Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009191.1 Corchorus capsularis cultivar CVL-1 contig09212, 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: 33121
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:812 original size:324 final size:321
Alignment explanation
Indices: 34--973 Score: 1365
Period size: 322 Copynumber: 2.9 Consensus size: 321
24 CGAACCCCGG
* * *
34 CTCAATTTTGCAAGATTTTTGACGTAAAGACTCCTTGAAGGATCTATATTCATCTAAGCAAATGT
1 CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAGTATCTATATTCATCTAAGCAAATGT
*
99 CAGTCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAGATAGAA
66 CAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTA-ATAGAA
164 ATTAATTCGGAAATAAAATT-AGAAAAATGATATTAGAAGCGTGAAAAGACCATCAATCTCTTTG
130 ATTAATTCGGAAATAAAATTGA-AAAAATGATATTAGAAGCGTGAAAAGACCATCAATCTCTTTG
* *
228 GTGTTGAATTATATATTTTTTTTGAGTATTGTGGCAAAAAATTGAGAAATACTTTTCGGGTCAGT
194 CTGTTGAATTATATATTTTTTTTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTCGGGTCAGT
* *
293 TTTTAGCCGAAATCGTGTATTAAACATCACGGTTTTTGGCTAAAAACGTATTCCGAGTACCTG
259 TTTTAGCCGAAATCGTGTATTAACCATCACGGTTTTTGGCTAAAAACGTATTCCGAGTACCTA
*
356 CTCAATTTTGCAAT-ATTTTTGGCGTAAAGACTCCTTGAAGTATCTATATTCATCTAACCAAATG
1 CTCAATTTTGC-ATGATTTTTGGCGTAAAGACTCCTTGAAGTATCTATATTCATCTAAGCAAATG
420 TCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGA
65 TCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAA-TAGA
* *
485 AATTTATTCGGAAATAAAATTGAAAAAATGATATTAGAAGCATGAAAAGACCATCAATCTCTTTG
129 AATTAATTCGGAAATAAAATTGAAAAAATGATATTAGAAGCGTGAAAAGACCATCAATCTCTTTG
*
550 CTGTTGAATTATATATTTTTTTTAAGTATTGTGGCAAAAAATTGAGAAAAAGCTTTTCGGGTCAG
194 CTGTTGAATTATATATTTTTTTTGAGTATTGTGGCAAAAAATTGAGAAAAA-CTTTTCGGGTCAG
* * *
615 TTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGT-TTCGGAG-CCCT
258 TTTTTAGCCGAAATCGTGTATTAACCATCACGGTTTTTGGCTAAAAA--CGTATTCCGAGTACCT
678 AA
321 -A
* * *
680 CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCAT-TGATGCAAATG
1 CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAGTATCTATATTCATCT-AAGCAAATG
* * ** * *
744 TTAGGCA-AGTTGGATATAAGGATTTGTTTTTACGAGCATCAAAATCTTGTTTCGAATTAATAAG
65 TCAGCCACA-TTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAAT-AG
* * * * * *
808 AAATTAATTCGGCAATAAAAAATGAAAAAACGATATTAAAAGCGTGAAAA-ACCCGTCAATCTTT
128 AAATTAATTCGGAAAT-AAAATTGAAAAAATGATATTAGAAGCGTGAAAAGA-CCATCAATCTCT
* * * * *
872 TTGGC-GTTGAATTATATATGTTTTCTGTGTATTGTGGCAGAAAATTGAGAAAAAAACTGTTCGG
191 TT-GCTGTTGAATTATATATTTTTTTTGAGTATTGTGGCAAAAAATTGAG--AAAAACTTTTCGG
936 GTCAGTTTTTAGCCGAAATCGTGTATTAACCATCACGG
253 GTCAGTTTTTAGCCGAAATCGTGTATTAACCATCACGG
974 CTCAATTTTG
Statistics
Matches: 562, Mismatches: 40, Indels: 28
0.89 0.06 0.04
Matches are distributed among these distances:
321 1 0.00
322 229 0.41
323 68 0.12
324 130 0.23
325 83 0.15
326 46 0.08
327 5 0.01
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (321 bp):
CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAGTATCTATATTCATCTAAGCAAATGT
CAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATAGAAA
TTAATTCGGAAATAAAATTGAAAAAATGATATTAGAAGCGTGAAAAGACCATCAATCTCTTTGCT
GTTGAATTATATATTTTTTTTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTCGGGTCAGTTT
TTAGCCGAAATCGTGTATTAACCATCACGGTTTTTGGCTAAAAACGTATTCCGAGTACCTA
Found at i:1221 original size:294 final size:294
Alignment explanation
Indices: 680--1267 Score: 860
Period size: 294 Copynumber: 2.0 Consensus size: 294
670 GGAGCCCTAA
* * * **
680 CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATTGATGCAAATGT
1 CTCAATTTTGCAAGATTTTTGGCGCAAAGACTACTTGAAATAGCTATATTCATTGAACCAAATGT
* *
745 TAGGCAAGTTGGATATAAGGATTTGTTTTTACGAGCATCAAAATCTTGTTTCGAATTAATAAGAA
66 CAGGCAAGTTGGATATAAGGATTTGTTTTTACGAGCATCAAAATCTTATTTCGAATTAATAAGAA
**
810 ATTAATTCGGCAATAAAAAATGAAAAAACGATATTAAAAGCGTGAAAAACCCGTCAATCTTTTTG
131 ATTAATTCGAAAATAAAAAATGAAAAAACGATATTAAAAGCGTGAAAAACCCGTCAATCTTTTTG
*
875 GCGTTGAATTATATATGTTTTCTGTGTATTGTGGCAGAAAATTGAGAAAAAAACTGTTCGGGTCA
196 GCGTTGAATTATATATGTTTTCTGAGTATTGTGGCAGAAAATTGAGAAAAAAACTGTTCGGGTCA
*
940 GTTTTTAGCCGAAATCGTGTATTAACCATCACGG
261 GTTTTTAGCCGAAATCGTGTACTAACCATCACGG
* *
974 CTCAATTTTGCAAGATTTTTGGCGTAAAGACTACTTGAAGTAGCTATATTCATCT-AACCAAATG
1 CTCAATTTTGCAAGATTTTTGGCGCAAAGACTACTTGAAATAGCTATATTCAT-TGAACCAAATG
* ** ** * *
1038 TCAGTCACA-TTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTTTATTTAATTAG
65 TCAGGCA-AGTTGGATATAAGGATTTGTTTTTACGAGCATCAAAATCTTATTTCGAATTAATAAG
* * * * *
1102 AAATTAATTCGAAAAT-AAAATTGGAAAAATGATATTAGAAGCGTGAAAAGA-CCTTCAATCTTT
129 AAATTAATTCGAAAATAAAAAATGAAAAAACGATATTAAAAGCGTGAAAA-ACCCGTCAATCTTT
* * *
1165 TTGGTGTTGAATTATATATGTTTTCTGAGTATTGTTGCAGAAAATTGAGAAAAAAAACTTTTCGG
193 TTGGCGTTGAATTATATATGTTTTCTGAGTATTGTGGCAGAAAATTGAG-AAAAAAACTGTTCGG
1230 GTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGG
257 GTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGG
1268 TTTTTTGCTA
Statistics
Matches: 262, Mismatches: 28, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
293 86 0.33
294 174 0.66
295 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (294 bp):
CTCAATTTTGCAAGATTTTTGGCGCAAAGACTACTTGAAATAGCTATATTCATTGAACCAAATGT
CAGGCAAGTTGGATATAAGGATTTGTTTTTACGAGCATCAAAATCTTATTTCGAATTAATAAGAA
ATTAATTCGAAAATAAAAAATGAAAAAACGATATTAAAAGCGTGAAAAACCCGTCAATCTTTTTG
GCGTTGAATTATATATGTTTTCTGAGTATTGTGGCAGAAAATTGAGAAAAAAACTGTTCGGGTCA
GTTTTTAGCCGAAATCGTGTACTAACCATCACGG
Found at i:2014 original size:324 final size:323
Alignment explanation
Indices: 974--5104 Score: 4880
Period size: 322 Copynumber: 12.8 Consensus size: 323
964 ACCATCACGG
* * * * * *
974 CTCAATTTTGCAAGATTTTTGGCGTAAAGACTACTTGAAGTAGCTATATTCATCTAACCAAATGT
1 CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * * **
1039 CAGTCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTTTATTTAATTAGAA
66 CAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* * *
1104 ATTAATTCGAAAATAAAATTGGAAAAATGATATTAGAAGCGTGAAAAGACCTTCAATCTTTTTGG
131 ATTAATTCGGAAA-AAAATTGGAAAAACGATATTAGAAGCGTGAAAAGACCGTCAATCTTTTTGG
* * * *
1169 TGTTGAATTATATATGTTTTCTGAGTATTGTTGCAGAAAATTGAGAAAAAAAACTTTTCGGGTCA
195 CGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG--AAAAAACTTTTCGGGTCA
* * * * *
1234 GTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACACATTTCGGAGCCCTA
258 GTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCTG
1299 A
323 A
* * * *
1300 CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATATATATTCATTGAACCAAATGT
1 CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * * * *
1365 TAGGCAAATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAATTAATCAGAA
66 CAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* * *
1430 ATTAATTCGGCAAAAAAACTGAAAAAACGATATTAGAAGGGTGAAAA-ACCCGTCAATCTTTTTG
131 ATTAATTCGG-AAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGA-CCGTCAATCTTTTTG
* * * * **
1494 GCGATGAATTATATATGTTTTCTGAGTATTGTGGTAGAAAATTGAGAAAAAAAAAATTTCGGGTC
194 GCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG--AAAAAACTTTTCGGGTC
* * * * * * * *
1559 AGTTTTTAGCCAAAATCGTGTACTGACCATCACTGTTTTTAGCTAAAAACACATTCCGAAGCCCC
257 AGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCT
1624 GA
322 GA
* * *
1626 CCCAATTTTGCATGATTTTTTGTGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
1 CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * * **
1691 CAGTCATATTCGATATAAGGATTTGTTTTTTA-GAGCATCTCAATCTTGTTTCGATTTAATTTCA
66 CAGCCATATTGGATATAAGGATTTG-TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* * * * * * *
1755 AATTAATTCGGAAATAAAATTAGAAAAATGATATTAGAAGCGTGAACATACCATCAATATTTTGG
130 AATTAATTCGGAAA-AAAATTGGAAAAACGATATTAGAAGCGTGAAAAGACCGTCAATCTTTTTG
* * * * *
1820 GCGTTGAATAATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACATTTCGGGACTG
194 GCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAG
* * * *
1885 TTTTTAGCCGAAATCGTGTACTAACCTTCACGGTTTGTGGCTAAAAACGCATTCCGGAGCACTGA
259 TTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGA
* * *
1950 CTCAATTTTACATGATTTTTGGCGCAAAAACTCCTTGAAATAT-TCATATTCATCGAACCAAATC
1 CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCT-ATATTCATCGAACCAAATC
* ** * * * *
2014 TCAGCCATATTGGATATAAGGAATTGTTTTTTTGAGAATCTCAATCTTGTTTCGATTTTATTATA
65 TCAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* * *
2079 TATTAATTCGG--GAAAA-TGGAAAAACGATATTAGAAGCGTGAAAAG-CCTGTAAATCTTTTTG
130 AATTAATTCGGAAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGACC-GTCAATCTTTTTG
* * * *
2140 GCGTTGAATTATATATTTTTTATCAATACTGTGGCAAAAAATTGA-AATAAAA-TCTTTCGGGTC
194 GCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAA-AAAACT-TTTCGGGTC
* * * * * * * *
2203 ACTTTTTAGCCGAAATTGTGTACTAACCATCATTGTTTTTTTGCTAAAAACGTGTTTCAGAGCCC
257 AGTTTTTAGCCGAAATCGTGTACTAACCATCA-CGGTTTTTGGCTAAAAACGCGTTCCGGAGCCC
*
2268 GGA
321 TGA
** *
2271 CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGATGTATCTATATTCATC-AACCAAATGT
1 CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * ** * *
2335 CAGCCACATTGGATATAAGGA-TTGTTTTTACGAGCATCTGAATCTTTTTTTTTATTTAATCATA
66 CAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATC-TTGTTTCGATTTAATTAGA
* * * * * * *
2399 AATTAATTCGGAAAAAAAATGGAAAAATGATATTAGAAGCATGAAAAGACCATCAATATATTGGG
130 AATTAATTCGGAAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGACCGTCAATCTTTTTGG
* *
2464 CGTTGAATTATATATTTTTTCTAAGTATTGTGGCAAAAAATTAAGAAAAAACTTTTCGGGTCAGT
195 CGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGT
* ** *
2529 TTTTAGCCGAAATCGTGTATTAACCATCACGGTTTTTGGCTAAAAACGTATTCC-GAGTCCC-GG
260 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAG-CCCTGA
* * * *
2592 CTCAATTTTGCATGATTTTTTGCGTAAATACTCTTTGAAATATCTATATTC-TCTAACCAAATCT
1 CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * *
2656 CAGCCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTGGATTTAATTAGAA
66 CAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* *
2721 ATTAATTCGGAAATAAAATTGGAAAAATGATATTAGAAGCGTGAAAAGACCATCAATC-TTTTGG
131 ATTAATTCGGAAA-AAAATTGGAAAAACGATATTAGAAGCGTGAAAAGACCGTCAATCTTTTTGG
* *
2785 TCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAAAACTTTCCGGGAT
195 -CGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG--AAAAAACTTTTCGGG-T
* * *
2850 -AGTTTTTAGCCGAAATCGTGTACTAACTATCACGATTTTTGGCTAAAAACGCGTTCCGGAGCAC
256 CAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCC
2914 TGA
321 TGA
* *
2917 CTCAATTTTGCATGATTCTTGGCGCAAAGACTCCTTGAAATAT-TCATATTCATCGAACCAAATC
1 CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCT-ATATTCATCGAACCAAATC
* ** * * *
2981 TCAGCCATAATGGATATAAGGATTTGTTTTTTTGAGCATCTAAATCTTCTTTCGATTTTATTAGA
65 TCAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* *
3046 TATTAATTCGG-AAAAAA-TGG-AAAACGATATTAGAAGCGTGAAAAGCCCGTCAATC-TTTTGG
130 AATTAATTCGGAAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGACCGTCAATCTTTTTGG
* * * *
3107 CATTGAATTATATA-TTTTTATGAGTATTGTGGCAAAAAACTGAGAAAAAACTTTTCGGGTCAGA
195 CGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGT
* ** * * * * *
3171 TTTTAGCCGAAACCAAGTACTAACTATCATGGTTTTTCGCTAAAAACGTGTTTCGGAGCCCTGA
260 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGA
* * * * * * *
3235 CTCAATTTTACATGATTTTTGTCGCAAAAACTTCTTGAAATATCTATATTCATTGAACCAAATGT
1 CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* *
3300 CAGCCAAATTGGATATAAGGATTTGTTTTTACGAGCATATGAATCTTGTTTCGATTTAATTAGAA
66 CAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* * * *
3365 ATTAATTCCGCAAAAAAA-TGAAAAAATGATATTAGAAGCGAGAAAA-ACACGTCAATCTTTTTG
131 ATTAATT-CGGAAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGAC-CGTCAATCTTTTTG
* *
3428 GCGTTGAATTATATAGTTTTTCTGAGTATTTTGGCAAAAAATTGAGAGAAAAAAACTTTTCGGGT
194 GCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT--GAG-AAAAAACTTTTCGGGT
* * * *
3493 CAGTTTTTAGCTGAAATCGTGTACTAACCATCACGG-TTCTGGCTAAAAACGCATTCCGGATCCC
256 CAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCC
* *
3557 CGT
321 TGA
* * * * *
3560 CTTAATTTT-CCTAATTTTTTGCGTAAAGACTCCTTGAAATATCTATATTCATTGAACCAAATCT
1 CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * * *
3624 CAACCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTTATTAGAA
66 CAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* * *
3689 ATTAATTCAG-AAAAAA-TGGAAAAACGATGTTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGC
131 ATTAATTCGGAAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGACCGTCAATCTTTTTGGC
* * * * *
3752 ATTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAAAACTGAGATAAAATTTTTCGGGTCAG
196 GTTGAATTATATATTTTTTCTGAGTATTGTGGC--AAAAAATTGAGAAAAAACTTTTCGGGTCAG
* * * *
3817 TTTTTATCCGAAATCGTGTACTAACTATCACGGTTTTTGGCTAAAAACGCGTTTCGTAGCCCTGA
259 TTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGA
* *
3882 CTCAATTTTGCATGATTTTTGGCGTAAATACTCCTTG-AAT-T-T-TA-T--T-GAACCAAATGT
1 CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * *
3939 CAGTCATATTTGATATAAGGATTTGTTTTTACGAGCATAC-GAATCTTGTTTCGATTTAATCAGA
66 CAGCCATATTGGATATAAGGATTTGTTTTTACGAGCAT-CTGAATCTTGTTTCGATTTAATTAGA
* * * *
4003 AATTAATTCGGCAAAAAAA-TGAAAAAACGATATTGGAAACGTGAAAA-ACCCATCAATCTTTTT
130 AATTAATTCGG-AAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGA-CCGTCAATCTTTTT
4066 GGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAACTTTTCGGGT
193 GGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG--AAAAAACTTTTCGGGT
* * * * *
4131 CAGTTTTTAGTCGAAATCATGTACTAACTATCACGGTTTTTGGCTAAAAACGCGTTCTGAAGCCC
256 CAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCC
* *
4196 CGG
321 TGA
* *
4199 CTCAATTTTCCATGATTTTTTGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
1 CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * ** *
4264 CAGCCGTATTGGATATAAGGATTTGTTTTTTCGAGCATCTCTATCTTGTTTCGATTTTATTAGAA
66 CAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* *
4329 ATTAATTCGGAAAAAAA-TGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATATTTTTGGC
131 ATTAATTCGGAAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGACCGTCAATCTTTTTGGC
* * * * * *
4393 ATTGAATTATATAATTTTTATGAGTATTGTGGCAAAAAATTGAGATAAAATTTTTCGGATCAGTT
196 GTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAG-T
* * * *
4458 TTTTA-CCGAAATCGTGTACTAACTATCACGGTTTTTGGCTAAAAATGCGTTTCGTAGCCCTGA
260 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGA
* * * * * * * *
4521 GTCAATTTCGCATGATTTTTGGCGCAAAAACTCCTTGAAATATCTATATTCTTTGAACTAAATGT
1 CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * * *
4586 CAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATATGAATCTTGTTTTGATTTAATCAGAA
66 CAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* * * *
4651 ATTAATTCGGCAAAAAGA-TGAAAAAACGATATTAGAAGCGTGAAAA-ACCCGTTAATCTTTTTA
131 ATTAATTCGG-AAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGA-CCGTCAATCTTTTTG
* * **
4714 GCGTTGAATTATATA-TTTTTCTGAGTATTGTGGGACAAAATTGAGAAAAAA-AATTCGGGTCAG
194 GCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAG
* * *
4777 TTTTTAGCCGAAATCGTGTACTAAGCATCACGGATTTTTGACTAAAAACGTC-TTCC-GAGGTCA
259 TTTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTTTGGCTAAAAACG-CGTTCCGGA-G-CC
*
4840 CAG-
320 CTGA
** * * *** * * *
4843 CTCTGTTTTGCATGGTTTTTTGCGCCGAGACTCCTTGAAATATCTTTATT-ACTCTAATCAAAT-
1 CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCA-TCGAACCAAATC
* * * * * *
4906 TTAGACCACATTGGATTTAAGGATTTGTTTTTACGTGCATCAGAATCTTGTTTCTATTTAATTAG
65 TCAG-CCATATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
* * * * * *
4971 AAATTAATTCAGAAAAATA-T-GAAAAACGATATTAAAAGAGTGAAAAGTCC-TCCAATTTTTTT
129 AAATTAATTCGGAAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGACCGT-CAATCTTTTT
* * * * * * *
5033 GGCATTGAATTATATATATTTTTATGAGTATTTTTGCCAAAAATTGAGGAAAAA-TATTTCGGGC
193 GGCGTTGAATTATATAT-TTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACT-TTTCGGGT
5097 CA-TTTTTA
256 CAGTTTTTA
5105 CCATCATTGT
Statistics
Matches: 3275, Mismatches: 452, Indels: 160
0.84 0.12 0.04
Matches are distributed among these distances:
315 85 0.03
316 2 0.00
317 186 0.06
318 194 0.06
319 29 0.01
320 262 0.08
321 324 0.10
322 686 0.21
323 252 0.08
324 475 0.15
325 164 0.05
326 606 0.19
327 10 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (323 bp):
CTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
CAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
ATTAATTCGGAAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGACCGTCAATCTTTTTGGC
GTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTT
TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGA
Found at i:3433 original size:965 final size:968
Alignment explanation
Indices: 974--5104 Score: 5017
Period size: 965 Copynumber: 4.3 Consensus size: 968
964 ACCATCACGG
* * * * * * *
974 CTCAATTTTGCAAGATTTTTGGCGTAAAGACTACTTGAAGTA-GCTATATTCATCTAACCAAATG
1 CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATTC-ATATTCATCGAACCAAATC
* * * * **
1038 TCAGTCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTTTATTTAATTAGA
65 TCAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGA
* * * *
1103 AATTAATTCGAAAATAAAATTGGAAAAATGATATTAGAAGCGTGAAAAGACCTTCAATCTTTTTG
130 AATTAATTCG-GAA-AAAA-TGG-AAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTG
* * * *
1168 GTGTTGAATTATATATGTTTTCTGAGTATTGTTGCAGAAAATTGAGAAAAAAAACTTTTCGGGTC
191 GCGTTGAATTATATAT-TTTTATGAGTATTGTGGCAAAAAATTGAG--AAAAAACTTTTCGGGTC
* * *
1233 AGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACACATTTCGGAGCCCT
253 AGTTTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGAGCCCT
* *
1298 AACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATATATATTCATTGAACCAAAT
318 GACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATTGAACCAAAT
* * *
1363 GTTAGGCAAATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAATTAATCAG
383 GTCAGCCAAATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAG
* * * *
1428 AAATTAATTCGGCAAAAAAACTGAAAAAACGATATTAGAAGGGTGAAAAACCCGTCAATCTTTTT
448 AAATTAATTCCGCAAAAAAA-TGAAAAAACGATATTAGAAGCGAGAAAAACCCGTCAATATTTTT
* * * * * **
1493 GGCGATGAATTATATATGTTTTCTGAGTATTGTGGTAGAAAATTGAGAAAAAAAAAATTTCGGGT
512 GGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAGAAAAAACTTTTCGGGT
* * * * * *
1558 CAGTTTTTAGCCAAAATCGTGTACTGACCATCACTGTTTTTAGCTAAAAACACATTCCGAAGCCC
577 CAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTCCGAAGTCC
* * *
1623 CGACCCAATTTTGCATGATTTTTTGTGTAAAGACTCCTTGAAATATCTATATTCATC-GAACCAA
642 CGGCTCAATTTTGCATGATTTTTTGCGTAAAGACTCCTTGAAATATCTATATTCATCTGAACCAA
* * *
1687 ATCTCAGTCATATTCGATATAAGGATTTGTTTTTTAGAGCATCTCAATCTTGTTTCGATTTAATT
707 ATCTCAGCCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATT
** * * * * *
1752 TCAAATTAATTCGGAAATAAAATTAGAAAAATGATATTAGAAGCGTGAACATACCATCAATATTT
772 AGAAATTAATTCGGAAA-AAAA-TGGAAAAACGATATTAGAAGCGTGAAAAGACCATCAATCTTT
* * * * * *
1817 TGGGCGTTGAATAATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACATTTCGGGA
835 TTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGT
* * * *
1882 CTGTTTTTAGCCGAAATCGTGTACTAACCT-TCACGGTTTGTGGCTAAAAACGCATTCCGGAGCA
900 CAGTTTTTAGCCGAAATCGTGTACTAACCTATCACGATTTTTGGCTAAAAACGCGTTCCGGAGCA
1946 CTGA
965 CTGA
* *
1950 CTCAATTTTACATGATTTTTGGCGCAAAAACTCCTTGAAATATTCATATTCATCGAACCAAATCT
1 CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATTCATATTCATCGAACCAAATCT
* ** * * * * *
2015 CAGCCATATTGGATATAAGGAATTGTTTTTTTGAGAATCTCAATCTTGTTTCGATTTTATTATAT
66 CAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAA
* * *
2080 ATTAATTCGG-GAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCTGTAAATCTTTTTGGCGT
131 ATTAATTCGGAAAAAATGG-AAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGT
* * * *
2144 TGAATTATATATTTTTTATCAATACTGTGGCAAAAAATTGA-AATAAAA-TCTTTCGGGTCACTT
195 TGAATTATATA-TTTTTATGAGTATTGTGGCAAAAAATTGAGAA-AAAACT-TTTCGGGTCAGTT
** * * * * *
2207 TTTAGCCGAAATTGTGTACTAACCATCATTGTTTTTTTGCTAAAAACGTGTTTCAGAGCCCGGAC
257 TTTAGCCGAAATCATGTACTAACCATCA-CGGTTTTTTGCTAAAAACGCGTTTCGGAGCCCTGAC
* ** *
2272 TCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGATGTATCTATATTCA-TCAACCAAATGTC
321 TCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATTGAACCAAATGTC
* * ** *
2336 AGCCACATTGGATATAAGGA-TTGTTTTTACGAGCATCTGAATCTTTTTTTTTATTTAATCATAA
386 AGCCAAATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATC-TTGTTTCGATTTAATCAGAA
* * * * * * *
2400 ATTAATTCGGAAAAAAAATGGAAAAATGATATTAGAAGC-ATGAAAAGA-CCATCAATATATTGG
450 ATTAATTCCGCAAAAAAATGAAAAAACGATATTAGAAGCGA-GAAAA-ACCCGTCAATATTTTTG
*
2463 GCGTTGAATTATATATTTTTTCTAAGTATTGTGGCAAAAAATT-A-AGAAAAAACTTTTCGGGTC
513 GCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAGAAAAAACTTTTCGGGTC
* *
2526 AGTTTTTAGCCGAAATCGTGTATTAACCATCACGGTTTTTGGCTAAAAACGTATTCCG-AGTCCC
578 AGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTCCGAAGTCCC
* *
2590 GGCTCAATTTTGCATGATTTTTTGCGTAAATACTCTTTGAAATATCTATATTC-TCT-AACCAAA
643 GGCTCAATTTTGCATGATTTTTTGCGTAAAGACTCCTTGAAATATCTATATTCATCTGAACCAAA
*
2653 TCTCAGCCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTGGATTTAATTA
708 TCTCAGCCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTA
*
2718 GAAATTAATTCGGAAATAAAATTGGAAAAATGATATTAGAAGCGTGAAAAGACCATCAATC-TTT
773 GAAATTAATTCGGAAA-AAAA-TGGAAAAACGATATTAGAAGCGTGAAAAGACCATCAATCTTTT
2782 TGGTCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAAAACTTTCCGG
836 TGG-CGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAAAA-TTT-CGG
2847 GAT-AGTTTTTAGCCGAAATCGTGTACTAA-CTATCACGATTTTTGGCTAAAAACGCGTTCCGGA
898 G-TCAGTTTTTAGCCGAAATCGTGTACTAACCTATCACGATTTTTGGCTAAAAACGCGTTCCGGA
2910 GCACTGA
962 GCACTGA
*
2917 CTCAATTTTGCATGATTCTTGGCGCAAAGACTCCTTGAAATATTCATATTCATCGAACCAAATCT
1 CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATTCATATTCATCGAACCAAATCT
* ** * * *
2982 CAGCCATAATGGATATAAGGATTTGTTTTTTTGAGCATCTAAATCTTCTTTCGATTTTATTAGAT
66 CAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAA
*
3047 ATTAATTCGGAAAAAATGGAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATC-TTTTGGCATT
131 ATTAATTCGGAAAAAATGGAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTT
* *
3111 GAATTATATATTTTTATGAGTATTGTGGCAAAAAACTGAGAAAAAACTTTTCGGGTCAGATTTTA
196 GAATTATATATTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTA
* * * * * *
3176 GCCGAAACCAAGTACTAACTATCATGGTTTTTCGCTAAAAACGTGTTTCGGAGCCCTGACTCAAT
261 GCCGAAATCATGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGAGCCCTGACTCAAT
* * * *
3241 TTTACATGATTTTTGTCGCAAAAACTTCTTGAAATATCTATATTCATTGAACCAAATGTCAGCCA
326 TTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATTGAACCAAATGTCAGCCA
* *
3306 AATTGGATATAAGGATTTGTTTTTACGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAAT
391 AATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAAT
* * *
3371 TCCGCAAAAAAATGAAAAAATGATATTAGAAGCGAGAAAAACACGTCAATCTTTTTGGCGTTGAA
456 TCCGCAAAAAAATGAAAAAACGATATTAGAAGCGAGAAAAACCCGTCAATATTTTTGGCGTTGAA
* *
3436 TTATATAGTTTTTCTGAGTATTTTGGCAAAAAATTGAGAGAAAAAAACTTTTCGGGTCAGTTTTT
521 TTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAG-AAAAAACTTTTCGGGTCAGTTTTT
* * * * *
3501 AGCTGAAATCGTGTACTAACCATCACGG-TTCTGGCTAAAAACGCATTCCGGA-TCCCCGTCTTA
585 AGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTCCGAAGT-CCCGGCTCA
* * *
3564 ATTTT-CCTAATTTTTTGCGTAAAGACTCCTTGAAATATCTATATTCAT-TGAACCAAATCTCAA
649 ATTTTGCATGATTTTTTGCGTAAAGACTCCTTGAAATATCTATATTCATCTGAACCAAATCTCAG
*
3627 CCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTTATTAGAAATT
714 CCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATT
* * * * *
3692 AATTCAG-AAAAAATGGAAAAACGATGTTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCATTG
779 AATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGACCATCAATCTTTTTGGCGTTG
* * **
3756 AATTATATATTTTTTATGAGTATTGTGGCAAAAAAAACTGAGATAAAATTTTTCGGGTCAGTTTT
844 AATTATATATTTTTTATGAGTATTGTGGC--AAAAAATTGAGAAAAAAAATTTCGGGTCAGTTTT
* * * * *
3821 TATCCGAAATCGTGTACTAA-CTATCACGGTTTTTGGCTAAAAACGCGTTTCGTAGCCCTGA
907 TAGCCGAAATCGTGTACTAACCTATCACGATTTTTGGCTAAAAACGCGTTCCGGAGCACTGA
* * *
3882 CTCAATTTTGCATGATTTTTGGCGTAAATACTCCTTG-AAT-TT--TA-T--T-GAACCAAATGT
1 CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATTCATATTCATCGAACCAAATCT
* * * *
3939 CAGTCATATTTGATATAAGGATTTGTTTTTACGAGCATAC-GAATCTTGTTTCGATTTAATCAGA
66 CAGCCATATTGGATATAAGGATTTGTTTTTACGAGCAT-CTAAATCTTGTTTCGATTTAATTAGA
* * * * *
4003 AATTAATTCGGCAAAAAAATGAAAAAACGATATTGGAAACGTGAAAAACCCATCAATCTTTTTGG
130 AATTAATTCGG--AAAAAATG-GAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGG
*
4068 CGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAACTTTTCGGGTCA
192 CGTTGAATTATATA-TTTTTATGAGTATTGTGGCAAAAAATTGAG--AAAAAACTTTTCGGGTCA
* * * * *
4133 GTTTTTAGTCGAAATCATGTACTAACTATCACGGTTTTTGGCTAAAAACGCG-TTCTGAAGCCCC
254 GTTTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTC-GGAGCCCT
* * * * *
4197 GGCTCAATTTTCCATGATTTTTTGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAAT
318 GACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATTGAACCAAAT
* ** * ** * *
4262 CTCAGCCGTATTGGATATAAGGATTTGTTTTTTCGAGCATCTCTATCTTGTTTCGATTTTATTAG
383 GTCAGCCAAATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAG
* * * *
4327 AAATTAATT-CGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATATTTTTG
448 AAATTAATTCCGCAAAAAAATGAAAAAACGATATTAGAAGCGAGAAAAACCCGTCAATATTTTTG
* * * * * *
4391 GCATTGAATTATATAATTTTTATGAGTATTGTGGCAAAAAATT--GAGATAAAATTTTTCGGATC
513 GCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAGAAAAAACTTTTCGGGTC
* * * * *
4454 AGTTTTTTA-CCGAAATCGTGTACTAACTATCACGGTTTTTGGCTAAAAATGCGTTTCGTAG-CC
578 AG-TTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTCCGAAGTCC
* * * * * *
4517 CTGAG-TCAATTTCGCATGATTTTTGGCGCAAAAACTCCTTGAAATATCTATATTC-TTTGAACT
642 C-G-GCTCAATTTTGCATGATTTTTTGCGTAAAGACTCCTTGAAATATCTATATTCATCTGAACC
* * * * * *
4580 AAATGTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATATGAATCTTGTTTTGATTTAA
705 AAATCTCAGCCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAA
* * * * *
4645 TCAGAAATTAATTCGGCAAAAAGATGAAAAAACGATATTAGAAGCGTGAAAA-ACCCGTTAATCT
770 TTAGAAATTAATTCGG-AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGA-CCATCAATCT
* * * *
4709 TTTTAGCGTTGAATTATATA-TTTTTCTGAGTATTGTGGGACAAAATTGAGAAAAAAAA-TTCGG
833 TTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGG
* *
4772 GTCAGTTTTTAGCCGAAATCGTGTACTAAGC-ATCACGGATTTTTGACTAAAAACGTC-TTCC-G
898 GTCAGTTTTTAGCCGAAATCGTGTACTAACCTATCAC-GATTTTTGGCTAAAAACG-CGTTCCGG
*
4834 AGGTCACAG-
961 A-G-CACTGA
** * * ** * * *
4843 CTCTGTTTTGCATGGTTTTTTGCGCCGAGACTCCTTGAAATA-TCTTTATT-ACTCTAATCAAAT
1 CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATTC-ATATTCA-TCGAACCAAAT
* * * * *
4906 -TTAGACCACATTGGATTTAAGGATTTGTTTTTACGTGCATC-AGAATCTTGTTTCTATTTAATT
64 CTCAG-CCATATTGGATATAAGGATTTGTTTTTACGAGCATCTA-AATCTTGTTTCGATTTAATT
* * * * * *
4969 AGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGAGTGAAAAGTCC-TCCAATTTTTTT
127 AGAAATTAATTCGGAAAAA-ATGGAAAACGATATTAGAAGCGTGAAAAGCCCGT-CAATCTTTTT
* * * * * *
5033 GGCATTGAATTATATATATTTTTATGAGTATTTTTGCCAAAAATTGAGGAAAAA-TATTTCGGGC
190 GGCGTTGAA-T-TATATATTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAACT-TTTCGGGT
5097 CA-TTTTTA
252 CAGTTTTTA
5105 CCATCATTGT
Statistics
Matches: 2750, Mismatches: 333, Indels: 155
0.85 0.10 0.05
Matches are distributed among these distances:
957 73 0.03
958 2 0.00
959 8 0.00
960 114 0.04
961 121 0.04
962 148 0.05
963 109 0.04
964 336 0.12
965 551 0.20
966 133 0.05
967 418 0.15
968 188 0.07
969 172 0.06
970 105 0.04
971 75 0.03
972 76 0.03
973 5 0.00
976 115 0.04
977 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (968 bp):
CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATTCATATTCATCGAACCAAATCT
CAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAA
ATTAATTCGGAAAAAATGGAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTT
GAATTATATATTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTA
GCCGAAATCATGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGAGCCCTGACTCAAT
TTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATTGAACCAAATGTCAGCCA
AATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAAT
TCCGCAAAAAAATGAAAAAACGATATTAGAAGCGAGAAAAACCCGTCAATATTTTTGGCGTTGAA
TTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAGAAAAAACTTTTCGGGTCAGTTTTTA
GCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTCCGAAGTCCCGGCTCAAT
TTTGCATGATTTTTTGCGTAAAGACTCCTTGAAATATCTATATTCATCTGAACCAAATCTCAGCC
ATATTGGATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAA
TTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGACCATCAATCTTTTTGGCGTTGAA
TTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCAGTTTTTAGC
CGAAATCGTGTACTAACCTATCACGATTTTTGGCTAAAAACGCGTTCCGGAGCACTGA
Found at i:6537 original size:42 final size:43
Alignment explanation
Indices: 6490--6582 Score: 152
Period size: 43 Copynumber: 2.2 Consensus size: 43
6480 TAAGGCCATA
* *
6490 CATATATGCTCTGTTTTCTATGG-AAATTAGTCAATTTTAGCT
1 CATATATGCTCTGTTTTCTATGGAAAATGAGTCAATTTCAGCT
6532 CATATATGCTCTGTTTTCTATGGAAAATGAGTCAATTTCAGCT
1 CATATATGCTCTGTTTTCTATGGAAAATGAGTCAATTTCAGCT
*
6575 TATATATG
1 CATATATG
6583 AACAATTGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 23 0.49
43 24 0.51
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (43 bp):
CATATATGCTCTGTTTTCTATGGAAAATGAGTCAATTTCAGCT
Found at i:10843 original size:1 final size:1
Alignment explanation
Indices: 10837--10861 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
10827 TTCCCATCTG
10837 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
10862 GGAAAAGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16531 original size:21 final size:20
Alignment explanation
Indices: 16505--16550 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
16495 AACACAGTTT
16505 AGAGAGAGAAAGGA-AAAGAAA
1 AGAGAGAGAAA-GACAAAG-AA
*
16526 AGAGAGAGACAGACAAAGAA
1 AGAGAGAGAAAGACAAAGAA
16546 AGAGA
1 AGAGA
16551 AAAGAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.63, C:0.04, G:0.33, T:0.00
Consensus pattern (20 bp):
AGAGAGAGAAAGACAAAGAA
Found at i:17223 original size:14 final size:14
Alignment explanation
Indices: 17204--17232 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17194 ATTTGGTATT
17204 TTCTTTAGATAATA
1 TTCTTTAGATAATA
17218 TTCTTTAGATAATA
1 TTCTTTAGATAATA
17232 T
1 T
17233 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (14 bp):
TTCTTTAGATAATA
Found at i:18961 original size:10 final size:10
Alignment explanation
Indices: 18946--18972 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
18936 AAATAAAAAG
18946 GTAGTTTATA
1 GTAGTTTATA
18956 GTAGTTTATA
1 GTAGTTTATA
18966 GTAGTTT
1 GTAGTTT
18973 TCTTTTTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (10 bp):
GTAGTTTATA
Done.