Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016177.1 Corchorus capsularis cultivar CVL-1 contig16198, 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: 15146
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:1983 original size:667 final size:662
Alignment explanation
Indices: 712--2539 Score: 2598
Period size: 667 Copynumber: 2.7 Consensus size: 662
702 TAATGGTTAA
* * * * **
712 TACACGATTTCGGTTAAAATTTTGCAAAAATTTACCCGAAATAATTTTCC-CAAATTTTTTACCA
1 TACACGATTTCGGCTAAAATTTTGTAAAAATTGACCTGAAATAATTTTCCTC-AATTTTTGGCCA
776 CGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATA
65 CGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATA
* * *
841 TCGGTTTTCCAATTTTTTCCGAATTAATTTCTAATTCAATCGAAACATGATTCAGATGCTCGTAA
130 TTGGTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAA
* * *
906 AAACAAATTTTTAAATCCATTGTGGTTAAGATTTGATTAGATGGATATAGATATTTCAATGAAAC
195 AAACAAATCTTTAAATCCAATGTGGTTAAGATTTGATTAGATGGATATAGATATTTCAATGAGAC
* * *
971 TTGGCGCCAAAAAATCATGCAAAACGGAGCCGGGACTCAAAAACGTGTTTTTAGTTAAAAATTGT
260 TTGGCGCC-AAAAATCATGCAAAACAGAGCCGGGACTCAGAAACGCGTTTTTAGTTAAAAATTGT
1036 GA---T-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACACAAAACATTTCTCCTCAA-TT
324 GATGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACACAAAACATTTCTCCT-AATTT
* *
1096 TCCGGCCACCATACTTATAAAAAATATATAATTCAACT-CCAAAAAGATTGAAGAGCTTTTCACG
388 TCC-GCCACCATACTAATAAAAAATATATAATTCAA-TGTCAAAAAGATTGAAGAGCTTTTCACG
1160 CTTCTAATATTGTTTTTTTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCAAAACCGGATTG
451 CTTCTAATA---TTTTTTTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCAAAACCGGATTG
1225 AGATGCTCGTAAAAACAAATCCTTAAATCCAAGATGGCTGAGATTTCGTTAGATAAATATAGATA
513 AGATGCTCGTAAAAACAAATCCTTAAATCCAAGATGGCTGAGATTTCGTTAGATAAATATAGATA
* * * *
1290 TTTCAATGAGTCTTTGCGCCAAAAATCATGTAAAATTGAGCCGGAGTCCCGGAACGCGTTTTTTA
578 TTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGAGTCCCGGAACGCG-TTTTCA
1355 GCCAAAAACCATGAT-ATAACCG
642 GCCAAAAACCATGATAATAA--G
*
1377 TACACGATTTCGGCTAAAATTTTGTAAAAATTGACCTGAAAGAATTTTCCTCAATTTTTGGCCAC
1 TACACGATTTCGGCTAAAATTTTGTAAAAATTGACCTGAAATAATTTTCCTCAATTTTTGGCCAC
* *
1442 GATACTGATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTATAATAT
66 GATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATAT
* * *
1507 TGGTTTTCCTATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGATTTAGATTCTCGTA
131 TGGTTTTCCTA--TTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTA
*
1572 AAAACAAATCTTTGAATCCAATGTGGTTAAGATTTGATTAGATGGATATAGATATTTCAATGAGA
194 AAAACAAATCTTTAAATCCAATGTGGTTAAGATTTGATTAGATGGATATAGATATTTCAATGAGA
* *
1637 CTTGGCACCAAAAATCATGCAAAACAGAGCCGGGACTCAGAAACGGGTTTTTAGTTAAAAATTGT
259 CTTGGCGCCAAAAATCATGCAAAACAGAGCCGGGACTCAGAAACGCGTTTTTAGTTAAAAATTGT
* * * * *
1702 GATCGTTAGTACACAATTTCGGTTAAAATTTTGTAAAAATTGATACAAAACATTTCTCCTTATTT
324 GAT-GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACACAAAACATTTCTCCTAATTT
*
1767 TCCGCCACCATACTCATAAAAAATATATAATTCAATGTCAAAAAGATTGAAGAGCTTTTCACGCT
388 TCCGCCACCATACTAATAAAAAATATATAATTCAATGTCAAAAAGATTGAAGAGCTTTTCACGCT
*
1832 TCTAATATTTTTTTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATG
453 TCTAATATTTTTTTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCAAAACCGGATTGAGATG
* *
1897 CTCGTAAAAGCAAATCCTTAAATCCAATG-TGGCTGATATTTCGTTAGATAAATATAGATATTTC
518 CTCGTAAAAACAAATCCTTAAATCCAA-GATGGCTGAGATTTCGTTAGATAAATATAGATATTTC
* * *
1961 AATGAGTCTTGGTGCCAAAAATCATGCAAAACTGAGCTGGAGTCTCGGAACGCGTTTTCAGCCAA
582 AATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGAGTCCCGGAACGCGTTTTCAGCCAA
* *
2026 AAACCGTGATAATTAG
647 AAACCATGATAATAAG
* * *
2042 TACATGATTTCAGCTAAAATTTTGTAAAAATTGACCTGAAATAATTTTCCTCAATTTTTGGCCAT
1 TACACGATTTCGGCTAAAATTTTGTAAAAATTGACCTGAAATAATTTTCCTCAATTTTTGGCCAC
** * *
2107 GATACTCATAAAAAATATATAATTCAATACCAAAAATATTGAAAGGCTATTCACGCTTCTAATA-
66 GATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATAT
* * * * * *
2171 TCGTATTTCCTATTTTTTCTGAATTAATTCCTAATTGAATCGAAACATTATTCATATGCTCGTAA
131 TGGT-TTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAA
* * * *
2236 AAACAAATCCTTAAATCCAATGTGGGTAAGGTTTGGTTAGATGGATATAGATATTTCAATGAGAC
195 AAACAAATCTTTAAATCCAATGTGGTTAAGATTTGATTAGATGGATATAGATATTTCAATGAGAC
* * * * * * * * *
2301 TTGGCGCAAAAAATCTTGCAAAGCTGAGCTGGGGCTCCGGAACGCATTTTTAGTTAAAAATTGTG
260 TTGGCGCCAAAAATCATGCAAAACAGAGCCGGGACTCAGAAACGCGTTTTTAGTTAAAAATTGTG
** ** * *
2366 ATGGTTAAAACACGATTTCAACTAAAATTTTGCAAAAATTGACCCTAGAA-ATTTCTCCTCAATT
325 AT-GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACAC-AAAACATTTCTCCT-AATT
** * * * * * **
2430 TTGGGCCACAATACTAATAAAAAATATATAACTCAACGTCAAAAAGACTGAAGTGCTTCCCACGC
387 TTCCGCCACCATACTAATAAAAAATATATAATTCAATGTCAAAAAGATTGAAGAGCTTTTCACGC
*** *
2495 TTCTAATATCGCTTTTCCTACTTTTTTCCGAATTAATTTCTAATT
452 TTCTAATATTTTTTTTTCTA-TTTTTTCCGAATTAATTTCTAATT
2540 TAAAAATTAT
Statistics
Matches: 1044, Mismatches: 103, Indels: 32
0.89 0.09 0.03
Matches are distributed among these distances:
663 203 0.19
664 80 0.08
665 279 0.27
666 75 0.07
667 285 0.27
668 1 0.00
669 1 0.00
670 67 0.06
671 53 0.05
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (662 bp):
TACACGATTTCGGCTAAAATTTTGTAAAAATTGACCTGAAATAATTTTCCTCAATTTTTGGCCAC
GATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATAT
TGGTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAA
AACAAATCTTTAAATCCAATGTGGTTAAGATTTGATTAGATGGATATAGATATTTCAATGAGACT
TGGCGCCAAAAATCATGCAAAACAGAGCCGGGACTCAGAAACGCGTTTTTAGTTAAAAATTGTGA
TGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACACAAAACATTTCTCCTAATTTTCC
GCCACCATACTAATAAAAAATATATAATTCAATGTCAAAAAGATTGAAGAGCTTTTCACGCTTCT
AATATTTTTTTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCAAAACCGGATTGAGATGCTC
GTAAAAACAAATCCTTAAATCCAAGATGGCTGAGATTTCGTTAGATAAATATAGATATTTCAATG
AGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGAGTCCCGGAACGCGTTTTCAGCCAAAAAC
CATGATAATAAG
Found at i:2385 original size:332 final size:330
Alignment explanation
Indices: 707--2539 Score: 2034
Period size: 332 Copynumber: 5.5 Consensus size: 330
697 GACCGTAATG
* * *
707 GTTAATACACGATTTCGGTTAAAATTTTGCAAAAATTTACCCGAAATAATTTTCC-CAAATTTTT
1 GTTAATACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAATAATTTTCCTC-AATTTTT
**
771 TACCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAA-AGGCTTTTCACGCTT
65 GGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGA-GCTTTTCACGCTT
* *
835 CTAATATCGGTTTTCCAATTTTTTCCGAATTAATTTCTAATTCAATCGAAACATGATTCAGATGC
129 CTAATATC-GTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGC
** * * *
900 TCGTAAAAACAAATTTTTAAATCCATTGTGGTTAAGATTTGATTAGATGGATATAGATATTTCAA
193 TCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGGATATAGATATTTCAA
* * * *** *
965 TGAAACTTGGCGCCAAAAAATCATGCAAAACGGAGCCGGGACTCAAAAACGTGTTTTTAGTTAAA
258 TGAGACTTGGCGCC-AAAAATCATGCAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTAGTTAAA
1030 AATTGTGAT
322 AATTGTGAT
1039 G----TACACGATTTCGGCTAAAATTTTGCAAAAATTGACAC--AAA-ACATTTCTCCTCAATTT
1 GTTAATACACGATTTCGGCTAAAATTTTGCAAAAATTGAC-CTGAAATA-ATTT-TCCTCAATTT
** * * *
1097 CCGGCCACCATACTTATAAAAAATATATAATTCAACTCCAAAAAGATTGAAGAGCTTTTCACGCT
63 TTGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGAGCTTTTCACGCT
* * * ** *
1162 TCTAATATTGTTTTTTTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCAAAACCGGATTGAG
128 TCTAATATCG----TTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAG
* * **
1227 ATGCTCGTAAAAACAAATCCTTAAATCCAA-GATGGCTGAGATTTCGTTAGATAAATATAGATAT
189 ATGCTCGTAAAAACAAATCCTTAAATCCAATG-TGGCTAAGATTTGGTTAGATGGATATAGATAT
* * * * *
1291 TTCAATGAGTCTTTGCGCCAAAAATCATGTAAAATTGAGCCGGAG-TCCCGGAACGCGTTTTTTA
253 TTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCT-CCGGAACGCG-TTTTTA
** ***
1355 GCCAAAAACCATGAT
316 GTTAAAAATTGTGAT
* * *
1370 -ATAACCGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCTGAAAGAATTTTCCTCAATTT
1 GTTAA---TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAATAATTTTCCTCAATTT
*
1434 TTGGCCACGATACTGATAAAAAATATATAATTCAACGCCAAAAAGATTGAA-AGGCTTTTCACGC
63 TTGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGA-GCTTTTCACGC
* * * *
1498 TTATAATATTGGTTTTCCTATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGATTTAG
127 TTCTAATA-TCGTTTTCCTA--TTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAG
* * * * *
1563 ATTCTCGTAAAAACAAATCTTTGAATCCAATGTGGTTAAGATTTGATTAGATGGATATAGATATT
189 ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGGATATAGATATT
* * * * * *
1628 TCAATGAGACTTGGCACCAAAAATCATGCAAAACAGAGCCGGGACTCAGAAACGGGTTTTTAGTT
254 TCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTAGTT
1693 AAAAATTGTGAT
319 AAAAATTGTGAT
* * * * * *
1705 CGTTAGTACACAATTTCGGTTAAAATTTTGTAAAAATTGA--T-ACAAAACATTTCTCCT-TATT
1 -GTTAATACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGA-AATA-ATTT-TCCTCAATT
** * * *
1766 TTCCGCCACCATACTCATAAAAAATATATAATTCAATGTCAAAAAGATTGAAGAGCTTTTCACGC
62 TTTGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGAGCTTTTCACGC
** * ** *
1831 TTCTAATATTTTTTTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGATTGAGAT
127 TTCTAATA-TCGTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGAT
* * * * **
1896 GCTCGTAAAAGCAAATCCTTAAATCCAATGTGGCTGATATTTCGTTAGATAAATATAGATATTTC
191 GCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGGATATAGATATTTC
* * * * * **
1961 AATGAGTCTTGGTGCCAAAAATCATGCAAAACTGAGCTGGAG-TCTCGGAACGCGTTTTCAGCCA
256 AATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCTC-CGGAACGCGTTTTTAGTTA
**
2025 AAAACCGTGAT
320 AAAATTGTGAT
* * * * *
2036 AATTAGTACATGATTTCAGCTAAAATTTTGTAAAAATTGACCTGAAATAATTTTCCTCAATTTTT
1 -GTTAATACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAATAATTTTCCTCAATTTTT
* ** * *
2101 GGCCATGATACTCATAAAAAATATATAATTCAATACCAAAAATATTGAA-AGGCTATTCACGCTT
65 GGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGA-GCTTTTCACGCTT
* * * * *
2165 CTAATATCGTATTTCCTATTTTTTCTGAATTAATTCCTAATTGAATCGAAACATTATTCATATGC
129 CTAATATCGT-TTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGC
* *
2230 TCGTAAAAACAAATCCTTAAATCCAATGTGGGTAAGGTTTGGTTAGATGGATATAGATATTTCAA
193 TCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGGATATAGATATTTCAA
* * * * *
2295 TGAGACTTGGCGCAAAAAATCTTGCAAAGCTGAGCTGGGGCTCCGGAACGCATTTTTAGTTAAAA
258 TGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTAGTTAAAA
2360 ATTGTGAT
323 ATTGTGAT
* ** *
2368 GGTTAAAACACGATTTCAACTAAAATTTTGCAAAAATTGACCCTAGAAAT--TTCTCCTCAATTT
1 -GTTAATACACGATTTCGGCTAAAATTTTGCAAAAATTGA-CCT-GAAATAATTTTCCTCAATTT
* * * * * * * **
2431 TGGGCCACAATACTAATAAAAAATATATAACTCAACGTCAAAAAGACTGAAGTGCTTCCCACGCT
63 TTGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGAGCTTTTCACGCT
2496 TCTAATATCGCTTTTCCTACTTTTTTCCGAATTAATTTCTAATT
128 TCTAATATCG-TTTTCCTA-TTTTTTCCGAATTAATTTCTAATT
2540 TAAAAATTAT
Statistics
Matches: 1255, Mismatches: 199, Indels: 93
0.81 0.13 0.06
Matches are distributed among these distances:
326 1 0.00
327 8 0.01
328 105 0.08
329 4 0.00
330 30 0.02
331 323 0.26
332 347 0.28
333 112 0.09
334 50 0.04
335 16 0.01
336 137 0.11
337 112 0.09
338 9 0.01
339 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (330 bp):
GTTAATACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAATAATTTTCCTCAATTTTTG
GCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCT
AATATCGTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCG
TAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGGATATAGATATTTCAATGA
GACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTAGTTAAAAATT
GTGAT
Found at i:2653 original size:27 final size:28
Alignment explanation
Indices: 2594--2660 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
2584 GAAAAATACA
* *
2594 AAAAATTATATTTTAATAATGGTATAGTT
1 AAAAA-TATATTTTAATAATGGAAAAGTT
*
2623 -AAAATATATTTTAATAAT-GAAAATTT
1 AAAAATATATTTTAATAATGGAAAAGTT
2649 AAAAATATATTT
1 AAAAATATATTT
2661 GAAAAAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.15
27 25 0.74
28 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (28 bp):
AAAAATATATTTTAATAATGGAAAAGTT
Found at i:2749 original size:94 final size:95
Alignment explanation
Indices: 2585--2760 Score: 257
Period size: 94 Copynumber: 1.9 Consensus size: 95
2575 AATATATTTG
* ** *
2585 AAAAATACAAAAAATTATATTTTAATAATGGTATAGTTAAAATATATTTTAATAATGAAAATTTA
1 AAAAATACAAAAAATTATATTCTAATAATGACATAATTAAAATATATTTTAATAATGAAAATTTA
2650 AAAATATATTTGAAAAAATAGTACAATCAA
66 AAAATATATTTGAAAAAATAGTACAATCAA
* * *
2680 AAAATATACATAAAATTGTATTCTAATAATGACATAATT-AAA-ATATTTTAATAATGACAATTT
1 AAAA-ATACAAAAAATTATATTCTAATAATGACATAATTAAAATATATTTTAATAATGAAAATTT
*
2743 AGAAATATATTTGAAAAA
65 AAAAATATATTTGAAAAA
2761 GGGGTATAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
94 37 0.51
95 7 0.10
96 28 0.39
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (95 bp):
AAAAATACAAAAAATTATATTCTAATAATGACATAATTAAAATATATTTTAATAATGAAAATTTA
AAAATATATTTGAAAAAATAGTACAATCAA
Found at i:3076 original size:37 final size:37
Alignment explanation
Indices: 2987--3082 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 37
2977 TCTAGAACCC
* * *
2987 AAATAGGACGTTGGAGACGAAGACAAAAAGCAAACTT
1 AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
** * *
3024 AAATACAATGATTGGAAACAAAGACAAAAGGCAAAATT
1 AAATAGGACG-TTGGAAACAAAGACAAAAAGCAAAATT
3062 AAATAGGACGTTGGAAACAAA
1 AAATAGGACGTTGGAAACAAA
3083 AAGGCAAATT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
37 18 0.38
38 30 0.62
ACGTcount: A:0.53, C:0.11, G:0.21, T:0.15
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
Found at i:3234 original size:31 final size:31
Alignment explanation
Indices: 3179--3274 Score: 140
Period size: 31 Copynumber: 3.1 Consensus size: 31
3169 TGACAATTTA
**
3179 GAAATATGTTTTAAAAA-ACTGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATTG
* *
3209 GAAATATATTTTAAAAATAAGGGTACAATTA
1 GAAATATGTTTTAAAAATAAGGGTACAATTG
*
3240 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATTG
3271 GAAA
1 GAAA
3275 ACATAAAGTT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
30 16 0.28
31 42 0.72
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATTG
Found at i:4279 original size:20 final size:20
Alignment explanation
Indices: 4254--4291 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4244 TTTTTGGGGA
4254 TTACTAAATACCGCCCCCTT
1 TTACTAAATACCGCCCCCTT
**
4274 TTACTAGGTACCGCCCCC
1 TTACTAAATACCGCCCCC
4292 ATTTGGACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.42, G:0.11, T:0.26
Consensus pattern (20 bp):
TTACTAAATACCGCCCCCTT
Found at i:4616 original size:33 final size:32
Alignment explanation
Indices: 4592--4751 Score: 182
Period size: 33 Copynumber: 4.8 Consensus size: 32
4582 GCGATCCGCG
*
4592 TGCGACCCAGCCATGGGCAGGTCGCGACCAGAT
1 TGCGACCCA-CCATGGGCTGGTCGCGACCAGAT
4625 TGCGACCCACCATGGTGCTGGTCGCGACCAGAT
1 TGCGACCCACCATGG-GCTGGTCGCGACCAGAT
*
4658 TGCGACCCACCATGGTGC-GGATCACGACCAGAT
1 TGCGACCCACCATGG-GCTGG-TCGCGACCAGAT
**
4691 TGCGACCCATACCAT-GGCTGGTCGCGATCC-GCG
1 TGCGACCC--ACCATGGGCTGGTCGCGA-CCAGAT
*
4724 TGCGACCCAGCCATGGGCGGGTCGCGAC
1 TGCGACCCA-CCATGGGCTGGTCGCGAC
4752 TAGCCCTTTT
Statistics
Matches: 113, Mismatches: 6, Indels: 17
0.83 0.04 0.12
Matches are distributed among these distances:
31 1 0.01
32 13 0.12
33 89 0.79
34 5 0.04
35 5 0.04
ACGTcount: A:0.19, C:0.34, G:0.32, T:0.15
Consensus pattern (32 bp):
TGCGACCCACCATGGGCTGGTCGCGACCAGAT
Found at i:4648 original size:66 final size:64
Alignment explanation
Indices: 4569--4751 Score: 228
Period size: 66 Copynumber: 2.8 Consensus size: 64
4559 CGCGTTCCTC
* *
4569 ACCACGGCGGGTCGCGATCCGCGTGCGACCCAGCCATGGGCAGGTCGCGACCAGATTGCGACCC-
1 ACCATGGCTGGTCGCGATCCGCGTGCGACCCAGCCATGGGC-GGTCGCGACCAGATTGCGACCCA
** *
4633 ACCATGGTGCTGGTCGCGA-CCAGATTGCGACCCA-CCATGGTGCGGATCACGACCAGATTGCGA
1 ACCAT-G-GCTGGTCGCGATCC-GCGTGCGACCCAGCCATGG-GCGG-TCGCGACCAGATTGCGA
4696 CCCA
61 CCCA
4700 TACCATGGCTGGTCGCGATCCGCGTGCGACCCAGCCATGGGCGGGTCGCGAC
1 -ACCATGGCTGGTCGCGATCCGCGTGCGACCCAGCCATGGGC-GGTCGCGAC
4752 TAGCCCTTTT
Statistics
Matches: 101, Mismatches: 8, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
64 4 0.04
65 11 0.11
66 70 0.69
67 11 0.11
68 5 0.05
ACGTcount: A:0.18, C:0.35, G:0.33, T:0.14
Consensus pattern (64 bp):
ACCATGGCTGGTCGCGATCCGCGTGCGACCCAGCCATGGGCGGTCGCGACCAGATTGCGACCCA
Found at i:6510 original size:13 final size:13
Alignment explanation
Indices: 6488--6517 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6478 CGGTAATATT
6488 TTATACTATTATA
1 TTATACTATTATA
*
6501 TTATATTATTATA
1 TTATACTATTATA
6514 TTAT
1 TTAT
6518 TACATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATACTATTATA
Found at i:10132 original size:31 final size:31
Alignment explanation
Indices: 10094--10152 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
10084 AGTTTTGAGA
*
10094 AACTTTTGAAACGCCTATTTTACCCTTATTT
1 AACTTTTGAAACGCCTATTATACCCTTATTT
* *
10125 AACTTTTGAAATGCCTATTATATCCTTA
1 AACTTTTGAAACGCCTATTATACCCTTA
10153 GTTTTTTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (31 bp):
AACTTTTGAAACGCCTATTATACCCTTATTT
Done.