Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010350.1 Corchorus capsularis cultivar CVL-1 contig10371, 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: 176294
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:98 original size:2 final size:2
Alignment explanation
Indices: 61--86 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
51 TAGACTGCCA
61 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
87 GTTTGTATAT
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:10123 original size:19 final size:19
Alignment explanation
Indices: 10099--10164 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
10089 ATCACCAACA
10099 GGTGATCCTAATCAAATAG
1 GGTGATCCTAATCAAATAG
*
10118 GGTGAT-CTAAGATCACCAACA-
1 GGTGATCCT-A-ATCA--AATAG
*
10139 TGTGATCCTAATCAAATAG
1 GGTGATCCTAATCAAATAG
10158 GGTGATC
1 GGTGATC
10165 TGAAATCATC
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
18 5 0.14
19 13 0.35
20 8 0.22
21 6 0.16
22 5 0.14
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (19 bp):
GGTGATCCTAATCAAATAG
Found at i:10144 original size:40 final size:40
Alignment explanation
Indices: 10084--10165 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
10074 AGATCACCAC
10084 CTAAGATCACCAACAGGTGATCCTAATCAAATAGGGTGAT
1 CTAAGATCACCAACAGGTGATCCTAATCAAATAGGGTGAT
*
10124 CTAAGATCACCAACATGTGATCCTAATCAAATAGGGTGAT
1 CTAAGATCACCAACAGGTGATCCTAATCAAATAGGGTGAT
10164 CT
1 CT
10166 GAAATCATCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (40 bp):
CTAAGATCACCAACAGGTGATCCTAATCAAATAGGGTGAT
Found at i:14945 original size:18 final size:18
Alignment explanation
Indices: 14919--14953 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14909 CGAAGTCACA
* *
14919 CATCTTCATCGGCGTCAT
1 CATCATCATCGCCGTCAT
14937 CATCATCATCGCCGTCA
1 CATCATCATCGCCGTCA
14954 AATACTTCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.37, G:0.14, T:0.29
Consensus pattern (18 bp):
CATCATCATCGCCGTCAT
Found at i:15056 original size:18 final size:18
Alignment explanation
Indices: 15020--15057 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
15010 AGTTGTTGCT
*
15020 TCTTCCTCATCATCGTCC
1 TCTTCCTCATCATCCTCC
*
15038 TCTTCCTCATCTTCCTCC
1 TCTTCCTCATCATCCTCC
15056 TC
1 TC
15058 ACCACTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.47, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCCTCATCATCCTCC
Found at i:31625 original size:16 final size:17
Alignment explanation
Indices: 31595--31627 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31585 TTTTAATACG
*
31595 TAAATTAGAATAAGAAT
1 TAAATTAGAACAAGAAT
31612 TAAA-TAGAACAAGAAT
1 TAAATTAGAACAAGAAT
31628 GTCTTTGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.61, C:0.03, G:0.12, T:0.24
Consensus pattern (17 bp):
TAAATTAGAACAAGAAT
Found at i:34379 original size:29 final size:30
Alignment explanation
Indices: 34329--34392 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
34319 GTTGAGGGGG
*
34329 CAAAATGTCTCAAAATTGAAATTTATGGGA
1 CAAAATGTCTCAAAATTGAAATTTATAGGA
* *
34359 TAAAATGTC-CAATATTGAAATTTATAGGA
1 CAAAATGTCTCAAAATTGAAATTTATAGGA
34388 CAAAA
1 CAAAA
34393 CATCCAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (30 bp):
CAAAATGTCTCAAAATTGAAATTTATAGGA
Found at i:34398 original size:29 final size:29
Alignment explanation
Indices: 34343--34399 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
34333 ATGTCTCAAA
* * **
34343 ATTGAAATTTATGGGATAAAATGTCCAAT
1 ATTGAAATTTATAGGACAAAACATCCAAT
34372 ATTGAAATTTATAGGACAAAACATCCAA
1 ATTGAAATTTATAGGACAAAACATCCAA
34400 ACACTATAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.30
Consensus pattern (29 bp):
ATTGAAATTTATAGGACAAAACATCCAAT
Found at i:34663 original size:30 final size:30
Alignment explanation
Indices: 34607--34716 Score: 141
Period size: 32 Copynumber: 3.6 Consensus size: 30
34597 TTGAAAGGAT
*
34607 AACTTCATTACTACTTTTTTTCTTTGGCATCA
1 AACTTCATTGCTACTTTTTTT-TTTGGCA-CA
*
34639 AACTTCATTGCTAC-TTTTTTTTTGGCAGAAA
1 AACTTCATTGCTACTTTTTTTTTTGGC--ACA
*
34670 AACTTCATTGCTACTTTTTTTTTTTGCACA
1 AACTTCATTGCTACTTTTTTTTTTGGCACA
*
34700 AACTTTATTGCTACTTT
1 AACTTCATTGCTACTTT
34717 AGGAGTGTGG
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
30 24 0.34
31 21 0.30
32 25 0.36
ACGTcount: A:0.23, C:0.19, G:0.08, T:0.50
Consensus pattern (30 bp):
AACTTCATTGCTACTTTTTTTTTTGGCACA
Found at i:41947 original size:13 final size:13
Alignment explanation
Indices: 41929--41953 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41919 ACTTTTTGCA
41929 GAATGATGAATTT
1 GAATGATGAATTT
41942 GAATGATGAATT
1 GAATGATGAATT
41954 GACTGCTGAA
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:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (13 bp):
GAATGATGAATTT
Found at i:71338 original size:1 final size:1
Alignment explanation
Indices: 71332--71361 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
71322 CACTCAATTT
71332 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
71362 GCACAAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:72109 original size:2 final size:2
Alignment explanation
Indices: 72104--72140 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
72094 TTATTACTAT
72104 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
72141 GAACTTCGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:76518 original size:27 final size:27
Alignment explanation
Indices: 76488--76579 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 27
76478 CCAATTCTCA
76488 TTTCTTGCTTCTTAATCATTCTCTCTG
1 TTTCTTGCTTCTTAATCATTCTCTCTG
*
76515 TTTC-TGC-TCTTAGATTC-TTCTTCCCAATTCTCA
1 TTTCTTGCTTCTTA-A-TCATTC-T--C---TCT-G
76548 TTTCTTGCTTCTTAATCATTCTCTCTG
1 TTTCTTGCTTCTTAATCATTCTCTCTG
76575 TTTCT
1 TTTCT
76580 GCAGTGTTCT
Statistics
Matches: 51, Mismatches: 2, Indels: 24
0.66 0.03 0.31
Matches are distributed among these distances:
25 5 0.10
26 7 0.14
27 12 0.24
28 3 0.06
29 1 0.02
31 1 0.02
32 3 0.06
33 7 0.14
34 7 0.14
35 5 0.10
ACGTcount: A:0.12, C:0.27, G:0.07, T:0.54
Consensus pattern (27 bp):
TTTCTTGCTTCTTAATCATTCTCTCTG
Found at i:76556 original size:60 final size:60
Alignment explanation
Indices: 76463--76581 Score: 229
Period size: 60 Copynumber: 2.0 Consensus size: 60
76453 ATCCATTTTA
*
76463 CTTAGTTTCTTCTTCCCAATTCTCATTTCTTGCTTCTTAATCATTCTCTCTGTTTCTGCT
1 CTTAGATTCTTCTTCCCAATTCTCATTTCTTGCTTCTTAATCATTCTCTCTGTTTCTGCT
76523 CTTAGATTCTTCTTCCCAATTCTCATTTCTTGCTTCTTAATCATTCTCTCTGTTTCTGC
1 CTTAGATTCTTCTTCCCAATTCTCATTTCTTGCTTCTTAATCATTCTCTCTGTTTCTGC
76582 AGTGTTCTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.13, C:0.29, G:0.07, T:0.52
Consensus pattern (60 bp):
CTTAGATTCTTCTTCCCAATTCTCATTTCTTGCTTCTTAATCATTCTCTCTGTTTCTGCT
Found at i:81545 original size:18 final size:18
Alignment explanation
Indices: 81522--81558 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
81512 ACTTTTAGTT
81522 TGTATTTTGGTATTAATC
1 TGTATTTTGGTATTAATC
81540 TGTATTTTGGTATTAATC
1 TGTATTTTGGTATTAATC
81558 T
1 T
81559 CTAGTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.05, G:0.16, T:0.57
Consensus pattern (18 bp):
TGTATTTTGGTATTAATC
Found at i:96126 original size:334 final size:333
Alignment explanation
Indices: 95510--101766 Score: 8354
Period size: 333 Copynumber: 18.8 Consensus size: 333
95500 TTTTTCGTGT
* * * * * * * *
95510 CAAGACTCGTTGAAGTATTTGTATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGAATTTG
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGGATTAG
* * * ** * * * **
95575 TTTTTGCAAGCATCTGAATCTTGTGTCGATTTAATTAGAAAGTAATTCGGAAAAATAAATGGGAT
66 TTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGG-AAAA-AAATAAGA-
* **
95640 AAA-T-GATATTACAAGCGTGAAAATCCCTTCAATATTTTTGGTGTTGAATTATATATATTTTAT
128 AAATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTAT
* *
95703 GAGTATTGTGGCAAAAAATTGAGCAAAAATTTCTCGGGTCAATTTTTGCAAAATTTTAGCTGAAA
193 GAGTATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAA
* * * * *
95768 TCGTATACTAACCATCATAGTTTTTGGCCAAAAACGCGTTTCGGGATCCCAATTCAGTTT-TCAA
258 TCGTGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCGGGATCCCAACTCAGTTTGT--A
*
95832 TGATTTTTTGCGC
321 TGATTTTTTACGC
* * *
95845 CAAGACTCATTGAATTATTTGTATTCATCTAGCCAAATCCCAGTCACATTGTATTTAAGGATTAG
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGGATTAG
*
95910 TTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATTAGAAAA
66 TTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAAGAAAA
* * * **
95975 TTCAATATTAGACGTGTGAAAATCCCTTCAATATTTTTGGTGTTGAATTATATATATTTTATGAG
131 TTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATGAG
*
96040 TATTGTGGCAAAAAATTGAGCAAAAA-TTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCG
196 TATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCG
* *
96104 TGTACTAACCAATCACAGTTTTTGGCCAAAAATGCGTTCCGGGCTCCCAACTCAGTTTGTATGAA
261 TGTACTAACC-ATCACAGTTTTTGGCCAAAAATGCGTTCCGGGATCCCAACTCAGTTTGTATGAT
*
96169 TTTTTACAC
325 TTTTTACGC
* * *
96178 CAAGACTCATTG-ATATATCTGTATTCATTTAGCCAAATCTCAGTCACATTGGATTTATGGATTT
1 CAAGACTCATTGAAT-TATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGGATTA
* * * * *
96242 GTTTATACAAGCATCAGATACTGTTTTCGATTTAATTAAAAATTAATTT-GAAAAAAATATA-AA
65 GTTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATA-AGAA
* * * *
96305 AATTCGATATTAGATGTGTGAAAATCCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATG
129 AATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATG
* * *
96370 ATTATTGTGGCAAAAAATTAAGCAAAAATTTTTCGGGTCAATTTTTAC-AAATTTTAGCCGAAAT
194 AGTATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAT
* *
96434 CGTGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCGGGGTCCCAACTCTGTTTGTATGA
259 CGTGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCGGGATCCCAACTCAGTTTGTATGA
96499 TTTTTTACGC
324 TTTTTTACGC
* * * *
96509 CAAGACTCAATGAAATATCTGTATTCATTTAGCCAAATCTCAGTCACATTGGATTTAAGGATTTG
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGGATTAG
* * * *
96574 TTTCTACAAGCATCACAAACCGGTTTCGATTTAATTTGAAATTAATTTGGAAAAAAGTAAGAAAA
66 TTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAAGAAAA
* * * * *
96639 TTTGATATTAGACGCTTGAAAATCGCTTCAATATTTTTGGCGTTGAATTATATATATTTTATGAG
131 TTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATGAG
* * * *
96704 TATTGTGGCAAAAAATTTAGCAAAAATTTTTCGGGTCAATTTTTGCAAAAATTTAACTGAAATCG
196 TATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCG
*
96769 TGTACTAACCATCACAG-TTTTGGCCAAAAACT-CGTTCCGGGATCCCAATTCAGTTT-TCAGTG
261 TGTACTAACCATCACAGTTTTTGGCCAAAAA-TGCGTTCCGGGATCCCAACTCAGTTTGT-A-TG
*
96831 ATTTTTTGCGC
323 ATTTTTTACGC
* * * * * *
96842 CTAGACTCATTGAGTTATCTGTATTTATCTAGGCAAATCCCAGTCACATCGGATTTAAGGATTAG
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGGATTAG
*
96907 TTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAACAAAATAGGAAA
66 TTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAA-AAAATAAGAAA
* * * * * *
96972 ATTCGATATTAGACGCGTGAAAATGCCTTAAATATTTTTGGCATTGAATTACATATTTTTTATGT
130 ATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATGA
* *
97037 GTATTGTGGCAGAAAATTGAGCAAACATTTTTCGGGTCAATTTTTGCAAAA-TTTA-CCTGAAAT
195 GTATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCC-GAAAT
** *
97100 --T-TTGT-ACCATCATAGTTTTTGGCCAAAAATGCGTTCCGAGG-TCCCAACTCAGTTTGTATG
259 CGTGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCG-GGATCCCAACTCAGTTTGTATG
97160 ATTTTTTACGC
323 ATTTTTTACGC
** * * * * *
97171 CTGGACTCATTGAGTTATCTGTAGTCATCTAGACAAATCTCAGTCACATTAGATTTGAGGAATT-
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGG-ATTA
* * *
97235 GTTTCTACATGCATCAAAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAAGAAA
65 GTTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAAGAAA
* * **
97300 ATTCGATATTAGAAGCCTGAAAATCCCTTAAATATTTTTGGTGTTGAATTTATATATATTTTATG
130 ATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAA-TTATATATATTTTATG
* * *
97365 AGTATTGTGGCAAAAAATTGAGCAAAAACTTTTCGGGTCAATTTTTGCAAAATTTTAACTGAAAT
194 AGTATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAT
* ** * * *
97430 TGAATACTAACCATCACAGTTTTTGGGCCAAAAACGCGTTCCGGGATCCCAATTCAGTTTCGAAT
259 CGTGTACTAACCATCACAGTTTTT-GGCCAAAAATGCGTTCCGGGATCCCAACTCAGTTT-GTAT
* *
97495 GATTTTTTGCGT
322 GATTTTTTACGC
* *
97507 CAAGACTCATTGAATTTTCTGTATTCATCTAGCCAAATCCCAGTCACATTGGATTTAAGGATTAG
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGGATTAG
* * *
97572 TTTTTACAAGCTTCAGAAACCGGTTTCAATTTAATTAGAAATTAATTAGGAAAAAAATAAGAAAA
66 TTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAAGAAAA
* * * * *
97637 TTCGATATTAGACGTGTGAAAATGCCTTAAATACTTTTGGCATTGAATTATATATATTTTATGAG
131 TTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATGAG
*
97702 TATTGTGGCAAAAAATCGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCG
196 TATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCG
*
97767 TGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCGGGGTCCCAACTCAGTTTGTATGATT
261 TGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCGGGATCCCAACTCAGTTTGTATGATT
97832 TTTTACGC
326 TTTTACGC
* * * * *
97840 TAAGACTCATTCAAATATCTGTATTCATGTAGCCAAATCTCAGTCACATTAGATTTAAGGAATT-
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGG-ATTA
* * * *
97904 GTTTCTACAAGCATCAGAAACCTGTTTCGATTTAAATAGAAATTGATTTGGAAAAAAATAAGAAA
65 GTTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAAGAAA
* ** * * *
97969 ATTCGATATTATAAGCCAGAAAATCCCTTCAATATTTTTGGCTTTGATTTATATATGTTTTATGA
130 ATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATGA
* * ** *
98034 GTATTGTGGCTAAAAATTGAACAAAAATTTTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATT
195 GTATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC
* *
98099 GTGTACTAACCATCACAGTTTTTGGCAAAAAATGCGTTCCGGGGTCCCAACTCAGTTTGTATGAT
260 GTGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCGGGATCCCAACTCAGTTTGTATGAT
98164 TTTTTACGC
325 TTTTTACGC
* * * *
98173 TAAGACTCATTCAAATATCTGTATTCATTTAGCCAAATCTCAGTCACATTGGATTTAAGGAATT-
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGG-ATTA
* * *
98237 GTTTCTACAAGCATCAGAAACCTGTTTCGATTTAAATAGAAATTAATTTGGAAAAAAATAAGAAA
65 GTTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAAGAAA
* * * *
98302 ATTCGATATTAGAAGCCTGAAAATCCCTTCAATATTTTTGGCATTGATTTATATATGTTTTATAA
130 ATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATGA
** * * * *
98367 GTATTAAGGCAAAAAATTGAACAAAAATTTTTCGGCTCAATTTTTACAAAATTTTAGCCGAAATT
195 GTATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC
* * *
98432 GTGTACTAACCATCATAGTTTTTGGCAAAAAATGCGTTCCGGGGTCCCAACTCAGTTTGTATGAT
260 GTGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCGGGATCCCAACTCAGTTTGTATGAT
*
98497 TCTTTACGC
325 TTTTTACGC
* * * *
98506 TAAGACTCATTGAAGTATCTGTATTCATTTAGCCAAATCTCAGTCACATTGGATTTAAGGATTTG
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGGATTAG
* *
98571 TTTATACAAGCATCAGATACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAAATAAGAAA
66 TTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGG-AAAAAAATAAGAAA
** *
98636 ATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGTGTTGAATAATATATATTTTATGA
130 ATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATGA
*
98701 GTATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATC
195 GTATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC
* * * *
98766 GTATACTAACCATCACAGTTTTTGGCCAAAAACGCGTTTCGGGATCCCAATTCAGTTT-TCAATG
260 GTGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCGGGATCCCAACTCAGTTTGT--ATG
*
98830 ATTTTTTGCGC
323 ATTTTTTACGC
* * *
98841 CAAGAATCATTGAATAATCTGTATTCATCTAGCCAAATCCCAGTCACATTGGATTTAAGGATTAG
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGGATTAG
*
98906 -TTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAGTTAATTTGGAAAAAAAATAAGAAA
66 TTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGG-AAAAAAATAAGAAA
* * * *
98970 ATTCGATATTAGACGCGTGACAATCCCTTAAATATTTTTGGCATTGAATTATAAATATTTTATGA
130 ATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATGA
* * * * *
99035 GTATTGTGGTAAAAAATTGAGCAAAAACTTTTCGGGTCAATTTTTACAAAA-TTGA-CGTGTAAA
195 GTATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGC-CG-AAA
* *
99098 TCGTGTACTTACCATCACAGTTTTTGGCCAAAAATGCGTTCCGATG-TCCCAACTCAGTTTGTAT
258 TCGTGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCG-GGATCCCAACTCAGTTTGTAT
*
99162 GATTTTTTACAC
322 GATTTTTTACGC
* * * *
99174 CAAGACTCATTG-ATATATCTGTATTCATTTAGCCAAATCTCAGTCATATTGGATTTAAGAATTT
1 CAAGACTCATTGAAT-TATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGGATTA
* * * * * *
99238 GTTTATACAAGCGTCAGATACTGTTTTTGATTTAATTA-AAATTAATTT-G-AAAAAATATA-AA
65 GTTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATA-AGAA
* * * * * *
99299 AATTCGATATTAGAAGTGTGAAAATTCCTTCAATCTTTTTGGCATTTATTTATATATGTTTTATG
129 AATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATG
* * *
99364 AGTATGGTGGCAAAAAATTGAACAAAAATTTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAAT
194 AGTATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAT
* * *
99429 TGTGTACTGACCATCACAGTTTTTGGCCAAAAATGCGTTCCGGGGTCCCAACTCAGTTTGTATGA
259 CGTGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCGGGATCCCAACTCAGTTTGTATGA
99494 TTTTTTACGC
324 TTTTTTACGC
* * * * *
99504 TAAGACTCATTCAAATATCTGTATTCATTTAGCCAAATCTCAGTCACATTGGATTTAAGGATTTG
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGGATTAG
* * *
99569 TTTTTACAAGCATCAGATACCGGTTTCGATTTAATTAGAAATTAATTAGGAAAAAAATTAGAAAA
66 TTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAAGAAAA
* **
99634 TTCGATATTAGACGCGTGAAAATCCCTTCAATATTTTTGGTGTTGAATTATATATATTTTATGAG
131 TTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATGAG
*
99699 TATTGTGGCAAAAAATTGAGCAAAAA-TTTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATCG
196 TATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCG
* * * * * **
99763 TATACTAACCATCAAAGTTTTTGGCCAAAAACGCGTTCCGGGATCTCAATTCAGTTTCCAATGAT
261 TGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCGGGATCCCAACTCAGTTT-GTATGAT
** *
99828 TTTTTGTGT
325 TTTTTACGC
* * * *
99837 CAAGGCTCATTGAGTTATCTGTATTCATCTAGCCAAATCCCAGTCACATTGGATTTAAGGAATAG
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGGATTAG
99902 -TTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAAAATAAGAA
66 TTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGG--AAAAAAATAAGAA
* * * * *
99966 AATTTGATATTAGACGCGTGAAAATGCCTTAAATATTTTTGGCATTGAATTACATAGT-TTTTAT
129 AATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATA-TATTTTAT
* * *
100030 GAGTATTGTGGCAAAAAATTGAGCAAACATTTTTCGGGTCAATTTTTGGAAAA-TTTA-CCTTAA
193 GAGTATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCC-GAA
* ** * * *
100093 GTTTTGTACTAACCAACATAGTTTTTGGCCAAAAATGAGTTCCGAGG-TCCCAACTCAGTTTGTA
257 ATCGTGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCG-GGATCCCAACTCAGTTTGTA
100157 TGATTTTTTACGC
321 TGATTTTTTACGC
* * * **
100170 CTAGACTCATTGAGTTATCTGTAGTCATCTAGCCAAATCTCAGTCACATTATATTTAAGGAATT-
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGG-ATTA
* * *
100234 GTTTCTACAAGCATCAGAAACCTGTTTCGATTTAATTAGAAATTAATTTCGAAAAAAATAAGAAA
65 GTTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAAGAAA
* * * * * *
100299 ATTCGATATTTGAAGCCTGAAAATCTCTTCAAAATTTTTGGCATTGATTTATATATGTTTTATGA
130 ATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATGA
* * *
100364 GTTTTGTGGCAAAAAATTGAACAAAAATTTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATC
195 GTATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC
* *
100429 GTGTACTAACCATCACAGTTTTTGGCAAAAAATGCGTTCCGTGG-TCCCGACTCAGTTTGTATGA
260 GTGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCG-GGATCCCAACTCAGTTTGTATGA
100493 TTTTTTACGC
324 TTTTTTACGC
* * * * * * * *
100503 TAAAATTCATTGAAATATCTGTATTCATTTAGCCAAATTTTAGTGACATTGGATTTAAGGAATT-
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGG-ATTA
* *
100567 GTTTCTACAAGCATCAGATACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAAATAAGAA
65 GTTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGG-AAAAAAATAAGAA
* * * * * **
100632 ACTTAGATATTTGAAGCCTGAAAATACCTTCAATATTTTTGGTGTTGAATTATATATATTTTATG
129 AATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATG
* * * *
100697 AGTATTATGGCAAAAAAAATTGAGGAAAAACTTTTCGGGTCAATTTTTGCAAAATTTTAGCTG-A
194 AGTATTGTGGC--AAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAA
* * * * * * * **
100761 ATCGTATACTAAGCATCGCAGATTTTGGCCAAAAACGCGTTCCGAGATCCCAATTCAGTTTCCAA
257 ATCGTGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCGGGATCCCAACTCAGTTT-GTA
**
100826 TGATTTTTTGTGC
321 TGATTTTTTACGC
* * *
100839 CAAGACTCATTGAGTTATCTGTATTTATCTAGCCAAATCCCAGTCACATTGGATTTAAGGATTAG
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGGATTAG
* * *
100904 TTTTTACAAGCTTCAGAAACCGGTTTCAATTTAATTAGAAATTAATTAGGAAAAAAATAAGAAAA
66 TTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAAGAAAA
* * * * *
100969 TTCGATATTAGACGTGTGAAAATGCCTTAAATACTTTTGGCATTGAATTATATATATTTTATGAG
131 TTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATGAG
* * * * *
101034 TATTGTGTCAAAAAATCGAACAAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATT
196 TATTGTGGCAAAAAATTGAGC-AAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC
* * * * * * * **
101099 GTATACTAACCATCATAGTTTTTGGCAAAAAACGCGTTCCGGGATCTCAATTCACTTTCCAATGA
260 GTGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCGGGATCCCAACTCAGTTT-GTATGA
**
101164 TTTTTTGTGC
324 TTTTTTACGC
* *
101174 CAAGGCTCATTGAGTTATCTGTATTCATCTAGCCAAATC-CTAGTCACATTGGATTTAAGGATTA
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTC-AGTCACATTGGATTTAAGGATTA
* * *
101238 GTTTTTACAAGCTTCAGAAACCGGTTATCGATTTAATTAGAAATTAATTAGGAAAAAAATTAGAA
65 GTTTTTACAAGCATCAGAAACCGGTT-TCGATTTAATTAGAAATTAATTTGGAAAAAAATAAGAA
* * * *
101303 AATTCGATATTAGACGCGTGAAAATGCCTTAAATACTTTTGGCATTGAATTATATATATTTTATG
129 AATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATG
* * *
101368 ATTATTGTTGCAAAAAATTAAGCAAAAATTTTTCGGGTCAATTTTTGC-AAATTTTAGCCGAAAT
194 AGTATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAT
* * * * * *
101432 CGTGTACTAACCATCATAGTTTTGGGCCAAAAACGCATTCTGGGGTCCCAACTCAGTTTGTATGA
259 CGTGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCGGGATCCCAACTCAGTTTGTATGA
**
101497 TTTTGGACGC
324 TTTTTTACGC
* * *
101507 CAAGACTCATTGAAATATCTGTATTCATTTAGCCAAATCTCAGTCACATTAGATTTAAGGAATT-
1 CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGG-ATTA
* * *
101571 GTTTCTACAAGCATCAGAAACCTGTTTCGATTTAATTAGAAATTAATTTCGAAAAAAATAAGAAA
65 GTTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAAGAAA
* ** * *
101636 ATTCGATATTAGAAGCGTGAAAATCCCTTTAATATTTTTGGTGTTGAATTTTATATGTTTTATGA
130 ATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATGA
* * *
101701 GTATTGTTGCAAAAAATTGAGCAAAAATTTTTCAGGTCAATTTTTGCAAAATTTTAGCTGAAATC
195 GTATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC
101766 G
260 G
101767 AGTCACTTTA
Statistics
Matches: 5272, Mismatches: 573, Indels: 156
0.88 0.10 0.03
Matches are distributed among these distances:
328 53 0.01
329 188 0.04
330 324 0.06
331 183 0.03
332 674 0.13
333 1667 0.32
334 1112 0.21
335 638 0.12
336 433 0.08
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (333 bp):
CAAGACTCATTGAATTATCTGTATTCATCTAGCCAAATCTCAGTCACATTGGATTTAAGGATTAG
TTTTTACAAGCATCAGAAACCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAAGAAAA
TTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGCATTGAATTATATATATTTTATGAG
TATTGTGGCAAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCG
TGTACTAACCATCACAGTTTTTGGCCAAAAATGCGTTCCGGGATCCCAACTCAGTTTGTATGATT
TTTTACGC
Found at i:101934 original size:219 final size:219
Alignment explanation
Indices: 101548--102061 Score: 920
Period size: 219 Copynumber: 2.3 Consensus size: 219
101538 GCCAAATCTC
* * * *
101548 AGTCACATTAGATTTAAGGAATTGTTTCTACAAGCATCAGAAACCTGTTTCGATTTAATTAGAAA
1 AGTCACTTTAGATTTAAGGAATTTTTTCTACAGGCATCAGAAACCGGTTTCGATTTAATTAGAAA
* *
101613 TTAATTTCGAAAAAAATAAGAAAATTCGATATTAGAAGCGTGAAAATCCCTTTAATATTTTTGGT
66 TTAATTTGGAAAAAAATAAGAAAATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGT
* * *
101678 GTTGAATTTTATATGTTTTATGAGTATTGTTGCAAAAAATTGAGCAAAAATTTTTCAGGTCAATT
131 GTTGAATTATATATATTTTATGAGTATTGTGGCAAAAAATTGAGCAAAAATTTTTCAGGTCAATT
101743 TTTGCAAAATTTTAGCTGAAATCG
196 TTTGCAAAATTTTAGCTGAAATCG
101767 AGTCACTTTAGATTTAAGGAATTTTTTCTACAGGCATCAGAAACCGGTTTCGATTTAATTAGAAA
1 AGTCACTTTAGATTTAAGGAATTTTTTCTACAGGCATCAGAAACCGGTTTCGATTTAATTAGAAA
*
101832 TTAATTTGGAAAAAAATAAGAAAATTCGATATTATAAGCGTGAAAATCCCTTCAATATTTTTGGT
66 TTAATTTGGAAAAAAATAAGAAAATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGT
*
101897 GTTGAATTATATATATTTTATGAGTATTGTGGCAAAAAATTGAGCAAAAATTTTTCTGGTCAATT
131 GTTGAATTATATATATTTTATGAGTATTGTGGCAAAAAATTGAGCAAAAATTTTTCAGGTCAATT
101962 TTTGCAAAATTTTAGCTGAAATCG
196 TTTGCAAAATTTTAGCTGAAATCG
*
101986 AGTCACTTTAGATTTAAGGAATTTTTTCTACAGGCATCAAAAACCGGTTTCGATTTAATTAGAAA
1 AGTCACTTTAGATTTAAGGAATTTTTTCTACAGGCATCAGAAACCGGTTTCGATTTAATTAGAAA
102051 TTAATTTGGAA
66 TTAATTTGGAA
102062 TTCGTGTACT
Statistics
Matches: 283, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
219 283 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (219 bp):
AGTCACTTTAGATTTAAGGAATTTTTTCTACAGGCATCAGAAACCGGTTTCGATTTAATTAGAAA
TTAATTTGGAAAAAAATAAGAAAATTCGATATTAGAAGCGTGAAAATCCCTTCAATATTTTTGGT
GTTGAATTATATATATTTTATGAGTATTGTGGCAAAAAATTGAGCAAAAATTTTTCAGGTCAATT
TTTGCAAAATTTTAGCTGAAATCG
Found at i:111627 original size:249 final size:249
Alignment explanation
Indices: 111189--111688 Score: 1000
Period size: 249 Copynumber: 2.0 Consensus size: 249
111179 CCACGGGAAC
111189 CAGCAAGCGCAGAATCAAGAAAGCGTTGATCATGTGGAATTCTTCATTGAATAATACTAGAAACA
1 CAGCAAGCGCAGAATCAAGAAAGCGTTGATCATGTGGAATTCTTCATTGAATAATACTAGAAACA
111254 TATGTTTGAGAACAGAAACTTAGCAATTTGGTTGTTGAATCTGAATTAAAAGTGAAGTAAAATAT
66 TATGTTTGAGAACAGAAACTTAGCAATTTGGTTGTTGAATCTGAATTAAAAGTGAAGTAAAATAT
111319 CCTGAGACACGAAGCTATCTTTGTCTCTCATTTATCATTGCTAATTATGTTGAAAGAAGAAACTA
131 CCTGAGACACGAAGCTATCTTTGTCTCTCATTTATCATTGCTAATTATGTTGAAAGAAGAAACTA
111384 AATATAAGAAAATATGTACTCTACCTCCCATGAATCTTTAAAACTACCATTCAT
196 AATATAAGAAAATATGTACTCTACCTCCCATGAATCTTTAAAACTACCATTCAT
111438 CAGCAAGCGCAGAATCAAGAAAGCGTTGATCATGTGGAATTCTTCATTGAATAATACTAGAAACA
1 CAGCAAGCGCAGAATCAAGAAAGCGTTGATCATGTGGAATTCTTCATTGAATAATACTAGAAACA
111503 TATGTTTGAGAACAGAAACTTAGCAATTTGGTTGTTGAATCTGAATTAAAAGTGAAGTAAAATAT
66 TATGTTTGAGAACAGAAACTTAGCAATTTGGTTGTTGAATCTGAATTAAAAGTGAAGTAAAATAT
111568 CCTGAGACACGAAGCTATCTTTGTCTCTCATTTATCATTGCTAATTATGTTGAAAGAAGAAACTA
131 CCTGAGACACGAAGCTATCTTTGTCTCTCATTTATCATTGCTAATTATGTTGAAAGAAGAAACTA
111633 AATATAAGAAAATATGTACTCTACCTCCCATGAATCTTTAAAACTACCATTCAT
196 AATATAAGAAAATATGTACTCTACCTCCCATGAATCTTTAAAACTACCATTCAT
111687 CA
1 CA
111689 TACAATTTGA
Statistics
Matches: 251, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
249 251 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (249 bp):
CAGCAAGCGCAGAATCAAGAAAGCGTTGATCATGTGGAATTCTTCATTGAATAATACTAGAAACA
TATGTTTGAGAACAGAAACTTAGCAATTTGGTTGTTGAATCTGAATTAAAAGTGAAGTAAAATAT
CCTGAGACACGAAGCTATCTTTGTCTCTCATTTATCATTGCTAATTATGTTGAAAGAAGAAACTA
AATATAAGAAAATATGTACTCTACCTCCCATGAATCTTTAAAACTACCATTCAT
Found at i:128600 original size:30 final size:29
Alignment explanation
Indices: 128536--128605 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
128526 ACACCGAACC
***
128536 GTCAAATAAGCCCCTGAACAATTATTTCA
1 GTCAAATAAGCCCCTGAACAATTATAAAA
**
128565 GTCAAATAAGCCCCTGAACTCTTAATAAAA
1 GTCAAATAAGCCCCTGAACAATT-ATAAAA
128595 GTCAAATAAGC
1 GTCAAATAAGC
128606 TATGTTGCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.24
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACAATTATAAAA
Found at i:141613 original size:20 final size:21
Alignment explanation
Indices: 141588--141627 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
141578 CTTAGACATT
141588 GAACCTATTCTGG-TCAAAAA
1 GAACCTATTCTGGCTCAAAAA
*
141608 GAACCTATTTTGGCTCAAAA
1 GAACCTATTCTGGCTCAAAA
141628 TACATGGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (21 bp):
GAACCTATTCTGGCTCAAAAA
Found at i:155136 original size:2 final size:2
Alignment explanation
Indices: 155116--155157 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
155106 CTTTATGAGG
* *
155116 AT AT AT AA AT AT -T AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
155157 A
1 A
155158 ACATAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Done.