Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020747.1 Corchorus olitorius cultivar O-4 contig20780, 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: 7874
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Found at i:1366 original size:561 final size:555
Alignment explanation
Indices: 237--1308 Score: 1471
Period size: 561 Copynumber: 1.9 Consensus size: 555
227 TATTTCAATT
237 TTTTTTTTGCTTTGAATTGTGTATTTTTTCCAAAAATATTTTTTTTATTATTGCATGATTTTTGA
1 TTTTTTTTGCTTTGAATTGTGTATTTTTTCCAAAAATA-TTTTTTTATTATTGCATGATTTTTGA
** * * * * * * *
302 TTTAAATAATCCTTGAAATATCTCTATTCATCGCATAAAATCCCAGGCTTGTTTGATTTAAGTAT
65 CGTAAATAATCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCCATATTCGATTTAAGTAT
*
367 TTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAGTTAAAAATTAATTCGGAAAAAAATGGAA
130 TTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAATTCGGAAAAAAATGGAA
*
432 AAAACAATATTAGAAGCGTGAAAAGCCCGTCAATATTTTTGACATTGAATTATATAATTTTTGCT
195 AAAACAATATTAGAAGCGTGAAAACCCCGTCAATATTTTTGACATTGAATTATATAATTTTTGCT
* * *
497 GAGTATTGTGGCAAAAAATTGAGAAAAATTTTGGATCAGTTTTTAGCCGAAAATCATGTACTCAC
260 GAGTATTGTGGCAAAAAATTGAGAAAAATTTTCGAACAGTTTTTAGCCGAAAATCATGTACTAAC
* ** * * * *
562 CATCACGGCTTTGGGCTAAAAACGCGTTTCGTGGGCCCCGGCTTAGTTTTGCATATTTTTGGCAG
325 CATCACGGCTTTGGCCTAAAAACGCGTTTCCCGAGCCCCGACTCAATTTTGCATATTTTTGGCAG
* * *
627 AAAAACTCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCTCTCAGCCACATTAGATTTAA
390 AAAAACTCCTTAAAATATCTATATTCATCAAACCAA---CA-G-TCTCAGCCACATTAGATATAA
*
692 GGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGATTAGGAAAAAAAA
450 GGATTTGTTTTTACGAGCATCTGAATATTATTTCGATTTAATTAGAAATAGATTAGGAAAAAAAA
* *
757 AAAGGAAAGAAAAATGATATTTAAAGCGAGAAAATTATTTCAA
515 AAAGG-AAGAAAAATCATATTTAAAGCGAGAAAATTATAT-AA
* *
800 TTTTTTTTGCTTTGAATTGTGTATTTTTTCCGAAAATA-TTTTTTATTTTTGCATGATTTTTGAC
1 TTTTTTTTGCTTTGAATTGTGTATTTTTTCCAAAAATATTTTTTTATTATTGCATGATTTTTGAC
* *
864 GTAAATACTCCTTGAATTATCTATATTCATCGAACAAAATCCCAGCCATATTCGATTTAAGTATT
66 GTAAATAATCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCCATATTCGATTTAAGTATT
*
929 TGTTTTTACGAGCATTTGAATCTTGTTTCAATTTAATTAAAAATTAATTCGGAAAAAAAATGG-A
131 TGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAATTCGG-AAAAAAATGGAA
* * * * * * *
993 AAAACGATATTAGAAGCGTTAAAACCCCGTCAATCTTTTTGGCGTTGAATTATGT-ATTTTTTCT
195 AAAACAATATTAGAAGCGTGAAAACCCCGTCAATATTTTTGACATTGAATTATATAATTTTTGCT
1057 GAGTATTGTGGCAAAAAATTGAGAAAAACCTTTTCCGAACAGTTTTTAGCCG-AAATCGA-GTAC
260 GAGTATTGTGGCAAAAAATTGAGAAAAA--TTTT-CGAACAGTTTTTAGCCGAAAATC-ATGTAC
* * * *
1120 TAACCATCATGGTTTTTGCCTAAAAACGCG-TTCCCGAGCCCTGACTCAATTTTGCATAATTTTT
321 TAACCATCACGGCTTTGGCCTAAAAACGCGTTTCCCGAGCCCCGACTCAATTTTGCAT-ATTTTT
* * * * *
1184 GG-TGCAAAGATTCCTTAAAATATCTATATTCATCAAACCAA-A-TGTCAGCCACATTGGATATA
385 GGCAG-AAAAACTCCTTAAAATATCTATATTCATCAAACCAACAGTCTCAGCCACATTAGATATA
* * *
1246 AGGATTTGTTTTTATGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTA-ATTCGGAAAAA
449 AGGATTTGTTTTTACGAGCATCTGAATATTATTTCGATTTAATTAGAAA-TAGATTAGGAAAAA
1309 TGATATTAAA
Statistics
Matches: 452, Mismatches: 49, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
555 73 0.16
556 2 0.00
558 1 0.00
560 36 0.08
561 199 0.44
562 88 0.19
563 53 0.12
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (555 bp):
TTTTTTTTGCTTTGAATTGTGTATTTTTTCCAAAAATATTTTTTTATTATTGCATGATTTTTGAC
GTAAATAATCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCCATATTCGATTTAAGTATT
TGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAATTCGGAAAAAAATGGAAA
AAACAATATTAGAAGCGTGAAAACCCCGTCAATATTTTTGACATTGAATTATATAATTTTTGCTG
AGTATTGTGGCAAAAAATTGAGAAAAATTTTCGAACAGTTTTTAGCCGAAAATCATGTACTAACC
ATCACGGCTTTGGCCTAAAAACGCGTTTCCCGAGCCCCGACTCAATTTTGCATATTTTTGGCAGA
AAAACTCCTTAAAATATCTATATTCATCAAACCAACAGTCTCAGCCACATTAGATATAAGGATTT
GTTTTTACGAGCATCTGAATATTATTTCGATTTAATTAGAAATAGATTAGGAAAAAAAAAAAGGA
AGAAAAATCATATTTAAAGCGAGAAAATTATATAA
Found at i:4530 original size:320 final size:323
Alignment explanation
Indices: 3940--4719 Score: 885
Period size: 320 Copynumber: 2.4 Consensus size: 323
3930 TATTTTTTAT
* * ** *
3940 TTTTGCATGA-TTTTTGACGTAAATACTCCTTGAAATATCTATATTCATCGAAGAAAATCCCAGC
1 TTTTGCATGATTTTTTG-CG-AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGC
* * * * * *
4004 CACGTTCG-ATTCAAGTATTTGTTTTTACGAGTATCTGAATCTTGTTTCAATTTAATTAAAAATT
64 CACATTAGAATT-AAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * * * *
4068 AATTCAGAAAAAAAATGGAAAAACAATATTAGAGGCGTGAAAAGCCCGTCAATATATTTGGCATT
128 AATTCACAAAAAAAATGGAAAAACAATATTAAAAGCGTGAAAAGACCATCAATATATTTGGCATT
* * * *
4133 GAATTATATATTTTTTCTGAGTATTGTGGCAAAAATTGAGAAAAAAAACTTTTCCAATCTGTTTT
193 GAATTATATATTTTTTCTGAATATTGTGGCAAAAATTCAGAAAAAAAAATTTT-C-ATCAGTTTT
* * *
4198 TAGCCGAAATCGTGT-GTTA-CATCACAG-TTTTAGGCTTAAAACGCG-TTCCCGAGCCCCGACT
256 TAGCCGAAATCGTGTACTAACCATCACAGTTTTTAGGCTAAAAACGCGTTTCCCGAGCCCCGACT
4259 TAA
321 TAA
* * *
4262 TTTTGCATGATTTTTTGCGCAAAGACACCTTGAAATATCTATATTCATCAAACCAAATATCAACC
1 TTTTGCATGATTTTTTGCG-AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCC
* * *
4327 ACATTGGAAATAAGGATTT-ATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
65 ACATTAGAATTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* ** * * * **
4391 TTC-CAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGACCATGAATCTTTTTGGTGTTGA
130 TTCACAAAAAAAATGGAAAAACAATATTAAAAGCGTGAAAAGACCATCAATATATTTGGCATTGA
*
4455 ATTATATATTTTTTCTGAATATTGTGGCAAAAAATTCAGAAAAAAAAATTTGT-TTCAGTTTTTA
195 ATTATATATTTTTTCTGAATATTGTGGC-AAAAATTCAGAAAAAAAAATTT-TCATCAGTTTTTA
** * ** * *
4519 GCCGAAAATCGTGTACTAACCATCATGGTTTTTGGGCTAAAAACGCGTTTCGGGGGCCCCGGCTT
258 GCCG-AAATCGTGTACTAACCATCACAGTTTTTAGGCTAAAAACGCGTTTCCCGAGCCCCGACTT
*
4584 AG
322 AA
* *
4586 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAATCTCAGGAT
1 TTTTGCATGATTTTTTGC-GAAAGACTCCTTGAAATATCTATATTCATC--A--AA-C-CA-AAT
* * *
4651 CTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTAAATATTGTTTCGATTTAATTAG
58 CTCAGCCACATTAGAATTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
4716 AAAT
123 AAAT
4720 AGATGCGGTA
Statistics
Matches: 383, Mismatches: 57, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
319 13 0.03
320 84 0.22
321 66 0.17
322 68 0.18
323 24 0.06
324 59 0.15
325 1 0.00
326 1 0.00
328 2 0.01
329 1 0.00
330 2 0.01
331 23 0.06
332 39 0.10
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (323 bp):
TTTTGCATGATTTTTTGCGAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCA
CATTAGAATTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAAT
TCACAAAAAAAATGGAAAAACAATATTAAAAGCGTGAAAAGACCATCAATATATTTGGCATTGAA
TTATATATTTTTTCTGAATATTGTGGCAAAAATTCAGAAAAAAAAATTTTCATCAGTTTTTAGCC
GAAATCGTGTACTAACCATCACAGTTTTTAGGCTAAAAACGCGTTTCCCGAGCCCCGACTTAA
Found at i:4899 original size:890 final size:877
Alignment explanation
Indices: 3776--5650 Score: 3039
Period size: 890 Copynumber: 2.1 Consensus size: 877
3766 TTTTAGTGCA
* **
3776 ACATTAGATTTAAGAATTTGTTTTTATAAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGA
1 ACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGA
*
3841 TTCGGAAAAAAAAAGATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTTGCT
66 TTCGGAAAAAAAAAGAAAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTTGCT
3906 TTGAATTGTGTATTTTTCCGAAAATATTTTTTATTTTTGCATGATTTTTGACGTAAATACTCCTT
131 TTGAATTGTGTATTTTTCCGAAAATATTTTTTATTTTTGCATGATTTTTGACGTAAATACTCCTT
* *
3971 GAAATATCTATATTCATCGAAGAAAATCCCAGCCACGTTCGATTCAAGTATTTGTTTTTACGAGT
196 GAAATATCTATATTCATCGAACAAAATCCCAGCCACGTTCGATTCAAGTATTTGTTTTTACGAGC
4036 ATCTGAATCTTGTTTCAATTTAATTAAAAATTAATTCAGAAAAAAAATGGAAAAACAATATTAGA
261 ATCTGAATCTTGTTTCAATTTAATTAAAAATTAATTC-GAAAAAAAATGGAAAAACAATATTAGA
* * * *
4101 GGCGTGAAAAGCCCGTCAATATATTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGG-CAA
325 AGCGTGAAAAG-CCGTCAATATATTTGACATTGAATTATATATTTTCTCTGAGTATTGTGGTAAA
* * *
4165 AAATTGAGAAAAAAAACTTTTCCAATCTGTTTTTAGCCGAAATCGTGT-GTTA-CATCACAGTTT
389 AAATTGAG-AAAAAAACTTTTCCAATCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTT
*
4228 TAGGCTTAAAACGCGTTCCCGAGCCCCGACTTAATTTTGCATGATTTTTTGCGCAAAGACACCTT
453 TAGGCTTAAAACGCGTTCCCGAGCCCCGACTTAATTTTGCATGATTTTTTGCGCAAAGACACCAT
*
4293 GAAATATCTATATTCATCAAACCAAATATCAACCACATTGGAAATAAGGATTT-ATTTTACGAGC
518 GAAATATCTATATTCATCAAACCAAATATCAACCACATTCGAAATAAGGATTTGATTTTACGAGC
4357 ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCC-AAAAAAATTGGAAAAATGATATTAAA
583 ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCCGAAAAAAATTGGAAAAATGATATTAAA
*
4421 AGCGTGAAAAGACCATGAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAATATTGTGGCAAA
648 AGCGTGAAAAGACCATGAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAATATCGTGGCAAA
4486 AAATTCAGAAAAAAAAATTTGTTTCAGTTTTTAGCCGAAAATCGTGTACTAACCATCATGGTTTT
713 AAATTCAGAAAAAAAAATTTGTTTCAGTTTTTAGCCGAAAATCGTGTACTAACCATCATGGTTTT
*
4551 TGGGCTAAAAACGCGTTTCGGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCAGAAAGACTCCT
778 TGGGCTAAAAACGCGTTTCGGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGAAAGACTCCT
* *
4616 TGAAATATCTATATTCATCTAACCAATCTCAGGATCTCAGCC
843 TGAAATATCTATATACATC--A--AA-C-CA-AATCTCAGCC
*
4658 ACATTAGATTTAAGGATTTGTTTTTACGAGCATCTAAATATTGTTTCGATTTAATTAGAAATAGA
1 ACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGA
*
4723 TGCGGTAAAAAAAAAGAAAAAGAAAGAGAAATGATATTTAAAGCGAG-AAAATATTTCAA-TTTT
66 TTCGG-AAAAAAAAAG--AAAG--A-A-AAATGATATTTAAAGCGAGAAAAATATTTCAATTTTT
*
4786 TTTTGCTTTGAATTGTGTATTTTTTTCCGAAAATTTTTTTTTATTTTTGCATGATTTTTGACGTA
124 TTTTGCTTTGAATTGTGTA--TTTTTCCGAAAA-TATTTTTTATTTTTGCATGATTTTTGACGTA
*
4851 AATACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCCACGTTCGATTTAAGTATTTGT
186 AATACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCCACGTTCGATTCAAGTATTTGT
* *
4916 TTTTACGAGCGTCTGAATCTTGTTTCAATTTAATTAAAAATTAATTCGGAAAAAAATGGAAAAAC
251 TTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAATTCGAAAAAAAATGGAAAAAC
* *
4981 AATATTAGAAGCGTGAAAAGCCGTTAATATTTTTGACATTGAATTATATATTTTCTCTGAGTATT
316 AATATTAGAAGCGTGAAAAGCCGTCAATATATTTGACATTGAATTATATATTTTCTCTGAGTATT
*
5046 GTGGTAAAAAATTGAGAAAAAAACTTTTCCGATCAGTTTTTAGCCGAAATCGTGTACTAACCATC
381 GTGGTAAAAAATTGAGAAAAAAACTTTTCCAATCAGTTTTTAGCCGAAATCGTGTACTAACCATC
* * * **
5111 ACGGTTTTTGGCTTAAAACGTGTTCCCGAGCCCCGACTTAATTTTGCATGATTTTTTGTTCAAAG
446 ACAGTTTTAGGCTTAAAACGCGTTCCCGAGCCCCGACTTAATTTTGCATGATTTTTTGCGCAAAG
* * * * *
5176 ACTCCATGAAATATCTATATTCATCAAACCAAATGTCAGCCACATTCGATATAAGGATTTGTTTT
511 ACACCATGAAATATCTATATTCATCAAACCAAATATCAACCACATTCGAAATAAGGATTTGATTT
5241 TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCCGAAAAAAATTGGAAAAATGA
576 TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCCGAAAAAAATTGGAAAAATGA
*
5306 TATTAAAAGCGTGAAAAGACCATGAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATCG
641 TATTAAAAGCGTGAAAAGACCATGAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAATATCG
5371 TGGCAAAAAATTCAGAAAAAAAAATTTGTTTCAGTTTTTAGCCGAAAATCGTGTACTAACCATCA
706 TGGCAAAAAATTCAGAAAAAAAAATTTGTTTCAGTTTTTAGCCGAAAATCGTGTACTAACCATCA
*
5436 TGGTTTTTTGGCTAAAAACGCGTTTCGGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGAAA
771 TGGTTTTTGGGCTAAAAACGCGTTTCGGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGAAA
*
5501 GACTCCTTGAAATATCTATATACATCAAACCAAATGTCAGCC
836 GACTCCTTGAAATATCTATATACATCAAACCAAATCTCAGCC
* * * * *
5543 ACATTGGATATAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAAAAATTA-
1 ACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAA-TAG
*** * *
5607 ATTCGGAAAAAAAAA-TTGGAAAAATGATATTAAAAGCGTGAAAA
65 ATTCGGAAAAAAAAAGAAAGAAAAATGATATTTAAAGCGAGAAAA
5651 GATCATCAAT
Statistics
Matches: 923, Mismatches: 53, Indels: 38
0.91 0.05 0.04
Matches are distributed among these distances:
877 17 0.02
878 4 0.00
879 1 0.00
881 1 0.00
882 65 0.07
883 10 0.01
884 9 0.01
885 71 0.08
886 4 0.00
887 25 0.03
888 97 0.11
889 79 0.09
890 257 0.28
891 48 0.05
892 235 0.25
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (877 bp):
ACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGA
TTCGGAAAAAAAAAGAAAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTTGCT
TTGAATTGTGTATTTTTCCGAAAATATTTTTTATTTTTGCATGATTTTTGACGTAAATACTCCTT
GAAATATCTATATTCATCGAACAAAATCCCAGCCACGTTCGATTCAAGTATTTGTTTTTACGAGC
ATCTGAATCTTGTTTCAATTTAATTAAAAATTAATTCGAAAAAAAATGGAAAAACAATATTAGAA
GCGTGAAAAGCCGTCAATATATTTGACATTGAATTATATATTTTCTCTGAGTATTGTGGTAAAAA
ATTGAGAAAAAAACTTTTCCAATCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTAG
GCTTAAAACGCGTTCCCGAGCCCCGACTTAATTTTGCATGATTTTTTGCGCAAAGACACCATGAA
ATATCTATATTCATCAAACCAAATATCAACCACATTCGAAATAAGGATTTGATTTTACGAGCATC
TGAATCTTGTTTCGATTTAATTAGAAATTAATTCCGAAAAAAATTGGAAAAATGATATTAAAAGC
GTGAAAAGACCATGAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAATATCGTGGCAAAAAA
TTCAGAAAAAAAAATTTGTTTCAGTTTTTAGCCGAAAATCGTGTACTAACCATCATGGTTTTTGG
GCTAAAAACGCGTTTCGGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGA
AATATCTATATACATCAAACCAAATCTCAGCC
Found at i:5535 original size:326 final size:326
Alignment explanation
Indices: 4830--5982 Score: 1536
Period size: 326 Copynumber: 3.5 Consensus size: 326
4820 TTTTTTTTAT
* * * * *
4830 TTTTGCATGATTTTTGAC-GTAAATACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGC
1 TTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGC
* * * * *
4894 CACGTTCGATTTAAGTATTTGTTTTTACGAGCGTCTGAATCTTGTTTCAATTTAATTAAAAATTA
65 CACATTCGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTA
** * * * * ***
4959 ATTCGG-AAAAAAA-TGGAAAAACAATATTAGAAGCGTGAAAAG-CCGTTAATATTTTTGACATT
130 ATTCGGAAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTT
* * * *
5021 GAATTATATATTTTCTCTGAGTATTGTGGTAAAAAATTGAGAAAAAAACTTTTCCGATCAGTTTT
195 GAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAATTTT--GATCAGTTTT
* * * ** *
5086 TAGCCG-AAATCGTGTACTAACCATCACGG-TTTTTGGCTTAAAACGTG-TTCCCGAGCCCCGAC
258 TAGCCGAAAATCGTGTACTAACCATCATGGTTTTTTGGCTAAAAACGCGTTTCGGGGGCCCCGAC
*
5148 TTAA
323 TTAG
* *** * *
5152 TTTTGCATGATTTTTTGTTCAAAGACTCCATGAAATATCTATATTCATCAAACCAAATGTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCC
*
5217 ACATTCGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
66 ACATTCGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAA
* *
5282 TTCCG-AAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGACCATGAATCTTTTTGGTGTTG
131 TTCGGAAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTG
* * *
5346 AATTATATATTTTTTCTGAGTATCGTGGCAAAAAATTCAGAAAAAAAAATTTGTTTCAGTTTTTA
196 AATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAATTTTG-ATCAGTTTTTA
5411 GCCGAAAATCGTGTACTAACCATCATGGTTTTTTGGCTAAAAACGCGTTTCGGGGGCCCCGACTT
260 GCCGAAAATCGTGTACTAACCATCATGGTTTTTTGGCTAAAAACGCGTTTCGGGGGCCCCGACTT
5476 AG
325 AG
* *
5478 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATACATCAAACCAAATGTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCC
* *
5543 ACATTGGATATAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAAAAATTAA
66 ACATTCGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAA
*
5608 TTCGGAAAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGATCATCAATCTTTTTGGTGTT
131 TTCGG-AAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTT
*
5673 GAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAG-AAAAAAATTTTGGGTCAGTTTTT
195 GAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAATTTT-GATCAGTTTTT
* * * *
5737 TGCCGAAAATCGTGTACTAACCATCATGGTTTTTGGGCTAAAAATGCGTTTCGGGGGCCCCG-GT
259 AGCCGAAAATCGTGTACTAACCATCATGGTTTTTTGGCTAAAAACGCGTTTCGGGGGCCCCGACT
5801 TAG
324 TAG
* *
5804 TTTTGCATGATTTTTGGCAGGAAGACTCCTTGAAATATCTATATTCATCTAACCAATCTCAGGAT
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATC--A--AA-C-CA-AAT
* * * * *
5869 CTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTAAATATTGTTTCGATTTAATTAG
59 CTCAGCCACATTCGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAA
* * * *
5934 AAA-TAGATTCGGAAAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAA
124 AAATTA-ATTCGGAAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAA
5983 ATATTTCAAT
Statistics
Matches: 740, Mismatches: 73, Indels: 26
0.88 0.09 0.03
Matches are distributed among these distances:
322 125 0.17
323 40 0.05
324 83 0.11
325 16 0.02
326 191 0.26
327 78 0.11
328 98 0.13
330 2 0.00
331 1 0.00
332 37 0.05
333 69 0.09
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (326 bp):
TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCC
ACATTCGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAA
TTCGGAAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTG
AATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAATTTTGATCAGTTTTTAG
CCGAAAATCGTGTACTAACCATCATGGTTTTTTGGCTAAAAACGCGTTTCGGGGGCCCCGACTTA
G
Found at i:6290 original size:570 final size:561
Alignment explanation
Indices: 5478--6543 Score: 1450
Period size: 570 Copynumber: 1.9 Consensus size: 561
5468 CCCGACTTAG
* * * ***
5478 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATACATCAAACCAAATGTCAGCC
1 TTTTGCATGACTTTTGGAAGAAAGACTCCTTGAAATATCTATATACATCAAACAAAACCCCAGCC
* * *
5543 ACATTGGATATAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAAAAATTAA
66 ACATTCGATATAAGGATTTGTTTTTACGAGAATCTGAATCTTATTTCAATTTAATTAAAAATTAA
* * ***
5608 TTCGGAAAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGATCATCAATCTTTTTGGTGTT
131 TTCGGAAAAAAAAATTGGAAAAACGATATTAAAAGCGTGAAAAGATCATCAATATTTTTGACATT
* *
5673 GAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAG-AAAAAAA-TTTT-GGGTCAGTTT
196 GAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAACTTTTCCGATCAGTTT
* * * * ** *
5735 TTTGCCGAAAATCGTGTACTAACCATCATGGTTTTTGGGCTAAAAATGCGTTTCGGGGGCCCCG-
261 TTAGCCG-AAATCGTATACTAACCATCACGGTTTTT-GGCTAAAAACGCG-TTCCCGAGCCCCGA
* * *
5799 GTTAGTTTTGCATGA-TTTTTG-GCAGGAAGACTCCTTGAAATATCTATATTCATCTAACCAATC
323 CTCAATTTTGCATGATTTTTTGCGCA--AAGACTCCTTGAAATATCTATATTCATC--A--AA-C
* * *
5862 TCAGGATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTAAATATTGTTTCGATT
381 T-A-AATCTCAGCCACATTAGATATAAGGATTTGCTTTTACGAGCATCTAAATATTGTTTCGATT
*
5927 TAATTAGAAA-TAGATTCGGAAAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCA
444 TAATTAGAAATTA-ATTCGG---AAAAAATAGAAAAATGATATTAAAAGCGAGAAAAATATTTCA
5991 ATTTTTTTTATTTTTTTGCGTTGAATTGTGTATTTTTTGCCGAAAATATTTTTTTAT
505 ATTTTTTTTATTTTTTTGCGTTGAATTGTGTATTTTTTGCCGAAAATATTTTTTTAT
* *
6048 TTTTGCATGACTTTT-GAAGTAAATACTCCTTGAAATATCTATATTCATCAAACAAAACCCCAGC
1 TTTTGCATGACTTTTGGAAG-AAAGACTCCTTGAAATATCTATATACATCAAACAAAACCCCAGC
* * * *
6112 CACGTTCGATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTATTTCAATTTAATTAAAAATTA
65 CACATTCGATATAAGGATTTGTTTTTACGAGAATCTGAATCTTATTTCAATTTAATTAAAAATTA
* * *
6177 ATTCGGAAAAAAAAA-TGTAAAAACGATATTAGAAGCGTGAAAAG-TCCGTCAATATTTTTGACA
130 ATTCGGAAAAAAAAATTGGAAAAACGATATTAAAAGCGTGAAAAGAT-CATCAATATTTTTGACA
*
6240 TTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAAACTTTTCCGATCAG
194 TTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAG-AAAAAAAACTTTTCCGATCAG
* *
6305 TTTTTAGCCGAAATCGTATACTAACCATCACGGTTTTTTGCTGAAAACGCGTTCCCGAGCCCCGA
258 TTTTTAGCCGAAATCGTATACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCGA
* *
6370 CTCAATTTTGCATTATTTTTTGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACTAAATGT
323 CTCAATTTTGCATGATTTTTTGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACTAAATCT
* * *
6435 CAGCCACATTGGATATAAGGATTTGCTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
388 CAGCCACATTAGATATAAGGATTTGCTTTTACGAGCATCTAAATATTGTTTCGATTTAATTAGAA
* *
6500 ATTAATTCGGAAAAAATGGAAAAATGATATTAAAAGCGTGAAAA
453 ATTAATTCGGAAAAAATAGAAAAATGATATTAAAAGCGAGAAAA
6544 GACCATCAAT
Statistics
Matches: 437, Mismatches: 49, Indels: 29
0.85 0.10 0.06
Matches are distributed among these distances:
561 31 0.07
564 70 0.16
565 3 0.01
566 2 0.00
567 2 0.00
568 1 0.00
569 84 0.19
570 135 0.31
571 56 0.13
572 36 0.08
573 17 0.04
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (561 bp):
TTTTGCATGACTTTTGGAAGAAAGACTCCTTGAAATATCTATATACATCAAACAAAACCCCAGCC
ACATTCGATATAAGGATTTGTTTTTACGAGAATCTGAATCTTATTTCAATTTAATTAAAAATTAA
TTCGGAAAAAAAAATTGGAAAAACGATATTAAAAGCGTGAAAAGATCATCAATATTTTTGACATT
GAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAACTTTTCCGATCAGTTT
TTAGCCGAAATCGTATACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACTC
AATTTTGCATGATTTTTTGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACTAAATCTCAG
CCACATTAGATATAAGGATTTGCTTTTACGAGCATCTAAATATTGTTTCGATTTAATTAGAAATT
AATTCGGAAAAAATAGAAAAATGATATTAAAAGCGAGAAAAATATTTCAATTTTTTTTATTTTTT
TGCGTTGAATTGTGTATTTTTTGCCGAAAATATTTTTTTAT
Done.