Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1452
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: 52499
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Found at i:1444 original size:40 final size:40
Alignment explanation
Indices: 1296--1493 Score: 290
Period size: 40 Copynumber: 5.2 Consensus size: 40
1286 AACCCAACTA
* *
1296 CCTTC-GGATTTAG-CCGGATATAG-CAACTCGCAC-AATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
1333 CCTTC-GGACTTAGCCCGG---TA-TCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1368 CCTTCGGGACTTAGCCCGGAT-TAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1407 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
1447 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1487 CCTTCGG
1 CCTTCGG
1494 ATCTTAGTCC
Statistics
Matches: 150, Mismatches: 3, Indels: 13
0.90 0.02 0.08
Matches are distributed among these distances:
34 7 0.05
35 12 0.08
36 13 0.09
37 12 0.08
38 6 0.04
39 36 0.24
40 64 0.43
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:1448 original size:79 final size:76
Alignment explanation
Indices: 1296--1511 Score: 284
Period size: 79 Copynumber: 2.8 Consensus size: 76
1286 AACCCAACTA
* *
1296 CCTTC-GGATTTAG-CCGGATATAG-CAACTCGCAC-AATGCCTTC-GGACTTAGCCCGGTATCA
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGTATCA
1356 CTAGCACAAATG
65 CTAGCACAAATG
1368 CCTTCGGGACTTAGCCCGGAT-TAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGG---TA-
1432 TCACTAGCACAAATG
62 TCACTAGCACAAATG
* *
1447 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATGCCTTC-GGATCTTAGTCCGGTTATC
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGA-CTTAGCCCGG-TATC
1511 A
64 A
1512 TTCGAATAAT
Statistics
Matches: 128, Mismatches: 5, Indels: 17
0.85 0.03 0.11
Matches are distributed among these distances:
72 5 0.04
73 17 0.13
74 16 0.12
75 13 0.10
77 3 0.02
78 4 0.03
79 39 0.30
80 31 0.24
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (76 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGTATCAC
TAGCACAAATG
Found at i:9318 original size:40 final size:40
Alignment explanation
Indices: 9195--9398 Score: 299
Period size: 40 Copynumber: 5.2 Consensus size: 40
9185 AACCCAAGTA
* * * *
9195 CCTTCGGAATTTAG-CCGGATATAG-CAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
9234 CCTTCGGGACTTAG-CCGGACATAGTCACT-GCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
9272 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
9312 CCTTCGGGACTTAGCCCGGATATAATCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
9352 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
9392 CCTTCGG
1 CCTTCGG
9399 ATCTTAGTCC
Statistics
Matches: 154, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
38 22 0.14
39 38 0.25
40 94 0.61
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:14139 original size:27 final size:27
Alignment explanation
Indices: 14109--14436 Score: 347
Period size: 27 Copynumber: 12.2 Consensus size: 27
14099 AAAGTAGTCC
*
14109 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCATTTTACCCT
* * *
14136 CGATATATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCATTTTACCCT
** * *
14163 CGATTTTTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCATTTTACCCT
*
14190 CGATTTATAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCATTTTACCCT
* * *
14217 -TAGTTTACAAAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCATTTTACCCT
* *
14244 CGATTTATAGAATTACTATTTTACCCT
1 CGATTTACAGAATTACCATTTTACCCT
* ** * *
14271 CGTTTTTTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCATTTTACCCT
* * *
14298 TGATTTACAAAATTATCATTTTACCCT
1 CGATTTACAGAATTACCATTTTACCCT
*
14325 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCATTTTACCCT
*
14352 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCATTTTACCCT
* * * *
14379 CAATTTACA-AAATATCGTTTTACCCT
1 CGATTTACAGAATTACCATTTTACCCT
*
14405 CGATTTATAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCATTTTACCCT
*
14432 TGATT
1 CGATT
14437 GTGAAATTAC
Statistics
Matches: 255, Mismatches: 41, Indels: 10
0.83 0.13 0.03
Matches are distributed among these distances:
26 24 0.09
27 229 0.90
28 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.42
Consensus pattern (27 bp):
CGATTTACAGAATTACCATTTTACCCT
Found at i:14202 original size:81 final size:81
Alignment explanation
Indices: 14109--14436 Score: 383
Period size: 81 Copynumber: 4.1 Consensus size: 81
14099 AAAGTAGTCC
* * * * *
14109 CGATTTACAGAATTACCGTTTTACCCTCGATATATAGAATTACCGTTTTACCCTCGATTTTTAAA
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTATAAA
*
14174 ATTACCGTTTTACCCT
66 ATTACCATTTTACCCT
* * * * *
14190 CGATTTATAGAATTACCATTTTACCCT-TAGTTTACAAAATTACTATTTTACCCTCGATTTATAG
1 CGATTTACAGAATTACCGTTTTACCCTCGA-TTTACAAAATTACCATTTTACCCTCGATTTATAA
*
14254 AATTACTATTTTACCCT
65 AATTACCATTTTACCCT
* ** * * * * *
14271 CGTTTTTTAAAATTACCGTTTTACCCTTGATTTACAAAATTATCATTTTACCCTC-AGTTTACAG
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGA-TTTATAA
*
14335 AATTACTATTTTACCCT
65 AATTACCATTTTACCCT
* * * *
14352 CGATTTACAGAATTACCGTTTTACCCTCAATTTACAAAA-TATCGTTTTACCCTCGATTTATAGA
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTATAAA
14416 ATTACCATTTTACCCT
66 ATTACCATTTTACCCT
*
14432 TGATT
1 CGATT
14437 GTGAAATTAC
Statistics
Matches: 213, Mismatches: 30, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
80 42 0.20
81 170 0.80
82 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.42
Consensus pattern (81 bp):
CGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTATAAA
ATTACCATTTTACCCT
Found at i:14471 original size:27 final size:27
Alignment explanation
Indices: 14441--14636 Score: 230
Period size: 27 Copynumber: 7.3 Consensus size: 27
14431 TTGATTGTGA
*
14441 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
14468 AATTTCCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
14495 AATTACTGAAATACCCTTATAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
14522 AATTACCAAAATATCCCTGTAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
14549 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
14576 AAATACCGAAATACTCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
14603 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
14630 AATTACC
1 AATTACC
14637 ATTTTGCCCG
Statistics
Matches: 142, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 142 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:14902 original size:27 final size:26
Alignment explanation
Indices: 14835--14917 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 26
14825 CGGAGGAAGC
*
14835 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
*
14862 GTTCTAGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * ** *
14888 GTATTTGGTGACTCTATCACAATATTT
1 GT-TCTGGTGGCTCTGCCACAATATCT
14915 GTT
1 GTT
14918 GACCGATTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
26 10 0.21
27 37 0.79
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:15037 original size:22 final size:22
Alignment explanation
Indices: 15005--15063 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
14995 CCCGTTATTA
*
15005 ATGGCTATGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
15027 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
15049 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
15064 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:15258 original size:27 final size:25
Alignment explanation
Indices: 15228--15301 Score: 67
Period size: 27 Copynumber: 2.8 Consensus size: 25
15218 TAGGTGGGTT
*
15228 TGCCACATTATCTGATTCTGGTGGCTC
1 TGCCACA-TATCTG-TTCTGGTGACTC
* *
15255 TGCCATAATATCTTTATCTGGTGACTC
1 TGCCA-CATATCTGT-TCTGGTGACTC
*
15282 TGTCACGATATCTGTTCTGG
1 TGCCAC-ATATCTGTTCTGG
15302 CAGCCATGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
26 6 0.16
27 31 0.82
28 1 0.03
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (25 bp):
TGCCACATATCTGTTCTGGTGACTC
Found at i:15453 original size:6 final size:6
Alignment explanation
Indices: 15444--15605 Score: 165
Period size: 6 Copynumber: 26.8 Consensus size: 6
15434 CTGTCACGTA
* * *
15444 ATTCTG ATTCTG ATTCTG ATTCTG -TTACTA ATACTG ATTTTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG
* *
15492 ATTCTG -TTACTG ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTG
1 ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
*
15541 ATTCTG ATTCTG -TTACTA ATAT-TG ATTCTG ATTCTG ATTCTG -TTGCTG
1 ATTCTG ATTCTG ATT-CTG AT-TCTG ATTCTG ATTCTG ATTCTG ATT-CTG
15589 ATTCTG ATTCTG ATTCT
1 ATTCTG ATTCTG ATTCT
15606 CATTTTGGTT
Statistics
Matches: 131, Mismatches: 12, Indels: 26
0.78 0.07 0.15
Matches are distributed among these distances:
5 10 0.08
6 111 0.85
7 8 0.06
8 2 0.02
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:15488 original size:30 final size:30
Alignment explanation
Indices: 15419--15605 Score: 224
Period size: 30 Copynumber: 6.4 Consensus size: 30
15409 TTGCATTCAC
* * *
15419 ATTCTCATTCTGATTCTGTCACGTAATTCTG
1 ATTCTGATTCTGATTCTGTTAC-TAATACTG
15450 ATTCTGATTCTGATTCTGTTACTAATACTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
*
15480 ATTTTGATTCTGATTCTG----T--TACTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
* *
15504 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTA-CTAATACTG
*
15535 ATTCTGATTCTGATTCTGTTACTAATATTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
* * *
15565 ATTCTGATTCTGATTCTGTTGCTGATTCTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
15595 ATTCTGATTCT
1 ATTCTGATTCT
15606 CATTTTGGTT
Statistics
Matches: 136, Mismatches: 13, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
24 22 0.16
26 1 0.01
29 1 0.01
30 68 0.50
31 44 0.32
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (30 bp):
ATTCTGATTCTGATTCTGTTACTAATACTG
Found at i:15538 original size:25 final size:24
Alignment explanation
Indices: 15484--15546 Score: 99
Period size: 25 Copynumber: 2.6 Consensus size: 24
15474 ATACTGATTT
* *
15484 TGATTCTGATTCTGTTACTGATTC
1 TGATTCTGATTCTGTCACTAATTC
15508 TGATTCTGATTCTGTCACCTAATTC
1 TGATTCTGATTCTGTCA-CTAATTC
15533 TGATTCTGATTCTG
1 TGATTCTGATTCTG
15547 ATTCTGTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 16 0.44
25 20 0.56
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.48
Consensus pattern (24 bp):
TGATTCTGATTCTGTCACTAATTC
Found at i:15567 original size:85 final size:85
Alignment explanation
Indices: 15419--15605 Score: 329
Period size: 85 Copynumber: 2.2 Consensus size: 85
15409 TTGCATTCAC
* * *
15419 ATTCTCATTCTGATTCTGTCACGTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTT
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
15484 TGATTCTGATTCTGTTACTG
66 TGATTCTGATTCTGTTACTG
*
15504 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATATTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
*
15569 TGATTCTGATTCTGTTGCTG
66 TGATTCTGATTCTGTTACTG
15589 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
15606 CATTTTGGTT
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 97 1.00
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (85 bp):
ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
TGATTCTGATTCTGTTACTG
Found at i:15623 original size:30 final size:30
Alignment explanation
Indices: 15419--15626 Score: 207
Period size: 30 Copynumber: 7.1 Consensus size: 30
15409 TTGCATTCAC
* * *
15419 ATTCTCATTCTGATTCTGTCACGTAATTCTG
1 ATTCTGATTCTGATTCTGTTAC-CAATTCTG
* *
15450 ATTCTGATTCTGATTCTGTTACTAATACTG
1 ATTCTGATTCTGATTCTGTTACCAATTCTG
*
15480 ATTTTGATTCTGATTCTGTT----A--CTG
1 ATTCTGATTCTGATTCTGTTACCAATTCTG
*
15504 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTACC-AATTCTG
*
15535 ATTCTGATTCTGATTCTGTTACTAATAT-TG
1 ATTCTGATTCTGATTCTGTTACCAAT-TCTG
* **
15565 ATTCTGATTCTGATTCTGTTGCTGATTCTG
1 ATTCTGATTCTGATTCTGTTACCAATTCTG
* *
15595 ATTCTGATTCTCATTTTGGTT-CCAATTCTG
1 ATTCTGATTCTGATTCT-GTTACCAATTCTG
15625 AT
1 AT
15627 AATGTTTCTT
Statistics
Matches: 153, Mismatches: 14, Indels: 21
0.81 0.07 0.11
Matches are distributed among these distances:
24 21 0.14
26 1 0.01
29 2 0.01
30 81 0.53
31 48 0.31
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (30 bp):
ATTCTGATTCTGATTCTGTTACCAATTCTG
Found at i:16498 original size:17 final size:17
Alignment explanation
Indices: 16476--16510 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
16466 CTTAATCTCT
16476 TACACACTTATACAAAA
1 TACACACTTATACAAAA
16493 TACACACTTATACAAAA
1 TACACACTTATACAAAA
16510 T
1 T
16511 CAAAAGCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (17 bp):
TACACACTTATACAAAA
Found at i:18748 original size:30 final size:30
Alignment explanation
Indices: 18714--18774 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
18704 TCCTTAACTC
18714 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
18744 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
18774 A
1 A
18775 GGCTCGGCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:32168 original size:39 final size:40
Alignment explanation
Indices: 32068--32252 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
32058 TCGAATGATG
* *
32068 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
32107 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
32148 TTCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
32187 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
32226 AACCGGGCTATGTCCCGGAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
32253 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:32233 original size:79 final size:81
Alignment explanation
Indices: 32069--32250 Score: 221
Period size: 79 Copynumber: 2.3 Consensus size: 81
32059 CGAATGATGT
* *
32069 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT
*
32133 GTGCGAGTTACTAATT
66 GTGCGAGTTACTAATA
* * * **
32149 TCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCATT
32211 TGTGCGAGTTACT-ATAA
65 TGTGCGAGTTACTAAT-A
* *
32228 CCGGGCTATGTCCCGGAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
32251 TGAACGAGTA
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
78 3 0.03
79 58 0.67
80 26 0.30
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.26
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTAATA
Found at i:32274 original size:79 final size:78
Alignment explanation
Indices: 32102--32275 Score: 192
Period size: 79 Copynumber: 2.2 Consensus size: 78
32092 GTGCTAAGTG
* **
32102 ACTATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAATTTCGGGCTAAGCCCGAAGG
1 ACTATATCCGG-TTAAGATCCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGG
**
32167 CATTGGTGCGAGTT
65 CATTGGAACGAGTT
* * *
32181 ACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGG
1 ACTATATCC-GGTTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGA
*
32244 AGGCATTTGAACGAG-T
62 AGGCATTGGAACGAGTT
32260 AGCTATATCCGGTTAA
1 A-CTATATCCGGTTAA
32276 ATTCTGAAGG
Statistics
Matches: 80, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
78 3 0.04
79 52 0.65
80 25 0.31
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (78 bp):
ACTATATCCGGTTAAGATCCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGC
ATTGGAACGAGTT
Found at i:35606 original size:40 final size:39
Alignment explanation
Indices: 35544--35706 Score: 186
Period size: 40 Copynumber: 4.1 Consensus size: 39
35534 AAACCAAGTA
* * *
35544 CCTTCGGGATTTA-ACCGGATATAGCTAGTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAGTCGCACAAATG
* *
35583 CCTTCGGGACTTAGCCCGGATATAGTAGCTAGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAG-TCGCACAAATG
* *
35623 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGT-AGTCGCACAAATG
* *
35663 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGT-AGTCGCACAAATG
35703 CCTT
1 CCTT
35707 TGTTATCATC
Statistics
Matches: 108, Mismatches: 12, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
39 16 0.15
40 91 0.84
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGATATAGTAGTCGCACAAATG
Found at i:43991 original size:40 final size:39
Alignment explanation
Indices: 43929--44192 Score: 293
Period size: 40 Copynumber: 6.6 Consensus size: 39
43919 CGGATGATAA
* * *
43929 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAATT
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGT-ACTAATT
*
43969 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAATT
* *
44009 CCAGGCTAAGTCCTGAAGGCATTTGTGCGAGCTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAATT
*
44049 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAAT-T
* * * *
44089 CCAGGCTAAGTCCCGAAGGCATTTGTGTGAGTTA-TTATA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAATT
* *
44128 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTACA-A
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTA-ATT
*
44168 CCAGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
44193 AGCTATTGGC
Statistics
Matches: 198, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
39 34 0.17
40 160 0.81
41 4 0.02
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTAATT
Found at i:44065 original size:80 final size:80
Alignment explanation
Indices: 43932--44192 Score: 343
Period size: 80 Copynumber: 3.3 Consensus size: 80
43922 ATGATAACCG
* * *
43932 GGCTAAGTCCCG-AGAGCATTTGAGCTAG-TGGCTAATTTCGGGCTAAGTCCCGAAGGCATTTGT
1 GGCTAAGTCCCGAAG-GCATTTGTGCGAGCT-ACTAATTTCGGGCTAAGTCCCGAAGGCATTTGT
43995 GCGAGCTACTAATTCCA
64 GCGAGCTACTAATTCCA
*
44012 GGCTAAGTCCTGAAGGCATTTGTGCGAGCTACTAATTTCGGGCTAAGTCCCGAAGGCATTTGTGC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATTTCGGGCTAAGTCCCGAAGGCATTTGTGC
44077 GAGCTACT-ATATCCA
66 GAGCTACTAAT-TCCA
* * * **
44092 GGCTAAGTCCCGAAGGCATTTGTGTGAGTTA-TTATACCGGGCTAAGTCCCGAAGGCATTTGTGC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATTTCGGGCTAAGTCCCGAAGGCATTTGTGC
* * *
44156 AAGTTACTACA-ACCA
66 GAGCTACTA-ATTCCA
44171 GGCTAAGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
44193 AGCTATTGGC
Statistics
Matches: 163, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
79 63 0.39
80 96 0.59
81 4 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATTTCGGGCTAAGTCCCGAAGGCATTTGTGC
GAGCTACTAATTCCA
Done.