Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4408.1
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: 61881
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.29
Warning! 3249 characters in sequence are not A, C, G, or T
Found at i:1319 original size:18 final size:18
Alignment explanation
Indices: 1293--1378 Score: 73
Period size: 18 Copynumber: 4.6 Consensus size: 18
1283 AAATTGAAAG
*
1293 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
*
1311 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
1329 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
1347 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
1368 AAAAGAAAAAG
1 AAAAGAAAAAG
1379 CGAAAAAAGA
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
18 33 0.63
19 5 0.10
20 8 0.15
21 6 0.12
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.06
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:1321 original size:6 final size:6
Alignment explanation
Indices: 1289--1378 Score: 65
Period size: 6 Copynumber: 14.7 Consensus size: 6
1279 AAAGAAATTG
* * ** **
1289 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATCGAA AAAGTG
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* * *
1336 AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA AAAG
1379 CGAAAAAAGA
Statistics
Matches: 63, Mismatches: 18, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
5 3 0.05
6 49 0.78
7 7 0.11
8 4 0.06
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:1360 original size:14 final size:13
Alignment explanation
Indices: 1339--1376 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
1329 AAAAGTGAGA
1339 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
1351 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
1366 GAAAAAGAAAA
1 GAAAAAGAAAA
1377 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:1430 original size:33 final size:33
Alignment explanation
Indices: 1393--1455 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1383 AAAAGAAATT
1393 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
1426 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
1456 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:3248 original size:10 final size:10
Alignment explanation
Indices: 3233--3257 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3223 AGTTTTTCCC
3233 AGCTCGATTT
1 AGCTCGATTT
3243 AGCTCGATTT
1 AGCTCGATTT
3253 AGCTC
1 AGCTC
3258 ACATGAGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (10 bp):
AGCTCGATTT
Found at i:6973 original size:13 final size:13
Alignment explanation
Indices: 6955--6979 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6945 TGGTCATCAT
6955 GGTGTGAACACAA
1 GGTGTGAACACAA
6968 GGTGTGAACACA
1 GGTGTGAACACA
6980 TGATCAATAC
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:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:9480 original size:18 final size:18
Alignment explanation
Indices: 9459--9508 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
9449 AAACTCTTTT
9459 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
9477 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
9495 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
9509 TTTGTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:9509 original size:24 final size:24
Alignment explanation
Indices: 9434--9511 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
9424 CTTGTTCACA
*
9434 TTCTTTCTCTCTCTCAAACTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
* * * *
9458 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTCTCTCTCTCAATCTCTTT
* *
9482 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
9506 TTCTTT
1 TTCTTT
9512 GTCTTTCATT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.59
Consensus pattern (24 bp):
TTCTTTCTCTCTCTCAATCTCTTT
Found at i:10586 original size:17 final size:17
Alignment explanation
Indices: 10559--10591 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
10549 TATGTTCAAA
10559 TTTTCAGATTTTGTTTTT
1 TTTTCAGATTTT-TTTTT
10577 TTTTCA-ATTTTTTTT
1 TTTTCAGATTTTTTTT
10592 GAAACTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTCAGATTTTTTTTT
Found at i:11284 original size:11 final size:11
Alignment explanation
Indices: 11264--11295 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
11254 GGTCACATAG
*
11264 TAAAGTGCTAT
1 TAAAGGGCTAT
11275 TAAAGGGCTAT
1 TAAAGGGCTAT
11286 TAAAGGGCTA
1 TAAAGGGCTA
11296 ATTATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.28
Consensus pattern (11 bp):
TAAAGGGCTAT
Found at i:14645 original size:24 final size:24
Alignment explanation
Indices: 14613--14663 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
14603 ATGTATCGAC
14613 AAAAGCTAAAATGCCAAAAAGCCG
1 AAAAGCTAAAATGCCAAAAAGCCG
* *
14637 AAAAGCTAAAATGCCGAAAAGCTG
1 AAAAGCTAAAATGCCAAAAAGCCG
14661 AAA
1 AAA
14664 GTTTGGCTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.18, G:0.18, T:0.10
Consensus pattern (24 bp):
AAAAGCTAAAATGCCAAAAAGCCG
Found at i:14647 original size:16 final size:16
Alignment explanation
Indices: 14628--14659 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
14618 CTAAAATGCC
14628 AAAAAGCCGAAAAGCT
1 AAAAAGCCGAAAAGCT
*
14644 AAAATGCCGAAAAGCT
1 AAAAAGCCGAAAAGCT
14660 GAAAGTTTGG
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:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (16 bp):
AAAAAGCCGAAAAGCT
Found at i:14949 original size:28 final size:29
Alignment explanation
Indices: 14886--14986 Score: 143
Period size: 28 Copynumber: 3.6 Consensus size: 29
14876 TGAATATGAC
* *
14886 TGGGCCTAACGGGCCACATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
*
14915 TGGGCCTAATGGGCCATATACA-GTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
*
14943 TGGGCCTAATGGGCCATATAAATATGA-T
1 TGGGCCTAATGGGCCATATAAATGTGATT
*
14971 TGGGCTTAATGGGCCA
1 TGGGCCTAATGGGCCA
14987 GATACAGGTA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
28 43 0.66
29 22 0.34
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATGTGATT
Found at i:14957 original size:57 final size:56
Alignment explanation
Indices: 14886--14993 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 56
14876 TGAATATGAC
* *
14886 TGGGCCTAACGGGCCACATAAATGTGATTTGGGCCTAATGGGCCATATACAGTGATT
1 TGGGCCTAACGGGCCACATAAATATGA-TTGGGCCTAATGGGCCAGATACAGTGATT
* * *
14943 TGGGCCTAATGGGCCATATAAATATGATTGGGCTTAATGGGCCAGATACAG
1 TGGGCCTAACGGGCCACATAAATATGATTGGGCCTAATGGGCCAGATACAG
14994 GTATGTGAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
56 22 0.48
57 24 0.52
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.26
Consensus pattern (56 bp):
TGGGCCTAACGGGCCACATAAATATGATTGGGCCTAATGGGCCAGATACAGTGATT
Found at i:18444 original size:48 final size:48
Alignment explanation
Indices: 18388--18483 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
18378 CTCGTGGTCC
18388 GAATGAATTACGAATTCCTTCGGCCATAAATAGTGTTACCATGTTTCA
1 GAATGAATTACGAATTCCTTCGGCCATAAATAGTGTTACCATGTTTCA
18436 GAATGAATTACGAATTCCTTCGGCCATAAATAGTGTTACCATGTTTCA
1 GAATGAATTACGAATTCCTTCGGCCATAAATAGTGTTACCATGTTTCA
18484 AGAGCTCGGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (48 bp):
GAATGAATTACGAATTCCTTCGGCCATAAATAGTGTTACCATGTTTCA
Found at i:19845 original size:15 final size:15
Alignment explanation
Indices: 19825--19879 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
19815 ACTCTCCTCA
*
19825 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
19840 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
19855 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
19869 TTCTTTT-TCTC
1 TTCTTTTCTCTC
19880 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:31542 original size:30 final size:30
Alignment explanation
Indices: 31508--31604 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
31498 AGCTCACTCC
31508 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
31538 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* **
31568 CAGCTCAACTTTAGCTCACGAGCTAAAATT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
31598 TAGCTCA
1 TAGCTCA
31605 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:35352 original size:29 final size:29
Alignment explanation
Indices: 35315--35405 Score: 121
Period size: 29 Copynumber: 3.2 Consensus size: 29
35305 TGAATGTTAC
*
35315 TGGGCCTAACGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
** *
35344 TGGGCCTAATGGGCCATATGCAGGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* *
35373 TGGGCCTAATGGGCCATATCAATATGA-T
1 TGGGCCTAATGGGCCATATAAATGTGATT
35401 TGGGC
1 TGGGC
35406 TTTATAGGCC
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
28 6 0.11
29 48 0.89
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATGTGATT
Found at i:36021 original size:20 final size:20
Alignment explanation
Indices: 35975--36021 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
35965 AGCTCGTTTC
*
35975 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
35995 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
36015 CAGCTCA
1 CAGCTCA
36022 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:37902 original size:30 final size:30
Alignment explanation
Indices: 37808--37903 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
37798 AGCTCACTTC
37808 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
37838 TA-CTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
37867 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
37897 TAGCTCA
1 TAGCTCA
37904 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
28 1 0.02
29 20 0.40
30 29 0.58
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:39562 original size:21 final size:22
Alignment explanation
Indices: 39536--39585 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
39526 GTAGTTATAA
39536 AAAAAAGTAT-ATAAAAAAATC-
1 AAAAAAGTATGA-AAAAAAATCG
* *
39557 AAAAAAATTTGAAAAAAAATCG
1 AAAAAAGTATGAAAAAAAATCG
39579 AAAAAAG
1 AAAAAAG
39586 AGAGAGGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.72, C:0.04, G:0.08, T:0.16
Consensus pattern (22 bp):
AAAAAAGTATGAAAAAAAATCG
Found at i:40522 original size:21 final size:21
Alignment explanation
Indices: 40496--40545 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
40486 ACATTCTTGT
40496 AAAGAAAAAACAAAGAAAAG-A
1 AAAGAAAAAACAAA-AAAAGAA
* *
40517 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAACAAAAAAAGAA
40538 AAAGAAAA
1 AAAGAAAA
40546 TGAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAACAAAAAAAGAA
Found at i:40531 original size:6 final size:5
Alignment explanation
Indices: 40496--40563 Score: 59
Period size: 5 Copynumber: 13.0 Consensus size: 5
40486 ACATTCTTGT
* *
40496 AAAGA AAAAA CAAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA
1 AAAGA AAAGA -AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA
40543 AAATGA AATA-A AAAGA AAAGA
1 AAA-GA AA-AGA AAAGA AAAGA
40564 GAGGCAAGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
4 4 0.08
5 29 0.56
6 18 0.35
7 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:40536 original size:15 final size:14
Alignment explanation
Indices: 40507--40563 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
40497 AAGAAAAAAC
40507 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
40523 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
40538 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
40554 AAAGAAAAGA
1 AAAGAAAAGA
40564 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:40662 original size:12 final size:12
Alignment explanation
Indices: 40636--40680 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
40626 AAAACAAAAA
*
40636 GAAAAAGAAAAT
1 GAAAAAGAGAAT
* *
40648 GAAAATGAGATT
1 GAAAAAGAGAAT
40660 GAAAAAGAGAAT
1 GAAAAAGAGAAT
40672 GAAAAAGAG
1 GAAAAAGAG
40681 TTTGAGAGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.11
Consensus pattern (12 bp):
GAAAAAGAGAAT
Found at i:40663 original size:24 final size:24
Alignment explanation
Indices: 40636--40694 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
40626 AAAACAAAAA
*
40636 GAAAAAGAAAATGAAAATGAGATT
1 GAAAAAGAAAATGAAAAAGAGATT
* *
40660 GAAAAAGAGAATGAAAAAGAGTTT
1 GAAAAAGAAAATGAAAAAGAGATT
* *
40684 GAGAGAGAAAA
1 GAAAAAGAAAA
40695 AGAATGTGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (24 bp):
GAAAAAGAAAATGAAAAAGAGATT
Found at i:40712 original size:17 final size:18
Alignment explanation
Indices: 40689--40729 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
40679 AGTTTGAGAG
*
40689 AGAAAAAGAA-TGTGAAAA
1 AGAAAAAAAAGTG-GAAAA
40707 AGAAAAAAAAGTGGAAAA
1 AGAAAAAAAAGTGGAAAA
40725 AGAAA
1 AGAAA
40730 TTGAGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.07
Consensus pattern (18 bp):
AGAAAAAAAAGTGGAAAA
Found at i:45237 original size:23 final size:22
Alignment explanation
Indices: 45185--45237 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
45175 TCCACGTCTT
*
45185 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
45207 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
45230 TTTCTTTT
1 TTTCTTTT
45238 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:54147 original size:15 final size:14
Alignment explanation
Indices: 54111--54165 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
54101 TCTATTGATC
54111 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
54125 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
54139 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
54154 GAAAGAAAAGAA
1 GAGA-AAAAGAA
54166 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:57556 original size:102 final size:102
Alignment explanation
Indices: 57412--57615 Score: 399
Period size: 102 Copynumber: 2.0 Consensus size: 102
57402 TTTAGTTTAA
*
57412 TTACAAAGTTTTAATGTGTCTTGACTAAGACAAATTTATTAGTGGCTGCTAGTTAATTTGTCTTA
1 TTACAAAGTTTTAATGTGTCTTGACTAAGACAAATTTATTAGTGGCTGCTAATTAATTTGTCTTA
57477 GCCGAATTAATGTGCAGAATTTTAATATGTCCAGCTG
66 GCCGAATTAATGTGCAGAATTTTAATATGTCCAGCTG
57514 TTACAAAGTTTTAATGTGTCTTGACTAAGACAAATTTATTAGTGGCTGCTAATTAATTTGTCTTA
1 TTACAAAGTTTTAATGTGTCTTGACTAAGACAAATTTATTAGTGGCTGCTAATTAATTTGTCTTA
57579 GCCGAATTAATGTGCAGAATTTTAATATGTCCAGCTG
66 GCCGAATTAATGTGCAGAATTTTAATATGTCCAGCTG
57616 CTGATTTCAT
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (102 bp):
TTACAAAGTTTTAATGTGTCTTGACTAAGACAAATTTATTAGTGGCTGCTAATTAATTTGTCTTA
GCCGAATTAATGTGCAGAATTTTAATATGTCCAGCTG
Found at i:61055 original size:15 final size:14
Alignment explanation
Indices: 61035--61082 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
61025 CTCATTTTCA
61035 TCTTTTTCTTTTATT
1 TCTTTTTCTTTT-TT
*
61050 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTT
*
61064 TCTCATTTCTTTTTT
1 TCT-TTTTCTTTTTT
61079 TCTT
1 TCTT
61083 CTCTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:61087 original size:22 final size:21
Alignment explanation
Indices: 61035--61093 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
61025 CTCATTTTCA
* *
61035 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
61056 TCTTTTTCTCTCATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
*
61077 T-TTCTTCTCTCAATTTC
1 TCTTTTTCTCTC-ATTTC
61094 ATTCAAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCTCATTTCTTTT
Found at i:61407 original size:34 final size:34
Alignment explanation
Indices: 61366--61431 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
61356 GCATTTGTAG
61366 AGACATGATTACCTTCTTGTATATCATCTCGGGT
1 AGACATGATTACCTTCTTGTATATCATCTCGGGT
*
61400 AGACATGATTACCTTTTTGTATATCATCTCGG
1 AGACATGATTACCTTCTTGTATATCATCTCGG
61432 AAGGACTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (34 bp):
AGACATGATTACCTTCTTGTATATCATCTCGGGT
Done.