Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018426.1 Corchorus olitorius cultivar O-4 contig18459, 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: 122379
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:28 original size:2 final size:2
Alignment explanation
Indices: 21--46 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11 AATTTATTCA
21 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
47 CTTTGGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3245 original size:16 final size:15
Alignment explanation
Indices: 3215--3259 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
3205 TACCATCCAT
*
3215 AATATATCCTTAAAA
1 AATAAATCCTTAAAA
3230 AATAAATCCTTTAAAA
1 AATAAATCC-TTAAAA
* *
3246 AATACATTCTTAAA
1 AATAAATCCTTAAA
3260 TATCCTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAAATCCTTAAAA
Found at i:3453 original size:19 final size:19
Alignment explanation
Indices: 3433--3468 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3423 TATTAATCAT
*
3433 TTTA-ATATTATATTTTTA
1 TTTATATATTACATTTTTA
3451 TTTATATATTACATTTTT
1 TTTATATATTACATTTTT
3469 GCTTAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATATATTACATTTTTA
Found at i:3607 original size:13 final size:13
Alignment explanation
Indices: 3589--3615 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3579 AAATATAATA
3589 AATATGATTTATG
1 AATATGATTTATG
3602 AATATGATTTATG
1 AATATGATTTATG
3615 A
1 A
3616 GGTTATAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (13 bp):
AATATGATTTATG
Found at i:5204 original size:18 final size:18
Alignment explanation
Indices: 5181--5215 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5171 ACAAAATTTG
5181 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
5199 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
5216 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:5496 original size:35 final size:34
Alignment explanation
Indices: 5415--5500 Score: 111
Period size: 35 Copynumber: 2.4 Consensus size: 34
5405 TTATATAAAC
*
5415 GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
1 GAACAC-TAAATGAACAATAAACGAGTCTGTTCAT
*
5450 GAACACTTAAATGAACAATAAACGAGTCTGTAATTAT
1 GAACAC-TAAATGAACAATAAACGAGTCTGT--TCAT
5487 GAACA-TAAATGAAC
1 GAACACTAAATGAAC
5501 TGAACACATC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
35 40 0.85
37 7 0.15
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.24
Consensus pattern (34 bp):
GAACACTAAATGAACAATAAACGAGTCTGTTCAT
Found at i:6645 original size:2 final size:2
Alignment explanation
Indices: 6638--6678 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
6628 AGATGTTCAA
*
6638 AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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 AT AT A
6679 AAGTTGCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14652 original size:91 final size:92
Alignment explanation
Indices: 14495--14681 Score: 331
Period size: 91 Copynumber: 2.0 Consensus size: 92
14485 CAACAGATTG
*
14495 AAATTCACCAGTTCTAGAGGCATCATTACCATCCTTAAGATCTGCATTGCATCTAACTAGCGCAT
1 AAATTCACCAGTTCTAGAGGCATCATTACCATCCTTAAGATCTGCATTGCATCTAACTAGCACAT
*
14560 TAGCAGATGGCTCCGTGACTGCATAT-
66 TAGCAGATGGCTCCGAGACTGCATATC
* *
14586 AAATTCACTAGTTCTAGAGGCATCATTGCCATCCTTAAGATCTGCATTGCATCTAACTAGCACAT
1 AAATTCACCAGTTCTAGAGGCATCATTACCATCCTTAAGATCTGCATTGCATCTAACTAGCACAT
14651 TAGCAGATGGCTCCGAGACTGCATATC
66 TAGCAGATGGCTCCGAGACTGCATATC
14678 AAAT
1 AAAT
14682 GAAAAATAAC
Statistics
Matches: 91, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
91 87 0.96
92 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (92 bp):
AAATTCACCAGTTCTAGAGGCATCATTACCATCCTTAAGATCTGCATTGCATCTAACTAGCACAT
TAGCAGATGGCTCCGAGACTGCATATC
Found at i:36191 original size:37 final size:37
Alignment explanation
Indices: 36141--36211 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
36131 TGTCTCATAG
*
36141 GTCAAAGAAACAATCTTCTACCATTGTTATGTAGTAT
1 GTCAAAGAAACAATCTTCCACCATTGTTATGTAGTAT
36178 GTCAAAGAAACAATCTTCCACCATTGTTATGTAG
1 GTCAAAGAAACAATCTTCCACCATTGTTATGTAG
36212 CATGAAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (37 bp):
GTCAAAGAAACAATCTTCCACCATTGTTATGTAGTAT
Found at i:38621 original size:4 final size:4
Alignment explanation
Indices: 38612--38640 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
38602 AGTCCTCAAC
38612 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
38641 AAGAGTGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:47571 original size:354 final size:354
Alignment explanation
Indices: 46922--47632 Score: 1422
Period size: 354 Copynumber: 2.0 Consensus size: 354
46912 GACCACCCTT
46922 AAATTCTATGAGCATGCATCTGCCACTAATTTTACTTAGGAAACTCCTACCAAGTACCAATTATT
1 AAATTCTATGAGCATGCATCTGCCACTAATTTTACTTAGGAAACTCCTACCAAGTACCAATTATT
46987 TTACTGATTATAGAGTTTGAAGCTCCATCATATCCTGGGAGGAGTTTAAAGTACCGCTTTATACA
66 TTACTGATTATAGAGTTTGAAGCTCCATCATATCCTGGGAGGAGTTTAAAGTACCGCTTTATACA
47052 TTCATCAAGTATCATGATTTCACAAGCTTCATTTAAAACATTTCAAAAGATTTCAACATATAAAA
131 TTCATCAAGTATCATGATTTCACAAGCTTCATTTAAAACATTTCAAAAGATTTCAACATATAAAA
47117 ATCTAGCAAGACAAGTGAGAAAACATAGAGATATCAGTGTTATCACCAGACACAGCTAACAATTT
196 ATCTAGCAAGACAAGTGAGAAAACATAGAGATATCAGTGTTATCACCAGACACAGCTAACAATTT
47182 AACATCCAAAGTAGCTCTGAAATTCAACTTAAATTAAGAGGCCAAAATAGAAACCAATATATGAG
261 AACATCCAAAGTAGCTCTGAAATTCAACTTAAATTAAGAGGCCAAAATAGAAACCAATATATGAG
47247 AAATTAAATCAACATTTCATCAACAAGTC
326 AAATTAAATCAACATTTCATCAACAAGTC
47276 AAATTCTATGAGCATGCATCTGCCACTAATTTTACTTAGGAAACTCCTACCAAGTACCAATTATT
1 AAATTCTATGAGCATGCATCTGCCACTAATTTTACTTAGGAAACTCCTACCAAGTACCAATTATT
47341 TTACTGATTATAGAGTTTGAAGCTCCATCATATCCTGGGAGGAGTTTAAAGTACCGCTTTATACA
66 TTACTGATTATAGAGTTTGAAGCTCCATCATATCCTGGGAGGAGTTTAAAGTACCGCTTTATACA
47406 TTCATCAAGTATCATGATTTCACAAGCTTCATTTAAAACATTTCAAAAGATTTCAACATATAAAA
131 TTCATCAAGTATCATGATTTCACAAGCTTCATTTAAAACATTTCAAAAGATTTCAACATATAAAA
47471 ATCTAGCAAGACAAGTGAGAAAACATAGAGATATCAGTGTTATCACCAGACACAGCTAACAATTT
196 ATCTAGCAAGACAAGTGAGAAAACATAGAGATATCAGTGTTATCACCAGACACAGCTAACAATTT
47536 AACATCCAAAGTAGCTCTGAAATTCAACTTAAATTAAGAGGCCAAAATAGAAACCAATATATGAG
261 AACATCCAAAGTAGCTCTGAAATTCAACTTAAATTAAGAGGCCAAAATAGAAACCAATATATGAG
47601 AAATTAAATCAACATTTCATCAACAAGTC
326 AAATTAAATCAACATTTCATCAACAAGTC
47630 AAA
1 AAA
47633 ATATCTTTGG
Statistics
Matches: 357, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
354 357 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (354 bp):
AAATTCTATGAGCATGCATCTGCCACTAATTTTACTTAGGAAACTCCTACCAAGTACCAATTATT
TTACTGATTATAGAGTTTGAAGCTCCATCATATCCTGGGAGGAGTTTAAAGTACCGCTTTATACA
TTCATCAAGTATCATGATTTCACAAGCTTCATTTAAAACATTTCAAAAGATTTCAACATATAAAA
ATCTAGCAAGACAAGTGAGAAAACATAGAGATATCAGTGTTATCACCAGACACAGCTAACAATTT
AACATCCAAAGTAGCTCTGAAATTCAACTTAAATTAAGAGGCCAAAATAGAAACCAATATATGAG
AAATTAAATCAACATTTCATCAACAAGTC
Found at i:51596 original size:16 final size:15
Alignment explanation
Indices: 51563--51605 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
51553 ACCGTTTAAT
*
51563 ATATA-TATATATAT
1 ATATACTATATATAA
51577 ATATACTATATACTAA
1 ATATACTATATA-TAA
*
51593 ATATACTAAATAT
1 ATATACTATATAT
51606 TATTTGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.20
15 7 0.28
16 13 0.52
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATACTATATATAA
Found at i:56651 original size:56 final size:56
Alignment explanation
Indices: 56565--56678 Score: 192
Period size: 56 Copynumber: 2.0 Consensus size: 56
56555 TATCTGTTTC
*
56565 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTAACTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCATAACTCTACTTAATTATT
* **
56621 CTTTCACACAATAAATGTTATAATAAATCCTATCCCTATATTTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCATAACTCTACTTAATTATT
56677 CT
1 CT
56679 ACAAAATAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCATAACTCTACTTAATTATT
Found at i:56803 original size:42 final size:42
Alignment explanation
Indices: 56744--56824 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
56734 TAAGGATCGG
56744 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
56786 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
56825 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:59562 original size:17 final size:17
Alignment explanation
Indices: 59531--59571 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
59521 CTCACGCGGT
59531 AAAAAAAAAAGGAAAAG
1 AAAAAAAAAAGGAAAAG
*
59548 AGAAAAGAAAA-GAAAAG
1 A-AAAAAAAAAGGAAAAG
59565 AAAAAAA
1 AAAAAAA
59572 TTAGATAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 8 0.38
18 8 0.38
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGGAAAAG
Found at i:68600 original size:62 final size:62
Alignment explanation
Indices: 68529--68654 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
68519 TCTTCCATCT
*
68529 ATCAATCTTCTTCTTTCCATATCTCCGTTTTGTTTGTTTCCTGAGAAAGTTCAGAAGAAGAA
1 ATCAATCTTCTTCTTTCCATATCTCCGTTTTGTTTGTTTCCCGAGAAAGTTCAGAAGAAGAA
68591 ATCAATCTTCTTCTTTCCATATCTCCGTTTTGTTTGTTTCCCGAGAAAGTTCAGAAGAAGAA
1 ATCAATCTTCTTCTTTCCATATCTCCGTTTTGTTTGTTTCCCGAGAAAGTTCAGAAGAAGAA
68653 AT
1 AT
68655 TGCAGAAACT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (62 bp):
ATCAATCTTCTTCTTTCCATATCTCCGTTTTGTTTGTTTCCCGAGAAAGTTCAGAAGAAGAA
Found at i:72746 original size:13 final size:13
Alignment explanation
Indices: 72728--72753 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
72718 TTTATTTCTT
72728 TCTCAAAGCAAAA
1 TCTCAAAGCAAAA
72741 TCTCAAAGCAAAA
1 TCTCAAAGCAAAA
72754 GCAAGGATTC
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:0.54, C:0.23, G:0.08, T:0.15
Consensus pattern (13 bp):
TCTCAAAGCAAAA
Found at i:73061 original size:22 final size:21
Alignment explanation
Indices: 73036--73112 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 21
73026 TATTTTTATG
*
73036 AAATTTTGATAATTGCCCTATT
1 AAATTTTGATAATT-CCCTATA
* * *
73058 AAATTTTGGTAA-CCACCATATG
1 AAATTTTGATAATTC-CC-TATA
*
73080 AAATTTTGATAATTACCTATA
1 AAATTTTGATAATTCCCTATA
*
73101 AAATTGTGATAA
1 AAATTTTGATAA
73113 ACTCCAAAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
20 1 0.02
21 16 0.36
22 27 0.61
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
AAATTTTGATAATTCCCTATA
Found at i:73185 original size:20 final size:21
Alignment explanation
Indices: 73140--73202 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
73130 GATAACCTAA
* *
73140 CTATGAAATTTTAATAAACTTTC
1 CTATG-AATTTTGATAATC-TTC
73163 CTATGAATTTTG-TAATCTTC
1 CTATGAATTTTGATAATCTTC
*
73183 CTATGATTTTTGATAATCTT
1 CTATGAATTTTGATAATCTT
73203 TGTGTGAGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 14 0.39
21 11 0.31
22 6 0.17
23 5 0.14
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (21 bp):
CTATGAATTTTGATAATCTTC
Found at i:74134 original size:35 final size:35
Alignment explanation
Indices: 74073--74144 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 35
74063 AATCTTAAAC
* *
74073 TCTCTAAACACTTTAAGACCCCACTAACTCCAGTA
1 TCTCCAAACACTTTAAGACCCCACTAACTCCAATA
* * *
74108 TCTCCAAACACTTTAATATCCTACTAACTCCAATA
1 TCTCCAAACACTTTAAGACCCCACTAACTCCAATA
74143 TC
1 TC
74145 AAAGAGGATC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.29
Consensus pattern (35 bp):
TCTCCAAACACTTTAAGACCCCACTAACTCCAATA
Found at i:74885 original size:15 final size:15
Alignment explanation
Indices: 74865--74893 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
74855 TGACAAGAAC
74865 TAATCAATACTATAT
1 TAATCAATACTATAT
74880 TAATCAATACTATA
1 TAATCAATACTATA
74894 CTTAGACGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATCAATACTATAT
Found at i:75166 original size:3 final size:3
Alignment explanation
Indices: 75158--75242 Score: 170
Period size: 3 Copynumber: 28.3 Consensus size: 3
75148 TTAAATCATA
75158 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
75206 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
75243 TATAGTAGAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:83294 original size:15 final size:16
Alignment explanation
Indices: 83268--83317 Score: 70
Period size: 15 Copynumber: 3.3 Consensus size: 16
83258 AAAGGAAGTC
*
83268 TCTTCCTTCCTTCCCA
1 TCTTCTTTCCTTCCCA
83284 T-TTCTTTCCTTCCC-
1 TCTTCTTTCCTTCCCA
83298 TCTTCTTTCCTTCCCA
1 TCTTCTTTCCTTCCCA
83314 -CTTC
1 TCTTC
83318 CACCGTACCA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 1 0.03
15 29 0.94
16 1 0.03
ACGTcount: A:0.04, C:0.46, G:0.00, T:0.50
Consensus pattern (16 bp):
TCTTCTTTCCTTCCCA
Found at i:84050 original size:15 final size:15
Alignment explanation
Indices: 84030--84076 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
84020 CAGATTTAAT
84030 ATAAGTGACAAAAAC
1 ATAAGTGACAAAAAC
84045 ATAAGTGACAAAAAC
1 ATAAGTGACAAAAAC
84060 ATAAGTGACAAAAAC
1 ATAAGTGACAAAAAC
84075 AT
1 AT
84077 TACTTTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.15
Consensus pattern (15 bp):
ATAAGTGACAAAAAC
Found at i:109751 original size:16 final size:17
Alignment explanation
Indices: 109730--109765 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
109720 TCATTTACTA
*
109730 TTTTCATTTC-TTTTAT
1 TTTTCATTCCTTTTTAT
109746 TTTTCATTCCTTTTTAT
1 TTTTCATTCCTTTTTAT
109763 TTT
1 TTT
109766 CTTTTAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTCATTCCTTTTTAT
Found at i:111445 original size:20 final size:20
Alignment explanation
Indices: 111420--111480 Score: 97
Period size: 20 Copynumber: 3.0 Consensus size: 20
111410 CAACAATCAA
111420 AAGAAATTTGAGAGAGACAG
1 AAGAAATTTGAGAGAGACAG
*
111440 AAGAAATTCT-AAAGAGACAG
1 AAGAAATT-TGAGAGAGACAG
111460 AAGAAATTTGAGAGAGACAG
1 AAGAAATTTGAGAGAGACAG
111480 A
1 A
111481 GATCAGAGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.52, C:0.07, G:0.26, T:0.15
Consensus pattern (20 bp):
AAGAAATTTGAGAGAGACAG
Found at i:113751 original size:56 final size:56
Alignment explanation
Indices: 113665--113778 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
113655 TATCTTTTTC
113665 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTAACTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTAACTCTACTTAATTATT
**
113721 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATTTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTAACTCTACTTAATTATT
113777 CT
1 CT
113779 ACAAAATAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTAACTCTACTTAATTATT
Found at i:113903 original size:42 final size:42
Alignment explanation
Indices: 113844--113924 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
113834 TAAGGATCGG
113844 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
113886 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
113925 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:115696 original size:29 final size:29
Alignment explanation
Indices: 115653--115708 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
115643 ATCCAATCTG
*
115653 TCTACCAATATACGTGCTACATAATTCCA
1 TCTACCAATAAACGTGCTACATAATTCCA
*
115682 TCTACCAATAAACGTGTTACATAATTC
1 TCTACCAATAAACGTGCTACATAATTC
115709 TTTAGTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (29 bp):
TCTACCAATAAACGTGCTACATAATTCCA
Found at i:116008 original size:2 final size:2
Alignment explanation
Indices: 116003--116035 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
115993 TGTGTGTGTC
116003 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 T
116036 GATGTTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.