Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020774.1 Corchorus olitorius cultivar O-4 contig20807, 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: 39420
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:11180 original size:61 final size:62
Alignment explanation
Indices: 11061--11182 Score: 212
Period size: 61 Copynumber: 2.0 Consensus size: 62
11051 AATAAGTTGA
11061 AGTTGAAGGTTAAGGATGTCAAGAATCATAAAATCCAATGACGAGTTTCATTACATATATTG
1 AGTTGAAGGTTAAGGATGTCAAGAATCATAAAATCCAATGACGAGTTTCATTACATATATTG
*
11123 AGTTGAAGGTTGAGGATGTCAA-AGATCAT-AAATCCAATGACGAGTTTCATTACATATATT
1 AGTTGAAGGTTAAGGATGTCAAGA-ATCATAAAATCCAATGACGAGTTTCATTACATATATT
11183 ATTACTAATG
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
61 32 0.55
62 26 0.45
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (62 bp):
AGTTGAAGGTTAAGGATGTCAAGAATCATAAAATCCAATGACGAGTTTCATTACATATATTG
Found at i:23508 original size:45 final size:46
Alignment explanation
Indices: 23457--23551 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 46
23447 TCATTCTAGG
* * *
23457 ATTATAAAGTTACTTTTATTCAGCAT-TACTTAATTTCTTAAGCTA
1 ATTATAAAGTTACTTTTAATCAGCATCTAATTAATTTATTAAGCTA
23502 ATTATAAAGTTACTTTTAATCAGCATCACTAATTAATTTATTAAGCTA
1 ATTATAAAGTTACTTTTAATCAGCAT--CTAATTAATTTATTAAGCTA
23550 AT
1 AT
23552 AATATGACGA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
45 25 0.57
48 19 0.43
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (46 bp):
ATTATAAAGTTACTTTTAATCAGCATCTAATTAATTTATTAAGCTA
Found at i:23668 original size:19 final size:19
Alignment explanation
Indices: 23641--23677 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
23631 AAATTAACAA
*
23641 TTCTCATGTATACGTATAG
1 TTCTCATGTATACATATAG
*
23660 TTCTTATGTATACATATA
1 TTCTCATGTATACATATA
23678 TATGCAATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.46
Consensus pattern (19 bp):
TTCTCATGTATACATATAG
Found at i:26549 original size:18 final size:18
Alignment explanation
Indices: 26526--26561 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
26516 GCTTTTTATG
26526 GGGCTTTTCGAAAGCATA
1 GGGCTTTTCGAAAGCATA
26544 GGGCTTTTCGAAAGCATA
1 GGGCTTTTCGAAAGCATA
26562 AAAGATGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (18 bp):
GGGCTTTTCGAAAGCATA
Found at i:28334 original size:322 final size:318
Alignment explanation
Indices: 27768--28660 Score: 1129
Period size: 322 Copynumber: 2.8 Consensus size: 318
27758 TGGAAAAAAC
* * ** *
27768 ACTCATAAAAATATATATAATTCAACGCCAAAAAAATTGGAGGACTTTTCACGCTTTTAATATCG
1 ACTCAGAAAAA-ATATATAATTCAACGCCAAAAAGATTACAGG-CTTTTCACGCTTCTAATATCG
* ** *
27833 TTTTTCATATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCTGATGCAC-ATAAA
64 TTTTTCAT-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGA-AAA
* * * *
27897 AACAAATCCTTAAATCCAATGTGGCCT-AGATTTGATTAGACTAATAA-AGATATTTCAAGGAGT
127 AACAAATCCTTATATCCAATATGG-CTGAGATTTGGTTCGA-TAA-AATAGATATTTCAAGGAGT
* * * * * * *
27960 CTCAGCACCAAAAACCATGAAAAACAGAGCCGTGACCCCGAAAGCCGTTTTTAGTCA-AAATCCG
189 CTTAGCGCCAAAAATCATGCAAAACTGAGCCGTG-CCCCGAACG-CGTTTTTAGCCAGAAA-CCG
* * *
28024 AGATGGTTAGTACATGATTT-CGGCTAAAAACTGACCCG-AAAG-TTTCTCTCAATTTTTTGCCA
251 AGATGGTTAGTACACGATTTAC-GCTAAAAACGGACCCGAAAAGTTTTCTCTCAAATTTTTGCCA
28086 CAAT
315 CAAT
* *
28090 ACTCAGAAAAAATATATAATTCAACTCCAAAAAGATTAACAGGCTTTTCATGCTTCTAATATCGT
1 ACTCAGAAAAAATATATAATTCAACGCCAAAAAGATT-ACAGGCTTTTCACGCTTCTAATATCGT
*
28155 TTTTCATTTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAGAA
65 TTTTCA--TTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAA
28220 ACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCGATGAAAATAGATATTTCAAGGAGTCTT
128 ACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCGAT-AAAATAGATATTTCAAGGAGTCTT
* * * **
28285 TGCGCCAAAAATCATGCAAAATTGAGCCAGTGCTCCGTAACGCGTTTTTAGCCAGAAACCGTTAT
192 AGCGCCAAAAATCATGCAAAACTGAGCC-GTGCCCCG-AACGCGTTTTTAGCCAGAAACCGAGAT
*
28350 GGTTAGTACACGATTTACGCTAAAAACGGACCCGAAAAGTTTTTTCTCAAATTTTTGCCACAAT
255 GGTTAGTACACGATTTACGCTAAAAACGGACCCGAAAAGTTTTCTCTCAAATTTTTGCCACAAT
*
28414 ACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGT
1 ACTCAGAAAAAATATATAATTCAACGCCAAAAAGATT-ACAGGCTTTTCACGCTTCTAATATCGT
* * *
28479 TTTTCCA-TTTTTTTCGGAATTAATTTCTAATTAAGTCGAAACAAGATTGAGATGCTTGAAAAAA
65 TTTT-CATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAA
* * *
28543 CAAAT-CTATATATTCAATATGACTGAGATTTGGTTCGATAAATATAGATATTTCAAGGAGCCTT
129 CAAATCCT-TATATCCAATATGGCTGAGATTTGGTTCGATAAA-ATAGATATTTCAAGGAGTCTT
* * * *
28607 AACGACAAAAATCTTGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCA
192 AGCGCCAAAAATCATGCAAAACTGAGCC-GTGCCCC-GAACGCGTTTTTAGCCA
28661 CAAGCCGTGA
Statistics
Matches: 503, Mismatches: 51, Indels: 34
0.86 0.09 0.06
Matches are distributed among these distances:
321 60 0.12
322 337 0.67
323 17 0.03
324 87 0.17
325 2 0.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (318 bp):
ACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTACAGGCTTTTCACGCTTCTAATATCGTT
TTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACA
AATCCTTATATCCAATATGGCTGAGATTTGGTTCGATAAAATAGATATTTCAAGGAGTCTTAGCG
CCAAAAATCATGCAAAACTGAGCCGTGCCCCGAACGCGTTTTTAGCCAGAAACCGAGATGGTTAG
TACACGATTTACGCTAAAAACGGACCCGAAAAGTTTTCTCTCAAATTTTTGCCACAAT
Found at i:28752 original size:2 final size:2
Alignment explanation
Indices: 28747--28775 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28737 CTCAATCCAA
28747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28776 AAATTTTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30381 original size:325 final size:324
Alignment explanation
Indices: 29191--30415 Score: 931
Period size: 325 Copynumber: 3.7 Consensus size: 324
29181 TGAGACGATT
* * * * * * *
29191 TTTTTTTTCTCAATTTTTTTGCGACAATAGTCATAAAAAATATATAATTTAACGCCAAAAAAATT
1 TTTTTTTTCTCAA-TATTTTGCCACAATACTC--AGAAAATATACAATTCAACACCAAAAAAATT
* ** * * ** * * * * * **
29256 GAAGGATTTTTCACACTTCTAATATTGTTTTTCCATTTTTTTTCGAATTAATTTATAGTTAAAAC
63 GACGGGCTTTTCACGCTTTTAATATCATTTTTCCAATTTTTTCCGAATTTATTTCTAATTAAATT
* * * * * * * * *
29321 AAAACAAAATTCAGATGCTCGTAAAAATAAATCGTTAAATCGAATTTGGCTGGGATTTGGTTCGA
128 GAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGGGAATTGGTTAGA
* * * * *
29386 TGAATATAGATATTTCAAGGAGTCTTTACACC-AAAATCATGCAAAATTGTGCCGGGG-TCCCGG
193 TGAATATAGATATTTCAAGGAGTCTTT-CGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCGA
*** * * * * * * * *
29449 AATGTGGTTTTAGCAAAAAAACCGTGATAGTTAGTAAAGGATTTCAGGGAAAGTTTTGC-AAAAA
257 AACACGTTTTTAGCCAAAAAACCATGATGGTCAGTACACGA-TT---------TTTGGCTAAAAA
*
29513 CTGACCCAA-AA-
312 CTGAGCCAATAAG
** * * * * ** *
29524 ------AACTCAATTTTTTGCCATAATAGTCAGAAAAAAATACAAAATTCAA-TGCAAAAAAAAT
1 TTTTTTTTCTCAATATTTTGCCACAATACTCAG-AAAATATAC--AATTCAACACCAAAAAAATT
**** ** * * * *
29582 GAAATACTTTTCTTGCTTTAAATATCATTTTT-CAATTTTTTCCGAATCTAATTCTAATTAAATC
63 GACGGGCTTTTCACGCTTTTAATATCATTTTTCCAATTTTTTCCGAATTTATTTCTAATTAAATT
* * * *
29646 GAAACAATATTCAGATGCTCGTAAAAGCAAATCCTTAAATCTAATGTGGCTGAGAGCCTGAGATT
128 GAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT--G-G---GA-ATT
*
29711 GGTTAGATGAACATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGG
186 GGTTAGATGAATATAGATATTTCAAGGAGTCTTTC-GCCAAAAATCATGCAAAACTGAGCCGGGG
* * *
29776 CCCCCGAAACGCGTTTTTAGCCCAAAACCCATGATGGTCAGTACACGATTTTTGGCTAAAAACTG
250 CCCCCGAAACACGTTTTTAGCCAAAAAACCATGATGGTCAGTACACGATTTTTGGCTAAAAACTG
***
29841 AGCCAATTTTT
315 AGCCAA-TAAG
* *
29852 TTTTTTTTCTGAATATTTTGCCACAATACTCAGAAAATATACAATTCAACACCAAAAAAATTGAT
1 TTTTTTTTCTCAATATTTTGCCACAATACTCAGAAAATATACAATTCAACACCAAAAAAATTGAC
* * *
29917 GGTCTTTTCACGCTTTTAATATCATTTTTCTAATTTTTTCCGAATTAATTTCTAATTAAATTGAA
66 GGGCTTTTCACGCTTTTAATATCATTTTTCCAATTTTTTCCGAATTTATTTCTAATTAAATTGAA
* * * ** * *
29982 ACAAGATTCAAAAGCTCGTAAAAACAAATCCTTATATCCAATGTGGCAGACACTTGGTTTGATGA
131 ACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGGGAATTGGTTAGATGA
* * * * *
30047 ATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGG-CTCGGGAAC
196 ATATAGATATTTCAAGGAGTCTTT-CGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCGAAAC
* * * * * *
30111 ACGTTTTTTG-TAAAAAACCGTGATGGTTAGTACACGA-TTTTGGCTAAAAACTGATCGGAA-AA
260 ACGTTTTTAGCCAAAAAACCATGATGGTCAGTACACGATTTTTGGCTAAAAACTGAGC-CAATAA
30173 G
324 G
* * * * * *
30174 TTTTTTTTCTCAATTTTTTGCCACAATACTCTGGAAAAATTTATAATTCAACGCCAAAAAGATTG
1 TTTTTTTTCTCAATATTTTGCCACAATACTC-AG-AAAATATACAATTCAACACCAAAAAAATTG
* * * *
30239 ACGGGCTTTTCACGCTTCTT-TTATCGTTTTTCCATTTTTTTCCGAATTTATTTTATAATTAAAT
64 ACGGGCTTTTCACGCTT-TTAATATCATTTTTCCAATTTTTTCCGAATTTA-TTTCTAATTAAAT
* * * * * * *
30303 TGAAACAAGATTCAAATGCACGTAAAAACAAATACTTAAATCGAACGTGGCTGGGATTTTGTTCG
127 TGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGGGAATTGGTTAG
* * *
30368 ATGAATATAGATATTTC-AGAAAGTATTTACGTCAAAAATCATGCAAAA
192 ATGAATATAGATATTTCAAG-GAGTCTTT-CGCCAAAAATCATGCAAAA
30416 ACAAAAAAAA
Statistics
Matches: 719, Mismatches: 141, Indels: 72
0.77 0.15 0.08
Matches are distributed among these distances:
322 29 0.04
323 19 0.03
324 98 0.14
325 210 0.29
326 108 0.15
327 14 0.02
328 1 0.00
331 11 0.02
332 70 0.10
333 104 0.14
334 55 0.08
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (324 bp):
TTTTTTTTCTCAATATTTTGCCACAATACTCAGAAAATATACAATTCAACACCAAAAAAATTGAC
GGGCTTTTCACGCTTTTAATATCATTTTTCCAATTTTTTCCGAATTTATTTCTAATTAAATTGAA
ACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGGGAATTGGTTAGATGA
ATATAGATATTTCAAGGAGTCTTTCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCGAAACA
CGTTTTTAGCCAAAAAACCATGATGGTCAGTACACGATTTTTGGCTAAAAACTGAGCCAATAAG
Found at i:30971 original size:565 final size:555
Alignment explanation
Indices: 29921--30980 Score: 1346
Period size: 565 Copynumber: 1.9 Consensus size: 555
29911 ATTGATGGTC
* * *
29921 TTTTCACGCTTTTAATATCATTTTTCTAATTTTTTCCGAATTAATTTCTAATTAAATTGAAACAA
1 TTTTCACGCTTTAAATATCATTTTTCTAATTTTTTCCGAATTAACTTCTAATTAAATCGAAACAA
* * *
29986 GATTCAAAAGCTCGTAAAAACAAATCCTTATATCCAATGTGGCAGACACTTGGTTTGATGAATAT
66 GATTCAAAAGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCAGACAATTGGTTAGATGAATAT
* * * * * *
30051 AGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAACACGTT
131 AGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCCGAAACACGTT
* * * * * * **
30116 TTTTGTAAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGATCGGAAAAGTTTTTTT
196 TTTAGCAAAAAACCATAATGGTTAGTACACGATTTTGACTAAAAACTGAACCCAAAAGTTTTTTT
* * * * *
30181 TCTCAATTTTTTGCCACAATACTCTGGAAAAATTTATAATTCAACGCCAAAAAGATTGACGGGCT
261 TCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTAACGGGCT
* * * * *
30246 TTTCACGCTTCTTTTATCGTTTTTCCATTTTTTTCCGAATTTATTTTATAATTAAATTGAAACAA
326 TTTCACGCTTCTTATATCATTTTTCCATTTTTTTCCGAAATTAATTTATAATTAAATCGAAACAA
* * ** *
30311 GATTCAAATGCACGTAAAAACAAATACTTAAATCGAACGTGGCTGGGATTTTGTTCGATGAATAT
391 GATTCAAATGCACGTAAAAACAAATACTTAAATCCAACGTGACTGACATTTGGTTCGATGAATAT
*
30376 AGATATTTCAGAAAGTATTTACGTCAAAAATCATGCAAAAACAAAAAAAAATATTTTCGGCAAAA
456 AGATATTTCAGAAAGTATTTACGCCAAAAATCATGCAAAAACAAAAAAAAATATTTTCGGCAAAA
30441 AATATACATTTCAACGCAAAAAAAAAAAGAAATAT
521 AATATACATTTCAACGCAAAAAAAAAAAGAAATAT
* *
30476 TTTTCTCGCTTTAAATATCATTTTTCTATTTTTTTTCCGAA-TATACTTCTAATTAAATCGAAAC
1 TTTTCACGCTTTAAATATCATTTTTCTA-ATTTTTTCCGAATTA-ACTTCTAATTAAATCGAAAC
* * * * **
30540 AATATTCAGATGCTCGTAAAAA-AAATCTTTAAATTTAATGTGGCTGAGAGCCTGAGATTGGTTA
64 AAGATTCAAAAGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC--AGA--C--A-ATTGGTTA
30604 GATGAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAACTGAGCCGGGACCCC
122 GATGAATATAGATATTTCAAGGAGTCTTTGC-GCCAAAAATCATGCAAAACTGAGCCGGG-CCCC
*
30668 CGAAACACGTTTTTAGCCCAAAAACCATAATGGTTAGGTACACGATTTTCGACTAAAAACT-AAC
185 CGAAACACGTTTTTAG-CAAAAAACCATAATGGTTA-GTACACGATTTT-GACTAAAAACTGAAC
* *
30732 CCAGAA-TTTTTTTTCCTGAA-TTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAA
247 CCAAAAGTTTTTTTT-CTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAA
* *
30795 AAAGATTAATGGTCTTTTCACGCTT-TTAATATCATTTTTCCAAATTTTTTTCC-AAATTAATTT
311 AAAGATTAACGGGCTTTTCACGCTTCTT-ATATCATTTTTCC--ATTTTTTTCCGAAATTAATTT
* * * * * *
30858 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGACTGAC
373 ATAATTAAATCGAAACAAGATTCAAATGCACGTAAAAACAAATACTTAAATCCAACGTGACTGAC
* * * * *
30923 ATTTGGTTTGATGAATATAGATATTTCA-AGGAGTCTTTGCGCCAAAAATTATGCAAAA
438 ATTTGGTTCGATGAATATAGATATTTCAGA-AAGTATTTACGCCAAAAATCATGCAAAA
30981 TTGAGTCGGG
Statistics
Matches: 426, Mismatches: 60, Indels: 28
0.83 0.12 0.05
Matches are distributed among these distances:
555 46 0.11
556 48 0.11
557 3 0.01
559 1 0.00
561 2 0.00
562 61 0.14
563 17 0.04
564 96 0.23
565 132 0.31
566 20 0.05
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (555 bp):
TTTTCACGCTTTAAATATCATTTTTCTAATTTTTTCCGAATTAACTTCTAATTAAATCGAAACAA
GATTCAAAAGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCAGACAATTGGTTAGATGAATAT
AGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCCGAAACACGTT
TTTAGCAAAAAACCATAATGGTTAGTACACGATTTTGACTAAAAACTGAACCCAAAAGTTTTTTT
TCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTAACGGGCT
TTTCACGCTTCTTATATCATTTTTCCATTTTTTTCCGAAATTAATTTATAATTAAATCGAAACAA
GATTCAAATGCACGTAAAAACAAATACTTAAATCCAACGTGACTGACATTTGGTTCGATGAATAT
AGATATTTCAGAAAGTATTTACGCCAAAAATCATGCAAAAACAAAAAAAAATATTTTCGGCAAAA
AATATACATTTCAACGCAAAAAAAAAAAGAAATAT
Found at i:37699 original size:328 final size:316
Alignment explanation
Indices: 36875--38109 Score: 987
Period size: 323 Copynumber: 3.8 Consensus size: 316
36865 TGACGTAAAT
* * * * ** ** * *
36875 ACTCCTTGAAATATCTATATTCATCAAAACAAAATCCCAGCCATGTTCTATTTAA-GTATTTGTT
1 ACTCCTTAAAATATCTACATTCATCAAATC-AAATCTCAGCCACATTAGATATAAGGAATTTGTT
* * *
36939 TTTACGAGACATCTGAATCTTGTTTCAATTTAATTAAAAATTAATTCAGAAAAAAATGGAAAAAT
65 TTTACGAG-CATCTGAATCTTGTTTCGATTTAATTAAAAA-TAATTCGGAAAAAAAT-TAAAAAT
* * * * *
37004 GATA-ATAGAAGTGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTA
127 GATATTTA-AAGCGTGAAAAG-ACATCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTA
* *
37068 TTGTGG-AAAAAAATTGAGAAATAACTTTTCGGATCAGTTTTTAGCCGAAATCGTGTACTAACCA
190 TTGTGGCAAAAAAATTGAGAAA-AAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACT----A
*
37132 TCACGGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACTCAATTTTGTATGATTTTTGGCGCAA
250 TCACGGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACTCAATTTTGTATGATTTTTGGAGCAA
37197 CG
315 CG
* *
37199 ACTCCTTAAAATATCTACATTCATCAAATCAAATGTCAGCCACATTGGATATAAGGAATTT-TTT
1 ACTCCTTAAAATATCTACATTCATCAAATCAAATCTCAGCCACATTAGATATAAGGAATTTGTTT
* *
37263 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATTGGAAAAATG
66 TTACGAGCATCTGAATCTTGTTTCGATTTAATTA-AAAATAATTCGGAAAAAAATT--AAAAATG
* *
37328 ATATTAAAAGCGTGAAAAGACCATCAATATTTTTGGTGTTGAATTATATATTTTTTCTGAGTATT
128 ATATTTAAAGCGTGAAAAGA-CATCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTATT
* * ** *
37393 TTGGCAAAAAAATTCAGAAAAAAAATTCGGGTCAGTTTTTAGCCGAAAATCGTGTACGT-T-ATG
192 GTGGCAAAAAAATTGAGAAAAAATTTTCGGGTCAGTTTTTAGCCG-AAATCGTGTAC-TATCACG
** * *
37456 GTTTTTGTGCTAAAAACGCGTTTCGGGGGCCCC-AGCTCAGTTTT-TCATGATTTTTGGTAG--A
255 GTTTTTG-GCTAAAAACGCG-TTCCCGAGCCCCGA-CTCAATTTTGT-ATGATTTTTGG-AGCAA
37517 CAG
315 C-G
* * * *
37520 ACTCCTTGAAATATCTATATTCATCTAACCAATCTCAGACTCTTAGCCACATTAGAT-TCAAGG-
1 ACTCCTTAAAATATCTACATTCATC--A--AA--TCA-AATCTCAGCCACATTAGATAT-AAGGA
*
37583 ATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAATAGATTCGGAAAAAAATAT
58 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATA-ATTCGGAAAAAAAT-T
* * ** * * * *
37648 AAGAATGATATTTAAAGCGAGAAAAGTATTTCAATTTTTTTTTGCGTTGAATTGTGTATTTTTTC
121 AAAAATGATATTTAAAGCGTGAAAAG-ACATCAA-TATTTTTGGCGTTGAATTATATATTTTTTC
* * *
37713 TGACTATTGTGGCAAAAAAAATTGAGGAAAAATTTTTCGGGTCAGTTTTTGCGAAACTTTCGCTG
184 TGAGTATTGTGGC-AAAAAAATTGA-GAAAAAATTTTCGGGTCAGTTTTT-----A-----GCCG
* * * * * * * *
37778 AAATCCTATACTAACCATCACGGTTTTTTGCTAAAACCACGTT-CCGGGACCCCGGCTCAGTTTT
237 AAATCGTGTACT----ATCACGGTTTTTGGCTAAAAACGCGTTCCCGAG-CCCCGACTCAATTTT
* * * *
37842 GCATGA-TTTTGGCGTAAAG
297 GTATGATTTTTGGAGCAACG
* * * * * * * * * * *
37861 ACTCCTTGAAATATCTATATTCATCGAACCAAATCCCAACCAAATTCGATTTAACG-ATTTATTT
1 ACTCCTTAAAATATCTACATTCATCAAATCAAATCTCAGCCACATTAGATATAAGGAATTTGTTT
* * * * *
37925 TTACGAGCATATGAATCTTGTTTCGTTTTAATTAGAAATTAATTCGG-AAAAAATGGAAAAACGA
66 TTACGAGCATCTGAATCTTGTTTCGATTTAATTA-AAAATAATTCGGAAAAAAAT-TAAAAATGA
* * * * * * *
37989 TA-TTAGAAGTGTGAAAA-ATCCTTCAATTTTTTTGGCATTAAATTATATATTTTTTATGACTAT
129 TATTTA-AAGCGTGAAAAGA--CATCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTAT
* ** *
38052 TGTCGC-AAAAAATTGAGAAAAAAATTTTTCGTCTCAATTTTTAGCCGAAATCGTGTAC
191 TGTGGCAAAAAAATTGAG-AAAAAA-TTTTCGGGTCAGTTTTTAGCCGAAATCGTGTAC
38110 GTTTGGCTAA
Statistics
Matches: 745, Mismatches: 108, Indels: 119
0.77 0.11 0.12
Matches are distributed among these distances:
319 9 0.01
320 17 0.02
321 64 0.09
322 41 0.06
323 117 0.16
324 58 0.08
325 3 0.00
326 1 0.00
327 40 0.05
328 105 0.14
329 12 0.02
330 36 0.05
331 15 0.02
332 39 0.05
333 29 0.04
334 60 0.08
335 9 0.01
337 2 0.00
338 1 0.00
339 9 0.01
340 4 0.01
341 35 0.05
342 20 0.03
343 11 0.01
344 8 0.01
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (316 bp):
ACTCCTTAAAATATCTACATTCATCAAATCAAATCTCAGCCACATTAGATATAAGGAATTTGTTT
TTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAATTCGGAAAAAAATTAAAAATGATA
TTTAAAGCGTGAAAAGACATCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGG
CAAAAAAATTGAGAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTATCACGGTTTTT
GGCTAAAAACGCGTTCCCGAGCCCCGACTCAATTTTGTATGATTTTTGGAGCAACG
Found at i:37973 original size:334 final size:338
Alignment explanation
Indices: 37455--38082 Score: 767
Period size: 334 Copynumber: 1.9 Consensus size: 338
37445 TGTACGTTAT
* * * * *
37455 GGTTTTTGTGCTAAAAACGCGTTTCGGGGGCCCCAGCTCAGTTTTTCATGATTTTTGGTAGACAG
1 GGTTTTTGTGCTAAAAACACGTTTCCGGGACCCCAGCTCAGTTTTGCATGATTTTGGGTAGACAG
* * *
37520 ACTCCTTGAAATATCTATATTCATCTAACCAATCTCAGACTCTTAGCCACATTAGATTCAAGGAT
66 ACTCCTTGAAATATCTATATTCATCGAACCAATCCCAGACTC-TA--CACATTAGATTCAACGAT
* * *
37585 TTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAATAGATTCGGAAAAAAATATAA
128 TTATTTTTACGAGCATATGAATATTGTTTCGATTTAATTAAAAATAGATTCGG-AAAAAATAGAA
* * * * * * * * * *
37650 GAATGATATTTA-AAGCGAGAAAAGTATTTCAATTTTTTTTTGCGTTGAATTGTGTATTTTTTCT
192 AAACGATA-TTAGAAGCGAGAAAAATACTTCAA-TTTTTTTGGCATTAAATTATATATTTTTTAT
* *
37714 GACTATTGTGGCAAAAAAAATTGAG-GAAAAATTTTTCGGGTCAGTTTTTGCGAAACTTTCGCTG
255 GACTATTGTCGC--AAAAAATTGAGAAAAAAATTTTTCGGGTCAGTTTTTGCGAAACTTTCGCTG
37778 AAATCCTATACTAACCATCAC
318 AAATCCTATACTAACCATCAC
* *
37799 GGTTTTT-TGCTAAAACCACG-TTCCGGGACCCCGGCTCAGTTTTGCATGATTTTGGCGTA-A-A
1 GGTTTTTGTGCTAAAAACACGTTTCCGGGACCCCAGCTCAGTTTTGCATGATTTTGG-GTAGACA
* *
37860 GACTCCTTGAAATATCTATATTCATCGAACCAAATCCCA-AC-C-A-A-ATTCGATTTAACGATT
65 GACTCCTTGAAATATCTATATTCATCGAACC-AATCCCAGACTCTACACATTAGATTCAACGATT
* * * *
37920 TATTTTTACGAGCATATGAATCTTGTTTCGTTTTAATTAGAAATTA-ATTCGGAAAAAATGGAAA
129 TATTTTTACGAGCATATGAATATTGTTTCGATTTAATTA-AAAATAGATTCGGAAAAAATAGAAA
* * *
37984 AACGATATTAGAAGTGTGAAAAATCCTTCAATTTTTTTGGCATTAAATTATATATTTTTTATGAC
193 AACGATATTAGAAGCGAGAAAAATACTTCAATTTTTTTGGCATTAAATTATATATTTTTTATGAC
38049 TATTGTCGCAAAAAATTGAGAAAAAAATTTTTCG
258 TATTGTCGCAAAAAATTGAGAAAAAAATTTTTCG
38083 TCTCAATTTT
Statistics
Matches: 245, Mismatches: 34, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
330 11 0.04
331 12 0.05
332 39 0.16
333 30 0.12
334 54 0.22
335 6 0.02
338 1 0.00
340 1 0.00
341 33 0.13
342 37 0.15
343 14 0.06
344 7 0.03
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (338 bp):
GGTTTTTGTGCTAAAAACACGTTTCCGGGACCCCAGCTCAGTTTTGCATGATTTTGGGTAGACAG
ACTCCTTGAAATATCTATATTCATCGAACCAATCCCAGACTCTACACATTAGATTCAACGATTTA
TTTTTACGAGCATATGAATATTGTTTCGATTTAATTAAAAATAGATTCGGAAAAAATAGAAAAAC
GATATTAGAAGCGAGAAAAATACTTCAATTTTTTTGGCATTAAATTATATATTTTTTATGACTAT
TGTCGCAAAAAATTGAGAAAAAAATTTTTCGGGTCAGTTTTTGCGAAACTTTCGCTGAAATCCTA
TACTAACCATCAC
Found at i:39387 original size:325 final size:324
Alignment explanation
Indices: 38576--39412 Score: 1170
Period size: 324 Copynumber: 2.6 Consensus size: 324
38566 ATCGTTTACT
* * *
38576 CATCACGGCTTATGGCTAAAAACGCG-TTCTGG-GCCCCGGCTCAGTTTTGCAAGATTTTTGGCG
1 CATCACGG-TTTTGGCTAAAAACGCGTTTC-GGAGCCCCGGCTCAATTTTGCATGATTTTTGGCG
* * * *
38639 T-AAAGGCTCCTTGAAATATCTATATTCATGGAACCAAATCTCAGTCATATTGAATA-TATGGAT
64 TCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGGATATTA-GGAT
* * * *
38702 TTGTTTTTTCGAGCATCTCAATCTTTTTTTGACTTAATTAGAAATTAATTCGGGAAAAAATGGAA
128 TTGTTTTTTCGAGCATCTCAATCTTATTTTGATTTAATTAGAAATTAATTCGGAAAAAAAAGGAA
*
38767 AAACGATATTAGAAGCGTGAAAAGCCCATCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGA
193 AAACGATATTAGAAGCGTGAAAAGCCCATCAATCTTTTTGCCGTTGAATTATATATTTTTTCTGA
* * * *
38832 GTATTGTAGGCAAAAATTTGAGAAAAAAACTTTTCGGGTCCGTTTTTAGCCGAAATTGTGTACTA
258 GTATTGTAGGCAAAAAATTGAGAAAAAAACTTTTCGGGTCCGTTTTTAGCCAAAATCGTGTACAA
38897 AC
323 AC
* * * * *
38899 CATCACAGTTTATGGCTAAAAACGCGTTCCGGAGCCCCGACTCAATTTTTCATGATTTTTGGTG-
1 CATCACGGTTT-TGGCTAAAAACGCGTTTCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGT
* * * * *
38963 CAAAGACTCATTGAAATATCTATTTTCATCTAACCAAATCTTAGCCATATTGGATATAAGGATTT
65 CAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGGATATTAGGATTT
* *
39028 GTTTTTTCGAGCACCTCAATCTTGTTTTGATTTAATTAGAAATTAATTCGGAAAAAAAAAGGAAA
130 GTTTTTTCGAGCATCTCAATCTTATTTTGATTTAATTAGAAATTAATTCGG-AAAAAAAAGGAAA
39093 AACGATATTAGAAGCGTGAAAAGCCCATCAATCTTTTTGCCGTTGAATTATATATTTTTTCTGAG
194 AACGATATTAGAAGCGTGAAAAGCCCATCAATCTTTTTGCCGTTGAATTATATATTTTTTCTGAG
* * *
39158 TATTGT-GGCAAAAAATTG-GTATAAAAA-TTTTTGGGTCGGTTTTTAGCCAAAATCGTGTACAA
259 TATTGTAGGCAAAAAATTGAG-AAAAAAACTTTTCGGGTCCGTTTTTAGCCAAAATCGTGTACAA
39220 AC
323 AC
39222 CATCACGGTTTTGGCTAAAAACGCGTTTCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGTC
1 CATCACGGTTTTGGCTAAAAACGCGTTTCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGTC
* ** * *
39287 AAAGTCTCCTTGATTTATCTATATTCATCGAATCAAATGTCAGCCACT-TTGGATATTAGGATTT
66 AAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCA-TATTGGATATTAGGATTT
* * *
39351 GTTTTTAACGAGTCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCGGGAAAAAAAA
130 GTTTTT-TCGAG-CATCTCAATCTTATTTTGATTTAATTAGAAATTAATTC-GGAAAAAAAA
39413 TTGAAAAA
Statistics
Matches: 452, Mismatches: 50, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
322 50 0.11
323 125 0.28
324 151 0.33
325 124 0.27
326 2 0.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (324 bp):
CATCACGGTTTTGGCTAAAAACGCGTTTCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGTC
AAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGGATATTAGGATTTG
TTTTTTCGAGCATCTCAATCTTATTTTGATTTAATTAGAAATTAATTCGGAAAAAAAAGGAAAAA
CGATATTAGAAGCGTGAAAAGCCCATCAATCTTTTTGCCGTTGAATTATATATTTTTTCTGAGTA
TTGTAGGCAAAAAATTGAGAAAAAAACTTTTCGGGTCCGTTTTTAGCCAAAATCGTGTACAAAC
Done.