Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014688.1 Corchorus capsularis cultivar CVL-1 contig14709, 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: 126954
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:9397 original size:18 final size:18
Alignment explanation
Indices: 9374--9411 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
9364 GGAAGCTTCT
9374 AACTTGTTTTCAATATGC
1 AACTTGTTTTCAATATGC
9392 AACTTGTTTTCAATATGC
1 AACTTGTTTTCAATATGC
9410 AA
1 AA
9412 ATATCTTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (18 bp):
AACTTGTTTTCAATATGC
Found at i:22522 original size:13 final size:13
Alignment explanation
Indices: 22506--22548 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
22496 ACTCCCACCT
22506 TTAACTTGCTTAA
1 TTAACTTGCTTAA
*
22519 TTAATTTGCTTGAA
1 TTAACTTGCTT-AA
*
22533 -AAACTTGCTTAA
1 TTAACTTGCTTAA
22545 TTAA
1 TTAA
22549 TAATACTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 2 0.08
13 20 0.83
14 2 0.08
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (13 bp):
TTAACTTGCTTAA
Found at i:22561 original size:26 final size:26
Alignment explanation
Indices: 22508--22561 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
22498 TCCCACCTTT
* *
22508 AACTTGCTTAATTAATTTGCTTGAAA
1 AACTTGCTTAATTAATATACTTGAAA
*
22534 AACTTGCTTAATTAATAATACTTTAAA
1 AACTTGCTTAATTAAT-ATACTTGAAA
22561 A
1 A
22562 TTAATAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (26 bp):
AACTTGCTTAATTAATATACTTGAAA
Found at i:29343 original size:16 final size:16
Alignment explanation
Indices: 29324--29373 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
29314 TGCTCTGTTT
29324 TTTTCAAACTCTGATC
1 TTTTCAAACTCTGATC
** * *
29340 TTTT--TGCTCTGTTT
1 TTTTCAAACTCTGATC
29354 TTTTCAAACTCTGATC
1 TTTTCAAACTCTGATC
29370 TTTT
1 TTTT
29374 TGCTCTGTTT
Statistics
Matches: 24, Mismatches: 8, Indels: 4
0.67 0.22 0.11
Matches are distributed among these distances:
14 10 0.42
16 14 0.58
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.56
Consensus pattern (16 bp):
TTTTCAAACTCTGATC
Found at i:29346 original size:30 final size:30
Alignment explanation
Indices: 29312--29383 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
29302 ATTAATGACA
29312 TTTGCTCTGTTTTTTTCAAACTCTGATCTT
1 TTTGCTCTGTTTTTTTCAAACTCTGATCTT
29342 TTTGCTCTGTTTTTTTCAAACTCTGATCTT
1 TTTGCTCTGTTTTTTTCAAACTCTGATCTT
29372 TTTGCTCTGTTT
1 TTTGCTCTGTTT
29384 CCTTGACTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.11, C:0.19, G:0.11, T:0.58
Consensus pattern (30 bp):
TTTGCTCTGTTTTTTTCAAACTCTGATCTT
Found at i:31715 original size:24 final size:24
Alignment explanation
Indices: 31662--31717 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
31652 ATGGTTTATA
* *
31662 GGTGGAGGTGCGTAGGTTAAGAGC
1 GGTGGTGGTGCGTAGGATAAGAGC
*
31686 GGTGGTGGTGCGTAGGATAAGAGG
1 GGTGGTGGTGCGTAGGATAAGAGC
31710 GGTGGTGG
1 GGTGGTGG
31718 AAGTGTGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.18, C:0.05, G:0.55, T:0.21
Consensus pattern (24 bp):
GGTGGTGGTGCGTAGGATAAGAGC
Found at i:35471 original size:23 final size:23
Alignment explanation
Indices: 35441--35486 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
35431 AATGCAAAGA
35441 TGGATGGAACCCATATGGCATAT
1 TGGATGGAACCCATATGGCATAT
35464 TGGATGGAACCCATATGGCATAT
1 TGGATGGAACCCATATGGCATAT
35487 GGCTTGGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGATGGAACCCATATGGCATAT
Found at i:35997 original size:13 final size:13
Alignment explanation
Indices: 35979--36007 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
35969 GAAGTCTAGT
35979 CTCTTCTCTTTCG
1 CTCTTCTCTTTCG
35992 CTCTTCTCTTTCG
1 CTCTTCTCTTTCG
36005 CTC
1 CTC
36008 CAAGGTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.41, G:0.07, T:0.52
Consensus pattern (13 bp):
CTCTTCTCTTTCG
Found at i:38386 original size:30 final size:32
Alignment explanation
Indices: 38332--38397 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
38322 AACTTTATGT
* *
38332 TTTCCGATTGTATCCTTATTTTT-AAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAAACATA
38363 TTTCCAATTGTACCCTT-TTTTTAAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAAACATA
38394 TTTC
1 TTTC
38398 TTAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.48
Consensus pattern (32 bp):
TTTCCAATTGTACCCTTATTTTTAAAAACATA
Found at i:38676 original size:22 final size:22
Alignment explanation
Indices: 38648--38831 Score: 108
Period size: 22 Copynumber: 8.3 Consensus size: 22
38638 TGTCTCTATG
38648 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
38670 TGGTTATTATAATTCCATGAAGA
1 TGGTTATCAAAATTTCAT-AAGA
* * *
38693 -GATTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
38714 TGGTTACCAAAAGTTCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
38734 TGTAGTTATCAAAATTTCAT-AGA
1 TG--GTTATCAAAATTTCATAAGA
* *
38757 GTGGTTACCAAAATTTCATAGGA
1 -TGGTTATCAAAATTTCATAAGA
* * * *
38780 TCAGGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
38804 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAAGA
38826 TGGTTA
1 TGGTTA
38832 ATTATCACAA
Statistics
Matches: 130, Mismatches: 22, Indels: 20
0.76 0.13 0.12
Matches are distributed among these distances:
20 4 0.03
22 100 0.77
23 6 0.05
24 20 0.15
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:38808 original size:46 final size:43
Alignment explanation
Indices: 38650--38824 Score: 140
Period size: 44 Copynumber: 4.0 Consensus size: 43
38640 TCTCTATGTG
** * * *
38650 GTTATCAAAATTTCATA-AGATGGTTATTATAATTCCATGAAG-A
1 GTTATCAAAATTTCATAGAG-TGGTTACCAAAATTTCAT-AGGTA
* * *
38693 GATTATCAAAATTCCATAGTGTGGTTACCAAAAGTTCATAGTGTA
1 G-TTATCAAAATTTCATAGAGTGGTTACCAAAATTTCATAG-GTA
38738 GTTATCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGGATCA
1 GTTATCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGG-T-A
* * ***
38783 GGTTATTAAAATTTCTTAG-GTTGGTTATTGAAATTTCATAGG
1 -GTTATCAAAATTTCATAGAG-TGGTTACCAAAATTTCATAGG
38825 GTGGTTAATT
Statistics
Matches: 108, Mismatches: 16, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
43 3 0.03
44 66 0.61
45 5 0.05
46 34 0.31
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.37
Consensus pattern (43 bp):
GTTATCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGGTA
Found at i:38934 original size:22 final size:22
Alignment explanation
Indices: 38870--39257 Score: 123
Period size: 22 Copynumber: 17.5 Consensus size: 22
38860 AAAAAGATTT
* *
38870 CAAAATGTCATAGCGAGGTTATA
1 CAAAATTTCATAGAGAGGTTA-A
* * **
38893 C-GAATTTCATAGTGTTGTTAA
1 CAAAATTTCATAGAGAGGTTAA
38914 CAAAATTTCATTAGAG-GGTT-A
1 CAAAATTTCA-TAGAGAGGTTAA
* * * *
38935 CTAATACTTCATCGAGAGGTTAT
1 C-AAAATTTCATAGAGAGGTTAA
* * * *
38958 CAAAATTTTATAGTGTGGTTAT
1 CAAAATTTCATAGAGAGGTTAA
38980 CAAAATTTCATATGA-AGGTTATA
1 CAAAATTTCATA-GAGAGGTTA-A
* * * *
39003 AAAGTCTCAATTTCATAAATA-G-TAC
1 CAA-----AATTTCATAGAGAGGTTAA
* *
39028 CAAAATTTGATAGA-AGGTTAT
1 CAAAATTTCATAGAGAGGTTAA
* * * *
39049 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGAGAGGTTAA
* * *
39070 CGAAATTTCATAAAGGTAGGATTAT
1 CAAAATTTCATAGA-G-AGG-TTAA
* *
39095 CAAAATTT-ATATGA-AGATTAT
1 CAAAATTTCATA-GAGAGGTTAA
* * *
39116 CAAAATTTCATAGTGATGTTAT
1 CAAAATTTCATAGAGAGGTTAA
* * *
39138 CAAAATTTCAAAGCGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAA
* * * *
39160 CAAAATTACATA-ATGTGATTAT
1 CAAAATTTCATAGA-GAGGTTAA
* * *
39182 CAAAATTTCAAAGAGGGGTCAA
1 CAAAATTTCATAGAGAGGTTAA
* * * *
39204 CAAAATTTTATAAAGATGTTAT
1 CAAAATTTCATAGAGAGGTTAA
* *
39226 CAAAATTTCATAAAGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAA
*
39248 CAAATTTTCA
1 CAAAATTTCA
39258 AAATGTGATT
Statistics
Matches: 273, Mismatches: 67, Indels: 51
0.70 0.17 0.13
Matches are distributed among these distances:
19 1 0.00
20 20 0.07
21 30 0.11
22 179 0.66
23 11 0.04
24 4 0.01
25 14 0.05
26 2 0.01
27 2 0.01
28 10 0.04
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGAGAGGTTAA
Found at i:39182 original size:44 final size:44
Alignment explanation
Indices: 39091--39279 Score: 183
Period size: 44 Copynumber: 4.3 Consensus size: 44
39081 AAAGGTAGGA
* * *
39091 TTATCAAAATTT-ATATGA-AGATTATCAAAATTTCATAGTGATG
1 TTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGATG
* *
39134 TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATG-TG
1 TTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGATG
* * * * *
39177 ATTATCAAAATTTCAAAGAGGGGTCAACAAAATTTTATAAAGATG
1 -TTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGATG
* *
39222 TTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATG-TG
1 TTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGATG
39265 ATTA-CAAAAATTTCA
1 -TTATC-AAAATTTCA
39280 TAGTGGTATT
Statistics
Matches: 120, Mismatches: 19, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
43 19 0.16
44 97 0.81
45 4 0.03
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (44 bp):
TTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGATG
Found at i:39208 original size:66 final size:66
Alignment explanation
Indices: 39072--39259 Score: 166
Period size: 66 Copynumber: 2.8 Consensus size: 66
39062 GTGATTATCG
* * * * *
39072 AAATTTCATAAAGGTAGGATTATCAAAATT-TAT-ATGAAGATTATCAAAATTTCATAGTGATGT
1 AAATTTCATAAA-G-AGG-TTATCAAAATTACATAAAG-AGATTATCAAAATTTCAAAGAGAGGT
* *
39135 TATCA
62 CAACA
* * * *
39140 AAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATTATCAAAATTTCAAAGAGGGGTCAA
1 AAATTTCATAA-AGAGGTTATCAAAATTACATAAAGAGATTATCAAAATTTCAAAGAGAGGTCAA
39204 CA
65 CA
* * * * *
39206 AAATTTTATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAA
1 AAATTTCATAAAGAGGTTATCAAAATTACATAAAGAGATTATCAAAATTTCAAA
39260 ATGTGATTAC
Statistics
Matches: 99, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
65 11 0.11
66 72 0.73
67 8 0.08
68 8 0.08
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (66 bp):
AAATTTCATAAAGAGGTTATCAAAATTACATAAAGAGATTATCAAAATTTCAAAGAGAGGTCAAC
A
Found at i:39210 original size:88 final size:88
Alignment explanation
Indices: 39116--39279 Score: 233
Period size: 88 Copynumber: 1.9 Consensus size: 88
39106 TGAAGATTAT
** * *
39116 CAAAATTTCATAGTGATGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTCATAAAGATGTTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATGTGATT
39180 ATC-AAAATTTCAAAGAGGGGTCAA
65 A-CAAAAATTTCAAAGAGGGGTCAA
* * *
39204 CAAAATTTTATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTA
1 CAAAATTTCATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
39269 CAAAAATTTCA
66 CAAAAATTTCA
39280 TAGTGGTATT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
87 1 0.01
88 64 0.96
89 2 0.03
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (88 bp):
CAAAATTTCATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
CAAAAATTTCAAAGAGGGGTCAA
Found at i:39395 original size:19 final size:19
Alignment explanation
Indices: 39365--39429 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
39355 ATGGAGTAAT
*
39365 CAAAATTTCAGGGATGATAC
1 CAAAA-TTCAGGGAGGATAC
*
39385 CAAAATTCAGGGAGGATAT
1 CAAAATTCAGGGAGGATAC
* ** *
39404 CGAAATTCAGTAAGGATAT
1 CAAAATTCAGGGAGGATAC
39423 CAAAATT
1 CAAAATT
39430 TCATATGAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 34 0.87
20 5 0.13
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (19 bp):
CAAAATTCAGGGAGGATAC
Found at i:39443 original size:22 final size:22
Alignment explanation
Indices: 39415--39566 Score: 121
Period size: 22 Copynumber: 6.9 Consensus size: 22
39405 GAAATTCAGT
39415 AAGGATATCAAAATTTCATATG
1 AAGGATATCAAAATTTCATATG
39437 AAGGATATCAAAATTTCATATG
1 AAGGATATCAAAATTTCATATG
* * *
39459 AAGGTTATCAAATTTTCATAGTT
1 AAGGATATCAAAATTTCATA-TG
* * * *
39482 TA-GTTTTCAAAATTTCATAAG
1 AAGGATATCAAAATTTCATATG
* *
39503 AGGGTTATCAAAATTTCATA-G
1 AAGGATATCAAAATTTCATATG
* * * *
39524 TATGTAGATCAAAATTTCATAGG
1 -AAGGATATCAAAATTTCATATG
* *
39547 GA-GATTAACAAAATTTCATA
1 AAGGA-TATCAAAATTTCATA
39567 ATGAGGTAAT
Statistics
Matches: 105, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
21 2 0.02
22 100 0.95
23 3 0.03
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (22 bp):
AAGGATATCAAAATTTCATATG
Found at i:39477 original size:44 final size:44
Alignment explanation
Indices: 39415--39606 Score: 140
Period size: 44 Copynumber: 4.4 Consensus size: 44
39405 GAAATTCAGT
* *
39415 AAGGATATCAAAATTTCATATGAAGGATATCAAAATTTCATATG
1 AAGGTTATCAAAATTTCATATGAAGGATATCAAAATTTCATAAG
* ** * *
39459 AAGGTTATCAAATTTTCATAGTTTA-GTTTTCAAAATTTCATAAG
1 AAGGTTATCAAAATTTCATA-TGAAGGATATCAAAATTTCATAAG
* * * * *
39503 AGGGTTATCAAAATTTCATA-GTATGTAGATCAAAATTTCATAGG
1 AAGGTTATCAAAATTTCATATG-AAGGATATCAAAATTTCATAAG
* * * ** *
39547 GAGATTAACAAAATTTCATAATG-AGG-TAATCAAAAAATCATAGG
1 AAGGTTATCAAAATTTCAT-ATGAAGGAT-ATCAAAATTTCATAAG
* *
39591 GAGCTTATCAAAATTT
1 AAGGTTATCAAAATTT
39607 GTAGTTATTA
Statistics
Matches: 114, Mismatches: 28, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
44 110 0.96
45 3 0.03
46 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (44 bp):
AAGGTTATCAAAATTTCATATGAAGGATATCAAAATTTCATAAG
Found at i:39535 original size:66 final size:66
Alignment explanation
Indices: 39422--39545 Score: 169
Period size: 66 Copynumber: 1.9 Consensus size: 66
39412 AGTAAGGATA
* * *
39422 TCAAAATTTCATATGAAGGATATCAAAATTTCATATGAAGGTTATCAAATTTTCATAGTTTAGTT
1 TCAAAATTTCATAAGAAGGATATCAAAATTTCATATGAAGGTGATCAAAATTTCATAGTTTAGTT
39487 T
66 T
* * * *
39488 TCAAAATTTCATAAGAGGGTTATCAAAATTTCATA-GTATGTAGATCAAAATTTCATAG
1 TCAAAATTTCATAAGAAGGATATCAAAATTTCATATGAAGGT-GATCAAAATTTCATAG
39546 GGAGATTAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 4 0.08
66 46 0.92
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.38
Consensus pattern (66 bp):
TCAAAATTTCATAAGAAGGATATCAAAATTTCATATGAAGGTGATCAAAATTTCATAGTTTAGTT
T
Found at i:39559 original size:66 final size:65
Alignment explanation
Indices: 39423--39581 Score: 160
Period size: 66 Copynumber: 2.4 Consensus size: 65
39413 GTAAGGATAT
* * * * ** *
39423 CAAAATTTCATATGAAGGATATCAAAATTTCATATGAAGGTTATCAAATTTTCATAGTTTAGTTT
1 CAAAATTTCATAAG-AGGTTATCAAAATTTCATATGAAGGTGATCAAAATTTCATAGTGGAGTTA
*
39488 T
65 A
* *
39489 CAAAATTTCATAAGAGGGTTATCAAAATTTCATA-GTATGTAGATCAAAATTTCATAG-GGAGAT
1 CAAAATTTCATAAGA-GGTTATCAAAATTTCATATGAAGGT-GATCAAAATTTCATAGTGGAG-T
39552 TAA
63 TAA
*
39555 CAAAATTTCATAATGAGGTAATCAAAA
1 CAAAATTTCATAA-GAGGTTATCAAAA
39582 AATCATAGGG
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
65 7 0.09
66 69 0.88
67 2 0.03
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (65 bp):
CAAAATTTCATAAGAGGTTATCAAAATTTCATATGAAGGTGATCAAAATTTCATAGTGGAGTTAA
Found at i:42938 original size:53 final size:53
Alignment explanation
Indices: 42838--42937 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 53
42828 GACGTGGCAC
* **
42838 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
* **
42891 GCCACATGTACC-AAAAGTGACACATGTCACGCCATGTGTACCAAAAA
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAA
42938 ATGACACGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
52 30 0.73
53 11 0.27
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:61387 original size:2 final size:2
Alignment explanation
Indices: 61382--61406 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61372 ATAATAAAAA
61382 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
61407 TACAAGTGGC
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:61460 original size:2 final size:2
Alignment explanation
Indices: 61453--61509 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
61443 TTACCTAGGT
* * *
61453 TA TA TA TA TA TA TA TA T- TA CA TA CA TA CA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61494 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
61510 CTCCAATAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:66558 original size:20 final size:20
Alignment explanation
Indices: 66533--66574 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
66523 AATTATCTCC
66533 CATTGATATTCCCCAAACTG
1 CATTGATATTCCCCAAACTG
66553 CATTGATATTCCCCAAACTG
1 CATTGATATTCCCCAAACTG
66573 CA
1 CA
66575 GGGGAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.29
Consensus pattern (20 bp):
CATTGATATTCCCCAAACTG
Found at i:97470 original size:22 final size:23
Alignment explanation
Indices: 97442--97484 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
97432 TCCTAGGAGT
97442 AGGTTTTACT-TTCCTACCAGAA
1 AGGTTTTACTATTCCTACCAGAA
97464 AGGTTTTACTATTCCTACCAG
1 AGGTTTTACTATTCCTACCAG
97485 GATTAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (23 bp):
AGGTTTTACTATTCCTACCAGAA
Found at i:102197 original size:2 final size:2
Alignment explanation
Indices: 102190--102226 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
102180 GAAAAATGAA
102190 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
102227 CACACTTCAC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:105419 original size:2 final size:2
Alignment explanation
Indices: 105410--105445 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
105400 TATCTCTTCT
105410 TA TA -A 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
105446 CTTAATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:107816 original size:24 final size:24
Alignment explanation
Indices: 107789--107836 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
107779 AATCTCTAAC
107789 ACTTTCAACTTGAACATAATTGGT
1 ACTTTCAACTTGAACATAATTGGT
*
107813 ACTTTCAACTTGAACGTAATTGGT
1 ACTTTCAACTTGAACATAATTGGT
107837 TTTGAATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (24 bp):
ACTTTCAACTTGAACATAATTGGT
Found at i:107888 original size:30 final size:30
Alignment explanation
Indices: 107839--107912 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 30
107829 TAATTGGTTT
*
107839 TGAATCAATAAGA-TTTTTTTTG-GCACA-A
1 TGAATCAATAAGATTTTTTTTTGAG-AAATA
107867 TGAATCAATAAGATTTTTTTTTGAGAAATA
1 TGAATCAATAAGATTTTTTTTTGAGAAATA
107897 TGAATCAATAAGATTT
1 TGAATCAATAAGATTT
107913 AGAATACCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 13 0.31
29 11 0.26
30 18 0.43
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.41
Consensus pattern (30 bp):
TGAATCAATAAGATTTTTTTTTGAGAAATA
Found at i:109973 original size:1 final size:1
Alignment explanation
Indices: 109967--109994 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
109957 TGGATTAGAA
109967 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
109995 GTCTTGAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:115731 original size:49 final size:49
Alignment explanation
Indices: 115659--115760 Score: 204
Period size: 49 Copynumber: 2.1 Consensus size: 49
115649 CAAGGCCTTG
115659 TCACTTGATCTTAGTCAAAACGCTGAGAAAGGTATCATAGACTTTCATT
1 TCACTTGATCTTAGTCAAAACGCTGAGAAAGGTATCATAGACTTTCATT
115708 TCACTTGATCTTAGTCAAAACGCTGAGAAAGGTATCATAGACTTTCATT
1 TCACTTGATCTTAGTCAAAACGCTGAGAAAGGTATCATAGACTTTCATT
115757 TCAC
1 TCAC
115761 GAACAAGAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (49 bp):
TCACTTGATCTTAGTCAAAACGCTGAGAAAGGTATCATAGACTTTCATT
Found at i:123138 original size:20 final size:19
Alignment explanation
Indices: 123124--123172 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 19
123114 AATTGTAATC
123124 GATAAATAAATATTGAGAT
1 GATAAATAAATATTGAGAT
* *
123143 GATAAATGAATA-T-A-TT
1 GATAAATAAATATTGAGAT
123159 GATAAATAAATATT
1 GATAAATAAATATT
123173 TTAAATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 2 0.08
18 1 0.04
19 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (19 bp):
GATAAATAAATATTGAGAT
Done.