Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016358.1 Corchorus olitorius cultivar O-4 contig16391, 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: 5544
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:939 original size:323 final size:320
Alignment explanation
Indices: 285--1109 Score: 885
Period size: 323 Copynumber: 2.5 Consensus size: 320
275 ATTTTTTTTT
* * * * * **
285 GTTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATTTATCGAACAAAATCCCAGC
1 GTTTTGCATGATTTTTGGCG-AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGC
* * * ** * * * *
350 CACGTTCGATTTAAGTATTTGTTTTTACAATTATCTTAATCTTGTTTCAATTTAATTAAAAATTA
65 CACATTAGATTTAAGGATTTGTTTTTACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTA
* * * *
415 ATTCGGGAAAAAAACTGG-AAAAATGATATTTGACGCGTGAAAAGCCTGTCAATCTTTTTGGCGT
130 ATTC-GGAAAAAAA-TGGAAAAAATGATATTTAAAGCGTGAAAAGCCTATCAATCTTTTTGGCGG
* * * *
479 TGAATTATATATTTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAACATTTCCGATCAGTTTT
193 GGAATTATATATGTTTTCTGAGTATTATAGCAAAAAATTCAGAAAAAACATTTCCGATCAGTTTT
*
544 TAGACGAAATCGTGTGCTACGCATCACAATTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACTCA
258 TAGACGAAATCG-GTGCTACG-ATCACAATTTTGGGCTAAAAACGCGTTCCCGAGCCCCGACTCA
*
609 ATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGC
1 GTTTTGCATGATTTTTGGCG-AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGC
* * *
674 CACATTGGATATAAGGATTTGTTTTTACAAGCATCTGAATCATGTTTCGATATAATTAGAAATTA
65 CACATTAGATTTAAGGATTTGTTTTTACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTA
* * * * *
739 ATTTGGAAAAAATTGGAAAAAATGATATTAAAAGCGTGAAAAGACC-ATCATTCTTTTTGGTGGG
130 ATTCGGAAAAAAATGGAAAAAATGATATTTAAAGCGTGAAAAG-CCTATCAATCTTTTTGGCGGG
* * * *
803 GAATTATGTATGTTTTCTGAGTATTATGGCAAAAAAAATTCAGAAAAAA-ATATTCGGGTCAGTT
194 GAATTATATATGTTTTCTGAGTATTATAGC--AAAAAATTCAGAAAAAACAT-TTCCGATCAGTT
* * *** ** * *
867 TTTAGCCGAAAATC-GTG-TACG-TTATGGTTTTGGGGCTAAAAACGCGTTTCGGGGGCCCCGGC
256 TTTAGACG-AAATCGGTGCTACGATCACAATTTT-GGGCTAAAAACGCG-TTCCCGAGCCCCGAC
929 TCA
318 TCA
* *
932 GTTTTGCATGATTTTTGGCAGAAAGTCTCCTTGAAATATCTATATTCATCTAACCAATCTCAGGC
1 GTTTTGCATGATTTTTGGC-GAAAGACTCCTTGAAATATCTATATTCATCAAACCAA----A---
* * *
997 TGTCAGCGACATTAGATTTAAGGATTTGTTTTTACGAGCATCTG-ATTATTGTTTCGATTTAATT
58 TGTCAGCCACATTAGATTTAAGGATTTGTTTTTACAAGCATCTGAATCA-TGTTTCGATTTAATT
** *
1061 AGAAA-TAGATTCGGAAAAAAATATAAAAAA-GATATTTAAAGCGAGAAAA
122 AGAAATTA-ATTCGGAAAAAAATGGAAAAAATGATATTTAAAGCGTGAAAA
1110 ATTTCTTCTT
Statistics
Matches: 421, Mismatches: 62, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
321 6 0.01
322 16 0.04
323 140 0.33
324 121 0.29
325 33 0.08
326 5 0.01
327 1 0.00
329 22 0.05
330 77 0.18
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (320 bp):
GTTTTGCATGATTTTTGGCGAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
ACATTAGATTTAAGGATTTGTTTTTACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAA
TTCGGAAAAAAATGGAAAAAATGATATTTAAAGCGTGAAAAGCCTATCAATCTTTTTGGCGGGGA
ATTATATATGTTTTCTGAGTATTATAGCAAAAAATTCAGAAAAAACATTTCCGATCAGTTTTTAG
ACGAAATCGGTGCTACGATCACAATTTTGGGCTAAAAACGCGTTCCCGAGCCCCGACTCA
Found at i:1712 original size:321 final size:323
Alignment explanation
Indices: 1163--1855 Score: 905
Period size: 321 Copynumber: 2.2 Consensus size: 323
1153 TTTTTTTTGT
** * *
1163 TTTTGCATGATTTTTGATGTAAATACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCC
1 TTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAAACAAAATCCCAGCC
* *
1228 ACATTCGATTTAAGTATTTGTTTTCACGAACATCTAAATCTTGTTTCAATTTAATTAAAAATTAA
66 ACATTCGATATAAGGATTTGTTTTCACGAACATCTAAATCTTGTTTCAATTTAATTAAAAATTAA
** * * * *
1293 TTTGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTCAC
131 TTAAGAAAAAAATGGAAAAACGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTCAA
* * * *
1358 TTATATATTTTTTCTGAGTATTGTGGCAAAAATTGA-GAAAAAAATTTTCTGATCAGTTTTTAGC
196 TTATATATTTTTTATGAGTATTGTGGCAAAAATTCAGGAAAAAAA--ATCGGATCAGTTTTTAGC
* * *
1422 CG-AAATCGTGTACTTACCATCACGGTTTTT-GGCTAAAAACGC-ATTCCTGAGCCACGACTCAA
259 AGAAAATCGTGTACTAACCATCACAGTTTTTGGGCTAAAAACGCGATTCCTGAGCCACGACTCAA
* * **
1484 TTTTGCATGATTTTTGGCGTAAAGATTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
1 TTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAAACAAAATCCCAGCC
* ** * *
1549 ACATTGGATATAAGGATTTGTATTT-ACGAGTATCTGAATCTTGTTTCAATTTAATTAGAAATTA
66 ACATTCGATATAAGGATTTGT-TTTCACGAACATCTAAATCTTGTTTCAATTTAATTAAAAATTA
* * *
1613 ATTAAGAAAAAATTGG-AAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGA
130 ATTAAGAAAAAAATGGAAAAACGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTCA
*
1677 ATTATATATTTTTTATGAGTATTGTGGCAAAAAATTCAGGAAAAAAAATCGGGTCAGTTTTTAGC
195 ATTATATATTTTTTATGAGTATTGTGGC-AAAAATTCAGGAAAAAAAATCGGATCAGTTTTTAGC
* * * * * * * *
1742 AGAAAATCGTGTACTAACCATCATAGTTTTTGGGCTGAAAACGCGTTTCGTGGGCCCCGGCTCAG
259 AGAAAATCGTGTACTAACCATCACAGTTTTTGGGCTAAAAACGCGATTCCTGAGCCACGACTCAA
* * *
1807 TTTTGAATGATTTTTGGCAG-AAAGACTCCGTGAAATATCTATTTTCATC
1 TTTTGCATGATTTTTGGC-GTAAAGACTCCTTGAAATATCTATATTCATC
1856 GAAGCAATCT
Statistics
Matches: 321, Mismatches: 44, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
320 85 0.26
321 156 0.49
322 22 0.07
323 57 0.18
324 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (323 bp):
TTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAAACAAAATCCCAGCC
ACATTCGATATAAGGATTTGTTTTCACGAACATCTAAATCTTGTTTCAATTTAATTAAAAATTAA
TTAAGAAAAAAATGGAAAAACGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTCAA
TTATATATTTTTTATGAGTATTGTGGCAAAAATTCAGGAAAAAAAATCGGATCAGTTTTTAGCAG
AAAATCGTGTACTAACCATCACAGTTTTTGGGCTAAAAACGCGATTCCTGAGCCACGACTCAA
Found at i:1785 original size:874 final size:876
Alignment explanation
Indices: 203--1921 Score: 2640
Period size: 874 Copynumber: 2.0 Consensus size: 876
193 TGTTTCGATT
*
203 TAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTGCGTTGAATTGTGTATTTTTTG
1 TAAAAAAGATATTTAAAGCGAGAAAAATATTTC-A-TTTTTTTGCGTTGAATTGTGTATTTTTTG
*
268 AGAAAATATTTTTTTTTGTTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATTTA
64 AG-AAATATTTTTTTTTGTTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATTCA
* * * *
333 TCGAACAAAATCCCAGCCACGTTCGATTTAAGTATTTGTTTTTACAATTATCTTAATCTTGTTTC
128 TCGAACAAAATCCCAGCCACATTCGATTTAAGTATTTGTTTTCACAATCATCTAAATCTTGTTTC
* * * *
398 AATTTAATTAAAAATTAATTCGGGAAAAAAACTGGAAAAATGATATTTGACGCGTGAAAAGCCTG
193 AATTTAATTAAAAATTAATTCGGGAAAAAAACTGGAAAAACGATATTAGAAGCGTGAAAAGCCCG
*
463 TCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAAC
258 TCAATCTTTTTGGCGTTCAATTATATATTTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAAC
* *
528 ATTTCCGATCAGTTTTTAGACGAAATCGTGTGCTACGCATCACAATTTTTGGCTAAAAACGCGTT
323 ATTTCCGATCAGTTTTTAGACGAAATCGTGTACTACGCATCACAATTTTTGGCTAAAAACGCATT
*
593 CCCGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCAT
388 CCCGAGCCACGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCAT
* *
658 CAAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTACAAGCATCTGAATCATGTTTCG
453 CAAACCAAATGTCAGCCACATTGGATATAAGGATTTGTATTTACAAGCATCTGAATCATGTTTCA
**
723 ATATAATTAGAAATTAATTTGGAAAAAATTGGAAAAAATGATATTAAAAGCGTGAAAAGACCATC
518 ATATAATTAGAAATTAATTAAGAAAAAATTGG-AAAAATGATATTAAAAGCGTGAAAAGACCATC
* * *
788 ATTCTTTTTGGTGGGGAATTATGTATGTTTTCTGAGTATTATGGCAAAAAAAATTCAGAAAAAAA
582 AATCTTTTTGGTGGGGAATTATATATGTTTTATGAGTATTATGGC-AAAAAAATTCAGAAAAAAA
* *
853 TATTCGGGTCAGTTTTTAGCCGAAAATCGTGTACGTTATGGTTTTGGGGCTAAAAACGCGTTTCG
646 TATTCGGGTCAGTTTTTAGCAGAAAATCGTGTACGTTATAGTTTTGGGGCTAAAAACGCGTTTCG
* * * *
918 GGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGTCTCCTTGAAATATCTATATTCATCT
711 GGGGCCCCGGCTCAGTTTTGAATGATTTTTGGCAGAAAGACTCCGTGAAATATCTATATTCATCG
* * * * *
983 AACCAATCTCAGGCTGTCAGCGACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGATTATTG
776 AACCAATCTCAGGCTCTCAGCCACATTACATTTAAGGATTTGTTTTTACAAGCATCTGAATATTG
1048 TTTCGATTTAATTAGAAATAGATTCGGAAAAAAATA
841 TTTCGATTTAATTAGAAATAGATTCGGAAAAAAATA
*
1084 TAAAAAAGATATTTAAAGCGAGAAAAATTTCTTC-TTTTTTTGCGTTGAATTGTGTATTTTTTGC
1 TAAAAAAGATATTTAAAGCGAGAAAAATAT-TTCATTTTTTTGCGTTGAATTGTGTATTTTTTG-
* *
1148 CG--A-ATTTTTTTTTGTTTTTGCATGATTTTTGATGTAAATACTCCTTGAAATATCTATATTCA
64 AGAAATATTTTTTTTTG-TTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATTCA
1210 TCGAACAAAATCCCAGCCACATTCGATTTAAGTATTTGTTTTCACGAA-CATCTAAATCTTGTTT
128 TCGAACAAAATCCCAGCCACATTCGATTTAAGTATTTGTTTTCAC-AATCATCTAAATCTTGTTT
*
1274 CAATTTAATTAAAAATTAATT-TGGAAAAAAA-TGGAAAAACGATATTAGAAGCGTGAAAAGCCC
192 CAATTTAATTAAAAATTAATTCGGGAAAAAAACTGGAAAAACGATATTAGAAGCGTGAAAAGCCC
* * *
1337 GTCAATCTTTTTGGTGTTCACTTATATATTTTTTCTGAGTATTGTGGC-AAAAATTGAGAAAAAA
257 GTCAATCTTTTTGGCGTTCAATTATATATTTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAA
* * **
1401 -ATTTTCTGATCAGTTTTTAGCCGAAATCGTGTACTTAC-CATCACGGTTTTTGGCTAAAAACGC
322 CA-TTTCCGATCAGTTTTTAGACGAAATCGTGTAC-TACGCATCACAATTTTTGGCTAAAAACGC
* * *
1464 ATTCCTGAGCCACGACTCAATTTTGCATGATTTTTGGCGTAAAGATTCCTTGAAATATCTATATT
385 ATTCCCGAGCCACGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATT
* * *
1529 CATCAAACCAAATGTCAGCCACATTGGATATAAGGATTTGTATTTACGAGTATCTGAATCTTGTT
450 CATCAAACCAAATGTCAGCCACATTGGATATAAGGATTTGTATTTACAAGCATCTGAATCATGTT
*
1594 TCAATTTAATTAGAAATTAATTAAGAAAAAATTGG-AAAATGATATTAAAAGCGTGAAAAGACCA
515 TCAATATAATTAGAAATTAATTAAGAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGACCA
** * *
1658 TCAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTGTGGC-AAAAAATTCAGGAAAAA
580 TCAATCTTTTTGGTGGGGAATTATATATGTTTTATGAGTATTATGGCAAAAAAATTCA-GAAAAA
* *
1722 AA-A-TCGGGTCAGTTTTTAGCAGAAAATCGTGTAC-TAACCATCATAGTTTTTGGGCTGAAAAC
644 AATATTCGGGTCAGTTTTTAGCAGAAAATCGTGTACGT-----T-ATAGTTTTGGGGCTAAAAAC
*
1784 GCGTTTCGTGGGCCCCGGCTCAGTTTTGAATGATTTTTGGCAGAAAGACTCCGTGAAATATCTAT
703 GCGTTTCGGGGGCCCCGGCTCAGTTTTGAATGATTTTTGGCAGAAAGACTCCGTGAAATATCTAT
* *
1849 TTTCATCGAAGCAATCTCAGGCTCTCAGCCACATTACATTTAAGGATTTGTTTTTACAAGCATCT
768 ATTCATCGAACCAATCTCAGGCTCTCAGCCACATTACATTTAAGGATTTGTTTTTACAAGCATCT
1914 GAATATTG
833 GAATATTG
1922 CGTTGAATTA
Statistics
Matches: 766, Mismatches: 59, Indels: 33
0.89 0.07 0.04
Matches are distributed among these distances:
868 1 0.00
869 30 0.04
870 11 0.01
871 8 0.01
872 69 0.09
873 2 0.00
874 363 0.47
875 75 0.10
876 20 0.03
877 124 0.16
878 2 0.00
879 29 0.04
880 1 0.00
881 28 0.04
882 3 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (876 bp):
TAAAAAAGATATTTAAAGCGAGAAAAATATTTCATTTTTTTGCGTTGAATTGTGTATTTTTTGAG
AAATATTTTTTTTTGTTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATTCATCG
AACAAAATCCCAGCCACATTCGATTTAAGTATTTGTTTTCACAATCATCTAAATCTTGTTTCAAT
TTAATTAAAAATTAATTCGGGAAAAAAACTGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCA
ATCTTTTTGGCGTTCAATTATATATTTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAACATT
TCCGATCAGTTTTTAGACGAAATCGTGTACTACGCATCACAATTTTTGGCTAAAAACGCATTCCC
GAGCCACGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAA
ACCAAATGTCAGCCACATTGGATATAAGGATTTGTATTTACAAGCATCTGAATCATGTTTCAATA
TAATTAGAAATTAATTAAGAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATC
TTTTTGGTGGGGAATTATATATGTTTTATGAGTATTATGGCAAAAAAATTCAGAAAAAAATATTC
GGGTCAGTTTTTAGCAGAAAATCGTGTACGTTATAGTTTTGGGGCTAAAAACGCGTTTCGGGGGC
CCCGGCTCAGTTTTGAATGATTTTTGGCAGAAAGACTCCGTGAAATATCTATATTCATCGAACCA
ATCTCAGGCTCTCAGCCACATTACATTTAAGGATTTGTTTTTACAAGCATCTGAATATTGTTTCG
ATTTAATTAGAAATAGATTCGGAAAAAAATA
Found at i:2556 original size:324 final size:323
Alignment explanation
Indices: 1963--2790 Score: 1038
Period size: 324 Copynumber: 2.5 Consensus size: 323
1953 TTTTTTTTGT
* * * * **
1963 TTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATACATCGAACAAAATCCCAGCC
1 TTTTGCATGATTTTTGGCG-AAAGACTCCTTGAAATATCTATATTCATCTAACAAAATGTCAGCC
* * *
2028 AC-GTACGATTTAAGTATTTGTTTTTACGAGCATATGAATATTGTTTCGATTTAATTAAAAAGTA
65 ACATTA-GATTTAAGGATTTGTTTTTACGAGCATATGAATATTGTTTCGATTTAATTAAAAATTA
* * * *
2092 ATTCGTAAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTG
129 ATTCGGAAAAAAATTGGAAAAATGATATTAGAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTG
* **
2157 AATTATATATTATTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCCGATCAGTTTTTA
194 AATTATATATTATTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAC-AATCCGATCAGTTTTTA
* *
2222 GCCGAAATCGTGTACT-ACCATCACGGTTTTT-GGCTAAAAAACGC-ATTCCTGAGCCACCGACT
258 ACCGAAATCGTGTACTAACCATCACGGTTTTTGGGCT-AAAAACGCGATTCCGGAGCC-CCGACT
2284 CAA
321 CAA
* * *
2287 TTTTGCATGATTTTTGGCGCAAAGATTCCTTGAAATATCTATATTCATCTAACCAAATGTCAACC
1 TTTTGCATGATTTTTGGCG-AAAGACTCCTTGAAATATCTATATTCATCTAACAAAATGTCAGCC
* * * * * *
2352 ACATTGGATATAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAA-TAAGAAATTC
65 ACATTAGATTTAAGGATTTGTTTTTACGAGCATATGAATATTGTTTCGATTTAATTAA-AAATTA
*
2416 ATTCGGAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTG
129 ATTCGGAAAAAAATTGGAAAAATGATATTAGAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTG
* * * *
2481 AATTATATATTTTTTCTGAGTATTGTGGCCAAAAATTCAGGAAAAAA-AATCGGGTCAGTTTTTA
194 AATTATATATTATTTCTGAGTATTGTGGCAAAAAATTCA-GAAAAAACAATCCGATCAGTTTTTA
* * * * *
2545 ACCGAAAATCGTGTACTAACCATCATGGTTTTTGGGCTTAAAACGCGTTTCGGGGGCCCCGACTC
258 ACCG-AAATCGTGTACTAACCATCACGGTTTTTGGGCTAAAAACGCGATTCCGGAGCCCCGACTC
*
2610 AG
322 AA
* * * * *
2612 TTTTGAATGATTTTTGGCAGAAAGACTCCGTGGAATATCTATTTTCATCTAAGAAATCTCAGGCT
1 TTTTGCATGATTTTTGGC-GAAAGACTCCTTGAAATATCTATATTCATCTAACAAA----A---T
*
2677 CTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATATGAATATTGTTTCGATTTAATTAA
58 GTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATATGAATATTGTTTCGATTTAATTAA
** *
2742 AAATTAATTTAGAAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAG
123 AAATTAATTCGGAAAAAAATTGGAAAAATGATATTAGAAGCGTGAAAAG
2791 CCCGTTAATC
Statistics
Matches: 430, Mismatches: 58, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
323 19 0.04
324 212 0.49
325 84 0.20
326 12 0.03
329 1 0.00
332 99 0.23
333 3 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (323 bp):
TTTTGCATGATTTTTGGCGAAAGACTCCTTGAAATATCTATATTCATCTAACAAAATGTCAGCCA
CATTAGATTTAAGGATTTGTTTTTACGAGCATATGAATATTGTTTCGATTTAATTAAAAATTAAT
TCGGAAAAAAATTGGAAAAATGATATTAGAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAA
TTATATATTATTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAACAATCCGATCAGTTTTTAACC
GAAATCGTGTACTAACCATCACGGTTTTTGGGCTAAAAACGCGATTCCGGAGCCCCGACTCAA
Found at i:2699 original size:805 final size:796
Alignment explanation
Indices: 1123--2726 Score: 2706
Period size: 805 Copynumber: 2.0 Consensus size: 796
1113 TCTTCTTTTT
* *
1123 TTGCGTTGAATTGTGTATTTTTTGCCGAATTTTTTTTTGTTTTTGCATGATTTTTGATGTAAATA
1 TTGCGTTGAATTATGTATTTTTTGCCGAATTTTTTTTTGTTTTTGCATGATTTTTGACGTAAATA
* *
1188 CTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCCACATTCGATTTAAGTATTTGTTTTC
66 CTCCTTGAAATATCTATATACATCGAACAAAATCCCAGCCACATACGATTTAAGTATTTGTTTTC
* * * *
1253 ACGAACATCTAAATCTTGTTTCAATTTAATTAAAAATTAATTTGGAAAAAAATGGAAAAACGATA
131 ACGAACATATAAATATTGTTTCAATTTAATTAAAAAGTAATTCGGAAAAAAATGGAAAAACGATA
* *
1318 TTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTCACTTATATATTTTTTCTGAGTATTGTG
196 TTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTCAATTATATATTATTTCTGAGTATTGTG
*
1383 GCAAAAATTGAGAAAAAAATTTTCTGATCAGTTTTTAGCCGAAATCGTGTACTTACCATCACGGT
261 GCAAAAATTGAGAAAAAAATTTTCCGATCAGTTTTTAGCCGAAATCGTGTACTTACCATCACGGT
*
1448 TTTTGGCTAAAAACGCATTCCTGAGCCACGACTCAATTTTGCATGATTTTTGGCGTAAAGATTCC
326 TTTTGGCTAAAAACGCATTCCTGAGCCACGACTCAATTTTGCATGATTTTTGGCGCAAAGATTCC
* *
1513 TTGAAATATCTATATTCATCAAACCAAATGTCAGCCACATTGGATATAAGGATTTGTATTTACGA
391 TTGAAATATCTATATTCATCAAACCAAATGTCAACCACATTGGATATAAGGATTTGTATTTACAA
* *
1578 GTATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTAAGAAAAAATTGGAAAATGATATTAAA
456 GCATCTGAATCTTGTTTCAATTTAATAAGAAATTAATTAAGAAAAAATTGGAAAATGATATTAAA
1643 AGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTGTGGCAAA
521 AGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTGTGGCAAA
*
1708 AAATTCAGGAAAAAAAATCGGGTCAGTTTTTAGCAGAAAATCGTGTACTAACCATCATAGTTTTT
586 AAATTCAGGAAAAAAAATCGGGTCAGTTTTTAACAGAAAATCGTGTACTAACCATCATAGTTTTT
* *
1773 GGGCTGAAAACGCGTTTCGTGGGCCCCGGCTCAGTTTTGAATGATTTTTGGCAGAAAGACTCCGT
651 GGGCTGAAAACGCGTTTCGGGGGCCCCGACTCAGTTTTGAATGATTTTTGGCAGAAAGACTCCGT
*
1838 GAAATATCTATTTTCATCGAAGCAATCTCAGGCTCTCAGCCACATTACATTTAAGGATTTGTTTT
716 GAAATATCTATTTTCATCGAAGAAATCTCAGGCTCTCAGCCACATTACATTTAAGGATTTGTTTT
*
1903 TACAAGCATCTGAATA
781 TACAAGCATATGAATA
*
1919 TTGCGTTGAATTATGTCTTTTTTGCCGAAAATACTTTTTTTTGTTTTTGCATGATTTTTGACGTA
1 TTGCGTTGAATTATGTATTTTTTGCCG--AAT--TTTTTTTTGTTTTTGCATGATTTTTGACGTA
*
1984 AATACTCCTTGAAATATCTATATACATCGAACAAAATCCCAGCCACGTACGATTTAAGTATTTGT
62 AATACTCCTTGAAATATCTATATACATCGAACAAAATCCCAGCCACATACGATTTAAGTATTTGT
* * * * *
2049 TTTTACGAGCATATGAATATTGTTTCGATTTAATTAAAAAGTAATTCGTAAAAAAATTGGAAAAA
127 TTTCACGAACATATAAATATTGTTTCAATTTAATTAAAAAGTAATTCGGAAAAAAA-TGGAAAAA
*
2114 CGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTGAATTATATATTATTTCTGAGTA
191 CGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTCAATTATATATTATTTCTGAGTA
*
2179 TTGTGGCAAAAAATTGAGAAAAAACTTTTCCGATCAGTTTTTAGCCGAAATCGTGTAC-TACCAT
256 TTGTGGC-AAAAATTGAGAAAAAAATTTTCCGATCAGTTTTTAGCCGAAATCGTGTACTTACCAT
2243 CACGGTTTTTGGCTAAAAAACGCATTCCTGAGCCACCGACTCAATTTTGCATGATTTTTGGCGCA
320 CACGGTTTTTGGCT-AAAAACGCATTCCTGAGCCA-CGACTCAATTTTGCATGATTTTTGGCGCA
*
2308 AAGATTCCTTGAAATATCTATATTCATCTAACCAAATGTCAACCACATTGGATATAAGGATTTGT
383 AAGATTCCTTGAAATATCTATATTCATCAAACCAAATGTCAACCACATTGGATATAAGGATTTGT
* * * **
2373 TTTTACAAGCATCTGAATCTTGTTTCGATTTAATAAGAAATTCATTCGGAAAAAAATTGGAAAAA
448 ATTTACAAGCATCTGAATCTTGTTTCAATTTAATAAGAAATTAATTAAG-AAAAAATTGG-AAAA
*
2438 TGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTA
511 TGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTA
* *
2503 TTGTGGCCAAAAATTCAGGAAAAAAAATCGGGTCAGTTTTTAACCGAAAATCGTGTACTAACCAT
576 TTGTGGCAAAAAATTCAGGAAAAAAAATCGGGTCAGTTTTTAACAGAAAATCGTGTACTAACCAT
* *
2568 CATGGTTTTTGGGCTTAAAACGCGTTTCGGGGGCCCCGACTCAGTTTTGAATGATTTTTGGCAGA
641 CATAGTTTTTGGGCTGAAAACGCGTTTCGGGGGCCCCGACTCAGTTTTGAATGATTTTTGGCAGA
* * *
2633 AAGACTCCGTGGAATATCTATTTTCATCTAAGAAATCTCAGGCTCTCAGCCACATTAGATTTAAG
706 AAGACTCCGTGAAATATCTATTTTCATCGAAGAAATCTCAGGCTCTCAGCCACATTACATTTAAG
*
2698 GATTTGTTTTTACGAGCATATGAATA
771 GATTTGTTTTTACAAGCATATGAATA
2724 TTG
1 TTG
2727 TTTCGATTTA
Statistics
Matches: 753, Mismatches: 45, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
796 25 0.03
798 3 0.00
800 139 0.18
801 97 0.13
802 68 0.09
803 132 0.18
804 10 0.01
805 279 0.37
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (796 bp):
TTGCGTTGAATTATGTATTTTTTGCCGAATTTTTTTTTGTTTTTGCATGATTTTTGACGTAAATA
CTCCTTGAAATATCTATATACATCGAACAAAATCCCAGCCACATACGATTTAAGTATTTGTTTTC
ACGAACATATAAATATTGTTTCAATTTAATTAAAAAGTAATTCGGAAAAAAATGGAAAAACGATA
TTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTCAATTATATATTATTTCTGAGTATTGTG
GCAAAAATTGAGAAAAAAATTTTCCGATCAGTTTTTAGCCGAAATCGTGTACTTACCATCACGGT
TTTTGGCTAAAAACGCATTCCTGAGCCACGACTCAATTTTGCATGATTTTTGGCGCAAAGATTCC
TTGAAATATCTATATTCATCAAACCAAATGTCAACCACATTGGATATAAGGATTTGTATTTACAA
GCATCTGAATCTTGTTTCAATTTAATAAGAAATTAATTAAGAAAAAATTGGAAAATGATATTAAA
AGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTGTGGCAAA
AAATTCAGGAAAAAAAATCGGGTCAGTTTTTAACAGAAAATCGTGTACTAACCATCATAGTTTTT
GGGCTGAAAACGCGTTTCGGGGGCCCCGACTCAGTTTTGAATGATTTTTGGCAGAAAGACTCCGT
GAAATATCTATTTTCATCGAAGAAATCTCAGGCTCTCAGCCACATTACATTTAAGGATTTGTTTT
TACAAGCATATGAATA
Found at i:2857 original size:83 final size:83
Alignment explanation
Indices: 2718--2873 Score: 240
Period size: 83 Copynumber: 1.9 Consensus size: 83
2708 TACGAGCATA
* * *
2718 TGAATATTGTTTCGATTTAATTAAAAATTAATTTAGAAAAAAAATGGAAAAATGATATTAGAAGC
1 TGAATATTGTTTCAATTTAATTAAAAATTAATTCAGAAAAAAAATGGAAAAATGATATTAAAAGC
2783 GTGAAAAGCCCGTTAATC
66 GTGAAAAGCCCGTTAATC
* ** * *
2801 TGAATCTTGTTTCAATTTAATTGGAAATTAATTCGGAAAAAAATTGGAAAAATGATATTAAAAGC
1 TGAATATTGTTTCAATTTAATTAAAAATTAATTCAGAAAAAAAATGGAAAAATGATATTAAAAGC
2866 GTGAAAAG
66 GTGAAAAG
2874 ACCATCAATC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 65 1.00
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (83 bp):
TGAATATTGTTTCAATTTAATTAAAAATTAATTCAGAAAAAAAATGGAAAAATGATATTAAAAGC
GTGAAAAGCCCGTTAATC
Found at i:5319 original size:331 final size:330
Alignment explanation
Indices: 4705--5399 Score: 1133
Period size: 331 Copynumber: 2.1 Consensus size: 330
4695 ATCCACGTTC
* * * * *
4705 GATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTTACTCGGA
1 GATTTAAG-ATTTATTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAAGTAACTCGGA
* *
4770 AAAAAATTGGAAAAATAATATTAAAAGCATGAAAAGCCCGTCAATCATTTTGGCGTTGAATTTTA
65 AAAAAATTGGAAAAACAATATTAAAAGCATGAAAAGCCCGTCAATCATTTTGGCGTTGAATTATA
4835 TATTTTTTATGAGTATTATGGCAAAAAATTGAGAAAAAACTTTTCCAATCAGTTTTTAGCCGAAA
130 TATTTTTTATGAGTATTATGGCAAAAAATTGAGAAAAAACTTTTCCAATCAGTTTTTAGCCGAAA
*
4900 ATCGTGGACTAACCGTCACGGTTTTTGGCTAAAAAAACGTTCCCGAGCCCCGACTCAATTTTGCA
195 ATCGTGGACTAACCGTCACGATTTTTGGCTAAAAAAACGTTCCCGAGCCCCGACTCAATTTTGCA
* * *
4965 TGGTTTTTCGCGCAAAGACTCCTTGAAATATCTATATTTATCTAACCAATCTCAGGCTCTCAGCC
260 TGGTTTTTCGCGCAAAAACTCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCTCTCAACC
5030 ACATTA
325 ACATTA
* * *
5036 GATTTAAGGATTTATTTTTACGAGCATATGAATATTGTTTCGATTTAATTAAAAAGTAATTCGTA
1 GATTTAA-GATTTATTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAAGTAACTCGGA
* * * *
5101 AAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATA
65 AAAAAATTGGAAAAACAATATTAAAAGCATGAAAAGCCCGTCAATCATTTTGGCGTTGAATTATA
* * * *
5166 TATTTTTTCTGAGTATTGTGGCAAAAAATTGTGAAAAAACTTTTCCGATCAGTTTTTAGCCGAAA
130 TATTTTTTATGAGTATTATGGCAAAAAATTGAGAAAAAACTTTTCCAATCAGTTTTTAGCCGAAA
*
5231 ATCGTGTACTAACCGTCACGATTTTTGGCTAAAAAAACGTTCCCGAGCCCCGACTCAATTTTGCA
195 ATCGTGGACTAACCGTCACGATTTTTGGCTAAAAAAACGTTCCCGAGCCCCGACTCAATTTTGCA
* *
5296 TGGTTTTTGGTGCAAAAACTCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCTCTCAACC
260 TGGTTTTTCGCGCAAAAACTCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCTCTCAACC
5361 ACATTA
325 ACATTA
5367 GATTT-A-ATTTATTTTTACGAGCATCTGAATATT
1 GATTTAAGATTTATTTTTACGAGCATCTGAATATT
5400 CACTACTAGA
Statistics
Matches: 337, Mismatches: 26, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
328 26 0.08
330 1 0.00
331 309 0.92
332 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Consensus pattern (330 bp):
GATTTAAGATTTATTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAAGTAACTCGGAA
AAAAATTGGAAAAACAATATTAAAAGCATGAAAAGCCCGTCAATCATTTTGGCGTTGAATTATAT
ATTTTTTATGAGTATTATGGCAAAAAATTGAGAAAAAACTTTTCCAATCAGTTTTTAGCCGAAAA
TCGTGGACTAACCGTCACGATTTTTGGCTAAAAAAACGTTCCCGAGCCCCGACTCAATTTTGCAT
GGTTTTTCGCGCAAAAACTCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCTCTCAACCA
CATTA
Done.