Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1656
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: 116196
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:659 original size:15 final size:16
Alignment explanation
Indices: 641--670 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
631 ATTTCCTTTC
641 TTCTTTCTT-TTTATT
1 TTCTTTCTTGTTTATT
656 TTCTTTCTTGTTTAT
1 TTCTTTCTTGTTTAT
671 CTATCAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.13, G:0.03, T:0.77
Consensus pattern (16 bp):
TTCTTTCTTGTTTATT
Found at i:8368 original size:23 final size:23
Alignment explanation
Indices: 8342--8403 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
8332 TCAAATTAGA
* *
8342 TTTGACTGATACGTTGATTGGTT
1 TTTGACCGATACATTGATTGGTT
8365 TTTGACCGATACATTGATTGGTT
1 TTTGACCGATACATTGATTGGTT
* *
8388 TTTGACCAATTCATTG
1 TTTGACCGATACATTG
8404 GTTTTAACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.45
Consensus pattern (23 bp):
TTTGACCGATACATTGATTGGTT
Found at i:9509 original size:2 final size:2
Alignment explanation
Indices: 9502--9529 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9492 AAAATAGGAA
9502 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9530 GAAAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18042 original size:2 final size:2
Alignment explanation
Indices: 18030--18060 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18020 TGCTTTTTGT
*
18030 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18061 GATAACCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:25372 original size:29 final size:23
Alignment explanation
Indices: 25315--25360 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
25305 TATATTGGGT
25315 GATGTTAGTTCAAGTTCATCACA
1 GATGTTAGTTCAAGTTCATCACA
25338 GATGTTAGTTCAAGTTCATCACA
1 GATGTTAGTTCAAGTTCATCACA
25361 TCGAGGGTTG
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:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (23 bp):
GATGTTAGTTCAAGTTCATCACA
Found at i:26049 original size:13 final size:13
Alignment explanation
Indices: 26031--26062 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
26021 TAGTTTTTAG
26031 AAAATGAAAACAA
1 AAAATGAAAACAA
*
26044 AAAATGAAAATAA
1 AAAATGAAAACAA
26057 AAAATG
1 AAAATG
26063 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.75, C:0.03, G:0.09, T:0.12
Consensus pattern (13 bp):
AAAATGAAAACAA
Found at i:30669 original size:10 final size:10
Alignment explanation
Indices: 30650--30681 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
30640 TAAATCCCTT
30650 TTACAATTTA
1 TTACAATTTA
*
30660 TTACACTTTA
1 TTACAATTTA
30670 TTACAATTTA
1 TTACAATTTA
30680 TT
1 TT
30682 GGATTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.53
Consensus pattern (10 bp):
TTACAATTTA
Found at i:30888 original size:75 final size:76
Alignment explanation
Indices: 30804--30955 Score: 207
Period size: 76 Copynumber: 2.0 Consensus size: 76
30794 AAAATGCAGC
** * * *
30804 CATA-TTTTTTTCAAAAAAATCATTAAAATGGACTACTCATTTATTGGATTATATTTTAATATAA
1 CATATTTTTTTTCAAAAAAATCATTAAAATAAACTACTCATTTATTGAATTATACTTTAATACAA
30868 ATCCTACCGCA
66 ATCCTACCGCA
* * *
30879 CATATTTTTTTTCAAAAAATTCATTAAAATAAATTACTTATTTATTGAATTATACTTTAATACAA
1 CATATTTTTTTTCAAAAAAATCATTAAAATAAACTACTCATTTATTGAATTATACTTTAATACAA
* *
30944 ATCTTACTGCA
66 ATCCTACCGCA
30955 C
1 C
30956 GTGTTTGACA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
75 4 0.06
76 62 0.94
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.42
Consensus pattern (76 bp):
CATATTTTTTTTCAAAAAAATCATTAAAATAAACTACTCATTTATTGAATTATACTTTAATACAA
ATCCTACCGCA
Found at i:30991 original size:95 final size:95
Alignment explanation
Indices: 30879--31089 Score: 259
Period size: 95 Copynumber: 2.2 Consensus size: 95
30869 TCCTACCGCA
* *
30879 CATATTTTTTTTCAAAAAATTCATTAAAATAAATTACTT-ATTTATT-GAATTATACTTTAATAC
1 CATA-TTTTTTTAAAAAAATTCATTAAAATAAACTA-TTCATTTATTAG-ATTATACTTTAATAC
*
30942 AAAT-CT-TACTGCACGTGTTTGACAAAATACAAT
63 AAATCCTGT-C-GCACATGTTTGACAAAATACAAT
* *
30975 CATATTTTTTTAAAAAAATTCATTAAAATGAACTATTCATTTATTAGATTATACTTTAATATAAA
1 CATATTTTTTTAAAAAAATTCATTAAAATAAACTATTCATTTATTAGATTATACTTTAATACAAA
* * ** *
31040 TCCTGTCGTATATGTTTGACAAAATGTAGT
66 TCCTGTCGCACATGTTTGACAAAATACAAT
31070 CATATTTTTTTAAAAAAATT
1 CATATTTTTTTAAAAAAATT
31090 ATTTATATAT
Statistics
Matches: 101, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
94 2 0.02
95 90 0.89
96 8 0.08
97 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.43
Consensus pattern (95 bp):
CATATTTTTTTAAAAAAATTCATTAAAATAAACTATTCATTTATTAGATTATACTTTAATACAAA
TCCTGTCGCACATGTTTGACAAAATACAAT
Found at i:31515 original size:2 final size:2
Alignment explanation
Indices: 31508--31545 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
31498 AATCAAGTTT
31508 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31546 TATTTTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:32418 original size:13 final size:13
Alignment explanation
Indices: 32374--32421 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
32364 AAATTAATTT
32374 TTTTAATTTATATA
1 TTTT-ATTTATATA
*
32388 TTTATACGTTATAT-
1 TTT-TA-TTTATATA
32402 TTTTATTTATATA
1 TTTTATTTATATA
32415 TTTTATT
1 TTTTATT
32422 AAAATTGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 6 0.21
13 9 0.31
14 7 0.24
15 7 0.24
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (13 bp):
TTTTATTTATATA
Found at i:34417 original size:24 final size:24
Alignment explanation
Indices: 34368--34418 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
34358 TATGATTTAA
* * *
34368 AAATAAATTAATACATAATTTTTT
1 AAATAAATTAATAAATAATATATT
34392 AAATAAATTAATTAAATAA-ATATT
1 AAATAAATTAA-TAAATAATATATT
34416 AAA
1 AAA
34419 ATTATAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
AAATAAATTAATAAATAATATATT
Found at i:34425 original size:28 final size:29
Alignment explanation
Indices: 34391--34452 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 29
34381 CATAATTTTT
* *
34391 TAAATAAATTAATTAAATAAATATTAAAATTA
1 TAAATAAATTAA--AAATATATA-AAAAATTA
34423 TAAATAAATTAAAAATATATAAAAAATTA
1 TAAATAAATTAAAAATATATAAAAAATTA
34452 T
1 T
34453 TTATATTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 8 0.29
30 8 0.29
32 12 0.43
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
TAAATAAATTAAAAATATATAAAAAATTA
Found at i:34428 original size:19 final size:19
Alignment explanation
Indices: 34404--34451 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
34394 ATAAATTAAT
*
34404 TAAATAAATATTAAAAT-TA
1 TAAATAAAT-TAAAAATATA
34423 TAAATAAATTAAAAATATA
1 TAAATAAATTAAAAATATA
34442 TAAA-AAATTA
1 TAAATAAATTA
34452 TTTATATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAATAAATTAAAAATATA
Found at i:34433 original size:17 final size:17
Alignment explanation
Indices: 34413--34451 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
34403 TTAAATAAAT
34413 ATTAAAAT-TATAAATAA
1 ATTAAAATATATAAA-AA
34430 ATTAAAAATATATAAAAA
1 ATT-AAAATATATAAAAA
34448 ATTA
1 ATTA
34452 TTTATATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.20
18 10 0.50
19 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTAAAATATATAAAAA
Found at i:35337 original size:54 final size:54
Alignment explanation
Indices: 35269--35379 Score: 127
Period size: 55 Copynumber: 2.1 Consensus size: 54
35259 TATATAAAAA
* * * * *
35269 TATATAAAATTTATCATATTT-TAATTAAATATTACTATTATAAATA-TTTTATT
1 TATAAAAAATTTATCAAATTTATAAGTAAAAATTACTAAT-TAAATATTTTTATT
**
35322 TATAAAAATATTTATCAAATTTATAAGTAAAAATTTTTAATTAAATATTTTTATT
1 TATAAAAA-ATTTATCAAATTTATAAGTAAAAATTACTAATTAAATATTTTTATT
35377 TAT
1 TAT
35380 TTGATAGTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
53 7 0.15
54 18 0.38
55 23 0.48
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (54 bp):
TATAAAAAATTTATCAAATTTATAAGTAAAAATTACTAATTAAATATTTTTATT
Found at i:35691 original size:31 final size:31
Alignment explanation
Indices: 35653--35723 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
35643 TTGACTGGTG
35653 GCGAGTCCATATGGACTTGCTATCCTATGTA
1 GCGAGTCCATATGGACTTGCTATCCTATGTA
35684 GCGAGTCCATATGGACTTGCTATCCTATGTA
1 GCGAGTCCATATGGACTTGCTATCCTATGTA
35715 GCGAGTCCA
1 GCGAGTCCA
35724 CGTGGAACAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.30
Consensus pattern (31 bp):
GCGAGTCCATATGGACTTGCTATCCTATGTA
Found at i:35856 original size:22 final size:22
Alignment explanation
Indices: 35830--35871 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
35820 TGTGTATAGA
35830 TATTAATTGAAAATTATTTAAT
1 TATTAATTGAAAATTATTTAAT
* *
35852 TATTAATTTAAAATTTTTTA
1 TATTAATTGAAAATTATTTA
35872 TATTTAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTAATTGAAAATTATTTAAT
Found at i:36107 original size:25 final size:24
Alignment explanation
Indices: 36079--36141 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
36069 AATTTTAAAA
*
36079 TAAATATTTATATTATATTATGTAT
1 TAAATATTTATATTATATTATAT-T
*
36104 TAAATATTT-TATATGTATTATATT
1 TAAATATTTATAT-TATATTATATT
*
36128 TAAATAATTATATT
1 TAAATATTTATATT
36142 TAAAATTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 13 0.39
25 20 0.61
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (24 bp):
TAAATATTTATATTATATTATATT
Found at i:36612 original size:16 final size:16
Alignment explanation
Indices: 36587--36617 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36577 TGCTTTAATA
36587 ATTATATTTTATTTGC
1 ATTATATTTTATTTGC
*
36603 ATTATTTTTTATTTG
1 ATTATATTTTATTTG
36618 ATAATCGTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.68
Consensus pattern (16 bp):
ATTATATTTTATTTGC
Found at i:36667 original size:35 final size:34
Alignment explanation
Indices: 36628--36733 Score: 83
Period size: 35 Copynumber: 3.0 Consensus size: 34
36618 ATAATCGTAT
36628 TTAATTTGTTATATGTTTATATAATTTTTAATATA
1 TTAATTTGTTATAT-TTTATATAATTTTTAATATA
** *
36663 TTAATAAGTTATA--TTATATAAATTTTAA-ATA
1 TTAATTTGTTATATTTTATATAATTTTTAATATA
*
36694 TTGATATTTTTGTTATATTATTTATATTAATTTTTTATAT
1 TT-A-A--TTTGTTATA-T-TTTATA-TAATTTTTAATAT
36734 TATATTATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
31 5 0.09
32 15 0.28
33 1 0.02
35 18 0.33
39 5 0.09
40 8 0.15
41 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (34 bp):
TTAATTTGTTATATTTTATATAATTTTTAATATA
Found at i:36720 original size:20 final size:20
Alignment explanation
Indices: 36692--36746 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
36682 AAATTTTAAA
*
36692 TATTGATATTTTTGTTATAT
1 TATTTATATTTTTGTTATAT
*
36712 TATTTATATTAATTTTTTATAT
1 TATTTATATT--TTTGTTATAT
36734 TATATTAT-TTTTT
1 TAT-TTATATTTTT
36747 TAGTATCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
22 14 0.47
23 4 0.13
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (20 bp):
TATTTATATTTTTGTTATAT
Found at i:36738 original size:18 final size:18
Alignment explanation
Indices: 36628--36748 Score: 63
Period size: 18 Copynumber: 6.6 Consensus size: 18
36618 ATAATCGTAT
* *
36628 TTAATTTGTTATATGTTTA
1 TTAATTTTTTATAT-TATA
36647 TATAA-TTTTTA-A-TATA
1 T-TAATTTTTTATATTATA
***
36663 TTAATAAGTTATATTATA
1 TTAATTTTTTATATTATA
* **
36681 TAAATTTTAAATATTGATA
1 TTAATTTTTTATATT-ATA
36700 TT--TTTGTTATATTATTTATA
1 TTAATTT-TT-TA-TA-TTATA
36720 TTAATTTTTTATATTATA
1 TTAATTTTTTATATTATA
*
36738 TTATTTTTTTA
1 TTAATTTTTTA
36749 GTATCATATG
Statistics
Matches: 76, Mismatches: 15, Indels: 23
0.67 0.13 0.20
Matches are distributed among these distances:
15 3 0.04
16 7 0.09
17 4 0.05
18 30 0.39
19 13 0.17
20 12 0.16
21 4 0.05
22 3 0.04
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (18 bp):
TTAATTTTTTATATTATA
Found at i:37902 original size:24 final size:24
Alignment explanation
Indices: 37818--37902 Score: 79
Period size: 24 Copynumber: 3.5 Consensus size: 24
37808 GTTTTTACTC
*
37818 TATTTAAAAT-TTTTTTATTTAAAA
1 TATTTAAAATATTTTTTAATT-AAA
37842 TATATTAAAATATTATTTTATATT-AA
1 TAT-TTAAAATATT-TTTTA-ATTAAA
*
37868 TATTT-ATATATTTTTTAATTAAA
1 TATTTAAAATATTTTTTAATTAAA
37891 T-TCTTAAAATAT
1 TAT-TTAAAATAT
37903 ATTTATCTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
22 4 0.08
23 10 0.20
24 14 0.27
25 9 0.18
26 7 0.14
27 5 0.10
28 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTTAAAATATTTTTTAATTAAA
Found at i:43458 original size:22 final size:22
Alignment explanation
Indices: 43432--43473 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
43422 AATTTTTATT
43432 TAAAT-ATAATTATAAAAATATA
1 TAAATCATAA-TATAAAAATATA
*
43454 TAAATCTTAATATAAAAATA
1 TAAATCATAATATAAAAATA
43474 ATGTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAATCATAATATAAAAATATA
Found at i:45405 original size:22 final size:22
Alignment explanation
Indices: 45374--45430 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
45364 ACTGTTTAAA
*
45374 TAATA-AAAAATTATTTAAATA-
1 TAATATAAAAA-TATATAAATAT
45395 TAATTATAAAAATATATAAATAT
1 TAA-TATAAAAATATATAAATAT
45418 TAATATAAAAATA
1 TAATATAAAAATA
45431 AAATTTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 3 0.09
22 21 0.66
23 8 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAATATAAAAATATATAAATAT
Found at i:45561 original size:20 final size:20
Alignment explanation
Indices: 45536--45579 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
45526 CACTTTTATG
45536 ATTAATATTACTCATTATTC
1 ATTAATATTACTCATTATTC
45556 ATTAATATTACTCATTATTC
1 ATTAATATTACTCATTATTC
45576 ATTA
1 ATTA
45580 TTGCTCTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTAATATTACTCATTATTC
Found at i:51216 original size:3 final size:3
Alignment explanation
Indices: 51208--51241 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
51198 TAATGATTTC
51208 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
51242 TTTTTATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:51246 original size:8 final size:8
Alignment explanation
Indices: 51211--51258 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 8
51201 TGATTTCTTA
51211 TTATTATT
1 TTATTATT
51219 ATTATTATT
1 -TTATTATT
51228 ATTATTATT
1 -TTATTATT
*
51237 TTATTTTT
1 TTATTATT
*
51245 TTATATAGT
1 TTAT-TATT
51254 TTATT
1 TTATT
51259 CTCACTATGG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
8 12 0.34
9 23 0.66
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (8 bp):
TTATTATT
Found at i:52052 original size:142 final size:141
Alignment explanation
Indices: 51794--52060 Score: 419
Period size: 142 Copynumber: 1.9 Consensus size: 141
51784 GGTTTTGAAT
* *
51794 TTGGTTATGCTCTGGACCATGCCATTGGGGATAAATACAACGGTACTGTATGCTAGCATTTACAT
1 TTGGCTATGCTCTGAACCATGCCATTGGGGATAAATACAACGGTACTGTATGCTAGCATTTACAT
* *
51859 ATCCTTTTTGAAGATACATTATGAATATAGACCTTGCCACTATGGTAAAAGTGGTCATAGTCTAG
66 ATCCTTTTTGAAGATACATTATGAATATAAACCTTGCCACTAGGGTAAAAGTGGTCATAGTCTAG
51924 TGTTATTTGAC
131 TGTTATTTGAC
* * * *
51935 TTGGCTATGTTCTGAACCTTGCCATTAGGGGATAAATACAATGGTATTGTATGCTAGCATTTACA
1 TTGGCTATGCTCTGAACCATGCCATT-GGGGATAAATACAACGGTACTGTATGCTAGCATTTACA
* *
52000 TATCCTTTTTG-AGATTATATTATGAATATAAACCTTGCCACTAGGGTGAAAGTGGTCATAG
65 TATCCTTTTTGAAGA-TACATTATGAATATAAACCTTGCCACTAGGGTAAAAGTGGTCATAG
52061 CCCAATTTGA
Statistics
Matches: 114, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
141 25 0.22
142 89 0.78
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (141 bp):
TTGGCTATGCTCTGAACCATGCCATTGGGGATAAATACAACGGTACTGTATGCTAGCATTTACAT
ATCCTTTTTGAAGATACATTATGAATATAAACCTTGCCACTAGGGTAAAAGTGGTCATAGTCTAG
TGTTATTTGAC
Found at i:54101 original size:2 final size:2
Alignment explanation
Indices: 54094--54121 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54084 TAGGATTGCA
54094 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54122 GTACTTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55168 original size:3 final size:3
Alignment explanation
Indices: 55160--55202 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
55150 TTTTGCATTG
55160 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
55203 AGTTTTGGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:56116 original size:38 final size:36
Alignment explanation
Indices: 56062--56168 Score: 99
Period size: 37 Copynumber: 2.8 Consensus size: 36
56052 GTCATAGGTT
56062 AAAACAAAAATCACTATTCTAATCCGGTGGCACGGCTC
1 AAAACAAAAAT-ACTATTCT-ATCCGGTGGCACGGCTC
** * *
56100 AAAACAAAAACTACTATTCCTA-CCAATGGCACGGGTT
1 AAAACAAAAA-TACTATT-CTATCCGGTGGCACGGCTC
**
56137 GGAACAAAAATTACTATTCTTATCCGGTGGCA
1 AAAACAAAAA-TACTATTC-TATCCGGTGGCA
56169 TAGTAAAAAC
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
36 1 0.02
37 28 0.50
38 24 0.43
39 3 0.05
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.23
Consensus pattern (36 bp):
AAAACAAAAATACTATTCTATCCGGTGGCACGGCTC
Found at i:56183 original size:31 final size:31
Alignment explanation
Indices: 56141--56288 Score: 161
Period size: 31 Copynumber: 4.8 Consensus size: 31
56131 CGGGTTGGAA
* *
56141 CAAAAATTACTATTCTTATCCGGTGGCATAG
1 CAAAAACTACTATTCTTATCCGGTGGCATGG
* * *
56172 TAAAAACTACTATTCTTATCCGGTGGCACGA
1 CAAAAACTACTATTCTTATCCGGTGGCATGG
* * * **
56203 CAAAAATTACTATTCTTAACAGGCAGCATGG
1 CAAAAACTACTATTCTTATCCGGTGGCATGG
* *
56234 CAACAACCACTATTCTTATCCGGTGGCATGG
1 CAAAAACTACTATTCTTATCCGGTGGCATGG
* * *
56265 TAAAAACCACTATTCTTAACCGGT
1 CAAAAACTACTATTCTTATCCGGT
56289 AACACGATTT
Statistics
Matches: 94, Mismatches: 23, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 94 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (31 bp):
CAAAAACTACTATTCTTATCCGGTGGCATGG
Found at i:61856 original size:38 final size:36
Alignment explanation
Indices: 61780--61894 Score: 124
Period size: 38 Copynumber: 3.1 Consensus size: 36
61770 CTGTGGTATA
* *
61780 GGTTAGAACAAAAACCACTATTCTAATCCT-GTGACAC
1 GGTTAGAACAAAAACTACTATTCTAAT--TGGTGGCAC
61817 GGTTCAGAACAAAAACTACTATTCTAATATGGTGGCAC
1 GGTT-AGAACAAAAACTACTATTCTAAT-TGGTGGCAC
* * *
61855 GGGTTGGAACAAAAACTACTATTTTTATTCGGTGGCAC
1 -GGTTAGAACAAAAACTACTATTCTAATT-GGTGGCAC
61893 GG
1 GG
61895 AAAAATCACT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
37 8 0.12
38 56 0.82
39 4 0.06
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (36 bp):
GGTTAGAACAAAAACTACTATTCTAATTGGTGGCAC
Found at i:61943 original size:31 final size:30
Alignment explanation
Indices: 61865--62003 Score: 127
Period size: 30 Copynumber: 4.6 Consensus size: 30
61855 GGGTTGGAAC
* *
61865 AAAAACTACTATTTTTATTCGGTGGCACGG
1 AAAAACTACTATTCTTATCCGGTGGCACGG
*
61895 AAAAA-TCACTATCCTTATCCGGTGGCACGG
1 AAAAACT-ACTATTCTTATCCGGTGGCACGG
* * *
61925 TAAAAACTGCTATTCTTATCCTGTAGCACGG
1 -AAAAACTACTATTCTTATCCGGTGGCACGG
* * * **
61956 CAAGACCACTATTCTTATCCAATGGCACGG
1 AAAAACTACTATTCTTATCCGGTGGCACGG
* *
61986 TAAAAACCATTATTCTTA
1 -AAAAACTACTATTCTTA
62004 ACTGGTAGCA
Statistics
Matches: 88, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
29 1 0.01
30 48 0.55
31 38 0.43
32 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (30 bp):
AAAAACTACTATTCTTATCCGGTGGCACGG
Found at i:61966 original size:61 final size:61
Alignment explanation
Indices: 61865--62016 Score: 169
Period size: 61 Copynumber: 2.5 Consensus size: 61
61855 GGGTTGGAAC
* * * * **
61865 AAAAACTACTATTTTTATTCGGTGGCACGGAAAAATCACTATCCTTATCCGGTGGCACGGT
1 AAAAACTACTATTCTTATCCGGTAGCACGGAAAAACCACTATCCTTATCCAATGGCACGGT
* * * * *
61926 AAAAACTGCTATTCTTATCCTGTAGCACGGCAAGACCACTATTCTTATCCAATGGCACGGT
1 AAAAACTACTATTCTTATCCGGTAGCACGGAAAAACCACTATCCTTATCCAATGGCACGGT
* * * *
61987 AAAAACCATTATTCTTAACTGGTAGCACGG
1 AAAAACTACTATTCTTATCCGGTAGCACGG
62017 TTTGAAACTA
Statistics
Matches: 74, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
61 74 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (61 bp):
AAAAACTACTATTCTTATCCGGTAGCACGGAAAAACCACTATCCTTATCCAATGGCACGGT
Found at i:65675 original size:32 final size:32
Alignment explanation
Indices: 65633--65711 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
65623 TATATAAATT
65633 AAAATAGTAAGATTTGCTAACCTTGATTTTAA
1 AAAATAGTAAGATTTGCTAACCTTGATTTTAA
* * *
65665 AAAATGGTAAGGTTTGTTAACCTTGATTTTAA
1 AAAATAGTAAGATTTGCTAACCTTGATTTTAA
*
65697 AAAACAGTAAGATTT
1 AAAATAGTAAGATTT
65712 ACTTATCTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.37
Consensus pattern (32 bp):
AAAATAGTAAGATTTGCTAACCTTGATTTTAA
Found at i:66816 original size:17 final size:16
Alignment explanation
Indices: 66794--66836 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
66784 ATTAATTAAG
66794 TTTTATTTATTTAATTT
1 TTTTATTTATTT-ATTT
66811 TTTTATTTATTTATTT
1 TTTTATTTATTTATTT
66827 TTTTCATTTA
1 TTTT-ATTTA
66837 AGTGTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 8 0.32
17 17 0.68
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTTATTTATTT
Found at i:67665 original size:15 final size:15
Alignment explanation
Indices: 67634--67683 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
67624 CTATCTATAT
* *
67634 TTTTTAAAAATAT-A
1 TTTTTAAATATTTAA
67648 TTTTTAAATATTTAA
1 TTTTTAAATATTTAA
67663 TTTTT-AATAATTTAA
1 TTTTTAAAT-ATTTAA
67678 TATTTT
1 T-TTTT
67684 TATTAAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 14 0.45
15 13 0.42
16 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTAAATATTTAA
Found at i:73051 original size:2 final size:2
Alignment explanation
Indices: 73039--73076 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
73029 GTTGGACTGA
73039 AT AT A- AT AT AT AT 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 AT AT AT AT AT AT AT A
73077 AGTTAATCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:73917 original size:21 final size:23
Alignment explanation
Indices: 73893--73942 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
73883 TTTTTTATTT
73893 TTTATATAAA-A-GATATTATAA
1 TTTATATAAAGATGATATTATAA
* *
73914 TTTAGAATAAAGATTATATTATAA
1 TTTA-TATAAAGATGATATTATAA
73938 TTTAT
1 TTTAT
73943 TTAGAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 4 0.17
22 5 0.22
23 1 0.04
24 13 0.57
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (23 bp):
TTTATATAAAGATGATATTATAA
Found at i:75456 original size:148 final size:148
Alignment explanation
Indices: 75188--75480 Score: 507
Period size: 148 Copynumber: 2.0 Consensus size: 148
75178 TCAAAGTCAG
* *
75188 AGTTATGTTAATTGATTGAAGAATATTAATACTTTCTTCACGCGTTCATGAATCGGTAACACATC
1 AGTTATATTAATTGATTGAAGAATATTAATACTTTCTTCACGCGTTCACGAATCGGTAACACATC
75253 ATTAATTGATATTATTTTTGAATGAGTACAATAAGGATGCTAATAATCTTTTCACATGTAATTAT
66 ATTAATTGATATTATTTTTGAATGAGTACAATAAGGATGCTAATAATCTTTTCACATGTAATTAT
75318 CTATACTTAATTTGACAC
131 CTATACTTAATTTGACAC
* *
75336 AGTTATATTAATTGATTGGAGAATATTAATACTTTCTTCATGCGTTCACGAATC-GTCAACACAT
1 AGTTATATTAATTGATTGAAGAATATTAATACTTTCTTCACGCGTTCACGAATCGGT-AACACAT
* * *
75400 CATTAATTGATATTATTTTTGAATGAGTACAATGAGGATGCTGATAATGTTTTCACATGTAATTA
65 CATTAATTGATATTATTTTTGAATGAGTACAATAAGGATGCTAATAATCTTTTCACATGTAATTA
75465 TCTATACTTAATTTGA
130 TCTATACTTAATTTGA
75481 TGTTATGTTT
Statistics
Matches: 137, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
147 2 0.01
148 135 0.99
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (148 bp):
AGTTATATTAATTGATTGAAGAATATTAATACTTTCTTCACGCGTTCACGAATCGGTAACACATC
ATTAATTGATATTATTTTTGAATGAGTACAATAAGGATGCTAATAATCTTTTCACATGTAATTAT
CTATACTTAATTTGACAC
Found at i:75771 original size:3 final size:3
Alignment explanation
Indices: 75763--75792 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
75753 TTTTATTGAG
75763 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
75793 GAAGTACATA
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):
TAT
Found at i:77165 original size:29 final size:29
Alignment explanation
Indices: 77127--77183 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
77117 TATCTCTTTA
*
77127 AATTCAATTTT-AGTGATGTGAATTTTATTT
1 AATTCAATTTTCA-TAATGTG-ATTTTATTT
77157 AATT-AATTTTCATAATGTGATTTTATT
1 AATTCAATTTTCATAATGTGATTTTATT
77184 ATTGATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 8 0.32
29 12 0.48
30 5 0.20
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.54
Consensus pattern (29 bp):
AATTCAATTTTCATAATGTGATTTTATTT
Found at i:78972 original size:15 final size:16
Alignment explanation
Indices: 78945--78984 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
78935 ATTTAAAAAA
*
78945 TTAAAAGTA-ATATT-
1 TTAAAAATATATATTC
78959 TTAAAAATATATATTC
1 TTAAAAATATATATTC
78975 TT-AAAATATA
1 TTAAAAATATA
78985 GTATCATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 8 0.35
15 13 0.57
16 2 0.09
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (16 bp):
TTAAAAATATATATTC
Found at i:80228 original size:19 final size:19
Alignment explanation
Indices: 80204--80269 Score: 64
Period size: 19 Copynumber: 3.3 Consensus size: 19
80194 AAATTTTAAA
80204 ATATTTATATATTTATATC
1 ATATTTATATATTTATATC
*
80223 ATATTTATATTATTTTTTTAT-
1 ATATTTATA-TA--TTTATATC
80244 ATTATGTTATAT-TTTATATC
1 A-TAT-TTATATATTTATATC
80264 ATATTT
1 ATATTT
80270 TAATTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
18 2 0.05
19 18 0.46
20 3 0.08
21 1 0.03
22 10 0.26
23 5 0.13
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.64
Consensus pattern (19 bp):
ATATTTATATATTTATATC
Found at i:80242 original size:41 final size:41
Alignment explanation
Indices: 80197--80283 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 41
80187 ACTATATAAA
*
80197 TTTTAAAATAT-TTATATATTTATATCATA-TTTATATTATTT
1 TTTTAAAATATGTTATAT-TTTATATCATATTTTA-ATTAATT
* *
80238 TTTTATATTATGTTATATTTTATATCATATTTTAATTAATT
1 TTTTAAAATATGTTATATTTTATATCATATTTTAATTAATT
80279 TTTTA
1 TTTTA
80284 TATTCTATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
41 31 0.76
42 10 0.24
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (41 bp):
TTTTAAAATATGTTATATTTTATATCATATTTTAATTAATT
Found at i:80253 original size:18 final size:17
Alignment explanation
Indices: 80204--80268 Score: 50
Period size: 17 Copynumber: 4.0 Consensus size: 17
80194 AAATTTTAAA
*
80204 ATATTTATATATTTATATC
1 ATATTT-TATA-TTATATT
80223 ATA-TTTATA-T-TATT
1 ATATTTTATATTATATT
*
80237 -T-TTTTATATTATGTT
1 ATATTTTATATTATATT
*
80252 ATATTTTATATCATATT
1 ATATTTTATATTATATT
80269 TTAATTAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
13 7 0.19
14 4 0.11
15 4 0.11
16 1 0.03
17 16 0.43
18 2 0.05
19 3 0.08
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (17 bp):
ATATTTTATATTATATT
Found at i:80284 original size:41 final size:42
Alignment explanation
Indices: 80208--80287 Score: 128
Period size: 41 Copynumber: 1.9 Consensus size: 42
80198 TTTAAAATAT
*
80208 TTATATATTTATATCATATTTATATTATTTTTTTATATTATG
1 TTATATATTTATATCATATTTATATTAATTTTTTATATTATG
80250 TTATAT-TTTATATCATATTT-TAATTAATTTTTTATATT
1 TTATATATTTATATCATATTTAT-ATTAATTTTTTATATT
80288 CTATTCATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 1 0.03
41 29 0.81
42 6 0.17
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (42 bp):
TTATATATTTATATCATATTTATATTAATTTTTTATATTATG
Found at i:82984 original size:13 final size:13
Alignment explanation
Indices: 82966--82996 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
82956 AGATTTTTTT
82966 ATATTATAATAAA
1 ATATTATAATAAA
*
82979 ATATTATAGTAAA
1 ATATTATAATAAA
82992 ATATT
1 ATATT
82997 CATGTTCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (13 bp):
ATATTATAATAAA
Found at i:83444 original size:17 final size:19
Alignment explanation
Indices: 83403--83446 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
83393 TAAAATATTA
*
83403 ATAT-AAATTTTTTTTAAT
1 ATATAAAATTTTTCTTAAT
83421 ATATAAAATTTTTCTTAA-
1 ATATAAAATTTTTCTTAAT
83439 AT-TAAAAT
1 ATATAAAAT
83447 AACAAATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 6 0.25
18 6 0.25
19 12 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
ATATAAAATTTTTCTTAAT
Found at i:88251 original size:25 final size:25
Alignment explanation
Indices: 88223--88272 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
88213 CTATTTACAT
88223 TTAGAACTTGAGCTGAGTTTCTTAA
1 TTAGAACTTGAGCTGAGTTTCTTAA
*
88248 TTAGAATTTGAGCTGAGTTTCTTAA
1 TTAGAACTTGAGCTGAGTTTCTTAA
88273 CTGGAGGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (25 bp):
TTAGAACTTGAGCTGAGTTTCTTAA
Found at i:95449 original size:32 final size:32
Alignment explanation
Indices: 95407--95485 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
95397 TATATAAATT
95407 AAAATAGTAAGATTTGCTAACCTTGATTTTAA
1 AAAATAGTAAGATTTGCTAACCTTGATTTTAA
* * *
95439 AAAATGGTAAGGTTTGTTAACCTTGATTTTAA
1 AAAATAGTAAGATTTGCTAACCTTGATTTTAA
*
95471 AAAACAGTAAGATTT
1 AAAATAGTAAGATTT
95486 AGTTATCTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.37
Consensus pattern (32 bp):
AAAATAGTAAGATTTGCTAACCTTGATTTTAA
Found at i:96584 original size:17 final size:16
Alignment explanation
Indices: 96562--96604 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
96552 ATTAATTAAG
96562 TTTTATTTATATAATTT
1 TTTTATTTAT-TAATTT
*
96579 TTTTATTTATTTATTT
1 TTTTATTTATTAATTT
96595 TTTTCATTTA
1 TTTT-ATTTA
96605 AGTGTTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTATTTATTAATTT
Found at i:98588 original size:21 final size:22
Alignment explanation
Indices: 98560--98608 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
98550 AGTGAGATGC
98560 TATTTAC-TTTTAAAAATTACTA
1 TATTTACTTTTTAAAAATTA-TA
*
98582 T-TTTACTTTTTAAATATTATA
1 TATTTACTTTTTAAAAATTATA
98603 TATTTA
1 TATTTA
98609 TATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTTACTTTTTAAAAATTATA
Found at i:98651 original size:13 final size:13
Alignment explanation
Indices: 98633--98657 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
98623 TACACACACA
98633 AAAATTATATATT
1 AAAATTATATATT
98646 AAAATTATATAT
1 AAAATTATATAT
98658 AATATTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATTATATATT
Found at i:105371 original size:148 final size:148
Alignment explanation
Indices: 105103--105395 Score: 507
Period size: 148 Copynumber: 2.0 Consensus size: 148
105093 TCAAAGTCAG
* *
105103 AGTTATGTTAATTGATTGAAGAATATTAATACTTTCTTCACGCGTTCATGAATCGGTAACACATC
1 AGTTATATTAATTGATTGAAGAATATTAATACTTTCTTCACGCGTTCACGAATCGGTAACACATC
105168 ATTAATTGATATTATTTTTGAATGAGTACAATAAGGATGCTAATAATCTTTTCACATGTAATTAT
66 ATTAATTGATATTATTTTTGAATGAGTACAATAAGGATGCTAATAATCTTTTCACATGTAATTAT
105233 CTATACTTAATTTGACAC
131 CTATACTTAATTTGACAC
* *
105251 AGTTATATTAATTGATTGGAGAATATTAATACTTTCTTCATGCGTTCACGAATC-GTCAACACAT
1 AGTTATATTAATTGATTGAAGAATATTAATACTTTCTTCACGCGTTCACGAATCGGT-AACACAT
* * *
105315 CATTAATTGATATTATTTTTGAATGAGTACAATGAGGATGCTGATAATGTTTTCACATGTAATTA
65 CATTAATTGATATTATTTTTGAATGAGTACAATAAGGATGCTAATAATCTTTTCACATGTAATTA
105380 TCTATACTTAATTTGA
130 TCTATACTTAATTTGA
105396 TGTTATGTTT
Statistics
Matches: 137, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
147 2 0.01
148 135 0.99
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (148 bp):
AGTTATATTAATTGATTGAAGAATATTAATACTTTCTTCACGCGTTCACGAATCGGTAACACATC
ATTAATTGATATTATTTTTGAATGAGTACAATAAGGATGCTAATAATCTTTTCACATGTAATTAT
CTATACTTAATTTGACAC
Found at i:105686 original size:3 final size:3
Alignment explanation
Indices: 105678--105707 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
105668 TTTTATTGAG
105678 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
105708 GAAGTACATA
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):
TAT
Found at i:107079 original size:29 final size:29
Alignment explanation
Indices: 107041--107097 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
107031 TATCTCTTTA
*
107041 AATTCAATTTT-AGTGATGTGAATTTTATTT
1 AATTCAATTTTCA-TAATGTG-ATTTTATTT
107071 AATT-AATTTTCATAATGTGATTTTATT
1 AATTCAATTTTCATAATGTGATTTTATT
107098 ATTGATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 8 0.32
29 12 0.48
30 5 0.20
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.54
Consensus pattern (29 bp):
AATTCAATTTTCATAATGTGATTTTATTT
Found at i:108887 original size:15 final size:16
Alignment explanation
Indices: 108860--108899 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
108850 ATTTAAAAAA
*
108860 TTAAAAGTA-ATATT-
1 TTAAAAATATATATTC
108874 TTAAAAATATATATTC
1 TTAAAAATATATATTC
108890 TT-AAAATATA
1 TTAAAAATATA
108900 GTATCATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 8 0.35
15 13 0.57
16 2 0.09
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (16 bp):
TTAAAAATATATATTC
Found at i:110142 original size:19 final size:19
Alignment explanation
Indices: 110118--110183 Score: 64
Period size: 19 Copynumber: 3.3 Consensus size: 19
110108 AAATTTTAAA
110118 ATATTTATATATTTATATC
1 ATATTTATATATTTATATC
*
110137 ATATTTATATTATTTTTTTAT-
1 ATATTTATA-TA--TTTATATC
110158 ATTATGTTATAT-TTTATATC
1 A-TAT-TTATATATTTATATC
110178 ATATTT
1 ATATTT
110184 TAATTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
18 2 0.05
19 18 0.46
20 3 0.08
21 1 0.03
22 10 0.26
23 5 0.13
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.64
Consensus pattern (19 bp):
ATATTTATATATTTATATC
Found at i:110156 original size:41 final size:41
Alignment explanation
Indices: 110111--110197 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 41
110101 ACTATATAAA
*
110111 TTTTAAAATAT-TTATATATTTATATCATA-TTTATATTATTT
1 TTTTAAAATATGTTATAT-TTTATATCATATTTTA-ATTAATT
* *
110152 TTTTATATTATGTTATATTTTATATCATATTTTAATTAATT
1 TTTTAAAATATGTTATATTTTATATCATATTTTAATTAATT
110193 TTTTA
1 TTTTA
110198 TATTCTATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
41 31 0.76
42 10 0.24
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (41 bp):
TTTTAAAATATGTTATATTTTATATCATATTTTAATTAATT
Found at i:110167 original size:18 final size:17
Alignment explanation
Indices: 110118--110182 Score: 50
Period size: 17 Copynumber: 4.0 Consensus size: 17
110108 AAATTTTAAA
*
110118 ATATTTATATATTTATATC
1 ATATTT-TATA-TTATATT
110137 ATA-TTTATA-T-TATT
1 ATATTTTATATTATATT
*
110151 -T-TTTTATATTATGTT
1 ATATTTTATATTATATT
*
110166 ATATTTTATATCATATT
1 ATATTTTATATTATATT
110183 TTAATTAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
13 7 0.19
14 4 0.11
15 4 0.11
16 1 0.03
17 16 0.43
18 2 0.05
19 3 0.08
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (17 bp):
ATATTTTATATTATATT
Found at i:110198 original size:41 final size:42
Alignment explanation
Indices: 110122--110201 Score: 128
Period size: 41 Copynumber: 1.9 Consensus size: 42
110112 TTTAAAATAT
*
110122 TTATATATTTATATCATATTTATATTATTTTTTTATATTATG
1 TTATATATTTATATCATATTTATATTAATTTTTTATATTATG
110164 TTATAT-TTTATATCATATTT-TAATTAATTTTTTATATT
1 TTATATATTTATATCATATTTAT-ATTAATTTTTTATATT
110202 CTATTCATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 1 0.03
41 29 0.81
42 6 0.17
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (42 bp):
TTATATATTTATATCATATTTATATTAATTTTTTATATTATG
Found at i:112893 original size:13 final size:13
Alignment explanation
Indices: 112875--112905 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
112865 AGATTTTTTT
112875 ATATTATAATAAA
1 ATATTATAATAAA
*
112888 ATATTATAGTAAA
1 ATATTATAATAAA
112901 ATATT
1 ATATT
112906 CATGTTCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (13 bp):
ATATTATAATAAA
Found at i:113352 original size:17 final size:19
Alignment explanation
Indices: 113310--113354 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
113300 CTTAAAATAT
*
113310 TATAT-AAATTTTTTTTAA
1 TATATAAAATTTTTCTTAA
113328 TATATAAAATTTTTCTTAA
1 TATATAAAATTTTTCTTAA
113347 -AT-TAAAAT
1 TATATAAAAT
113355 AACAAATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 6 0.24
18 7 0.28
19 12 0.48
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATAAAATTTTTCTTAA
Done.