Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010515.1 Corchorus capsularis cultivar CVL-1 contig10536, 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: 159500
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:914 original size:326 final size:319
Alignment explanation
Indices: 16--2454 Score: 2537
Period size: 326 Copynumber: 7.5 Consensus size: 319
6 AATGATATTA
* * *
16 ATTAGAAGCGTGAAAAACCCATCAATCTTTTTGGCGTTGAATTATTTAATTTTTCTCAATA-GTT
1 ATTAGAAGCGTGAAAAACCCATCAATCTTTTTGGCGTTGAATTATAT-ATTTTTCTGAATATTTT
* * * * *
80 TGAAAAAAATTGAGAAAAAAAACTTTTCGGGTTAACTCTTAGCCGAAATCGTGTATTAAAACATC
65 TGAAAAAAATTGAG--AAAAAACTTTTCGGGTTAATTTTTAGCTGAAATCGTGTACT-AACCATC
* * ** * * * *
145 ACTGCTTTTTGCTATAATTGCGTTTTGGGGCTCCGGTTCTGTTTTGCATGACTTTTGGCAGAACA
127 AC-GGTTTTTGCTAGAAACGCGTTTCGGGGCTCCGGCTCAGTTTTGCATGATTTTTGGCAGAA-A
*
210 ACTCCTTGAAATATCTATATTCATCTAACCAAATCTAAGTCACAACGGATTTAAGGATTTGTTTT
190 ACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACAACGGATTTAAGGATTTGTTTT
* *
275 TACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATAAATTCGAAAAAAAATGAAAATATGAT
255 TACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATAAATTCGAAAAAAAATGAAAAAACGAT
* ** * *
340 ATAAGAAGCGTGAAAGCCCCATTAATCTTTTTGGCGTTCAATTATATATTTTTCTGAATATTTTC
1 ATTAGAAGCGTGAAAAACCCATCAATCTTTTTGGCGTTGAATTATATATTTTTCTGAATATTTT-
** * **
405 CAAAAAAAATTG-G-AAAAACTCTTCGGGCCAGA-TTTTAGCTGAAATCGTGTACTAACCATCAC
65 TGAAAAAAATTGAGAAAAAACTTTTCGGGTTA-ATTTTTAGCTGAAATCGTGTACTAACCATCAC
* * * * * *
467 GGTTTTTGGCTTA-AAACGCGTTTCCGGCCTCCGGCTCTA-TTTTACATAATATTTGGCAGAACG
129 GGTTTTT-GC-TAGAAACGCGTTTCGGGGCTCCGGCTC-AGTTTTGCATGATTTTTGGCAGAA-A
* *
530 ACTCCTTGAAATATTTATATTCATCTAACCAAATATCAGTCACAACGGATTTAAGGATTTGTTTT
190 ACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACAACGGATTTAAGGATTTGTTTT
* *
595 TACGAGCATCTGAATTTTATTTCGATTTAATTTGAAATAAATTCGAAAAAAAAATGAAAAAACGA
255 TACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATAAATTCG-AAAAAAAATGAAAAAACGA
660 T
319 T
* * * *
661 ATTAGAAACGTTAAAAACCCATCAATCTTTTTGACGTTGAATTATATTATTTTCTCTCAATATTT
1 ATTAGAAGCGTGAAAAACCCATCAATCTTTTTGGCGTTGAATTATA-TATTTT-TCTGAATATTT
*
726 TTG-AAAAAATTGAGAAAAAAAAAACTTTTCGGGTTAATTCTTAGCTGAAATCGTGTACTAA-CA
64 TTGAAAAAAATTGAG----AAAAAACTTTTCGGGTTAATTTTTAGCTGAAATCGTGTACTAACCA
* * ** * *
789 TCACTGCTTTTTGCTAGAAATGTATTTCGGGGCTCCGGCTCTGTTTTGCATGACTTTTGGCAGAA
125 TCAC-GGTTTTTGCTAGAAACGCGTTTCGGGGCTCCGGCTCAGTTTTGCATGATTTTTGGCAGAA
*
854 CAACTCCTTGAAATATCTATATTCAGCTAACCAAATCTCAGTCACAACGGATTTAAGGATTTGTT
189 -AACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACAACGGATTTAAGGATTTGTT
** *
919 TTTACGAGCCCCTAAATCTTGTTTCGATTTAATTTGAAATAAATTCGAAAAAAAAAATG-AAAAA
253 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATAAATTCG--AAAAAAAATGAAAAAA
983 CGAT
316 CGAT
* * * * *
987 ATTAAAAGTGTGAAAATCCCATCAATCATTTTGGCGTTGAATTATATTATTTTCCTGAATATTTT
1 ATTAGAAGCGTGAAAAACCCATCAATCTTTTTGGCGTTGAATTATA-TATTTTTCTGAATATTTT
** * * * * * *
1052 CCAGAAAAATTGAG-AAAAACTCTTCGGGTCAGTTTTTAGCTGAAACCGTGTAATAACCATCACG
65 TGAAAAAAATTGAGAAAAAACTTTTCGGGTTAATTTTTAGCTGAAATCGTGTACTAACCATCACG
* *
1116 GTTTTTGGCTAAAAACGCGTTTCAGGGCTCCGGCTCTA-TTTTGCATGATTTTTGGCAGAAAGAC
130 GTTTTT-GCTAGAAACGCGTTTCGGGGCTCCGGCTC-AGTTTTGCATGATTTTTGGCAGAAA-AC
* * *
1180 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACAATGGATTTATGGATTTATTTTTA
192 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACAACGGATTTAAGGATTTGTTTTTA
*
1245 CGAGAATCTGAATCTTGTTTCGATTTAATTTGAAATAAATTCG-AAAAAAATGAAAAAAAAAAAC
257 CGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATAAATTCGAAAAAAAATG------AAAAA-
1309 ACGAT
315 ACGAT
* *
1314 ATTAGAAGCGTGAAAAACCCATCAATATTTTTGGCGCTGAATTATATATTTTTCTGAATA-TTTT
1 ATTAGAAGCGTGAAAAACCCATCAATCTTTTTGGCGTTGAATTATATATTTTTCTGAATATTTTT
* * * ** * *
1378 GCAAAAAAATTGAGAGAAAACTTTCCAGGTTAATTTTTAGCCAAAATCGTGTACCAACTATCACG
66 G-AAAAAAATTGAGAAAAAACTTTTCGGGTTAATTTTTAGCTGAAATCGTGTACTAACCATCACG
* * * * *
1443 GTTTTTGGCTGGAAACGCCTTTCGGGGCTCAGTCTCAGTTTTGCATGATATTTGGCAGAAAGACT
130 GTTTTT-GCTAGAAACGCGTTTCGGGGCTCCGGCTCAGTTTTGCATGATTTTTGGCAGAAA-ACT
* * * * **
1508 CCTTGAAATGTCTATATTCGTCTAGCCAAATCTCAGCCACATTGGATTTAAGGATTT-TCTTTT-
193 CCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACAACGGATTTAAGGATTTGT-TTTTA
* ** *
1571 TGAGCATCTGAATCTTGTTTCGATTTAATTTGAAA-AAATTCGGGAAAAAAAA-G-GGAAATGAT
257 CGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATAAATTC--GAAAAAAAATGAAAAAACGAT
* * * * * *
1633 ATTAGAAGCTTG-AAAACCCATTCAATTTTTTTGGCATTGAGTTATATATTTTTCTGAGTATTGT
1 ATTAGAAGCGTGAAAAACCCA-TCAATCTTTTTGGCGTTGAATTATATATTTTTCTGAATATTTT
* * * * * *
1697 GGCAAAATAATTGA-AGAAAAATTTTTCGAGTCAGTTTTGTAAAATGTTAGCTGAAATCGTGTGC
65 TG-AAAAAAATTGAGA-AAAAACTTTTCG-G---G---T-T-AATTTTTAGCTGAAATCGTGTAC
* * * ** * * *
1761 TAACTATCACGGTTTTTGCCTACAAACGCGTTCCGGAACCCCGGCTCAATTTGGCATGATTTTTG
119 TAACCATCACGGTTTTTG-CTAGAAACGCGTTTCGGGGCTCCGGCTCAGTTTTGCATGATTTTTG
* * * * * * *
1826 GC-GCAAAAACTCTTTGAAATATC---ATTCATCAAACAAAATCCCAGCCACATCGGATATAAGG
183 GCAG--AAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACAACGGATTTAAGG
* * * * * * * *
1887 ATTTGTTTTTACGAACTTCTGAATTTTTTTTCGATTTAATTAGAAATTAATTTTG-AAAAGAATG
246 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAA-TAAATTCGAAAAAAAAT-
1951 GAAAAAACGAT
309 GAAAAAACGAT
* * * * * * * * *
1962 ATTAGAAGCGTGATAATCTC-TCATTCATTTTGACGTCGAATTTTATATTTTTCTGAATATTTTC
1 ATTAGAAGCGTGAAAAACCCATCAATCTTTTTGGCGTTGAATTATATATTTTTCTGAATATTTTT
* * * * * * * * *
2026 CAGAAAAATTGAG-AAAAACTCTTCGAGTCAGTTTTTAGCTGAAATTGTGTACTAAGCATCACAG
66 GAAAAAAATTGAGAAAAAACTTTTCGGGTTAATTTTTAGCTGAAATCGTGTACTAACCATCACGG
* * * * * *
2090 TTTTGGGATAAAAACGCGTTTCCGGGCCCCGGCTAAGTTTTGCATGATTTTTGGCAGAAAGACTC
131 TTTT-TGCTAGAAACGCGTTTCGGGGCTCCGGCTCAGTTTTGCATGATTTTTGGCAGAAA-ACTC
* ** * *
2155 CTTGAAATATCTATATTCATCTAACCAAATCTCAGTCATATTGGATTGAAGGATTTATTTTTACG
194 CTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACAACGGATTTAAGGATTTGTTTTTACG
* *
2220 GGCATCTGAATCTTTTTTCGATTTAATTTGAAAT-AATGTCG--AAAAAATGAAAAAACGAT
259 AGCATCTGAATCTTGTTTCGATTTAATTTGAAATAAAT-TCGAAAAAAAATGAAAAAACGAT
* *
2279 ATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATA-TTT
1 ATTAGAAGCGTGAAAAACCCATCAATCTTTTTGGCGTTGAATTATATA-TTTTTCTGAATATTTT
*
2343 TGCAAAAAAAATTGAGAAAAAAAACTTTTCGGGTTAATTTTTAGCCGAAATCGTGTACTAACCAT
65 TG--AAAAAAATTGAG--AAAAAACTTTTCGGGTTAATTTTTAGCTGAAATCGTGTACTAACCAT
* ** *
2408 CACGGTTTTTTGCTGGAAACATGTTTCGGGGCTCCGTCTCAGTTTTG
126 CACGG-TTTTTGCTAGAAACGCGTTTCGGGGCTCCGGCTCAGTTTTG
2455 TAGTTAAGGA
Statistics
Matches: 1751, Mismatches: 285, Indels: 159
0.80 0.13 0.07
Matches are distributed among these distances:
316 3 0.00
317 112 0.06
318 43 0.02
319 81 0.05
320 257 0.15
321 143 0.08
322 162 0.09
323 93 0.05
324 49 0.03
325 31 0.02
326 332 0.19
327 290 0.17
328 44 0.03
329 104 0.06
330 7 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (319 bp):
ATTAGAAGCGTGAAAAACCCATCAATCTTTTTGGCGTTGAATTATATATTTTTCTGAATATTTTT
GAAAAAAATTGAGAAAAAACTTTTCGGGTTAATTTTTAGCTGAAATCGTGTACTAACCATCACGG
TTTTTGCTAGAAACGCGTTTCGGGGCTCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAACTCCT
TGAAATATCTATATTCATCTAACCAAATCTCAGTCACAACGGATTTAAGGATTTGTTTTTACGAG
CATCTGAATCTTGTTTCGATTTAATTTGAAATAAATTCGAAAAAAAATGAAAAAACGAT
Found at i:1400 original size:648 final size:642
Alignment explanation
Indices: 16--2417 Score: 2687
Period size: 646 Copynumber: 3.7 Consensus size: 642
6 AATGATATTA
* * * *
16 ATTAGAAGCGTGAAAAACCCATCAATCTTTTTGGCGTTGAATTATTTAATTTTTCTCAATAGTTT
1 ATTAGAAGCGTGAAAAACCCATCAATATTTTTGACGTTGAATTATAT-ATTTTTCTCAATATTTT
* *
81 GAAAAAAATTGAGAAAAAAAACTTTTCGGGTTAACTCTTAGCCGAAATCGTGTATTAAAACATCA
65 GAAAAAAATTGAG-AAAAAAACTTTTCGGGTTAATTCTTAGCCGAAATCGTGTACT--AACATCA
* ** * * *
146 CTGCTTTTTGCTATAATTGCGTTTTGGGGCTCCGGTTCTGTTTTGCATGACTTTTGGCAGAACA-
127 CTGCTTTTTGCTAGAAACGCGTTTCGGGGCTCCGGCTCAGTTTTGCATGACTTTTGGCAGAA-AG
* *
210 ACTCCTTGAAATATCTATATTCATCTAACCAAATCTAAGTCACAACGGATTTAAGGATTTGTTTT
191 ACTCCTTGAAATATCTATATTCAGCTAACCAAATCTCAGTCACAACGGATTTAAGGATTTGTTTT
*
275 TACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATAAATTCGAAAAAAAATGAAAATATGAT
256 TACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATAAATTCGAAAAAAAATGAAAA-ACGAT
* * *
340 A-TAAGAAGCGTGAAAGCCCCATTAATCTTTTTGGCGTTCAATTATATATTTTTCTGAATATTTT
320 ATTAA-AAGCGTGAAA-ACCCATCAATCTTTTTGGCGTTGAATTATATATTTTTCTGAATATTTT
* *
404 CCAAAAAAAATTG-GAAAAACTCTTCGGGCCAGATTTTAGCTGAAATCGTGTACTAACCATCACG
383 CC-AAAAAAATTGAGAAAAACTCTTCGGGTCAGTTTTTAGCTGAAATCGTGTACTAACCATCACG
* * * * * *
468 GTTTTTGGCTTAAAACGCGTTTCCGGCCTCCGGCTCTATTTTACATAATATTTGGCAGAACGACT
447 GTTTTTGGCTAAAAACGCGTTTCCGGACTCCGGCTCTATTTTGCATGATTTTTGGCAGAAAGACT
* * *
533 CCTTGAAATATTTATATTCATCTAACCAAATATCAGTCACAACGGATTTAAGGATTTGTTTTTAC
512 CCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACAATGGATTTAAGGATTTGTTTTTAC
* *
598 GAGCATCTGAATTTTATTTCGATTTAATTTGAAATAAATTCG-AAAAAA--AAATGAAAAAACGA
577 GAGAATCTGAATTTTATTTCGATTTAATTTGAAATAAATTCGAAAAAAATGAAAAGAAAAAACGA
660 T
642 T
* * *
661 ATTAGAAACGTTAAAAACCCATCAATCTTTTTGACGTTGAATTATATTATTTTCTCTCAATATTT
1 ATTAGAAGCGTGAAAAACCCATCAATATTTTTGACGTTGAATTATA-TATTTT-TCTCAATA-TT
*
726 TTG-AAAAAATTGAGAAAAAAAAAACTTTTCGGGTTAATTCTTAGCTGAAATCGTGTACTAACAT
63 TTGAAAAAAATTGAG---AAAAAAACTTTTCGGGTTAATTCTTAGCCGAAATCGTGTACTAACAT
* ** *
790 CACTGCTTTTTGCTAGAAATGTATTTCGGGGCTCCGGCTCTGTTTTGCATGACTTTTGGCAGAAC
125 CACTGCTTTTTGCTAGAAACGCGTTTCGGGGCTCCGGCTCAGTTTTGCATGACTTTTGGCAGAA-
855 A-ACTCCTTGAAATATCTATATTCAGCTAACCAAATCTCAGTCACAACGGATTTAAGGATTTGTT
189 AGACTCCTTGAAATATCTATATTCAGCTAACCAAATCTCAGTCACAACGGATTTAAGGATTTGTT
** *
919 TTTACGAGCCCCTAAATCTTGTTTCGATTTAATTTGAAATAAATTCGAAAAAAAAAATGAAAAAC
254 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATAAATTCG--AAAAAAAATGAAAAAC
* * *
984 GATATTAAAAGTGTGAAAATCCCATCAATCATTTTGGCGTTGAATTATATTATTTTCCTGAATAT
317 GATATTAAAAGCGTGAAAA-CCCATCAATCTTTTTGGCGTTGAATTATA-TATTTTTCTGAATAT
* * *
1049 TTTCCAGAAAAATTGAGAAAAACTCTTCGGGTCAGTTTTTAGCTGAAACCGTGTAATAACCATCA
380 TTTCCAAAAAAATTGAGAAAAACTCTTCGGGTCAGTTTTTAGCTGAAATCGTGTACTAACCATCA
* *
1114 CGGTTTTTGGCTAAAAACGCGTTTCAGGGCTCCGGCTCTATTTTGCATGATTTTTGGCAGAAAGA
445 CGGTTTTTGGCTAAAAACGCGTTTCCGGACTCCGGCTCTATTTTGCATGATTTTTGGCAGAAAGA
* *
1179 CTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACAATGGATTTATGGATTTATTTTT
510 CTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACAATGGATTTAAGGATTTGTTTTT
* * *
1244 ACGAGAATCTGAATCTTGTTTCGATTTAATTTGAAATAAATTCGAAAAAAATGAAAAAAAAAAAC
575 ACGAGAATCTGAATTTTATTTCGATTTAATTTGAAATAAATTCGAAAAAAATG-AAAAGAAAAA-
1309 ACGAT
638 ACGAT
* * *
1314 ATTAGAAGCGTGAAAAACCCATCAATATTTTTGGCGCTGAATTATATATTTTTCTGAATATTTTG
1 ATTAGAAGCGTGAAAAACCCATCAATATTTTTGACGTTGAATTATATATTTTTCTCAATATTTTG
* * * * * *
1379 CAAAAAAATTGAG-AGAAAACTTTCCAGGTTAATTTTTAGCCAAAATCGTGTACCAACTATCAC-
66 -AAAAAAATTGAGAAAAAAACTTTTCGGGTTAATTCTTAGCCGAAATCGTGTACTAAC-ATCACT
* * * * *
1442 GGTTTTTGGCTGGAAACGCCTTTCGGGGCTCAGTCTCAGTTTTGCATGA-TATTTGGCAGAAAGA
129 GCTTTTT-GCTAGAAACGCGTTTCGGGGCTCCGGCTCAGTTTTGCATGACT-TTTGGCAGAAAGA
* * * **
1506 CTCCTTGAAATGTCTATATTC-GTCTAGCCAAATCTCAGCCACATTGGATTTAAGGATTT-TCTT
192 CTCCTTGAAATATCTATATTCAG-CTAACCAAATCTCAGTCACAACGGATTTAAGGATTTGT-TT
* ** *
1569 TT-TGAGCATCTGAATCTTGTTTCGATTTAATTTGAAA-AAATTCGGGAAAAAAAA-GGGAAATG
255 TTACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATAAATTC--GAAAAAAAATGAAAAACG
* * * * * *
1631 ATATTAGAAGCTTGAAAACCCATTCAATTTTTTTGGCATTGAGTTATATATTTTTCTGAGTATTG
318 ATATTAAAAGCGTGAAAACCCA-TCAATCTTTTTGGCGTTGAATTATATATTTTTCTGAATATT-
** * * * * *
1696 TGGCAAAATAATTGAAGAAAAATTTTTCGAGTCAGTTTTGTAAAATGTTAGCTGAAATCGTGTGC
381 TTCCAAAAAAATTG-AGAAAAACTCTTCGGGTCAG---T-T----T-TTAGCTGAAATCGTGTAC
* * * * * *
1761 TAACTATCACGGTTTTTGCCTACAAACGCG-TTCCGGAACCCCGGCTCAATTTGGCATGATTTTT
436 TAACCATCACGGTTTTTGGCTAAAAACGCGTTTCCGG-ACTCCGGCTCTATTTTGCATGATTTTT
* * * * * * *
1825 GGC-GCAAAAACTCTTTGAAATATC---ATTCATCAAACAAAATCCCAGCCAC-ATCGGATATAA
500 GGCAG-AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACAAT-GGATTTAA
* * * * * *
1885 GGATTTGTTTTTACGA-ACTTCTGAATTTTTTTTCGATTTAATTAGAAATTAATTTTGAAAAGAA
563 GGATTTGTTTTTACGAGA-ATCTGAATTTTATTTCGATTTAATTTGAAA-TAAATTCGAAAAAAA
1949 TG----GAAAAAACGAT
626 TGAAAAGAAAAAACGAT
* * * * * * *
1962 ATTAGAAGCGTGATAATCTC-TCATTCA-TTTTGACGTCGAATTTTATATTTTTCTGAATATTTT
1 ATTAGAAGCGTGAAAAACCCATCAAT-ATTTTTGACGTTGAATTATATATTTTTCTCAATATTTT
* * * * * * * * *
2025 CCAGAAAAATTGAG--AAAAACTCTTCGAGTCAGTTTTTAGCTGAAATTGTGTACTAAGCATCAC
65 -GAAAAAAATTGAGAAAAAAACTTTTCGGGTTAATTCTTAGCCGAAATCGTGTACTAA-CATCAC
* * * * * * * *
2088 AG-TTTTGGGATAAAAACGCGTTTCCGGGCCCCGGCTAAGTTTTGCATGATTTTTGGCAGAAAGA
128 TGCTTTT-TGCTAGAAACGCGTTTCGGGGCTCCGGCTCAGTTTTGCATGACTTTTGGCAGAAAGA
* * ** * *
2152 CTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCATATTGGATTGAAGGATTTATTTTT
192 CTCCTTGAAATATCTATATTCAGCTAACCAAATCTCAGTCACAACGGATTTAAGGATTTGTTTTT
* *
2217 ACGGGCATCTGAATCTTTTTTCGATTTAATTTGAAAT-AATGTCG--AAAAAATGAAAAAACGAT
257 ACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATAAAT-TCGAAAAAAAATG-AAAAACGAT
* *
2279 ATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTT
320 ATTAAAAGCGTGAAAA-CCCATCAATCTTTTTGGCGTTGAATTATATA-TTTTTCTGAATATTTT
* * * * *
2344 GCAAAAAAAATTGAGAAAAAAAACTTTTCGGGTTAATTTTTAGCCGAAATCGTGTACTAACCATC
383 -CCAAAAAAATTGAG---AAAAACTCTTCGGGTCAGTTTTTAGCTGAAATCGTGTACTAACCATC
2409 ACGGTTTTT
444 ACGGTTTTT
2418 TGCTGGAAAC
Statistics
Matches: 1510, Mismatches: 185, Indels: 129
0.83 0.10 0.07
Matches are distributed among these distances:
640 32 0.02
641 1 0.00
644 6 0.00
645 67 0.04
646 432 0.29
647 195 0.13
648 383 0.25
649 132 0.09
650 6 0.00
651 8 0.01
652 28 0.02
653 114 0.08
654 14 0.01
655 7 0.00
656 85 0.06
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (642 bp):
ATTAGAAGCGTGAAAAACCCATCAATATTTTTGACGTTGAATTATATATTTTTCTCAATATTTTG
AAAAAAATTGAGAAAAAAACTTTTCGGGTTAATTCTTAGCCGAAATCGTGTACTAACATCACTGC
TTTTTGCTAGAAACGCGTTTCGGGGCTCCGGCTCAGTTTTGCATGACTTTTGGCAGAAAGACTCC
TTGAAATATCTATATTCAGCTAACCAAATCTCAGTCACAACGGATTTAAGGATTTGTTTTTACGA
GCATCTGAATCTTGTTTCGATTTAATTTGAAATAAATTCGAAAAAAAATGAAAAACGATATTAAA
AGCGTGAAAACCCATCAATCTTTTTGGCGTTGAATTATATATTTTTCTGAATATTTTCCAAAAAA
ATTGAGAAAAACTCTTCGGGTCAGTTTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGC
TAAAAACGCGTTTCCGGACTCCGGCTCTATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAAT
ATCTATATTCATCTAACCAAATCTCAGTCACAATGGATTTAAGGATTTGTTTTTACGAGAATCTG
AATTTTATTTCGATTTAATTTGAAATAAATTCGAAAAAAATGAAAAGAAAAAACGAT
Found at i:3506 original size:29 final size:29
Alignment explanation
Indices: 3468--3525 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
3458 TTTCGTTTTT
3468 AAAAGTTAAGGGGAT-AATTTGTCCCAAAA
1 AAAAGTTAAGGGG-TCAATTTGTCCCAAAA
3497 AAAAGTTAAGGGGTCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGTCAATTTGTCCCAAAA
3526 TGGATAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (29 bp):
AAAAGTTAAGGGGTCAATTTGTCCCAAAA
Found at i:25371 original size:2 final size:2
Alignment explanation
Indices: 25364--25389 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25354 GAGTTATACT
25364 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
25390 AATCAAAAGG
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):
TA
Found at i:29698 original size:15 final size:15
Alignment explanation
Indices: 29678--29708 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29668 GAAACTGATC
29678 TGCTATAATATATAA
1 TGCTATAATATATAA
29693 TGCTATAATATATAA
1 TGCTATAATATATAA
29708 T
1 T
29709 TAATGACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (15 bp):
TGCTATAATATATAA
Found at i:32594 original size:30 final size:30
Alignment explanation
Indices: 32554--32616 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
32544 CCATCAGAAA
32554 AGGACTTATTTAGCC-TTTT-TAAAGAGTTC
1 AGGACTTATTTAGCCATTTTGTAAA-AGTTC
* *
32583 AGGAGCTTATTTGGCCATTTTGTATAAGTTC
1 AGGA-CTTATTTAGCCATTTTGTAAAAGTTC
32614 AGG
1 AGG
32617 GGCCTTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.14
30 10 0.34
31 12 0.41
32 3 0.10
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (30 bp):
AGGACTTATTTAGCCATTTTGTAAAAGTTC
Found at i:36127 original size:45 final size:45
Alignment explanation
Indices: 36052--36141 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
36042 AAAAGACAAA
*
36052 ATGTTGAATTGTTCTACGTTGAACTGTATTTTT-TAGTCAAATGGT
1 ATGTTGAATTGTTCTACGTTGAACTATATTTTTAT-GTCAAATGGT
*
36097 ATGTTGAATTGTTCTAC-TTTAATCTATATTTTTATGTCAAATGGT
1 ATGTTGAATTGTTCTACGTTGAA-CTATATTTTTATGTCAAATGGT
36142 TAATATTTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 4 0.10
45 36 0.88
46 1 0.02
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49
Consensus pattern (45 bp):
ATGTTGAATTGTTCTACGTTGAACTATATTTTTATGTCAAATGGT
Found at i:48361 original size:27 final size:26
Alignment explanation
Indices: 48318--48368 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
48308 TTTTTAAAGA
48318 TTTTTTTTGTCTAAACTATCTTCATT
1 TTTTTTTTGTCTAAACTATCTTCATT
48344 TTTTTTTTGGT-TACAACTATCTTCA
1 TTTTTTTT-GTCTA-AACTATCTTCA
48369 ATCAATGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.20, C:0.16, G:0.06, T:0.59
Consensus pattern (26 bp):
TTTTTTTTGTCTAAACTATCTTCATT
Found at i:52341 original size:34 final size:34
Alignment explanation
Indices: 52298--52363 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
52288 ATCAACTAAT
*
52298 TCTATTGGACCTGAGCCTTGGTCCAAGTTCTAGA
1 TCTATTGGACCTGAGCCTTGATCCAAGTTCTAGA
52332 TCTATTGGACCTGAGCCTTGATCCAAGTTCTA
1 TCTATTGGACCTGAGCCTTGATCCAAGTTCTA
52364 TAAAGTCTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33
Consensus pattern (34 bp):
TCTATTGGACCTGAGCCTTGATCCAAGTTCTAGA
Found at i:64845 original size:29 final size:30
Alignment explanation
Indices: 64778--64834 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
64768 TAGTTTGATG
* *
64778 GGACAAAACGTCCCAAAATTGAAGTTCAAT
1 GGACAAAATGTCCCAAAATTAAAGTTCAAT
64808 GGACAAAATGT-CCAAAATTAAAGTTCA
1 GGACAAAATGTCCCAAAATTAAAGTTCA
64835 TGAGGCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.21
Consensus pattern (30 bp):
GGACAAAATGTCCCAAAATTAAAGTTCAAT
Found at i:64851 original size:29 final size:29
Alignment explanation
Indices: 64789--64852 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
64779 GACAAAACGT
* *
64789 CCCAAAATTGAAGTTCAATGGACAAAATG
1 CCCAAAATTAAAGTTCAATGGACAAAATA
* *
64818 TCCAAAATTAAAGTTC-ATGAGGCAAAATA
1 CCCAAAATTAAAGTTCAATG-GACAAAATA
64847 CCCAAA
1 CCCAAA
64853 CGCTGTAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 3 0.10
29 26 0.90
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.20
Consensus pattern (29 bp):
CCCAAAATTAAAGTTCAATGGACAAAATA
Found at i:65609 original size:54 final size:54
Alignment explanation
Indices: 65495--65613 Score: 148
Period size: 54 Copynumber: 2.2 Consensus size: 54
65485 GTCAGTGCCG
* *
65495 GAACTTGGACCAGAGTTGGTGACAGCATCAGTAAATGCATGGCCTTTTCCACCA
1 GAACTTGGACCAGAGTTGGTGACAGCATCAGTAAATGCATGACCTTCTCCACCA
* * * * ** * *
65549 GGACTTGGGCCTGAGTTGGTGACAGCTTTGGTAAATGCATGACCTTCTCCTCCT
1 GAACTTGGACCAGAGTTGGTGACAGCATCAGTAAATGCATGACCTTCTCCACCA
65603 GAACTTGGACC
1 GAACTTGGACC
65614 TCCGGTCTTG
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (54 bp):
GAACTTGGACCAGAGTTGGTGACAGCATCAGTAAATGCATGACCTTCTCCACCA
Found at i:72276 original size:13 final size:14
Alignment explanation
Indices: 72252--72280 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
72242 AGATTATAAA
72252 ATTTTTGTGAGGAT
1 ATTTTTGTGAGGAT
72266 ATTTTTG-GAGGAT
1 ATTTTTGTGAGGAT
72279 AT
1 AT
72281 AGGAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (14 bp):
ATTTTTGTGAGGAT
Found at i:77854 original size:11 final size:11
Alignment explanation
Indices: 77838--77872 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
77828 TTTTTCTGTT
77838 TTTTGTTTTTG
1 TTTTGTTTTTG
*
77849 TTTTGTTTTCG
1 TTTTGTTTTTG
77860 TTTTGTTTTTG
1 TTTTGTTTTTG
77871 TT
1 TT
77873 GCACTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:89780 original size:2 final size:2
Alignment explanation
Indices: 89773--89806 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
89763 AAATTAAGCA
89773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89807 GAATACTGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102793 original size:28 final size:28
Alignment explanation
Indices: 102727--102809 Score: 105
Period size: 28 Copynumber: 2.8 Consensus size: 28
102717 TTAATGCCCT
*
102727 TTTTGTCCCCTAAACTTGTTATGATTTTGATG
1 TTTTG-CCCCTAAACTTG-CA--ATTTTGATG
102759 TTTTGCCCCTAAACTT-CAATTTTGGATG
1 TTTTGCCCCTAAACTTGCAATTTT-GATG
102787 TTTTGCCCCTAAACTTGCAATTT
1 TTTTGCCCCTAAACTTGCAATTT
102810 GGAACCATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
27 5 0.10
28 20 0.42
29 7 0.15
31 11 0.23
32 5 0.10
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.46
Consensus pattern (28 bp):
TTTTGCCCCTAAACTTGCAATTTTGATG
Found at i:112790 original size:2 final size:2
Alignment explanation
Indices: 112783--112831 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
112773 AACAAGTCGC
112783 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
112825 AG AG AG A
1 AG AG AG A
112832 AAGGGTGAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:113051 original size:17 final size:18
Alignment explanation
Indices: 113029--113068 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
113019 GTTTTTTAAT
113029 GTTTT-GGC-TTTGGGTGG
1 GTTTTGGGCTTTTGGG-GG
113046 GTTTTGGGCTTTTGGGGG
1 GTTTTGGGCTTTTGGGGG
113064 GTTTT
1 GTTTT
113069 TAGTTTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.24
18 10 0.48
19 6 0.29
ACGTcount: A:0.00, C:0.05, G:0.45, T:0.50
Consensus pattern (18 bp):
GTTTTGGGCTTTTGGGGG
Found at i:132660 original size:34 final size:34
Alignment explanation
Indices: 132607--132671 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
132597 TGAAAGCTCC
* * *
132607 ATTAGTTTCCATCAATGATCCTACAATCCTATTA
1 ATTAATTTCCATCAATGATCCCACAAACCTATTA
*
132641 ATTAATTTCTATCAATGATCCCACAAACCTA
1 ATTAATTTCCATCAATGATCCCACAAACCTA
132672 AAAAAATTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (34 bp):
ATTAATTTCCATCAATGATCCCACAAACCTATTA
Found at i:133429 original size:2 final size:2
Alignment explanation
Indices: 133422--133454 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
133412 TTAGGATAAG
133422 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 T
133455 GTGTTTATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:146728 original size:3 final size:3
Alignment explanation
Indices: 146720--146745 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
146710 TTTAATTAGT
146720 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
146746 TACTAACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:147728 original size:29 final size:29
Alignment explanation
Indices: 147694--147768 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
147684 CTCTCCGTTT
*
147694 AATCAAAGAAAGGATATTCTTGCCA-AAAA
1 AATCAAAGAAAGGATACTCTT-CCAGAAAA
*
147723 AATCAAAGAAAGGATACTCTTTCAGAAAA
1 AATCAAAGAAAGGATACTCTTCCAGAAAA
*
147752 AGTCAAAGAAAGGATAC
1 AATCAAAGAAAGGATAC
147769 AATTGAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 2 0.05
29 40 0.95
ACGTcount: A:0.52, C:0.13, G:0.16, T:0.19
Consensus pattern (29 bp):
AATCAAAGAAAGGATACTCTTCCAGAAAA
Found at i:147779 original size:28 final size:28
Alignment explanation
Indices: 147694--147779 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 28
147684 CTCTCCGTTT
**
147694 AATCAAAGAAAGGATA-TTCTTGCCAAAAA
1 AATCAAAGAAAGGATACTAATT--CAAAAA
**
147723 AATCAAAGAAAGGATACTCTTTCAGAAAA
1 AATCAAAGAAAGGATACTAATTCA-AAAA
* *
147752 AGTCAAAGAAAGGATAC-AATTGAAAAA
1 AATCAAAGAAAGGATACTAATTCAAAAA
147779 A
1 A
147780 TAAATAGTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
27 5 0.10
28 5 0.10
29 36 0.73
30 3 0.06
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.19
Consensus pattern (28 bp):
AATCAAAGAAAGGATACTAATTCAAAAA
Found at i:148990 original size:51 final size:52
Alignment explanation
Indices: 148914--149019 Score: 160
Period size: 51 Copynumber: 2.1 Consensus size: 52
148904 ATTCTCCTAC
* *
148914 TAAGATAAAGAACAATTAGATTGAGAGTGAAAAGTGC-ATCATTAACTAGTG
1 TAAGATAAAGAACAATTAGATTGAGAATAAAAAGTGCAATCATTAACTAGTG
* * *
148965 TAAGATAAATAACAATTGGATTGAGAATAAAAAGTGCAATCATTGACTAGTG
1 TAAGATAAAGAACAATTAGATTGAGAATAAAAAGTGCAATCATTAACTAGTG
149017 TAA
1 TAA
149020 CTAGTGTAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 33 0.67
52 16 0.33
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (52 bp):
TAAGATAAAGAACAATTAGATTGAGAATAAAAAGTGCAATCATTAACTAGTG
Found at i:150468 original size:33 final size:33
Alignment explanation
Indices: 150425--150488 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
150415 ATATTACCCT
150425 CTTCCAGTCAAAATGGATTCTTGGCTGGTTCTC
1 CTTCCAGTCAAAATGGATTCTTGGCTGGTTCTC
*
150458 CTTCCGGTCAAAATGGATTCTTGGCTGGTTC
1 CTTCCAGTCAAAATGGATTCTTGGCTGGTTC
150489 GTCTGCCGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (33 bp):
CTTCCAGTCAAAATGGATTCTTGGCTGGTTCTC
Done.