Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold435
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: 524057
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 3
Found at i:445331 original size:115 final size:115
Alignment explanation
Indices: 445129--445359 Score: 462
Period size: 115 Copynumber: 2.0 Consensus size: 115
445119 TCCGCCCTTT
445129 TAGTTAAATCAGGGGGCTCTGTTGCGTGAATACGAACTTAACAAAAGTTGGATGCATGCTTCAGA
1 TAGTTAAATCAGGGGGCTCTGTTGCGTGAATACGAACTTAACAAAAGTTGGATGCATGCTTCAGA
445194 TTCCCTGTCCTACATTTTTAGCAACGGTTATTCGGGTAGTTTTGAACTGC
66 TTCCCTGTCCTACATTTTTAGCAACGGTTATTCGGGTAGTTTTGAACTGC
445244 TAGTTAAATCAGGGGGCTCTGTTGCGTGAATACGAACTTAACAAAAGTTGGATGCATGCTTCAGA
1 TAGTTAAATCAGGGGGCTCTGTTGCGTGAATACGAACTTAACAAAAGTTGGATGCATGCTTCAGA
445309 TTCCCTGTCCTACATTTTTAGCAACGGTTATTCGGGTAGTTTTGAACTGC
66 TTCCCTGTCCTACATTTTTAGCAACGGTTATTCGGGTAGTTTTGAACTGC
445359 T
1 T
445360 CCAACGTAGT
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 116 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (115 bp):
TAGTTAAATCAGGGGGCTCTGTTGCGTGAATACGAACTTAACAAAAGTTGGATGCATGCTTCAGA
TTCCCTGTCCTACATTTTTAGCAACGGTTATTCGGGTAGTTTTGAACTGC
Found at i:446182 original size:3 final size:3
Alignment explanation
Indices: 446174--446223 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
446164 TTCTTTTCCT
*
446174 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
446222 TT
1 TT
446224 TTCTATTTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:446411 original size:28 final size:28
Alignment explanation
Indices: 446380--446437 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
446370 ATTAAAAAAC
*
446380 ATATAAT-TGATAATTAAATTGTAAGTTA
1 ATATAATAT-ATAATTAAATTGCAAGTTA
* *
446408 ATATGATATATAATTTAATTGCAAGTTA
1 ATATAATATATAATTAAATTGCAAGTTA
446436 AT
1 AT
446438 CTGTTAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (28 bp):
ATATAATATATAATTAAATTGCAAGTTA
Found at i:447135 original size:21 final size:22
Alignment explanation
Indices: 447099--447155 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
447089 ATGTCGGTAG
*
447099 TTACAATTATGTTATTAATAAT
1 TTACTATTATGTTATTAATAAT
* *
447121 TTATTATTAT-TTATTAATCAT
1 TTACTATTATGTTATTAATAAT
447142 TTACTATTATGTTA
1 TTACTATTATGTTA
447156 CTTATCATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (22 bp):
TTACTATTATGTTATTAATAAT
Found at i:447436 original size:22 final size:23
Alignment explanation
Indices: 447406--447454 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
447396 TTATATCTTT
447406 TATTAATAAT-TTATAAAATTTAC
1 TATTAATAATATTA-AAAATTTAC
**
447429 TATT-ATAATATTAACTATTTAC
1 TATTAATAATATTAAAAATTTAC
447451 TATT
1 TATT
447455 GTTTTGTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTAATAATATTAAAAATTTAC
Found at i:447553 original size:11 final size:11
Alignment explanation
Indices: 447531--447576 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
447521 ATTAATGTGC
447531 TATTAATA-AT
1 TATTAATATAT
*
447541 TAGTAATATAT
1 TATTAATATAT
447552 TATTAATCAT-T
1 TATTAAT-ATAT
447563 TATTAATATAT
1 TATTAATATAT
447574 TAT
1 TAT
447577 AAAAAAATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 9 0.29
11 20 0.65
12 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (11 bp):
TATTAATATAT
Found at i:447572 original size:22 final size:21
Alignment explanation
Indices: 447508--447576 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 21
447498 TCTTTACCTG
* * *
447508 TTATTTATAATTTATTAATGTG
1 TTATTAAT-ATTTATTAATATA
* * *
447530 CTATTAATAATTAGTAATATA
1 TTATTAATATTTATTAATATA
447551 TTATTAATCATTTATTAATATA
1 TTATTAAT-ATTTATTAATATA
447573 TTAT
1 TTAT
447577 AAAAAAATCT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 16 0.43
22 21 0.57
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (21 bp):
TTATTAATATTTATTAATATA
Found at i:452320 original size:3 final size:3
Alignment explanation
Indices: 452312--452340 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
452302 AAATAAAGCC
452312 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
452341 AATCTTTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:454669 original size:16 final size:16
Alignment explanation
Indices: 454650--454680 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
454640 CTTGTTAATT
454650 AATTTTATTATTACTC
1 AATTTTATTATTACTC
454666 AATTTTATTATTACT
1 AATTTTATTATTACT
454681 TTAATTAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTTTATTATTACTC
Found at i:457274 original size:29 final size:28
Alignment explanation
Indices: 457242--457390 Score: 101
Period size: 29 Copynumber: 5.0 Consensus size: 28
457232 AAATACAAAT
*
457242 AAAATTATATTTATATTGAACAATAATTA
1 AAAATTATATTTATATT-AAAAATAATTA
* *
457271 AAAATTATTTTTAT-TTTAAAATAATTA
1 AAAATTATATTTATATTAAAAATAATTA
*
457298 CTAAAATTATATATATTAAATTTAAAATATATATT-
1 --AAAA-T-TATAT-TTATA-TTAAAA-ATA-ATTA
457333 AAAA-TATATTTATATTAAATAATAATTA
1 AAAATTATATTTATATTAAA-AATAATTA
*
457361 AATATTAT-TTGTAT-TTAAAAAATTAATTA
1 AAAATTATATT-TATATT-AAAAA-TAATTA
457390 A
1 A
457391 TTAAAAAAAA
Statistics
Matches: 97, Mismatches: 8, Indels: 30
0.72 0.06 0.22
Matches are distributed among these distances:
27 12 0.12
28 19 0.20
29 38 0.39
30 6 0.06
31 4 0.04
32 3 0.03
33 4 0.04
34 5 0.05
35 3 0.03
36 3 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
AAAATTATATTTATATTAAAAATAATTA
Found at i:457336 original size:33 final size:34
Alignment explanation
Indices: 457285--457352 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 34
457275 TTATTTTTAT
457285 TTTAAAATAATTACTAAAAT-TATATATATTAAA
1 TTTAAAATAATTACTAAAATATATATATATTAAA
* *
457318 TTTAAAAT-ATATATTAAAATATATTTATATTAAA
1 TTTAAAATAAT-TACTAAAATATATATATATTAAA
457352 T
1 T
457353 AATAATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 2 0.06
33 16 0.52
34 13 0.42
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (34 bp):
TTTAAAATAATTACTAAAATATATATATATTAAA
Found at i:457360 original size:90 final size:91
Alignment explanation
Indices: 457200--457385 Score: 245
Period size: 90 Copynumber: 2.1 Consensus size: 91
457190 ATATTGAATG
* *
457200 AATTATTAAAATTATAATTATATTAAATAATAAAATACAAATAAAATTATATTTATATTGAACAA
1 AATTACTAAAATTATAATTATATTAAATAATAAAATACAAATAAAATTATATTTATATTAAACAA
*
457265 TAATTAAAAATTATTTTTATTTTAAAA
66 TAATTAAAAATTATTTGTA-TTTAAAA
* * * *
457292 TAATTACTAAAATTAT-A-TATATTAAAT-TTAAAATATATATTAAAA-TATATTTATATTAAAT
1 -AATTACTAAAATTATAATTATATTAAATAATAAAATACA-AATAAAATTATATTTATATTAAAC
*
457353 AATAATTAAATATTATTTGTATTTAAAA
64 AATAATTAAAAATTATTTGTATTTAAAA
457381 AATTA
1 AATTA
457386 ATTAATTAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
88 5 0.06
89 7 0.08
90 41 0.49
91 16 0.19
92 1 0.01
93 14 0.17
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (91 bp):
AATTACTAAAATTATAATTATATTAAATAATAAAATACAAATAAAATTATATTTATATTAAACAA
TAATTAAAAATTATTTGTATTTAAAA
Found at i:457366 original size:34 final size:32
Alignment explanation
Indices: 457286--457367 Score: 85
Period size: 34 Copynumber: 2.5 Consensus size: 32
457276 TATTTTTATT
* *
457286 TTAAAATAATTACTAAAATTATATATATTAAA
1 TTAAAATAAATATTAAAATTATATATATTAAA
* *
457318 TTTAAAATATATATTAAAATATATTTATATTAAA
1 -TTAAAATAAATATTAAAAT-TATATATATTAAA
457352 -TAATAATTAAATATTA
1 TTAA-AA-TAAATATTA
457368 TTTGTATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 3 0.07
33 18 0.44
34 20 0.49
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (32 bp):
TTAAAATAAATATTAAAATTATATATATTAAA
Found at i:460675 original size:62 final size:62
Alignment explanation
Indices: 460556--460677 Score: 174
Period size: 62 Copynumber: 2.0 Consensus size: 62
460546 AAAGTTACTA
* * *
460556 AATATTAAGAATATAATATTGATAAAATAATTAAAATATAAAATAAATATATATTTTAAATG
1 AATATTAAGAATATAATATTGATAAAATAATTAAAATAGAAAATAAACACATATTTTAAATG
* * *
460618 AATATTAAGAATATAATA-TGAATAAAGTAATTAAAATAGAACATAAACACATGTTTTAAA
1 AATATTAAGAATATAATATTG-ATAAAATAATTAAAATAGAAAATAAACACATATTTTAAA
460678 ATTTATATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 2 0.04
62 51 0.96
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (62 bp):
AATATTAAGAATATAATATTGATAAAATAATTAAAATAGAAAATAAACACATATTTTAAATG
Found at i:467500 original size:2 final size:2
Alignment explanation
Indices: 467493--467517 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
467483 AAACAAATGA
467493 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
467518 AGGGATGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:469543 original size:24 final size:24
Alignment explanation
Indices: 469515--469580 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
469505 TGCTCTTAAT
* *
469515 TAAAAATACATTTG-TTGAATTGAA
1 TAAAAATAC-TATGATTCAATTGAA
*
469539 TAAAAATACTATGATTCATTTGAA
1 TAAAAATACTATGATTCAATTGAA
469563 TAAAAATACTATGATTCA
1 TAAAAATACTATGATTCA
469581 TTCTTTCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 3 0.08
24 35 0.92
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (24 bp):
TAAAAATACTATGATTCAATTGAA
Found at i:469581 original size:24 final size:24
Alignment explanation
Indices: 469534--469582 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
469524 ATTTGTTGAA
469534 TTGAATAAAAATACTATGATTCAT
1 TTGAATAAAAATACTATGATTCAT
469558 TTGAATAAAAATACTATGATTCAT
1 TTGAATAAAAATACTATGATTCAT
469582 T
1 T
469583 CTTTCTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (24 bp):
TTGAATAAAAATACTATGATTCAT
Found at i:470738 original size:22 final size:22
Alignment explanation
Indices: 470713--470755 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
470703 ATCATAATTA
470713 TTATTT-AATAATAAAAATATTT
1 TTATTTAAAT-ATAAAAATATTT
*
470735 TTATTTAAATATAAAATTATT
1 TTATTTAAATATAAAAATATT
470756 AATATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATTTAAATATAAAAATATTT
Found at i:470754 original size:16 final size:16
Alignment explanation
Indices: 470735--470771 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
470725 AAAAATATTT
470735 TTATTTAA-ATATAAAA
1 TTATTTAATATA-AAAA
470751 TTA-TTAATATAAAAA
1 TTATTTAATATAAAAA
470766 TTATTT
1 TTATTT
470772 TTTATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATTTAATATAAAAA
Found at i:472057 original size:52 final size:55
Alignment explanation
Indices: 471998--472111 Score: 128
Period size: 56 Copynumber: 2.1 Consensus size: 55
471988 TAGTAAAGTA
*
471998 ATATTATA-TAGATA-TTTATTAT-TAAAAAGTTA-ATTTAATGAATTTAATATTT
1 ATATTATATTAGATATTTTATTATATAAAAA-TTATATTTAAAGAATTTAATATTT
* * * * *
472050 ATATTATATTTATATATTTTATTATATCATAATTATATTTAAAGTATTTTATATTT
1 ATATTATA-TTAGATATTTTATTATATAAAAATTATATTTAAAGAATTTAATATTT
472106 ATATTA
1 ATATTA
472112 ATTTTTAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
52 8 0.16
54 5 0.10
55 11 0.22
56 27 0.53
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (55 bp):
ATATTATATTAGATATTTTATTATATAAAAATTATATTTAAAGAATTTAATATTT
Found at i:472062 original size:6 final size:6
Alignment explanation
Indices: 472039--472136 Score: 53
Period size: 6 Copynumber: 16.5 Consensus size: 6
472029 AATTTAATGA
* * *
472039 ATTTAAT ATTTAT A-TTAT ATTTAT ATATTTT A-TTAT A-TCAT AATTAT
1 ATTT-AT ATTTAT ATTTAT ATTTAT AT-TTAT ATTTAT ATTTAT ATTTAT
** * * *
472086 ATTTA- AAGTAT -TTTAT ATTTAT ATTAAT TTTTAAT ATTAAT AATTTAT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTT-AT ATTTAT -ATTTAT
472134 ATT
1 ATT
472137 ATAAAAATTT
Statistics
Matches: 69, Mismatches: 15, Indels: 15
0.70 0.15 0.15
Matches are distributed among these distances:
5 19 0.28
6 33 0.48
7 17 0.25
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (6 bp):
ATTTAT
Found at i:472072 original size:18 final size:18
Alignment explanation
Indices: 472039--472076 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
472029 AATTTAATGA
472039 ATTTAATATTTATATTAT
1 ATTTAATATTTATATTAT
472057 ATTTATATATTT-TATTAT
1 ATTTA-ATATTTATATTAT
472075 AT
1 AT
472077 CATAATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTAATATTTATATTAT
Found at i:472147 original size:48 final size:45
Alignment explanation
Indices: 472053--472148 Score: 106
Period size: 48 Copynumber: 2.1 Consensus size: 45
472043 AATATTTATA
* * *
472053 TTATATTTATATATTTTATTATATCATAATTATATTTAAAGTATT
1 TTATATTTATATATTTTAATATATAATAATTATATTTAAAGAATT
472098 TTATATTTATATTAATTTTTAATAT-TAATAATTTATATTATAAA-AATT
1 TTATATTTATA-T-A-TTTTAATATATAATAA-TTATATT-TAAAGAATT
472146 TTA
1 TTA
472149 AAATATATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
45 11 0.26
46 1 0.02
47 6 0.14
48 21 0.49
49 4 0.09
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (45 bp):
TTATATTTATATATTTTAATATATAATAATTATATTTAAAGAATT
Found at i:472210 original size:29 final size:29
Alignment explanation
Indices: 472039--472212 Score: 84
Period size: 29 Copynumber: 6.1 Consensus size: 29
472029 AATTTAATGA
* *
472039 ATTTAATAT-TTATATTATATTT-ATA-T
1 ATTTTATATATTATATAATATTTAATATT
* * *
472065 ATTTTATTATATCATAATTATATTTAA-AGT
1 ATTTTA-TATATTAT-ATAATATTTAATATT
*
472095 ATTTTATAT-TTATATTAATTTTTAATATT
1 ATTTTATATATTATA-TAATATTTAATATT
* * *
472124 AATAATT-TATATTATA-AAAATTTTAAAATAT
1 -AT-TTTATATATTATATAATA-TTTAATAT-T
*
472155 ATATTCATGATA-TATAT-AT-TTT-A-ATT
1 AT-TTTAT-ATATTATATAATATTTAATATT
*
472181 ATTTTATATATTATATCATATTTAATATT
1 ATTTTATATATTATATAATATTTAATATT
472210 ATT
1 ATT
472213 AAATTTACTT
Statistics
Matches: 114, Mismatches: 14, Indels: 37
0.69 0.08 0.22
Matches are distributed among these distances:
24 3 0.03
25 9 0.08
26 10 0.09
27 9 0.08
28 16 0.14
29 26 0.23
30 24 0.21
31 14 0.12
32 3 0.03
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (29 bp):
ATTTTATATATTATATAATATTTAATATT
Found at i:472611 original size:35 final size:35
Alignment explanation
Indices: 472554--472634 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
472544 TTTTTGATAG
* *
472554 TATTTTAA-TTATTTTTTAATTTTATATTAATATTA-
1 TATTTTAATTTATCTCTTAATTTTATATT-AT-TTAT
472589 TATTTTAATTTATCTCTT-ATTTTATATTATTTAT
1 TATTTTAATTTATCTCTTAATTTTATATTATTTAT
*
472623 TATTATAATTTA
1 TATTTTAATTTA
472635 ATTTTAACTA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 3 0.07
34 13 0.32
35 18 0.44
36 7 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.65
Consensus pattern (35 bp):
TATTTTAATTTATCTCTTAATTTTATATTATTTAT
Found at i:474021 original size:3 final size:3
Alignment explanation
Indices: 474015--474044 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
474005 CATCATAATT
474015 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
474045 AGCTTGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:474753 original size:17 final size:17
Alignment explanation
Indices: 474706--474759 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
474696 TATTTTTATA
474706 TTAATATTTATAATAAAAT
1 TTAA-ATTTA-AATAAAAT
**
474725 TTAAATAAAAATAAAAT
1 TTAAATTTAAATAAAAT
* *
474742 TTTAATTTAAATCAAAT
1 TTAAATTTAAATAAAAT
474759 T
1 T
474760 AATTTTATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
17 22 0.76
18 3 0.10
19 4 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAATTTAAATAAAAT
Found at i:475268 original size:6 final size:6
Alignment explanation
Indices: 475259--475295 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
475249 TATTTTTATT
475259 AAAATA AAAATA AAAATA AAAAT- AAAA-A AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
475296 TGCACGGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 8 0.28
6 21 0.72
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:475512 original size:23 final size:23
Alignment explanation
Indices: 475482--475529 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
475472 ACATTTCGTC
475482 AATCAAGGCACTCAATTGAAAGA
1 AATCAAGGCACTCAATTGAAAGA
475505 AATCAAGGCACTCAATTGAAAGA
1 AATCAAGGCACTCAATTGAAAGA
475528 AA
1 AA
475530 CCCTTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (23 bp):
AATCAAGGCACTCAATTGAAAGA
Found at i:479013 original size:173 final size:175
Alignment explanation
Indices: 478744--479070 Score: 631
Period size: 173 Copynumber: 1.9 Consensus size: 175
478734 ATTTGGTTGC
478744 CTTTTTTTTTTTTTTTGGGTATGGCCTTTGATTTGGAAACTGGAATAATAATGTGTTTGGTATTT
1 CTTTTTTTTTTTTTTTGGGTATGGCCTTTGATTTGGAAACTGGAATAATAATGTGTTTGGTATTT
478809 TGATTGCATGAGGTTGGTTTGATCAGTATCTAGAAATTATGATTTTGATGTAATTC-TTTTTGTT
66 TGATTGCATGAGGTTGGTTTGATCAGTATCTAGAAATTATGATTTTGATGTAATTCTTTTTTGTT
478873 AATACTTTGTATTGATATTAATTATGATATTTGGTTGCCTTTTTT
131 AATACTTTGTATTGATATTAATTATGATATTTGGTTGCCTTTTTT
478918 CTTTTTTTTTTTTTTT-GGTATGGCCTTTGATTTGGAAACTGGAATAATAATGTGTTTGGTATTT
1 CTTTTTTTTTTTTTTTGGGTATGGCCTTTGATTTGGAAACTGGAATAATAATGTGTTTGGTATTT
*
478982 TGATTGCATGAGGTTGGTTTGATCAGTATCTAGAAATTATGATTTTGATTTAATTCTTTTTTGTT
66 TGATTGCATGAGGTTGGTTTGATCAGTATCTAGAAATTATGATTTTGATGTAATTCTTTTTTGTT
479047 AATACTTTGTATTGATATTAATTA
131 AATACTTTGTATTGATATTAATTA
479071 AAATGCCATT
Statistics
Matches: 151, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
173 103 0.68
174 48 0.32
ACGTcount: A:0.23, C:0.06, G:0.19, T:0.52
Consensus pattern (175 bp):
CTTTTTTTTTTTTTTTGGGTATGGCCTTTGATTTGGAAACTGGAATAATAATGTGTTTGGTATTT
TGATTGCATGAGGTTGGTTTGATCAGTATCTAGAAATTATGATTTTGATGTAATTCTTTTTTGTT
AATACTTTGTATTGATATTAATTATGATATTTGGTTGCCTTTTTT
Found at i:479410 original size:23 final size:23
Alignment explanation
Indices: 479383--479428 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
479373 GCTAAGCATA
479383 AAATCGAACAATCAAAGGTTAGC
1 AAATCGAACAATCAAAGGTTAGC
479406 AAATCGAACAATCAAAGGTTAGC
1 AAATCGAACAATCAAAGGTTAGC
479429 TCTGATACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (23 bp):
AAATCGAACAATCAAAGGTTAGC
Found at i:479700 original size:56 final size:56
Alignment explanation
Indices: 479614--479721 Score: 207
Period size: 56 Copynumber: 1.9 Consensus size: 56
479604 TGTGACGCCT
*
479614 TTATCACAGACTTATTCACCATTTTTGTTGACTCCGCCCTCAAGAAGTTCAAGCCC
1 TTATCACAAACTTATTCACCATTTTTGTTGACTCCGCCCTCAAGAAGTTCAAGCCC
479670 TTATCACAAACTTATTCACCATTTTTGTTGACTCCGCCCTCAAGAAGTTCAA
1 TTATCACAAACTTATTCACCATTTTTGTTGACTCCGCCCTCAAGAAGTTCAA
479722 CGTACCTCAC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (56 bp):
TTATCACAAACTTATTCACCATTTTTGTTGACTCCGCCCTCAAGAAGTTCAAGCCC
Found at i:491477 original size:21 final size:21
Alignment explanation
Indices: 491336--491477 Score: 99
Period size: 21 Copynumber: 6.7 Consensus size: 21
491326 TGGTATAAAG
* *
491336 TTTTAATAAATTTTTATATGA
1 TTTTAATAACTTTTTATATAA
* ***
491357 TTTTGATAACTTCAAAGTATAA
1 TTTTAATAACTTTTTA-TATAA
*
491379 TTTTAATAAATATTTT-TATAA
1 TTTTAATAACT-TTTTATATAA
* *
491400 TTTTTTATAA-TATTTGATATAA
1 -TTTTAATAACT-TTTTATATAA
* **
491422 TTTTAATAACGTTAGATATAA
1 TTTTAATAACTTTTTATATAA
*
491443 TTTTAATAATTTTTTATATAA
1 TTTTAATAACTTTTTATATAA
**
491464 TTTTGGTAACTTTT
1 TTTTAATAACTTTT
491478 GTGTGTAACT
Statistics
Matches: 93, Mismatches: 23, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
21 66 0.71
22 26 0.28
23 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (21 bp):
TTTTAATAACTTTTTATATAA
Found at i:491515 original size:20 final size:20
Alignment explanation
Indices: 491492--491540 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
491482 GTAACTTTTA
*
491492 ATATAATTTGGTAATATTTG
1 ATATAATTTGATAATATTTG
* *
491512 ATATGATTTGATAATGTTTG
1 ATATAATTTGATAATATTTG
491532 ATATAATTT
1 ATATAATTT
491541 TGATGGCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (20 bp):
ATATAATTTGATAATATTTG
Found at i:491636 original size:99 final size:98
Alignment explanation
Indices: 491407--491666 Score: 244
Period size: 99 Copynumber: 2.7 Consensus size: 98
491397 TAATTTTTTA
* * * * * * * * **
491407 TAATATTTGATATAATTTTAATAACGTTAGATATAATTTTAATAATTTTTTATATAATTTTGGTA
1 TAATATTTGATATGA-CTTGATAATGTTTGATATAATTTTGATAACTTTTGATATAATTTTAATA
* * *
491472 A-CTTT--TGTGTG-TAACTTTTAATATAATTTGG
65 ATCTTTGATATTTGATAAC-CTTAATATAATTTGG
* **
491503 TAATATTTGATATGATTTGATAATGTTTGATATAATTTTGATGGCTTTTG-TAATAATTTTAATA
1 TAATATTTGATATGACTTGATAATGTTTGATATAATTTTGATAACTTTTGAT-ATAATTTTAATA
491567 ATCTTTGATATTTGATAACCTTAATATAATTTGG
65 ATCTTTGATATTTGATAACCTTAATATAATTTGG
* * * * *
491601 CTAATTTTTG-TAATTACTTGATAATTTTTTATATAATTTTTATAACTTTTGATATAATTTTAAT
1 -TAATATTTGAT-ATGACTTGATAATGTTTGATATAATTTTGATAACTTTTGATATAATTTTAAT
491665 AA
64 AA
491667 AATTCAATGT
Statistics
Matches: 134, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
94 1 0.01
95 38 0.28
96 18 0.13
98 19 0.14
99 57 0.43
100 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.10, T:0.52
Consensus pattern (98 bp):
TAATATTTGATATGACTTGATAATGTTTGATATAATTTTGATAACTTTTGATATAATTTTAATAA
TCTTTGATATTTGATAACCTTAATATAATTTGG
Found at i:491645 original size:21 final size:21
Alignment explanation
Indices: 491621--491666 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
491611 TAATTACTTG
* * *
491621 ATAATTTTTTATATAATTTTT
1 ATAACTTTTGATATAATTTTA
491642 ATAACTTTTGATATAATTTTA
1 ATAACTTTTGATATAATTTTA
491663 ATAA
1 ATAA
491667 AATTCAATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
ATAACTTTTGATATAATTTTA
Found at i:492104 original size:21 final size:21
Alignment explanation
Indices: 492080--492119 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
492070 TATCATTTCT
492080 TGTAATATTAG-TAACATTTAA
1 TGTAAT-TTAGATAACATTTAA
*
492101 TGTAATTTTGATAACATTT
1 TGTAATTTAGATAACATTT
492120 GTTATACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (21 bp):
TGTAATTTAGATAACATTTAA
Found at i:492269 original size:20 final size:20
Alignment explanation
Indices: 492103--492425 Score: 97
Period size: 21 Copynumber: 14.8 Consensus size: 20
492093 ACATTTAATG
492103 TAATTTTGATAACATTTGTTATA
1 TAATTTTGATAAC--TT-TTATA
* *
492126 CTATATTTTTGATAAATTTTAGCA
1 -TA-A-TTTTGATAACTTTTA-TA
*
492150 -AATTTTGATAA-TCTTGATA
1 TAATTTTGATAACT-TTTATA
*
492169 TAAATTT-AGTAACTTTTAATA
1 TAATTTTGA-TAACTTTT-ATA
**
492190 TAATTTCAATAACTTTTGATA
1 TAATTTTGATAACTTTT-ATA
**
492211 TAATTCTTAGA-ATTTTTTATA
1 TAATT-TT-GATAACTTTTATA
*
492232 TAATTTTGATAACATTTATA
1 TAATTTTGATAACTTTTATA
492252 TAATTTT-AGTGAA-TTTTAATA
1 TAATTTTGA-T-AACTTTT-ATA
*
492273 TAATTTTGTTTAACATTTGATATGATAA
1 TAATTTTG-ATAAC--TT--T-T-AT-A
* *
492301 TGTAACTTTTTGATAGCCTTTATA
1 --TAA--TTTTGATAACTTTTATA
* *
492325 TAATTTTCATAACTATTGATA
1 TAATTTTGATAACT-TTTATA
* *
492346 TAATTTT-AGCAATTTTTAATA
1 TAATTTTGA-TAACTTTT-ATA
* *
492367 TAAATTT-AGTAGCTTTTAATA
1 TAATTTTGA-TAACTTTT-ATA
492388 TAA-TTTGAATAACTTTTAATA
1 TAATTTTG-ATAACTTTT-ATA
*
492409 TAATTTTGATAAATTTT
1 TAATTTTGATAACTTTT
492426 TTAATAACAT
Statistics
Matches: 230, Mismatches: 35, Indels: 71
0.68 0.10 0.21
Matches are distributed among these distances:
19 6 0.03
20 56 0.24
21 108 0.47
22 17 0.07
23 4 0.02
24 8 0.03
25 3 0.01
26 11 0.05
27 4 0.02
28 1 0.00
29 1 0.00
30 3 0.01
31 3 0.01
32 5 0.02
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.50
Consensus pattern (20 bp):
TAATTTTGATAACTTTTATA
Found at i:492276 original size:21 final size:21
Alignment explanation
Indices: 492166--492279 Score: 110
Period size: 21 Copynumber: 5.5 Consensus size: 21
492156 GATAATCTTG
*
492166 ATATAAATTTAGTAACTTTTA
1 ATATAATTTTAGTAACTTTTA
* * *
492187 ATATAATTTCAATAACTTTTG
1 ATATAATTTTAGTAACTTTTA
* *
492208 ATATAATTCTTAG-AATTTTTT
1 ATATAATT-TTAGTAACTTTTA
*
492229 ATATAATTTT-GATAACATTT-
1 ATATAATTTTAG-TAACTTTTA
492249 ATATAATTTTAGTGAA-TTTTA
1 ATATAATTTTAGT-AACTTTTA
492270 ATATAATTTT
1 ATATAATTTT
492280 GTTTAACATT
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
19 1 0.01
20 16 0.21
21 57 0.75
22 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (21 bp):
ATATAATTTTAGTAACTTTTA
Found at i:492287 original size:42 final size:43
Alignment explanation
Indices: 492082--492424 Score: 169
Period size: 42 Copynumber: 7.9 Consensus size: 43
492072 TCATTTCTTG
* * *
492082 TAATATTAGT-AACATTTAATGTAATTTTGATAACATTTGTTATA
1 TAATTTTAGTGAACTTTTAATATAATTTTGATAACATTTG--ATA
* * **
492126 CTATATTTTTGAT-AAATTTTAGCA-AATTTTGAT-A-ATCTTGATA
1 -TA-ATTTTAG-TGAACTTTTAATATAATTTTGATAACAT-TTGATA
* ** *
492169 TAAATTTAGT-AACTTTTAATATAATTTCAATAACTTTTGATA
1 TAATTTTAGTGAACTTTTAATATAATTTTGATAACATTTGATA
* *
492211 TAATTCTTA--GAATTTTTTATATAATTTTGATAACATTT-ATA
1 TAATT-TTAGTGAACTTTTAATATAATTTTGATAACATTTGATA
*
492252 TAATTTTAGTGAA-TTTTAATATAATTTTGTTTAACATTTGATATGA
1 TAATTTTAGTGAACTTTTAATATAATTTTG-ATAACATTTG--AT-A
** * *
492298 TAATGTAACTTTTTGATAGCCTTT-ATATAATTTTCATAAC-TATTGATA
1 TAAT-T---TTAGTGA-A-CTTTTAATATAATTTTGATAACAT-TTGATA
* * * * * *
492346 TAATTTTAG-CAATTTTTAATATAAATTT-AGTAGCTTTTAATA
1 TAATTTTAGTGAACTTTTAATATAATTTTGA-TAACATTTGATA
* *
492388 TAATTTGAAT-AACTTTTAATATAATTTTGATAA-ATTT
1 TAATTTTAGTGAACTTTTAATATAATTTTGATAACATTT
492425 TTTAATAACA
Statistics
Matches: 228, Mismatches: 42, Indels: 60
0.69 0.13 0.18
Matches are distributed among these distances:
40 12 0.05
41 42 0.18
42 90 0.39
43 10 0.04
44 4 0.02
45 8 0.04
46 19 0.08
47 9 0.04
48 5 0.02
49 2 0.01
50 6 0.03
51 8 0.04
52 10 0.04
53 3 0.01
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.50
Consensus pattern (43 bp):
TAATTTTAGTGAACTTTTAATATAATTTTGATAACATTTGATA
Found at i:492367 original size:21 final size:21
Alignment explanation
Indices: 492322--492415 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
492312 GATAGCCTTT
* *
492322 ATATAATTTTCA-TAACTATTG
1 ATATAATTTT-AGTAACTTTTA
* *
492343 ATATAATTTTAGCAATTTTTA
1 ATATAATTTTAGTAACTTTTA
* *
492364 ATATAAATTTAGTAGCTTTTA
1 ATATAATTTTAGTAACTTTTA
* *
492385 ATATAATTTGAATAACTTTTA
1 ATATAATTTTAGTAACTTTTA
492406 ATATAATTTT
1 ATATAATTTT
492416 GATAAATTTT
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
20 1 0.02
21 58 0.98
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (21 bp):
ATATAATTTTAGTAACTTTTA
Found at i:492415 original size:11 final size:10
Alignment explanation
Indices: 492380--492469 Score: 54
Period size: 11 Copynumber: 8.2 Consensus size: 10
492370 ATTTAGTAGC
492380 TTTTAATATAA
1 TTTTAATA-AA
* *
492391 TTTGAATAAC
1 TTTTAATAAA
492401 TTTTAATATAA
1 TTTTAATA-AA
*
492412 TTTTGATAAA
1 TTTTAATAAA
492422 TTTTTTAATAACA
1 --TTTTAATAA-A
*
492435 TTTATAATAAT
1 TTT-TAATAAA
492446 TTTTATATAATA
1 TTTTA-ATAA-A
* *
492458 TTATAAGAAA
1 TTTTAATAAA
492468 TT
1 TT
492470 CAATATTAAG
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
10 15 0.24
11 28 0.45
12 18 0.29
13 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.51
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:493376 original size:3 final size:3
Alignment explanation
Indices: 493368--493418 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
493358 CAACAAACAA
493368 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
493416 AAT
1 AAT
493419 TGGATCCTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:493747 original size:22 final size:23
Alignment explanation
Indices: 493710--493760 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
493700 ATAATATTTA
*
493710 AAAATAAATAAATAT-AGTACAAT
1 AAAA-AAATAAATATAAATACAAT
493733 ATAAAAAAT-AATATAAATACAAT
1 A-AAAAAATAAATATAAATACAAT
493756 AAAAA
1 AAAAA
493761 TAAATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 9 0.36
23 13 0.52
24 3 0.12
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.24
Consensus pattern (23 bp):
AAAAAAATAAATATAAATACAAT
Found at i:493763 original size:27 final size:27
Alignment explanation
Indices: 493709--493764 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
493699 CATAATATTT
* * *
493709 AAAAATAAATAAATATAGTACAATATA
1 AAAAATAAATAAATACAATACAAAATA
493736 AAAAATAATATAAATACAATA-AAAATA
1 AAAAATAA-ATAAATACAATACAAAATA
493763 AA
1 AA
493765 TTAACTTGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (27 bp):
AAAAATAAATAAATACAATACAAAATA
Found at i:494022 original size:14 final size:15
Alignment explanation
Indices: 494003--494031 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
493993 TTTATAACTT
494003 TATGATAT-ATTAAA
1 TATGATATGATTAAA
494017 TATGATATGATTAAA
1 TATGATATGATTAAA
494032 AAAATAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (15 bp):
TATGATATGATTAAA
Found at i:494308 original size:17 final size:17
Alignment explanation
Indices: 494269--494312 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
494259 TAGATATAGA
*
494269 AAATTATATTATTATTT
1 AAATAATATTATTATTT
494286 ATAATAATATT-TTATATT
1 A-AATAATATTATTAT-TT
494304 AAATAATAT
1 AAATAATAT
494313 ATAATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAATAATATTATTATTT
Found at i:496519 original size:112 final size:112
Alignment explanation
Indices: 496322--496540 Score: 411
Period size: 112 Copynumber: 2.0 Consensus size: 112
496312 AAGTTATATT
496322 ACTTACAATTTCAAGTTGATTGTATGCATCTGGTACTTACTAGCTGTTGTAAAGTCAGAATAAAT
1 ACTTACAATTTCAAGTTGATTGTATGCATCTGGTACTTACTAGCTGTTGTAAAGTCAGAATAAAT
496387 TTTAGGATCACCATGCTATTTAAAGTTAGGATTGAAAGTCATCAATG
66 TTTAGGATCACCATGCTATTTAAAGTTAGGATTGAAAGTCATCAATG
* *
496434 ACTTAGAATTTCAAGTTGATTGTATGCATCTGGTACTTACTAGCTGTTGTAAAGTCAGGATAAAT
1 ACTTACAATTTCAAGTTGATTGTATGCATCTGGTACTTACTAGCTGTTGTAAAGTCAGAATAAAT
*
496499 TTTAGGATCATCATGCTATTTAAAGTTAGGATTGAAAGTCAT
66 TTTAGGATCACCATGCTATTTAAAGTTAGGATTGAAAGTCAT
496541 TTAATCTGCA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 104 1.00
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (112 bp):
ACTTACAATTTCAAGTTGATTGTATGCATCTGGTACTTACTAGCTGTTGTAAAGTCAGAATAAAT
TTTAGGATCACCATGCTATTTAAAGTTAGGATTGAAAGTCATCAATG
Found at i:504328 original size:16 final size:16
Alignment explanation
Indices: 504307--504338 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
504297 ATATTTTTAC
*
504307 TTTTAAATTTTTAAAA
1 TTTTAAAGTTTTAAAA
504323 TTTTAAAGTTTTAAAA
1 TTTTAAAGTTTTAAAA
504339 GCATTTATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTTAAAGTTTTAAAA
Found at i:511568 original size:2 final size:2
Alignment explanation
Indices: 511561--511600 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
511551 ATCAAGGCTA
* *
511561 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
511601 GCTAAGATGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:515163 original size:89 final size:89
Alignment explanation
Indices: 515009--515188 Score: 261
Period size: 89 Copynumber: 2.0 Consensus size: 89
514999 AAGCATAACC
* * * * *
515009 TAGTATCAATAAGAGAGTAAGAAGTGAGGACCCTAAAAACACAGTAAAAAGAAGCTCGAACTTGA
1 TAGTATCAATAAAACAGTAAGAAGTCAGCACCCTAAAAACACAGTAAAAAGAAGCTCAAACTTGA
*
515074 TGCAATAACCTTTTAGCATGATGG
66 TGCAATAACCATTTAGCATGATGG
* *
515098 TAGTATCAATAAAACAGTAAGAAGTCAGCACCCTAGAAACACAGTAAAAAGAAGCTCAAATTTGA
1 TAGTATCAATAAAACAGTAAGAAGTCAGCACCCTAAAAACACAGTAAAAAGAAGCTCAAACTTGA
* **
515163 TGCCATAACCATTTAGTGTGATGG
66 TGCAATAACCATTTAGCATGATGG
515187 TA
1 TA
515189 ATAAATGCAC
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 80 1.00
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (89 bp):
TAGTATCAATAAAACAGTAAGAAGTCAGCACCCTAAAAACACAGTAAAAAGAAGCTCAAACTTGA
TGCAATAACCATTTAGCATGATGG
Found at i:517619 original size:18 final size:19
Alignment explanation
Indices: 517564--517628 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 19
517554 AGATTGTTTA
*
517564 ATTAAA-AAAGAATTTAAAT
1 ATTAAATAAATAA-TTAAAT
517583 ATTAAATAAATAATT-AAT
1 ATTAAATAAATAATTAAAT
* *
517601 ATTCAATAAGT-ATTAAAT
1 ATTAAATAAATAATTAAAT
517619 A-T-AATAAATA
1 ATTAAATAAATA
517629 TTTATAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 6 0.15
17 4 0.10
18 16 0.41
19 8 0.21
20 5 0.13
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (19 bp):
ATTAAATAAATAATTAAAT
Found at i:517685 original size:18 final size:18
Alignment explanation
Indices: 517662--517698 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
517652 CTAAATGGTA
517662 TGATCTTTAAGAGAGATC
1 TGATCTTTAAGAGAGATC
*
517680 TGATCTTTAATAGAGATC
1 TGATCTTTAAGAGAGATC
517698 T
1 T
517699 AATGGGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (18 bp):
TGATCTTTAAGAGAGATC
Done.