Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold153
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: 3137677
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 11 of 24
Found at i:1510381 original size:19 final size:17
Alignment explanation
Indices: 1510357--1510401 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
1510347 AATTTAACTC
1510357 AATTAAATAATTATTTATT
1 AATTAAATAA-TATTT-TT
1510376 AATTAAAATAATATTTTT
1 AATT-AAATAATATTTTT
*
1510394 ATTTAAAT
1 AATTAAAT
1510402 TTAATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.17
18 5 0.21
19 9 0.38
20 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTAAATAATATTTTT
Found at i:1511003 original size:45 final size:45
Alignment explanation
Indices: 1510943--1511081 Score: 269
Period size: 45 Copynumber: 3.1 Consensus size: 45
1510933 TTAATAAAAA
1510943 ATATCTAACTATTTGTTTGATGTAAAAAACTTTCTACCATTAAAT
1 ATATCTAACTATTTGTTTGATGTAAAAAACTTTCTACCATTAAAT
1510988 ATATCTAACTATTTGTTTGATGTAAAAAACTTTCTACCATTAAAT
1 ATATCTAACTATTTGTTTGATGTAAAAAACTTTCTACCATTAAAT
*
1511033 ATATCTAACTATTTGTTTGATGTAAAAAACTTTCTACTATTAAAT
1 ATATCTAACTATTTGTTTGATGTAAAAAACTTTCTACCATTAAAT
1511078 ATAT
1 ATAT
1511082 ATTGAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 93 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.43
Consensus pattern (45 bp):
ATATCTAACTATTTGTTTGATGTAAAAAACTTTCTACCATTAAAT
Found at i:1512437 original size:20 final size:19
Alignment explanation
Indices: 1512414--1512488 Score: 55
Period size: 22 Copynumber: 3.7 Consensus size: 19
1512404 TTTTTATTAA
1512414 TTATTTATTACATTTAATAT
1 TTATTTATTA-ATTTAATAT
*
1512434 TTATTAAATATATATTTAAT-T
1 TTATT-TAT-TA-ATTTAATAT
*
1512455 TTATTT-TTAATTGAATAAT
1 TTATTTATTAATTTAAT-AT
1512474 TTAATTTAATTAATT
1 TT-ATTT-ATTAATT
1512489 GAACTGATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
17 6 0.14
18 2 0.05
19 4 0.09
20 9 0.20
21 8 0.18
22 15 0.34
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (19 bp):
TTATTTATTAATTTAATAT
Found at i:1512455 original size:27 final size:27
Alignment explanation
Indices: 1512406--1512483 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
1512396 AAATCATGTT
*
1512406 TTTATTAATTATTTA-TTACATTTAATA
1 TTTATTAATTATATATTTA-ATTTAATA
*
1512433 TTTATTAAATATATATTTAATTT--TA
1 TTTATTAATTATATATTTAATTTAATA
1512458 TTT-TTAATTGA-ATAATTTAATTTAAT
1 TTTATTAATT-ATAT-ATTTAATTTAAT
1512484 TAATTGAACT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
24 7 0.16
25 15 0.35
27 18 0.42
28 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (27 bp):
TTTATTAATTATATATTTAATTTAATA
Found at i:1513690 original size:50 final size:50
Alignment explanation
Indices: 1513657--1513757 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 50
1513647 AAATTGTACA
* *
1513657 TAATTTTTTATCAAATTTTATAAAACAATAAATAATATTTGAGTTCAAAG
1 TAATTTTTTATCAAATTTTATAAAACAATAAATAATATTTAAATTCAAAG
* *
1513707 TAATTTTTTATCAAATTTTATAAAACAATAAATAATATTTGAGTTCAAAG
1 TAATTTTTTATCAAATTTTATAAAACAATAAATAATATTTAAATTCAAAG
1513757 T
1 T
1513758 CAAGTCGTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (50 bp):
TAATTTTTTATCAAATTTTATAAAACAATAAATAATATTTAAATTCAAAG
Found at i:1514500 original size:3 final size:3
Alignment explanation
Indices: 1514492--1514541 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1514482 TTCAACAATT
1514492 TTA TTA TTA TTA 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
1514540 TT
1 TT
1514542 TAATGGTCTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1514765 original size:2 final size:2
Alignment explanation
Indices: 1514758--1514791 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1514748 GGTTACATGA
1514758 AT AT AT 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 AT AT AT
1514792 CAGCAACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1514914 original size:22 final size:23
Alignment explanation
Indices: 1514871--1514924 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
1514861 TTATAATTTT
*
1514871 TATATATT-TTATATTTATTTAA
1 TATAGATTATTATATTTATTTAA
*
1514893 TTTA-ATTATTATATTT-TATTAA
1 TATAGATTATTATATTTAT-TTAA
1514915 TATAGATTAT
1 TATAGATTAT
1514925 GTATGATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 4 0.15
22 18 0.67
23 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TATAGATTATTATATTTATTTAA
Found at i:1514974 original size:26 final size:26
Alignment explanation
Indices: 1514945--1515028 Score: 71
Period size: 28 Copynumber: 3.1 Consensus size: 26
1514935 TTTTTGAGTT
*
1514945 AATTAAAAATATTTAATTATATAGAA
1 AATTAAAAATATTTAATTATATAAAA
* *
1514971 AATT-TAAATATTTTAATATGTATAAAA
1 AATTAAAAATA-TTTAAT-TATATAAAA
* * *
1514998 AAATAAAATATTTTTAATTAATATAATA
1 AATTAAAA-ATATTTAATT-ATATAAAA
1515026 AAT
1 AAT
1515029 ATATCACATC
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
25 5 0.11
26 10 0.23
27 11 0.25
28 16 0.36
29 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
AATTAAAAATATTTAATTATATAAAA
Found at i:1514994 original size:27 final size:26
Alignment explanation
Indices: 1514950--1515023 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 26
1514940 GAGTTAATTA
* *
1514950 AAAATA-TTTAATTATATAGAAAATT
1 AAAATATTTTAATTATATAAAAAAAT
* *
1514975 TAAATATTTTAATATGTATAAAAAAAT
1 AAAATATTTTAAT-TATATAAAAAAAT
1515002 AAAATATTTTTAATTAATATAA
1 AAAATA-TTTTAATT-ATATAA
1515024 TAAATATATC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
25 5 0.13
26 6 0.15
27 16 0.41
28 12 0.31
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (26 bp):
AAAATATTTTAATTATATAAAAAAAT
Found at i:1515391 original size:17 final size:17
Alignment explanation
Indices: 1515264--1515411 Score: 58
Period size: 18 Copynumber: 8.5 Consensus size: 17
1515254 TAAAATAATT
1515264 AAAATATAATATAATACA
1 AAAATATAATATAATA-A
1515282 AAAA-ATAATATAAATATTTTA
1 AAAATATAATAT-AATA----A
* *
1515303 AAAA-ATTATATAATAC
1 AAAATATAATATAATAA
* * *
1515319 GAATTATTAATAT-AT-C
1 AAAATA-TAATATAATAA
* *
1515335 AAAAT-TTATATAAATAT
1 AAAATATAATAT-AATAA
**
1515352 AAAATATTTTA-AAT-A
1 AAAATATAATATAATAA
*
1515367 AAATTATAATATAATAA
1 AAAATATAATATAATAA
1515384 AAAATATAAATATAATATA
1 AAAATAT-AATATAATA-A
*
1515403 AATATATAA
1 AAAATATAA
1515412 ATTATTAAAT
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
14 5 0.05
15 8 0.08
16 14 0.14
17 22 0.22
18 28 0.28
19 7 0.07
20 4 0.04
21 11 0.11
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (17 bp):
AAAATATAATATAATAA
Found at i:1515395 original size:18 final size:19
Alignment explanation
Indices: 1515364--1515413 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
1515354 AATATTTTAA
*
1515364 ATAAAATTAT-AATATAAT
1 ATAAAAATATAAATATAAT
1515382 A-AAAAATATAAATATAAT
1 ATAAAAATATAAATATAAT
*
1515400 ATAAATATATAAAT
1 ATAAAAATATAAAT
1515414 TATTAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 7 0.25
18 10 0.36
19 11 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAAAATATAAATATAAT
Found at i:1515406 original size:29 final size:28
Alignment explanation
Indices: 1515341--1515430 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 28
1515331 TATCAAAATT
* *
1515341 TATATAA-ATATAAAATATTTTAAATAAAA
1 TATATAATATATAAAA-A-ATTAAATATAA
1515370 T-TATAATATAATAAAAAATATAAATATAA
1 TATATAATAT-ATAAAAAAT-TAAATATAA
** *
1515399 TATA-AATATATAAATTATTAAATTTAA
1 TATATAATATATAAAAAATTAAATATAA
1515426 TATAT
1 TATAT
1515431 TTTACCTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
27 12 0.24
28 13 0.25
29 18 0.35
30 8 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
TATATAATATATAAAAAATTAAATATAA
Found at i:1517333 original size:19 final size:20
Alignment explanation
Indices: 1517286--1517339 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1517276 TTAAATAAAT
*
1517286 TATTAATTAATATATATTTA
1 TATTTATTAATATATATTTA
*
1517306 TATTATATTAATAT-TTTTTA
1 TATT-TATTAATATATATTTA
1517326 TATTTATTAATATA
1 TATTTATTAATATA
1517340 ATAATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 9 0.30
20 13 0.43
21 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTATTAATATATATTTA
Found at i:1517362 original size:14 final size:14
Alignment explanation
Indices: 1517339--1517376 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1517329 TTATTAATAT
1517339 AATAAT-TTTAAAA
1 AATAATATTTAAAA
*
1517352 AATAATATTTAATA
1 AATAATATTTAAAA
*
1517366 TATAATATTTA
1 AATAATATTTA
1517377 TAATTCTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATAATATTTAAAA
Found at i:1517580 original size:12 final size:11
Alignment explanation
Indices: 1517565--1517611 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 11
1517555 AAAAATGCAT
1517565 TTAAAATAATAA
1 TTAAAATAA-AA
1517577 TT--AATAAAA
1 TTAAAATAAAA
1517586 TTCAAAATAAAA
1 TT-AAAATAAAA
1517598 TTAAAATTAAAA
1 TTAAAA-TAAAA
1517610 TT
1 TT
1517612 TACTTAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.13
10 5 0.16
11 4 0.13
12 18 0.58
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (11 bp):
TTAAAATAAAA
Found at i:1517846 original size:12 final size:14
Alignment explanation
Indices: 1517819--1517861 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 14
1517809 ATTTTTTATT
1517819 TATTAATATTTAAA
1 TATTAATATTTAAA
1517833 TATTAAT-TTT-AA
1 TATTAATATTTAAA
1517845 TATTAA-A--TAAA
1 TATTAATATTTAAA
1517856 TATTAA
1 TATTAA
1517862 ACATAATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 1 0.04
11 8 0.30
12 8 0.30
13 3 0.11
14 7 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATTAATATTTAAA
Found at i:1517985 original size:14 final size:15
Alignment explanation
Indices: 1517961--1517989 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1517951 TTTTACTAAT
1517961 TTAATTTAATTTTTA
1 TTAATTTAATTTTTA
1517976 TTAA-TTAATTTTTA
1 TTAATTTAATTTTTA
1517990 ATTTTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTAATTTAATTTTTA
Found at i:1517989 original size:21 final size:20
Alignment explanation
Indices: 1517945--1518014 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
1517935 ATATGTAAAA
* *
1517945 TAATTTTTTTACTAATTTAATT
1 TAATTTTTTTATTAA--TATTT
1517967 TAATTTTTATTAATTAAT-TTT
1 TAATTTTT-TT-ATTAATATTT
*
1517988 TAATTTTTTTATTCATATTT
1 TAATTTTTTTATTAATATTT
1518008 TAATTTT
1 TAATTTT
1518015 AATATATATC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.12
20 12 0.29
21 10 0.24
22 9 0.21
23 2 0.05
24 4 0.10
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TAATTTTTTTATTAATATTT
Found at i:1518417 original size:2 final size:2
Alignment explanation
Indices: 1518410--1518437 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1518400 TTTCATATTT
1518410 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1518438 AAAACAAAAA
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):
TA
Found at i:1519474 original size:13 final size:14
Alignment explanation
Indices: 1519456--1519486 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1519446 ATTCGAAAAA
1519456 TTATATTT-AATAT
1 TTATATTTAAATAT
1519469 TTATATTTAAATAT
1 TTATATTTAAATAT
1519483 TTAT
1 TTAT
1519487 GAGATGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATATTTAAATAT
Found at i:1521621 original size:15 final size:15
Alignment explanation
Indices: 1521601--1521630 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1521591 TATTAGCAGA
1521601 TGTTAATGTTGTTTC
1 TGTTAATGTTGTTTC
1521616 TGTTAATGTTGTTTC
1 TGTTAATGTTGTTTC
1521631 CCATGTGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.20, T:0.60
Consensus pattern (15 bp):
TGTTAATGTTGTTTC
Found at i:1525533 original size:22 final size:22
Alignment explanation
Indices: 1525506--1525564 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
1525496 AATAAAATTT
1525506 TAATAAAATAATTATTATGTAG
1 TAATAAAATAATTATTATGTAG
1525528 TAATAAAATAATTATTATGTAG
1 TAATAAAATAATTATTATGTAG
*
1525550 TAATGAAATAATTAT
1 TAATAAAATAATTAT
1525565 AATTTTAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (22 bp):
TAATAAAATAATTATTATGTAG
Found at i:1528880 original size:18 final size:18
Alignment explanation
Indices: 1528857--1528891 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1528847 ATTTTGATTT
*
1528857 AAAAAAAATCTAAAAAGA
1 AAAAAAAATCGAAAAAGA
1528875 AAAAAAAATCGAAAAAG
1 AAAAAAAATCGAAAAAG
1528892 TTTTATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.77, C:0.06, G:0.09, T:0.09
Consensus pattern (18 bp):
AAAAAAAATCGAAAAAGA
Found at i:1534753 original size:26 final size:25
Alignment explanation
Indices: 1534697--1534747 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
1534687 TTATTTAAAA
1534697 ATAA-TAAATTAAAAAATATATTTT
1 ATAATTAAATTAAAAAATATATTTT
1534721 ATAATTAAATTTAAAAAATATTATTTT
1 ATAATTAAA-TTAAAAAATA-TATTTT
1534748 TTATTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 4 0.17
25 4 0.17
26 10 0.42
27 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATAATTAAATTAAAAAATATATTTT
Found at i:1536800 original size:2 final size:2
Alignment explanation
Indices: 1536793--1536817 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1536783 TATAATTCTA
1536793 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
1536818 CACATATAAT
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:1537248 original size:2 final size:2
Alignment explanation
Indices: 1537241--1537273 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1537231 AAAAGTTCTT
1537241 TA TA TA TA 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 TA T
1537274 TATTCGACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1538303 original size:3 final size:3
Alignment explanation
Indices: 1538295--1538340 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1538285 TCACATCTTT
1538295 TTA 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 TTA T
1538341 GTTTGTTTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1539939 original size:21 final size:20
Alignment explanation
Indices: 1539909--1539949 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1539899 AATATTTTAT
*
1539909 TTAATTTTAATTATAAAAATA
1 TTAATATTAA-TATAAAAATA
1539930 TTAATATTAATATAAAAATA
1 TTAATATTAATATAAAAATA
1539950 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATATTAATATAAAAATA
Found at i:1540344 original size:17 final size:17
Alignment explanation
Indices: 1540310--1540351 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1540300 CTATTTAATC
* * *
1540310 AAATATATATTTATATT
1 AAATATTTATTAAAATT
1540327 AAATATTTATTAAAATT
1 AAATATTTATTAAAATT
1540344 -AATATTTA
1 AAATATTTA
1540352 ATTTTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATATTTATTAAAATT
Found at i:1540876 original size:27 final size:29
Alignment explanation
Indices: 1540845--1540979 Score: 95
Period size: 27 Copynumber: 4.7 Consensus size: 29
1540835 ATAATATGAT
1540845 TATAATATAAAAATTAATATT-AAATATAA
1 TATAATATAAAAATTAATATTAAAATAT-A
* * * *
1540874 TAAAATATATAAA-T-ATTTTAAAATTTA
1 TATAATATAAAAATTAATATTAAAATATA
*
1540901 TATAATATAAATTATTAATATATTAAAATATA
1 TATAATATAAA-AATT-A-ATATTAAAATATA
*
1540933 TATGAATAT-AAAA-T-AT-TTTAAATATGA
1 TAT-AATATAAAAATTAATATTAAAATAT-A
*
1540960 TTATAATATAAAAATAAATA
1 -TATAATATAAAAATTAATA
1540980 AACATAATAC
Statistics
Matches: 81, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
26 8 0.10
27 22 0.27
28 14 0.17
29 12 0.15
30 3 0.04
31 1 0.01
32 16 0.20
33 5 0.06
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (29 bp):
TATAATATAAAAATTAATATTAAAATATA
Found at i:1540881 original size:10 final size:9
Alignment explanation
Indices: 1540848--1541000 Score: 54
Period size: 8 Copynumber: 17.1 Consensus size: 9
1540838 ATATGATTAT
1540848 AATATA-AA
1 AATATATAA
*
1540856 AATTAATATTA
1 AA-T-ATATAA
1540867 AATATAATAA
1 AATAT-ATAA
1540877 AATATAT-A
1 AATATATAA
*
1540885 AATATTTTAA
1 AATA-TATAA
*
1540895 AATTTAT-A
1 AATATATAA
*
1540903 TA-ATATAA
1 AATATATAA
*
1540911 ATTAT-TAA
1 AATATATAA
*
1540919 TATAT-TAA
1 AATATATAA
*
1540927 AATATATAT
1 AATATATAA
*
1540936 GA-ATATAA
1 AATATATAA
* *
1540944 AATATTTTA
1 AATATATAA
*
1540953 AATATGATTAT
1 AATAT-A-TAA
1540964 AATATA-AA
1 AATATATAA
*
1540972 AATAAATAA
1 AATATATAA
*
1540981 ACATA-ATACG
1 A-ATATATA-A
1540991 AATATATAA
1 AATATATAA
1541000 A
1 A
1541001 TTATTAAATT
Statistics
Matches: 104, Mismatches: 25, Indels: 31
0.65 0.16 0.19
Matches are distributed among these distances:
7 3 0.03
8 35 0.34
9 33 0.32
10 24 0.23
11 9 0.09
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (9 bp):
AATATATAA
Found at i:1540902 original size:54 final size:57
Alignment explanation
Indices: 1540837--1541009 Score: 173
Period size: 59 Copynumber: 3.1 Consensus size: 57
1540827 TTAATTATAT
* *
1540837 AATATGATTATAATATAAAAATTAATATTAAATATAATA-AAATATATAAATATTTTA
1 AATATTATTATAATATAAAAATTAATATTAAA-ATAATACGAATATATAAATATTTTA
* *
1540894 AA-ATT-TATATAATATAAATTATTAATATATTAAAATATATATGAATATA-AAATATTTTA
1 AATATTAT-TATAATATAAA-AATT-A-ATATTAAAATA-ATACGAATATATAAATATTTTA
* *
1540953 AATATGATTATAATATAAAAA-TAA-A-TAAACATAATACGAATATATAAAT-TATTA
1 AATATTATTATAATATAAAAATTAATATTAAA-ATAATACGAATATATAAATATTTTA
1541007 AAT
1 AAT
1541010 TTACTTAAAA
Statistics
Matches: 99, Mismatches: 7, Indels: 23
0.77 0.05 0.18
Matches are distributed among these distances:
54 21 0.21
55 9 0.09
56 14 0.14
57 6 0.06
58 5 0.05
59 24 0.24
60 19 0.19
61 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.39
Consensus pattern (57 bp):
AATATTATTATAATATAAAAATTAATATTAAAATAATACGAATATATAAATATTTTA
Found at i:1540921 original size:32 final size:32
Alignment explanation
Indices: 1540868--1540949 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 32
1540858 TTAATATTAA
* * *
1540868 ATATAATA-AAATATATAAATATTTTAAAATTT
1 ATATAATATAAAT-TATTAATATATTAAAATAT
1540900 ATATAATATAAATTATTAATATATTAAAATAT
1 ATATAATATAAATTATTAATATATTAAAATAT
*
1540932 ATATGAATATAAAATATT
1 ATAT-AATATAAATTATT
1540950 TTAAATATGA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
32 28 0.64
33 16 0.36
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (32 bp):
ATATAATATAAATTATTAATATATTAAAATAT
Found at i:1540930 original size:60 final size:56
Alignment explanation
Indices: 1540837--1540979 Score: 166
Period size: 60 Copynumber: 2.5 Consensus size: 56
1540827 TTAATTATAT
1540837 AATATGATTATAATATAAAAATTAATATTAAATATA-ATAAAATATATAAATATTTTA
1 AATATGATTATAATATAAAAATTAATATTAAATATATAT-AAATATA-AAATATTTTA
* * *
1540894 AA-AT-TTATATAATATAAATTATTAATATATTAAAATATATATGAATATAAAATATTTTA
1 AATATGAT-TATAATATAAA-AATT-A-ATATT-AAATATATATAAATATAAAATATTTTA
*
1540953 AATATGATTATAATATAAAAATAAATA
1 AATATGATTATAATATAAAAATTAATA
1540980 AACATAATAC
Statistics
Matches: 72, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
55 1 0.01
56 13 0.18
57 8 0.11
58 2 0.03
59 19 0.26
60 26 0.36
61 3 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (56 bp):
AATATGATTATAATATAAAAATTAATATTAAATATATATAAATATAAAATATTTTA
Found at i:1543644 original size:20 final size:19
Alignment explanation
Indices: 1543619--1543674 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
1543609 ATTATAACTC
*
1543619 ATAATTCATAAATAAATTTA
1 ATAATT-ATAAATAAATATA
*
1543639 ATAATTTTAAATATAATATA
1 ATAATTATAAATA-AATATA
*
1543659 ATTATTATAAAATAAA
1 ATAATTAT-AAATAAA
1543675 AATTAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 6 0.20
20 19 0.63
21 5 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAATTATAAATAAATATA
Found at i:1546825 original size:11 final size:11
Alignment explanation
Indices: 1546801--1546830 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1546791 TTTATTTTAT
1546801 TAAAATAA-AA
1 TAAAATAATAA
1546811 TAAAATAATAA
1 TAAAATAATAA
1546822 TAAAATAAT
1 TAAAATAAT
1546831 TATTATGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:1548844 original size:18 final size:19
Alignment explanation
Indices: 1548808--1548854 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1548798 TTAGAGTTAA
*
1548808 TAAAGTTTATTTAAATTTG
1 TAAAATTTATTTAAATTTG
1548827 TAAAATTTATTT-AATTTG
1 TAAAATTTATTTAAATTTG
1548845 TAAGAATTTA
1 TAA-AATTTA
1548855 AATTTAATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (19 bp):
TAAAATTTATTTAAATTTG
Found at i:1549228 original size:31 final size:30
Alignment explanation
Indices: 1549191--1549251 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
1549181 AATTTGAATA
1549191 AAAATTTTAAATTAAATTAAAA-AAATTTATT
1 AAAA-TTTAAATT-AATTAAAATAAATTTATT
*
1549222 AAAATTTAAATTTATTAAAATTAAATTTAT
1 AAAATTTAAATTAATTAAAA-TAAATTTAT
1549252 CACATACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 7 0.26
30 8 0.30
31 12 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
AAAATTTAAATTAATTAAAATAAATTTATT
Found at i:1549247 original size:15 final size:16
Alignment explanation
Indices: 1549213--1549251 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1549203 TAAATTAAAA
1549213 AAATTTATTAAAATTT
1 AAATTTATTAAAATTT
1549229 AAATTTATTAAAA-TT
1 AAATTTATTAAAATTT
1549244 AAATTTAT
1 AAATTTAT
1549252 CACATACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATTTATTAAAATTT
Found at i:1550890 original size:2 final size:2
Alignment explanation
Indices: 1550883--1550922 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1550873 CATGCTAACT
1550883 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1550923 GAGAGAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1550927 original size:2 final size:2
Alignment explanation
Indices: 1550922--1550960 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1550912 ATATATATAT
1550922 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1550961 ATAAGGTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1552935 original size:2 final size:2
Alignment explanation
Indices: 1552928--1552966 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1552918 TCTATTCTAT
1552928 TA TA TA TA TA TA TA 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 TA TA TA TA T
1552967 CACAAGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1553608 original size:3 final size:3
Alignment explanation
Indices: 1553602--1553638 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1553592 TTAATTTTTT
1553602 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 T
1553639 ATATCCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1553837 original size:36 final size:36
Alignment explanation
Indices: 1553787--1553890 Score: 106
Period size: 36 Copynumber: 2.9 Consensus size: 36
1553777 AAAGGAAAAA
* *
1553787 AATTTATGTATTTATATATATTTTTTGATATA-TAA-
1 AATTTATATTTTTATATATATTTTTT-ATATATTAAT
*
1553822 AATATTATATTTTTATATAAATTTTTTATATATTAAT
1 AAT-TTATATTTTTATATATATTTTTTATATATTAAT
* * *
1553859 AATTTGTTTTTATTTTATATATTTTTT-TATAT
1 AATTTATATTT-TTATATATATTTTTTATATAT
1553891 GTATATATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
35 8 0.14
36 34 0.59
37 16 0.28
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (36 bp):
AATTTATATTTTTATATATATTTTTTATATATTAAT
Found at i:1553860 original size:19 final size:18
Alignment explanation
Indices: 1553838--1553890 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
1553828 ATATTTTTAT
1553838 ATAAATTTTTTATATATTA
1 ATAAATTTTTT-TATATTA
* *
1553857 ATAATTTGTTTTTAT-TTT
1 ATAAATT-TTTTTATATTA
*
1553875 ATATATTTTTTTATAT
1 ATAAATTTTTTTATAT
1553891 GTATATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 7 0.25
18 8 0.29
19 9 0.32
20 4 0.14
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
ATAAATTTTTTTATATTA
Found at i:1555075 original size:19 final size:22
Alignment explanation
Indices: 1555034--1555089 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1555024 ATATTCTTTT
*
1555034 TAATATATTAAAATATTAAT-AA
1 TAATATATT-AATTATTAATAAA
*
1555056 -AAT-TATTAATTATTATTAAA
1 TAATATATTAATTATTAATAAA
1555076 TAATATATTAATTA
1 TAATATATTAATTA
1555090 ATCTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 8 0.28
20 6 0.21
21 6 0.21
22 9 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATATATTAATTATTAATAAA
Found at i:1555350 original size:21 final size:21
Alignment explanation
Indices: 1555311--1555374 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
1555301 AGTATATAAT
* **
1555311 TATTTTAAATTAAAATTTAAA
1 TATTTTAAATTTATTTTTAAA
*
1555332 TATTTTAAATTTATTTTTATTA
1 TATTTTAAATTTATTTTTA-AA
* *
1555354 TAATTTAATTTTAATTTTTAA
1 TATTTTAAATTT-ATTTTTAA
1555375 GTCTATCTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
21 16 0.47
22 11 0.32
23 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTAAATTTATTTTTAAA
Found at i:1555542 original size:29 final size:29
Alignment explanation
Indices: 1555487--1555544 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1555477 TTAATTGTTA
* *
1555487 TTATATTTATATATTTTATTATATTATAT
1 TTATATTTAAATATTTTATAATATTATAT
*
1555516 TTATATTTAAAATATTTTA-AATTTTATAT
1 TTATATTT-AAATATTTTATAATATTATAT
1555545 ATTGATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
TTATATTTAAATATTTTATAATATTATAT
Found at i:1555557 original size:25 final size:25
Alignment explanation
Indices: 1555529--1555577 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1555519 TATTTAAAAT
*
1555529 ATTTTAAATT-TTATATATTGATATA
1 ATTTCAAATTATTATATATT-ATATA
*
1555554 ATTTCAAATTATTTTATATTATAT
1 ATTTCAAATTATTATATATTATAT
1555578 TTACGTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTTCAAATTATTATATATTATATA
Found at i:1556872 original size:16 final size:16
Alignment explanation
Indices: 1556851--1556899 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1556841 TATTATTATA
1556851 ATTAATTATAATAAAT
1 ATTAATTATAATAAAT
*
1556867 ATTAATAAT-ATAAATT
1 ATTAATTATAATAAA-T
* *
1556883 ATAAATTATAAAAAAT
1 ATTAATTATAATAAAT
1556899 A
1 A
1556900 ATTATGACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 5 0.19
16 18 0.67
17 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAATTATAATAAAT
Found at i:1556882 original size:25 final size:25
Alignment explanation
Indices: 1556828--1556887 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
1556818 ATTAAACGTA
1556828 ATAAATT-TAAAAATATTATTATAAT
1 ATAAATTATAAAAATATTA-TATAAT
1556853 -T-AATTATAATAAATATTA-ATAAT
1 ATAAATTATAA-AAATATTATATAAT
1556876 ATAAATTATAAA
1 ATAAATTATAAA
1556888 TTATAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
23 9 0.29
24 6 0.19
25 16 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAAATTATAAAAATATTATATAAT
Found at i:1557057 original size:7 final size:7
Alignment explanation
Indices: 1557045--1557140 Score: 60
Period size: 7 Copynumber: 13.7 Consensus size: 7
1557035 AAAAATAATA
1557045 AAATTTT
1 AAATTTT
1557052 AAATTTT
1 AAATTTT
*
1557059 AAA-TAT
1 AAATTTT
1557065 ATAA-TTT
1 A-AATTTT
*
1557072 ATATTTT
1 AAATTTT
1557079 --ATTTT
1 AAATTTT
1557084 AAATTTT
1 AAATTTT
1557091 ATCAATTATT
1 A--AATT-TT
1557101 AAATTTT
1 AAATTTT
1557108 -AATTTT
1 AAATTTT
1557114 -AATATTT
1 AAAT-TTT
*
1557121 ATGATTTT
1 A-AATTTT
*
1557129 TAATTTT
1 AAATTTT
1557136 AAATT
1 AAATT
1557141 ATGTTTTTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
5 5 0.07
6 13 0.18
7 38 0.53
8 7 0.10
9 6 0.08
10 3 0.04
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (7 bp):
AAATTTT
Found at i:1557070 original size:21 final size:21
Alignment explanation
Indices: 1557037--1557079 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
1557027 TTTTAATTAA
1557037 AAATAATAAAATTTTAAATTTT
1 AAATAATAAAA-TTTAAATTTT
* *
1557059 AAAT-ATATAATTTATATTTT
1 AAATAATAAAATTTAAATTTT
1557079 A
1 A
1557080 TTTTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
21 5 0.26
22 4 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATAATAAAATTTAAATTTT
Found at i:1557132 original size:22 final size:20
Alignment explanation
Indices: 1557104--1557150 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
1557094 AATTATTAAA
1557104 TTTTAATTTTAATATTTATGAT
1 TTTTAATTTTAA-A-TTATGAT
*
1557126 TTTTAATTTTAAATTATGTT
1 TTTTAATTTTAAATTATGAT
1557146 TTTTA
1 TTTTA
1557151 TATAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 11 0.46
21 1 0.04
22 12 0.50
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (20 bp):
TTTTAATTTTAAATTATGAT
Found at i:1561283 original size:32 final size:31
Alignment explanation
Indices: 1561247--1561307 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1561237 TTATTTTCAT
*
1561247 AATAATATTTTATATTTTTATAATTAAATTTA
1 AATAATATTTT-TAATTTTATAATTAAATTTA
* *
1561279 AATAATATTTTTAATTTTATGATTTAATT
1 AATAATATTTTTAATTTTATAATTAAATT
1561308 AGCACGAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (31 bp):
AATAATATTTTTAATTTTATAATTAAATTTA
Found at i:1561669 original size:19 final size:19
Alignment explanation
Indices: 1561645--1561703 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 19
1561635 TATTATTAAT
1561645 TATATAAATATAAATATAA
1 TATATAAATATAAATATAA
1561664 TATAT-AATATTAAATATGTAA
1 TATATAAATA-TAAATA--TAA
*
1561685 AATTCATAAATATAAATAT
1 TA-T-ATAAATATAAATAT
1561704 TACACATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
18 4 0.12
19 11 0.33
21 5 0.15
22 1 0.03
23 8 0.24
24 4 0.12
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
TATATAAATATAAATATAA
Found at i:1563121 original size:15 final size:15
Alignment explanation
Indices: 1563100--1563136 Score: 60
Period size: 13 Copynumber: 2.6 Consensus size: 15
1563090 AGAATAATTC
1563100 AATATATATAT-A-A
1 AATATATATATGATA
1563113 AATATATATATGATA
1 AATATATATATGATA
1563128 AATATATAT
1 AATATATAT
1563137 TTTAACAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.50
14 1 0.05
15 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AATATATATATGATA
Found at i:1564327 original size:24 final size:26
Alignment explanation
Indices: 1564300--1564351 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
1564290 CGACACGTGA
1564300 ATAATATAA-AAAAATAATTAAA-AT
1 ATAATATAATAAAAATAATTAAATAT
* *
1564324 ATAATATAATATAAATATTTAAATAT
1 ATAATATAATAAAAATAATTAAATAT
1564350 AT
1 AT
1564352 TAAAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.38
25 11 0.46
26 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
ATAATATAATAAAAATAATTAAATAT
Found at i:1564811 original size:17 final size:18
Alignment explanation
Indices: 1564780--1564817 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1564770 TATGATATAA
*
1564780 AAAATTAAAATATAATAT
1 AAAATTAAAAAATAATAT
1564798 AAAA-TAAAAAATAATAT
1 AAAATTAAAAAATAATAT
1564815 AAA
1 AAA
1564818 TATATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATTAAAAAATAATAT
Found at i:1564826 original size:17 final size:16
Alignment explanation
Indices: 1564791--1564852 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
1564781 AAATTAAAAT
*
1564791 ATAATATAAAATAAAAA
1 ATAATATAAAAT-ATAA
1564808 ATAATATAAATATATAA
1 ATAATATAAA-ATATAA
* *
1564825 AT-ATATTAAAATTTAT
1 ATAATA-TAAAATATAA
1564841 ATAATATAAAAT
1 ATAATATAAAAT
1564853 TTTAATTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 15 0.38
17 22 0.56
18 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATATAAAATATAA
Found at i:1564830 original size:16 final size:16
Alignment explanation
Indices: 1564785--1564897 Score: 51
Period size: 16 Copynumber: 6.9 Consensus size: 16
1564775 TATAAAAAAT
1564785 TAAA-ATAT-AATATA
1 TAAATATATAAATATA
*
1564799 -AAATA-AAAAATAATA
1 TAAATATATAAAT-ATA
1564814 TAAATATATAAATATA
1 TAAATATATAAATATA
*
1564830 TTAAAATTTATATAATATA
1 -T-AAATATATA-AATATA
* * *
1564849 -AAAT-TTTAATTTTA
1 TAAATATATAAATATA
1564863 TTAAAATTTATATAAATATA
1 -T-AAA--TATATAAATATA
1564883 T-AATATTATAAATAT
1 TAAATA-TATAAATAT
1564898 TATTATAACA
Statistics
Matches: 75, Mismatches: 9, Indels: 28
0.67 0.08 0.25
Matches are distributed among these distances:
13 4 0.05
14 8 0.11
15 8 0.11
16 21 0.28
17 11 0.15
18 8 0.11
19 8 0.11
20 7 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATATATAAATATA
Found at i:1564847 original size:33 final size:34
Alignment explanation
Indices: 1564808--1564902 Score: 122
Period size: 33 Copynumber: 2.8 Consensus size: 34
1564798 AAAATAAAAA
1564808 ATAATATAAATA-TATAAATATATTAAAATTTAT
1 ATAATATAAATATTATAAATATATTAAAATTTAT
* * *
1564841 ATAATATAAA-ATTTTAATTTTATTAAAATTTAT
1 ATAATATAAATATTATAAATATATTAAAATTTAT
1564874 ATAAATATATAATATTATAAATATTATTA
1 AT-AATATA-AATATTATAAATA-TATTA
1564903 TAACATAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
32 1 0.02
33 30 0.59
34 6 0.12
35 2 0.04
36 7 0.14
37 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
ATAATATAAATATTATAAATATATTAAAATTTAT
Found at i:1564940 original size:28 final size:27
Alignment explanation
Indices: 1564802--1564940 Score: 66
Period size: 28 Copynumber: 4.8 Consensus size: 27
1564792 TAATATAAAA
1564802 TAAAAAATA-ATATAAATATATAAATATAT
1 TAAAAAATATATATAAA-A-ATAAA-ATAT
* * ** *
1564831 TAAAATTTATATAATATAAAATTTTAATTT
1 TAAAA--AATAT-ATATAAAAATAAAATAT
* * * *
1564861 TATTAAAATTTATATAAATATATAATAT
1 TA-AAAAATATATATAAAAATAAAATAT
*
1564889 T-ATAAATATTATTATAACATAATAAAATAT
1 TAAAAAATA-TA-TATAA-A-AATAAAATAT
1564919 TAAAAAATATATAATAAAAATA
1 TAAAAAATATAT-ATAAAAATA
1564941 CACAAATTAC
Statistics
Matches: 81, Mismatches: 18, Indels: 23
0.66 0.15 0.19
Matches are distributed among these distances:
26 4 0.05
27 2 0.02
28 23 0.28
29 11 0.14
30 20 0.25
31 13 0.16
32 1 0.01
33 7 0.09
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (27 bp):
TAAAAAATATATATAAAAATAAAATAT
Found at i:1566639 original size:2 final size:2
Alignment explanation
Indices: 1566632--1566664 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1566622 ATTTGATCTT
1566632 TA TA TA TA 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 TA T
1566665 GTTCTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1568394 original size:20 final size:19
Alignment explanation
Indices: 1568344--1568395 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1568334 ATAATATTTA
*
1568344 AAATATTATATATTTATAT
1 AAATATTATATATTAATAT
*
1568363 AAATTTTAATATATTAATAAT
1 AAATATT-ATATATTAAT-AT
*
1568384 TAATATTATATA
1 AAATATTATATA
1568396 AATTTTAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 6 0.22
20 14 0.52
21 7 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATATTATATATTAATAT
Found at i:1568394 original size:32 final size:34
Alignment explanation
Indices: 1568335--1568403 Score: 99
Period size: 32 Copynumber: 2.1 Consensus size: 34
1568325 TATGTCATAA
1568335 TAATATTTAAAATATTATATATTTATATAAATTT
1 TAATATTTAAAATATTATATATTTATATAAATTT
*
1568369 TAATATATTAATA-ATTA-ATA-TTATATAAATTT
1 TAATAT-TTAAAATATTATATATTTATATAAATTT
1568401 TAA
1 TAA
1568404 GATAAATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 15 0.45
33 3 0.09
34 10 0.30
35 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
TAATATTTAAAATATTATATATTTATATAAATTT
Found at i:1568761 original size:25 final size:26
Alignment explanation
Indices: 1568716--1568808 Score: 77
Period size: 25 Copynumber: 3.7 Consensus size: 26
1568706 TTTAACACAT
* *
1568716 ATAAATTATACAA-ATTAAATTTTAA
1 ATAAATTATAAAATATTTAATTTTAA
* *
1568741 ATAAATTA-AAAATATTTAATTATAG
1 ATAAATTATAAAATATTTAATTTTAA
** *
1568766 ATTCAGTATAAAAT-TTTAATTATTAA
1 ATAAATTATAAAATATTTAATT-TTAA
*
1568792 AAAAATTA-AAAATATTT
1 ATAAATTATAAAATATTT
1568809 TCTATCGATA
Statistics
Matches: 51, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
24 3 0.06
25 34 0.67
26 14 0.27
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
ATAAATTATAAAATATTTAATTTTAA
Found at i:1568998 original size:2 final size:2
Alignment explanation
Indices: 1568993--1569031 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1568983 TTAATTGCAC
1568993 AT AT AT 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
1569032 AACTTTAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1569605 original size:16 final size:16
Alignment explanation
Indices: 1569556--1569612 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
1569546 TTTAATATTT
*
1569556 AAAA-AAATTTAAATA
1 AAAATAAATTTATATA
*
1569571 AAAATATTAAATT-TA-A
1 AAAATA--AATTTATATA
1569587 AAAATAAATTTATATA
1 AAAATAAATTTATATA
1569603 AAAATAAATT
1 AAAATAAATT
1569613 CGTTTAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
14 4 0.12
15 6 0.18
16 19 0.56
17 1 0.03
18 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATAAATTTATATA
Found at i:1570417 original size:14 final size:14
Alignment explanation
Indices: 1570400--1570436 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1570390 AAATTTGAAT
1570400 ATAAAAATCATTTA
1 ATAAAAATCATTTA
*
1570414 ATAAAAAT-AATTA
1 ATAAAAATCATTTA
1570427 A-AAAAATCAT
1 ATAAAAATCAT
1570437 CCAAACCACT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
12 6 0.30
13 6 0.30
14 8 0.40
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAAAATCATTTA
Found at i:1571424 original size:17 final size:17
Alignment explanation
Indices: 1571416--1571453 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1571406 TTTTATTAAT
1571416 TAATATTTTTAATATAA
1 TAATATTTTTAATATAA
*
1571433 TAATATTATT-ATA-AA
1 TAATATTTTTAATATAA
1571448 TAATAT
1 TAATAT
1571454 GTTAACTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 3 0.15
17 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATATTTTTAATATAA
Found at i:1574798 original size:15 final size:15
Alignment explanation
Indices: 1574774--1574805 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1574764 AGTGTCAAGC
*
1574774 TTGTTGTTTTTGCTG
1 TTGTTCTTTTTGCTG
1574789 TTGTTCTTTTTGCTG
1 TTGTTCTTTTTGCTG
1574804 TT
1 TT
1574806 TCGATTGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.09, G:0.22, T:0.69
Consensus pattern (15 bp):
TTGTTCTTTTTGCTG
Found at i:1577429 original size:16 final size:16
Alignment explanation
Indices: 1577408--1577439 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1577398 AAGGTTTAAC
*
1577408 AGATCAGGTGAGACAG
1 AGATCAGGTGAAACAG
1577424 AGATCAGGTGAAACAG
1 AGATCAGGTGAAACAG
1577440 GTTAAACAAC
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:0.41, C:0.12, G:0.34, T:0.12
Consensus pattern (16 bp):
AGATCAGGTGAAACAG
Found at i:1577663 original size:25 final size:26
Alignment explanation
Indices: 1577619--1577668 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
1577609 TTACTTTTTT
*
1577619 ATTTTATTTTTCTTGTTTTTTGATTA
1 ATTTTATTTTTCTTGATTTTTGATTA
*
1577645 ATTTTGTTTTT-TTGATTTTTGATT
1 ATTTTATTTTTCTTGATTTTTGATT
1577669 TTATTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.14, C:0.02, G:0.10, T:0.74
Consensus pattern (26 bp):
ATTTTATTTTTCTTGATTTTTGATTA
Found at i:1579429 original size:55 final size:55
Alignment explanation
Indices: 1579333--1579439 Score: 133
Period size: 55 Copynumber: 1.9 Consensus size: 55
1579323 GGCAATTAGT
* *
1579333 GTGACTTGATATCGCTTAAAATTATGGTGTTGCCTTAGTGGCGATCAGAATTTGG
1 GTGACTTGATATCACTTAAAATTATGGTGATGCCTTAGTGGCGATCAGAATTTGG
* * * * * * *
1579388 GTGACTTGTTATCATTTAAAGTTGTGGTGATGTCTTGGTGGCTATCAGAATT
1 GTGACTTGATATCACTTAAAATTATGGTGATGCCTTAGTGGCGATCAGAATT
1579440 GGAATGGCTT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 43 1.00
ACGTcount: A:0.22, C:0.11, G:0.27, T:0.39
Consensus pattern (55 bp):
GTGACTTGATATCACTTAAAATTATGGTGATGCCTTAGTGGCGATCAGAATTTGG
Found at i:1582490 original size:19 final size:18
Alignment explanation
Indices: 1582468--1582530 Score: 76
Period size: 17 Copynumber: 3.6 Consensus size: 18
1582458 CATTTTAATC
*
1582468 TTTTTATTTTTTTGATTAA
1 TTTTGATTTTTTT-ATTAA
1582487 TTTTGATTTTTTTATTAA
1 TTTTGATTTTTTTATTAA
*
1582505 TTTTG-TTTTATTATT-A
1 TTTTGATTTTTTTATTAA
*
1582521 TTTTAATTTT
1 TTTTGATTTT
1582531 ATAACAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
16 5 0.12
17 13 0.32
18 10 0.25
19 12 0.30
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTTGATTTTTTTATTAA
Found at i:1583063 original size:19 final size:18
Alignment explanation
Indices: 1583039--1583101 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1583029 AAACCGTAAC
1583039 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
1583058 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
1583071 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
1583090 TGTATCGATACA
1 TGTATCGATACA
1583102 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:1583076 original size:13 final size:13
Alignment explanation
Indices: 1583058--1583082 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1583048 ACATAAGTGT
1583058 TGTATCGATACAA
1 TGTATCGATACAA
1583071 TGTATCGATACA
1 TGTATCGATACA
1583083 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1583080 original size:32 final size:32
Alignment explanation
Indices: 1583039--1583109 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
1583029 AAACCGTAAC
1583039 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1583071 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1583103 TGTATCG
1 TGTATCG
1583110 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1590927 original size:26 final size:25
Alignment explanation
Indices: 1590897--1590982 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 25
1590887 TCAGAATTTG
1590897 GGTGACTTGGTGTCACTTAAAGTTAT
1 GGTGACTTGGTGTCACTTAAAGTT-T
* * *
1590923 GGTGATGTCTTGGTGGTGA-TCAAAATTT
1 GGTGA---CTTGGT-GTCACTTAAAGTTT
1590951 GAGTGACTTGGTGTCACTTAAAGTTGT
1 G-GTGACTTGGTGTCACTTAAAGTT-T
1590978 GGTGA
1 GGTGA
1590983 TGTCTTGGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
25 3 0.06
26 21 0.45
27 2 0.04
28 2 0.04
29 16 0.34
30 3 0.06
ACGTcount: A:0.22, C:0.09, G:0.31, T:0.37
Consensus pattern (25 bp):
GGTGACTTGGTGTCACTTAAAGTTT
Found at i:1590927 original size:55 final size:55
Alignment explanation
Indices: 1590843--1591023 Score: 254
Period size: 55 Copynumber: 3.3 Consensus size: 55
1590833 GGCAGTTAGT
* * * * * *
1590843 GTGACTTGATGTCATTTAAAGTTGTGGTGATGCCTTAGTGGCGATCAGAATTTGG
1 GTGACTTGGTGTCACTTAAAGTTGTGGTGATGTCTTGGTGGCGATCAAAATTTGA
* *
1590898 GTGACTTGGTGTCACTTAAAGTTATGGTGATGTCTTGGTGGTGATCAAAATTTGA
1 GTGACTTGGTGTCACTTAAAGTTGTGGTGATGTCTTGGTGGCGATCAAAATTTGA
*
1590953 GTGACTTGGTGTCACTTAAAGTTGTGGTGATGTCTTGGTGGCGATCAAAATTGGA
1 GTGACTTGGTGTCACTTAAAGTTGTGGTGATGTCTTGGTGGCGATCAAAATTTGA
* **
1591008 ATGGTTTGGTGTCACT
1 GTGACTTGGTGTCACT
1591024 AATAATAATA
Statistics
Matches: 112, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 112 1.00
ACGTcount: A:0.22, C:0.10, G:0.31, T:0.37
Consensus pattern (55 bp):
GTGACTTGGTGTCACTTAAAGTTGTGGTGATGTCTTGGTGGCGATCAAAATTTGA
Found at i:1590936 original size:29 final size:28
Alignment explanation
Indices: 1590902--1590992 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 28
1590892 ATTTGGGTGA
1590902 CTTGGTGTCACTTAAAGTTATGGTGATGT
1 CTTGGTGTCACTTAAAGTT-TGGTGATGT
* * *
1590931 CTTGGTGGTGA-TCAAAATTTGAGTGA---
1 CTTGGT-GTCACTTAAAGTTTG-GTGATGT
1590957 CTTGGTGTCACTTAAAGTTGTGGTGATGT
1 CTTGGTGTCACTTAAAGTT-TGGTGATGT
1590986 CTTGGTG
1 CTTGGTG
1590993 GCGATCAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
25 3 0.06
26 16 0.33
27 2 0.04
28 2 0.04
29 23 0.47
30 3 0.06
ACGTcount: A:0.20, C:0.10, G:0.31, T:0.40
Consensus pattern (28 bp):
CTTGGTGTCACTTAAAGTTTGGTGATGT
Found at i:1598115 original size:46 final size:46
Alignment explanation
Indices: 1598064--1598154 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
1598054 TCATATCTTA
*
1598064 ATTTATCTCATGTTTTGTATAATTTGTTATAATAATTTTATTTTTT
1 ATTTATCTCATGTTTTGTATAATTTGTCATAATAATTTTATTTTTT
1598110 ATTTATCTCATGTTTTGTATAATTTGTCATAATAATTTTATTTTT
1 ATTTATCTCATGTTTTGTATAATTTGTCATAATAATTTTATTTTT
1598155 ACTCTTAACT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.62
Consensus pattern (46 bp):
ATTTATCTCATGTTTTGTATAATTTGTCATAATAATTTTATTTTTT
Found at i:1598271 original size:14 final size:14
Alignment explanation
Indices: 1598254--1598292 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
1598244 GTTATTTTTT
1598254 ATTTTTAATGATGA
1 ATTTTTAATGATGA
*
1598268 ATTTTTAA--AAGA
1 ATTTTTAATGATGA
1598280 ATTTTTAATGATG
1 ATTTTTAATGATG
1598293 TATATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 11 0.52
14 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
ATTTTTAATGATGA
Found at i:1599048 original size:20 final size:20
Alignment explanation
Indices: 1599023--1599060 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1599013 ATTATTTTTG
1599023 TATTATA-ATCTTATTTAAGT
1 TATTATACA-CTTATTTAAGT
1599043 TATTATACACTTATTTAA
1 TATTATACACTTATTTAA
1599061 ATTTTTTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (20 bp):
TATTATACACTTATTTAAGT
Found at i:1603051 original size:20 final size:20
Alignment explanation
Indices: 1603026--1603079 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1603016 CTACCACTGT
* *
1603026 TTGTATCGATACATGGCACA
1 TTGTATCGATACATGACAAA
*
1603046 TTGTATCGATACATGATAAA
1 TTGTATCGATACATGACAAA
1603066 TTGTATCGATACAT
1 TTGTATCGATACAT
1603080 TGCTTCAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGACAAA
Found at i:1609235 original size:13 final size:13
Alignment explanation
Indices: 1609217--1609252 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1609207 ATGTTTTTTA
1609217 TATCGATACAATG
1 TATCGATACAATG
* *
1609230 TATCGATGCATTG
1 TATCGATACAATG
1609243 TATCGATACA
1 TATCGATACA
1609253 TGGGTTACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:1611742 original size:20 final size:20
Alignment explanation
Indices: 1611654--1611747 Score: 68
Period size: 20 Copynumber: 4.5 Consensus size: 20
1611644 TACATGTTCT
1611654 TTGTATCGATACATGTACA-A
1 TTGTATCGATACATG-ACACA
*
1611674 TTGTATCGATACATGAAAC-
1 TTGTATCGATACATGACACA
* * * *
1611693 TGGTAGTAGCTACCCT-ACCACTA
1 TTGTA-TCGATA-CATGA-CAC-A
1611716 TTTGTATCGATACATGACACA
1 -TTGTATCGATACATGACACA
1611737 TTGTATCGATA
1 TTGTATCGATA
1611748 TAATATATTG
Statistics
Matches: 56, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
19 6 0.11
20 31 0.55
21 5 0.09
22 5 0.09
23 5 0.09
24 4 0.07
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATGACACA
Found at i:1613874 original size:32 final size:32
Alignment explanation
Indices: 1613838--1613902 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1613828 TATGGTTTTG
1613838 TGGCTAATGCTTATGATTTTTTTTTTTCCAGA
1 TGGCTAATGCTTATGATTTTTTTTTTTCCAGA
1613870 TGGCTAATGCTTATGATTTTTTTTTTTCCAGA
1 TGGCTAATGCTTATGATTTTTTTTTTTCCAGA
1613902 T
1 T
1613903 AAATCCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.18, C:0.12, G:0.15, T:0.54
Consensus pattern (32 bp):
TGGCTAATGCTTATGATTTTTTTTTTTCCAGA
Found at i:1614893 original size:25 final size:25
Alignment explanation
Indices: 1614857--1614904 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
1614847 TCATAATTAT
1614857 ATTTAAATATTTAT-ATTTATATAA
1 ATTTAAATATTTATAATTTATATAA
1614881 ATTTAATATATTTATAATTTATAT
1 ATTTAA-ATATTTATAATTTATAT
1614905 TATATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 6 0.27
25 8 0.36
26 8 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTTAAATATTTATAATTTATATAA
Found at i:1614911 original size:31 final size:33
Alignment explanation
Indices: 1614854--1614915 Score: 101
Period size: 31 Copynumber: 1.9 Consensus size: 33
1614844 TTATCATAAT
1614854 TATATTTAAATATTTATATTTATATAAATTTAA
1 TATATTTAAATATTTATATTTATATAAATTTAA
*
1614887 TATATTTATA-ATTTATA-TTATATAAATTT
1 TATATTTAAATATTTATATTTATATAAATTT
1614916 TAAAATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 12 0.43
32 7 0.25
33 9 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TATATTTAAATATTTATATTTATATAAATTTAA
Found at i:1614917 original size:16 final size:16
Alignment explanation
Indices: 1614860--1614917 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 16
1614850 TAATTATATT
1614860 TAAATATTTATATTTATA
1 TAAAT-TTTATA-TTATA
1614878 TAAATTTAATATATT-TA
1 TAAATTT--TATATTATA
1614895 T-AA-TTTATATTATA
1 TAAATTTTATATTATA
1614909 TAAATTTTA
1 TAAATTTTA
1614918 AAATTTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 6 0.17
14 3 0.09
15 4 0.11
16 6 0.17
17 5 0.14
18 7 0.20
19 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAAATTTTATATTATA
Found at i:1614926 original size:31 final size:32
Alignment explanation
Indices: 1614855--1614926 Score: 94
Period size: 31 Copynumber: 2.2 Consensus size: 32
1614845 TATCATAATT
* *
1614855 ATATTTAAATATTTATATTTATATAAATTTAAT
1 ATATTTATA-ATTTATATTTATATAAATTTAAA
1614888 ATATTTATAATTTATA-TTATATAAATTTTAAA
1 ATATTTATAATTTATATTTATATAAA-TTTAAA
1614920 AT-TTTAT
1 ATATTTAT
1614927 TTAACTAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 14 0.39
32 14 0.39
33 8 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
ATATTTATAATTTATATTTATATAAATTTAAA
Found at i:1615080 original size:21 final size:22
Alignment explanation
Indices: 1615038--1615081 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1615028 GGGGGGGGGC
* **
1615038 AGGAAAGAAAGAAATAGCAAGG
1 AGGAAAGAAAGAAAAAAAAAGG
1615060 AGGAAA-AAAGAAAAAAAAAGG
1 AGGAAAGAAAGAAAAAAAAAGG
1615081 A
1 A
1615082 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.68, C:0.02, G:0.27, T:0.02
Consensus pattern (22 bp):
AGGAAAGAAAGAAAAAAAAAGG
Found at i:1615165 original size:29 final size:28
Alignment explanation
Indices: 1615108--1615180 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 28
1615098 CGTATTTGTA
*
1615108 TTATTTTTTATATATAAAATATTATATTT
1 TTATTTTTTATATATAAAATATTACA-TT
1615137 TTATATTTTTATATAT-AAATAATT-CATT
1 TTAT-TTTTTATATATAAAAT-ATTACATT
*
1615165 TTATTTTATATATATA
1 TTATTTTTTATATATA
1615181 TTTATATGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 10 0.26
28 6 0.15
29 9 0.23
30 14 0.36
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
TTATTTTTTATATATAAAATATTACATT
Found at i:1615181 original size:29 final size:29
Alignment explanation
Indices: 1615112--1615181 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
1615102 TTTGTATTAT
*
1615112 TTTTTATATATA-AAATATTATATTTTTA
1 TTTTTATATATATAAATATTACATTTTTA
1615140 TATTTT-TATATATAAATAATT-CA-TTTTA
1 T-TTTTATATATATAAAT-ATTACATTTTTA
1615168 TTTTATATATATAT
1 TTTT-TATATATAT
1615182 TTATATGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
27 3 0.08
28 14 0.39
29 16 0.44
30 3 0.08
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTTATATATATAAATATTACATTTTTA
Found at i:1616073 original size:4 final size:4
Alignment explanation
Indices: 1616064--1616128 Score: 66
Period size: 4 Copynumber: 17.2 Consensus size: 4
1616054 TATTTTTGTC
*
1616064 AAGA AAGA AAGA AA-A AAGA AAGA AAGA AAGA AA-A GAGA AA-A AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
* * *
1616109 AA-A AGGA AACA AAAA AAGA A
1 AAGA AAGA AAGA AAGA AAGA A
1616129 TAAAATTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
3 10 0.20
4 40 0.80
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:1616084 original size:15 final size:15
Alignment explanation
Indices: 1616064--1616117 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
1616054 TATTTTTGTC
1616064 AAGAAAGAAAGAAAA
1 AAGAAAGAAAGAAAA
1616079 AAGAAAGAAAGAAAGAA
1 AAGAAAGAAAG-AA-AA
*
1616096 AAGAGAAAAAAGAAAA
1 AAGA-AAGAAAGAAAA
*
1616112 AGGAAA
1 AAGAAA
1616118 CAAAAAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 13 0.38
16 7 0.21
17 8 0.24
18 6 0.18
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAGAAAGAAAGAAAA
Found at i:1616088 original size:19 final size:19
Alignment explanation
Indices: 1616064--1616110 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
1616054 TATTTTTGTC
1616064 AAGAAAGAAAGAAAAAAGA
1 AAGAAAGAAAGAAAAAAGA
*
1616083 AAGAAAGAAAGAAAAGAGA
1 AAGAAAGAAAGAAAAAAGA
1616102 AA-AAAGAAA
1 AAGAAAGAAA
1616111 AAGGAAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
AAGAAAGAAAGAAAAAAGA
Found at i:1616123 original size:26 final size:26
Alignment explanation
Indices: 1616071--1616133 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
1616061 GTCAAGAAAG
*
1616071 AAAGAAAAAAGAAAGAAAGAAAGAAA
1 AAAGAAAAAAGAAAGAAAGAAAAAAA
* *
1616097 AGAGAAAAAAGAAA-AAGGAAACAAAA
1 AAAGAAAAAAGAAAGAAAGAAA-AAAA
1616123 AAAGAATAAAA
1 AAAGAA-AAAA
1616134 TTATGTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 6 0.19
26 21 0.68
27 4 0.13
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (26 bp):
AAAGAAAAAAGAAAGAAAGAAAAAAA
Found at i:1616194 original size:19 final size:19
Alignment explanation
Indices: 1616172--1616233 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
1616162 ATTTAAATTA
1616172 TTATATTTTTGTATATTTT
1 TTATATTTTTGTATATTTT
* **
1616191 TTATATATTAATA-ATTTT
1 TTATATTTTTGTATATTTT
* *
1616209 TTTTATTTCATGTATA-TTT
1 TTATATTT-TTGTATATTTT
1616228 TTATAT
1 TTATAT
1616234 GTACGTGTAT
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
18 11 0.34
19 20 0.62
20 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (19 bp):
TTATATTTTTGTATATTTT
Found at i:1617153 original size:24 final size:26
Alignment explanation
Indices: 1617112--1617160 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
1617102 CCATGTTCAT
1617112 ATTATTTTTTTATCATATTATATTTTA
1 ATTATTTTTTTA-CATATTATATTTTA
*
1617139 ATTA-TTTTTTA-ATATTGTATTT
1 ATTATTTTTTTACATATTATATTT
1617161 GTGTTATACC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 10 0.48
26 7 0.33
27 4 0.19
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (26 bp):
ATTATTTTTTTACATATTATATTTTA
Found at i:1617273 original size:15 final size:14
Alignment explanation
Indices: 1617199--1617284 Score: 65
Period size: 15 Copynumber: 6.0 Consensus size: 14
1617189 TGTATAAATT
1617199 TTTTATATAATTAAA
1 TTTTAT-TAATTAAA
1617214 TTTTA--AATTTTAAA
1 TTTTATTAA--TTAAA
1617228 -TTTA-TATATTAAA
1 TTTTATTA-ATTAAA
*
1617241 TATTT-TTAAATAAA
1 T-TTTATTAATTAAA
1617255 TTTTATTAATTATAA
1 TTTTATTAATTA-AA
1617270 TTTTATTTAATTAAA
1 TTTTA-TTAATTAAA
1617285 AATTTATAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 20
0.73 0.02 0.25
Matches are distributed among these distances:
12 2 0.03
13 12 0.20
14 18 0.31
15 20 0.34
16 7 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTATTAATTAAA
Found at i:1619039 original size:2 final size:2
Alignment explanation
Indices: 1619032--1619068 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1619022 CGAAAAGTTA
1619032 AT AT 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 A
1619069 CACAAATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1620379 original size:35 final size:35
Alignment explanation
Indices: 1620340--1620406 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
1620330 ATTTTTAACG
*
1620340 TAAATATAATTATAATAAATATTT-ATTATTTAATA
1 TAAATAAAATTATAAT-AATATTTAATTATTTAATA
* *
1620375 TAAATAAAATTTTAATAATTTTTAATTATTTA
1 TAAATAAAATTATAATAATATTTAATTATTTA
1620407 TAATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 6 0.21
35 22 0.79
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
TAAATAAAATTATAATAATATTTAATTATTTAATA
Found at i:1621230 original size:38 final size:37
Alignment explanation
Indices: 1621164--1621237 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 37
1621154 TTAATTCAAC
1621164 TTAAATTAATATATAAATAAATAAAAAATAATTTTAT
1 TTAAATTAATATATAAATAAATAAAAAATAATTTTAT
1621201 TTAAATTTAAT-TATAAAT-AATAATTAAAATAATTTTA
1 TTAAA-TTAATATATAAATAAATAA--AAAATAATTTTA
1621238 ATATTATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
36 5 0.15
37 12 0.35
38 17 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (37 bp):
TTAAATTAATATATAAATAAATAAAAAATAATTTTAT
Found at i:1621481 original size:37 final size:37
Alignment explanation
Indices: 1621432--1621504 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
1621422 AAACCGTAGG
** *
1621432 TTAATTAATTGTTTTTGTTAAAGTTAATTAATCATGA
1 TTAATTAATTGTTTTAATTAAAGTTAATTAACCATGA
1621469 TTAATTAATTGTTTTAATTAAAGTTAATTAACCATG
1 TTAATTAATTGTTTTAATTAAAGTTAATTAACCATG
1621505 GTTAGTCCCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (37 bp):
TTAATTAATTGTTTTAATTAAAGTTAATTAACCATGA
Found at i:1622194 original size:2 final size:2
Alignment explanation
Indices: 1622187--1622216 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1622177 AATGAGTTAC
1622187 AT 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 AT
1622217 TAATAGGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1622265 original size:17 final size:18
Alignment explanation
Indices: 1622240--1622281 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1622230 ATTTATGTTA
*
1622240 TATAAATTTTGAT-ATAT
1 TATATATTTTGATCATAT
*
1622257 TATATATTTTTATCATAT
1 TATATATTTTGATCATAT
1622275 T-TATATT
1 TATATATT
1622282 ATTTTTTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TATATATTTTGATCATAT
Found at i:1622300 original size:22 final size:24
Alignment explanation
Indices: 1622252--1622303 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
1622242 TAAATTTTGA
1622252 TATATTATATATTTTTATCATATT
1 TATATTATATATTTTTATCATATT
*
1622276 TATATTAT-T-TTTTGTATCGTA-T
1 TATATTATATATTTT-TATCATATT
1622298 TATATT
1 TATATT
1622304 TTAATTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 11 0.42
23 7 0.27
24 8 0.31
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (24 bp):
TATATTATATATTTTTATCATATT
Found at i:1622316 original size:11 final size:12
Alignment explanation
Indices: 1622295--1622327 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1622285 TTTTGTATCG
1622295 TATTATATTTTA
1 TATTATATTTTA
*
1622307 -ATTATTTTTTA
1 TATTATATTTTA
1622318 TATTATATTT
1 TATTATATTT
1622328 ATGTCATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TATTATATTTTA
Found at i:1622812 original size:19 final size:20
Alignment explanation
Indices: 1622784--1622826 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1622774 AGACTTAGAC
1622784 TAAAACAATA-ATTTTTAAT
1 TAAAACAATATATTTTTAAT
* *
1622803 TAAAATAATATATTTTTATT
1 TAAAACAATATATTTTTAAT
1622823 TAAA
1 TAAA
1622827 TTTAATTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAAACAATATATTTTTAAT
Found at i:1623734 original size:9 final size:9
Alignment explanation
Indices: 1623720--1623751 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1623710 TTAAAAATAT
1623720 TTTATTATA
1 TTTATTATA
1623729 TTTATTAT-
1 TTTATTATA
1623737 TTT-TTATA
1 TTTATTATA
1623745 TTTATTA
1 TTTATTA
1623752 AATATAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 4 0.19
8 6 0.29
9 11 0.52
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTATTATA
Found at i:1623745 original size:16 final size:17
Alignment explanation
Indices: 1623717--1623751 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1623707 TACTTAAAAA
1623717 TATTTTATTATATTTAT
1 TATTTTATTATATTTAT
1623734 TATTTT-TTATATTTAT
1 TATTTTATTATATTTAT
1623750 TA
1 TA
1623752 AATATAGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTATTATATTTAT
Found at i:1623884 original size:2 final size:2
Alignment explanation
Indices: 1623877--1623913 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1623867 AGTGGGGAAG
1623877 AT AT 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 A
1623914 AAGAGTAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1624161 original size:11 final size:11
Alignment explanation
Indices: 1624145--1624171 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1624135 ATTTTATATA
1624145 TTTATATAATT
1 TTTATATAATT
1624156 TTTATATAATT
1 TTTATATAATT
1624167 TTTAT
1 TTTAT
1624172 CTATTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTATATAATT
Found at i:1624361 original size:8 final size:8
Alignment explanation
Indices: 1624350--1624385 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
1624340 AAAATTTTAT
*
1624350 TTATACAA
1 TTATATAA
1624358 TTATTATAA
1 TTA-TATAA
1624367 TTATATAA
1 TTATATAA
1624375 TTATATAA
1 TTATATAA
1624383 TTA
1 TTA
1624386 AATTTAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (8 bp):
TTATATAA
Found at i:1624376 original size:17 final size:16
Alignment explanation
Indices: 1624350--1624385 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1624340 AAAATTTTAT
1624350 TTATACAATTATTATAA
1 TTATACAATTA-TATAA
*
1624367 TTATATAATTATATAA
1 TTATACAATTATATAA
1624383 TTA
1 TTA
1624386 AATTTAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATACAATTATATAA
Found at i:1628794 original size:11 final size:11
Alignment explanation
Indices: 1628780--1628814 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1628770 AAAATAATTT
1628780 TTATATTTATA
1 TTATATTTATA
*
1628791 TTATATTTATG
1 TTATATTTATA
*
1628802 TTATAATTATA
1 TTATATTTATA
1628813 TT
1 TT
1628815 TAAAATGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
TTATATTTATA
Done.