Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011413.1 Corchorus capsularis cultivar CVL-1 contig11434, 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: 72221
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7084 original size:33 final size:34
Alignment explanation
Indices: 7019--7103 Score: 111
Period size: 33 Copynumber: 2.5 Consensus size: 34
7009 AAGGGAGCTT
*
7019 AAAAAGACCATTCATTATGTAGAAATAATAAAAAA
1 AAAAAGACCATTCATT-TGCAGAAATAATAAAAAA
*
7054 AAAAAGACCATTCATTTGCA-AAA-AAGTAAAAAT
1 AAAAAGACCATTCATTTGCAGAAATAA-TAAAAAA
*
7087 ACAAAGACCATTCATTT
1 AAAAAGACCATTCATTT
7104 ATTCCCACGT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
32 2 0.04
33 25 0.54
34 3 0.07
35 16 0.35
ACGTcount: A:0.55, C:0.13, G:0.08, T:0.24
Consensus pattern (34 bp):
AAAAAGACCATTCATTTGCAGAAATAATAAAAAA
Found at i:9267 original size:7 final size:7
Alignment explanation
Indices: 9255--9303 Score: 53
Period size: 7 Copynumber: 6.6 Consensus size: 7
9245 TCATGAATTA
9255 AAAAAAT
1 AAAAAAT
9262 AAAAAAT
1 AAAAAAT
9269 AAAAAAT
1 AAAAAAT
9276 AAAATAAAAT
1 --AA-AAAAT
*
9286 AAAAAAG
1 AAAAAAT
*
9293 AAACAAT
1 AAAAAAT
9300 AAAA
1 AAAA
9304 TTGTCCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 26 0.74
8 2 0.06
9 2 0.06
10 5 0.14
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:9285 original size:24 final size:24
Alignment explanation
Indices: 9257--9304 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
9247 ATGAATTAAA
*
9257 AAAATAAAAAATAAAAAATAAAAT
1 AAAATAAAAAAGAAAAAATAAAAT
*
9281 AAAATAAAAAAGAAACAATAAAAT
1 AAAATAAAAAAGAAAAAATAAAAT
9305 TGTCCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (24 bp):
AAAATAAAAAAGAAAAAATAAAAT
Found at i:9291 original size:19 final size:20
Alignment explanation
Indices: 9255--9304 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
9245 TCATGAATTA
9255 AAAAAATAAAA-AATAAAA-
1 AAAAAATAAAATAATAAAAG
9273 AATAAAATAAAATAA-AAAAG
1 AA-AAAATAAAATAATAAAAG
*
9293 AAACAATAAAAT
1 AAAAAATAAAAT
9305 TGTCCAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.07
19 22 0.79
20 4 0.14
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAAAATAAAATAATAAAAG
Found at i:21040 original size:13 final size:13
Alignment explanation
Indices: 21022--21046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21012 AGGGTAGTAA
21022 TATAAAATAATAT
1 TATAAAATAATAT
21035 TATAAAATAATA
1 TATAAAATAATA
21047 AGGACAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TATAAAATAATAT
Found at i:25665 original size:18 final size:18
Alignment explanation
Indices: 25638--25676 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25628 ATTCTGTTGT
25638 AGAAAATGAAGAAGAA-GA
1 AGAAAATGAAG-AGAATGA
*
25656 AGAAAGTGAAGAGAATGA
1 AGAAAATGAAGAGAATGA
25674 AGA
1 AGA
25677 GGAAGCTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.08
Consensus pattern (18 bp):
AGAAAATGAAGAGAATGA
Found at i:27838 original size:22 final size:22
Alignment explanation
Indices: 27796--27838 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
27786 TCATATCAGA
* *
27796 ATGTTAAATTTTGATCATTTTC
1 ATGTTAAAGTTTGAACATTTTC
27818 ATGTT-AAGTTTGAACACTTTT
1 ATGTTAAAGTTTGAACA-TTTT
27839 AGTGTTGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.51
Consensus pattern (22 bp):
ATGTTAAAGTTTGAACATTTTC
Found at i:29578 original size:44 final size:44
Alignment explanation
Indices: 29515--29606 Score: 184
Period size: 44 Copynumber: 2.1 Consensus size: 44
29505 CCGTCCTCCC
29515 TATATTCAATAAGACATTCCCTTGATTATAAATTTATAATTTAT
1 TATATTCAATAAGACATTCCCTTGATTATAAATTTATAATTTAT
29559 TATATTCAATAAGACATTCCCTTGATTATAAATTTATAATTTAT
1 TATATTCAATAAGACATTCCCTTGATTATAAATTTATAATTTAT
29603 TATA
1 TATA
29607 ACAGTGCTAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (44 bp):
TATATTCAATAAGACATTCCCTTGATTATAAATTTATAATTTAT
Found at i:32794 original size:49 final size:49
Alignment explanation
Indices: 32728--32960 Score: 283
Period size: 49 Copynumber: 4.7 Consensus size: 49
32718 AAAAAATTTT
*
32728 ATATAATATATATTTAAAATATATTATATATATGTTTTTATTATATATAA
1 ATAT-ATATAAATTTAAAATATATTATATATATGTTTTTATTATATATAA
32778 ATATATATAAATTTAAAATATATTATATATATGTTTTTATTATATATAA
1 ATATATATAAATTTAAAATATATTATATATATGTTTTTATTATATATAA
* * *
32827 ATATATATAAATTTAAAATATATTATATATAT-TATAAATATATTTTCTATAA
1 ATATATATAAATTTAAAATATATTATATATATGT-T---TTTATTATATATAA
* * * *
32879 ATATATTTAAA-ATATATTATATATATTATATATGTTTTTATTATATATAA
1 ATATATATAAATTTAAAATATAT-TA-TATATATGTTTTTATTATATATAA
* *
32929 ATAAATA-AAATTTAAAATATAGTTAAATATAT
1 ATATATATAAATTTAAAATATA-TTATATATAT
32961 TTAAAAAAAC
Statistics
Matches: 157, Mismatches: 17, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
48 1 0.01
49 86 0.55
50 29 0.18
51 9 0.06
52 23 0.15
53 8 0.05
54 1 0.01
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (49 bp):
ATATATATAAATTTAAAATATATTATATATATGTTTTTATTATATATAA
Found at i:32927 original size:2 final size:2
Alignment explanation
Indices: 32727--32911 Score: 74
Period size: 2 Copynumber: 99.5 Consensus size: 2
32717 TAAAAAATTT
* * * * *
32727 TA TA TA -A TA TA TA TT TA -A AA TA TA T- TA TA TA TA TG TT TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
32766 TA T- TA TA TA TA AA TA TA TA TA AA TT TA -A AA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
32805 TA TA TG TT TT TA T- TA TA TA TA AA TA TA TA TA AA TT TA -A AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
32845 TA TA T- TA TA TA TA T- TA TA AA TA TA T- TT TC TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
32884 TT TA -A AA TA TA T- TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32912 GTTTTTATTA
Statistics
Matches: 137, Mismatches: 32, Indels: 28
0.70 0.16 0.14
Matches are distributed among these distances:
1 14 0.10
2 123 0.90
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34320 original size:7 final size:7
Alignment explanation
Indices: 34308--34340 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
34298 AGTTTGTGAG
34308 TTCTTTT
1 TTCTTTT
34315 TTC-TTT
1 TTCTTTT
34321 TTC-TTT
1 TTCTTTT
34327 TTCTTTT
1 TTCTTTT
34334 TTCTTTT
1 TTCTTTT
34341 AATTTATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTCTTTT
Found at i:34329 original size:12 final size:13
Alignment explanation
Indices: 34312--34340 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34302 TGTGAGTTCT
34312 TTTTTC-TTTTTC
1 TTTTTCTTTTTTC
34324 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
34337 TTTT
1 TTTT
34341 AATTTATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:42417 original size:75 final size:73
Alignment explanation
Indices: 42177--42473 Score: 495
Period size: 73 Copynumber: 4.0 Consensus size: 73
42167 CCCTCTCCTT
* * * *
42177 CTTCCCTAGTTCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAATTTGCATCCGCAAAT
1 CTTCCCTAATCCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAATTTGCATCCCCAAAG
42242 TCACTAAA
66 TCACTAAA
*
42250 CTTCCCTAAACCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAATTTGCATCCCCAAAG
1 CTTCCCTAATCCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAATTTGCATCCCCAAAG
*
42315 CCACTAAA
66 TCACTAAA
* *
42323 CTTCCCTAATGCTACAATGGGTTTACATTAAAATGTTTAATAACACAAAATTTTTGCATCCCCAA
1 CTTCCCTAATCCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAA--TTTGCATCCCCAA
42388 AGTCACTAAA
64 AGTCACTAAA
*
42398 CTTCCCTAATCCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAATTTGCATCTCCAAAG
1 CTTCCCTAATCCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAATTTGCATCCCCAAAG
42463 TCACTAAA
66 TCACTAAA
42471 CTT
1 CTT
42474 GAATTTTTGT
Statistics
Matches: 209, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
73 139 0.67
75 70 0.33
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (73 bp):
CTTCCCTAATCCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAATTTGCATCCCCAAAG
TCACTAAA
Found at i:42443 original size:148 final size:146
Alignment explanation
Indices: 42177--42473 Score: 504
Period size: 148 Copynumber: 2.0 Consensus size: 146
42167 CCCTCTCCTT
* * * *
42177 CTTCCCTAGTTCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAATTTGCATCCGCAAAT
1 CTTCCCTAATGCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAATTTGCATCCCCAAAG
42242 TCACTAAACTTCCCTAAACCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAATTTGCAT
66 TCACTAAACTTCCCTAAACCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAATTTGCAT
42307 CCCCAAAGCCACTAAA
131 CCCCAAAGCCACTAAA
*
42323 CTTCCCTAATGCTACAATGGGTTTACATTAAAATGTTTAATAACACAAAATTTTTGCATCCCCAA
1 CTTCCCTAATGCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAA--TTTGCATCCCCAA
*
42388 AGTCACTAAACTTCCCTAATCCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAATTTGC
64 AGTCACTAAACTTCCCTAAACCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAATTTGC
* *
42453 ATCTCCAAAGTCACTAAA
129 ATCCCCAAAGCCACTAAA
42471 CTT
1 CTT
42474 GAATTTTTGT
Statistics
Matches: 141, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
146 47 0.33
148 94 0.67
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (146 bp):
CTTCCCTAATGCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAATTTGCATCCCCAAAG
TCACTAAACTTCCCTAAACCTACAATGGGTTTACATTAAAATGTTCAATAACACAAAATTTGCAT
CCCCAAAGCCACTAAA
Found at i:45526 original size:34 final size:34
Alignment explanation
Indices: 45487--45556 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
45477 ATCGGTTTAG
45487 TGAGAGTAAAATTGGTTACTGTACGGATTAGATT
1 TGAGAGTAAAATTGGTTACTGTACGGATTAGATT
45521 TGAGAGTAAAATTGGTTACTGTACGGATTAGATT
1 TGAGAGTAAAATTGGTTACTGTACGGATTAGATT
45555 TG
1 TG
45557 TTACTGTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (34 bp):
TGAGAGTAAAATTGGTTACTGTACGGATTAGATT
Found at i:47406 original size:2 final size:2
Alignment explanation
Indices: 47399--47475 Score: 57
Period size: 2 Copynumber: 43.5 Consensus size: 2
47389 CCGTTTAGCA
* *
47399 AT AT AT AT A- AT -T AA AT AT AT AT -T TT AT AT AT AT A- AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
47436 AT AT CT A- AT AT AT AT A- AT -T AT AT AT AT A- AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47473 AT A
1 AT A
47476 ATTATTAAAC
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
1 10 0.17
2 50 0.83
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:47426 original size:21 final size:21
Alignment explanation
Indices: 47398--47479 Score: 83
Period size: 23 Copynumber: 3.7 Consensus size: 21
47388 ACCGTTTAGC
47398 AATATATATAATTAAATATAT
1 AATATATATAATTAAATATAT
* * * *
47419 ATTTTATATATATAATAATATCT
1 AATATATATA-ATTA-AATATAT
47442 AATATATATAATTATATATATAAT
1 AATATATATAATTA-A-ATAT-AT
47466 AATATATATAATTA
1 AATATATATAATTA
47480 TTAAACGGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 8 0.16
22 8 0.16
23 18 0.37
24 15 0.31
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (21 bp):
AATATATATAATTAAATATAT
Found at i:47439 original size:19 final size:19
Alignment explanation
Indices: 47424--47477 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
47414 TATATATTTT
47424 ATATATATAATAATATCTA
1 ATATATATAATAATATCTA
*
47443 ATATATATAATTATATATATA
1 ATATATATAA-TA-ATATCTA
47464 ATA-ATATATATAAT
1 ATATATATA-ATAAT
47478 TATTAAACGG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 12 0.39
20 9 0.29
21 10 0.32
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATATATAATAATATCTA
Found at i:47444 original size:10 final size:10
Alignment explanation
Indices: 47398--47477 Score: 64
Period size: 9 Copynumber: 8.3 Consensus size: 10
47388 ACCGTTTAGC
47398 AATATAT-AT
1 AATATATAAT
47407 AAT-TA-AAT
1 AATATATAAT
**
47415 -ATATATTTT
1 AATATATAAT
47424 ATATATATAAT
1 A-ATATATAAT
*
47435 AATATCTAAT
1 AATATATAAT
47445 -ATATATAATT
1 AATATATAA-T
47455 ATATATATAAT
1 A-ATATATAAT
47466 AATATAT-AT
1 AATATATAAT
47475 AAT
1 AAT
47478 TATTAAACGG
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
7 2 0.04
8 6 0.11
9 16 0.28
10 15 0.26
11 10 0.18
12 8 0.14
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (10 bp):
AATATATAAT
Found at i:47460 original size:31 final size:30
Alignment explanation
Indices: 47412--47470 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 30
47402 TATATAATTA
*
47412 AATATATATTTTATATATATAATAATATCT
1 AATATATATATTATATATATAATAATATCT
47442 AATATATATAATTATATATATAATAATAT
1 AATATATAT-ATTATATATATAATAATAT
47471 ATATAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (30 bp):
AATATATATATTATATATATAATAATATCT
Found at i:49768 original size:20 final size:21
Alignment explanation
Indices: 49735--49773 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
49725 TTACAAAGAA
49735 AACTCACAATTCCGTGAGAGT
1 AACTCACAATTCCGTGAGAGT
49756 AACTCAC-ATTCCGTGAGA
1 AACTCACAATTCCGTGAGA
49774 TAGAACCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (21 bp):
AACTCACAATTCCGTGAGAGT
Found at i:69668 original size:228 final size:227
Alignment explanation
Indices: 69246--70280 Score: 1189
Period size: 228 Copynumber: 4.5 Consensus size: 227
69236 AGATAAGCCT
* * * * * * * *
69246 TTGCTGATCTGG-GGGAATCCCTTCCTTGTCCTGAATCTTTGCCTTGACATTATCAATTGTATCA
1 TTGCTGGTCTGGAGGG-ATCCCTTCCTTGTCCTGGATCTTGGCCTTGACGTTATCGATGGTGTCG
* * * * * * *
69310 GAACTTTCAACCTCCAGGGTGATTGTTTTCCCTGTCAAGGTCTTAACGAAA-ATCTGCATACCTC
65 GAACTCTCGACCTCCAGGGTGATGGTTTTCCCGGTCAGGGTTTTAAC-AAAGATCTGCATACCGC
* * ** * *
69374 CCCTG-AGCCTCAAGACAAGATGAAGGGTCGACTCCTTTTGGATGTTGTAATCGGCCAAGGTACG
129 CAC-GAAGACGGAGGACAAGATGGAGGGTCGACTCCTTTTGGATGTTGTAATCGGCCAAGGTACG
69438 GCCGTCCTCGAGCTGTTTCCCGGCGAAGATGAGACG
193 GCCGTCCTCGAGCTGTTT-CCGGCGAAGATGAGACG
* * * * * * * *
69474 TTGCTGGTCTGGTGGGATTCCTTCTTTGTCCTGAATCTTTGCCTTGACGTTGTCGATTGTGTCAG
1 TTGCTGGTCTGGAGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTGACGTTATCGATGGTGTCGG
* * * * * *
69539 AACTCTCGACCTCCAAGGTTATGGTTTTGCCGGTCAGGGTTTTAACAAAGATTTGCATGCCTCCA
66 AACTCTCGACCTCCAGGGTGATGGTTTTCCCGGTCAGGGTTTTAACAAAGATCTGCATACCGCCA
* * *
69604 CGAAGGCGGAGGACAAGGTGGAGGGTTGACTCCTTTTGGATGTTGTAATCGGCCAAGGTACGGCC
131 CGAAGACGGAGGACAAGATGGAGGGTCGACTCCTTTTGGATGTTGTAATCGGCCAAGGTACGGCC
*
69669 GTCCTCGAGCTGTTTACCGGCGAAGATAAGACG
196 GTCCTCGAGCTGTTT-CCGGCGAAGATGAGACG
* * * * * *
69702 CTGCTGATCTGGAGGAATTCCC-TCCTTGTCTTGGATCTTGGCTTTGACATTATCGATGGTGTCG
1 TTGCTGGTCTGGAGGGA-TCCCTTCCTTGTCCTGGATCTTGGCCTTGACGTTATCGATGGTGTCG
* * * * * *
69766 GAGCTCTCGACTTCGAGGGTGATGGTTTTCCCGGTTAGGGTTTTGACAAAGATTTGCATACCGCC
65 GAACTCTCGACCTCCAGGGTGATGGTTTTCCCGGTCAGGGTTTTAACAAAGATCTGCATACCGCC
* * * * *
69831 GCGAAGACGGAGGACAAGGTGGAGGGTCGACTCCTTCTGGATGTTGTAGTCAGCCAAGGTACGGC
130 ACGAAGACGGAGGACAAGATGGAGGGTCGACTCCTTTTGGATGTTGTAATCGGCCAAGGTACGGC
* *
69896 CGTCCTCAAGCTGCTTTCCGGCGAAGATCAGACG
195 CGTCCTCGAGCTG-TTTCCGGCGAAGATGAGACG
* * * * * * *
69930 TTGCTGGTCTGGTGGGATGCCTTCTTTGTCCTGGATCTTGGCTTTAACGTTGTCGATCGTGTCGG
1 TTGCTGGTCTGGAGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTGACGTTATCGATGGTGTCGG
* * * * * * * *
69995 AACTCTCGACTTCGAGGGTGATGGTCTTGCCGGTCAAGGTCTTGACGAAGATCTGCATACCGCCA
66 AACTCTCGACCTCCAGGGTGATGGTTTTCCCGGTCAGGGTTTTAACAAAGATCTGCATACCGCCA
*
70060 CGAAGACGGAGGACAAGATGGAGCGTCGACTCCTTTTGGATGTTGTAATCGGCCAAGGTACGGCC
131 CGAAGACGGAGGACAAGATGGAGGGTCGACTCCTTTTGGATGTTGTAATCGGCCAAGGTACGGCC
70125 GTCCTCGAGCTGTTTTCCGGCGAAGATGAGACG
196 GTCCTCGAGCTG-TTTCCGGCGAAGATGAGACG
* * * *
70158 CTGCTGGTCGGGAGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTATCGATGGTATCGG
1 TTGCTGGTCTGGAGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTGACGTTATCGATGGTGTCGG
* * * * * * *
70223 AACTCTCGACCTCGAGAGTTATTGTCTTT-CCGGTGAGGGTTTTCACGAAGATCTGCAT
66 AACTCTCGACCTCCAGGGTGATGGT-TTTCCCGGTCAGGGTTTTAACAAAGATCTGCAT
70281 CTTTCAGAAA
Statistics
Matches: 692, Mismatches: 108, Indels: 14
0.85 0.13 0.02
Matches are distributed among these distances:
227 7 0.01
228 674 0.97
229 11 0.02
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (227 bp):
TTGCTGGTCTGGAGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTGACGTTATCGATGGTGTCGG
AACTCTCGACCTCCAGGGTGATGGTTTTCCCGGTCAGGGTTTTAACAAAGATCTGCATACCGCCA
CGAAGACGGAGGACAAGATGGAGGGTCGACTCCTTTTGGATGTTGTAATCGGCCAAGGTACGGCC
GTCCTCGAGCTGTTTCCGGCGAAGATGAGACG
Found at i:70027 original size:456 final size:456
Alignment explanation
Indices: 69247--70280 Score: 1335
Period size: 456 Copynumber: 2.3 Consensus size: 456
69237 GATAAGCCTT
* * * * * *
69247 TGCTGATCTGGG-GGAATCCCTTCCTTGTCCTGAATCTTTGCCTTGACATTATCAATTGTATCAG
1 TGCTGATC-GGGAGGAATCCCTTCCTTGTCTTGGATCTTGGCCTTGACATTATCGATGGTATCGG
* * * * * * * * * * *
69311 AACTTTCAACCTCCAGGGTGATTGT-TTTCCCTGTCAAGGTCTTAACGAAA-ATCTGCATACCTC
65 AACTCTCGACCTCGAGAGTGATGGTCTTT-CCGGTGAGGGTTTTCAC-AAAGATCTGCATACCGC
* * ** * * *
69374 CCCTG-AGCCTCAAGACAAGATGAAGGGTCGACTCCTTTTGGATGTTGTAATCGGCCAAGGTACG
128 CGC-GAAGACGGAGGACAAGATGAAGGGTCGACTCCTTCTGGATGTTGTAATCAGCCAAGGTACG
* * *
69438 GCCGTCCTCGAGCTGTTTCCCGGCGAAGATGAGACGTTGCTGGTCTGGTGGGATTCCTTCTTTGT
192 GCCGTCCTCAAGCTGTTTCCCGGCGAAGATCAGACGTTGCTGGTCTGGTGGGATGCCTTCTTTGT
* * * * *
69503 CCTGAATCTTTGCCTTGACGTTGTCGATTGTGTCAGAACTCTCGACCTCCAAGGTTATGGTTTTG
257 CCTGAATCTTGGCCTTAACGTTGTCGATCGTGTCAGAACTCTCGACCTCCAAGGTGATGGTCTTG
* * * * * * * * *
69568 CCGGTCAGGGTTTTAACAAAGATTTGCATGCCTCCACGAAGGCGGAGGACAAGGTGGAGGGTTGA
322 CCGGTCAAGGTCTTAACAAAGATCTGCATACCGCCACGAAGACGGAGGACAAGATGGAGCGTCGA
69633 CTCCTTTTGGATGTTGTAATCGGCCAAGGTACGGCCGTCCTCGAGCTGTTTACCGGCGAAGATAA
387 CTCCTTTTGGATGTTGTAATCGGCCAAGGTACGGCCGTCCTCGAGCTGTTTACCGGCGAAGATAA
69698 GACGC
452 GACGC
* * *
69703 TGCTGATCTGGAGGAATTCCC-TCCTTGTCTTGGATCTTGGCTTTGACATTATCGATGGTGTCGG
1 TGCTGATCGGGAGGAA-TCCCTTCCTTGTCTTGGATCTTGGCCTTGACATTATCGATGGTATCGG
* * * * * *
69767 AGCTCTCGACTTCGAGGGTGATGGT-TTTCCCGGTTAGGGTTTTGACAAAGATTTGCATACCGCC
65 AACTCTCGACCTCGAGAGTGATGGTCTTT-CCGGTGAGGGTTTTCACAAAGATCTGCATACCGCC
* * *
69831 GCGAAGACGGAGGACAAGGTGGAGGGTCGACTCCTTCTGGATGTTGTAGTCAGCCAAGGTACGGC
129 GCGAAGACGGAGGACAAGATGAAGGGTCGACTCCTTCTGGATGTTGTAATCAGCCAAGGTACGGC
69896 CGTCCTCAAGCTGCTTT-CCGGCGAAGATCAGACGTTGCTGGTCTGGTGGGATGCCTTCTTTGTC
194 CGTCCTCAAGCTG-TTTCCCGGCGAAGATCAGACGTTGCTGGTCTGGTGGGATGCCTTCTTTGTC
* * * * * *
69960 CTGGATCTTGGCTTTAACGTTGTCGATCGTGTCGGAACTCTCGACTTCGAGGGTGATGGTCTTGC
258 CTGAATCTTGGCCTTAACGTTGTCGATCGTGTCAGAACTCTCGACCTCCAAGGTGATGGTCTTGC
* *
70025 CGGTCAAGGTCTTGACGAAGATCTGCATACCGCCACGAAGACGGAGGACAAGATGGAGCGTCGAC
323 CGGTCAAGGTCTTAACAAAGATCTGCATACCGCCACGAAGACGGAGGACAAGATGGAGCGTCGAC
* *
70090 TCCTTTTGGATGTTGTAATCGGCCAAGGTACGGCCGTCCTCGAGCTGTTTTCCGGCGAAGATGAG
388 TCCTTTTGGATGTTGTAATCGGCCAAGGTACGGCCGTCCTCGAGCTGTTTACCGGCGAAGATAAG
70155 ACGC
453 ACGC
* * *
70159 TGCTGGTCGGGAGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTATCGATGGTATCGGA
1 TGCTGATCGGGAGGAATCCCTTCCTTGTCTTGGATCTTGGCCTTGACATTATCGATGGTATCGGA
* * *
70224 ACTCTCGACCTCGAGAGTTATTGTCTTTCCGGTGAGGGTTTTCACGAAGATCTGCAT
66 ACTCTCGACCTCGAGAGTGATGGTCTTTCCGGTGAGGGTTTTCACAAAGATCTGCAT
70281 CTTTCAGAAA
Statistics
Matches: 497, Mismatches: 74, Indels: 14
0.85 0.13 0.02
Matches are distributed among these distances:
455 10 0.02
456 477 0.96
457 10 0.02
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (456 bp):
TGCTGATCGGGAGGAATCCCTTCCTTGTCTTGGATCTTGGCCTTGACATTATCGATGGTATCGGA
ACTCTCGACCTCGAGAGTGATGGTCTTTCCGGTGAGGGTTTTCACAAAGATCTGCATACCGCCGC
GAAGACGGAGGACAAGATGAAGGGTCGACTCCTTCTGGATGTTGTAATCAGCCAAGGTACGGCCG
TCCTCAAGCTGTTTCCCGGCGAAGATCAGACGTTGCTGGTCTGGTGGGATGCCTTCTTTGTCCTG
AATCTTGGCCTTAACGTTGTCGATCGTGTCAGAACTCTCGACCTCCAAGGTGATGGTCTTGCCGG
TCAAGGTCTTAACAAAGATCTGCATACCGCCACGAAGACGGAGGACAAGATGGAGCGTCGACTCC
TTTTGGATGTTGTAATCGGCCAAGGTACGGCCGTCCTCGAGCTGTTTACCGGCGAAGATAAGACG
C
Found at i:72180 original size:2 final size:2
Alignment explanation
Indices: 72175--72215 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
72165 GTAAAAAAAC
72175 AT AT AT AT -T A- AT AT 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 AT AT AT AT AT AT AT AT
72215 A
1 A
72216 GTTGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.