Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010144.1 Corchorus capsularis cultivar CVL-1 contig10165, 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: 50839
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:36 original size:6 final size:6
Alignment explanation
Indices: 15--49 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
5 ATATATATAT
*
15 ATATTA ATA-TA TTATTA ATATTA ATATTA ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
50 GATTGGTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
ATATTA
Found at i:1058 original size:7 final size:7
Alignment explanation
Indices: 1046--1071 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1036 CTATATCTAA
1046 GCCCCAG
1 GCCCCAG
1053 GCCCCAG
1 GCCCCAG
1060 GCCCCAG
1 GCCCCAG
1067 GCCCC
1 GCCCC
1072 GACTCTCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.62, G:0.27, T:0.00
Consensus pattern (7 bp):
GCCCCAG
Found at i:3207 original size:2 final size:2
Alignment explanation
Indices: 3200--3225 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3190 CTTTCTCTTT
3200 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3226 GTCACCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9332 original size:6 final size:6
Alignment explanation
Indices: 9321--9349 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
9311 TAAGTATCGA
9321 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
9350 TGGCATGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:13029 original size:1 final size:1
Alignment explanation
Indices: 13023--13048 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
13013 TGTCCCTCAC
13023 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
13049 GAGAAATGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:25951 original size:3 final size:3
Alignment explanation
Indices: 25943--25984 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
25933 TATTTAACTA
25943 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
25985 TAAAAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:26480 original size:22 final size:24
Alignment explanation
Indices: 26441--26486 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
26431 TGATTAATCA
* *
26441 CCGTACATATATTAAAGATTTTCT
1 CCGTAAATATATTAAAGAATTTCT
26465 CCGTAAATATA-T-AAGAATTTCT
1 CCGTAAATATATTAAAGAATTTCT
26487 TGAATATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 1 0.05
24 10 0.50
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (24 bp):
CCGTAAATATATTAAAGAATTTCT
Found at i:26935 original size:166 final size:166
Alignment explanation
Indices: 26646--26961 Score: 517
Period size: 166 Copynumber: 1.9 Consensus size: 166
26636 TGAATCATTT
* * * * * *
26646 GTCAATTGAGAAATGACCAAAAAGTTTATTTATTTAATCCCCTTAAGAATAAAAAGTTAGGACAT
1 GTCAATTGAGAAATAACCAAAAAGTCTAGTTATTGAATCCCCTCAAGAATAAAAAGTTAGAACAT
* *
26711 TTAAGTAATCTGTCAAGTAGGTAAAGACGAAAAAAATTAGTTATCCAGCTCATCATTAATCCGGG
66 TTAAGTAATCTGTCAAGTAGGAAAAGACGAAAAAAATTAATTATCCAGCTCATCATTAATCCGGG
26776 GTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
131 GTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
*
26812 GTCAATTGAGAAATAACCAAAAAGTCTAGTTATTGAATCCCCTCAAGAATTAAAAGTTAGAACAT
1 GTCAATTGAGAAATAACCAAAAAGTCTAGTTATTGAATCCCCTCAAGAATAAAAAGTTAGAACAT
* *
26877 TTAAGTAATCTGTCAAGTGGGAAAAGACGAAAAAAATTAATTATCTC-GCTCCTCATTAATCCGG
66 TTAAGTAATCTGTCAAGTAGGAAAAGACGAAAAAAATTAATTATC-CAGCTCATCATTAATCCGG
26941 GGTAGGGATCTTTTAGTAATT
130 GGTAGGGATCTTTTAGTAATT
26962 ATACATGTTT
Statistics
Matches: 138, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
166 137 0.99
167 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (166 bp):
GTCAATTGAGAAATAACCAAAAAGTCTAGTTATTGAATCCCCTCAAGAATAAAAAGTTAGAACAT
TTAAGTAATCTGTCAAGTAGGAAAAGACGAAAAAAATTAATTATCCAGCTCATCATTAATCCGGG
GTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:27052 original size:21 final size:21
Alignment explanation
Indices: 27026--27070 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27016 AAATACTGGA
*
27026 TTGCTAAACAGCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
**
27047 TTGCTATTCACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
27068 TTG
1 TTG
27071 ACGCTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.33, G:0.13, T:0.36
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:27457 original size:33 final size:32
Alignment explanation
Indices: 27407--27524 Score: 111
Period size: 33 Copynumber: 3.6 Consensus size: 32
27397 CCCCACCAGT
27407 GCCGTCCC-CCTGGGGCGG-CTGAGCCATGGCCAA
1 GCCG-CCCTCCTGGGGCGGCCT-A-CCATGGCCAA
*
27440 GCCGCCCTCCTGGGGCGGCACTACCATGGCCAG
1 GCCGCCCTCCTGGGGCGGC-CTACCATGGCCAA
27473 GCCG-CCTCCCTGGGGCGGCCTTACCATGG--ATA
1 GCCGCCCT-CCTGGGGCGGCC-TACCATGGCCA-A
*
27505 GACCGCCCCCCTGGGGCGGC
1 G-CCGCCCTCCTGGGGCGGC
27525 ACCGGTACTA
Statistics
Matches: 74, Mismatches: 3, Indels: 16
0.80 0.03 0.17
Matches are distributed among these distances:
31 1 0.01
32 8 0.11
33 60 0.81
34 3 0.04
35 2 0.03
ACGTcount: A:0.11, C:0.42, G:0.35, T:0.13
Consensus pattern (32 bp):
GCCGCCCTCCTGGGGCGGCCTACCATGGCCAA
Found at i:27677 original size:32 final size:32
Alignment explanation
Indices: 27585--27668 Score: 150
Period size: 32 Copynumber: 2.6 Consensus size: 32
27575 AAAAAGCTTT
*
27585 GCCGCCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGA
27617 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGA
*
27649 GCCGTCCTAGTGGGGAGGCT
1 GCCGTCCTAGTGGGGCGGCT
27669 CCGCGTGGCT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.12, C:0.29, G:0.44, T:0.15
Consensus pattern (32 bp):
GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGA
Found at i:28306 original size:28 final size:28
Alignment explanation
Indices: 28266--28323 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
28256 AAAACTGAGC
*
28266 CATTGCTTTTATTCCGCACTCTCTCTGA
1 CATTGCTTTTATTCCGCACTCTCTCCGA
*
28294 CATTGCTTTTATTCCGCATTCTCTCCGA
1 CATTGCTTTTATTCCGCACTCTCTCCGA
28322 CA
1 CA
28324 ATGATCCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.16, C:0.33, G:0.10, T:0.41
Consensus pattern (28 bp):
CATTGCTTTTATTCCGCACTCTCTCCGA
Found at i:30050 original size:11 final size:12
Alignment explanation
Indices: 30016--30058 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
30006 AAGAGAGAAT
30016 CAAGGAAGATTA
1 CAAGGAAGATTA
30028 CAAGGAAGATTA
1 CAAGGAAGATTA
30040 CAAGG-AGATTA
1 CAAGGAAGATTA
*
30051 CCAGGAAG
1 CAAGGAAG
30059 GTTCCCTGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 10 0.34
12 19 0.66
ACGTcount: A:0.47, C:0.12, G:0.28, T:0.14
Consensus pattern (12 bp):
CAAGGAAGATTA
Found at i:31156 original size:30 final size:30
Alignment explanation
Indices: 31035--31482 Score: 538
Period size: 30 Copynumber: 14.6 Consensus size: 30
31025 AGTCTCCAAA
* *
31035 TGACACCAGAAGTTGTCATGATAAATCT-CCAT
1 TGACACCAGAAGTTGTCATGAT---TTTGCAAT
* * *
31067 TGACACCAGAAGTTGTCAATGGTGTTACAAT
1 TGACACCAGAAGTTGTC-ATGATTTTGCAAT
* * * *
31098 TGACACCAGAAGTTGTCAATAATCTTACAAA
1 TGACACCAGAAGTTGTC-ATGATTTTGCAAT
* * * *
31129 TGACACCAGAAGTTGTCATGGTCTTACAAA
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
* * *
31159 TGACACCAGAAGTTGTCAATAATCTTACAAT
1 TGACACCAGAAGTTGTC-ATGATTTTGCAAT
*
31190 TGACACCAAAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
*
31220 TGACACCAGAAGTTGTCATGATTTTGGAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
31250 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
31280 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
*
31310 TGACACTAGAAGTTGTCATGATTTTTGCAAT
1 TGACACCAGAAGTTGTCATGA-TTTTGCAAT
31341 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
*
31371 TGACACCAGAAATTGTCATGATTTTTGCAAT
1 TGACACCAGAAGTTGTCATGA-TTTTGCAAT
**
31402 TGACACTTGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
* ** * * * *
31432 TGATACTTGAAGATGTTATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGA-TTT-TGCAAT
31464 TGACACCAGAAGTTGTCAT
1 TGACACCAGAAGTTGTCAT
31483 ATACACCATG
Statistics
Matches: 373, Mismatches: 36, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
30 201 0.54
31 132 0.35
32 36 0.10
33 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATTTTGCAAT
Found at i:31165 original size:61 final size:60
Alignment explanation
Indices: 31035--31483 Score: 497
Period size: 61 Copynumber: 7.3 Consensus size: 60
31025 AGTCTCCAAA
* * * *
31035 TGACACCAGAAGTTGTCATGATAAATC-T-CCATTGACACCAGAAGTTGTCAATGGTGTTACAAT
1 TGACACCAGAAGTTGTC---AT-AATCTTGCAATTGACACCAGAAGTTGTC-ATGATTTTGCAAT
* * * * * *
31098 TGACACCAGAAGTTGTCAATAATCTTACAAATGACACCAGAAGTTGTCATGGTCTTACAAA
1 TGACACCAGAAGTTGTC-ATAATCTTGCAATTGACACCAGAAGTTGTCATGATTTTGCAAT
* *
31159 TGACACCAGAAGTTGTCAATAATCTTACAATTGACACCAAAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTC-ATAATCTTGCAATTGACACCAGAAGTTGTCATGATTTTGCAAT
* * *
31220 TGACACCAGAAGTTGTCATGATTTTGGAATTGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATAATCTTGCAATTGACACCAGAAGTTGTCATGATTTTGCAAT
* * *
31280 TGACACCAGAAGTTGTCATGATTTTGCAATTGACACTAGAAGTTGTCATGATTTTTGCAAT
1 TGACACCAGAAGTTGTCATAATCTTGCAATTGACACCAGAAGTTGTCATGA-TTTTGCAAT
* * *
31341 TGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAATTGTCATGATTTTTGCAAT
1 TGACACCAGAAGTTGTCATAATCTTGCAATTGACACCAGAAGTTGTCATGA-TTTTGCAAT
** * * * ** * * * *
31402 TGACACTTGAAGTTGTCATGATTTTGCAATTGATACTTGAAGATGTTATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATAATCTTGCAATTGACACCAGAAGTTGTCATGA-TTT-TGCAAT
31464 TGACACCAGAAGTTGTCATA
1 TGACACCAGAAGTTGTCATA
31484 TACACCATGA
Statistics
Matches: 349, Mismatches: 33, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
60 91 0.26
61 200 0.57
62 41 0.12
63 17 0.05
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (60 bp):
TGACACCAGAAGTTGTCATAATCTTGCAATTGACACCAGAAGTTGTCATGATTTTGCAAT
Found at i:31266 original size:121 final size:120
Alignment explanation
Indices: 31031--31482 Score: 487
Period size: 121 Copynumber: 3.7 Consensus size: 120
31021 TCAAAGTCTC
* * * *
31031 CAAATGACACCAGAAGTTGTCATGATAAATC-TCCATTGACACCAGAAGTTGTCAATGGTGTTAC
1 CAAATGACACCAGAAGTTGTCA--AT-AATCTTCAATTGACACCAGAAGTTGTC-ATGATTTTGC
* * * * *
31095 AATTGACACCAGAAGTTGTCAATAATCTTACAAATGACACCAGAAGTTGTCATGGTCTTA
62 AATTGACACCAGAAGTTGTC-ATGATTTTGCAATTGACACCAGAAGTTGTCATGATCTTA
*
31155 CAAATGACACCAGAAGTTGTCAATAATCTTACAATTGACACCAAAAGTTGTCATGATTTTGCAAT
1 CAAATGACACCAGAAGTTGTCAATAATCTT-CAATTGACACCAGAAGTTGTCATGATTTTGCAAT
* * *
31220 TGACACCAGAAGTTGTCATGATTTTGGAATTGACACCAGAAGTTGTCATGATTTTG
65 TGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATCTTA
* * * *
31276 CAATTGACACCAGAAGTTGTC-ATGATTTTGCAATTGACACTAGAAGTTGTCATGATTTTTGCAA
1 CAAATGACACCAGAAGTTGTCAATAATCTT-CAATTGACACCAGAAGTTGTCATGA-TTTTGCAA
* * *
31340 TTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAATTGTCATGATTTTTG
64 TTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGA-TCTTA
* ** * * * ** * * * *
31398 CAATTGACACTTGAAGTTGTC-ATGATTTTGCAATTGATACTTGAAGATGTTATAATTTTATTCA
1 CAAATGACACCAGAAGTTGTCAATAATCTT-CAATTGACACCAGAAGTTGTCATGA-TTT-TGCA
31462 ATTGACACCAGAAGTTGTCAT
63 ATTGACACCAGAAGTTGTCAT
31483 ATACACCATG
Statistics
Matches: 294, Mismatches: 29, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
120 29 0.10
121 113 0.38
122 87 0.30
123 43 0.15
124 22 0.07
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (120 bp):
CAAATGACACCAGAAGTTGTCAATAATCTTCAATTGACACCAGAAGTTGTCATGATTTTGCAATT
GACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATCTTA
Found at i:33597 original size:33 final size:33
Alignment explanation
Indices: 33534--33597 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
33524 ATACTGAATA
**
33534 ATATTGCCCCTGAAGAGGCACAAATTCATGAGC
1 ATATTGCCCCTGAAGAGGCACAAACCCATGAGC
* * *
33567 ATATTGCCCCTGTAGTGGCATAAACCCATGA
1 ATATTGCCCCTGAAGAGGCACAAACCCATGA
33598 AAAGATCACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (33 bp):
ATATTGCCCCTGAAGAGGCACAAACCCATGAGC
Found at i:35569 original size:120 final size:124
Alignment explanation
Indices: 35268--35582 Score: 349
Period size: 127 Copynumber: 2.5 Consensus size: 124
35258 AAAGTGCGTT
*
35268 GCACTCTTTTTCCCTTATGATCGGTTTTGTCCCACAGGGTTTTCCGACTTAAGGTTTTTAATGAG
1 GCACTCTTTTTCCCTTATGATCGGTTTTGTCCCACTGGGTTTTCCGACTTAAGGTTTTTAATGAG
* * * * * *
35333 GCAACAATAGCACATTTAGATGTAATTGTCCTGAAGACATTTACATGGACTTAATTGCTCTA
66 GCAAAAAGAGCACATGTAGA-GTAATTGTCCAGAAGACA--TAAATGGACTTAATTGATCTA
* * * **
35395 GCACTCTTTTTCCCTTCTGTTCGGTTTTGTCCCACTAGGTTTTCCGACACAAGGTTTTTAATGAG
1 GCACTCTTTTTCCCTTATGATCGGTTTTGTCCCACTGGGTTTTCCGACTTAAGGTTTTTAATGAG
* * *
35460 GCAATAAAGAGCACATGTA-A-TATTTGTCCAGAAGACA-AAATGGACTTGATATGATGTA
66 GCAA-AAAGAGCACATGTAGAGTAATTGTCCAGAAGACATAAATGGACTTAAT-TGATCTA
* * *
35518 -CTC-CTTTTT-CCTTATGA-CTGGTTTTGTCCCATTGGGTTTTCC-AGCTTAAGGTTTTTAACG
1 GCACTCTTTTTCCCTTATGATC-GGTTTTGTCCCACTGGGTTTTCCGA-CTTAAGGTTTTTAATG
35578 AGGCA
64 AGGCA
35583 CTAGCTACAT
Statistics
Matches: 161, Mismatches: 23, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
119 2 0.01
120 45 0.28
121 6 0.04
122 13 0.08
123 5 0.03
125 15 0.09
127 64 0.40
128 11 0.07
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (124 bp):
GCACTCTTTTTCCCTTATGATCGGTTTTGTCCCACTGGGTTTTCCGACTTAAGGTTTTTAATGAG
GCAAAAAGAGCACATGTAGAGTAATTGTCCAGAAGACATAAATGGACTTAATTGATCTA
Found at i:47646 original size:221 final size:213
Alignment explanation
Indices: 47250--47675 Score: 726
Period size: 221 Copynumber: 2.0 Consensus size: 213
47240 ATTGAAGTAG
*
47250 GTAACATGATGAGGTTTTTAGTTGTAGACAGCAGCATTTGGTATGTTAAAATAAGCAACAGCGAG
1 GTAACATGATGAGGTTTTTAGCTGTAGACAGCAGCATTTGGTATGTTAAAATAAGCAACAGCGAG
*
47315 GCGGTATACATTTAGATATATATAAATAGAGAAATAACAAGAAAGATGTATTTAACTCTCACTTC
66 GCGGCATACATTTAGATATATATAAATAGAGAAATAACAAGAAAGATGTATTTAACTCTCACTTC
47380 CAAATGCTGTTGGTTGAAGTTGTATTACTGCCAAAAAATCTGTCTATGTATCTCTCAACTGGCTA
131 CAAATGCTGTTGGTTGAAGTTGTATTACTGCCAAAAAATCTGTCTATGTATCTCTCAACTGGCTA
47445 TAGTAATTACATTTAGCT
196 TAGTAATTACATTTAGCT
*
47463 GTAACATGATGAGGTTTTTAGCTGTAGACAGCAGCATTTGGTATGTTAAAATAGGCAACAGCGAG
1 GTAACATGATGAGGTTTTTAGCTGTAGACAGCAGCATTTGGTATGTTAAAATAAGCAACAGCGAG
* *
47528 GCGGCGTACATTTAGATATATATAAATTAATAAATAGATAAATAACAAGAAAGATGTATTTAACT
66 GCGGCATACATTTAG----ATAT--A-T-ATAAATAGAGAAATAACAAGAAAGATGTATTTAACT
*
47593 CTCACTTGCAAATGCTGTTGGTTGAAGTTGTATTACTGCCAAAAAATCTGTCTATGTATCTCTCA
123 CTCACTTCCAAATGCTGTTGGTTGAAGTTGTATTACTGCCAAAAAATCTGTCTATGTATCTCTCA
47658 ACTGGCTATAGTAATTAC
188 ACTGGCTATAGTAATTAC
47676 CTTCACTCAT
Statistics
Matches: 199, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
213 76 0.38
217 4 0.02
219 1 0.01
220 1 0.01
221 117 0.59
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (213 bp):
GTAACATGATGAGGTTTTTAGCTGTAGACAGCAGCATTTGGTATGTTAAAATAAGCAACAGCGAG
GCGGCATACATTTAGATATATATAAATAGAGAAATAACAAGAAAGATGTATTTAACTCTCACTTC
CAAATGCTGTTGGTTGAAGTTGTATTACTGCCAAAAAATCTGTCTATGTATCTCTCAACTGGCTA
TAGTAATTACATTTAGCT
Found at i:50806 original size:32 final size:33
Alignment explanation
Indices: 50627--50797 Score: 283
Period size: 33 Copynumber: 5.2 Consensus size: 33
50617 TTTGCCCTTA
*
50627 GCCAC-GCGGAGTCTCCCCACTAGGACGGCTCT
1 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
50659 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
1 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
50692 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
1 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
* *
50725 GCCACAGCGGAGCCTCCCCACTAGGACGGCTTT
1 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
* *
50758 GCCACGGC-TAGCCGCCCCACTAGGACGGCTCT
1 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
50790 GCCACGGC
1 GCCACGGC
50798 TAGCCGCCCT
Statistics
Matches: 131, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
32 34 0.26
33 97 0.74
ACGTcount: A:0.16, C:0.42, G:0.29, T:0.13
Consensus pattern (33 bp):
GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
Done.