Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009091.1 Corchorus capsularis cultivar CVL-1 contig09112, 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: 41038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:76 original size:48 final size:49
Alignment explanation
Indices: 11--384 Score: 380
Period size: 48 Copynumber: 7.8 Consensus size: 49
1 CACCACCCGT
*
11 CCACTCTCCACCACCACCATACTACTACAAATCCCCACCACCACCATCG
1 CCACTCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCATCG
*
60 CCA-TCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACC--CG
1 CCACTCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCATCG
*
106 TCCACTCTCCTCCACCACCATACTACTACAAGTCCCCACCACCACCATCG
1 -CCACTCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCATCG
*
156 CCA-TCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCA--G
1 CCACTCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCATCG
* * * * * *
202 TCTATTCCCCTCCACCACCATACTACTACAAATCACCACCACCTCCAGTAG
1 -CCACTCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCA-TCG
** ** * * * *
253 --AGGCTCCAGCACCCACC-TACCACTACAAGTCCCCACCACCTCCATCA
1 CCACTCTCCTCCA-CCACCATACTACTACAAATCCCCACCACCACCATCG
* *
300 CCA-TCACCACCACCACCATACTACTACAAATCTCCC-CCACCACCA--G
1 CCACTCTCCTCCACCACCATACTACTACAAATC-CCCACCACCACCATCG
* * * *
346 TTCACTCTCCACCACC-CCCTACTACTACAAGTCCCCACC
1 -CCACTCTCCTCCACCACCATACTACTACAAATCCCCACC
385 TCCTCCCTCA
Statistics
Matches: 276, Mismatches: 32, Indels: 36
0.80 0.09 0.10
Matches are distributed among these distances:
46 6 0.02
47 30 0.11
48 222 0.80
49 15 0.05
50 2 0.01
51 1 0.00
ACGTcount: A:0.28, C:0.52, G:0.03, T:0.17
Consensus pattern (49 bp):
CCACTCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCATCG
Found at i:161 original size:96 final size:96
Alignment explanation
Indices: 1--244 Score: 425
Period size: 96 Copynumber: 2.5 Consensus size: 96
*
1 CACCACCCGTCCACTCTCCACCACCACCATACTACTACAAATCCCCACCACCACCATCGCCATCT
1 CACCACCCGTCCACTCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCATCGCCATCT
66 CCTCCTCCACCATACTACTACAAATCCCCAC
66 CCTCCTCCACCATACTACTACAAATCCCCAC
*
97 CACCACCCGTCCACTCTCCTCCACCACCATACTACTACAAGTCCCCACCACCACCATCGCCATCT
1 CACCACCCGTCCACTCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCATCGCCATCT
162 CCTCCTCCACCATACTACTACAAATCCCCAC
66 CCTCCTCCACCATACTACTACAAATCCCCAC
* * * * *
193 CACCACCAGTCTATTCCCCTCCACCACCATACTACTACAAATCACCACCACC
1 CACCACCCGTCCACTCTCCTCCACCACCATACTACTACAAATCCCCACCACC
245 TCCAGTAGAG
Statistics
Matches: 140, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 140 1.00
ACGTcount: A:0.28, C:0.52, G:0.02, T:0.17
Consensus pattern (96 bp):
CACCACCCGTCCACTCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCATCGCCATCT
CCTCCTCCACCATACTACTACAAATCCCCAC
Found at i:278 original size:144 final size:143
Alignment explanation
Indices: 15--390 Score: 456
Period size: 144 Copynumber: 2.6 Consensus size: 143
5 ACCCGTCCAC
* *
15 TCTCCACCACCACCATACTACTACAAATCCCCACCACCACCA-TCGCCATCTCCTCCTCCACCAT
1 TCTCCACCACCACCATACTACTACAAATCCCCACCACCACCAGT--CTATCTCCTCCACCACCAT
* * * * * *
79 ACTACTACAAATCCCCACCACCACCCGTCCACTCTCCTCCACCACCATACTACTACAAGTCCCCA
64 ACTACTACAAATCCCCACCACCTCCAGTACACGCTCCACCACCACCATACCACTACAAGTCCCCA
*
144 CCACCACCATCGCCA
129 CCACCACCATCACCA
* * *
159 TCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCAGTCTATTCCCCTCCACCACCATA
1 TCTCCACCACCACCATACTACTACAAATCCCCACCACCACCAGTCTA-TCTCCTCCACCACCATA
* * * *
224 CTACTACAAATCACCACCACCTCCAGTAGAGGCTCCAGCACCCACC-TACCACTACAAGTCCCCA
65 CTACTACAAATCCCCACCACCTCCAGTACACGCTCCACCA-CCACCATACCACTACAAGTCCCCA
*
288 CCACCTCCATCACCA
129 CCACCACCATCACCA
* * *
303 TCACCACCACCACCATACTACTACAAATCTCCC-CCACCACCAGT-TCACTCTCCACCACC-CCC
1 TCTCCACCACCACCATACTACTACAAATC-CCCACCACCACCAGTCT-A-TCTCCTCCACCACCA
* *
365 TACTACTACAAGTCCCCACCTCCTCC
63 TACTACTACAAATCCCCACCACCTCC
391 CTCACCCTCA
Statistics
Matches: 200, Mismatches: 27, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
143 28 0.14
144 163 0.81
145 9 0.05
ACGTcount: A:0.28, C:0.52, G:0.03, T:0.17
Consensus pattern (143 bp):
TCTCCACCACCACCATACTACTACAAATCCCCACCACCACCAGTCTATCTCCTCCACCACCATAC
TACTACAAATCCCCACCACCTCCAGTACACGCTCCACCACCACCATACCACTACAAGTCCCCACC
ACCACCATCACCA
Found at i:416 original size:95 final size:96
Alignment explanation
Indices: 18--441 Score: 303
Period size: 96 Copynumber: 4.4 Consensus size: 96
8 CGTCCACTCT
* * * * *
18 CCACCACCACCATACTACTACAAATCCCCACCACCACCA-T-CGCCATCTCCTCC-TCCACCATA
1 CCACCACCACCATACTACTACAAATCACCACCACCACCAGTAC-AC-GCTCCACCACCCACC-TA
* * * * *
80 CTACTACAAATCCCCACCACCACC--CGTCCACTCT
63 CCACTACAAGTCCCCACCACCTCCATC-ACCA-TCA
* * * * * * *
114 CCTCCACCACCATACTACTACAAGTCCCCACCACCACCA-T-CGCCATCTCCTCC-TCCACCATA
1 CCACCACCACCATACTACTACAAATCACCACCACCACCAGTAC-AC-GCTCCACCACCCACC-TA
* * * * *
176 CTACTACAAATCCCCACCACCACCAGTCTA--TTCC
63 CCACTACAAGTCCCCACCACCTCCA-TC-ACCATCA
* * * * *
210 CCTCCACCACCATACTACTACAAATCACCACCACCTCCAGTAGAGGCTCCAGCACCCACCTACCA
1 CCACCACCACCATACTACTACAAATCACCACCACCACCAGTACACGCTCCACCACCCACCTACCA
275 CTACAAGTCCCCACCACCTCCATCACCATCA
66 CTACAAGTCCCCACCACCTCCATCACCATCA
* * * * *
306 CCACCACCACCATACTACTACAAATCTCCCCCACCACCAGTTCACTCTCCACCACCC-CCTACTA
1 CCACCACCACCATACTACTACAAATCACCACCACCACCAGTACACGCTCCACCACCCACCTACCA
* * *
370 CTACAAGTCCCCACCTCCTCCCTCACCCTCA
66 CTACAAGTCCCCACCACCTCCATCACCATCA
* * * * * * *
401 CCCCCTCCCCCATACTACTACCACTCACCTCCCCCACCAGT
1 CCACCACCACCATACTACTACAAATCACCACCACCACCAGT
442 GAAGTCACCT
Statistics
Matches: 278, Mismatches: 42, Indels: 17
0.82 0.12 0.05
Matches are distributed among these distances:
94 1 0.00
95 69 0.25
96 201 0.72
97 6 0.02
99 1 0.00
ACGTcount: A:0.27, C:0.53, G:0.03, T:0.17
Consensus pattern (96 bp):
CCACCACCACCATACTACTACAAATCACCACCACCACCAGTACACGCTCCACCACCCACCTACCA
CTACAAGTCCCCACCACCTCCATCACCATCA
Found at i:10498 original size:11 final size:11
Alignment explanation
Indices: 10482--10525 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
10472 TATACTATAT
10482 CTAATTAATAA
1 CTAATTAATAA
*
10493 CTAATTAATAT
1 CTAATTAATAA
*
10504 CTAATTAATAG
1 CTAATTAATAA
*
10515 TTAATTAATAA
1 CTAATTAATAA
10526 TGAATAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (11 bp):
CTAATTAATAA
Found at i:10506 original size:22 final size:22
Alignment explanation
Indices: 10478--10524 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
10468 CCATTATACT
10478 ATATCTAATTAATAACTAATTA
1 ATATCTAATTAATAACTAATTA
**
10500 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAACTAATTA
10522 ATA
1 ATA
10525 ATGAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAACTAATTA
Found at i:11474 original size:2 final size:2
Alignment explanation
Indices: 11467--11494 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11457 AAATCTCACT
11467 TA 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 TA
11495 AAACTCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12110 original size:2 final size:2
Alignment explanation
Indices: 12103--12153 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
12093 TAAACAATTT
12103 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12145 TC TC -C TC TC
1 TC TC TC TC TC
12154 ATTTCATTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:13736 original size:137 final size:138
Alignment explanation
Indices: 13483--13760 Score: 495
Period size: 137 Copynumber: 2.0 Consensus size: 138
13473 AGGGCTTTTC
*
13483 TAAAATTATCTGTTAATTTATGATTCAATAATGTTGCATATATCCTAGTAATTGAATAGAAATAA
1 TAAAATTATCTGTTAAGTTATGATTCAATAATGTTGCA-ATATCCTAGTAATTGAATAGAAATAA
13548 AGAGGCCAACCAAGGAAGAACAAGCAGTATTTGAAGAGTCCGAGTTTTCTTGAAGGTGAAAAAGG
65 AGAGGCCAACCAAGGAAGAACAAGCAGTATTTGAAGAGTCCGAGTTTTCTTGAAGGTGAAAAAGG
13613 GATGATTAA
130 GATGATTAA
*
13622 TAAACTTATCTGTTAAGTTATGATTCAATAATGTTGC-ATATCCTAGTAATTGAATAGAAATAAA
1 TAAAATTATCTGTTAAGTTATGATTCAATAATGTTGCAATATCCTAGTAATTGAATAGAAATAAA
* * *
13686 GAGGCCAACCAAGGAAGACCAAGCAGTATTTGAAGAGTCTGAGTTTTCTTGAAGGTGAAAGAGGG
66 GAGGCCAACCAAGGAAGAACAAGCAGTATTTGAAGAGTCCGAGTTTTCTTGAAGGTGAAAAAGGG
13751 ATGATTAA
131 ATGATTAA
13759 TA
1 TA
13761 GAATCCAGCT
Statistics
Matches: 134, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
137 99 0.74
139 35 0.26
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.29
Consensus pattern (138 bp):
TAAAATTATCTGTTAAGTTATGATTCAATAATGTTGCAATATCCTAGTAATTGAATAGAAATAAA
GAGGCCAACCAAGGAAGAACAAGCAGTATTTGAAGAGTCCGAGTTTTCTTGAAGGTGAAAAAGGG
ATGATTAA
Found at i:14243 original size:2 final size:2
Alignment explanation
Indices: 14236--14262 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14226 TATTGTACCT
14236 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
14263 TCTTTTGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:18299 original size:33 final size:33
Alignment explanation
Indices: 18270--18686 Score: 458
Period size: 33 Copynumber: 12.6 Consensus size: 33
18260 CCCAGCCGCC
* *
18270 TGCTAATCCATATGGCCAACCTGGACAGCCAAG
1 TGCTAATCCTTATGGCCAACCTGCACAGCCAAG
* *
18303 TGCTAATCCTTACGGCCAACCTGGACAGCCAAG
1 TGCTAATCCTTATGGCCAACCTGCACAGCCAAG
* * *
18336 TGCCAATCCATATGGCCAACCTGGACAGCCAAG
1 TGCTAATCCTTATGGCCAACCTGCACAGCCAAG
* * * * *
18369 TGCCAATCCATACGGCCAACCTGGACAGCCAAC
1 TGCTAATCCTTATGGCCAACCTGCACAGCCAAG
* * * * *
18402 TGCCAATCCATACGGCCAGCCTGCACAGCCAAA
1 TGCTAATCCTTATGGCCAACCTGCACAGCCAAG
* * * * * *
18435 TGCCAATCCATACGGCCAGCCTGCACTGCCAAA
1 TGCTAATCCTTATGGCCAACCTGCACAGCCAAG
* * * * * *
18468 TGCCAATCCCTACGTCCAGCCTGCACAGCCAAA
1 TGCTAATCCTTATGGCCAACCTGCACAGCCAAG
* * *
18501 TGCTAATCCCTACGGTCAACCTGCACAGCCCAA-
1 TGCTAATCCTTATGGCCAACCTGCACAG-CCAAG
* *
18534 TGCCAATCCTTATGGCCAACCTGCACAGCCGAG
1 TGCTAATCCTTATGGCCAACCTGCACAGCCAAG
* * *
18567 TGCTAATCCTTATGGCCAACCTTCACACCCCAG
1 TGCTAATCCTTATGGCCAACCTGCACAGCCAAG
* *
18600 TGCTAATCCTTATGGCCAACCTGCACACCCCAG
1 TGCTAATCCTTATGGCCAACCTGCACAGCCAAG
*
18633 TGCTAATCCTTATGGCCAACCTGCACAGCCGAG
1 TGCTAATCCTTATGGCCAACCTGCACAGCCAAG
18666 TGCTAATCCTTATGGCCAACC
1 TGCTAATCCTTATGGCCAACC
18687 CACACAACCA
Statistics
Matches: 352, Mismatches: 30, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
32 3 0.01
33 345 0.98
34 4 0.01
ACGTcount: A:0.27, C:0.37, G:0.18, T:0.18
Consensus pattern (33 bp):
TGCTAATCCTTATGGCCAACCTGCACAGCCAAG
Found at i:19331 original size:12 final size:12
Alignment explanation
Indices: 19313--19357 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
19303 GATGGGTTCT
19313 GGAATGGGTATG
1 GGAATGGGTATG
* *
19325 GGTATGGGCATG
1 GGAATGGGTATG
* *
19337 GGCATGGGGATG
1 GGAATGGGTATG
19349 GGAATGGGT
1 GGAATGGGT
19358 GGTGCTCCTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.20, C:0.04, G:0.53, T:0.22
Consensus pattern (12 bp):
GGAATGGGTATG
Found at i:19337 original size:18 final size:18
Alignment explanation
Indices: 19313--19357 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
19303 GATGGGTTCT
*
19313 GGAATGGGTATGGGTATG
1 GGAATGGGTATGGGGATG
* *
19331 GGCATGGGCATGGGGATG
1 GGAATGGGTATGGGGATG
19349 GGAATGGGT
1 GGAATGGGT
19358 GGTGCTCCTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.04, G:0.53, T:0.22
Consensus pattern (18 bp):
GGAATGGGTATGGGGATG
Found at i:23894 original size:15 final size:15
Alignment explanation
Indices: 23874--23905 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
23864 GGAGACACCT
23874 ATCAGTGAAGTTTTA
1 ATCAGTGAAGTTTTA
23889 ATCAGTGAAGTTTTA
1 ATCAGTGAAGTTTTA
23904 AT
1 AT
23906 AATAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (15 bp):
ATCAGTGAAGTTTTA
Found at i:26394 original size:24 final size:25
Alignment explanation
Indices: 26344--26411 Score: 129
Period size: 25 Copynumber: 2.8 Consensus size: 25
26334 TAATGCTAAA
26344 GAAGAAATCACTAATTTTTTTTAGG
1 GAAGAAATCACTAATTTTTTTTAGG
26369 GAAGAAATCACTAATTTTTTTT-GG
1 GAAGAAATCACTAATTTTTTTTAGG
26393 GAAGAAATCACTAATTTTT
1 GAAGAAATCACTAATTTTT
26412 CATACAATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 21 0.49
25 22 0.51
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.40
Consensus pattern (25 bp):
GAAGAAATCACTAATTTTTTTTAGG
Found at i:29353 original size:24 final size:24
Alignment explanation
Indices: 29311--29356 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
29301 CAAAAGTTCA
***
29311 TATATTATATTATGGAGTATTAAT
1 TATATTATATTACAAAGTATTAAT
29335 TATATTATATTACAAAGTATTA
1 TATATTATATTACAAAGTATTA
29357 TTGAAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (24 bp):
TATATTATATTACAAAGTATTAAT
Found at i:34638 original size:35 final size:35
Alignment explanation
Indices: 34573--34639 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
34563 TTTAGTTAAT
**
34573 TGATCTAGGGTGATCTTTCTTCAGTGAATTTCGGC
1 TGATCTAGGGTGATCTTTCTTCAGCAAATTTCGGC
34608 TGATCTAGGGTGATCTTTCTAT-AGCAAATTTC
1 TGATCTAGGGTGATCTTTCT-TCAGCAAATTTC
34640 AATTGACCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 28 0.97
36 1 0.03
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.40
Consensus pattern (35 bp):
TGATCTAGGGTGATCTTTCTTCAGCAAATTTCGGC
Found at i:34653 original size:99 final size:97
Alignment explanation
Indices: 34537--34795 Score: 315
Period size: 99 Copynumber: 2.6 Consensus size: 97
34527 TTCTTTAGAC
* * * *
34537 TTTCAGTTGACCTAGGGCGGTCCATCTTTAGTTAATTGATCTAGGGTGATCTTTCTTCAGTGAAT
1 TTTCAATTGACCAAGGGCGGTCCATCTTAAGTTAATTGATCCAGGGTGATCTTTCTTCAGTGAAT
*
34602 TTCGGC-TGATCTAGGGTGATCTTTCTATAGCA-AA
66 CTC-GCTTGATCTAGGGTGA--TTTCTATA-CATAA
* * * ** *
34636 TTTCAATTGACCCAGGGCGGTCCATGTTCAGTTAATTGATCCAGGGCAATCTTTCTTCAGTGAGT
1 TTTCAATTGACCAAGGGCGGTCCATCTTAAGTTAATTGATCCAGGGTGATCTTTCTTCAGTGAAT
*
34701 CTCGCTTGATCTAGGGTGATTTCTCTACATTAA
66 CTCGCTTGATCTAGGGTGATTTCTATACA-TAA
* * *
34734 TTTCAAACTGACCAAGGGCGGTCCATCTCAAGTTAATTGATCCAGGGTGATCTTTTTTCAGT
1 TTTC-AATTGACCAAGGGCGGTCCATCTTAAGTTAATTGATCCAGGGTGATCTTTCTTCAGT
34796 TTATTTCAAT
Statistics
Matches: 138, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
96 2 0.01
97 7 0.05
98 8 0.06
99 121 0.88
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (97 bp):
TTTCAATTGACCAAGGGCGGTCCATCTTAAGTTAATTGATCCAGGGTGATCTTTCTTCAGTGAAT
CTCGCTTGATCTAGGGTGATTTCTATACATAA
Found at i:34839 original size:63 final size:62
Alignment explanation
Indices: 34706--34927 Score: 220
Period size: 64 Copynumber: 3.5 Consensus size: 62
34696 TGAGTCTCGC
* * *
34706 TTGATCTAGGGTGAT-TTCTCTACA-TTAATTTCAAACTGACCAAGGGCGGTCCATCTCAAGTTA
1 TTGATCCAGGGTGATCTT-TCTTCAGTTAATTTC-AA-TGACCAAGGGCGGTCCATCT-TAGTTA
34769 A
62 A
* * *
34770 TTGATCCAGGGTGATCTTTTTTCAGTTTATTTCAATTGACCTAGGGC-GTCCATCATTAGTTAA
1 TTGATCCAGGGTGATCTTTCTTCAGTTAATTTCAA-TGACCAAGGGCGGTCCATC-TTAGTTAA
* * * *
34833 TTGATCCAGGGTGGTCATTCTGCAGTTAAGGTTT-ACA-GACCCAGGGCGGTCCATCTTAAGTTA
1 TTGATCCAGGGTGATCTTTCTTCAGTTAA--TTTCA-ATGACCAAGGGCGGTCCATCTT-AGTTA
34896 A
62 A
*
34897 TTGATCCAGGGCGATCTTTCTTCAGTTAATT
1 TTGATCCAGGGTGATCTTTCTTCAGTTAATT
34928 GGTCCAGGGC
Statistics
Matches: 133, Mismatches: 17, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
62 2 0.02
63 48 0.36
64 70 0.53
65 13 0.10
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (62 bp):
TTGATCCAGGGTGATCTTTCTTCAGTTAATTTCAATGACCAAGGGCGGTCCATCTTAGTTAA
Found at i:34946 original size:29 final size:29
Alignment explanation
Indices: 34873--34949 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
34863 GTTTACAGAC
* *
34873 CCAGGGCGGTCCA-TCTTAAGTTAATTGAT
1 CCAGGGC-GACCATTCTTCAGTTAATTGAT
* * *
34902 CCAGGGCGATCTTTCTTCAGTTAATTGGT
1 CCAGGGCGACCATTCTTCAGTTAATTGAT
34931 CCAGGGCGACCATTCTTCA
1 CCAGGGCGACCATTCTTCA
34950 ATTTACTTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 2 0.05
29 38 0.95
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (29 bp):
CCAGGGCGACCATTCTTCAGTTAATTGAT
Found at i:34993 original size:8 final size:8
Alignment explanation
Indices: 34980--35025 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
34970 GTGGTTTTTC
34980 TTCAATTA
1 TTCAATTA
34988 TTCAATTA
1 TTCAATTA
**
34996 TTCAATGC
1 TTCAATTA
*
35004 TTCAATTC
1 TTCAATTA
*
35012 TCCAATTA
1 TTCAATTA
35020 TTCAAT
1 TTCAAT
35026 GCTTCAATCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.46
Consensus pattern (8 bp):
TTCAATTA
Found at i:35006 original size:24 final size:24
Alignment explanation
Indices: 34979--35057 Score: 122
Period size: 24 Copynumber: 3.3 Consensus size: 24
34969 GGTGGTTTTT
* *
34979 CTTCAATTATTCAATTATTCAATG
1 CTTCAATTCTCCAATTATTCAATG
35003 CTTCAATTCTCCAATTATTCAATG
1 CTTCAATTCTCCAATTATTCAATG
* *
35027 CTTCAATCCTCCAACTATTCAATG
1 CTTCAATTCTCCAATTATTCAATG
35051 CTTCAAT
1 CTTCAAT
35058 GACCTAGGGT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.41
Consensus pattern (24 bp):
CTTCAATTCTCCAATTATTCAATG
Found at i:35033 original size:16 final size:16
Alignment explanation
Indices: 34988--35057 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 16
34978 TCTTCAATTA
34988 TTCAATTATTCAATGC
1 TTCAATTATTCAATGC
* * **
35004 TTCAATTCTCCAATTA
1 TTCAATTATTCAATGC
** *
35020 TTCAATGCTTCAATCC
1 TTCAATTATTCAATGC
* *
35036 TCCAACTATTCAATGC
1 TTCAATTATTCAATGC
35052 TTCAAT
1 TTCAAT
35058 GACCTAGGGT
Statistics
Matches: 39, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.40
Consensus pattern (16 bp):
TTCAATTATTCAATGC
Found at i:35113 original size:36 final size:36
Alignment explanation
Indices: 35063--35440 Score: 245
Period size: 36 Copynumber: 10.6 Consensus size: 36
35053 TCAATGACCT
* * * *
35063 AGGGTGGCCTTTCTTCAATTCAGTCTGGAATGATCG
1 AGGGTGGTCGTTCTTCAGTTAAGTCTGGAATGATCG
* * ** * * *
35099 AGGGTAGTCGTTCTTCAGTTTA-T-TTCAGTTGACCC
1 AGGGTGGTCGTTCTTCAGTTAAGTCTGGA-ATGATCG
* * *
35134 AGGGTGGTCTTTCTTCAGTTTAAGTC-AGAACGATCG
1 AGGGTGGTCGTTCTTCAG-TTAAGTCTGGAATGATCG
* *
35170 AGGGTGGTCGTTCTTTAGTTCAGT-TCGGAATGATCG
1 AGGGTGGTCGTTCTTCAGTTAAGTCT-GGAATGATCG
** * * * *
35206 AGGGTGGTCGTTCTTCAGTCTATTTC-AG-TTGACCC
1 AGGGTGGTCGTTCTTCAGT-TAAGTCTGGAATGATCG
*
35241 AGGGTGGTCATTCTTCAGTTTAAGTC-GGAATGATCG
1 AGGGTGGTCGTTCTTCAG-TTAAGTCTGGAATGATCG
* * *
35277 AGGGTGGTCGTTCGTCAGTTAAGTCCGGAACGATCG
1 AGGGTGGTCGTTCTTCAGTTAAGTCTGGAATGATCG
* * * * * * * *
35313 AGGGTGGTCGTTCTTCAGTTTATTTTAG-TTAACCC
1 AGGGTGGTCGTTCTTCAGTTAAGTCTGGAATGATCG
* **
35348 AGGGTGGTCTTTCTTCAGTTTGCGT-TGGAATGATCG
1 AGGGTGGTCGTTCTTCAG-TTAAGTCTGGAATGATCG
* *
35384 AGGGTGGTCGTTCTTCAGTTTAGT-TCGGAATGATCC
1 AGGGTGGTCGTTCTTCAGTTAAGTCT-GGAATGATCG
* **
35420 AAGGTGGTTTTTCTTCAGTTA
1 AGGGTGGTCGTTCTTCAGTTA
35441 CTTATTCTAG
Statistics
Matches: 258, Mismatches: 70, Indels: 28
0.72 0.20 0.08
Matches are distributed among these distances:
34 2 0.01
35 85 0.33
36 167 0.65
37 4 0.02
ACGTcount: A:0.18, C:0.17, G:0.29, T:0.36
Consensus pattern (36 bp):
AGGGTGGTCGTTCTTCAGTTAAGTCTGGAATGATCG
Found at i:35146 original size:71 final size:72
Alignment explanation
Indices: 35055--35436 Score: 285
Period size: 71 Copynumber: 5.3 Consensus size: 72
35045 TCAATGCTTC
* * *
35055 AATGACCTAGGGTGGCCTTTCTTCAATTCAGTCTGGAATGATCGAGGGTAGTCGTTCTTCAGTTT
1 AATGACCCAGGGTGGTCTTTCTTCAATTCAGTCTGGAATGATCGAGGGTGGTCGTTCTTCAGTTT
35120 ATTTCAG
66 ATTTCAG
* * * * * *
35127 -TTGACCCAGGGTGGTCTTTCTTCAGTTTAAGTC-AGAACGATCGAGGGTGGTCGTTCTTTAGTT
1 AATGACCCAGGGTGGTCTTTCTTCA-ATTCAGTCTGGAATGATCGAGGGTGGTCGTTCTTCAGTT
* * *
35190 CAGTTCGG
65 TATTTCAG
* * * * ** * * * *
35198 AATGATCGAGGGTGGTCGTTCTTC-AGTCTA-T-TTCAGTTGACCCAGGGTGGTCATTCTTCAGT
1 AATGACCCAGGGTGGTCTTTCTTCAATTC-AGTCTGGA-ATGATCGAGGGTGGTCGTTCTTCAGT
** *
35260 TTAAGTCGG
64 TTATTTCAG
* * * * * * * *
35269 AATGATCGAGGGTGGTCGTTCGTCAGTTAAGTCCGGAACGATCGAGGGTGGTCGTTCTTCAGTTT
1 AATGACCCAGGGTGGTCTTTCTTCAATTCAGTCTGGAATGATCGAGGGTGGTCGTTCTTCAGTTT
*
35334 ATTTTAG
66 ATTTCAG
* * *
35341 -TTAACCCAGGGTGGTCTTTCTTCAGTTTGC-GT-TGGAATGATCGAGGGTGGTCGTTCTTCAGT
1 AATGACCCAGGGTGGTCTTTCTTCA-ATT-CAGTCTGGAATGATCGAGGGTGGTCGTTCTTCAGT
* *
35403 TTAGTTCGG
64 TTATTTCAG
* * *
35412 AATGATCCAAGGTGGTTTTTCTTCA
1 AATGACCCAGGGTGGTCTTTCTTCA
35437 GTTACTTATT
Statistics
Matches: 235, Mismatches: 64, Indels: 22
0.73 0.20 0.07
Matches are distributed among these distances:
70 3 0.01
71 155 0.66
72 76 0.32
73 1 0.00
ACGTcount: A:0.18, C:0.17, G:0.29, T:0.36
Consensus pattern (72 bp):
AATGACCCAGGGTGGTCTTTCTTCAATTCAGTCTGGAATGATCGAGGGTGGTCGTTCTTCAGTTT
ATTTCAG
Found at i:35249 original size:107 final size:107
Alignment explanation
Indices: 35063--35439 Score: 531
Period size: 107 Copynumber: 3.5 Consensus size: 107
35053 TCAATGACCT
* * * *
35063 AGGGTGGCCTTTCTTCAATTCAG-TCTGGAATGATCGAGGGTAGTCGTTCTTCAGTTTATTTCAG
1 AGGGTGGTCGTTCTTCAGTTCAGTTC-GGAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAG
* *
35127 TTGACCCAGGGTGGTCTTTCTTCAGTTTAAGTCAGAACGATCG
65 TTGACCCAGGGTGGTCTTTCTTCAGTTTAAGTCGGAATGATCG
* *
35170 AGGGTGGTCGTTCTTTAGTTCAGTTCGGAATGATCGAGGGTGGTCGTTCTTCAGTCTATTTCAGT
1 AGGGTGGTCGTTCTTCAGTTCAGTTCGGAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAGT
*
35235 TGACCCAGGGTGGTCATTCTTCAGTTTAAGTCGGAATGATCG
66 TGACCCAGGGTGGTCTTTCTTCAGTTTAAGTCGGAATGATCG
* * * * *
35277 AGGGTGGTCGTTCGTCAGTTAAGTCCGGAACGATCGAGGGTGGTCGTTCTTCAGTTTATTTTAGT
1 AGGGTGGTCGTTCTTCAGTTCAGTTCGGAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAGT
* ** *
35342 TAACCCAGGGTGGTCTTTCTTCAGTTTGCGTTGGAATGATCG
66 TGACCCAGGGTGGTCTTTCTTCAGTTTAAGTCGGAATGATCG
* * * **
35384 AGGGTGGTCGTTCTTCAGTTTAGTTCGGAATGATCCAAGGTGGTTTTTCTTCAGTT
1 AGGGTGGTCGTTCTTCAGTTCAGTTCGGAATGATCGAGGGTGGTCGTTCTTCAGTT
35440 ACTTATTCTA
Statistics
Matches: 240, Mismatches: 29, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
107 238 0.99
108 2 0.01
ACGTcount: A:0.18, C:0.17, G:0.29, T:0.36
Consensus pattern (107 bp):
AGGGTGGTCGTTCTTCAGTTCAGTTCGGAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAGT
TGACCCAGGGTGGTCTTTCTTCAGTTTAAGTCGGAATGATCG
Found at i:36442 original size:18 final size:20
Alignment explanation
Indices: 36421--36463 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
36411 GATGAAGAAT
36421 AAAAAGAA-G-AAAAGAAAA
1 AAAAAGAAGGAAAAAGAAAA
36439 AAAAAGAAGGAAAAAGAAAA
1 AAAAAGAAGGAAAAAGAAAA
36459 AAAAA
1 AAAAA
36464 ACGCAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.35
19 1 0.04
20 14 0.61
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAAGAAGGAAAAAGAAAA
Found at i:36445 original size:10 final size:10
Alignment explanation
Indices: 36430--36463 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
36420 TAAAAAGAAG
36430 AAAAGAAAAA
1 AAAAGAAAAA
**
36440 AAAAGAAGGA
1 AAAAGAAAAA
36450 AAAAGAAAAA
1 AAAAGAAAAA
36460 AAAA
1 AAAA
36464 ACGCAATTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:37948 original size:235 final size:235
Alignment explanation
Indices: 37537--38006 Score: 859
Period size: 235 Copynumber: 2.0 Consensus size: 235
37527 CTATATCTAT
*
37537 ATATTATATAAGTCTAAACTTCAAAAACTTTGACCTGAAATATCTAAAATACCATTTTTAACATA
1 ATATTATATAAGTCTAAACTTCAAAAACCTTGACCTGAAATATCTAAAATACCATTTTTAACATA
*
37602 AAGTTTTAGTTTTAAGTTTGAATGGTTAATAGGTAATTTAATATAAAAGGAAATATATATCTTCT
66 AAGTTTTAGTTTTAAGTTTAAATGGTTAATAGGTAATTTAATATAAAAGGAAATATATATCTTCT
* * *
37667 TAAACTTTTATTTAATTTCAGTCTCTTAATATCTAAAATAATTAAAGCTTACAGATACTATTATT
131 TAAACTTTTATTTAATTTCAATCTCTTAATATCTAAAAAAATTAAAGCTTACAAATACTATTATT
*
37732 ATTAGGTTAATTTTACGTTTTCTCAAAAAGAAAAAGCTAA
196 ATTAGGTTAATTCTACGTTTTCTCAAAAAGAAAAAGCTAA
* *
37772 ATATTATATAAGTCTAAACTTTAAAAACCTTGACCTGAAATATCTAAAATACCCTTTTTAACATA
1 ATATTATATAAGTCTAAACTTCAAAAACCTTGACCTGAAATATCTAAAATACCATTTTTAACATA
37837 AAGTTTTAGTTTTAAGTTTAAATGGTTAATAGGTAATTTAATATAAAAGGAAATATATATCTTCT
66 AAGTTTTAGTTTTAAGTTTAAATGGTTAATAGGTAATTTAATATAAAAGGAAATATATATCTTCT
37902 TAAACTTTTATTTAATTTCAATCTCTTAATATCTAAAAAAATTAAAGCTTACAAATACTATTATT
131 TAAACTTTTATTTAATTTCAATCTCTTAATATCTAAAAAAATTAAAGCTTACAAATACTATTATT
*
37967 ATTAGGTTAATTCTACGTTTTCTCAAAAAGAAAAGGCTAA
196 ATTAGGTTAATTCTACGTTTTCTCAAAAAGAAAAAGCTAA
38007 TTTTATGTTA
Statistics
Matches: 226, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
235 226 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.40
Consensus pattern (235 bp):
ATATTATATAAGTCTAAACTTCAAAAACCTTGACCTGAAATATCTAAAATACCATTTTTAACATA
AAGTTTTAGTTTTAAGTTTAAATGGTTAATAGGTAATTTAATATAAAAGGAAATATATATCTTCT
TAAACTTTTATTTAATTTCAATCTCTTAATATCTAAAAAAATTAAAGCTTACAAATACTATTATT
ATTAGGTTAATTCTACGTTTTCTCAAAAAGAAAAAGCTAA
Found at i:40724 original size:2 final size:2
Alignment explanation
Indices: 40717--40742 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40707 TGATAACATC
40717 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
40743 CTTTTTTAAT
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):
AT
Done.