Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015147.1 Corchorus capsularis cultivar CVL-1 contig15168, 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: 87301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2693 original size:321 final size:322
Alignment explanation
Indices: 3--8695 Score: 9415
Period size: 323 Copynumber: 27.2 Consensus size: 322
1 CA
* * * *
3 CAATTTTTGGCCACAATACTCAGAAAAAATGTATTATTCAATGCCAAAAAGATTGACGGGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
* * * *
68 CAAGATTCTAATA--GTTTCTTCA-TTTTTTTCCTAATTAATTTCTAATTAAATCGGAACAAGAT
66 CAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * * * * * *
130 TCAAAGGCTTGTAAAAACAAATCCTTATATCCAATGTGGCTGTCATTTGGTTTGATGAATATAGA
131 TGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATAGA
* * * * *
195 TATTTCAAGGGGTCTTTGTG-CATAAAATCATGCAAAATTGACCCGGGGCGCCAGAATGCGTTTT
196 TATTTCAAGGAGTCTTTGTGCCA-AAAATCATGCAAAATTGAGCCGGGGCTCCTGAACGCGTTTT
* * * * * * *
259 TAGCC-AATACTGTGATGATTAGTATAGGATTTCGGCAAAAAACTGACCCGAAATTTTTTTCCT
260 TAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTTTTT-CT
* * * * * * *
322 CAATTTTTTGTCACAATA-TACAGAGAAAATATTTAATTAAATGCCAAAAATATTGACAGGTTTT
1 CAATTTTTTGCCACAATACT-CAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTT
* * *
386 TCAAGCTTCTAATATCTTTTTTTTA-TTTTTTTCCGATTTAATTTCTAATTAAATCGAAACAAGA
65 TCAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGA
* *
450 TTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCGATGAATATAG
130 TTGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATAG
* * * * ** * * *
515 ATATTTCAAGGAGTCCTTATGCCAAAAATCTTACAAACCTGAGCCAGGGCTCCAGAAACACGTTT
195 ATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTG-AACGCGTTT
* * *
580 TTAACCCAAAAACC----------GT----GA-------TAAAAACTGACCCTAAAAGTTCTTTC
259 TT-AGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAA-TTTTTTC
624 T
322 T
* * * *
625 CAAATTTTTGCCACAATACTCAGAAAATATATATAATTCAATGCCAAAAAGATTGATGGGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
* * * *
690 CAAGTTTCTAATATAGTTTTTTCATTTTTTTTACCAAATTAATTTCTAATTAAATCTAAACAAGA
66 CAAGCTTCTAATATCGTTTTTTCATTTTTTTT-CCGAATTAATTTCTAATTAAATCGAAACAAGA
*
755 TTGAGATGCTCG-AAGAAACAAATCCTTATATCCAATATGGCTGAAATTTGGTTCGATGAATATA
130 TTGAGATGCTCGTAA-AAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATA
* ** * * * * * * * *
819 GATATTTTAAGGAGT-TCTTCAGCCAAAATTCTTTCAAAACT-ATGTCGGGGCTCCGGAAACACA
194 GATATTTCAAGGAGTCT-TTGTGCCAAAAATCATGCAAAATTGA-GCCGGGGCTCCTG-AACGCG
* * * *
882 TTTTTATCCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAAATTGACCCGAAATGTTTT
256 TTTTTA-GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAA-ATTTT
947 TTCT
319 TTCT
* * *
951 TAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCATAAAGATTGACGTGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
* * *
1016 CAAGCTTCTAATATCGTTTTTTTCTTCTTCTTTTTTCCAAATTAATTTCTAATTAAATCGAGACA
66 CAAGCTTCTAATATCG-TTTTTTC--ATT-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * * * * * *
1081 AGAATGAGATGCTC-AAAGAAAGAAATCCTTATATCAAATATAGCTGAGATTTGATTCGATGAAT
127 AGATTGAGATGCTCGTAA-AAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAAT
* * * * * *
1145 ATAGATATTTTAAGGAGTCATTCTGACAAAAATCATGC-AAATCTGAGCCGGGGCTCCCGAAACA
191 ATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAAT-TGAGCCGGGGCTCCTG-AACG
* * * * * ** *
1209 CATTTTCACCCAAAAAACCATGATGGTTATTACACGATTTCGATTAAAAACTGACAC-AAAAGGT
254 CGTTTTTAGCC-AAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAA--T
1273 TTTTTCT
316 TTTTTCT
* *
1280 CAATTTTTTGCCACAATACTCAG-AAAAATATATAATTTAACGCCAAAAAGATTGACGTGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
1344 CAAGCTTCTAATATCGTTTTTTCATTTTCTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGA
66 CAAGCTTCTAATATCGTTTTTTCATTTT-TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGA
* * * * * *
1409 TTCACATGCTCGTAAAAACATATCCTTATATACAATGTGGCTGACATTTGGTTAGAT-AATTATA
130 TTGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAA-TATA
* *
1473 GATATTTCAAGGAATCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTCCTGAACGCGTTT
194 GATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTGAACGCGTTT
* * * * * **
1538 TTAGCCAAAACCCTTGAAGGTTAGTACACGATTTTGGATAAAAACTGACATGAGAAATTTTTTCT
259 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGA-AAATTTTTTCT
* * * * * **
1603 CATTTTTTTGCCACAATACTTAGAGAAAA-ATATAATTTAATGCAAAAAAGATTAACATGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
** ** * * * *
1667 CAAGCTTCTAATATCG--GGTT-A-TTTTTCCCCAAATTAATTTGTAATAAAATCGTAACAAGAT
66 CAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * * * * ** *
1728 TCAGATGCTCGCAAAAACAAATCCTTGTGTCCAATGTGATTGACATTTGGTTCAATGAATATAGA
131 TGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATAGA
* * * * * *
1793 TACTTCAAGGAGTTTTTGTGCAAAAAATAATGCAAAATTCAGCCGGGGCTCCAGAACGCGTTTTT
196 TATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTGAACGCGTTTTT
* * *
1858 AGGCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAAACTGACCCGAAAAGTTTTATCT
261 AGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAA-TTTTTTCT
* * * * * * **
1921 GAATTTTTTGCCACAATACTTAGAAAAAATATACAATTTAACGCAAAAAAGATTAACATGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
*
1986 CAAGCTTCTAATA--------TCATTTTTTTTCCGAATTACTTTCTAATTAAATCGAAACAAGAT
66 CAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * ** * *
2043 TGACATGCTCTTAAAAGTAAATCCTTATATCCAATGTGGCTGACTTTTGGTTCGATGAATATAGA
131 TGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATAGA
* * * * *
2108 TATTTCAACGAGTCTTTGTGCCAAAAATTATGCAAAATTGACCCGGGACTCC-GAAAGGCGTTTT
196 TATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTG-AACGCGTTTT
* * * ** * * * *
2172 TAGCCAAAAACTGTGATGGCTAGTATATAATTTCGGCAAAAAACAGATCTGAAAATTATTTTCT
260 TAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATT-TTTTCT
** * * * * *
2236 CAATTTTTTGAAACAATACACAGAGAAAATATATAATTCAATGCCAAAAATATTGACGGGATTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
**
2301 CAAGCTTCTAATATATTTTTTTCA-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
66 CAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * * * * * *
2365 GGAGATGCTCGAAAAAACAAATACTTATATCTAATATGGCTGAGATTTGTTTCGATAAATATAGA
131 TGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATAGA
* * * *
2430 TATTTCAATGAGTCTTTGTGCTAAAAATCATGCAAAATTGAGTCGGGGCT-CTGAACGTGTTTTT
196 TATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTGAACGCGTTTTT
* * **
2494 AGCCAAAAACCGTGATGGTTAGTAAATGATTTCGGCTAAAAACTGACCCGAGAAGGTTTTTCT
261 AGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGA-AAATTTTTTCT
* * * * *
2557 GAATTTTTTGCCACAATAATCAGAAAACATATAT-ATTCAATGCCAAAAAGATTGACGGGTTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
* * * *
2621 CAAGCTTCCAATATCGTTTTTTCATTTTTTTTCCGAATCAGTTTTTAATTAAATCGAAA-AAGGA
66 CAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAA-GA
* * * * *
2685 ATGAGATGCTC-AAAGAAATAAATCCTTATATCCAAAATGGCTGAGATTTGGTTCGATGAATATA
130 TTGAGATGCTCGTAA-AAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATA
* * * * * * * *
2749 GAAATTTTAAGGAGTCATTCTGCCAAAAATCATGCAAAAATGAGCCGAGGCTCCCGAAACACGTT
194 GATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTG-AACGCGTT
* * *
2814 TTTA-CC-----CC---A-----ACGTACACGATTTCGGTTAAAAACTGACCTGAAATGTTTTTT
258 TTTAGCCAAAAACCGTGATGGTTA-GTACACGATTTCGGCTAAAAACTGACCCGAAA-ATTTTTT
2865 CT
321 CT
* * * * *
2867 CAATTTTTTGCCACAATACTCATAAAAAATTGTATTATTCAATGCCAAAAAGATTG-GGAGGCTT
1 CAATTTTTTGCCACAATACTCAGAAAAAA-TATATAATTTAATGCCAAAAAGATTGACG-GGCTT
* *
2931 TTCAAGCTTCTAATATAGTTTTTTC--TTTTTTTCCTAATTAATTTCTAATTAAATCGAAACAAG
64 TTCAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG
* * * * * * *
2994 ATTCAAAAGCTTGTAAAAACAAATCCTTATATCCAATGTGGCTGTCATTTGGTTTGATGAATATA
129 ATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATA
* * * * * * *
3059 TATATTTCAAGGGGTCTTTGTGCCCAAAATCATGCAAAATTCACCCGGGGCTCCAGAATGCGTTT
194 GATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTGAACGCGTTT
* * * *
3124 TTAGCCAAAAACTGTGATGGTTAGTATACGATTTTGGCAAAAAACTGACCCGAAAAATTTTTTTC
259 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCG-AAAA-TTTTTTC
3189 T
322 T
* * * * * * * *
3190 AAATTTTTTGTCACAATA-TGCAGAGAAAATATATAATTAAATGTCAAGAATATTGACTGGCTTT
1 CAATTTTTTGCCACAATACT-CAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTT
*
3254 TCAAGTTTCTAATATC-TTTTATTCA-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG
65 TCAAGCTTCTAATATCGTTTT-TTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG
* * *
3317 ATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATCGCTGAGATTTGGTTCGATGAATATA
129 ATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATA
** * * * * * * * *
3382 GATATTTCAATAAGTCCTTATGCCAAAAATCTTACAAAACTGAGCCAGGGCT-TTAGAAACACGT
194 GATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCT-G-AACGCGT
* * * * *
3446 TTTTACCCCAAAACCGTGATAGTTCGTACACGATTTCGGCTAAAAACTGACCCTAAAAGTTTTTT
257 TTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAA-TTTTTT
3511 CT
321 CT
* * *
3513 CAATTTTTTGCCACAATACTCAGAAAATATATATAATTCAATGCCTAAAAGATTGAC-GGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
* * *
3577 CAAGATTCTAATATCGTTTTTTCATTTTTTTACCAAATTAATTTCTAATTAAATCGAAACAAGAT
66 CAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
*
3642 TGAGATGCTCG-AAGAAACAAATCCTTATATCCAATATGGCTGAAATTTGGTTCGATGAATATAG
131 TGAGATGCTCGTAA-AAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATAG
** * * ** * * * * * *
3706 ATATTTTGAGGAATTTTTCAGCCAAAAATCTTTCAAAACT-ATGTCGGGGCTCCCGAAACACGTT
195 ATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGA-GCCGGGGCTCCTG-AACGCGTT
* * * *
3770 TTTACTCCAAAAACCGTGACGGTTAGTACACGA-TTCAGGCTAAAAA-TTACCCGAAATGTTTTT
258 TTTA-GCCAAAAACCGTGATGGTTAGTACACGATTTC-GGCTAAAAACTGACCCGAAA-ATTTTT
3833 TCT
320 TCT
* ** * *
3836 TAATTTTTTGCCACAATACTTGGAAAAAATATATAATTTAACGCCAAAAAGATTGACGTGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
* * *
3901 CAAGCTTCTAATATCGTTTTTTTCACTTTTTTTCCAAATTAATTTCTAATTAAATCGAGACAAGA
66 CAAGCTTCTAATATCG-TTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGA
* * * *
3966 ATGAGATGCTCG-AAGAAAGAAATCCTTATATCTAATATGGCTGAGATTTGGTTCGATGAATATA
130 TTGAGATGCTCGTAA-AAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATA
* * * * * * * *
4030 GATATGTT-AAGGAGTCATTCTGACAAAAATCATGCTAAACTGAGCCGGGGCTCCCGAAACACAT
194 GATAT-TTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTG-AACGCGT
* * * * *
4094 TTTCACCCAAAAAACCGTGATGGTTATTACACGATTTCGGTTAAAAACTAACCCGAAAAGTTTTT
257 TTTTAGCC-AAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAA-TTTTT
4159 TCT
320 TCT
* * *
4162 CAATTTTTTGCCACAATACTCAG-AAAAATATATAATTTAACGCCAAAAAGATTGACGTGCTTGT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
*
4226 CAAGCTTCTATTATCGTTTTTTCATTTTCTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGA
66 CAAGCTTCTAATATCGTTTTTTCATTTT-TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGA
* * *
4291 TTAAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTAGAT-AATTATA
130 TTGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAA-TATA
* *
4355 GATATTTCAAGGAATCTTTGTGCCAAAAATCATGCAAAATTGAGTCC-GGGCTCCTGAACGCATT
194 GATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAG-CCGGGGCTCCTGAACGCGTT
* * * * *
4419 TTCAGCTAAACACCGTGA-----CGTACACGATTTCGGCTAAAAACTTACCCAAGAAAATTTTTT
258 TTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCC--GAAAATTTTTT
4479 CT
321 CT
* * * * *
4481 CATTTTTTTGCCACAATACTCAGAGAAAA-ATATAATTTAATGCAAAAAAGATTAACGTGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
* * * *
4545 TAAGCTTCTAATATCGTTTTATTTTTATTTTTTTCCCGAATTAATTTCTAATTAAATCGTAACAA
66 CAAGCTTCTAATATCG--TT-TTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAA
* * * * * **
4610 GATTCAGATGCTCGCAAAAACAAATCCTTGTGTCCAATGTGATTGACATTTGGTTCGATGAATAT
128 GATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATAT
* * * * * * * *
4675 AGATACTTCAAGGTGTCTTTTTGCCAAAAATAATGCAAAATGGAGTCGGGACTCCAGAACGCGTT
193 AGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTGAACGCGTT
* * * * * *
4740 CTTAGCCAAAAACCGTGATGGTTAGCACATGATTTCGACTAAAAACTTACCCGAAAAGTTTTATC
258 TTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAA-TTTTTTC
4805 T
322 T
* * * * **
4806 GAATTTTTTACCACAATACTTAGAAAAAATATACAATTTAATGCCAAAAAGATT-ACCATGCTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGA-CGGGCTTT
* *
4870 TCAACCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTACTTTCTAATTAAATCGAAACAAGA
65 TCAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGA
* * * *
4935 TTGAGATGCTCGTAAAAATAAATCATTATATCCAATATGGCTTACTTTTGGTTCGATGAATATAG
130 TTGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATAG
* * * * * *
5000 ATATTTCAAGGAGTCTTTGTGCCAAAAATTATGCAAAATTGACCCAGTGCTCCGGAATGCGTTTT
195 ATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTGAACGCGTTTT
* * *
5065 TAGCCAAAAACTGTGATGGCTAGTATACGATTTCGGC-AAGAAACTGACCCGAAAATTATTTTCT
260 TAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAA-AAACTGACCCGAAAATT-TTTTCT
* * * * * *
5129 CAATTTTTTGCTACAATACACAGAGAGAATATATAATTCAATGCCAAAAATATTGACGGGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
5194 CAAGCTTCTAATA--------TCA--TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
66 CAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * * *
5249 GGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCGATAAATATAGA
131 TGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATAGA
* *
5314 TATTTCAAGGAGTTTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCT-CTGAACGCGTTTTT
196 TATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTGAACGCGTTTTT
* *
5378 AGCCAAAAACCGTGATGGTTAGTACATGATTTCGGCT----A---ACCCGAGAAGTTTTTTCT
261 AGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGA-AAATTTTTTCT
* * *
5434 CAATTTTTTGCCACAATAATCAGAAAAAAAATAT-ATTAAATGCCAAAAAGATTGACGGGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
* * *
5498 CAAGCTTCCAATATCGTTTTTTCATTTTTTTTTCCGAATCAATTTTTAATTAAATCGAAACAAGA
66 CAAGCTTCTAATATCGTTTTTTCA-TTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGA
* * * * *
5563 ATGAGATGCT--TAAAGAAATAAATCCATATATCCAATATGGTTGAGATTTGGTTCGATGAATAT
130 TTGAGATGCTCGT-AA-AAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATAT
* * * * * * * *
5626 AGAAATTTTAAGGAGTCATTCTGCCAAAAATCATGCAAAACTGAGCCGAGGCTCCCGAAACACGT
193 AGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTG-AACGCGT
* *
5691 TTTTA-CC-----CC---A-----ACGTACACGATTTCGGTTAAACACTGACCC-AAAATGTTTT
257 TTTTAGCCAAAAACCGTGATGGTTA-GTACACGATTTCGGCTAAAAACTGACCCGAAAA--TTTT
5741 TTCT
319 TTCT
* * * * *
5745 CAATTTTTTGCCATAATACTCAGAAAAAATGTATTATTCAATGCCAAAAAGATTGGCGGGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
*
5810 CAAGCTTCTAATA--GTTTTTTCATTTTTTTTTTCCTAATTAATTTCTAATTAAATCGAAACAAG
66 CAAGCTTCTAATATCGTTTTTTCA--TTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG
* * * * * * *
5873 ATTCAAATGCTTGTAAAAACAAATCCTTATATCCAATGTGGTTGTCATTTGGTTTGATGAATATA
129 ATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATA
* * * * * *
5938 GATATTTCAAGGGGTCTTTGTGCCCAAAATCATGGAAAATTGACCCGGGGCTCCAT-AATGCGTG
194 GATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCC-TGAACGCGTT
* * * *
6002 TTTAGCCAAAAACTGTGATGGTTAGTATACGATTTCGGCAAAAAACTAACCCGAAAATTTTTTTT
258 TTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAA--TTTTTT
6067 CT
321 CT
* * * * *
6069 CAATTTTTTGTCACAATA-TACAGAGAAAATATATAATTAAATGCCAAAAATATTGACAGGCTTT
1 CAATTTTTTGCCACAATACT-CAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTT
*
6133 TCAAGCTTCTAATATC-TTTTATTCA--TTTTTTCCGAATTAATTTGTAATTAAATCGAAACAAG
65 TCAAGCTTCTAATATCGTTTT-TTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG
* *
6195 ATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCGATGAATATA
129 ATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATA
* * * * * * * *
6260 GATATTTCAAGGAGTCCTTATGCCAAAAATCTTACAAAACTGAGTCAGGGCT-CTAGAAACACGT
194 GATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCT-G-AACGCGT
* * * * ** *
6324 TTTTACCCCAAAACCGTGATAGTTCGTACACGATTTCGGCTAAAAACTGACCATAAAAGTTCTTT
257 TTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAA-TTTTTT
6389 CT
321 CT
* * * * *
6391 GAATTTTTTGGCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAATATTGACGGGTTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
** * *
6456 CAATTTTCTAATATCTTTTTTTCA-TTTTTTTCCGAATTAACTTCTAATTAAATCGAAACAAGAT
66 CAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * * *
6520 TCAGATGCTCGTAAAAACAAATCCTTATATCAAATGTGGCTGACATTTGGTTAGAT-AATTATAG
131 TGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAA-TATAG
* * * * * **
6584 ATATTTCAAGGAATCTTTGTGCCAAAAATCATACAAAATCGAGTCGGGGATCCTGAACGTATTTT
195 ATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTGAACGCGTTTT
* *
6649 TAGCCAAAAACCGTG-TAGGTTAGTACACGATTTCTGCTAAAAACTGACCTGAGAAATTTTTTCT
260 TAGCCAAAAACCGTGAT-GGTTAGTACACGATTTCGGCTAAAAACTGACCCGA-AAATTTTTTCT
* * * * * * *
6713 CATTTTTTTGCCACAATGCTCAGAGAAAA-ATATAATTTAATGCAAAAAATATTAACGTGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
* * *
6777 AAAGCTTCTAATATCG-----T--TTTTTTTCCCGAATTAATTTCTAATTAAATCGTAACAAGAT
66 CAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * * * * ** *
6835 TCAGATGCTCGTAAAAACAAATCATTGTGTCCAATGTGATTGACATTTGGTTAGATGAATATAGA
131 TGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATAGA
* *
6900 TATTTCAAGGAGTCTTTGTGCCAAAAATAATGCAAAATTGAGCCGGGGCTCCAGAACGCGTTTTT
196 TATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTGAACGCGTTTTT
* * * * **
6965 GGCCAAAAACCGTGATGGTTAGTACACGATCTCGACTAAAAACTGACCCAAAAAGTTTAATCT
261 AGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAA-TTTTTTCT
* * * * **
7028 GAATTTTTTGCCACAATACTTAGAAAAAATATACAATTTAATGCCAAAAAGATTTACATGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
** *
7093 CAAGCTTCTAATATAATTTTTTCA-TTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGAT
66 CAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * * * *
7157 TCAGATGCTCGTAAAAA-AAATCCTTAGATCCAATATGGTTGACATTTAGTTCGATAAATATAGA
131 TGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATAGA
* * * * ** *
7221 TATTTCAAGGAGTATTTGTGCCAAAAGTCATGCAAAATTTAGTCATGGCTCC-GAAACACGTTTT
196 TATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTG-AACGCG-TTT
** * * * *
7285 TTCCCCAAAAACCGTGATGGTTTA-TACCCGATTTCGACTAAAAACTGATCCGAAAAGTTTTTCC
259 TTAGCCAAAAACCGTGATGG-TTAGTACACGATTTCGGCTAAAAACTGACCCGAAAA-TTTTTTC
7349 T
322 T
** * * * *
7350 CAGCTTTTTGCTACAATACCCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGTTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGG-CTTT
*** * * *
7415 TCTTTCTTCTAATGTCGTTTTTTCATTTTTTTTCCGAATTAATCTCTAATTAAATCGAAACAAAA
65 TCAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGA
* * * *
7480 TTGAGATGCTCGAAAAAACAAATCCTTATATCTAATATGGCTGAGATTTGGTTCGATGAGTATAG
130 TTGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATAG
* * * * ** * * * ** *
7545 ATTTTTTAAGGAGTATTTCTGTAAAAAATCATTCAAAATTGTGCCAGGGCTCTCCAAACACGTTT
195 ATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTC-CTGAACGCGTTT
* * *
7610 TTACCCTAAAAACCGTGATGGTTAGTACACGATTCCGGCTAAAAACTGACTCGAAAAGTTTTTTC
259 TTAGCC-AAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAA-TTTTTTC
7675 T
322 T
* * * *
7676 CAATTTTTTTCCACAATACTAAGAAAAAATATATAATTTAATGCCAAAAAGATTGTCGTGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
* * *
7741 CAAGCTTCTAATATCATATTTTCA-ATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
66 CAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * * * *
7805 TCAGATGCTCGTAAAAACAAATCCTTATTTCCAATCTGGCTGACATTTGGTTAGATAAATATAGA
131 TGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATAGA
** * *
7870 TATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTTTGTCGGGGCT-CTGAATGCGTTTTT
196 TATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTGAACGCGTTTTT
* * *
7934 AGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGACCCGGGAAGTTTTTTCT
261 AGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCC-GAAAATTTTTTCT
* * * * *
7997 CAATTTTTTGCCACAATAATCAGAAAAAATATATAATTTAACGCCAAAAACATTAACGTGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
* * * * * * *
8062 TAAGTTTGTAATATCGTTTTTTCAATTTTTTT-CGAATTATTTTCAAATTAAATCGTAACAAGAT
66 CAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * *
8126 TTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATATAGA
131 TGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATAGA
* * * * *
8191 TATTTCGAGGAGTCTTTGTGACAAAAATAATGCAAAATTGAGTCGGGGCTCCAGAACGCGTTTTT
196 TATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTGAACGCGTTTTT
*** * * *
8256 AGCCAAAATTTGTGATGTTTAGTACACGATTTCGGCTAAAAACTGACCCGATAATTTTATCT
261 AGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTCT
* * * * * * ***
8318 GAATTTTTTACCACAATACTTAGAAAAAATATACAATTTAACGCCAAAAAGATTAATATGCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
* *
8383 CAAGCTTCTAATATCGTCTTTTCA--TTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGAT
66 CAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * *
8446 TGAGATGCTCGTAAAAATAAATCCTTATATCCAATGTGGCTGACATTTGGTTCGATGAATATAAA
131 TGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATAGA
* * * * * *
8511 TATTTCAAGGAGTCTTTGTGTCAAAAATAATGCAAAATTGAGGCGGAGCT-CTGGAATGCGTTGT
196 TATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCT-GAACGCGTTTT
* * * * * ** *
8575 CAGCCAAAAACTGTGATAGTTAGTACACAATTTCGGCTAAGAACTGATCCAAAAAAAATTTTTCT
260 TAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGA-CC-CGAAAATTTTTTCT
* * * * * *
8640 TAATTTTTTACTACAATACTCAGAAAAAATATATAATTCAATGTCTAAAAGATTGA
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGA
8696 ATTATATAGC
Statistics
Matches: 7078, Mismatches: 1059, Indels: 471
0.82 0.12 0.05
Matches are distributed among these distances:
303 91 0.01
304 71 0.01
305 193 0.03
306 4 0.00
308 3 0.00
309 15 0.00
310 207 0.03
311 187 0.03
312 136 0.02
313 141 0.02
314 12 0.00
315 612 0.09
316 52 0.01
317 16 0.00
318 242 0.03
319 201 0.03
320 251 0.04
321 998 0.14
322 853 0.12
323 1091 0.15
324 433 0.06
325 648 0.09
326 327 0.05
327 14 0.00
328 64 0.01
329 209 0.03
330 7 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (322 bp):
CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTAATGCCAAAAAGATTGACGGGCTTTT
CAAGCTTCTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
TGAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGCTGACATTTGGTTCGATGAATATAGA
TATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCTGAACGCGTTTTT
AGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTCT
Found at i:15340 original size:2 final size:2
Alignment explanation
Indices: 15328--15395 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
15318 TCTAGCTCCA
15328 CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
15369 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
15396 ACCTTAGCTT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:15942 original size:104 final size:103
Alignment explanation
Indices: 15763--15965 Score: 343
Period size: 104 Copynumber: 2.0 Consensus size: 103
15753 TTGGGAAAAT
* * *
15763 TTGAACTTGTATTATCAATATGCACGTGATGAAAAAAAAATTGATTCCTTTCGTAAACATTTTAC
1 TTGAACTTGTATTATCAATATGCACATGATGAAAAAAAAATTGATTACTTTCATAAACATTTTAC
15828 CCTTGAGGCTGGGAAGAATCGAACTCTAACTACTGGAA
66 CCTTGAGGCTGGGAAGAATCGAACTCTAACTACTGGAA
15866 TTGAACTTGTATTATCAATATGCACATGATGAAAAAAAAAATTGATTACTTTCATAAACATTTTA
1 TTGAACTTGTATTATCAATATGCACATGATG-AAAAAAAAATTGATTACTTTCATAAACATTTTA
* * *
15931 CCTTTGAGGCTGTGAGGAATCGAACTCTAACTACT
65 CCCTTGAGGCTGGGAAGAATCGAACTCTAACTACT
15966 AGACTATCCA
Statistics
Matches: 93, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
103 30 0.32
104 63 0.68
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (103 bp):
TTGAACTTGTATTATCAATATGCACATGATGAAAAAAAAATTGATTACTTTCATAAACATTTTAC
CCTTGAGGCTGGGAAGAATCGAACTCTAACTACTGGAA
Found at i:45877 original size:16 final size:16
Alignment explanation
Indices: 45837--45962 Score: 119
Period size: 16 Copynumber: 7.7 Consensus size: 16
45827 TTGGTGACAT
45837 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
* **
45853 TACTGGGTGAGTATCT-
1 CACCAGGTGAGTAT-TG
45869 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
*
45885 CACCAGGTGAGCATTG
1 CACCAGGTGAGTATTG
*
45901 CACCAGGTGAGTGTTTG
1 CACCAGGTGAGT-ATTG
*
45918 TACCAGGTGAGTATTTG
1 CACCAGGTGAGTA-TTG
* * *
45935 TACCAGATGAGTGTTTG
1 CACCAGGTGAGT-ATTG
*
45952 TACCAGGTGAG
1 CACCAGGTGAG
45963 CATTTGTATT
Statistics
Matches: 91, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
15 1 0.01
16 48 0.53
17 42 0.46
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.29
Consensus pattern (16 bp):
CACCAGGTGAGTATTG
Found at i:45968 original size:17 final size:17
Alignment explanation
Indices: 45838--45970 Score: 139
Period size: 17 Copynumber: 8.1 Consensus size: 17
45828 TGGTGACATC
45838 ACCAGGTGAGTA-TTGT
1 ACCAGGTGAGTATTTGT
** * *
45854 ACTGGGTGAGTATCT-C
1 ACCAGGTGAGTATTTGT
*
45870 ACCAGGTGAGTA-TTGC
1 ACCAGGTGAGTATTTGT
* *
45886 ACCAGGTGAGCA-TTGC
1 ACCAGGTGAGTATTTGT
*
45902 ACCAGGTGAGTGTTTGT
1 ACCAGGTGAGTATTTGT
45919 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
* *
45936 ACCAGATGAGTGTTTGT
1 ACCAGGTGAGTATTTGT
*
45953 ACCAGGTGAGCATTTGT
1 ACCAGGTGAGTATTTGT
45970 A
1 A
45971 TTGGGTGAGT
Statistics
Matches: 97, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
15 1 0.01
16 46 0.47
17 50 0.52
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (17 bp):
ACCAGGTGAGTATTTGT
Found at i:72701 original size:60 final size:60
Alignment explanation
Indices: 72603--72721 Score: 186
Period size: 60 Copynumber: 2.0 Consensus size: 60
72593 TTCGACGTCT
* *
72603 GGCCGTTATTTGAACATTTTCGATAATGTTAGGTCCTTATTTGACCAAATTAAAAGATTG
1 GGCCCTTATTTGAACATTTTCGATAATGTTAAGTCCTTATTTGACCAAATTAAAAGATTG
* *
72663 GGCCCTTATTT-AAGCATTTTTGATACTGTTAAGTCCTTATTTGACCAAATTAAAAGATT
1 GGCCCTTATTTGAA-CATTTTCGATAATGTTAAGTCCTTATTTGACCAAATTAAAAGATT
72722 AAATCCTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
59 2 0.04
60 52 0.96
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (60 bp):
GGCCCTTATTTGAACATTTTCGATAATGTTAAGTCCTTATTTGACCAAATTAAAAGATTG
Found at i:72730 original size:60 final size:59
Alignment explanation
Indices: 72608--72742 Score: 180
Period size: 60 Copynumber: 2.2 Consensus size: 59
72598 CGTCTGGCCG
* ***
72608 TTATTTGAACATTTTCGATAATGTTAGGTCCTTATTTGACCAAATTAAAAGATTGGGCCC
1 TTATTT-AACATTTTCGATAATGTTAAGTCCTTATTTGACCAAATTAAAAGATTAAACCC
* * *
72668 TTATTTAAGCATTTTTGATACTGTTAAGTCCTTATTTGACCAAATTAAAAGATTAAATCC
1 TTATTTAA-CATTTTCGATAATGTTAAGTCCTTATTTGACCAAATTAAAAGATTAAACCC
72728 TTATTTAAACATTTT
1 TTATTT-AACATTTT
72743 GACAAACATT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 2 0.03
60 62 0.94
61 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (59 bp):
TTATTTAACATTTTCGATAATGTTAAGTCCTTATTTGACCAAATTAAAAGATTAAACCC
Found at i:72759 original size:60 final size:60
Alignment explanation
Indices: 72608--72766 Score: 171
Period size: 60 Copynumber: 2.6 Consensus size: 60
72598 CGTCTGGCCG
* * * ***
72608 TTATTTGAACATTTTCGATAA-TGTTAGGTCCTTATTTGACCAAATTAAAAGATTGGGCCC
1 TTATTTAAACATTTTTGA-AACTATTAGGTCCTTATTTGACCAAATTAAAAGATTAAACCC
* * * * *
72668 TTATTTAAGCATTTTTGATACTGTTAAGTCCTTATTTGACCAAATTAAAAGATTAAATCC
1 TTATTTAAACATTTTTGAAACTATTAGGTCCTTATTTGACCAAATTAAAAGATTAAACCC
72728 TTATTTAAACA-TTTTGACAAAC-ATTAGGTCCTTATTTGA
1 TTATTTAAACATTTTTG--AAACTATTAGGTCCTTATTTGA
72767 GCAATTAGCC
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
59 6 0.07
60 74 0.89
61 3 0.04
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (60 bp):
TTATTTAAACATTTTTGAAACTATTAGGTCCTTATTTGACCAAATTAAAAGATTAAACCC
Found at i:73457 original size:22 final size:22
Alignment explanation
Indices: 73429--73473 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
73419 AATCTACAGG
*
73429 TAAATACATTACAAACAATCAT
1 TAAATACATTACAAACAAGCAT
*
73451 TAAATACATTACCAACAAGCAT
1 TAAATACATTACAAACAAGCAT
73473 T
1 T
73474 TGCATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.20, G:0.02, T:0.27
Consensus pattern (22 bp):
TAAATACATTACAAACAAGCAT
Found at i:74450 original size:30 final size:28
Alignment explanation
Indices: 74379--74456 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
74369 GAACTTACAC
*
74379 AAAACGGCCAAATAAGCCCCTGAACTCT
1 AAAAAGGCCAAATAAGCCCCTGAACTCT
**
74407 -AATTGCAGCCAAATAAGCCCCTGAACTCTTT
1 AAAAAG--GCCAAATAAGCCCCTGAACTC--T
74438 AAAAAGGCCAAATAAGCCC
1 AAAAAGGCCAAATAAGCCC
74457 TTTTCTGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 3 0.07
29 21 0.51
30 13 0.32
31 1 0.02
32 3 0.07
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (28 bp):
AAAAAGGCCAAATAAGCCCCTGAACTCT
Found at i:74927 original size:30 final size:28
Alignment explanation
Indices: 74891--74980 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 28
74881 AGAAAAGGAT
74891 TTATTTGGCCTTTTTAAAGAGTTCAGGGGC
1 TTATTTGGCCTTTTT-AA-AGTTCAGGGGC
**
74921 TTATTTGG-CTGCAATTAAAGTTCAGGGGC
1 TTATTTGGCCT--TTTTAAAGTTCAGGGGC
*
74950 TTATTTGGCCGTTTTGTGTAAGTTCAGGGGC
1 TTATTTGGCC-TTTT-T-AAAGTTCAGGGGC
74981 CTTTTTGAGC
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
29 22 0.45
30 12 0.24
31 15 0.31
ACGTcount: A:0.19, C:0.13, G:0.29, T:0.39
Consensus pattern (28 bp):
TTATTTGGCCTTTTTAAAGTTCAGGGGC
Found at i:80453 original size:1 final size:1
Alignment explanation
Indices: 80447--80490 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
80437 GCTTGCAAGG
* * * *
80447 TTTTTTTTTTTTTTTGTTTTTGTTTTTGTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
80491 CAATGCAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:80525 original size:3 final size:3
Alignment explanation
Indices: 80517--80548 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
80507 GCTTTCCATC
80517 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
80549 TTTTCCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.