Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007777.1 Corchorus capsularis cultivar CVL-1 contig07798, 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: 2748
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Found at i:1009 original size:330 final size:331
Alignment explanation
Indices: 6--2735 Score: 3454
Period size: 330 Copynumber: 8.3 Consensus size: 331
1 TTTTT
* * * * *** *
6 TTTTTGACTTTGAATTATATA-TTTTCCTTAGTATTGTGGTAAAAAATTGAGGAAAAATTTTTCG
1 TTTTTGGCTTTGAATTATATACTTTTCATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCG
* * * * * * * *
70 GGTCTATTTTTGCAAAATTTTAGCCGAAATCGTGGATTAATCATCACGATTTTTTGCTAAAAACG
66 GGTCAATTTTTGCAAAATTTTGGCC-AAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATG
* * * * * * * * * *
135 CCTTTCCTG-GCCCCGGCTCCGTTTTGCATTATTTTTGGCAG-AAAGACTCCTTGAAATATCTAT
130 -CGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGC-GTCAAGACTCATTGAAATATATAC
** * * *
198 ATTCATCTAACCAAATCTCAGCCACAATGGATTTAATGATTT-TTTTTACGAGCATCT-GAATCT
193 ATTCATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCAT-TAGAATCA
* * * * * *
261 TGTTTCGATTTAATTAGAAATAAATTC-GAAAAAT-TTGGAAAAAT-GATATTAAAAGCGTGTAA
257 TG-TTCGATTTTATCAGAAATTAATTCGGAACAATATAGG-AAAATCGATATTAGAAGCGTG-AA
*
323 AA-CCCTTCAATTT
319 AAGCCCTTCAA-TC
* * * * ** *
336 TTTTTGACTTTGAATTATAT-TTTTTCCTGAGTATTGTGGCAAAAAATTGAGGAAAAATTTTTCG
1 TTTTTGGCTTTGAATTATATACTTTTCATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCG
* *
400 GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-T-A--ATCACGAGTTTTT-GCTAAAAAC
66 GGTCAATTTTTGCAAAATTTTGGCC-AAATCGTGTACTAACCATCACG-GTTTTTGGCTAAAAAT
* * * * * * * *
460 GCCTTTCGGGGCCCCGGCTCCA-TTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTA
129 GCGTTCCGGTGCTCCGGCT-CAGTTTTTCATGATTTTTGGC-GTCAAGACTCATTGAAATATATA
* *** *
523 TATTCATCTAACCAAATCTCAGCCAAAATGGATTTAAGGATTTGTTTTTACGAGCATCT-GAATC
192 CATTCATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCAT-TAGAATC
* * * * * *
587 -TAGTTTCGATTTAATTAGAAATAAATTC-GAAAAAT-TTGGAAAAAT-GATATTAAAAGCGTGT
256 AT-G-TTCGATTTTATCAGAAATTAATTCGGAACAATATAGG-AAAATCGATATTAGAAGCGTG-
*
648 AAAA-CCCTTCAAATTT
317 AAAAGCCCTTC-AA-TC
* * * * **
664 TTTTTGACTTTGAATTATATA-TTTTCCTGAGTATTGTGACAAAAAATTGAGGAAAAAT-TTTCG
1 TTTTTGGCTTTGAATTATATACTTTTCATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCG
* *
727 GGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTATTAATCATCACGGTTTTTGGCTAAAAATGC
66 GGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGC
* * * *
792 GTTCTGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGCCAAGAATCATTAAAATATATACATT
131 GTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGACTCATTGAAATATATACATT
* *
857 TATCTAACCAAATCTCAGCCACTTTGGATTTACGGATTTGATTTTACGAGCATTAGAATCATGTG
196 CATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGT-
* *
922 TTGATTTTATCAGAAATTAATTCGGAACTATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCC
260 TCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCC
*
987 TCCAATC
325 TTCAATC
* * * *
994 TTTTTGGCGTTGAATTATATACTTTTAATGAGTATTTTTGCCGAAAATTAAGGAAAAATATTTCG
1 TTTTTGGCTTTGAATTATATACTTTTCATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCG
* * * * ***
1059 GGTCAATTTTCGCAAAATTTTGGCCAAA-AGTAT-TTTGGCATCACGGTTTTTGGCTAAAAATGC
66 GGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGC
* * * *
1122 GTTCCGGTGCTCCGGCTCAGTTTCTCATGATTTTTGGCGTCAATACTCATTGAAATATCTATATT
131 GTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGACTCATTGAAATATATACATT
* * * **
1187 AATCTAACCAAATTTCAACCACTTTGGATTTAAGGATTTCCTTTTACGAGCATTAGAATC---TT
196 CATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGTT
1249 C-----TATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCT
261 CGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCT
1309 TCAATC
326 TCAATC
* * * *
1315 TTTTTGGCTTTGAATTATATATTTTTCATGAATATTTTGGCCGAAAATTGAGGAAAATTATTTCA
1 TTTTTGGCTTTGAATTATATACTTTTCATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCG
* *
1380 GGTCAATTTTTGCAAAATTCTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAATGC
66 GGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGC
*
1445 GTTCCGGTGCTCCGACTCAGTTTTTCATGA-TTTTGGCGTCAAGACTCATTGAAATATATACATT
131 GTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGACTCATTGAAATATATACATT
1509 CATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGTG
196 CATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGT-
* * *
1574 TCGATTTTATCAGAAATTAAGTCGGAACAAAATAGGAAAATCGATATTAGAAGCGTTAAAAGCCC
260 TCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCC
1639 TTCAATC
325 TTCAATC
* * * *
1646 TTTTTGGCTTTTACTTATATACTTTTTATGACTATTTTGGCCGAAAATTGAGGAAAAATATTTCG
1 TTTTTGGCTTTGAATTATATACTTTTCATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCG
* *
1711 GGTCAATTTTTGCAAAATTTTGACCAAATCGTG---T-ACCATCACGGTTTTTGGCTAAAAATGT
66 GGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGC
*
1772 GTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGAATCATTGAAATATATACATT
131 GTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGACTCATTGAAATATATACATT
* * *
1837 CATCTAACCAAATCTCAGCCACTTTAGAATTAAGGATTTGATTTTACGAGCATTAGAATTATGTG
196 CATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGT-
*
1902 TCGATTTTATCAGAAATTAAGTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCC
260 TCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCC
1967 TTTTTTTCAATC
325 -----TTCAATC
* * *
1979 TTTTTGGCTTTGACTTATATACTTTTTATGAGTATTTTGGCCGAAAATTGAGGTAAAATATTTCG
1 TTTTTGGCTTTGAATTATATACTTTTCATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCG
*
2044 GGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGT
66 GGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGC
* * * * * *
2109 GTTCTGGTGCTCCGGATCAGTTTTTCATGATTTTTGACGCCAAGACTCATTGAAATATCTATATT
131 GTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGACTCATTGAAATATATACATT
* * * * *
2174 AATCTAACCTAATCTAAGCCACTTTGGAGTTAAGGATTTGATTTTACGAGCAATAGAATC---TT
196 CATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGTT
*
2236 C-----TATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCTCT
261 CGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCT
*
2296 TGAATC
326 TCAATC
2302 TTTTTGGCTTTGAATTATATA-TATTTCATGAGTATTTTGGCCGAAAATTGAGG-AAAATAATTT
1 TTTTTGGCTTTGAATTATATACT-TTTCATGAGTATTTTGGCCGAAAATTGAGGAAAAAT-ATTT
* * *
2365 CGGGTAAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAATCATCACGGTTTTTGGCTAAATAT
64 CGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAT
*
2430 GCGTTCCGGTGCTCCGGCTCAAGTTTTTCATGATTTTTGGCGTCAAGACTCATTAAAATATATAC
129 GCGTTCCGGTGCTCCGGCTC-AGTTTTTCATGATTTTTGGCGTCAAGACTCATTGAAATATATAC
*
2495 ATTCATCTAACCAAATCTCAGCCACTTTGGATTTACGGATTTGATTTTACGAGCATTAGAATCAT
193 ATTCATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATCAT
* * *
2560 GTGTCGATTTTATCAGAAATTAATTCGGACCTATACAGGAAAATCGATATTAGAAGCGTGAAAAG
258 GT-TCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAG
2625 CCCTTCAATC
322 CCCTTCAATC
* *
2635 TTTTTGGCTTTGAATTATATACTTTTAATGAGTATTTTGGCCGAAAATTAAGGAAAAATATTTCG
1 TTTTTGGCTTTGAATTATATACTTTTCATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCG
*
2700 GGTCAATTTTCGCAAAATTTTGGCCAAATCGTGTAC
66 GGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTAC
2736 GGTTATCACG
Statistics
Matches: 2168, Mismatches: 173, Indels: 115
0.88 0.07 0.05
Matches are distributed among these distances:
321 146 0.07
322 95 0.04
323 191 0.09
324 96 0.04
325 6 0.00
326 120 0.06
327 181 0.08
328 280 0.13
329 12 0.01
330 389 0.18
331 200 0.09
332 54 0.02
333 252 0.12
334 7 0.00
336 1 0.00
337 138 0.06
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.36
Consensus pattern (331 bp):
TTTTTGGCTTTGAATTATATACTTTTCATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCG
GGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGC
GTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGACTCATTGAAATATATACATT
CATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGTT
CGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCT
TCAATC
Found at i:2346 original size:987 final size:979
Alignment explanation
Indices: 48--2735 Score: 3623
Period size: 987 Copynumber: 2.7 Consensus size: 979
38 ATTGTGGTAA
* * * * *
48 AAAATTGAGGAAAAATTTTTCGGGTCTATTTTTGCAAAATTTTAGCCGAAATCGTGGATTAATCA
1 AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCC-AAATCGTGTATTAACCA
* * * * * * *
113 TCACGATTTTTTGCTAAAAACGCCT-TTCCT-G-GCCCCGGCTCCGTTTTGCATTATTTTTGGCA
65 TCACGGTTTTTGGCTAAAAATG--TGTT-CTGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGC-
* * * * ** *
175 GAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAATGATTT
126 GCAAGACTCATTGAAATATCTATATTAATCTAACCAAATCTAAGCCACTTTGGATTTAAGGATTT
* * * * * *
240 TTTTTACGAGC-ATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-GAAAAAT-TTGGAAA
191 ATTTTACGAGCAAT-AGAATC----TTC----T-ATCAGAAATTAATTCGGAACAATATAGG-AA
* * * *
302 AAT-GATATTAAAAGCGTGTAAAA-CCCTTCAATTTTTTTTGACTTTGAATTATAT-TTTTTCCT
245 AATCGATATTAGAAGCGTG-AAAAGCCCTTCAA-TCTTTTTGGCTTTGAATTATATATTTTTCAT
* ** *
364 GAGTATTGTGGCAAAAAATTGAGGAAAAATT-TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAA
308 GAGTATTTTGGCCGAAAATTGAGG-AAAATTATTTCGGGTCAATTTTTGCAAAATTTTGGCC-AA
* * * * * *
428 ATCGTGTA-T-A-ATCACGAGTTTTT-GCTAAAAACGCCTTTCGGGGCCCCGGCTCCA-TTTTGC
371 ATCGTGTACTAACATCACG-GTTTTTGGCT-AAAATGCGTTCCGGTGCTCCGGCT-CAGTTTTTC
* * * * ***
488 ATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCAAAAT
433 ATGATTTTTGGC-GTCAAGACTCATTGAAATATATACATTCATCTAACCAAATCTCAGCCACTTT
* * * * *
552 GGATTTAAGGATTTGTTTTTACGAGCATCT-GAATC-TAGTTTCGATTTAATTAGAAATAAATTC
497 GGATTTAAGGATTTGATTTTACGAGCAT-TAGAATCAT-GTGTCGATTTTATCAGAAATTAATTC
* * * * *
615 -GAA-AAATTTGGAAAAAT-GATATTAAAAGCGTGTAAAA-CCCTTCAAATTTTTTTTGACTTTG
560 GGAACAAAATAGG-AAAATCGATATTAGAAGCGT-TAAAAGCCCTTC-AA-TCTTTTTGGCTTTG
** * * **
676 AATTATATA-TTTTCCTGAGTATTGTGACAAAAAATTGAGGAAAAAT-TTTCGGGTCAATTTTTG
621 AATTATATACTTTTAATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCGGGTCAATTTTTG
* *
739 CAAAATTTTGGCCAAATCGTGTATTAATCATCACGGTTTTTGGCTAAAAATGCGTTCTGGTGCTC
686 CAAAATTTTGGCCAAATCGTG---T-ACCATCACGGTTTTTGGCTAAAAATGCGTTCCGGTGCTC
*
804 CGGCTCAGTTTTTCATGATTTTTGGCGCCAAGAATCATTAAAATATATACATTTATCTAACCAAA
747 CGGCTCAGTTTTTCATGATTTTTGGCGCCAAGAATCATTAAAATATATACATTCATCTAACCAAA
* * * *
869 TCTCAGCCACTTTGGATTTACGGATTTGATTTTACGAGCATTAGAATCATGTGTTGATTTTATCA
812 TCTCAGCCACTTTAGAATTAAGGATTTGATTTTACGAGCATTAGAATCATGTGTCGATTTTATCA
* *
934 GAAATTAATTCGGAACTATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTT
877 GAAATTAAGTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTT
*
999 GGCGTTGAATTATATACTTTTAATGAGTATTTTTGCCG
942 GGCGTTGAATTATATACTTTTAATGAGTATTTTGGCCG
* * * * ***
1037 AAAATTAAGGAAAAATATTTCGGGTCAATTTTCGCAAAATTTTGGCCAAA-AGTAT-TTTGGCAT
1 AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTATTAACCAT
* * *
1100 CACGGTTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGCTCAGTTTCTCATGATTTTTGGCGTCAA
66 CACGGTTTTTGGCTAAAAATGTGTTCTGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCG-CAA
* * *
1165 TACTCATTGAAATATCTATATTAATCTAACCAAATTTCAA-CCACTTTGGATTTAAGGATTTCCT
130 GACTCATTGAAATATCTATATTAATCTAACCAAATCT-AAGCCACTTTGGATTTAAGGATTT-AT
*
1229 TTTACGAGCATTAGAATCTTCTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGA
193 TTTACGAGCAATAGAATCTTCTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGA
*
1294 AGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATATTTTTCATGAATATTTTGGCCGA
258 AGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATATTTTTCATGAGTATTTTGGCCGA
* *
1359 AAATTGAGGAAAATTATTTCAGGTCAATTTTTGCAAAATTCTGGCCAAATCGTGTACTAACCATC
323 AAATTGAGGAAAATTATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAA-CATC
*
1424 ACGGTTTTTGGCTGAAAATGCGTTCCGGTGCTCCGACTCAGTTTTTCATGA-TTTTGGCGTCAAG
387 ACGGTTTTTGGCT-AAAATGCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAG
1488 ACTCATTGAAATATATACATTCATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTT
451 ACTCATTGAAATATATACATTCATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTT
*
1553 TACGAGCATTAGAATCATGTGTCGATTTTATCAGAAATTAAGTCGGAACAAAATAGGAAAATCGA
516 TACGAGCATTAGAATCATGTGTCGATTTTATCAGAAATTAATTCGGAACAAAATAGGAAAATCGA
* * * *
1618 TATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGGCTTTTACTTATATACTTTTTATGACTATTT
581 TATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATACTTTTAATGAGTATTT
*
1683 TGGCCGAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGACCAAATCGTGTACC
646 TGGCCGAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACC
* *
1748 ATCACGGTTTTTGGCTAAAAATGTGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTC
711 ATCACGGTTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGCC
*
1813 AAGAATCATTGAAATATATACATTCATCTAACCAAATCTCAGCCACTTTAGAATTAAGGATTTGA
776 AAGAATCATTAAAATATATACATTCATCTAACCAAATCTCAGCCACTTTAGAATTAAGGATTTGA
*
1878 TTTTACGAGCATTAGAATTATGTGTCGATTTTATCAGAAATTAAGTCGGAACAATATAGGAAAAT
841 TTTTACGAGCATTAGAATCATGTGTCGATTTTATCAGAAATTAAGTCGGAACAATATAGGAAAAT
* * * *
1943 CGATATTAGAAGCGTGAAAAGCCCTTTTTTTCAATCTTTTTGGCTTTGACTTATATACTTTTTAT
906 CGATATTAGAAGCGTGAAAAGCCC-----TCCAATCTTTTTGGCGTTGAATTATATACTTTTAAT
2008 GAGTATTTTGGCCG
966 GAGTATTTTGGCCG
* *
2022 AAAATTGAGGTAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCAT
1 AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTATTAACCAT
* *
2087 CACGGTTTTTGGCTAAAAATGTGTTCTGGTGCTCCGGATCAGTTTTTCATGATTTTTGACGCCAA
66 CACGGTTTTTGGCTAAAAATGTGTTCTGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCG-CAA
* *
2152 GACTCATTGAAATATCTATATTAATCTAACCTAATCTAAGCCACTTTGGAGTTAAGGATTTGATT
130 GACTCATTGAAATATCTATATTAATCTAACCAAATCTAAGCCACTTTGGATTTAAGGATTT-ATT
2217 TTACGAGCAATAGAATCTTCTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAA
194 TTACGAGCAATAGAATCTTCTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAA
* * *
2282 GCGTGAAAAGCTCTTGAATCTTTTTGGCTTTGAATTATATATATTTCATGAGTATTTTGGCCGAA
259 GCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATATTTTTCATGAGTATTTTGGCCGAA
* *
2347 AATTGAGGAAAATAATTTCGGGTAAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAATCATCA
324 AATTGAGGAAAATTATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAA-CATCA
2412 CGGTTTTTGGCTAAATATGCGTTCCGGTGCTCCGGCTCAAGTTTTTCATGATTTTTGGCGTCAAG
388 CGGTTTTTGGCTAAA-ATGCGTTCCGGTGCTCCGGCTC-AGTTTTTCATGATTTTTGGCGTCAAG
* *
2477 ACTCATTAAAATATATACATTCATCTAACCAAATCTCAGCCACTTTGGATTTACGGATTTGATTT
451 ACTCATTGAAATATATACATTCATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTT
* * * *
2542 TACGAGCATTAGAATCATGTGTCGATTTTATCAGAAATTAATTCGGACCTATACAGGAAAATCGA
516 TACGAGCATTAGAATCATGTGTCGATTTTATCAGAAATTAATTCGGAACAAAATAGGAAAATCGA
*
2607 TATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATACTTTTAATGAGTATTT
581 TATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATACTTTTAATGAGTATTT
* *
2672 TGGCCGAAAATTAAGGAAAAATATTTCGGGTCAATTTTCGCAAAATTTTGGCCAAATCGTGTAC
646 TGGCCGAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTAC
2736 GGTTATCACG
Statistics
Matches: 1511, Mismatches: 149, Indels: 78
0.87 0.09 0.04
Matches are distributed among these distances:
978 13 0.01
979 52 0.03
980 289 0.19
981 4 0.00
982 130 0.09
983 85 0.06
984 63 0.04
985 96 0.06
986 109 0.07
987 355 0.23
988 16 0.01
989 299 0.20
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (979 bp):
AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTATTAACCAT
CACGGTTTTTGGCTAAAAATGTGTTCTGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGCAAG
ACTCATTGAAATATCTATATTAATCTAACCAAATCTAAGCCACTTTGGATTTAAGGATTTATTTT
ACGAGCAATAGAATCTTCTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGC
GTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATATTTTTCATGAGTATTTTGGCCGAAAA
TTGAGGAAAATTATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACATCACGG
TTTTTGGCTAAAATGCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGACTCA
TTGAAATATATACATTCATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGA
GCATTAGAATCATGTGTCGATTTTATCAGAAATTAATTCGGAACAAAATAGGAAAATCGATATTA
GAAGCGTTAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATACTTTTAATGAGTATTTTGGCC
GAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACCATCAC
GGTTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGCCAAGAA
TCATTAAAATATATACATTCATCTAACCAAATCTCAGCCACTTTAGAATTAAGGATTTGATTTTA
CGAGCATTAGAATCATGTGTCGATTTTATCAGAAATTAAGTCGGAACAATATAGGAAAATCGATA
TTAGAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATACTTTTAATGAGTATTTTG
GCCG
Found at i:2399 original size:656 final size:652
Alignment explanation
Indices: 6--2735 Score: 3325
Period size: 656 Copynumber: 4.2 Consensus size: 652
1 TTTTT
* ** * * *** *
6 TTTTTGACTTTGAATTATATATTTTCCTTAGTATTGTGGTAAAAAATTGAGGAAAAATTTTTCGG
1 TTTTTGGCTTTGAATTATATATTTTTATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCGG
* * * * * * * *
71 GTCTATTTTTGCAAAATTTTAGCCGAAATCGTGGATTAATCATCACGATTTTTTGCTAAAAACGC
66 GTCAATTTTTGCAAAATTTTGGCC-AAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATG-
* * * * * * * * * *
136 CTTTCCT-G-GCCCCGGCTCCGTTTTGCATTATTTTTGGCAG-AAAGACTCCTTGAAATATCTAT
129 CGTT-CTGGTGCTCCGGATCAGTTTTTCATGATTTTTGGC-GCCAAGACTCATTGAAATATATAC
** * * *
198 ATTCATCTAACCAAATCTCAGCCACAATGGATTTAATGATTT-TTTTTACGAGC-ATCTGAATCT
192 ATTCATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCAAT-AGAATC-
* * * * *
261 TGTTTCGATTTAATTAGAAATAAATTC-GAAAAAT-TTGGAAAAAT-GATATTAAAAGCGTGTAA
255 --TTTC---TT-ATCAGAAATTAATTCGGAACAATATAGG-AAAATCGATATTAGAAGCGTG-AA
* * * * * **
323 AA-CCCTTCAATTTTTTTTGACTTTGAATTATAT-TTTTTCCTGAGTATTGTGGCAAAAAATTGA
312 AAGCCCTTCAA-TCTTTTTGGCTTTGAATTATATACTTTTCATGAGTATTTTGGCCGAAAATTGA
* * * **
386 GGAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATAATCACGAGTTTTT
376 GGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAAATCGTGTACCATCACG-GTTTTT
* * * * * * * *
451 -GCTAAAAACGCCTTTCGGGGCCCCGGCTCCA-TTTTGCATGATTTTTGGCAG-AAAGACTCCTT
440 GGCTAAAAATGCGTTCCGGTGCTCCGGCT-CAGTTTTTCATGATTTTTGGC-GTCAAGACTCATT
* * *** *
513 GAAATATCTATATTCATCTAACCAAATCTCAGCCAAAATGGATTTAAGGATTTGTTTTTACGAGC
503 GAAATATATACATTCATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGC
* * * * * *
578 ATCT-GAATCTAGTTTCGATTTAATTAGAAATAAATTC-GAAAAAT-TTGGAAAAAT-GATATTA
568 AT-TAGAAT-TAGTGTCGATTTTATCAGAAATTAATTCGGAACAATATAGG-AAAATCGATATTA
* *
639 AAAGCGTGTAAAA-CCCTTCAAATTT
630 GAAGCGTG-AAAAGCCCTTC-AA-TC
* ** * * **
664 TTTTTGACTTTGAATTATATATTTTCCTGAGTATTGTGACAAAAAATTGAGGAAAAAT-TTTCGG
1 TTTTTGGCTTTGAATTATATATTTTTATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCGG
* *
728 GTCAATTTTTGCAAAATTTTGGCCAAATCGTGTATTAATCATCACGGTTTTTGGCTAAAAATGCG
66 GTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCG
* * * *
793 TTCTGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGCCAAGAATCATTAAAATATATACATTT
131 TTCTGGTGCTCCGGATCAGTTTTTCATGATTTTTGGCGCCAAGACTCATTGAAATATATACATTC
* *
858 ATCTAACCAAATCTCAGCCACTTTGGATTTACGGATTTGATTTTACGAGCATTAGAATCATGTGT
196 ATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCAATAGAATC-----T
* *
923 TGATTTTATCAGAAATTAATTCGGAACTATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCT
256 T--TCTTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCT
* * * * *
988 CCAATCTTTTTGGCGTTGAATTATATACTTTTAATGAGTATTTTTGCCGAAAATTAAGGAAAAAT
319 TCAATCTTTTTGGCTTTGAATTATATACTTTTCATGAGTATTTTGGCCGAAAATTGAGGAAAAAT
* ** * **
1053 ATTTCGGGTCAATTTTCGCAAAATTTTGGCCAAAAGTATTTTGGCATCACGGTTTTTGGCTAAAA
384 ATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAAA-TCGTGTACCATCACGGTTTTTGGCTAAAA
* * *
1118 ATGCGTTCCGGTGCTCCGGCTCAGTTTCTCATGATTTTTGGCGTCAATACTCATTGAAATATCTA
448 ATGCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGACTCATTGAAATATATA
* * * * **
1183 TATTAATCTAACCAAATTTCAACCACTTTGGATTTAAGGATTTCCTTTTACGAGCATTAG-A--A
513 CATTCATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATTA
*
1245 ---TC--TTCTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAG
578 GTGTCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAG
1305 CCCTTCAATC
643 CCCTTCAATC
* * *
1315 TTTTTGGCTTTGAATTATATATTTTTCATGAATATTTTGGCCGAAAATTGAGGAAAATTATTTCA
1 TTTTTGGCTTTGAATTATATATTTTT-ATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCG
* *
1380 GGTCAATTTTTGCAAAATTCTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAATGC
65 GGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGC
* *
1445 GTTCCGGTGCTCC-GACTCAGTTTTTCATGA-TTTTGGCGTCAAGACTCATTGAAATATATACAT
130 GTTCTGGTGCTCCGGA-TCAGTTTTTCATGATTTTTGGCGCCAAGACTCATTGAAATATATACAT
*
1508 TCATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGT
194 TCATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCAATAGAATC-T-T
* * *
1573 GTCGATTTTATCAGAAATTAAGTCGGAACAAAATAGGAAAATCGATATTAGAAGCGTTAAAAGCC
257 -TC----TTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCC
* * * *
1638 CTTCAATCTTTTTGGCTTTTACTTATATACTTTTTATGACTATTTTGGCCGAAAATTGAGGAAAA
317 CTTCAATCTTTTTGGCTTTGAATTATATACTTTTCATGAGTATTTTGGCCGAAAATTGAGGAAAA
*
1703 ATATTTCGGGTCAATTTTTGCAAAATTTTGACC-AAATCGTGTACCATCACGGTTTTTGGCTAAA
382 ATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAAATCGTGTACCATCACGGTTTTTGGCTAAA
* *
1767 AATGTGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGAATCATTGAAATATAT
447 AATGCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGACTCATTGAAATATAT
* *
1832 ACATTCATCTAACCAAATCTCAGCCACTTTAGAATTAAGGATTTGATTTTACGAGCATTAGAATT
512 ACATTCATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATT
*
1897 ATGTGTCGATTTTATCAGAAATTAAGTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAA
577 A-GTGTCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAA
1962 AGCCCTTTTTTTCAATC
641 AGCCC-----TTCAATC
* *
1979 TTTTTGGCTTTGACTTATATACTTTTTATGAGTATTTTGGCCGAAAATTGAGGTAAAATATTTCG
1 TTTTTGGCTTTGAATTATATA-TTTTTATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCG
*
2044 GGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGT
65 GGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGC
* * *
2109 GTTCTGGTGCTCCGGATCAGTTTTTCATGATTTTTGACGCCAAGACTCATTGAAATATCTATATT
130 GTTCTGGTGCTCCGGATCAGTTTTTCATGATTTTTGGCGCCAAGACTCATTGAAATATATACATT
* * * *
2174 AATCTAACCTAATCTAAGCCACTTTGGAGTTAAGGATTTGATTTTACGAGCAATAGAATC-TTC-
195 CATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCAATAGAATCTTTCT
* *
2237 TATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCTCTTGAATC
260 TATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATC
2302 TTTTTGGCTTTGAATTATATA-TATTTCATGAGTATTTTGGCCGAAAATTGAGG-AAAATAATTT
325 TTTTTGGCTTTGAATTATATACT-TTTCATGAGTATTTTGGCCGAAAATTGAGGAAAAAT-ATTT
* *
2365 CGGGTAAATTTTTGCAAAATTTTGGCC-AAATCGTGTACTAATCATCACGGTTTTTGGCTAAATA
388 CGGGTCAATTTTTGCAAAATTTTGGCCAAAATCGTGTAC----CATCACGGTTTTTGGCTAAAAA
*
2429 TGCGTTCCGGTGCTCCGGCTCAAGTTTTTCATGATTTTTGGCGTCAAGACTCATTAAAATATATA
449 TGCGTTCCGGTGCTCCGGCTC-AGTTTTTCATGATTTTTGGCGTCAAGACTCATTGAAATATATA
* *
2494 CATTCATCTAACCAAATCTCAGCCACTTTGGATTTACGGATTTGATTTTACGAGCATTAGAATCA
513 CATTCATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATTA
* * *
2559 TGTGTCGATTTTATCAGAAATTAATTCGGACCTATACAGGAAAATCGATATTAGAAGCGTGAAAA
578 -GTGTCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAA
2624 GCCCTTCAATC
642 GCCCTTCAATC
* *
2635 TTTTTGGCTTTGAATTATATACTTTTAATGAGTATTTTGGCCGAAAATTAAGGAAAAATATTTCG
1 TTTTTGGCTTTGAATTATATA-TTTTTATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCG
*
2700 GGTCAATTTTCGCAAAATTTTGGCCAAATCGTGTAC
65 GGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTAC
2736 GGTTATCACG
Statistics
Matches: 1829, Mismatches: 188, Indels: 112
0.86 0.09 0.05
Matches are distributed among these distances:
648 2 0.00
649 1 0.00
650 136 0.07
651 44 0.02
652 274 0.15
653 117 0.06
654 2 0.00
655 11 0.01
656 365 0.20
657 58 0.03
658 91 0.05
659 159 0.09
660 157 0.09
661 170 0.09
662 1 0.00
664 149 0.08
665 92 0.05
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.36
Consensus pattern (652 bp):
TTTTTGGCTTTGAATTATATATTTTTATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCGG
GTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCG
TTCTGGTGCTCCGGATCAGTTTTTCATGATTTTTGGCGCCAAGACTCATTGAAATATATACATTC
ATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCAATAGAATCTTTCTT
ATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCT
TTTTGGCTTTGAATTATATACTTTTCATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCGG
GTCAATTTTTGCAAAATTTTGGCCAAAATCGTGTACCATCACGGTTTTTGGCTAAAAATGCGTTC
CGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGACTCATTGAAATATATACATTCATC
TAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATTAGTGTCGAT
TTTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAA
TC
Done.