Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013392.1 Corchorus capsularis cultivar CVL-1 contig13413, 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: 131971
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:96 original size:21 final size:21
Alignment explanation
Indices: 35--112 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 21
25 GATGTTGTGC
* *
35 TTATCAAAATTTAATAGTG-AG
1 TTATCAAAATTT-CTAGGGAAG
* *
56 ATTAACAAAATTCTATAGGGAAG
1 -TTATCAAAATT-TCTAGGGAAG
* *
79 TTATCAACATTTCTAGGGAGG
1 TTATCAAAATTTCTAGGGAAG
100 TTATCAAAATTTC
1 TTATCAAAATTTC
113 ATAGTATGGT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 20 0.43
22 24 0.51
23 3 0.06
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCTAGGGAAG
Found at i:126 original size:22 final size:22
Alignment explanation
Indices: 98--139 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
88 TTTCTAGGGA
98 GGTTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGTAT
*
120 GGTTATCCAAATTTCATAGT
1 GGTTATCAAAATTTCATAGT
140 GTACAAAATC
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:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTAT
Found at i:258 original size:22 final size:22
Alignment explanation
Indices: 233--321 Score: 101
Period size: 22 Copynumber: 4.0 Consensus size: 22
223 TCACTATTTT
233 ATAGTGTGGTTATCAAAGTTTC
1 ATAGTGTGGTTATCAAAGTTTC
** * *
255 ATAGTGTGGAAATCAAAATTTA
1 ATAGTGTGGTTATCAAAGTTTC
277 ATAG-GATGGTTATCGAAA-TTTC
1 ATAGTG-TGGTTATC-AAAGTTTC
*
299 ATAGTGTGGGTATCAAAGTTTC
1 ATAGTGTGGTTATCAAAGTTTC
321 A
1 A
322 CAGGGATTAG
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
21 4 0.07
22 47 0.85
23 4 0.07
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (22 bp):
ATAGTGTGGTTATCAAAGTTTC
Found at i:1327 original size:2 final size:2
Alignment explanation
Indices: 1320--1344 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1310 AAGATTAGTG
1320 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1345 TCGGAACGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8547 original size:11 final size:10
Alignment explanation
Indices: 8528--8563 Score: 56
Period size: 11 Copynumber: 3.6 Consensus size: 10
8518 GTCTTCAATC
8528 TTTTTTTCTT
1 TTTTTTTCTT
8538 TTTCTTTTCTT
1 TTT-TTTTCTT
8549 TTTTTTT-TT
1 TTTTTTTCTT
8558 TTTTTT
1 TTTTTT
8564 GAGTAGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.32
10 7 0.28
11 10 0.40
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:8550 original size:19 final size:17
Alignment explanation
Indices: 8526--8562 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
8516 TGGTCTTCAA
8526 TCTTTTTTTCTTTTTCTTT
1 TCTTTTTTT-TTTTT-TTT
8545 TCTTTTTTTTTTTTTTT
1 TCTTTTTTTTTTTTTTT
8562 T
1 T
8563 TGAGTAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
19 9 0.50
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (17 bp):
TCTTTTTTTTTTTTTTT
Found at i:15163 original size:26 final size:26
Alignment explanation
Indices: 15134--15201 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
15124 TTCCTTCATT
15134 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
15160 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
15186 TTAAACACAAACTAAT
1 TTAATCATAAACTAAT
15202 AAACTAAGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.32
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:15288 original size:22 final size:22
Alignment explanation
Indices: 15263--15308 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
15253 ATTAAACAAA
15263 TTTTAAAAAAAAATTAAGAATT
1 TTTTAAAAAAAAATTAAGAATT
*** *
15285 TTTTCTTAAAAATTTAAGAATT
1 TTTTAAAAAAAAATTAAGAATT
15307 TT
1 TT
15309 AATTAACCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
TTTTAAAAAAAAATTAAGAATT
Found at i:15314 original size:21 final size:21
Alignment explanation
Indices: 15261--15314 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
15251 ATATTAAACA
*
15261 AATTTTAA-AAAAAAATTAAG
1 AATTTTAATTAAAAAATTAAG
** *
15281 AATTTTTTCTTAAAAATTTAAG
1 AA-TTTTAATTAAAAAATTAAG
15303 AATTTTAATTAA
1 AATTTTAATTAA
15315 CCAAACTGGG
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
20 2 0.08
21 12 0.46
22 12 0.46
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (21 bp):
AATTTTAATTAAAAAATTAAG
Found at i:15372 original size:12 final size:12
Alignment explanation
Indices: 15355--15388 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
15345 TTTCTTCTTC
15355 TTTTTTTTTAAA
1 TTTTTTTTTAAA
15367 TTTTTTTTTAAA
1 TTTTTTTTTAAA
* *
15379 ATATTTTTTA
1 TTTTTTTTTA
15389 CATCAACCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTTTTAAA
Found at i:15373 original size:13 final size:13
Alignment explanation
Indices: 15355--15387 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
15345 TTTCTTCTTC
15355 TTTTTTTTT-AAA
1 TTTTTTTTTAAAA
15367 TTTTTTTTTAAAA
1 TTTTTTTTTAAAA
*
15380 TATTTTTT
1 TTTTTTTT
15388 ACATCAACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTAAAA
Found at i:19386 original size:40 final size:40
Alignment explanation
Indices: 19331--19406 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
19321 TTAATCGATT
* *
19331 AAGGTTGGGTACTAATGAGTAATTTAGGATGGGCACCATA
1 AAGGTTAGGCACTAATGAGTAATTTAGGATGGGCACCATA
19371 AAGGTTAGGCACTAATGAGTAATTTAGGATGGGCAC
1 AAGGTTAGGCACTAATGAGTAATTTAGGATGGGCAC
19407 AACCATACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (40 bp):
AAGGTTAGGCACTAATGAGTAATTTAGGATGGGCACCATA
Found at i:25962 original size:6 final size:6
Alignment explanation
Indices: 25950--25994 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
25940 AAAATGATTC
* * *
25950 ATATAT CTATAT CTATCT ATATAT ATATAT ATATAT ATATAT ATA
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATA
25995 CGAGTTATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (6 bp):
ATATAT
Found at i:25968 original size:10 final size:10
Alignment explanation
Indices: 25950--25994 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
25940 AAAATGATTC
*
25950 ATATATCTAT
1 ATATATATAT
* *
25960 ATCTATCTAT
1 ATATATATAT
25970 ATATATATAT
1 ATATATATAT
25980 ATATATATAT
1 ATATATATAT
25990 ATATA
1 ATATA
25995 CGAGTTATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (10 bp):
ATATATATAT
Found at i:25974 original size:4 final size:4
Alignment explanation
Indices: 25950--25994 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
25940 AAAATGATTC
* * *
25950 ATAT ATCT ATAT CTAT CTAT ATAT ATAT ATAT ATAT ATAT ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
25995 CGAGTTATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:32282 original size:29 final size:29
Alignment explanation
Indices: 32250--32305 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
32240 CTAGTCGTAG
* *
32250 TTAGAGTAACTTGTAAGTTAAGTTTAGTC
1 TTAGAGTAAATTATAAGTTAAGTTTAGTC
*
32279 TTAGAGTAAATTATAATTTAAGTTTAG
1 TTAGAGTAAATTATAAGTTAAGTTTAG
32306 CCCTGAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.43
Consensus pattern (29 bp):
TTAGAGTAAATTATAAGTTAAGTTTAGTC
Found at i:52370 original size:16 final size:16
Alignment explanation
Indices: 52351--52454 Score: 156
Period size: 16 Copynumber: 6.6 Consensus size: 16
52341 GGGCGGGTTT
52351 GGGTTCGGGTATTTTC
1 GGGTTCGGGTATTTTC
52367 GGGTTCGGGTATTTTC
1 GGGTTCGGGTATTTTC
* * *
52383 GGATTCGGATTTTTTC
1 GGGTTCGGGTATTTTC
*
52399 GGGTTCGAGTA-TTTC
1 GGGTTCGGGTATTTTC
*
52414 GGGTTCGGATATTTTC
1 GGGTTCGGGTATTTTC
52430 GGGTTCGGGTATTTTC
1 GGGTTCGGGTATTTTC
52446 GGGTTCGGG
1 GGGTTCGGG
52455 CTCGGGTCGG
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
15 13 0.17
16 64 0.83
ACGTcount: A:0.09, C:0.12, G:0.37, T:0.42
Consensus pattern (16 bp):
GGGTTCGGGTATTTTC
Found at i:52428 original size:47 final size:48
Alignment explanation
Indices: 52351--52452 Score: 152
Period size: 47 Copynumber: 2.1 Consensus size: 48
52341 GGGCGGGTTT
* * *
52351 GGGTTCGGGTATTTTCGGGTTCGGGTATTTTCGGATTCGGATTTTTTC
1 GGGTTCGAGTATTTTCGGGTTCGGATATTTTCGGATTCGGATATTTTC
* *
52399 GGGTTCGAGTA-TTTCGGGTTCGGATATTTTCGGGTTCGGGTATTTTC
1 GGGTTCGAGTATTTTCGGGTTCGGATATTTTCGGATTCGGATATTTTC
52446 GGGTTCG
1 GGGTTCG
52453 GGCTCGGGTC
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 39 0.80
48 10 0.20
ACGTcount: A:0.09, C:0.13, G:0.35, T:0.43
Consensus pattern (48 bp):
GGGTTCGAGTATTTTCGGGTTCGGATATTTTCGGATTCGGATATTTTC
Found at i:53016 original size:31 final size:31
Alignment explanation
Indices: 52981--53052 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
52971 TAAATTGTAG
*
52981 CAAATTAAAACAAAT-TAAGTATTAAATTAAA
1 CAAATTAAAA-AAATGCAAGTATTAAATTAAA
* ** *
53012 CAAATCATCAAAATGCAAGTCTTAAATTAAA
1 CAAATTAAAAAAATGCAAGTATTAAATTAAA
53043 CAAATTAAAA
1 CAAATTAAAA
53053 GCTAATGGAC
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.58, C:0.11, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGCAAGTATTAAATTAAA
Found at i:53273 original size:16 final size:16
Alignment explanation
Indices: 53222--53279 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
53212 ATCTCGGGTT
* *
53222 CGGGTTCAGGTTCGGG
1 CGGGTTCGGGTACGGG
* ****
53238 CAGGTTCGGGTATTTT
1 CGGGTTCGGGTACGGG
53254 CGGGTTCGGGTACGGG
1 CGGGTTCGGGTACGGG
53270 CGGGTTCGGG
1 CGGGTTCGGG
53280 ACGTTGACTT
Statistics
Matches: 30, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.07, C:0.17, G:0.48, T:0.28
Consensus pattern (16 bp):
CGGGTTCGGGTACGGG
Found at i:58015 original size:28 final size:27
Alignment explanation
Indices: 57984--58045 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
57974 TGGCACGTGG
**
57984 CATTTTTAACACGTGATGTGCCATGTGT
1 CATTTTTAACACGTGACATGCCA-GTGT
** *
58012 CATTTTTTGCACGTGGCATGCCAGTGT
1 CATTTTTAACACGTGACATGCCAGTGT
58039 CATTTTT
1 CATTTTT
58046 TTGGTACACG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (27 bp):
CATTTTTAACACGTGACATGCCAGTGT
Found at i:58046 original size:28 final size:30
Alignment explanation
Indices: 58002--58062 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
57992 ACACGTGATG
58002 TGCCATGTGTCATTTTTT-G-CACGTGGCA
1 TGCCATGTGTCATTTTTTGGACACGTGGCA
58030 TGCCA-GTGTCATTTTTTTGGTACACGTGGCA
1 TGCCATGTGTCA-TTTTTTGG-ACACGTGGCA
58061 TG
1 TG
58063 TCACATCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 6 0.21
28 11 0.38
29 1 0.03
31 11 0.38
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.39
Consensus pattern (30 bp):
TGCCATGTGTCATTTTTTGGACACGTGGCA
Found at i:61980 original size:17 final size:17
Alignment explanation
Indices: 61960--62006 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
61950 AAGAGATCAC
61960 AAATATTCAATTAA-AAT
1 AAATATT-AATTAATAAT
*
61977 AAATATTGAAATAATAAT
1 AAATATT-AATTAATAAT
61995 AAATATTAATTA
1 AAATATTAATTA
62007 GAACTGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
AAATATTAATTAATAAT
Found at i:65650 original size:31 final size:31
Alignment explanation
Indices: 65595--65670 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 31
65585 ACGGTGTCTG
* * *
65595 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAATGAC
** *
65626 ACGTGGCATGCCACATGTTTCAAAAAATGGC
1 ACGTGGCATGCCACATGTACCAAAAAATGAC
* *
65657 ACATGACATGCCAC
1 ACGTGGCATGCCAC
65671 GTGCACAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17
Consensus pattern (31 bp):
ACGTGGCATGCCACATGTACCAAAAAATGAC
Found at i:68662 original size:63 final size:63
Alignment explanation
Indices: 68563--68688 Score: 207
Period size: 63 Copynumber: 2.0 Consensus size: 63
68553 AAAAGTCGAT
*
68563 TTCCAGCTTCCAAATCACTTTCAATGATTTCTCAACGCAGTTATCAATATCACGGTTGGTAAC
1 TTCCAGCTTCCAAATCACTTTCAATGATTTCTCAACGCAGTTATCAATATCACGGTTAGTAAC
* * * *
68626 TTCCAGTTTCCAAATTACTTTCAATGGTTTCTCAACGTAGTTATCAATATCACGGTTAGTAAC
1 TTCCAGCTTCCAAATCACTTTCAATGATTTCTCAACGCAGTTATCAATATCACGGTTAGTAAC
68689 CGGATTAGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.36
Consensus pattern (63 bp):
TTCCAGCTTCCAAATCACTTTCAATGATTTCTCAACGCAGTTATCAATATCACGGTTAGTAAC
Found at i:69495 original size:78 final size:78
Alignment explanation
Indices: 69344--69499 Score: 206
Period size: 78 Copynumber: 2.0 Consensus size: 78
69334 CAGGAGGCAA
* * *
69344 GTCGACAATAGAAAGCCAAGGGTGGAGATGGCTCATGGTGACCCTATTGAAAAACCTGTATCTGT
1 GTCGACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAACTGT
*
69409 TTGCAGAAATCCT
66 TCGCAGAAATCCT
* * * * *
69422 GTCGACAATAGAAAGCCAGGGGTGGAAATAGCTCGTGGTGGCCCTATTGAAAGATCTG-AACATG
1 GTCGACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAAC-TG
*
69486 TTCGTAGAAATCCT
65 TTCGCAGAAATCCT
69500 ATCTATGATA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
77 2 0.03
78 65 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (78 bp):
GTCGACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAACTGT
TCGCAGAAATCCT
Found at i:75403 original size:2 final size:2
Alignment explanation
Indices: 75396--75423 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
75386 ACATTAATTG
75396 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
75424 GAATATGTAT
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):
AT
Found at i:79988 original size:2 final size:2
Alignment explanation
Indices: 79981--80010 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
79971 ACTTACTTAC
79981 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
80011 AGTTACAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:84998 original size:34 final size:34
Alignment explanation
Indices: 84955--85101 Score: 192
Period size: 34 Copynumber: 4.4 Consensus size: 34
84945 ACAACAATTA
*
84955 GGATTTTGAGTTTTGAACATGAAACGCAGATTCT
1 GGATTTTGAGTTTTGAACATGAAATGCAGATTCT
*
84989 GGATTTTGAGTTTTGAACATGAGATGCAGATTCT
1 GGATTTTGAGTTTTGAACATGAAATGCAGATTCT
* *
85023 GGATTTTGAGTTTTGAACATGAGATGCAGATTTT
1 GGATTTTGAGTTTTGAACATGAAATGCAGATTCT
* * * *
85057 GAACTTTGAATTTTGAA-ATGAAATGCAAATT-T
1 GGATTTTGAGTTTTGAACATGAAATGCAGATTCT
*
85089 GAATTTTGA-TTTT
1 GGATTTTGAGTTTT
85102 CGAAAGGAAT
Statistics
Matches: 104, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
31 4 0.04
32 9 0.09
33 12 0.12
34 79 0.76
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.40
Consensus pattern (34 bp):
GGATTTTGAGTTTTGAACATGAAATGCAGATTCT
Found at i:85136 original size:40 final size:39
Alignment explanation
Indices: 85073--85178 Score: 110
Period size: 41 Copynumber: 2.7 Consensus size: 39
85063 TGAATTTTGA
**
85073 AATGAAATGCA-AATTTGAATTTTGA-TTTTCGAAAGGAATG
1 AATGAAATGCAGGTTTTGAATTTTGACTTTT-G-AA-GAATG
* *
85113 -TTGAAATGCATGTTTTGAATTTTGACTTTTGAAGAATG
1 AATGAAATGCAGGTTTTGAATTTTGACTTTTGAAGAATG
85151 AACATGAAATGCAGGTTTTGAATTTTGA
1 -A-ATGAAATGCAGGTTTTGAATTTTGA
85179 ACCATGAGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
38 5 0.09
39 11 0.20
40 13 0.23
41 27 0.48
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.39
Consensus pattern (39 bp):
AATGAAATGCAGGTTTTGAATTTTGACTTTTGAAGAATG
Found at i:85197 original size:28 final size:27
Alignment explanation
Indices: 85149--85206 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
85139 TTTTGAAGAA
*
85149 TGAACATGAAATGCAGGTTTTGAATTT
1 TGAACATGAAATGCAGATTTTGAATTT
* *
85176 TGAACCATGAGATGCTGATTTTGAATTT
1 TGAA-CATGAAATGCAGATTTTGAATTT
85204 TGA
1 TGA
85207 TATTTGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (27 bp):
TGAACATGAAATGCAGATTTTGAATTT
Found at i:85213 original size:35 final size:36
Alignment explanation
Indices: 84957--85242 Score: 145
Period size: 34 Copynumber: 8.2 Consensus size: 36
84947 AACAATTAGG
* * * * *
84957 ATTTTGA-GTTTTGAAC-ATGAAACGCAGATTCTGG
1 ATTTTGATATTTTGAACAATGAAATGCAAATTTTGA
* * * * *
84991 ATTTTGA-GTTTTGAAC-ATGAGATGCAGATTCTGG
1 ATTTTGATATTTTGAACAATGAAATGCAAATTTTGA
* * *
85025 ATTTTGA-GTTTTGAAC-ATGAGATGCAGATTTTGA
1 ATTTTGATATTTTGAACAATGAAATGCAAATTTTGA
*
85059 ACTTTGA-ATTTTG-A-AATGAAATGCAAA-TTTGA
1 ATTTTGATATTTTGAACAATGAAATGCAAATTTTGA
* * **
85091 ATTTTGAT-TTTCGAAAGGAATGTTGAAATGCATGTTTTGA
1 ATTTTGATATTTTG-AA-CAA---TGAAATGCAAATTTTGA
* * ***
85131 ATTTTGA-CTTTTGAAGAATGAACATG-AAATGCAG-
1 ATTTTGATATTTTGAACAATGAA-ATGCAAATTTTGA
* * * **
85165 GTTTTGA-ATTTTGAACCATGAGATGCTGATTTTGA
1 ATTTTGATATTTTGAACAATGAAATGCAAATTTTGA
*
85200 ATTTTGATA-TTTGAATAATGAAATGCAAATTTTGA
1 ATTTTGATATTTTGAACAATGAAATGCAAATTTTGA
85235 ATTTTGAT
1 ATTTTGAT
85243 TTTCGGATGG
Statistics
Matches: 203, Mismatches: 34, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
32 15 0.07
33 14 0.07
34 96 0.47
35 42 0.21
36 6 0.03
38 3 0.01
39 11 0.05
40 16 0.08
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (36 bp):
ATTTTGATATTTTGAACAATGAAATGCAAATTTTGA
Found at i:85264 original size:144 final size:140
Alignment explanation
Indices: 85026--85281 Score: 397
Period size: 144 Copynumber: 1.8 Consensus size: 140
85016 AGATTCTGGA
*
85026 TTTTGAGTTTTGAACATGAGATGCAGATTTTGAACTTTGAATTTTGAAATGAAATGCAAATTTGA
1 TTTTGAATTTTGAACATGAGATGCAGATTTTGAACTTTGAATTTTGAAATGAAATGCAAATTTGA
**
85091 ATTTTGATTTTCGAAAGGAATGTTGAAATGCATGTTTTGAATTTTGACTTTTGAAGAATGAACAT
66 ATTTTGATTTTCGAAAGGAATACTGAAATGCATGTTTTGAATTTTGACTTTTGAAGAATGAACAT
85156 GAAATGCAGG
131 GAAATGCAGG
* *
85166 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAATTTTG-ATATTTGAATAATGAAATGCAAAT
1 TTTTGAATTTTGAA-CATGAGATGCAGATTTTGAACTTTGAAT-TTTG-A-AATGAAATGCAAA-
* *
85230 TTTGAATTTTGATTTTCGGATGGAATACTGAAATGCATGTTTTGAATTTTGA
61 TTTGAATTTTGATTTTCGAAAGGAATACTGAAATGCATGTTTTGAATTTTGA
85282 TGCAAATATT
Statistics
Matches: 104, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
140 15 0.14
141 27 0.26
142 1 0.01
143 13 0.12
144 48 0.46
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.41
Consensus pattern (140 bp):
TTTTGAATTTTGAACATGAGATGCAGATTTTGAACTTTGAATTTTGAAATGAAATGCAAATTTGA
ATTTTGATTTTCGAAAGGAATACTGAAATGCATGTTTTGAATTTTGACTTTTGAAGAATGAACAT
GAAATGCAGG
Found at i:85294 original size:59 final size:60
Alignment explanation
Indices: 85222--85344 Score: 160
Period size: 62 Copynumber: 2.0 Consensus size: 60
85212 GAATAATGAA
* * * *
85222 ATGCAAATTTTGAATTTTGATTTTCG-GATGGAATACTGAAATGCA-TGTTTTGAATTTTG
1 ATGCAAATATTGAACTTTGATTTTCGAAATGGAATACTGAAATG-AGAGTTTTGAATTTTG
*
85281 ATGCAAATATTGAACTTTGATTTTCGAATAATGGAATGCTGAAATGAGAGTTTTGAATTTTG
1 ATGCAAATATTGAACTTTGATTTTCG-A-AATGGAATACTGAAATGAGAGTTTTGAATTTTG
85343 AT
1 AT
85345 TTTTGAAGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
59 24 0.44
61 1 0.02
62 30 0.55
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (60 bp):
ATGCAAATATTGAACTTTGATTTTCGAAATGGAATACTGAAATGAGAGTTTTGAATTTTG
Found at i:85386 original size:28 final size:28
Alignment explanation
Indices: 85355--85413 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
85345 TTTTGAAGAA
* *
85355 TGAACCATGAAATGGAGATTTTGAATTT
1 TGAACCATGAAATGCAGATTTTGAAATT
* * *
85383 TGAACTATGAGATGCTGATTTTGAAATT
1 TGAACCATGAAATGCAGATTTTGAAATT
85411 TGA
1 TGA
85414 TTTTTGAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (28 bp):
TGAACCATGAAATGCAGATTTTGAAATT
Found at i:85521 original size:74 final size:74
Alignment explanation
Indices: 85439--85821 Score: 653
Period size: 74 Copynumber: 5.2 Consensus size: 74
85429 TTTTGAAACC
** * *
85439 TAAACAAGGATTTGTTAAGATTCCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAA
1 TAAACAAGGATTTAATAAGAATCCTAAACAGGAATCTTAAACAAGATTTTGACGAGACACCTAAA
85504 CAGGGACCT
66 CAGGGACCT
85513 TAAACAAGGATTTAATAAGAAAT-CTAAACAGGAATCTTAAACAAGATTTTGACGAGACACCTAA
1 TAAACAAGGATTTAATAAG-AATCCTAAACAGGAATCTTAAACAAGATTTTGACGAGACACCTAA
85577 ACAGGGACCT
65 ACAGGGACCT
* * *
85587 TAAACAAGGATTTAAAAAGAAACCTAAATAGGAATCTTAAACAAGATTTTGACGAGACACCTAAA
1 TAAACAAGGATTTAATAAGAATCCTAAACAGGAATCTTAAACAAGATTTTGACGAGACACCTAAA
85652 CAGGGACCT
66 CAGGGACCT
*
85661 TAAACAAGGATTTAATAAGAAAT-CTAAACAAGAATCTTAAACAAGATTTTGACGAGACACCTAA
1 TAAACAAGGATTTAATAAG-AATCCTAAACAGGAATCTTAAACAAGATTTTGACGAGACACCTAA
85725 ACAGGGACCT
65 ACAGGGACCT
*
85735 TAAACAAGGATTTAATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGACGAGACACCTAAA
1 TAAACAAGGATTTAATAAGAATCCTAAACAGGAATCTTAAACAAGATTTTGACGAGACACCTAAA
85800 CAGGGACCT
66 CAGGGACCT
85809 TAAACAAGGATTT
1 TAAACAAGGATTT
85822 GACGAGAATG
Statistics
Matches: 292, Mismatches: 13, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
73 4 0.01
74 284 0.97
75 4 0.01
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.22
Consensus pattern (74 bp):
TAAACAAGGATTTAATAAGAATCCTAAACAGGAATCTTAAACAAGATTTTGACGAGACACCTAAA
CAGGGACCT
Found at i:85823 original size:37 final size:37
Alignment explanation
Indices: 85461--85828 Score: 377
Period size: 37 Copynumber: 9.9 Consensus size: 37
85451 TGTTAAGATT
* *
85461 CCTAAACAGGAATCTTAAACAAGATTTTGATGAGACA
1 CCTAAACAGGAACCTTAAACAAGATTTTGACGAGACA
* * ** *
85498 CCTAAACAGGGACCTTAAACAAGGA-TTTAATAAGAAA
1 CCTAAACAGGAACCTTAAACAA-GATTTTGACGAGACA
* *
85535 TCTAAACAGGAATCTTAAACAAGATTTTGACGAGACA
1 CCTAAACAGGAACCTTAAACAAGATTTTGACGAGACA
* * ** *
85572 CCTAAACAGGGACCTTAAACAAGGA-TTTAAAAAGAAA
1 CCTAAACAGGAACCTTAAACAA-GATTTTGACGAGACA
* *
85609 CCTAAATAGGAATCTTAAACAAGATTTTGACGAGACA
1 CCTAAACAGGAACCTTAAACAAGATTTTGACGAGACA
* * ** *
85646 CCTAAACAGGGACCTTAAACAAGGA-TTTAATAAGAAA
1 CCTAAACAGGAACCTTAAACAA-GATTTTGACGAGACA
* * *
85683 TCTAAACAAGAATCTTAAACAAGATTTTGACGAGACA
1 CCTAAACAGGAACCTTAAACAAGATTTTGACGAGACA
* * ** *
85720 CCTAAACAGGGACCTTAAACAAGGA-TTTAATAAGAAA
1 CCTAAACAGGAACCTTAAACAA-GATTTTGACGAGACA
*
85757 CCTAAACAGGAATCTTAAACAAGATTTTGACGAGACA
1 CCTAAACAGGAACCTTAAACAAGATTTTGACGAGACA
*
85794 CCTAAACAGGGACCTTAAACAAGGA-TTTGACGAGA
1 CCTAAACAGGAACCTTAAACAA-GATTTTGACGAGA
85829 ATGAATTTTT
Statistics
Matches: 265, Mismatches: 57, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
36 8 0.03
37 247 0.93
38 10 0.04
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.21
Consensus pattern (37 bp):
CCTAAACAGGAACCTTAAACAAGATTTTGACGAGACA
Found at i:87546 original size:14 final size:14
Alignment explanation
Indices: 87515--87579 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
87505 ACTGAAAACC
* **
87515 TTTTTGAAAACACA
1 TTTTTGAAAGCATT
87529 TTTTTGAAAGTCATTT
1 TTTTTGAAAG-CA-TT
87545 TTTTTGAAAGCATT
1 TTTTTGAAAGCATT
*
87559 TTCTTGAAA--ATT
1 TTTTTGAAAGCATT
*
87571 TTTTCGAAA
1 TTTTTGAAA
87580 AACGTTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
12 10 0.23
14 19 0.44
15 4 0.09
16 10 0.23
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (14 bp):
TTTTTGAAAGCATT
Found at i:87550 original size:16 final size:15
Alignment explanation
Indices: 87529--87560 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
87519 TGAAAACACA
87529 TTTTTGAAAGTCATTT
1 TTTTTGAAAG-CATTT
87545 TTTTTGAAAGCATTT
1 TTTTTGAAAGCATTT
87560 T
1 T
87561 CTTGAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.56
Consensus pattern (15 bp):
TTTTTGAAAGCATTT
Found at i:100693 original size:117 final size:117
Alignment explanation
Indices: 100487--100722 Score: 463
Period size: 117 Copynumber: 2.0 Consensus size: 117
100477 TCGTAACCAA
100487 TTCAAGTTTCTCGTCAATGAATCTATGGGAAAAGTTGAAGACTCTGCTCATATCAGAGCTTGTTT
1 TTCAAGTTTCTCGTCAATGAATCTATGGGAAAAGTTGAAGACTCTGCTCATATCAGAGCTTGTTT
100552 TGGCTGAAACCCAACTAAAATCAAAGCCCTGGAAGCCATAAAGCCTGGCTGT
66 TGGCTGAAACCCAACTAAAATCAAAGCCCTGGAAGCCATAAAGCCTGGCTGT
100604 TTCAAGTTTCTCGTCAATGAATCTATGGGAAAAGTTGAAGACTCTGCTCATATCAGAGCTTGTTT
1 TTCAAGTTTCTCGTCAATGAATCTATGGGAAAAGTTGAAGACTCTGCTCATATCAGAGCTTGTTT
*
100669 TGGCTGAAACCGAACTAAAATCAAAGCCCTGGAAGCCATAAAGCCTGGCTGT
66 TGGCTGAAACCCAACTAAAATCAAAGCCCTGGAAGCCATAAAGCCTGGCTGT
100721 TT
1 TT
100723 TTATAGAGGA
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 118 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (117 bp):
TTCAAGTTTCTCGTCAATGAATCTATGGGAAAAGTTGAAGACTCTGCTCATATCAGAGCTTGTTT
TGGCTGAAACCCAACTAAAATCAAAGCCCTGGAAGCCATAAAGCCTGGCTGT
Found at i:102405 original size:60 final size:60
Alignment explanation
Indices: 102273--102438 Score: 183
Period size: 60 Copynumber: 2.7 Consensus size: 60
102263 CTGACGCCAA
* *
102273 GCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTAATTATTTGGCCAAATTAAAAAATCTG
1 GCCCTTATTTGAGCATTTTCGATAACATTAGGCCC----TTATTTGGCCAAATTAAAAAATCTG
* * * *
102337 GCCCTTATTTGAGCATTTTCGATAACACTAGGCCCTTATTTGGTCAACTTAAAAGAT-TG
1 GCCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGGCCAAATTAAAAAATCTG
* * *
102396 GACGCTTATTTGAGCATTTTGGCA-AACATTAGGTCCTTATTTG
1 G-CCCTTATTTGAGCATTTTCG-ATAACATTAGGCCCTTATTTG
102439 AACAATTAAG
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
59 3 0.03
60 54 0.60
61 1 0.01
64 32 0.36
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGGCCAAATTAAAAAATCTG
Found at i:102615 original size:27 final size:27
Alignment explanation
Indices: 102585--102636 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
102575 TTTTGGTGTA
*
102585 GTTTAGT-GTTGTTAAGGAGTAGGAATT
1 GTTTAGTAG-TGTAAAGGAGTAGGAATT
*
102612 GTTTGGTAGTGTAAAGGAGTAGGAA
1 GTTTAGTAGTGTAAAGGAGTAGGAA
102637 AAATTGAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (27 bp):
GTTTAGTAGTGTAAAGGAGTAGGAATT
Found at i:103914 original size:127 final size:127
Alignment explanation
Indices: 103677--103907 Score: 365
Period size: 127 Copynumber: 1.8 Consensus size: 127
103667 ATTCTTTTAA
* * *
103677 TTAATTAAGTGTTAATTAATGGTTTGTAGAAAATTACTAAAACGAGGCGATAAAGTCTCATCAGA
1 TTAATTAAGTGTTAATTAATGATTTGTAGAAAATTACTAAAACGAGGCGATAAAGTCTCACCAAA
* * * *
103742 TTAAAAGTTGGAAGGACTGTTAAGTAATTTCATGTTGCTACAAAAAAGGTTTTATAACTCTT
66 TTAAAAATTAGAAAGACTGTTAAGTAATTTCACGTTGCTACAAAAAAGGTTTTATAACTCTT
* *
103804 TTAATTAAGTGTTAATTAATGATTTGTAGAAAATTACTAAAACGGGGTGAT-AAGCTCTCACCAA
1 TTAATTAAGTGTTAATTAATGATTTGTAGAAAATTACTAAAACGAGGCGATAAAG-TCTCACCAA
103868 ATTAAAAATTAGAAAGACTGTTAAGTAATTTCACGTTGCT
65 ATTAAAAATTAGAAAGACTGTTAAGTAATTTCACGTTGCT
103908 TAAAAAATAA
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
126 3 0.03
127 91 0.97
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (127 bp):
TTAATTAAGTGTTAATTAATGATTTGTAGAAAATTACTAAAACGAGGCGATAAAGTCTCACCAAA
TTAAAAATTAGAAAGACTGTTAAGTAATTTCACGTTGCTACAAAAAAGGTTTTATAACTCTT
Found at i:109949 original size:2 final size:2
Alignment explanation
Indices: 109938--109969 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
109928 AACTTATGCT
109938 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
109970 CTGCAGGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:114463 original size:22 final size:22
Alignment explanation
Indices: 114369--114531 Score: 129
Period size: 22 Copynumber: 7.5 Consensus size: 22
114359 GAGAAATTGA
* * *
114369 CAAAATCTCACAGGGAGGTTAT
1 CAAAATTTCATAGGTAGGTTAT
* * *
114391 CAAAA-ATCATAGG-AAGATA-
1 CAAAATTTCATAGGTAGGTTAT
*
114410 CAAAATTTCATAGGAAGGTTTAT
1 CAAAATTTCATAGGTAGG-TTAT
* *
114433 TAAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAGGTAGGTTAT
* * * *
114455 CAAAGTTTCATATGAAGTTTAT
1 CAAAATTTCATAGGTAGGTTAT
* *
114477 CACAATTTCATAGGTA-ATTAT
1 CAAAATTTCATAGGTAGGTTAT
*
114498 CAAAATTTTATAGGGT-GGTTAT
1 CAAAATTTCATA-GGTAGGTTAT
114520 CAAAATTTCATA
1 CAAAATTTCATA
114532 AAATATTCAA
Statistics
Matches: 110, Mismatches: 25, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
19 5 0.05
20 11 0.10
21 22 0.20
22 57 0.52
23 15 0.14
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGGTAGGTTAT
Found at i:118102 original size:2 final size:2
Alignment explanation
Indices: 118097--118124 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
118087 TATATATATA
118097 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
118125 AGACTTCAAG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:129834 original size:24 final size:24
Alignment explanation
Indices: 129807--129859 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
129797 GCATAATTTC
129807 TATTGAGATCAATTGATATGAGAA
1 TATTGAGATCAATTGATATGAGAA
* * *
129831 TATTGATATTAATTGATATTAGAA
1 TATTGAGATCAATTGATATGAGAA
129855 TATTG
1 TATTG
129860 CTTAGACGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.17, T:0.42
Consensus pattern (24 bp):
TATTGAGATCAATTGATATGAGAA
Found at i:131162 original size:20 final size:19
Alignment explanation
Indices: 131133--131173 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
131123 AATCCTCCCA
131133 ATTAATTATATATATATAT
1 ATTAATTATATATATATAT
*
131152 ATTACATTATATTTATATAT
1 ATTA-ATTATATATATATAT
131172 AT
1 AT
131174 ACTTAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTAATTATATATATATAT
Found at i:131930 original size:2 final size:2
Alignment explanation
Indices: 131925--131961 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
131915 TATTATGTTT
131925 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
131962 CTTTAATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.