Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1071
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: 46888
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Found at i:2464 original size:27 final size:27
Alignment explanation
Indices: 2433--2610 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
2423 TAAATTGTAC
2433 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
2460 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2486 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
2514 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
2542 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2569 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2596 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2611 GACTTAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:2547 original size:82 final size:81
Alignment explanation
Indices: 2434--2589 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
2424 AAATTGTACA
* *
2434 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
2498 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
2515 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
2580 TGCGAGTTGA
65 TGCGAATTGA
2590 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:2601 original size:82 final size:81
Alignment explanation
Indices: 2430--2610 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
2420 GATTAAATTG
* *
2430 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
2495 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
2511 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
2575 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
2593 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
2611 GACTTAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:10520 original size:27 final size:27
Alignment explanation
Indices: 10490--10665 Score: 192
Period size: 27 Copynumber: 6.5 Consensus size: 27
10480 AAATTGTACA
*
10490 GCACTAAGTGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGAATTGACTATGTT
* * *
10517 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGAATTGACTATGTT
* **
10544 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTT
* *
10571 GCACTAAGTGTGCGAGTTGACTATGTA
1 GCACTAAGTGTGCGAATTGACTATGTT
* *
10598 GCACTAAGTGTGCGAGTTTGATTATG-T
1 GCACTAAGTGTGCGA-ATTGACTATGTT
* * * *
10625 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAATTGACTATGTT
*
10652 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
10666 GACTTAATAT
Statistics
Matches: 127, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
26 8 0.06
27 111 0.87
28 8 0.06
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTT
Found at i:10550 original size:54 final size:54
Alignment explanation
Indices: 10489--10665 Score: 225
Period size: 54 Copynumber: 3.3 Consensus size: 54
10479 TAAATTGTAC
**
10489 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATG-TGCACTAAGTGTGCGAGTTGAATATGAT
* * * *
10544 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATG-TGCACTAAGTGTGCGAGTTGAATATGAT
* *
10597 AGCACTAAGTGTGCGAGTTTGATTATGTGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTTGACTATGTGCACTAAGTGTGCGAGTTGAATATGAT
*
10651 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
10666 GACTTAATAT
Statistics
Matches: 106, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
53 1 0.01
54 98 0.92
55 7 0.07
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTGACTATGTGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:10628 original size:81 final size:81
Alignment explanation
Indices: 10490--10644 Score: 240
Period size: 81 Copynumber: 1.9 Consensus size: 81
10480 AAATTGTACA
* *
10490 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
10555 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
** *
10571 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATG-TGCACTAAGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGA-AATGAATATGATGCACTAAGTG
*
10635 TGCGAGTTGA
65 TGCGAATTGA
10645 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
81 60 0.90
82 7 0.10
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:10656 original size:81 final size:81
Alignment explanation
Indices: 10486--10665 Score: 236
Period size: 81 Copynumber: 2.2 Consensus size: 81
10476 GATTAAATTG
* *
10486 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
10551 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
10567 TGCGGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATG-TGCACTA
1 TACAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGA-AATGAATATGATGCACTA
* **
10631 AGTGTGCGAGTTGATTA
65 AGTGTGCGAATTGACCA
* *
10648 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
10666 GACTTAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 77 0.92
82 7 0.08
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:12279 original size:56 final size:56
Alignment explanation
Indices: 12193--12305 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
12183 ATCTGAACAA
12193 AGCGCTTAGCTCAATCTACACCACTACGCTCTCGCTGCGCACTCTAGTTATAAACT
1 AGCGCTTAGCTCAATCTACACCACTACGCTCTCGCTGCGCACTCTAGTTATAAACT
12249 AGCGCTTAGCTCAATCTACACCACTACGCTCTCGCTGCGCACTCTAGTTATAAACT
1 AGCGCTTAGCTCAATCTACACCACTACGCTCTCGCTGCGCACTCTAGTTATAAACT
12305 A
1 A
12306 CACTAACATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.27
Consensus pattern (56 bp):
AGCGCTTAGCTCAATCTACACCACTACGCTCTCGCTGCGCACTCTAGTTATAAACT
Found at i:17273 original size:27 final size:27
Alignment explanation
Indices: 17227--17278 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
17217 CAGTAACAGT
*
17227 TGGGCCTAACCCATTAACAGAATCAAG
1 TGGGCCTAACCCAGTAACAGAATCAAG
17254 TGGGCCTAAGCCCAGT-ACAGAATCA
1 TGGGCCTAA-CCCAGTAACAGAATCA
17279 GTATCAGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (27 bp):
TGGGCCTAACCCAGTAACAGAATCAAG
Found at i:20561 original size:28 final size:28
Alignment explanation
Indices: 20522--20579 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
20512 AAATAATCAT
**
20522 AAAAATACGATATAAT-AATGATCATAAG
1 AAAAATACGATA-AATGAATGAAAATAAG
20550 AAAATATA-GATAAATGAATGAAAATAAG
1 AAAA-ATACGATAAATGAATGAAAATAAG
20578 AA
1 AA
20580 TAATTTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 3 0.12
28 20 0.77
29 3 0.12
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.22
Consensus pattern (28 bp):
AAAAATACGATAAATGAATGAAAATAAG
Found at i:20706 original size:21 final size:22
Alignment explanation
Indices: 20661--20706 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
20651 ACTAAAATAA
* *
20661 ATAATAAAAAATAGTAATAATT
1 ATAATAAAAAATAGTAAGAAAT
20683 ATAA-AAAAAATAGTAAGAAAT
1 ATAATAAAAAATAGTAAGAAAT
20704 ATA
1 ATA
20707 GGTAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (22 bp):
ATAATAAAAAATAGTAAGAAAT
Found at i:23089 original size:31 final size:31
Alignment explanation
Indices: 23046--23108 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
23036 CTTTTCACAC
23046 TTCATATGTCATAACACTGAGCCGAAGCCTT
1 TTCATATGTCATAACACTGAGCCGAAGCCTT
* ** *
23077 TTCATATTTCATATTACTGGGCCGAAGCCTT
1 TTCATATGTCATAACACTGAGCCGAAGCCTT
23108 T
1 T
23109 ACTGTAAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (31 bp):
TTCATATGTCATAACACTGAGCCGAAGCCTT
Found at i:23396 original size:24 final size:24
Alignment explanation
Indices: 23319--23395 Score: 111
Period size: 24 Copynumber: 3.2 Consensus size: 24
23309 GGCCTATCCT
23319 CTTTTAATAACTGGGGCA-AAAGCC
1 CTTTTAATAACTGGGGCATAAA-CC
*
23343 CTTTTAATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAACC
* *
23367 CTTTTGATAATTGGGGCATAAACC
1 CTTTTAATAACTGGGGCATAAACC
23391 CTTTT
1 CTTTT
23396 GCACTTCCTC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 46 0.96
25 2 0.04
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (24 bp):
CTTTTAATAACTGGGGCATAAACC
Found at i:23470 original size:20 final size:20
Alignment explanation
Indices: 23445--23511 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
23435 TTATGAACAC
*
23445 ATCATGTGCATATCATTCAT
1 ATCATGTGCATATCATACAT
*
23465 ATCATGTGCATAGCATACAT
1 ATCATGTGCATATCATACAT
*
23485 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
23505 ACCATGT
1 ATCATGT
23512 TTACTAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:23476 original size:11 final size:11
Alignment explanation
Indices: 23445--23500 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
23435 TTATGAACAC
23445 ATCATGTGCAT
1 ATCATGTGCAT
23456 ATCAT-T-CAT
1 ATCATGTGCAT
23465 ATCATGTGCAT
1 ATCATGTGCAT
* *
23476 AGCA--TACAT
1 ATCATGTGCAT
*
23485 GTCATGTGCAT
1 ATCATGTGCAT
23496 ATCAT
1 ATCAT
23501 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 14 0.40
10 2 0.06
11 19 0.54
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:31128 original size:31 final size:31
Alignment explanation
Indices: 31090--31151 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
31080 CTTTTCACAC
*
31090 TTCATATTTCATAACACTGGGCCGAAGCCTT
1 TTCATATTTCATAACACTGGGCCAAAGCCTT
**
31121 TTCATATTTCATATTACTGGGCCAAAGCCTT
1 TTCATATTTCATAACACTGGGCCAAAGCCTT
31152 CACTGTAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (31 bp):
TTCATATTTCATAACACTGGGCCAAAGCCTT
Found at i:31419 original size:47 final size:47
Alignment explanation
Indices: 31365--31461 Score: 176
Period size: 47 Copynumber: 2.1 Consensus size: 47
31355 TCTAGCCTCT
31365 TTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCC
* *
31412 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCC
31459 TTT
1 TTT
31462 TGCACTTCCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (47 bp):
TTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCC
Found at i:31463 original size:24 final size:24
Alignment explanation
Indices: 31358--31462 Score: 176
Period size: 24 Copynumber: 4.4 Consensus size: 24
31348 CTGGAGGTCT
*
31358 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
31383 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
31407 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
31430 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
31454 AGCCCTTTT
1 AGCCCTTTT
31463 GCACTTCCTC
Statistics
Matches: 77, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
23 23 0.30
24 50 0.65
25 4 0.05
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:31537 original size:20 final size:20
Alignment explanation
Indices: 31512--31578 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
31502 TTATGAACAC
31512 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
31532 ATCATGTGCATAGCATACAT
1 ATCATGTGCATATCATACAT
*
31552 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
31572 ACCATGT
1 ATCATGT
31579 TTACTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:35153 original size:30 final size:30
Alignment explanation
Indices: 35078--35153 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
35068 AATAGTCTAT
*
35078 ATTTTTATAATTTTTAAATGATCAAATCAA
1 ATTTTTATAATTTTTGAATGATCAAATCAA
35108 ATTTTTATAATTTTTGAATGATCAAATCAA
1 ATTTTTATAATTTTTGAATGATCAAATCAA
*
35138 ATTTTTATTATTTTTG
1 ATTTTTATAATTTTTG
35154 GGATGACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (30 bp):
ATTTTTATAATTTTTGAATGATCAAATCAA
Found at i:37381 original size:40 final size:40
Alignment explanation
Indices: 37337--37560 Score: 246
Period size: 40 Copynumber: 5.6 Consensus size: 40
37327 GCTCCTCGTT
*
37337 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
37377 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* *
37417 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* *
37456 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGG-TTATAGTAACTCGCA
* * * * *
37496 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
37537 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
37561 ACATCATTCA
Statistics
Matches: 161, Mismatches: 13, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
38 2 0.01
39 32 0.20
40 114 0.71
41 13 0.08
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:37439 original size:79 final size:78
Alignment explanation
Indices: 37337--37561 Score: 274
Period size: 79 Copynumber: 2.8 Consensus size: 78
37327 GCTCCTCGTT
* *
37337 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
37402 ATTTAGTAACTCGCA
64 ATTTAGTAACTCGCA
* * *
37417 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGG
*
37481 ATTTAGTATCTCGCA
64 ATTTAGTAACTCGCA
* * * * *
37496 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
37560 GA
63 GA
37562 CATCATTCAA
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
78 4 0.03
79 66 0.53
80 43 0.34
81 12 0.10
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
TTAGTAACTCGCA
Found at i:37521 original size:119 final size:120
Alignment explanation
Indices: 37337--37561 Score: 298
Period size: 119 Copynumber: 1.9 Consensus size: 120
37327 GCTCCTCGTT
37337 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
37402 ATTTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * * **
37456 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACC
* *
37518 CGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
63 CGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
37562 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
118 6 0.07
119 65 0.71
120 21 0.23
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:45263 original size:40 final size:40
Alignment explanation
Indices: 45219--45438 Score: 253
Period size: 40 Copynumber: 5.7 Consensus size: 40
45209 GCTCCTCGTT
* *
45219 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
45259 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
45299 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGT-A-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
*
45336 C-AA-GCCTTC-GGATCTTAGCCCGGAT-TAGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAACTCGCA
* * * *
45373 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
45414 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
45439 CATCATTCAA
Statistics
Matches: 156, Mismatches: 13, Indels: 22
0.82 0.07 0.12
Matches are distributed among these distances:
34 2 0.01
35 10 0.06
36 13 0.08
37 12 0.08
38 3 0.02
39 35 0.22
40 70 0.45
41 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:45376 original size:74 final size:80
Alignment explanation
Indices: 45219--45438 Score: 244
Period size: 79 Copynumber: 2.8 Consensus size: 80
45209 GCTCCTCGTT
*
45219 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
45284 ATTTAGTAACTCGCA
66 ATTTAGTAACTCGCA
* *
45299 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGT-A-TCGCAC-AA-GCCTTC-GGATCTTAGCCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
*
45357 GGA-TTAGTATCTCGCA
64 GGATTTAGTAACTCGCA
* * * * * *
45373 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CATAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCC
45436 GGA
64 GGA
45439 CATCATTCAA
Statistics
Matches: 123, Mismatches: 7, Indels: 21
0.81 0.05 0.14
Matches are distributed among these distances:
73 2 0.02
74 26 0.21
75 29 0.24
76 4 0.03
77 6 0.05
78 7 0.06
79 32 0.26
80 17 0.14
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATTTAGTAACTCGCA
Done.