Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1929
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: 58980
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:9123 original size:27 final size:27
Alignment explanation
Indices: 9093--9270 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
9083 ATATTAAGTC
* * *
9093 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
9120 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
9148 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
9175 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
9202 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
9229 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
9256 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9271 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 105 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:9177 original size:55 final size:54
Alignment explanation
Indices: 9093--9270 Score: 232
Period size: 54 Copynumber: 3.3 Consensus size: 54
9083 ATATTAAGTC
* * *
9093 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAA-T
* * * *
9148 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* ** *
9202 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
9256 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9271 GTACAATTTA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:9259 original size:81 final size:82
Alignment explanation
Indices: 9114--9269 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
9104 TGCTATATAA
* *
9114 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
9179 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
9196 TCAATTCGCACACTTAGTG-CATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
9259 ACACTTAGTGC
65 ACACTTAGTGC
9270 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 43 0.64
82 24 0.36
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Found at i:11592 original size:28 final size:28
Alignment explanation
Indices: 11560--11657 Score: 133
Period size: 28 Copynumber: 3.5 Consensus size: 28
11550 TAATAAGTTT
*
11560 GCACACCTAGTGCTTAATAATCAATCTC
1 GCACACTTAGTGCTTAATAATCAATCTC
11588 GCACACTTAGTGCTTAATAATCAATCTC
1 GCACACTTAGTGCTTAATAATCAATCTC
* * * * * *
11616 GCATACTTAGTGATTTACAATTAAACTC
1 GCACACTTAGTGCTTAATAATCAATCTC
11644 GCACACTTAGTGCT
1 GCACACTTAGTGCT
11658 AATCTCATTA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 61 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (28 bp):
GCACACTTAGTGCTTAATAATCAATCTC
Found at i:13282 original size:235 final size:235
Alignment explanation
Indices: 12863--13301 Score: 752
Period size: 235 Copynumber: 1.9 Consensus size: 235
12853 GGCTGTTATA
* *
12863 GAGGATTGGGTGGAGTCCACCACCCTAATAAAGAACACTCATTTTAAGTGAGTAGGGAGTTAATT
1 GAGGATTGGGTGGAGTCCACCACCCTAATAAAGAACACTCATTTCAAGTGAGAAGGGAGTTAATT
* *
12928 TATATTTATGTTATTTTACATTTATTACCTCATGAGATATGGTTTGATTATGGTGCTGTGAAGAC
66 TATATTTATGTTATTTTACATTTATTACCTCATGAGATATGGTTTAATTATGGTGCAGTGAAGAC
* * *
12993 ACTCAATGAGTTCATTTGAAATTTCAAGAGTTTGTCTAATGTTCGTAGGATTTGCAAGGTTGATC
131 ACTCAATAAGTTCATTTGAAATTTCAAGAGTTTGTCTAATGTTCGCAAGATTTGCAAGGTTGATC
13058 GAGGACTCAAAACAATATTTATAGTAAGCCGAGAAGCTTT
196 GAGGACTCAAAACAATATTTATAGTAAGCCGAGAAGCTTT
* *
13098 GAGGATTGGGTGGAGTCCACCGCCCTAATAAAGAACACTCGTTTCAAGTGAGAAGGGAGTTAATT
1 GAGGATTGGGTGGAGTCCACCACCCTAATAAAGAACACTCATTTCAAGTGAGAAGGGAGTTAATT
* *
13163 TATGTTTATGTTATTTTACATTTATTACCTCATGAGATATGGTTTAATTATGGTGCAGTGAAGAG
66 TATATTTATGTTATTTTACATTTATTACCTCATGAGATATGGTTTAATTATGGTGCAGTGAAGAC
* * *
13228 ACTCAATAAGTTCATTTGAACTTTCAAGAGTTTGTCTGATGTTCGCAAGATTTGCAAGGTTGATT
131 ACTCAATAAGTTCATTTGAAATTTCAAGAGTTTGTCTAATGTTCGCAAGATTTGCAAGGTTGATC
13293 GAGGACTCA
196 GAGGACTCA
13302 GAGGAGGGAC
Statistics
Matches: 190, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
235 190 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35
Consensus pattern (235 bp):
GAGGATTGGGTGGAGTCCACCACCCTAATAAAGAACACTCATTTCAAGTGAGAAGGGAGTTAATT
TATATTTATGTTATTTTACATTTATTACCTCATGAGATATGGTTTAATTATGGTGCAGTGAAGAC
ACTCAATAAGTTCATTTGAAATTTCAAGAGTTTGTCTAATGTTCGCAAGATTTGCAAGGTTGATC
GAGGACTCAAAACAATATTTATAGTAAGCCGAGAAGCTTT
Found at i:19643 original size:33 final size:33
Alignment explanation
Indices: 19606--19670 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
19596 GAGTTAGTTT
* *
19606 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGA
1 ATTAAATTTAGTTAAACTCAAATAAGTGTTAGA
* *
19639 ATTAATTTTAGTTAAACTTAAATAAGTGTTAG
1 ATTAAATTTAGTTAAACTCAAATAAGTGTTAG
19671 TAAATAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (33 bp):
ATTAAATTTAGTTAAACTCAAATAAGTGTTAGA
Found at i:22780 original size:27 final size:27
Alignment explanation
Indices: 22750--23056 Score: 284
Period size: 27 Copynumber: 11.4 Consensus size: 27
22740 ATTTGTGGGA
* *
22750 AAAATGACTGAACTACCC-CTAAATGGT
1 AAAATGACTGAAATACCCTC-AAAGGGT
** * *
22777 AAAATGACCAAAATACCTTCGAAGGGT
1 AAAATGACTGAAATACCCTCAAAGGGT
*
22804 AAAATGACTGAAATACCCTCGAAGGGT
1 AAAATGACTGAAATACCCTCAAAGGGT
** * *
22831 AAAATGACCAAAATATCCTCGAAGGGT
1 AAAATGACTGAAATACCCTCAAAGGGT
* * *
22858 AAAATGACTGAAATACCCCCGAAGGAT
1 AAAATGACTGAAATACCCTCAAAGGGT
* * *
22885 AAAATAATTGAAATACCCTCAAAGGTT
1 AAAATGACTGAAATACCCTCAAAGGGT
** ** *
22912 AATGTGACCAAAATTCCC-CTAAAGGGT
1 AAAATGACTGAAATACCCTC-AAAGGGT
22939 AAAATGACTGAAATACCC-CTAAAGGGT
1 AAAATGACTGAAATACCCTC-AAAGGGT
*
22966 AAAATGA-TCGAAATACCCTCGAAGGGT
1 AAAATGACT-GAAATACCCTCAAAGGGT
22993 AAAATGA-TCGAAATACCCTCAAAGGGT
1 AAAATGACT-GAAATACCCTCAAAGGGT
* * *
23020 AAAATGACCGAAATACCC-CTATAGTGT
1 AAAATGACTGAAATACCCTC-AAAGGGT
23047 AAAATGACTG
1 AAAATGACTG
23057 TTATACTTCT
Statistics
Matches: 233, Mismatches: 41, Indels: 12
0.81 0.14 0.04
Matches are distributed among these distances:
26 3 0.01
27 228 0.98
28 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (27 bp):
AAAATGACTGAAATACCCTCAAAGGGT
Found at i:22888 original size:81 final size:80
Alignment explanation
Indices: 22774--23038 Score: 325
Period size: 81 Copynumber: 3.3 Consensus size: 80
22764 ACCCCTAAAT
* **
22774 GGTAAAATGACCAAAATACCTTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGAC
1 GGTAAAATGACCGAAATACCCCCGAAGGGTAAAATGA-TGAAATACCCTCGAAGGGTAAAATGAC
*
22839 CAAAATATCCTCGAAG
65 CAAAATATCCTCAAAG
* * * * * **
22855 GGTAAAATGACTGAAATACCCCCGAAGGATAAAATAATTGAAATACCCTCAAAGGTTAATGTGAC
1 GGTAAAATGACCGAAATACCCCCGAAGGGTAAAATGA-TGAAATACCCTCGAAGGGTAAAATGAC
*
22920 CAAAAT-TCCCCTAAAG
65 CAAAATATCCTC-AAAG
* ** *
22936 GGTAAAATGACTGAAATACCCCTAAAGGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGAT
1 GGTAAAATGACCGAAATACCCCCGAAGGGTAAAATGAT-GAAATACCCTCGAAGGGTAAAATGAC
* *
23001 CGAAATACCCTCAAAG
65 CAAAATATCCTCAAAG
23017 GGTAAAATGACCGAAATACCCC
1 GGTAAAATGACCGAAATACCCC
23039 TATAGTGTAA
Statistics
Matches: 155, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
80 5 0.03
81 147 0.95
82 3 0.02
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (80 bp):
GGTAAAATGACCGAAATACCCCCGAAGGGTAAAATGATGAAATACCCTCGAAGGGTAAAATGACC
AAAATATCCTCAAAG
Found at i:23460 original size:28 final size:28
Alignment explanation
Indices: 23414--23527 Score: 149
Period size: 28 Copynumber: 4.0 Consensus size: 28
23404 CATTCTACTG
*
23414 ATTACCGTATTGGGCTAAGGCCCACACT
1 ATTACTGTATTGGGCTAAGGCCCACACT
*
23442 ATTACTATATTGAGG-TAAGGCCCACACT
1 ATTACTGTATTG-GGCTAAGGCCCACACT
* *
23470 ATTATTGTATTGGGCTAACGCCCACACACT
1 ATTACTGTATTGGGCTAA-GGCC-CACACT
*
23500 ATTACTGTAATGGGCTAAGGCCCACACT
1 ATTACTGTATTGGGCTAAGGCCCACACT
23528 GTACTGATAC
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 42 0.57
29 8 0.11
30 22 0.30
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (28 bp):
ATTACTGTATTGGGCTAAGGCCCACACT
Found at i:23522 original size:58 final size:56
Alignment explanation
Indices: 23420--23527 Score: 155
Period size: 58 Copynumber: 1.9 Consensus size: 56
23410 ACTGATTACC
* *
23420 GTATTGGGCTAAGGCCCACACTATTACTATATTGAGGTAAGGCCCACACTATTATT
1 GTATTGGGCTAAGCCCCACACTATTACTATAATGAGGTAAGGCCCACACTATTATT
*
23476 GTATTGGGCTAACGCCCACACACTATTACTGTAATG-GGCTAAGGCCCACACT
1 GTATTGGGCTAA-GCCC-CACACTATTACTATAATGAGG-TAAGGCCCACACT
23528 GTACTGATAC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
56 12 0.26
57 5 0.11
58 29 0.63
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (56 bp):
GTATTGGGCTAAGCCCCACACTATTACTATAATGAGGTAAGGCCCACACTATTATT
Found at i:30867 original size:162 final size:161
Alignment explanation
Indices: 30591--30911 Score: 552
Period size: 162 Copynumber: 2.0 Consensus size: 161
30581 GATACCTTAT
*
30591 TGGATTTGTACATCAAGTCGAAAACTTGATTCCTCACAAAATCGATCTCTCCAGCCCTCCTAAAT
1 TGGATTTGTACATCAAGTCGAAAACTTGATTCCTCACAAAATCGATCTCTCCAGCCCTCCTAAAC
* *
30656 AGTTTCAATCATCAATATTAGACTAAATACACTTATACTAAGCATCAATTTCATCTTTAAATCAA
66 ACTTTCAATCATCAATACTAGACTAAATACACTTATACTAAGCATCAATTTCATCTTTAAATCAA
*
30721 TTTCATAAAATTTTAGAAAATCAATTCATAC
131 TTTCATAAAATTCTAGAAAATCAATTCATAC
* *
30752 TGGATTTGTAACATCAAGTCGAAAACTTGATTCCTCACAAAATCGATCTTTCTAGCCCTCCTAAA
1 TGGATTTGT-ACATCAAGTCGAAAACTTGATTCCTCACAAAATCGATCTCTCCAGCCCTCCTAAA
* *
30817 CACTTTCAATCATCAATACTAGACTAAATACACTTCTATTAAGCATCAATTTCATCTTTAAATCA
65 CACTTTCAATCATCAATACTAGACTAAATACACTTATACTAAGCATCAATTTCATCTTTAAATCA
*
30882 ATTTCATAAAATTCTAGAAAATCGATTCAT
130 ATTTCATAAAATTCTAGAAAATCAATTCAT
30912 GAAGATGATG
Statistics
Matches: 150, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
161 9 0.06
162 141 0.94
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.34
Consensus pattern (161 bp):
TGGATTTGTACATCAAGTCGAAAACTTGATTCCTCACAAAATCGATCTCTCCAGCCCTCCTAAAC
ACTTTCAATCATCAATACTAGACTAAATACACTTATACTAAGCATCAATTTCATCTTTAAATCAA
TTTCATAAAATTCTAGAAAATCAATTCATAC
Found at i:31727 original size:20 final size:20
Alignment explanation
Indices: 31702--31743 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
31692 TTTAAAATTT
* *
31702 ATTTTTCAAATTTTTTTTTA
1 ATTTTTCAAATTATTGTTTA
*
31722 ATTTTTCAGATTATTGTTTA
1 ATTTTTCAAATTATTGTTTA
31742 AT
1 AT
31744 CGATTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (20 bp):
ATTTTTCAAATTATTGTTTA
Found at i:32752 original size:41 final size:41
Alignment explanation
Indices: 32700--32794 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
32690 TACTGTGTAT
* * **
32700 TGATTGCATGTAAGCATGTCACTGATTGTTACTGTACATAC
1 TGATTGCATGTAAGCATGCCACTAATTGTTACCATACATAC
*
32741 TGATTGCATGTAAGCATGCCACTAATTGTTACCATAGATAC
1 TGATTGCATGTAAGCATGCCACTAATTGTTACCATACATAC
*
32782 TGATTACATGTAA
1 TGATTGCATGTAA
32795 AGTATGACAC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (41 bp):
TGATTGCATGTAAGCATGCCACTAATTGTTACCATACATAC
Found at i:34141 original size:51 final size:51
Alignment explanation
Indices: 34064--34274 Score: 343
Period size: 51 Copynumber: 4.1 Consensus size: 51
34054 GCAATAGCAA
* ** * * **
34064 AGAGGGAGAGAGAGAATG-TCAATGGTGAGGAAGGTCTAGTGAAGGAAGGGG
1 AGAGGGAGAGAGAAAATGAT-GGTGGTGAGGGAGGTCTGGTGGGGGAAGGGG
34115 AGAGGGAGAGAGAAAATGATGGTGGTGAGGGAGGTCTGGTGGGGGAAGGGG
1 AGAGGGAGAGAGAAAATGATGGTGGTGAGGGAGGTCTGGTGGGGGAAGGGG
34166 AGAGGGAGAGAGAAAATGATGGTGGTGAGGGAGGTCTGGTGGGGGAAGGGG
1 AGAGGGAGAGAGAAAATGATGGTGGTGAGGGAGGTCTGGTGGGGGAAGGGG
34217 AGAGGGAGAGAGAAAATGATGGTGGTGAGGGAGGTCTGGTGGGGGAAGGGG
1 AGAGGGAGAGAGAAAATGATGGTGGTGAGGGAGGTCTGGTGGGGGAAGGGG
34268 AGAGGGA
1 AGAGGGA
34275 CAGGGATAAG
Statistics
Matches: 152, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
51 151 0.99
52 1 0.01
ACGTcount: A:0.30, C:0.02, G:0.55, T:0.13
Consensus pattern (51 bp):
AGAGGGAGAGAGAAAATGATGGTGGTGAGGGAGGTCTGGTGGGGGAAGGGG
Found at i:34374 original size:19 final size:19
Alignment explanation
Indices: 34345--34464 Score: 59
Period size: 19 Copynumber: 6.3 Consensus size: 19
34335 AATTTAAATT
* *
34345 TATTATTATATTTTTTGAA
1 TATTTTTATATTTTTTAAA
* *
34364 TTTTTTTATATATTTTAAA
1 TATTTTTATATTTTTTAAA
* * **
34383 TATTTATATATTATTT-CT
1 TATTTTTATATTTTTTAAA
***
34401 TATCAATA-ATTTTTT--A
1 TATTTTTATATTTTTTAAA
34417 TATTTTTATATTTTTTAAAA
1 TATTTTTATATTTTTT-AAA
*
34437 TTTATTATTATATTTTTTGAAAA
1 --TATTTTTATATTTTTT--AAA
34460 TATTT
1 TATTT
34465 ATGTAATTTT
Statistics
Matches: 75, Mismatches: 19, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
16 5 0.07
17 13 0.17
18 6 0.08
19 27 0.36
20 1 0.01
21 4 0.05
22 15 0.20
23 4 0.05
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TATTTTTATATTTTTTAAA
Found at i:34442 original size:22 final size:23
Alignment explanation
Indices: 34417--34460 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
34407 TAATTTTTTA
*
34417 TATTTTTATATTTTTT-AAAATT
1 TATTATTATATTTTTTGAAAATT
34439 TATTATTATATTTTTTGAAAAT
1 TATTATTATATTTTTTGAAAAT
34461 ATTTATGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TATTATTATATTTTTTGAAAATT
Found at i:34466 original size:22 final size:21
Alignment explanation
Indices: 34416--34474 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
34406 ATAATTTTTT
34416 ATATTT-TTATATTTTTTAAA
1 ATATTTATTATATTTTTTAAA
*
34436 ATTTATTATTATATTTTTTGAAA
1 ATAT-TTATTATATTTTTT-AAA
34459 ATATTTATGTA-ATTTT
1 ATATTTAT-TATATTTT
34475 ATATATTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 3 0.09
21 2 0.06
22 20 0.61
23 8 0.24
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (21 bp):
ATATTTATTATATTTTTTAAA
Found at i:34475 original size:51 final size:53
Alignment explanation
Indices: 34367--34482 Score: 132
Period size: 51 Copynumber: 2.2 Consensus size: 53
34357 TTTTGAATTT
* *
34367 TTTTATATATTTTAAATATTTATATATTATTTCTTATCAATAATTTTTTATAT
1 TTTTATATATTTTAAATATTTATATATTATTTCTTATCAATAATTTTATATAA
* * * *
34420 TTTTATATTTTTTAAA-ATTTAT-TATTATATT-TTTTGAA-AATATTTATGTAA
1 TTTTATATATTTTAAATATTTATATATTAT-TTCTTATCAATAAT-TTTATATAA
34471 TTTTATATATTT
1 TTTTATATATTT
34483 GTTAGAATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
50 3 0.06
51 28 0.52
52 8 0.15
53 15 0.28
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (53 bp):
TTTTATATATTTTAAATATTTATATATTATTTCTTATCAATAATTTTATATAA
Found at i:35411 original size:23 final size:23
Alignment explanation
Indices: 35368--35411 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
35358 TTAGATATTC
* *
35368 ACCCCTAATTATAGATCACTAAA
1 ACCCCTAATTACAGATAACTAAA
35391 ACCCTCTAATTACA-ATAACTA
1 ACCC-CTAATTACAGATAACTA
35412 TCCAAATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.27
Consensus pattern (23 bp):
ACCCCTAATTACAGATAACTAAA
Found at i:36947 original size:13 final size:13
Alignment explanation
Indices: 36929--36956 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
36919 ATTACTTTTT
36929 AGGTATTTAATAA
1 AGGTATTTAATAA
36942 AGGTATTTAATAA
1 AGGTATTTAATAA
36955 AG
1 AG
36957 AGAAAGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.36
Consensus pattern (13 bp):
AGGTATTTAATAA
Found at i:37050 original size:19 final size:19
Alignment explanation
Indices: 37016--37056 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
37006 GCCACAAAGA
*
37016 TTTATTTTGAATTTTAATAT
1 TTTAATTTGAATTTTAAT-T
37036 TTTAATTTGAA-TTTAATT
1 TTTAATTTGAATTTTAATT
37054 TTT
1 TTT
37057 TTCATGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 6 0.30
20 10 0.50
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTAATTTGAATTTTAATT
Found at i:37192 original size:23 final size:23
Alignment explanation
Indices: 37166--37214 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
37156 TATTTTACAT
*
37166 TTTCTAACAGAAAATCAATTCTC
1 TTTCTAACACAAAATCAATTCTC
37189 TTTCTAACACAAAATCAATTCTC
1 TTTCTAACACAAAATCAATTCTC
37212 TTT
1 TTT
37215 AATAGTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.39
Consensus pattern (23 bp):
TTTCTAACACAAAATCAATTCTC
Found at i:37444 original size:12 final size:13
Alignment explanation
Indices: 37418--37451 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
37408 AGTTTTATAA
37418 AAAAATTAAACAT
1 AAAAATTAAACAT
37431 AAAAATTAAA-AT
1 AAAAATTAAACAT
*
37443 AAGAATTAA
1 AAAAATTAA
37452 TTTGATGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (13 bp):
AAAAATTAAACAT
Found at i:38643 original size:50 final size:50
Alignment explanation
Indices: 38572--38704 Score: 144
Period size: 50 Copynumber: 2.6 Consensus size: 50
38562 TTGTATTGCT
* * *
38572 AATGTCATATCCTAGATATGGTCTTACATGGGAG-TTCTCATATCGGTGCC
1 AATGTCATATCCCAGACATGGTCTTAC-TGGGAGACTCTCATATCGGTGCC
* * *
38622 CATGTCATATCCCAGACATGGTCTTTC-GGGAGACCTCTCATCTCGGTGCC
1 AATGTCATATCCCAGACATGGTCTTACTGGGAGA-CTCTCATATCGGTGCC
* * *
38672 AACGCCATGTCCCAGACATGGTCTTACGTGGGA
1 AATGTCATATCCCAGACATGGTCTTAC-TGGGA
38705 TCTCATTCCC
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
48 5 0.07
50 59 0.87
52 4 0.06
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (50 bp):
AATGTCATATCCCAGACATGGTCTTACTGGGAGACTCTCATATCGGTGCC
Found at i:45025 original size:199 final size:199
Alignment explanation
Indices: 44685--45082 Score: 656
Period size: 199 Copynumber: 2.0 Consensus size: 199
44675 TTCACATACA
* *
44685 TTTCTCTAAATTTCTCTAGAAAGAATTCCCAATTTATCTGCTCATCAGGGGTCACACTTGTCAAC
1 TTTCTCTAAATTTCTCTAGAAAGAATTCCCAATCTATCTACTCATCAGGGGTCACACTTGTCAAC
*
44750 GTTTCGCACCATTGATACGCCTCCCCTACTAGCAAGGAGATTTCACACAAAAGACTATCCGCCGA
66 GTTTCGCACCATTGATACGCCTCCCCTACTAGCAAGGAGATTTCACAAAAAAGACTATCCGCCGA
* * * *
44815 CATGCACTTTAACTTATTAATTACCCTAAAAATGCGTGATAACCATTACTCTTCTACT-GTGGGG
131 CATGCACTTTAACTCATTAATTACCCAAAAAACGCGTGATAACCATTACTCTACT-CTCGTGGGG
44879 TCATT
195 TCATT
* * *
44884 TTTCTCTAAATTTCTCTAGACAGAATTCCCAATCTATCTACTCATCAGGGGTCACACTTGTTAGC
1 TTTCTCTAAATTTCTCTAGAAAGAATTCCCAATCTATCTACTCATCAGGGGTCACACTTGTCAAC
*
44949 GTTTCGCACCATTGATACGCCTCCCCTACTAGCAAGGAGATTTCACAAAAAAGACTGTCCGCC-A
66 GTTTCGCACCATTGATACGCCTCCCCTACTAGCAAGGAGATTTCACAAAAAAGACTATCCGCCGA
*
45013 GCATGCACTTTAACTCATTAATTACCCAAAAAACGCGTGATAACCATTACTCTACTGTCGTGGGG
131 -CATGCACTTTAACTCATTAATTACCCAAAAAACGCGTGATAACCATTACTCTACTCTCGTGGGG
45078 TCATT
195 TCATT
45083 GCCCTTATCC
Statistics
Matches: 185, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
198 2 0.01
199 183 0.99
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (199 bp):
TTTCTCTAAATTTCTCTAGAAAGAATTCCCAATCTATCTACTCATCAGGGGTCACACTTGTCAAC
GTTTCGCACCATTGATACGCCTCCCCTACTAGCAAGGAGATTTCACAAAAAAGACTATCCGCCGA
CATGCACTTTAACTCATTAATTACCCAAAAAACGCGTGATAACCATTACTCTACTCTCGTGGGGT
CATT
Found at i:51312 original size:39 final size:40
Alignment explanation
Indices: 51191--51372 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
51181 TTGAATGATG
* * * *
51191 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
51231 TCCGGACTAAGAT-CCGAAGGCA-TT-TGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
51269 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
51308 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
51349 -CCGGGCTATGT-CCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
51373 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
37 9 0.08
38 17 0.14
39 37 0.31
40 54 0.45
41 3 0.03
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:51325 original size:77 final size:80
Alignment explanation
Indices: 51191--51372 Score: 205
Period size: 77 Copynumber: 2.3 Consensus size: 80
51181 TTGAATGATG
*
51191 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGC-AT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
51254 T-TGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
51268 TTCCGGGCTAAGCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAA
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAA
*
51331 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* * *
51348 ACCGGGCTATGTCCGAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCATTTG
51373 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
76 1 0.01
77 33 0.37
78 21 0.24
79 33 0.37
80 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGATACTATA
Found at i:51379 original size:79 final size:76
Alignment explanation
Indices: 51244--51405 Score: 184
Period size: 79 Copynumber: 2.1 Consensus size: 76
51234 GGACTAAGAT
* **
51244 CCGAAGGCATTTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTA-CTAAA
1 CCGAAGGCATTTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAG-TAGCTAAA
*
51308 TCCGGGTTAAGTC
65 TCC-GGTTAAATC
* * *
51321 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCGAAGGCATTTGAACGAGTAGCTA
1 CCGAAGGC-ATT-TGCGAGATACTAAT-ACCGGGCTAAGCCCGAAGGCATTTGAACGAGTAGCTA
* *
51385 TATCCGGTTAAATT
63 AATCCGGTTAAATC
51399 CCGAAGG
1 CCGAAGG
51406 TACGTGATTT
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
77 8 0.11
78 21 0.29
79 43 0.60
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (76 bp):
CCGAAGGCATTTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTAGCTAAAT
CCGGTTAAATC
Done.