Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024024.1 Corchorus olitorius cultivar O-4 contig24057, 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: 96368
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:8280 original size:16 final size:16
Alignment explanation
Indices: 8261--8304 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
8251 ACCCGCTCGA
*
8261 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAAAT
* *
8277 ACCCGAGCCTGAAAAT
1 ACCCGAACCCGAAAAT
8293 ACCCGAACCCGA
1 ACCCGAACCCGA
8305 TGCAACCCGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.39, G:0.16, T:0.09
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:9137 original size:13 final size:12
Alignment explanation
Indices: 9101--9147 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
9091 TCAATCTTTA
*
9101 TATATATTGATAA
1 TATATATT-ATAT
*
9114 TA-ATGTTATAT
1 TATATATTATAT
9125 TATATTATTATAT
1 TATA-TATTATAT
9138 TATATATTAT
1 TATATATTAT
9148 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:9336 original size:16 final size:16
Alignment explanation
Indices: 9315--9371 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
9305 CTACCTGAGA
9315 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
**
9331 CCGAACCCG-ACTTAAC
1 CCGAACCCGAAAAT-AC
* *
9347 CCGAGCACGAAAATAC
1 CCGAACCCGAAAATAC
9363 CCGAACCCG
1 CCGAACCCG
9372 CCCAATTGCC
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
15 2 0.06
16 27 0.87
17 2 0.06
ACGTcount: A:0.37, C:0.40, G:0.16, T:0.07
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:11697 original size:22 final size:23
Alignment explanation
Indices: 11649--11697 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
11639 AGACAACACT
*
11649 ACTC-ATGAACTACTCGAGCTCG
1 ACTCGATGAACTACTCGAACTCG
* *
11671 CCTCGATGAA-TACTCGAATTCG
1 ACTCGATGAACTACTCGAACTCG
11693 ACTCG
1 ACTCG
11698 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (23 bp):
ACTCGATGAACTACTCGAACTCG
Found at i:12579 original size:22 final size:22
Alignment explanation
Indices: 12548--12593 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
12538 CGGCTCGACA
*
12548 AATTATAACAAAAAATAATAAG
1 AATTACAACAAAAAATAATAAG
12570 AATTACAACAAAAAATAATAAG
1 AATTACAACAAAAAATAATAAG
12592 AA
1 AA
12594 GATAAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.20
Consensus pattern (22 bp):
AATTACAACAAAAAATAATAAG
Found at i:12629 original size:30 final size:30
Alignment explanation
Indices: 12595--12694 Score: 71
Period size: 30 Copynumber: 3.2 Consensus size: 30
12585 TAATAAGAAG
12595 ATAAAAGAAACCACAAAATAATGAAATTGA
1 ATAAAAGAAACCACAAAATAATGAAATTGA
* * *
12625 ATAAAGGGGAAATTACAACAAAA-AAT--AATAAGAA
1 ATAAA--AG-AA--ACCACAAAATAATGAAAT-TG-A
*
12659 GATAAAAGAAACCACAAAATAATGAAATTTA
1 -ATAAAAGAAACCACAAAATAATGAAATTGA
12690 ATAAA
1 ATAAA
12695 GGGGAAAAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 22
0.64 0.09 0.27
Matches are distributed among these distances:
30 18 0.35
31 4 0.08
32 6 0.12
33 7 0.13
34 4 0.08
35 13 0.25
ACGTcount: A:0.64, C:0.08, G:0.11, T:0.17
Consensus pattern (30 bp):
ATAAAAGAAACCACAAAATAATGAAATTGA
Found at i:12646 original size:65 final size:65
Alignment explanation
Indices: 12570--12701 Score: 255
Period size: 65 Copynumber: 2.0 Consensus size: 65
12560 AAATAATAAG
12570 AATTACAACAAAAAATAATAAGAAGATAAAAGAAACCACAAAATAATGAAATTGAATAAAGGGGA
1 AATTACAACAAAAAATAATAAGAAGATAAAAGAAACCACAAAATAATGAAATTGAATAAAGGGGA
*
12635 AATTACAACAAAAAATAATAAGAAGATAAAAGAAACCACAAAATAATGAAATTTAATAAAGGGGA
1 AATTACAACAAAAAATAATAAGAAGATAAAAGAAACCACAAAATAATGAAATTGAATAAAGGGGA
12700 AA
1 AA
12702 AACAAAATAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.64, C:0.08, G:0.13, T:0.16
Consensus pattern (65 bp):
AATTACAACAAAAAATAATAAGAAGATAAAAGAAACCACAAAATAATGAAATTGAATAAAGGGGA
Found at i:12929 original size:25 final size:25
Alignment explanation
Indices: 12901--12951 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
12891 AAAAAGGGGG
12901 GAAAAGCCAAAAAGCAAATGGAAAA
1 GAAAAGCCAAAAAGCAAATGGAAAA
12926 GAAAAGCCAAAAAGCAAATGGAAAA
1 GAAAAGCCAAAAAGCAAATGGAAAA
12951 G
1 G
12952 GCAAGAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.63, C:0.12, G:0.22, T:0.04
Consensus pattern (25 bp):
GAAAAGCCAAAAAGCAAATGGAAAA
Found at i:14561 original size:2 final size:2
Alignment explanation
Indices: 14556--14582 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14546 GGAAGTAAGC
14556 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 T
14583 TTACGATTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28864 original size:22 final size:21
Alignment explanation
Indices: 28839--29379 Score: 239
Period size: 22 Copynumber: 25.2 Consensus size: 21
28829 AAATTTTTTT
28839 TAACCTCCTTATGAAATTTTGA
1 TAACCTCC-TATGAAATTTTGA
* * *
28861 TAACCTCCCTAAGGAATTTTAA
1 TAACCT-CCTATGAAATTTTGA
*
28883 AAACCTCACTATGAAATTTTGA
1 TAACCTC-CTATGAAATTTTGA
*
28905 TAA-CTTCTGAATGAAATTTTGA
1 TAACCTCCT--ATGAAATTTTGA
* * *
28927 TAACCAACACTATGAGATGTTGA
1 TAACC-TC-CTATGAAATTTTGA
* * *
28950 TAACCTTCATATGATATATTGA
1 TAACC-TCCTATGAAATTTTGA
* * * *
28972 TAACCACGTTATGAAAATTTAA
1 TAACCTC-CTATGAAATTTTGA
* *
28994 GAACCTCCATTTG-AATTGTT-A
1 TAACCTCC-TATGAAATT-TTGA
* * *
29015 GTAATCACACTCTGAAATTTTGA
1 -TAACCTC-CTATGAAATTTTGA
* * *
29038 TAATCACACTATGAAATTGTGA
1 TAACCTC-CTATGAAATTTTGA
* *
29060 TAACCTTGCTATAAAATTTTGA
1 TAACC-TCCTATGAAATTTTGA
*
29082 TAAACCTCCTTATAAAATTTT-A
1 T-AACCTCC-TATGAAATTTTGA
* *
29104 TAACCTTCTTATGAAATCTTGA
1 TAACC-TCCTATGAAATTTTGA
*
29126 TAA----CTA-CAAATTTTGA
1 TAACCTCCTATGAAATTTTGA
**
29142 TAACCTCCCTATGATTTTTTGA
1 TAACCT-CCTATGAAATTTTGA
* *
29164 TAACCTCATTATGAAATTTTGT
1 TAACCTC-CTATGAAATTTTGA
*
29186 TAATCTCCCTATGAAATTTTGA
1 TAACCT-CCTATGAAATTTTGA
* * * *
29208 TCTACATGCTATGAAATTTTGG
1 T-AACCTCCTATGAAATTTTGA
*
29230 TAACCCTCTTATGAAATTTTGA
1 TAA-CCTCCTATGAAATTTTGA
* **** *
29252 AAATAAACTACGAAATTTTGA
1 TAACCTCCTATGAAATTTTGA
*
29273 TAACCTTCATATGAAATTTTGA
1 TAACC-TCCTATGAAATTTTGA
* *
29295 TATCCTCC-CTGAAATTTTGA
1 TAACCTCCTATGAAATTTTGA
* * * *
29315 TTA-CTCCATAGTAAAAGTTTAA
1 TAACCTCC-TA-TGAAATTTTGA
* *
29337 TAACCTCC-CT--AA-TTTGG
1 TAACCTCCTATGAAATTTTGA
*
29354 TAACCATACTATGAAATTTTGA
1 TAACC-TCCTATGAAATTTTGA
29376 TAAC
1 TAAC
29380 TTCCCCATAA
Statistics
Matches: 383, Mismatches: 97, Indels: 78
0.69 0.17 0.14
Matches are distributed among these distances:
16 11 0.03
17 10 0.03
18 4 0.01
19 5 0.01
20 15 0.04
21 44 0.11
22 245 0.64
23 47 0.12
25 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
TAACCTCCTATGAAATTTTGA
Found at i:28972 original size:45 final size:44
Alignment explanation
Indices: 28889--28977 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 44
28879 TTAAAAACCT
* *
28889 CACTATGAAATTTTGATAACTTCTGAATGAAATTTTGATAACCAA
1 CACTATGAAATGTTGATAACTTCT-AATGAAATATTGATAACCAA
* *
28934 CACTATGAGATGTTGATAACCTTC-ATATGATATATTGATAACCA
1 CACTATGAAATGTTGATAA-CTTCTA-ATGAAATATTGATAACCA
28978 CGTTATGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 1 0.03
45 33 0.87
46 4 0.11
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (44 bp):
CACTATGAAATGTTGATAACTTCTAATGAAATATTGATAACCAA
Found at i:29203 original size:126 final size:129
Alignment explanation
Indices: 29027--29301 Score: 297
Period size: 126 Copynumber: 2.1 Consensus size: 129
29017 AATCACACTC
* * ** *
29027 TGAAATTTTGATAATCACACTATGAAATTGTGATAACCTTGCTATAAAATTTTGATAAACCTCCT
1 TGAAATTTTGATAACCTCACTATGAAATTGTGATAACCTCCCTATAAAATTTTGATAAACATCC-
* *
29092 TATAAAATTTT-ATAACCTTCTTATGAAATCTTG-AT-AACTAC-AAATTTTGATAACCTCCCTA
65 TATAAAATTTTGATAACCCTCTTATGAAATCTTGAATAAACTACGAAATTTTGATAACCTCCATA
** * * * * * ** *
29153 TGATTTTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACATGCT
1 TGAAATTTTGATAACCTCACTATGAAATTGTGATAACCTCCCTATAAAATTTTGATAAACATCCT
* * * *
29218 ATGAAATTTTGGTAACCCTCTTATGAAATTTTGAAAATAAACTACGAAATTTTGATAACCTTCAT
66 ATAAAATTTTGATAACCCTCTTATGAAATCTTG--AATAAACTACGAAATTTTGATAACCTCCAT
29283 A
129 A
*
29284 TGAAATTTTGATATCCTC
1 TGAAATTTTGATAACCTC
29302 CCTGAAATTT
Statistics
Matches: 119, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
125 10 0.08
126 68 0.57
129 2 0.02
130 6 0.05
131 33 0.28
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (129 bp):
TGAAATTTTGATAACCTCACTATGAAATTGTGATAACCTCCCTATAAAATTTTGATAAACATCCT
ATAAAATTTTGATAACCCTCTTATGAAATCTTGAATAAACTACGAAATTTTGATAACCTCCATA
Found at i:29344 original size:42 final size:42
Alignment explanation
Indices: 29263--29346 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
29253 AATAAACTAC
* * * * *
29263 GAAATTTTGATAACCTTCATATGAAATTTTGATATCCTCCCT
1 GAAATTTTGATAACCTCCATATAAAAGTTTAATAACCTCCCT
*
29305 GAAATTTTGATTA-CTCCATAGTAAAAGTTTAATAACCTCCCT
1 GAAATTTTGATAACCTCCATA-TAAAAGTTTAATAACCTCCCT
29347 AATTTGGTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 6 0.17
42 29 0.83
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (42 bp):
GAAATTTTGATAACCTCCATATAAAAGTTTAATAACCTCCCT
Found at i:29573 original size:22 final size:23
Alignment explanation
Indices: 29393--29587 Score: 81
Period size: 22 Copynumber: 8.9 Consensus size: 23
29383 CCCATAAACG
* *
29393 ACTATGAAATTTTGGTAATC-AC
1 ACTATGAAATTTTGATAATCTTC
* * * *
29415 ATTTTGAAAATTTGATAACCTT-
1 ACTATGAAATTTTGATAATCTTC
**
29437 TTTATGAAATTTTGATAACCTCTTC
1 ACTATGAAATTTTGATAA--TCTTC
* * **
29462 A-TA--AAATTTTGTTGA-CCCC
1 ACTATGAAATTTTGATAATCTTC
* *
29481 TCTATGAAATTTTGAT-ATTTTC
1 ACTATGAAATTTTGATAATCTTC
* * * *
29503 ATTATGTAATTTGGATAA-CCTC
1 ACTATGAAATTTTGATAATCTTC
* * **
29525 ACTTTGAAATATTGATAA-CAAC
1 ACTATGAAATTTTGATAATCTTC
29547 ACTATGAAATTTTGATAATCTTC
1 ACTATGAAATTTTGATAATCTTC
29570 -CTAT-AAATTTCT-ATAATC
1 ACTATGAAATTT-TGATAATC
29588 CGATCTCTAT
Statistics
Matches: 125, Mismatches: 37, Indels: 23
0.68 0.20 0.12
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 13 0.10
22 100 0.80
23 3 0.02
24 5 0.04
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (23 bp):
ACTATGAAATTTTGATAATCTTC
Found at i:29700 original size:22 final size:22
Alignment explanation
Indices: 29685--29746 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
29675 ATAACCTTCA
29685 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
** *
29707 TAAAAAATTTTAATAACCACAC
1 TATGAAATTTTGATAACCACAC
*
29729 TATGAAAATTTGATAACC
1 TATGAAATTTTGATAACC
29747 TCCCTACCTC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:29797 original size:22 final size:22
Alignment explanation
Indices: 29759--29818 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
29749 CCTACCTCCT
*
29759 TATGAAATTTTGTTAACCACAC
1 TATGAAATTTTGATAACCACAC
* *
29781 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCACAC
*
29803 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
29819 TCTCTTTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:29876 original size:22 final size:22
Alignment explanation
Indices: 29836--30035 Score: 99
Period size: 22 Copynumber: 9.0 Consensus size: 22
29826 GATAAACTTT
*
29836 CTATGAAATTGTGAA-AACCACA
1 CTATGAAATT-TTAATAACCACA
* **
29858 CTATGAAATTTCAATAACC-TT
1 CTATGAAATTTTAATAACCACA
**
29879 CTAAAAAATTTTAATAACCTGATC-
1 CTATGAAATTTTAATAACC--A-CA
**
29903 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTAATAACCACA
*
29925 CTATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTAATAAC--CACA
* **
29948 -TGTGAAATTTTGGTAACCACA
1 CTATGAAATTTTAATAACCACA
* * * *
29969 CTATGGAATATTGATAACCTC-
1 CTATGAAATTTTAATAACCACA
*
29990 CTCATGAAATTATAATAACCATC-
1 CT-ATGAAATTTTAATAACCA-CA
* * *
30013 TTATTAAATTTTGATAACCACA
1 CTATGAAATTTTAATAACCACA
30035 C
1 C
30036 AGAGACAAGA
Statistics
Matches: 136, Mismatches: 29, Indels: 26
0.71 0.15 0.14
Matches are distributed among these distances:
20 1 0.01
21 25 0.18
22 90 0.66
23 4 0.03
24 16 0.12
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTAATAACCACA
Found at i:29998 original size:44 final size:43
Alignment explanation
Indices: 29901--30000 Score: 146
Period size: 44 Copynumber: 2.3 Consensus size: 43
29891 AATAACCTGA
* *
29901 TCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACT
1 TCCTATGAAATTTTGGTAACCACACTATGAAATATTGATAACC
* *
29944 TCCATGTGAAATTTTGGTAACCACACTATGGAATATTGATAACC
1 TCC-TATGAAATTTTGGTAACCACACTATGAAATATTGATAACC
29988 TCCTCATGAAATT
1 TCCT-ATGAAATT
30001 ATAATAACCA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
43 4 0.08
44 46 0.92
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (43 bp):
TCCTATGAAATTTTGGTAACCACACTATGAAATATTGATAACC
Found at i:30009 original size:44 final size:44
Alignment explanation
Indices: 29917--30010 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 44
29907 GAAATTTTGG
* * * * **
29917 TAACCACACTATGAAATTTTGATAACTTCCATGTGAAATTTTGG
1 TAACCACACTATGAAATATTGATAACCTCCATATGAAATTATAA
*
29961 TAACCACACTATGGAATATTGATAACCTCC-TCATGAAATTATAA
1 TAACCACACTATGAAATATTGATAACCTCCAT-ATGAAATTATAA
30005 TAACCA
1 TAACCA
30011 TCTTATTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (44 bp):
TAACCACACTATGAAATATTGATAACCTCCATATGAAATTATAA
Found at i:30231 original size:19 final size:20
Alignment explanation
Indices: 30200--30237 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
30190 TATTGACATT
30200 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
30219 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
30238 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:31264 original size:2 final size:2
Alignment explanation
Indices: 31257--31290 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
31247 TTCGTACTTT
*
31257 TA TA TA TA GTA TA GA 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
31291 CAAATTCTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:33716 original size:37 final size:37
Alignment explanation
Indices: 33666--33739 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
33656 CGGGTTGACC
*
33666 CAAGTCAGGTTTTTTCCTTTTGTAAAATTAGGTACAA
1 CAAGTCAGGTTTTTTCCTTTGGTAAAATTAGGTACAA
33703 CAAGTCAGGTTTTTTCCTTTGGTAAAATTAGGTACAA
1 CAAGTCAGGTTTTTTCCTTTGGTAAAATTAGGTACAA
33740 TGTCTCTACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (37 bp):
CAAGTCAGGTTTTTTCCTTTGGTAAAATTAGGTACAA
Found at i:34513 original size:22 final size:23
Alignment explanation
Indices: 34482--34526 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
34472 AAGTTTTTAT
34482 TTTTTATCTTT-TTTCTCTTCTTC
1 TTTTTATCTTTCTTTCT-TTCTTC
34505 TTTTT-TCTTTCTTTCTTTCTTC
1 TTTTTATCTTTCTTTCTTTCTTC
34527 CTCCCTCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTTATCTTTCTTTCTTTCTTC
Found at i:34516 original size:14 final size:16
Alignment explanation
Indices: 34488--34522 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
34478 TTATTTTTTA
34488 TCTTTTTTCTCTTC-T
1 TCTTTTTTCTCTTCTT
34503 TCTTTTTTCT-TTCTT
1 TCTTTTTTCTCTTCTT
34518 TCTTT
1 TCTTT
34523 CTTCCTCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTTTTTTCTCTTCTT
Found at i:39599 original size:31 final size:31
Alignment explanation
Indices: 39553--39657 Score: 102
Period size: 31 Copynumber: 3.3 Consensus size: 31
39543 GAAGATTCTG
* *
39553 TTTTTTAATTATGTTTTGCATTTTTGTTTAA
1 TTTTTAAATTCTGTTTTGCATTTTTGTTTAA
* *
39584 TTTTTAAATTCTGTTTTGCATTTCTGTTTTA
1 TTTTTAAATTCTGTTTTGCATTTTTGTTTAA
* * * * *
39615 CTTTTCAATTCCGTTTTTCAATTTTGTTTTACA
1 TTTTTAAATTCTGTTTTGCATTTTTG-TTTA-A
39648 TTTTTCAAAT
1 TTTTT-AAAT
39658 AGATTTCAAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
31 47 0.81
32 3 0.05
33 5 0.09
34 3 0.05
ACGTcount: A:0.19, C:0.10, G:0.08, T:0.63
Consensus pattern (31 bp):
TTTTTAAATTCTGTTTTGCATTTTTGTTTAA
Found at i:44277 original size:15 final size:15
Alignment explanation
Indices: 44254--44320 Score: 52
Period size: 15 Copynumber: 4.7 Consensus size: 15
44244 TATCATTCAT
*
44254 AATATATCCTTCAAA
1 AATAAATCCTTCAAA
*
44269 AATAAATCCTTTAAA
1 AATAAATCCTTCAAA
* **
44284 AA-AAGA-CATTCTTA
1 AATAA-ATCCTTCAAA
44298 AAT--ATCCTTCAAA
1 AATAAATCCTTCAAA
44311 AATAAATCCT
1 AATAAATCCT
44321 AGGGATGCAA
Statistics
Matches: 38, Mismatches: 9, Indels: 10
0.67 0.16 0.18
Matches are distributed among these distances:
12 1 0.03
13 8 0.21
14 8 0.21
15 21 0.55
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.31
Consensus pattern (15 bp):
AATAAATCCTTCAAA
Found at i:45467 original size:18 final size:18
Alignment explanation
Indices: 45444--45491 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
45434 CGAATCGGAA
45444 TCGAACCCGAGTCCAAAC
1 TCGAACCCGAGTCCAAAC
45462 TCGAACCCGAGTCCAAAC
1 TCGAACCCGAGTCCAAAC
45480 TCGAACCCGAGT
1 TCGAACCCGAGT
45492 TCTACCCGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.31, C:0.38, G:0.19, T:0.12
Consensus pattern (18 bp):
TCGAACCCGAGTCCAAAC
Found at i:45681 original size:31 final size:29
Alignment explanation
Indices: 45608--45681 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
45598 TTATAAAAAT
* *
45608 CTCAATTTGATACCAAACGTTTAAACTAG
1 CTCAATTTGATACCAAACGTTCAAAATAG
* * * *
45637 CTCAAATTAATACCAAATGTTACAAAATCGG
1 CTCAATTTGATACCAAACGTT-CAAAAT-AG
45668 CTCAATTTGATACC
1 CTCAATTTGATACC
45682 TTTCTAGGCT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 18 0.51
30 4 0.11
31 13 0.37
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (29 bp):
CTCAATTTGATACCAAACGTTCAAAATAG
Found at i:47285 original size:26 final size:28
Alignment explanation
Indices: 47256--47314 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 28
47246 CAGGGCGTCA
*
47256 TCCTTCTAGATGGGAGACGGA-AA-TCT
1 TCCTTCTAGATGGCAGACGGATAATTCT
* *
47282 TCCTCCTAGATGGCAGATGGATAATTCT
1 TCCTTCTAGATGGCAGACGGATAATTCT
47310 TCCTT
1 TCCTT
47315 TTTCCTATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 18 0.67
27 2 0.07
28 7 0.26
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (28 bp):
TCCTTCTAGATGGCAGACGGATAATTCT
Found at i:64489 original size:25 final size:24
Alignment explanation
Indices: 64456--64504 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
64446 GTTGTTGCAG
*
64456 GAAATGGCGCAGGACTTGAGAGAA
1 GAAATGGCGCAGGACCTGAGAGAA
*
64480 GAAAGTGGCGCAGGGCCTGAGAGAA
1 GAAA-TGGCGCAGGACCTGAGAGAA
64505 AATAAGCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.35, C:0.14, G:0.41, T:0.10
Consensus pattern (24 bp):
GAAATGGCGCAGGACCTGAGAGAA
Found at i:67853 original size:19 final size:19
Alignment explanation
Indices: 67831--67882 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
67821 GGGCTGAAAT
67831 TAATTAATTATTAAATAAA
1 TAATTAATTATTAAATAAA
* * *
67850 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAAATAAA
67869 TAATT-ATTATTAAA
1 TAATTAATTATTAAA
67883 ATTACCACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
18 9 0.35
19 16 0.62
20 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TAATTAATTATTAAATAAA
Found at i:80706 original size:13 final size:13
Alignment explanation
Indices: 80688--80713 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
80678 CTTGGCATGA
80688 GTGATGATTTTTG
1 GTGATGATTTTTG
80701 GTGATGATTTTTG
1 GTGATGATTTTTG
80714 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:82453 original size:22 final size:22
Alignment explanation
Indices: 82428--82479 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
82418 TTTTCAACCT
*
82428 GTTCATCACGAGTTCTTCACTC
1 GTTCATCACAAGTTCTTCACTC
82450 GTTCATCACAAGTTCTTCACTC
1 GTTCATCACAAGTTCTTCACTC
82472 GTTCATCA
1 GTTCATCA
82480 ACTTTTCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.37
Consensus pattern (22 bp):
GTTCATCACAAGTTCTTCACTC
Found at i:86584 original size:18 final size:18
Alignment explanation
Indices: 86561--86605 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
86551 CTCCTCTTGC
86561 ATGAAAGCACTTCTTTTT
1 ATGAAAGCACTTCTTTTT
86579 ATGAAAGCACTTCTTTTT
1 ATGAAAGCACTTCTTTTT
86597 ATGAAAGCA
1 ATGAAAGCA
86606 ATTTTTTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (18 bp):
ATGAAAGCACTTCTTTTT
Found at i:86867 original size:4 final size:4
Alignment explanation
Indices: 86845--86882 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
86835 TCTAAGTATT
86845 AATC AATC -AT- AATC AAATC AATC AATC AATC AATC AAT
1 AATC AATC AATC AATC -AATC AATC AATC AATC AATC AAT
86883 ATATGCATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 4 0.13
4 23 0.74
5 4 0.13
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (4 bp):
AATC
Found at i:87065 original size:25 final size:25
Alignment explanation
Indices: 87035--87091 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
87025 AATTTATATT
87035 ATGCATGCTCATGTGATTTATTTAA
1 ATGCATGCTCATGTGATTTATTTAA
87060 ATGCATGCTCATGTGATTTATTTAA
1 ATGCATGCTCATGTGATTTATTTAA
87085 ATGCATG
1 ATGCATG
87092 AAATAAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (25 bp):
ATGCATGCTCATGTGATTTATTTAA
Found at i:87559 original size:21 final size:21
Alignment explanation
Indices: 87535--87589 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
87525 GGCATGGAAT
* *
87535 GGTGATGGCACGGGCATAGCC
1 GGTGGTGGCACGGGCATAACC
* *
87556 GGTGGTAGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATAACC
87577 GGTGGTGGCACGG
1 GGTGGTGGCACGG
87590 TGATTGGGCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.16, C:0.22, G:0.45, T:0.16
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATAACC
Found at i:90776 original size:27 final size:28
Alignment explanation
Indices: 90736--90808 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
90726 AATGGAGTGG
*
90736 AAATGACCACAATGCCCCCT-GAAGCAA
1 AAATGACCAAAATGCCCCCTAGAAGCAA
* ** *
90763 AAATGACTAAAATGCCCCCTAGGTGTAA
1 AAATGACCAAAATGCCCCCTAGAAGCAA
90791 AAATGACCAAAATGCCCC
1 AAATGACCAAAATGCCCC
90809 TGGATGTGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 18 0.46
28 21 0.54
ACGTcount: A:0.41, C:0.29, G:0.15, T:0.15
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCCTAGAAGCAA
Found at i:90809 original size:27 final size:27
Alignment explanation
Indices: 90736--90864 Score: 109
Period size: 27 Copynumber: 4.7 Consensus size: 27
90726 AATGGAGTGG
* * *
90736 AAATGACCACAATGCCCCCT-GAAGCAA
1 AAATGACCAAAATG-CCCCTGGATGTAA
*
90763 AAATGACTAAAATGCCCCCTAGG-TGTAA
1 AAATGACCAAAATG-CCCCT-GGATGTAA
**
90791 AAATGACCAAAATGCCCCTGGATGTGC
1 AAATGACCAAAATGCCCCTGGATGTAA
* * * *
90818 AAATGACTAAAACGCCCCTGGATTTTGA
1 AAATGACCAAAATGCCCCTGGA-TGTAA
90846 AAATGACCCAAAATGCCCC
1 AAATGA-CCAAAATGCCCC
90865 ATAGATGACC
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
26 2 0.02
27 46 0.55
28 25 0.30
29 11 0.13
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGATGTAA
Found at i:91177 original size:52 final size:50
Alignment explanation
Indices: 91113--91234 Score: 172
Period size: 50 Copynumber: 2.4 Consensus size: 50
91103 CGATCAATTT
* * *
91113 CTTTGAATTGTCTTCCACTCTAATATATTAAAAGGACCGTCTTCCGCATATC
1 CTTTGAACTGTCTACCAAT-TAA-ATATTAAAAGGACCGTCTTCCGCATATC
* * *
91165 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTAAATATTAAAAGGACCGTCTTCCGCATATC
91215 CTTTGAACTGTCTACCAATT
1 CTTTGAACTGTCTACCAATT
91235 CAATTCTATA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 46 0.72
51 2 0.03
52 16 0.25
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.36
Consensus pattern (50 bp):
CTTTGAACTGTCTACCAATTAAATATTAAAAGGACCGTCTTCCGCATATC
Found at i:91201 original size:50 final size:51
Alignment explanation
Indices: 91140--91247 Score: 191
Period size: 50 Copynumber: 2.1 Consensus size: 51
91130 CTCTAATATA
91140 TTAAAAGGACCGTCTTCCGCATATCCTTTGAACTGTCTACCAATTCAA-TC
1 TTAAAAGGACCGTCTTCCGCATATCCTTTGAACTGTCTACCAATTCAATTC
*
91190 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTC
1 TTAAAAGGACCGTCTTCCGCATATCCTTTGAACTGTCTACCAATTCAATTC
91241 TATAAAA
1 T-TAAAA
91248 AGGTAATGCA
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
50 47 0.85
51 3 0.05
52 5 0.09
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
TTAAAAGGACCGTCTTCCGCATATCCTTTGAACTGTCTACCAATTCAATTC
Found at i:91334 original size:50 final size:50
Alignment explanation
Indices: 91259--91491 Score: 369
Period size: 50 Copynumber: 4.7 Consensus size: 50
91249 GGTAATGCAC
* * * * *
91259 CGTATGGAAACAAATGTGACTTGTGGAAAAGCCCACGTTGATAATTGACT
1 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACT
* *
91309 CGTATGGAAACGAGTTTAGCTTGTGGAAAAGCCTGA-GTTGATAATTGACT
1 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC-CATGTTGATAATTGACT
*
91359 CGTATGGAAACGAGTTTGGCTTATGGAAAAGCCCATGTTGATAATTGACT
1 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACT
*
91409 CGTATGGAAACGAGTTTGGCTTATGGAAAAGCCCATGTTGATAATTGACT
1 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACT
91459 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
91492 TGTAGCATTC
Statistics
Matches: 171, Mismatches: 10, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
49 1 0.01
50 169 0.99
51 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.28
Consensus pattern (50 bp):
CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACT
Found at i:92288 original size:48 final size:48
Alignment explanation
Indices: 92166--92319 Score: 209
Period size: 48 Copynumber: 3.1 Consensus size: 48
92156 TCAATGTCCT
* * *
92166 TTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTA
1 TTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
* * * *
92214 GTTTGAAAAGCAAATTTCGATATTGAACTCACGAATGGAAAGCAATTTTA
1 --TTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
*
92264 TTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
1 TTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
92312 TTGTAAAA
1 TTG-AAAA
92320 CTTCATGTTC
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
48 46 0.51
49 4 0.04
50 41 0.45
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.32
Consensus pattern (48 bp):
TTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
Found at i:92900 original size:5 final size:5
Alignment explanation
Indices: 92884--92951 Score: 61
Period size: 5 Copynumber: 13.6 Consensus size: 5
92874 TCCATTCTCC
* **
92884 TTTGA TTTTGA TTTGA TTTGA TTT-- TCTGA TTTTGA TTTGA TTTTT TTTGA
1 TTTGA -TTTGA TTTGA TTTGA TTTGA TTTGA -TTTGA TTTGA TTTGA TTTGA
92934 -TTGA CTTTGA TTTGA TTT
1 TTTGA -TTTGA TTTGA TTT
92952 TTTTTTTTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
3 2 0.04
4 4 0.08
5 32 0.63
6 13 0.25
ACGTcount: A:0.16, C:0.03, G:0.16, T:0.65
Consensus pattern (5 bp):
TTTGA
Found at i:92918 original size:24 final size:23
Alignment explanation
Indices: 92884--92953 Score: 94
Period size: 24 Copynumber: 3.1 Consensus size: 23
92874 TCCATTCTCC
92884 TTTGATTTTGATTTGATTTGATT
1 TTTGATTTTGATTTGATTTGATT
92907 TTCTGATTTTGATTTGATTT--TT
1 TT-TGATTTTGATTTGATTTGATT
92929 TTTGA--TTGACTTTGATTTGATT
1 TTTGATTTTGA-TTTGATTTGATT
92951 TTT
1 TTT
92954 TTTTTTTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.09
20 8 0.19
21 3 0.07
22 9 0.21
23 2 0.05
24 17 0.40
ACGTcount: A:0.16, C:0.03, G:0.16, T:0.66
Consensus pattern (23 bp):
TTTGATTTTGATTTGATTTGATT
Found at i:94913 original size:16 final size:16
Alignment explanation
Indices: 94875--94906 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
94865 ACAGAGATTG
94875 ACAG-AAAGCAATTAA
1 ACAGAAAAGCAATTAA
94890 ACAGAAAAG-AATTAA
1 ACAGAAAAGCAATTAA
94905 AC
1 AC
94907 TGGAAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.12
Consensus pattern (16 bp):
ACAGAAAAGCAATTAA
Done.