGTGATGTTATACACGATTTCGGC
** *
26438 AATTTTTTTGCAAAAATTGACTCGAAAGATTTTTCCTTAATTTTTAACCGCAATACTCGTAAAAA
195 AAAATTTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTTTAACCGCAATACTCGTAAAAA
*
26503 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGCTTCTAATATCATTTTTTCAATTT
260 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTT
* *
26568 TTTCCCGAATTAATTTTTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAA
325 TTTCCCGAATTAATTTCTATTTAAATCGAAAAAAGATTCAGATGATCGTAAAAACAAATCCTTAA
*
26633 ATCCATTATGG-TGGATATTTGGTTAGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAA
390 ATCCATTGTGGCT-GATATTTGGTTAGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAA
* *
26697 TCATGCAATACTGAGCCGGGGCACCGGAACGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACAC
454 TCATGCAATACTGAGCCGGGGCACCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACAC
* * *
26762 GATTTCGGC-AATAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCGATTTTTAACAGAAATA
519 GATTTCGGCAAAT-ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTGTGAACAGAAATA
* * *
26826 CTTGTAAAAAATATATAATTCAACTCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCA-T
583 CTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCATCTAATATCATT
26890 TTTTTCAATTCTTTCCAA
648 TTTTTCAATTCTTTCC-A
*
26908 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCGTTAAATCCATT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATT
* * * *
26973 GTGGCTGAGATTTGGGATGATTAATATAAATAATTCAATGAGTCTTGGCGCCAAAAATCATGCAA
66 GTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTTTTGGCACCAAAAATCATGCAA
* *
27038 AACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGTTAGTACACGATTTCGGC
131 AACTGAACCGGGGCCTCGAAACGCGTTTTTAGCCAAAAACCGTGATGTTA-TACACGATTTCGGC
*
27103 AAAATTTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAA
195 AAAATTTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTTTAACCGCAATACTCGTAAAAA
27168 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTT
260 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTT
*
27233 GTTTCCCGAATTAATTTCTATTTAAATCGAAATAAGATTCAGATGATCGTAAAAACAAATCCTTA
325 -TTTCCCGAATTAATTTCTATTTAAATCGAAAAAAGATTCAGATGATCGTAAAAACAAATCCTTA
*
27298 AATCCATTGCGGCTGATATTTGGTTAGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAA
389 AATCCATTGTGGCTGATATTTGGTTAGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAA
*
27363 TCATGCAATACTGAGCCGGGGCATCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACAC
454 TCATGCAATACTGAGCCGGGGCACCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACAC
* * *
27428 GATTTCGGCAAATATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTGTGAACCGCAATAC
519 GATTTCGGCAAATATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTGTGAACAGAAATAC
* * *
27493 TCGTAAAAAATATATAATTCAACGGCAGAAAGATTGAAGGGCTTTTCAGGCATCTAATATCATTT
584 TCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCATCTAATATCA-TT
* *
27558 TTTTTCAATTTTTTCCG
648 TTTTTCAATTCTTTCCA
* ** * * * * * *
27575 TATTAATTTCCGATTTAATCGAAACATGATTCAGACGCTCGTAAAATCAAATCCTTAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATT
* * *
27640 GTGGCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTTTTGGCTCCAAAAATTATGCAA
66 GTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTTTTGGCACCAAAAATCATGCAA
* * * *
27705 AACTAAACCGGGACCTCGGAACGCGTTTTTAGCCAAAAACCGTGATAGTTAAATTACACTATTTC
131 AACTGAACCGGGGCCTCGAAACGCGTTTTTAGCCAAAAACCGTGAT-GTT--A-TACACGATTTC
*
27770 GGCAAAATTTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTTTAACCGCAATACTCATAA
192 GGCAAAATTTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTTTAACCGCAATACTCGTAA
** * *
27835 AAAATATATAATTCAAAACCAAAAAGATTGAAGGGCTTTTTACACTTCTAATATCATTTTTTCAA
257 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAA
27900 TTTTTTCCCGAATTAATTTCTATTTAAATCGAAACAAAAGATTCAGATGATCGTAAAAACAAATC
322 TTTTTTCCCGAATTAATTTCTATTTAAATCG-AA-AAAAGATTCAGATGATCGTAAAAACAAATC
*
27965 CTGAAATCCATTGTGGCTGATATTTGGTTAGATTAATATAGATATTTCAATGAGTCTTGGCGCCA
385 CTTAAATCCATTGTGGCTGATATTTGGTTAGATTAATATAGATATTTCAATGAGTCTTGGCGCCA
* * * * * * *
28030 AAAATCATGTAAAACTGAGGCGGGACCCCGGAACACGTTTTTAGCAAAAAACTGTTGATGGT
450 AAAATCATGCAATACTGAGCCGGGGCACCGGAACACGTTTTTAGCCAAAAACCG-TGATGGT
28092 AACCTAAACG
Statistics
Matches: 1074, Mismatches: 85, Indels: 30
0.90 0.07 0.03
Matches are distributed among these distances:
652 147 0.14
653 4 0.00
665 136 0.13
666 296 0.28
667 159 0.15
668 19 0.02
669 28 0.03
670 140 0.13
671 138 0.13
672 7 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (664 bp):
AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATT
GTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTTTTGGCACCAAAAATCATGCAA
AACTGAACCGGGGCCTCGAAACGCGTTTTTAGCCAAAAACCGTGATGTTATACACGATTTCGGCA
AAATTTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTTTAACCGCAATACTCGTAAAAAA
TATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTTT
TTCCCGAATTAATTTCTATTTAAATCGAAAAAAGATTCAGATGATCGTAAAAACAAATCCTTAAA
TCCATTGTGGCTGATATTTGGTTAGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATC
ATGCAATACTGAGCCGGGGCACCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
TTTCGGCAAATATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTGTGAACAGAAATACTC
GTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCATCTAATATCATTTTT
TTCAATTCTTTCCA
Found at i:27597 original size:334 final size:333
Alignment explanation
Indices: 26426--28091 Score: 2495
Period size: 333 Copynumber: 5.0 Consensus size: 333
26416 AGGCAAAAAC
* * * *
26426 CACGATTTCGGTAATTTTTTTGCAAAAATTGACTCGAAAGATTTTTCCTTAATTTTTAACCGCAA
1 CACGATTTCGGCAAATATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTTTAACCGCAA
*
26491 TACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGCTTCTAATATCA
66 TACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCA
*
26556 TTTTTTCAATTTTTTCCCGAATTAATTTTTATTTAAATCGAAACAAGATTCAGATGATCGTAAAA
131 TTTTTTCAATTTTTTCCCGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAA
*
26621 ACAAATCCTTAAATCCATTATGG-TGGATATTTGGTTAGATTAATATAGATATTTCAATGAGTCT
196 ACAAATCCTTAAATCCATTGTGGCT-GATATTTGGTTAGATTAATATAGATATTTCAATGAGTCT
* * *
26685 TGGCGCCAAAAATCATGCAATACTGAGCCGGGGCACCGGAACGCGTTTTTAGCCAAAAATCGTGA
260 TGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGA
26750 TGGTTAGTA
325 TGGTTAGTA
** * *
26759 CACGATTTCGGC-AATAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCGATTTTTAACAGAA
1 CACGATTTCGGCAAAT-ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTTTAACCGCA
* *
26823 ATACTTGTAAAAAATATATAATTCAACTCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATC
65 ATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATC
* ** *
26888 ATTTTTTCAATTCTTTCCAAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAA
130 ATTTTTTCAATTTTTTCCCGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAA
* * * * *
26953 AACAAATCGTTAAATCCATTGTGGCTGAGATTTGG-GATGATTAATATAAATAATTCAATGAGTC
195 AACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTA-GATTAATATAGATATTTCAATGAGTC
*
27017 TTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTG
259 TTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTG
27082 AT-GTTAGTA
324 ATGGTTAGTA
*
27091 CACGATTTCGGCAAA-ATTTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCA
1 CACGATTTCGGCAAATA-TTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTTTAACCGCA
27155 ATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATC
65 ATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATC
*
27220 ATTTTTTCAATTTGTTTCCCGAATTAATTTCTATTTAAATCGAAATAAGATTCAGATGATCGTAA
130 ATTTTTTCAATTT-TTTCCCGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAA
*
27285 AAACAAATCCTTAAATCCATTGCGGCTGATATTTGGTTAGATTAATATAGATATTTCAATGAGTC
194 AAACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTAGATTAATATAGATATTTCAATGAGTC
* ** *
27350 TTGGCGCCAAAAATCATGCAATACTGAGCCGGGGCATCGGAACACGTTTTTAGCCAAAAACCGTG
259 TTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTG
27415 ATGGTTAGTA
324 ATGGTTAGTA
* *
27425 CACGATTTCGGCAAATATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTGTGAACCGCAA
1 CACGATTTCGGCAAATATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTTTAACCGCAA
* * * *
27490 TACTCGTAAAAAATATATAATTCAACGGCAGAAAGATTGAAGGGCTTTTCAGGCATCTAATATCA
66 TACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCA
* * * * *
27555 TTTTTTTTCAATTTTTT-CCGTATTAATTTCCGATTT-AATCGAAACATGATTCAGACGCTCGTA
131 --TTTTTTCAATTTTTTCCCGAATTAATTT-CTATTTAAATCGAAACAAGATTCAGATGATCGTA
* * * * *
27618 AAATCAAATCCTTAAATCCAATGTGGCTGAGATTTGG-GATGATGAATATAGATATTTCAATGAG
193 AAAACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTA-GATTAATATAGATATTTCAATGAG
* * * * * * *
27682 TTTTGGCTCCAAAAATTATGCAAAACTAAACCGGGACCTCGGAACGCGTTTTTAGCCAAAAACCG
257 TCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCG
* *
27747 TGATAGTTAAATTA
322 TGATGGTT--AGTA
*
27761 CACTATTTCGGCAAA-ATTTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTTTAACCGCA
1 CACGATTTCGGCAAATA-TTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTTTAACCGCA
* ** * *
27825 ATACTCATAAAAAATATATAATTCAAAACCAAAAAGATTGAAGGGCTTTTTACACTTCTAATATC
65 ATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATC
27890 ATTTTTTCAATTTTTTCCCGAATTAATTTCTATTTAAATCGAAACAAAAGATTCAGATGATCGTA
130 ATTTTTTCAATTTTTTCCCGAATTAATTTCTATTTAAATCGAAAC--AAGATTCAGATGATCGTA
*
27955 AAAACAAATCCTGAAATCCATTGTGGCTGATATTTGGTTAGATTAATATAGATATTTCAATGAGT
193 AAAACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTAGATTAATATAGATATTTCAATGAGT
* * * * * *
28020 CTTGGCGCCAAAAATCATGTAAAACTGAGGCGGGACCCCGGAACACGTTTTTAGCAAAAAACTGT
258 CTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCG-
28085 TGATGGT
322 TGATGGT
28092 AACCTAAACG
Statistics
Matches: 1199, Mismatches: 112, Indels: 39
0.89 0.08 0.03
Matches are distributed among these distances:
331 1 0.00
332 141 0.12
333 461 0.38
334 303 0.25
335 30 0.03
336 131 0.11
337 125 0.10
338 7 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (333 bp):
CACGATTTCGGCAAATATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTTTAACCGCAA
TACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCA
TTTTTTCAATTTTTTCCCGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAA
ACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTAGATTAATATAGATATTTCAATGAGTCTT
GGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
GGTTAGTA
Found at i:30096 original size:8 final size:8
Alignment explanation
Indices: 30083--30113 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
30073 CATTCTAATT
30083 TTACTATC
1 TTACTATC
30091 TTACTATC
1 TTACTATC
30099 TTACTATC
1 TTACTATC
30107 TTACTAT
1 TTACTAT
30114 TATATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (8 bp):
TTACTATC
Found at i:32460 original size:334 final size:334
Alignment explanation
Indices: 31739--32620 Score: 995
Period size: 334 Copynumber: 2.6 Consensus size: 334
31729 GGCCTCGGTT
* *
31739 CATTGGATTTAAGGATTTGGTTTTTACGAGCAT-TTGAATCATGTTTCGATTTAATTAGAAATTA
1 CATTGAATTTAAGGATTT-GTTTTTACGAGCATCTT-AATCTTGTTTCGATTTAATTAGAAATTA
* * *
31803 ATTTGAAAAAAAA-AAGAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATCTTTTTGGAGTTA
64 ATTGGAAAAAAAATAAGAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATATTTTTGGAGTTG
* *
31867 AATTATATATTTTTAATGAGTATTGTGGCTAAAAATTGAGAAAAAGA--TTTCGGGTCAATTTTT
129 AATTATATATTTTTTATGAGTATT-TAGCTAAAAATTGAGAAAAA-ATCTTTCGGGTCAATTTTT
* * * * * *
31930 GCAAAATTTCAGCCGAAATCG-TGTACCATCACAGTTTTTTGGCTAAAAACGCATTGCAGGGCCT
192 ACAAAATTTTAGCCGAAATCGTTCTACCATCACAGGTTTTCGGCTAAAAACGCATTCCAGGGCCT
* * * * *
31994 CGAGTCAGTTTTGCATGATTTTTTGCGCCAAGACTCTTTGAAATATAGGTATCTATATTCATCTA
257 CAACTAAATTTTGCATGATTTTTTGCGCCAAGACTCCTTG-AATATA-GTATCTATATTCATCTA
**
32059 ACAAAATATTTGCCA
320 ACAAAATATGAGCCA
** * * * ** * *
32074 CATTGAATTTAAACATTTGATTTTCCGAGTATCAAAATCTTGTCTT-GATTTAATCATAAATTAA
1 CATTGAATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGT-TTCGATTTAATTAGAAATTAA
* ** * ** * *
32138 TTGGAAATAAAAATAGGAAAATTGATATTAGAAGCGTGAAAAAAG-TTTTCAATTTTTTTGGCGT
65 TTGGAAA-AAAAATAAGAAAAACGATATTAGAAGCGTG--AGAAGCCCTTCAATATTTTTGGAGT
* * *
32202 TGCATTATATATTTTTTATGAGTATTTCGCTAGAAATTGAGAAAAAATCTTTCGGGTCAATTTTT
127 TGAATTATATATTTTTTATGAGTATTTAGCTAAAAATTGAGAAAAAATCTTTCGGGTCAATTTTT
* * *
32267 ACAAAATTTTAGCCGAAATCGTTTACTAACCATCAC-GGTTTTCGGCTAAAAGCGCGTTCCGGGG
192 ACAAAATTTTAGCCGAAATCG-TT-CT-ACCATCACAGGTTTTCGGCTAAAAACGCATTCCAGGG
*
32331 CCT-AACTAAATTTTGCATGATTTTTTAGTGCCAAGACTCCTTG-A-A-A-TATCTATATTCATC
254 CCTCAACTAAATTTTGCATGATTTTTT-GCGCCAAGACTCCTTGAATATAGTATCTATATTCATC
* *
32391 TAACCAAATCTGAGCCA
318 TAACAAAATATGAGCCA
32408 CATTGAATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTAGAAATTAAT
1 CATTGAATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTAGAAATTAAT
* * * * *
32473 TCGG-AAAAAAGTAAGAAAAACAATATTAGAAGCGTTAGAAGCCCTTCAAAATTTTT-GATGTCG
66 T-GGAAAAAAAATAAGAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATATTTTTGGA-GTTG
* * * *
32536 AATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCAGGTCAATTTTTA
129 AATTATATATTTTTTATGAGTA-TTTAGCTAAAAATTGAGAAAAAATCTTTCGGGTCAATTTTTA
*
32601 CAAAATTTTAGCAG-AATCGT
193 CAAAATTTTAGCCGAAATCGT
32621 GTTGTTTTGA
Statistics
Matches: 455, Mismatches: 74, Indels: 40
0.80 0.13 0.07
Matches are distributed among these distances:
331 6 0.01
332 39 0.09
333 75 0.16
334 123 0.27
335 25 0.05
336 40 0.09
337 74 0.16
338 5 0.01
339 20 0.04
340 40 0.09
341 8 0.02
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (334 bp):
CATTGAATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTAGAAATTAAT
TGGAAAAAAAATAAGAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATATTTTTGGAGTTGAA
TTATATATTTTTTATGAGTATTTAGCTAAAAATTGAGAAAAAATCTTTCGGGTCAATTTTTACAA
AATTTTAGCCGAAATCGTTCTACCATCACAGGTTTTCGGCTAAAAACGCATTCCAGGGCCTCAAC
TAAATTTTGCATGATTTTTTGCGCCAAGACTCCTTGAATATAGTATCTATATTCATCTAACAAAA
TATGAGCCA
Found at i:32878 original size:2 final size:2
Alignment explanation
Indices: 32871--32896 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
32861 ACTCCTTGAA
32871 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
32897 TCATGTAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33269 original size:324 final size:318
Alignment explanation
Indices: 32887--35347 Score: 1711
Period size: 324 Copynumber: 7.6 Consensus size: 318
32877 ATATATATAT
* * *
32887 ATATATATATTCAT-GTAACCAAATCTCAGCCACATTGGATTTAAAGAGTTGTTTTTACGAGCAT
1 ATATCTATATTCATCG-AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
32951 CTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-G-AAAAAAAACGATATTAGAAGCGTGAAA
65 CTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAACGATATTAGAAGCGTGAAA
*
33014 AACCCTTCAAT-TTGTTTGGTGTTGAATTATATATATTTTTATTGAGTATTGTGGCAAAAATTTG
130 AACCCTTCAATCTT-TTTGGCGTTGAATTATATAT-TTTTT-TTGAGTATTGTGGCAAAAATTTG
* *
33078 AGGAAACTTTTCAGGTTAATTTTTACAAAATTTTAGCCGAAATCGTGCACTAACCGTCACTGTTT
192 AGGAAACTTTTCAGGTT--TTTTT-CAAAATTTTAGCCGAAATCGTGTACT-ACCATCAC-GTTT
* ** * *
33143 TTGGTTAAAAACGCG-TTCTGGAACCCCGACTCAATTTTGCGTGATTTTTGGCGCAAAGTCTCCT
252 TTGGCTAAAAACGCGTTTC-GGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCAAAGT-TCCT
33207 TGAA
315 TGAA
* *
33211 ACATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATC
1 ATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* * *
33276 TGAATCTTGTTTCGATTTAGTTAGAAATTAATTCGGGAAAATGGGAAAACGATATTAGAAGCGTG
66 TGAATCTTGTTTCGATTTAATTAGAAATAAATTC-GGAAAA---AAAAACGATATTAGAAGCGTG
* ** * * * *
33341 AAAAGCCCGCCAATGTTTTTGGCGTTGAATTGTAT-TTTATTCTGAGTATTGTGGCAAAAAATTT
127 AAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTTTGAGTATTGTGGC-AAAAATTT
* * * * ** *
33405 AGAAGAAAAAAATTTTC-GG-----GTC--AGTTATTAGTTGAAATCATGTACTAACAACCATCA
191 -G-AG--GAAACTTTTCAGGTTTTTTTCAAAATT-TTAGCCGAAATCGTGTACT----ACCATCA
* * * **
33462 TGGTTTTTGGGCTAAAAATGCGTTTCGGGGCCCCAACTCAGTTTTGCATGATTTTTGGCAAAAAG
247 -CGTTTTT-GGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCAAAG
*
33527 ACTCCTTGAA
310 -TTCCTTGAA
* * * *
33537 ATATCTATATTCATCTAACTAAATCTCAGCTATATTGGATTTAAGGATTTGTTTTTACGAGCATC
1 ATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* *
33602 TGAATCTTGTTTCGATTTAATTAGAAACAAATTGGAGAAAAATTGAAAAACGATATTAGAAGCGT
66 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCG-G-AAAA---AAAAACGATATTAGAAGCGT
* * ** *
33667 G-AAAACCCTTCAATTTTTGTTGG-TTTGAATTATAT-TTTTTCACTGAG-AAT-TGGCACAAAA
126 GAAAAACCCTTCAATCTTT-TTGGCGTTGAATTATATATTTTT-TTTGAGTATTGTGGCA-AAAA
* *
33727 -TTGAGGAAAAAATTTTCGAGTCAGTTTTTACTTTTTACAAAATTTTAGTCGAAA-CAGTGTACG
188 TTTGAGG--AAACTTTTC-AG---G---TT--TTTTT-CAAAATTTTAGCCGAAATC-GTGTAC-
* * * * *
33790 TTA-CATCACGGTTTTTTGCTAAAAATGTGTTTC-GGGCCCCGGCTCACG-TTTGCAT-A-TATT
239 -TACCATCAC-GTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCA-GTTTTGCATGATTTTT
* ** *
33850 GGCGTAAAGATTTTTTAAA
301 GGCGCAAAG-TTCCTTGAA
* * * * ** * *
33869 ATATTTATATTCATCGAATCAAATC-CAAGCCATATTGAATTTAAAAATTTATTTTTACAAGCAT
1 ATATCTATATTCATCGAACCAAATCTC-AGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
* * *
33933 CTTAA--TTGTTTCAATTTAATTAGAAATTAATTCGGAAAAGAAAATGAAAAAACGATATTAGAA
65 CTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-G----G-AAA--AAAAAACGATATTAGAA
* * * * * * *
33996 TCATGAAAAGCCCATT-AATCTTTTTGCCATTAAATTATATA-TTTTTTTGAGTATTATGGCAAA
122 GCGTGAAAAACCC-TTCAATCTTTTTGGCGTTGAATTATATATTTTTTTTGAGTATTGTGGC-AA
* * ** * ** *
34059 AAATTT-AGAAAAATATTT----TTCGTGT-AAGTTTTTAGCCGAAACCGTGTACGT----T-AC
185 AAATTTGAGGAAACT-TTTCAGGTTTTTTTCAAAATTTTAGCCGAAATCGTGTAC-TACCATCAC
* * * * **
34113 GGTTTTGGGCTAAAAACGCATTTCGGGGCCCTGCCTCAGTTTTGCATGATTTTTGGCGCAAAAAC
248 -GTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGC-AAAGT
34178 TCCTTGAA
311 TCCTTGAA
* * * *
34186 ATATCTTTATTAATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATT
1 ATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
*
34251 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAATAAATAAAAAAACGATATTAGAAGC
66 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG------AA-AAAAAAACGATATTAGAAGC
* * * * *
34316 GTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTAAGTATTGTGGCAAAAAA
124 GTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTTTGAGTATTGTGGCAAAAAT
* * * ** * *
34381 TTCAGGAAA-----AAGATTTTTTGGGTC-AGTTTTTAGCAGTAATCGTGTACTA-CATCACGAT
189 TTGAGGAAACTTTTCAGGTTTTTT---TCAAAATTTTAGCCGAAATCGTGTACTACCATCACG-T
* ** * * * *
34439 TTTTGAACTAAAAACGTATTTCAGGGCACCGGCTCAGTTTTGCATGATTTTTGGAAG-AAAGATT
250 TTTTG-GCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGG-CGCAAAG-TT
34503 CCTTGAA
312 CCTTGAA
* * * *
34510 ATATCTATATTCATCTAACAAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGTATC
1 ATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* * * *
34575 TGAATCTTGTTTCCATTCAATTAAAAATAAATTCGGAATAAAATGGAAAAACGATATTAGACGCG
66 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG---AAAA---AAAAACGATATTAGAAGCG
** * * *
34640 TGAAAAACTTTTCAATTTTTTTTGCGTTGAATTATATATTTGTTTT-AGTATTGTGGC-AAAATA
125 TGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTTTGAGTATTGTGGCAAAAAT-
* ** *
34703 TTGAGGAAAAACTTTTCGGGTCAGTTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCGTCAC
189 TTGAGG--AAACTTTTCAGGT---TTTTTTCAAAATTTTAGCCGAAATCGTGTACT-ACCATCAC
* * * * * * *
34768 AGTTTTTTTGCTAAAAACGCGTTCCGGAGCCCCGCCTCAATTTTGCAT-ATTTTTTGTGCAATGA
248 -G-TTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCAA--A
34832 G-TCCTTGAA
309 GTTCCTTGAA
* * * *
34841 ATATCTATATTCATCGAACCAAATCTCAGGCACATTGGATATAAGAATTT-TTTTTACAAGCATC
1 ATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* * * *
34905 TGAATCTTATTTCGATTTAATTAGAAATAAATTTGGAAAAAAATGGAAAAACGATTTTGGTAA-C
66 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG---AAAA---AAAAACGATATTAG-AAGC
* * * * * * *
34969 TTGAAAAACCCGTCAATCTTTTCGGTGTTGAATTA-ATTATTTTTTCTGAGTATTATGGAAAAAA
124 GTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATA-TATTTTTTTTGAGTATTGTGGCAAAAA
* * * **
35033 ATTGAGAAAAACTTTTC-GG-----GTC-AGTTTTTAGCCGAAATCGTG---TACCATCACGATT
188 TTTGAG-GAAACTTTTCAGGTTTTTTTCAAAATTTTAGCCGAAATCGTGTACTACCATCACG-TT
* * * * **
35088 TCTGACTAAAAACGCGTTTCGGGACCCTGACTCAGTTTTGCATGATTTTTGGCAAAAAGATTCCT
251 TTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCAAAG-TTCCT
35153 TGAA
315 TGAA
* * * * *
35157 ATGTCTATATTCATCTAACTAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGTATC
1 ATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* * * * * * *
35222 TGAATATTGTTTCGATTTGATTAATTCGGGAAAAAAAAT-GG----AACAACGATGTTAGAAGTG
66 TGAATCTTGTTTCGA--T--TTAATT--AGAAATAAATTCGGAAAAAAAAACGATATTAGAAGCG
* * * **
35282 TG-AAAAGCCTGTCAATCTTTTTGGCGTTGAATAATATATTTTTTCTGAGTATCATGGCAAAGAA
125 TGAAAAACCCT-TCAATCTTTTTGGCGTTGAATTATATATTTTTTTTGAGTATTGTGGCAAA-AA
35346 TT
188 TT
35348 AAGGAAAAAC
Statistics
Matches: 1712, Mismatches: 284, Indels: 293
0.75 0.12 0.13
Matches are distributed among these distances:
311 8 0.00
312 56 0.03
313 4 0.00
314 25 0.01
315 56 0.03
316 70 0.04
317 96 0.06
318 63 0.04
319 72 0.04
320 43 0.03
321 19 0.01
322 46 0.03
323 78 0.05
324 237 0.14
325 24 0.01
326 171 0.10
327 55 0.03
328 12 0.01
329 8 0.00
330 203 0.12
331 83 0.05
332 123 0.07
333 40 0.02
334 55 0.03
335 28 0.02
336 15 0.01
337 2 0.00
338 2 0.00
339 14 0.01
340 3 0.00
341 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (318 bp):
ATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
TGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAACGATATTAGAAGCGTGAAAA
ACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTTTGAGTATTGTGGCAAAAATTTGAGGA
AACTTTTCAGGTTTTTTTCAAAATTTTAGCCGAAATCGTGTACTACCATCACGTTTTTGGCTAAA
AACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCAAAGTTCCTTGAA
Found at i:35553 original size:316 final size:312
Alignment explanation
Indices: 33957--35560 Score: 894
Period size: 316 Copynumber: 5.0 Consensus size: 312
33947 TTTAATTAGA
* * * * * *
33957 AATTAATTC-GGAAAAGAAAATGAAAAAACGATATTAG-AATCATGAAAAGCCCATTAATCTTTT
1 AATTAATTCGGGAAAA-AAAATGGAAAAACGATGTTAGTAA-CTTGAAAAACCCGTCAATCTTTT
* * * * * * * * *
34020 TGCCATTAAATT-ATATATTTTTT-TGAGTATTATGGCAAAAAATTTAGAAAAATATTTTTCGTG
64 CGGCGTTGAATTAAT-TATTTTTTCTGAGTATCATGGAAAAAAATTAAG-AAAA-ACTTTTCGGG
* * * * * * *** * ** *
34083 TAAGTTTTTAGCCGAAACCGTGTA-CGTTACGGTTT-TGGGCTAAAAACGCATTTCGGGGCCCTG
126 TCACTTTTTAGCCGAAATCGTGTACCATCACGATTTCT-GAAAAAAAACGCGTCCCGGGACCCTG
* * * * * * *
34146 CCTCAGTTTTGCATGATTTTTGGCGCAAAA-ACTCCTTGAAATATCTTTATTAATCGAACCAAAT
190 ACTCAGTTTTGCATGATTTTTAGC-AAAAAGACTCCTTGAAATATCTATATTCATCTAACTAAAT
* * * * * * * *
34210 CTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATT
254 CTCACCCACATTGGATTTAAGAATTTGTTATTACGAGTATCTGAATATTATTTCGA--T--TT
* ** * * *
34273 AGAAATTAATTC-GGAAAATAAATAAAAAAACGATATTAG-AAGCGTGAAAAGCCCGTCAATCTT
1 ---AATTAATTCGGGAAAAAAAATGGAAAAACGATGTTAGTAA-CTTGAAAAACCCGTCAATCTT
* * ** * * * *
34336 TTTGGCGTTGAATT-ATATATTTTTTCTAAGTATTGTGGCAAAAAATTCAGGAAAAAGATTTTTT
62 TTCGGCGTTGAATTAAT-TATTTTTTCTGAGTATCATGGAAAAAAATT-AAG-AAAA-ACTTTTC
* * * * * ** * *
34400 GGGTCAGTTTTTAGCAGTAATCGTGTACTACATCACGATTTTTGAACTAAAAACGTATTTCAGGG
123 GGGTCACTTTTTAGCCGAAATCGTGTAC--CATCACGATTTCTGAA-AAAAAACG-CGTCCCGGG
* * *
34465 -CACC-GGCTCAGTTTTGCATGATTTTT-GGAAGAAAGATTCCTTGAAATATCTATATTCATCTA
184 AC-CCTGACTCAGTTTTGCATGATTTTTAGCAA-AAAGACTCCTTGAAATATCTATATTCATCTA
* * * * * * *
34527 ACAAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCCATT
247 ACTAAATCTCACCCACATTGGATTTAAGAATTTGTTATTACGAGTATCTGAATATTATTTCGA-T
34592 CAATT
311 ---TT
* * * * * *** *
34597 AAAAATAAATTC-GG-AATAAAATGGAAAAACGATATTAG-ACGCGTGAAAAACTTTTCAATTTT
1 ---AATTAATTCGGGAAAAAAAATGGAAAAACGATGTTAGTA-ACTTGAAAAACCCGTCAATCTT
** ** * * *
34659 TTTTGCGTTGAATT-ATATATTTGTTT-T-AGTATTGTGGCAAAATATTGAGGAAAAACTTTTCG
62 TTCGGCGTTGAATTAAT-TATTT-TTTCTGAGTATCATGGAAAAAAATT-AAGAAAAACTTTTCG
* * * * **
34721 GGTCAGTTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCGTCACAGTTTTTTTG-CTAAAAA
124 GGTCA-------C---TTTTTAGCCGAAATCGTG---T-ACCATCAC-G-ATTTCTGAAAAAAAA
* * * * * *** * *
34785 CGCGTTCC-GGAGCCCCGCCTCAATTTTGCAT-ATTTTTTGTGCAATGAGTCCTTGAAATATCTA
173 CGCGTCCCGGGA-CCCTGACTCAGTTTTGCATGATTTTTAGCAAAAAGACTCCTTGAAATATCTA
* * ** * * * * *
34848 TATTCATCGAACCAAATCTCAGGCACATTGGATATAAGAATTT-TTTTTACAAGCATCTGAATCT
237 TATTCATCTAACTAAATCTCACCCACATTGGATTTAAGAATTTGTTATTACGAGTATCTGAATAT
34912 TATTTCGATTT
302 TATTTCGATTT
** * *
34923 AATTAGAAATAAATTTGG-AAAAAAATGGAAAAACGATTTTGGTAACTTGAAAAACCCGTCAATC
1 AATT---AAT---TCGGGAAAAAAAATGGAAAAACGATGTTAGTAACTTGAAAAACCCGTCAATC
* * *
34987 TTTTCGGTGTTGAATTAATTATTTTTTCTGAGTATTATGGAAAAAAATTGAGAAAAACTTTTCGG
60 TTTTCGGCGTTGAATTAATTATTTTTTCTGAGTATCATGGAAAAAAATTAAGAAAAACTTTTCGG
* ** **
35052 GTCAGTTTTTAGCCGAAATCGTGTACCATCACGATTTCTGACTAAAAACGCGTTTCGGGACCCTG
125 GTCACTTTTTAGCCGAAATCGTGTACCATCACGATTTCTGAAAAAAAACGCGTCCCGGGACCCTG
* * *
35117 ACTCAGTTTTGCATGATTTTTGGCAAAAAGATTCCTTGAAATGTCTATATTCATCTAACTAAATC
190 ACTCAGTTTTGCATGATTTTTAGCAAAAAGACTCCTTGAAATATCTATATTCATCTAACTAAATC
* * *
35182 TCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGTATCTGAATATTGTTTCGATTT
255 TCACCCACATTGGATTTAAGAATTTGTTATTACGAGTATCTGAATATTATTTCGATTT
* * * * * *
35240 GATTAATTCGGGAAAAAAAATGGAACAACGATGTTAG-AAGTGTGAAAAGCCTGTCAATCTTTTT
1 AATTAATTCGGGAAAAAAAATGGAAAAACGATGTTAGTAACT-TGAAAAACCCGTCAATCTTTTC
* *
35304 GGCGTTGAA-TAATATATTTTTTCTGAGTATCATGGCAAAGAATTAAGGAAAAACTTTTCGGGTC
65 GGCGTTGAATTAAT-TATTTTTTCTGAGTATCATGGAAAAAAATTAA-GAAAAACTTTTCGGGTC
* * * * * * * *
35368 ACTTTTTAGTCGAAATCGTTTATTAATCATCATGGTTTTTGAAAAAAAATGCGTCCCGGGGCCAC
128 ACTTTTTAGCCGAAATCG--T-GT-ACCATCACGATTTCTGAAAAAAAACGCGTCCCGGGACC-C
* * *** *
35433 -GGCTCTA-TTTTGCATTATTTTTAGCACTGAGACTCCTTGAAATAT-TTTATTCATCTAA-TCA
188 TGACTC-AGTTTTGCATGATTTTTAGCAAAAAGACTCCTTGAAATATCTATATTCATCTAACT-A
* * ** * *
35494 AATCTCACCCACATTGGATTT-AGTGATTTGTTATTATGTTTATCTTAATCTTATTTCGATTT
251 AATCTCACCCACATTGGATTTAAG-AATTTGTTATTACGAGTATCTGAATATTATTTCGATTT
35556 AATTA
1 AATTA
35561 GAAATTAATT
Statistics
Matches: 1048, Mismatches: 176, Indels: 125
0.78 0.13 0.09
Matches are distributed among these distances:
311 10 0.01
312 76 0.07
313 33 0.03
314 8 0.01
315 35 0.03
316 142 0.14
317 95 0.09
318 63 0.06
319 34 0.03
320 62 0.06
321 4 0.00
322 22 0.02
323 77 0.07
324 130 0.12
325 7 0.01
326 5 0.00
329 5 0.00
330 116 0.11
331 86 0.08
332 28 0.03
333 2 0.00
334 8 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (312 bp):
AATTAATTCGGGAAAAAAAATGGAAAAACGATGTTAGTAACTTGAAAAACCCGTCAATCTTTTCG
GCGTTGAATTAATTATTTTTTCTGAGTATCATGGAAAAAAATTAAGAAAAACTTTTCGGGTCACT
TTTTAGCCGAAATCGTGTACCATCACGATTTCTGAAAAAAAACGCGTCCCGGGACCCTGACTCAG
TTTTGCATGATTTTTAGCAAAAAGACTCCTTGAAATATCTATATTCATCTAACTAAATCTCACCC
ACATTGGATTTAAGAATTTGTTATTACGAGTATCTGAATATTATTTCGATTT
Found at i:37093 original size:31 final size:31
Alignment explanation
Indices: 37058--37119 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
37048 ACTGGTACTG
37058 AGTATATATCTATTGAATTATGAAGATGCTA
1 AGTATATATCTATTGAATTATGAAGATGCTA
37089 AGTATATATCTATTGAATTATGAAGATGCTA
1 AGTATATATCTATTGAATTATGAAGATGCTA
37120 TTGACTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (31 bp):
AGTATATATCTATTGAATTATGAAGATGCTA
Found at i:42866 original size:8 final size:8
Alignment explanation
Indices: 42848--42881 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
42838 AATACCATCT
*
42848 TATCTTGC
1 TATCTTAC
*
42856 TATCTAAC
1 TATCTTAC
42864 TATCTTAC
1 TATCTTAC
42872 TATCTTAC
1 TATCTTAC
42880 TA
1 TA
42882 CTATATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.26, C:0.24, G:0.03, T:0.47
Consensus pattern (8 bp):
TATCTTAC
Found at i:43912 original size:322 final size:323
Alignment explanation
Indices: 43497--44302 Score: 947
Period size: 322 Copynumber: 2.5 Consensus size: 323
43487 CAACTGGCTC
* * * *
43497 AATTTTGCATGATTTTTGATGTAAATACTCCTTGAAATATCTATATTCATCGAACAAAATTCCAG
1 AATTTTGCATGATTTTTGACGTAAAAACTCCTTGAAATATCTATATTCATCAAACCAAATT-CAG
* * * * * * *
43562 CCACGTTTGATATAAGTATTTCTTTTTACGAGCATCTAAATTTTGTTTCAATTTAATTA-AACAT
65 CCACATTAGATATAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAA-AT
* * *
43626 TAATTCGGAAAAAAATGGAAAAACAATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTT
129 TAATTCGGAAAAAAATGGAAAAACAATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGCGTT
* * * * *
43691 GAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAA-ACTATTCTGATAAGTTTT
194 AAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAACA-AAATCGGATAAGTTTT
* * *
43755 TAGCCG-AAATCGTGCACTAACCATCACGGTTTTTGGCTAAAAACACATTCCCGAAC-CCCGACT
258 TAGCAGAAAAACGTGCACTAACCATCACGGTTTTGGGCTAAAAACACATTCCCGAACTCCCGACT
43818 A
323 A
* *
43819 AATTTTGCATTATTTTTGGCGTAAAAACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAG
1 AATTTTGCATGATTTTTGACGTAAAAACTCCTTGAAATATCTATATTCATCAAACCAAAT-TCAG
* * *
43884 CCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATT
65 CCACATTAGATATAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATT
* *** *
43949 AATTCGGAAAAGAATTGGAAAAGTGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTT
130 AATTCGGAAAA-AAATGGAAAAACAATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGCGTT
* *
44014 AAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAACAAAATCGGGTCAGTTTTT
194 AAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAACAAAATCGGATAAGTTTTT
* * ** * * * ** * *
44079 AGCAGAAAAACGTGTACTAACCATCATGGTTTTGGGCTAAAAATGCGTTTCGGGGCTCCCGGCTC
259 AGCAGAAAAACGTGCACTAACCATCACGGTTTTGGGCTAAAAACACATTCCCGAACTCCCGACTA
* ** * * *
44144 AGTTTTGCATGATTTTTGACACAAAGACTCCTTGTAATATCTATATTCATCTAACCAATCTCAGG
1 AATTTTGCATGATTTTTGACGTAAAAACTCCTTGAAATATCTATATTCATCAAACCAA----A--
* * * *
44209 CTTTGAGCCACATTATATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAAAT
60 --TTCAGCCACATTAGATATAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATT
*
44274 AGAAA-TAGATTCGGAAAAAAATAGAAAAA
123 AGAAATTA-ATTCGGAAAAAAATGGAAAAA
44303 ATGATATTTA
Statistics
Matches: 408, Mismatches: 61, Indels: 21
0.83 0.12 0.04
Matches are distributed among these distances:
322 122 0.30
323 108 0.26
324 40 0.10
325 56 0.14
329 1 0.00
331 10 0.02
332 70 0.17
333 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (323 bp):
AATTTTGCATGATTTTTGACGTAAAAACTCCTTGAAATATCTATATTCATCAAACCAAATTCAGC
CACATTAGATATAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTA
ATTCGGAAAAAAATGGAAAAACAATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGCGTTAA
ATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAACAAAATCGGATAAGTTTTTAG
CAGAAAAACGTGCACTAACCATCACGGTTTTGGGCTAAAAACACATTCCCGAACTCCCGACTA
Done.