Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011522.1 Corchorus capsularis cultivar CVL-1 contig11543, 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: 54535
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:24603 original size:218 final size:218
Alignment explanation
Indices: 24223--25639 Score: 1963
Period size: 218 Copynumber: 6.5 Consensus size: 218
24213 AAGTAAGTAC
* * * * *
24223 AAAAAATGTCACTCTCGAAAGAATTTTGGGATGGTGTATATGATTATTTGGGGATGATTAGAAAT
1 AAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAAT
* * * * *
24288 GAGTTGGATATAAAGTATATCAGC-TTGAGGATACTGAAGTTTTGTATTTTGTTTAACTATTAGA
66 GATTTGGGTATAAAGTATATCA-CTTTGGGGATACTGAA-TTTTGCATTTTGTTTAATTATTAGA
* ** * *
24352 TGACAGTAAATTCATATAGACATGG-TTATTCAATTGATTAGGATGAAAATATGGATTAAAACAC
129 TGACACTAAATTCATATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAGCAC
* *
24416 GTTTAAATCCAATTCTGGGTATATA
194 GTTTAAAGCCAATTTTGGGTATATA
* * * * *
24441 AAAAAATGTCAATCTCTAAAGAATTTGTGGATGATGGATATGGTTATGTGGGGATGATGAGAAAT
1 AAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAAT
* *
24506 GATTTGGGTATAGAGTATATCACTTTGGGGATATTGAATTTTGCATTTTGTTTAATTATTAGATG
66 GATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATG
* ** * *
24571 ACACCAAATTCATATAGACGGGGTCCATTCAATTAATTAAGATGAAAGTATGGATTAAAGCACGT
131 ACACTAAATTCATATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAGCACGT
*
24636 TTGAAGCCAATTTTGGGTATATAA
196 TTAAAGCCAATTTTGGGTATAT-A
* * *
24660 GAAAAAATGTCAATCTCTAATGAATTTGGGGATGATGCTTATGATTATTTGGGGATGATGAGAAA
1 -AAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAA
* * *
24725 TGATTTGGGTATAAAG--TATCAGTTTGGGGATACTGAAGTTTACATTTTGTTTAATTATTAGAT
65 TGATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGAT
* * * * *
24788 GACACTAAATTCATATAGACGAGGTTTATTCAATTAAATAGGATGAAATTATGAATTAAAGCATG
130 GACACTAAATTCATATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAGCACG
** *
24853 TTTAAAG-CAATTTTGGGCGTATT
195 TTTAAAGCCAATTTTGGGTATATA
* *
24876 AGAAAATGTCAATCTCTACAA-AATTTGGGGATGGTGCATATGATTATTTGGGGATGATGTGAAA
1 AAAAAATGTCAATCTCTA-AAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAA
* *
24940 TGATTTGGGTATAAAGTATATCAGTTTGCGGATACTGAATTTTGCATTTTGTTTAATTATTAGAT
65 TGATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGAT
* *
25005 GACACTAAATTCATATAGATGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAGCATG
130 GACACTAAATTCATATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAGCACG
*
25070 TTTAAAGCCAATTTTGGGTAT-GA
195 TTTAAAGCCAATTTTGGGTATATA
* * * * * *
25093 AAAAACTGTTAATCTCTAATGAATTTGGGGATGGTGGATATGATTATTTGGGGATGATGAAAAAC
1 AAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAAT
* *
25158 GATTTGGGTATAAAGTATATCTCTTTGGGGATATTGAATTTTGCATTTTG-TTAATTATTAGATG
66 GATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATG
** ** *
25222 TTACTAAATTCA-ATTAGACTAGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACG
131 ACACTAAATTCATA-TAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAGCACG
* * *
25286 TTTAAAGTCAATTTTGGGCACATA
195 TTTAAAGCCAATTTTGGGTATATA
* * *
25310 AAAAAATGTCAATCTCTAAAAAAATTTGGGGATGGTGCATATGATTATTTGGGGATGGTGGGAAA
1 AAAAAATGTCAATCTCT-AAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAA
*
25375 TGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGAT
65 TGATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGAT
* * * *
25440 GACACTAAACTCATATAGACGGGATTTATTCAATTAATTAGGATGAAAGTATGGATTAAAGCATG
130 GACACTAAATTCATATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAGCACG
25505 TTTAAAGCCAATTTTGGGTATATAA
195 TTTAAAGCCAATTTTGGGTATAT-A
* * *
25530 GAAAAAATGTCCATCTC-AAATGAATTTGGGGATGGTGCTTATGATTATTTGGGAATGATGAGAA
1 -AAAAAATGTCAATCTCTAAA-GAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAA
*
25594 ATGATTTGGGTATAGAGTATATCACTTTGGGGATACTGAATTTTGC
64 ATGATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGC
25640 GCATGCCTCA
Statistics
Matches: 1057, Mismatches: 125, Indels: 32
0.87 0.10 0.03
Matches are distributed among these distances:
215 74 0.07
216 89 0.08
217 286 0.27
218 345 0.33
219 91 0.09
220 157 0.15
221 15 0.01
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (218 bp):
AAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAAT
GATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATG
ACACTAAATTCATATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAGCACGT
TTAAAGCCAATTTTGGGTATATA
Found at i:25336 original size:435 final size:435
Alignment explanation
Indices: 24223--25639 Score: 2053
Period size: 435 Copynumber: 3.3 Consensus size: 435
24213 AAGTAAGTAC
* * * * * *
24223 AAAAAATGTCACTCTCGAAAGAATTTTGGGATGGTGTATATGATTATTTGGGGATGATTAGAAAT
1 AAAAAATGTCAATCTCTAATGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAAT
* * * * *
24288 GAGTTGGATATAAAGTATATCAGC-TTGAGGATACTGAAGTTTTGTATTTTGTTTAACTATTAGA
66 GATTTGGGTATAAAGTATATCA-CTTTGGGGATACTGAA-TTTTGCATTTTGTTTAATTATTAGA
* *
24352 TGACAGTAAATTCATATAGACATGG-TTATTCAATTGATTAGGATGAAAATATGGATTAAAACAC
129 TGACACTAAATTCATATAGACA-GGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACAC
* * * * * *
24416 GTTTAAA-TCCAATTCTGGGTATATAAAAAAATGTCAATCTCTAAAGAATTTGTGGATGATGGAT
193 GTTTAAAGT-CAATTTTGGGCATATAAAAAAATGTCAATCTCTAAAAAATTTGGGGATGGTGCAT
* * * * *
24480 ATGGTTATGTGGGGATGATGAGAAATGATTTGGGTATAGAGTATATCACTTTGGGGATATTGAAT
257 ATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAAT
* **
24545 TTTGCATTTTGTTTAATTATTAGATGACACCAAATTCATATAGACGGGGTCCATTCAATTAATTA
322 TTTGCATTTTGTTTAATTATTAGATGACACTAAATTCATATAGACGGGGTTTATTCAATTAATTA
* * *
24610 AGATGAAAGTATGGATTAAAGCACGTTTGAAGCCAATTTTGGGTATATAAG
387 GGATGAAAGTATGGATTAAAGCATGTTTAAAGCCAATTTTGGG-ATAT-AG
* *
24661 AAAAAATGTCAATCTCTAATGAATTTGGGGATGATGCTTATGATTATTTGGGGATGATGAGAAAT
1 AAAAAATGTCAATCTCTAATGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAAT
* * *
24726 GATTTGGGTATAAAG--TATCAGTTTGGGGATACTGAAGTTTACATTTTGTTTAATTATTAGATG
66 GATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATG
* * * * *
24789 ACACTAAATTCATATAGACGAGGTTTATTCAATTAAATAGGATGAAATTATGAATTAAAGCATGT
131 ACACTAAATTCATATAGAC-AGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGT
* * * *
24854 TTAAAG-CAATTTTGGGCGTATTAGAAAATGTCAATCTCTACAAAATTTGGGGATGGTGCATATG
195 TTAAAGTCAATTTTGGGCATATAAAAAAATGTCAATCTCTAAAAAATTTGGGGATGGTGCATATG
* *
24918 ATTATTTGGGGATGATGTGAAATGATTTGGGTATAAAGTATATCAGTTTGCGGATACTGAATTTT
260 ATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTT
*
24983 GCATTTTGTTTAATTATTAGATGACACTAAATTCATATAGATGGGGTTTATTCAATTAATTAGGA
325 GCATTTTGTTTAATTATTAGATGACACTAAATTCATATAGACGGGGTTTATTCAATTAATTAGGA
*
25048 TGAAAATATGGATTAAAGCATGTTTAAAGCCAATTTTGGG-TAT-G
390 TGAAAGTATGGATTAAAGCATGTTTAAAGCCAATTTTGGGATATAG
* * *
25092 AAAAAACTGTTAATCTCTAATGAATTTGGGGATGGTGGATATGATTATTTGGGGATGATGAAAAA
1 AAAAAA-TGTCAATCTCTAATGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAA
* * *
25157 CGATTTGGGTATAAAGTATATCTCTTTGGGGATATTGAATTTTGCATTTTG-TTAATTATTAGAT
65 TGATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGAT
**
25221 GTTACTAAATTCA-ATTAGACTAGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACAC
130 GACACTAAATTCATA-TAGAC-AGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACAC
*
25285 GTTTAAAGTCAATTTTGGGCACATAAAAAAATGTCAATCTCTAAAAAAATTTGGGGATGGTGCAT
193 GTTTAAAGTCAATTTTGGGCATATAAAAAAATGTCAATCTCT-AAAAAATTTGGGGATGGTGCAT
* *
25350 ATGATTATTTGGGGATGGTGGGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAAT
257 ATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAAT
* *
25415 TTTGCATTTTGTTTAATTATTAGATGACACTAAACTCATATAGACGGGATTTATTCAATTAATTA
322 TTTGCATTTTGTTTAATTATTAGATGACACTAAATTCATATAGACGGGGTTTATTCAATTAATTA
25480 GGATGAAAGTATGGATTAAAGCATGTTTAAAGCCAATTTTGGGTATATAAG
387 GGATGAAAGTATGGATTAAAGCATGTTTAAAGCCAATTTTGGG-ATAT-AG
* * * *
25531 AAAAAATGTCCATCTCAAATGAATTTGGGGATGGTGCTTATGATTATTTGGGAATGATGAGAAAT
1 AAAAAATGTCAATCTCTAATGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAAT
*
25596 GATTTGGGTATAGAGTATATCACTTTGGGGATACTGAATTTTGC
66 GATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGC
25640 GCATGCCTCA
Statistics
Matches: 875, Mismatches: 90, Indels: 28
0.88 0.09 0.03
Matches are distributed among these distances:
431 7 0.01
432 69 0.08
433 78 0.09
434 57 0.07
435 433 0.49
436 59 0.07
437 3 0.00
438 162 0.19
439 7 0.01
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (435 bp):
AAAAAATGTCAATCTCTAATGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAAT
GATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATG
ACACTAAATTCATATAGACAGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGTT
TAAAGTCAATTTTGGGCATATAAAAAAATGTCAATCTCTAAAAAATTTGGGGATGGTGCATATGA
TTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTG
CATTTTGTTTAATTATTAGATGACACTAAATTCATATAGACGGGGTTTATTCAATTAATTAGGAT
GAAAGTATGGATTAAAGCATGTTTAAAGCCAATTTTGGGATATAG
Found at i:26858 original size:218 final size:217
Alignment explanation
Indices: 26097--27157 Score: 1475
Period size: 218 Copynumber: 4.9 Consensus size: 217
26087 ATATTACTCG
* * * *
26097 TCATTCCCAAATAATCATAAGCAGCATCCCCAAATTCATTAGAGATTGACATTTTTTTCTTATAT
1 TCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACA--TTTTT-TTATAT
* * * * *
26162 ACCCAAAATTGGCTTCAAACATGCTTTAATCCATACTTTCATCTTAATTAATTGAATGAACCCCG
63 ACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAAT-AACCCCA
*
26227 TCTATATGAATTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTTAGTATCCCCAAACTGAT
127 TCTATATGAATTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTGAT
*
26292 ATACTTTATACCCAAATCATTTCCCA
192 ATACTTTATACCCAAATCATTTCTCA
* * * *
26318 CCATTCCCAAATAATCATATGCACCATCCCCAAATTTTTTAGAGATTGACATTTTTTTATATGCC
1 TCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTATATACC
* * * *
26383 CAAAATTGACTTTAAACGTGTTTTAATCCATATCTTCATCCTAATTAATTGAATAAACCCAGTCT
66 CAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAACCCCA-TCT
* * **
26448 A-ATTGAATTTAGTGACATCTAATAATT-AACAAAATGCAAAATTCAATA-CCCCAAAGAGATAT
130 ATA-TGAATTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTGATAT
*
26510 ACTTTATACCCAAATCGTTTCTCA
194 ACTTTATACCCAAATCATTTCTCA
* * * *
26534 TCATCCTCAAATAATCATATGCACCATCCCCAAATTCATTAGAGATTAACAATTTTTCTATATAC
1 TCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGAC-ATTTTTTTATATAC
* * *
26599 CCAAAATTGGCTTTAAACATGCTTTAGTCCATATCTTCATCCTAATTAATTGAATGAACCCCATC
65 CCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAAT-AACCCCATC
* *
26664 TATATGAATTTAATGTCATCTAATAATTAAACAAAATGCAAAATTCAATATCCCCAAACTGATAT
129 TATATGAATTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTGATAT
*
26729 ACTTTATACCCAACTCATTTCTCA
194 ACTTTATACCCAAATCATTTCTCA
* * *
26753 TCATCCCCAAATAATCATATGCACCATCCACAAAATCTTTCGAGATTGACATTTTTTTATATACC
1 TCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTATATACC
* *
26818 CAAAATTGGCTTTAAACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCAGTCT
66 CAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAACCCCA-TCT
* * * *
26883 AAATGAATTTAGTGACATCTAATAATTAAAGAAAATGCAAAATTCAGTATCCCCAAAGTGATATA
130 ATATGAATTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTGATATA
*
26948 CTTTATATCCAAATCATTTCTCA
195 CTTTATACCCAAATCATTTCTCA
* * * *
26971 TCATCCCCAAATAATCATATACACTATCCCCAAATTTTTTAGAGATTGACA-TTTTTTATATGCC
1 TCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTATATACC
* * * *
27035 CAAAATTGACTTTAAACGTGATTTAATCCATATTTTTCATCCTAATTAATTGAATAAGCCTCGTC
66 CAAAATTGGCTTTAAACGTGCTTTAATCCATA-TTTTCATCCTAATTAATTGAATAA-CCCCATC
* * * *
27100 TATATCAATTCT-GTTTTATCTAATAATTAAACAAAATGCAAAATTCAGTATCTCCAAA
129 TATATGAATT-TAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAA
27158 TTGTTTTTGT
Statistics
Matches: 749, Mismatches: 80, Indels: 25
0.88 0.09 0.03
Matches are distributed among these distances:
216 78 0.10
217 162 0.22
218 377 0.50
219 86 0.11
221 46 0.06
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (217 bp):
TCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTATATACC
CAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAACCCCATCTA
TATGAATTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTGATATAC
TTTATACCCAAATCATTTCTCA
Found at i:27039 original size:435 final size:432
Alignment explanation
Indices: 26097--27157 Score: 1590
Period size: 435 Copynumber: 2.4 Consensus size: 432
26087 ATATTACTCG
*
26097 TCATTCCCAAATAATCATA-AGCAGCATCCCCAAATTCATTAGAGATTGACATTTTTTTCTTATA
1 TCATCCCCAAATAATCATATA-CA-CATCCCCAAATTCATTAGAGATTGACA---TTTT-TTATA
* *
26161 TACCCAAAATTGGCTTCAAACATGCTTTAATCCATA-CTTTCATCTTAATTAATTGAATGAACCC
60 TACCCAAAATTGGCTTTAAACATGCTTTAATCCATATC-TTCATCCTAATTAATTGAATGAACCC
*
26225 CGTCTATATGAATTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTTAGTATCCCCAAACTG
124 CGTCTATATGAATTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTG
* * * *
26290 ATATACTTTATACCCAAATCATTTCCCACCATTCCCAAATAATCATATGCACCATCCCCAAATTT
189 ATATACTTTATACCCAAATCATTTCCCACCATCCCCAAATAATCATATGCACCATCCACAAAATC
*
26355 TTTAGAGATTGACATTTTTTTATATGCCCAAAATTGACTTTAAACGTGTTTTAATCCATATCTTC
254 TTTAGAGATTGACATTTTTTTATATACCCAAAATTGACTTTAAACGTGTTTTAATCCATATCTTC
*
26420 ATCCTAATTAATTGAATAAACCCAGTCTAATTGAATTTAGTGACATCTAATAATTAACAAAATGC
319 ATCCTAATTAATTGAATAAACCCAGTCTAAATGAATTTAGTGACATCTAATAATTAACAAAATGC
*
26485 AAAATTCAATACCCCAAAGAGATATACTTTATACCCAAATCGTTTCTCA
384 AAAATTCAATACCCCAAAGAGATATACTTTATACCCAAATCATTTCTCA
* * *
26534 TCATCCTCAAATAATCATATGCACCATCCCCAAATTCATTAGAGATTAACAATTTTTCTATATAC
1 TCATCCCCAAATAATCATATACA-CATCCCCAAATTCATTAGAGATTGAC-ATTTTT-TATATAC
* *
26599 CCAAAATTGGCTTTAAACATGCTTTAGTCCATATCTTCATCCTAATTAATTGAATGAACCCCATC
63 CCAAAATTGGCTTTAAACATGCTTTAATCCATATCTTCATCCTAATTAATTGAATGAACCCCGTC
* *
26664 TATATGAATTTAATGTCATCTAATAATTAAACAAAATGCAAAATTCAATATCCCCAAACTGATAT
128 TATATGAATTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTGATAT
* * * *
26729 ACTTTATACCCAACTCATTTCTCATCATCCCCAAATAATCATATGCACCATCCACAAAATCTTTC
193 ACTTTATACCCAAATCATTTCCCACCATCCCCAAATAATCATATGCACCATCCACAAAATCTTTA
* *
26794 GAGATTGACATTTTTTTATATACCCAAAATTGGCTTTAAACGTGTTTTAATCCATATTTTCATCC
258 GAGATTGACATTTTTTTATATACCCAAAATTGACTTTAAACGTGTTTTAATCCATATCTTCATCC
*
26859 TAATTAATTGAATAAACCCAGTCTAAATGAATTTAGTGACATCTAATAATTAAAGAAAATGCAAA
323 TAATTAATTGAATAAACCCAGTCTAAATGAATTTAGTGACATCTAATAATT-AACAAAATGCAAA
* * *
26924 ATTCAGTATCCCCAAAGTGATATACTTTATATCCAAATCATTTCTCA
387 ATTCAATA-CCCCAAAGAGATATACTTTATACCCAAATCATTTCTCA
** *
26971 TCATCCCCAAATAATCATATACACTATCCCCAAATTTTTTAGAGATTGACATTTTTTATATGCCC
1 TCATCCCCAAATAATCATATACAC-ATCCCCAAATTCATTAGAGATTGACATTTTTTATATACCC
* * * * *
27036 AAAATTGACTTTAAACGTGATTTAATCCATATTTTTCATCCTAATTAATTGAAT-AAGCCTCGTC
65 AAAATTGGCTTTAAACATGCTTTAATCCATA-TCTTCATCCTAATTAATTGAATGAA-CCCCGTC
* * * *
27100 TATATCAATTCT-GTTTTATCTAATAATTAAACAAAATGCAAAATTCAGTATCTCCAAA
128 TATATGAATT-TAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAA
27158 TTGTTTTTGT
Statistics
Matches: 566, Mismatches: 48, Indels: 21
0.89 0.08 0.03
Matches are distributed among these distances:
434 1 0.00
435 338 0.60
436 103 0.18
437 123 0.22
438 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (432 bp):
TCATCCCCAAATAATCATATACACATCCCCAAATTCATTAGAGATTGACATTTTTTATATACCCA
AAATTGGCTTTAAACATGCTTTAATCCATATCTTCATCCTAATTAATTGAATGAACCCCGTCTAT
ATGAATTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTGATATACT
TTATACCCAAATCATTTCCCACCATCCCCAAATAATCATATGCACCATCCACAAAATCTTTAGAG
ATTGACATTTTTTTATATACCCAAAATTGACTTTAAACGTGTTTTAATCCATATCTTCATCCTAA
TTAATTGAATAAACCCAGTCTAAATGAATTTAGTGACATCTAATAATTAACAAAATGCAAAATTC
AATACCCCAAAGAGATATACTTTATACCCAAATCATTTCTCA
Found at i:27312 original size:9 final size:9
Alignment explanation
Indices: 27298--27322 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
27288 CCGATGGGGT
27298 GTGGCGGTG
1 GTGGCGGTG
27307 GTGGCGGTG
1 GTGGCGGTG
27316 GTGGCGG
1 GTGGCGG
27323 AGGAGGAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.68, T:0.20
Consensus pattern (9 bp):
GTGGCGGTG
Found at i:28568 original size:22 final size:22
Alignment explanation
Indices: 28541--28582 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
28531 GACAAACCCA
*
28541 TAACCCGAATGACCCGAGAAGT
1 TAACCCGAATGACCCAAGAAGT
28563 TAACCCGAATGACCCAAGAA
1 TAACCCGAATGACCCAAGAA
28583 TTTTTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.29, G:0.19, T:0.12
Consensus pattern (22 bp):
TAACCCGAATGACCCAAGAAGT
Found at i:29951 original size:126 final size:128
Alignment explanation
Indices: 29737--29994 Score: 380
Period size: 126 Copynumber: 2.0 Consensus size: 128
29727 ATTTAAGAAA
*
29737 TATATTTTAAAAAATCTAATATATCTAAGTTTTTTAATTAAATTAGTAAAATGATAAAAATAAAA
1 TATATTTTAAAAAATCTAATATATATAAG-TTTTT-ATTAAATTAG-AAAATGATAAAAATAAAA
* *
29802 TAGATATAAAGATATTAGATTTAATTAAATGAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAA
63 TAGATATAAAGATATTAGATTTAATTAAAT-AAAAATAAACTTTTTAGTTGAGTAAAACTATAAA
29867 AG
127 AG
* *
29869 TATATTTTAAAAAATTCTAATATATATAAG-TTTT-TT-AATTA-AAAATGGTAAAAATAAAATT
1 TATATTTTAAAAAA-TCTAATATATATAAGTTTTTATTAAATTAGAAAATGATAAAAATAAAATA
* *
29930 GTTATAAGGATATTAGATTTAATTAAATAAAAATAAACTTTTTAGTTGAGTAAAACTATAAAAG
65 GATATAAAGATATTAGATTTAATTAAATAAAAATAAACTTTTTAGTTGAGTAAAACTATAAAAG
29994 T
1 T
29995 TTAAACAATG
Statistics
Matches: 118, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
125 35 0.30
126 44 0.37
128 5 0.04
129 2 0.02
131 4 0.03
132 14 0.12
133 14 0.12
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.38
Consensus pattern (128 bp):
TATATTTTAAAAAATCTAATATATATAAGTTTTTATTAAATTAGAAAATGATAAAAATAAAATAG
ATATAAAGATATTAGATTTAATTAAATAAAAATAAACTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:30782 original size:15 final size:16
Alignment explanation
Indices: 30754--30783 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30744 TATATAAACT
30754 TTAATTTTTCTTAGGC
1 TTAATTTTTCTTAGGC
30770 TTAATTTTT-TTAGG
1 TTAATTTTTCTTAGG
30784 AAATTGTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (16 bp):
TTAATTTTTCTTAGGC
Found at i:31186 original size:15 final size:15
Alignment explanation
Indices: 31166--31198 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
31156 CAATCGATTC
*
31166 CGAGCTTCTCATAAT
1 CGAGCTTCTCACAAT
31181 CGAGCTTCTCACAAT
1 CGAGCTTCTCACAAT
31196 CGA
1 CGA
31199 TTCTAGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (15 bp):
CGAGCTTCTCACAAT
Found at i:35717 original size:35 final size:32
Alignment explanation
Indices: 35669--35755 Score: 106
Period size: 35 Copynumber: 2.7 Consensus size: 32
35659 TCCAAGAATT
*
35669 AGTTTTTGTTTTTTCCGTTTTTTCTAAAAAAAAAA
1 AGTTTTT-CTTTTTCCGTTTTTTCT--AAAAAAAA
*
35704 AGTTTTTCCTTTTTCCGATTTTTCTAAAAAAAA
1 AGTTTTT-CTTTTTCCGTTTTTTCTAAAAAAAA
35737 AG-TTTTC-TTTTCCGTTTTT
1 AGTTTTTCTTTTTCCGTTTTT
35756 CCTTTTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 11 0.23
31 1 0.02
32 4 0.08
33 10 0.21
35 22 0.46
ACGTcount: A:0.25, C:0.13, G:0.08, T:0.54
Consensus pattern (32 bp):
AGTTTTTCTTTTTCCGTTTTTTCTAAAAAAAA
Found at i:35770 original size:38 final size:39
Alignment explanation
Indices: 35728--35801 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 39
35718 CCGATTTTTC
* *
35728 TAAAAAAAAAGTTTTCTTTTCCGTTT-TTCCTTTTAAAA
1 TAAAAAAAAAGTTTTATTTTCCGTTTCTGCCTTTTAAAA
* * *
35766 TAAAAAAATATTTTTATTTTCTGTTTCTGCCTTTTA
1 TAAAAAAAAAGTTTTATTTTCCGTTTCTGCCTTTTA
35802 TTTTATTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 22 0.73
39 8 0.27
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.51
Consensus pattern (39 bp):
TAAAAAAAAAGTTTTATTTTCCGTTTCTGCCTTTTAAAA
Found at i:39130 original size:5 final size:5
Alignment explanation
Indices: 39120--39144 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
39110 GCGCATCCAC
39120 CCATG CCATG CCATG CCATG CCATG
1 CCATG CCATG CCATG CCATG CCATG
39145 TCCGCACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (5 bp):
CCATG
Found at i:45512 original size:30 final size:30
Alignment explanation
Indices: 45476--45555 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 30
45466 CAAAGGATCA
45476 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGGCATCTTTGGTGCGATTCCTCCATCC
*
45506 AATGGCATCTTTGGTGCAATTCCTCCATCC
1 AATGGCATCTTTGGTGCGATTCCTCCATCC
* ***
45536 ATTGATGTCTTTGGTGCGAT
1 AATGGCATCTTTGGTGCGAT
45556 CGCATCTCCT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.36
Consensus pattern (30 bp):
AATGGCATCTTTGGTGCGATTCCTCCATCC
Found at i:47947 original size:6 final size:6
Alignment explanation
Indices: 47938--47970 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
47928 AAAACAAAGC
*
47938 AAATCT AAATCT ATATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
47971 GCAGATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATCT
Done.