Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 178 of 410
Found at i:54525855 original size:21 final size:21
Alignment explanation
Indices: 54525788--54525853 Score: 98
Period size: 21 Copynumber: 3.1 Consensus size: 21
54525778 AAGAGAAAAT
54525788 AAAG-AAAAGAAAAGAAAAGAA
1 AAAGAAAAAGAAAA-AAAAGAA
*
54525809 AAAGAAAAAGAAAAAGAAGAA
1 AAAGAAAAAGAAAAAAAAGAA
54525830 AAAGAAAAAGAAATAAAAAGAA
1 AAAGAAAAAGAAA-AAAAAGAA
54525852 AA
1 AA
54525854 GAGAGGCAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.56
22 18 0.44
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (21 bp):
AAAGAAAAAGAAAAAAAAGAA
Found at i:54525953 original size:30 final size:31
Alignment explanation
Indices: 54525919--54525998 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 31
54525909 AAAAAAGCAT
*
54525919 AAAGAAAATGAAAAAGAAA-ATGAGATTGAA
1 AAAGAAAATGAAAAAGAAATATGAGAGTGAA
* * *
54525949 AAAGAGAATG-AAAAGAAATCTGTGAGTGAA
1 AAAGAAAATGAAAAAGAAATATGAGAGTGAA
54525979 AAAGAAGAA-GAAAAAGAAAT
1 AAAGAA-AATGAAAAAGAAAT
54525999 TGAAACAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
29 8 0.19
30 23 0.55
31 11 0.26
ACGTcount: A:0.64, C:0.01, G:0.23, T:0.12
Consensus pattern (31 bp):
AAAGAAAATGAAAAAGAAATATGAGAGTGAA
Found at i:54528175 original size:30 final size:30
Alignment explanation
Indices: 54528080--54528176 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
54528070 AGCTCACTCC
*
54528080 TAGCTC-ACTTTCAACTCACGAGCTAAA-CAT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGC-T
* * * **
54528110 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
54528140 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
54528170 TAGCTCA
1 TAGCTCA
54528177 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
29 2 0.04
30 40 0.80
31 8 0.16
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:54530198 original size:30 final size:30
Alignment explanation
Indices: 54530164--54530260 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
54530154 TAAACTAAAA
54530164 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
54530194 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
54530224 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
54530254 TGAGCTA
1 TGAGCTA
54530261 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:54530759 original size:13 final size:13
Alignment explanation
Indices: 54530741--54530769 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54530731 CGGCTAACCT
54530741 ACATAATTAAATA
1 ACATAATTAAATA
54530754 ACATAATTAAATA
1 ACATAATTAAATA
54530767 ACA
1 ACA
54530770 CACAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:54531017 original size:21 final size:21
Alignment explanation
Indices: 54530993--54531032 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
54530983 GAAAAAGGAA
*
54530993 TGAGCTGAAACGAGCTAAATT
1 TGAGCTCAAACGAGCTAAATT
54531014 TGAGCTCAAACGAGCTAAA
1 TGAGCTCAAACGAGCTAAA
54531033 ACAAGCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (21 bp):
TGAGCTCAAACGAGCTAAATT
Found at i:54534237 original size:30 final size:31
Alignment explanation
Indices: 54534203--54534299 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
54534193 AGCTCACTCC
*
54534203 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
54534233 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
54534263 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
54534293 TAGCTCA
1 TAGCTCA
54534300 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:54536320 original size:30 final size:30
Alignment explanation
Indices: 54536286--54536382 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
54536276 TAAACTAAAA
54536286 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
54536316 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
54536346 TGAGCTAATG-TTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAA-GCTTTAGCTCGTGAGCT-AAAGT
54536376 TGAGCTA
1 TGAGCTA
54536383 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
29 1 0.02
30 43 0.86
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:54538513 original size:30 final size:30
Alignment explanation
Indices: 54538462--54538543 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 30
54538452 TCTTTTGTTT
*
54538462 CAATTTCTTTTTC-TTCTTCTTTTTCACTCA
1 CAATTTCTTTTTCATTC-TCTTTTTCAATCA
*
54538492 CAGATTTC-TTTTCATTCTCTTTTTCAATCT
1 CA-ATTTCTTTTTCATTCTCTTTTTCAATCA
* *
54538522 CATTTTCTTTTTCATTTTCTTT
1 CAATTTCTTTTTCATTCTCTTT
54538544 ATGCTTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 4 0.09
30 33 0.73
31 8 0.18
ACGTcount: A:0.13, C:0.23, G:0.01, T:0.62
Consensus pattern (30 bp):
CAATTTCTTTTTCATTCTCTTTTTCAATCA
Found at i:54538626 original size:15 final size:15
Alignment explanation
Indices: 54538606--54538673 Score: 68
Period size: 15 Copynumber: 4.3 Consensus size: 15
54538596 CTCTTGCCTC
54538606 TCTTTTCTTTT-TATT
1 TCTTTTCTTTTCT-TT
*
54538621 TCTTTTTCTTTT-TCT
1 TC-TTTTCTTTTCTTT
54538636 TCTTTTTCTTTTTCTTTT
1 TC-TTTTC-TTTTC-TTT
54538654 TCTTTTCTTTTCTTT
1 TCTTTTCTTTTCTTT
54538669 TCTTT
1 TCTTT
54538674 ATTTTCTCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
15 19 0.40
16 19 0.40
17 5 0.11
18 4 0.09
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (15 bp):
TCTTTTCTTTTCTTT
Found at i:54538628 original size:6 final size:6
Alignment explanation
Indices: 54538619--54538673 Score: 68
Period size: 6 Copynumber: 10.2 Consensus size: 6
54538609 TTTCTTTTTA
54538619 TTTCTT TTTCTT TTTC-- -TTCTT TTTCTT TTTCTT TTTC-T TTTC-T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
54538662 TTTC-T TTTCTT T
1 TTTCTT TTTCTT T
54538674 ATTTTCTCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.07
5 15 0.33
6 27 0.60
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:54538630 original size:21 final size:21
Alignment explanation
Indices: 54538608--54538673 Score: 98
Period size: 21 Copynumber: 3.1 Consensus size: 21
54538598 CTTGCCTCTC
54538608 TTTTCTTTTTATTTCTTTTTCT
1 TTTTCTTTTT-TTTCTTTTTCT
*
54538630 TTTTCTTCTTTTTCTTTTTCT
1 TTTTCTTTTTTTTCTTTTTCT
54538651 TTTTCTTTTCTTTTC-TTTTCT
1 TTTTCTTTT-TTTTCTTTTTCT
54538672 TT
1 TT
54538674 ATTTTCTCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
21 27 0.66
22 14 0.34
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTCTTTTTTTTCTTTTTCT
Found at i:54538683 original size:21 final size:22
Alignment explanation
Indices: 54538619--54538684 Score: 93
Period size: 21 Copynumber: 3.1 Consensus size: 22
54538609 TTTCTTTTTA
54538619 TTTCTTTTTCTTTTTCTTCT-T
1 TTTCTTTTTCTTTTTCTTCTCT
*
54538640 TTTCTTTTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTTTTCTTCTCT
54538662 TTTC-TTTTCTTTATT-TTCTCT
1 TTTCTTTTTCTTT-TTCTTCTCT
54538683 TT
1 TT
54538685 ACAAGAATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
21 34 0.83
22 7 0.17
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTCTTTTTCTTTTTCTTCTCT
Found at i:54541211 original size:30 final size:30
Alignment explanation
Indices: 54541177--54541273 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
54541167 TAAACTAAAA
54541177 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
54541207 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
54541237 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
54541267 TGAGCTA
1 TGAGCTA
54541274 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:54552777 original size:39 final size:39
Alignment explanation
Indices: 54552723--54552799 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
54552713 ATGCAGAACA
*
54552723 CATATTAATGATGTTCAAACTGTGACATAATTAAAGACT
1 CATATTAATGATGTTCAAACTATGACATAATTAAAGACT
54552762 CATATTAATGATGTTCAAACTATGACATAATTAAAGAC
1 CATATTAATGATGTTCAAACTATGACATAATTAAAGAC
54552800 ACAAACTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (39 bp):
CATATTAATGATGTTCAAACTATGACATAATTAAAGACT
Found at i:54562551 original size:30 final size:30
Alignment explanation
Indices: 54562454--54562552 Score: 87
Period size: 30 Copynumber: 3.3 Consensus size: 30
54562444 CAAGCTCACT
*
54562454 CCTAGCTC-ACTTTCAACTCACGAGCTAAA-
1 CCTAGCTCAACTTT-AGCTCACGAGCTAAAG
* * * **
54562483 CCTTAGCTCAACTTCAGCTTAGGAG-TTTAG
1 CC-TAGCTCAACTTTAGCTCACGAGCTAAAG
54562513 CCTCAGCTCAACTTTAGCTCACGAGCTAAAG
1 CCT-AGCTCAACTTTAGCTCACGAGCTAAAG
*
54562544 CGTAGCTCA
1 CCTAGCTCA
54562553 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
29 5 0.09
30 39 0.74
31 9 0.17
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.26
Consensus pattern (30 bp):
CCTAGCTCAACTTTAGCTCACGAGCTAAAG
Found at i:54565096 original size:21 final size:23
Alignment explanation
Indices: 54565062--54565106 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
54565052 ACATTCTTGT
54565062 AAAGAGAAAAC-AAAG-AAAAGA
1 AAAGAGAAAACAAAAGCAAAAGA
54565083 AAAGA-AAAACCAAAAGCAAAAGA
1 AAAGAGAAAA-CAAAAGCAAAAGA
54565106 A
1 A
54565107 GAAAAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.19
21 6 0.29
22 4 0.19
23 7 0.33
ACGTcount: A:0.76, C:0.09, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAGAGAAAACAAAAGCAAAAGA
Found at i:54565267 original size:30 final size:31
Alignment explanation
Indices: 54565204--54565274 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
54565194 TTTGAAAAGC
* *
54565204 AAAAAGAAA-ATGAGATTGAAAAAGAGAACG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
*
54565234 -AAAAGAAATTTGAGAGTGAAAAAGA-AGATG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGA-ACG
54565264 AAAAAGAAATT
1 AAAAAGAAATT
54565275 GAAACAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 9 0.26
30 16 0.46
31 10 0.29
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.14
Consensus pattern (31 bp):
AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
Found at i:54567412 original size:30 final size:31
Alignment explanation
Indices: 54567378--54567474 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
54567368 AGCTCACTCC
*
54567378 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
54567408 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
54567438 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
54567468 TAGCTCA
1 TAGCTCA
54567475 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:54570013 original size:21 final size:21
Alignment explanation
Indices: 54569979--54570049 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
54569969 ACATTCTTGT
54569979 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAAGAAAAGA
54570000 AAAGAAAAAGCAAAAGCAAAAG-
1 AAAGAAAAAGC-AAAG-AAAAGA
* *
54570022 -AAGAAAAAGAAAATAAATA-A
1 AAAGAAAAAGCAAAGAAA-AGA
54570042 AAAGAAAA
1 AAAGAAAA
54570050 GAGAGGCAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
19 3 0.07
20 8 0.19
21 22 0.52
22 4 0.10
23 5 0.12
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.03
Consensus pattern (21 bp):
AAAGAAAAAGCAAAGAAAAGA
Found at i:54570014 original size:6 final size:5
Alignment explanation
Indices: 54569990--54570051 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
54569980 AAGAGAAAAC
* *
54569990 AAAGA AAAGA AAAGAA AAAGCA AAAGCA AAAGA AGA-A AAAGA AAATA
1 AAAGA AAAGA AAAG-A AAAG-A AAAG-A AAAGA AAAGA AAAGA AAAGA
54570037 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
54570052 GAGGCAAGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
4 4 0.08
5 28 0.57
6 17 0.35
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:54570183 original size:30 final size:31
Alignment explanation
Indices: 54570120--54570190 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
54570110 TTTGAAAAGC
* *
54570120 AAAAAGAAA-ATGAGATTGAAAAAGAGAACG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
*
54570150 -AAAAGAAATTTGAGAGTGAAAAAGA-AGATG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGA-ACG
54570180 AAAAAGAAATT
1 AAAAAGAAATT
54570191 GAAACAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 9 0.26
30 16 0.46
31 10 0.29
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.14
Consensus pattern (31 bp):
AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
Found at i:54572392 original size:30 final size:30
Alignment explanation
Indices: 54572298--54572393 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
54572288 AGCTCACTCC
*
54572298 TAGCTC-ACTTTCA-CTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
54572327 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
54572357 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
54572387 TAGCTCA
1 TAGCTCA
54572394 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
29 9 0.18
30 38 0.76
31 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:54577066 original size:19 final size:19
Alignment explanation
Indices: 54577042--54577081 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54577032 AGCTCCCATG
54577042 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
54577061 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
54577080 TA
1 TA
54577082 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:54578341 original size:14 final size:14
Alignment explanation
Indices: 54578319--54578366 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
54578309 ACCTAAACCG
* *
54578319 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
54578333 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
54578347 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
54578361 ACCATT
1 ACCATT
54578367 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:54578735 original size:10 final size:10
Alignment explanation
Indices: 54578722--54578758 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
54578712 AGTTAAAAAA
54578722 AAAAAAAATC
1 AAAAAAAATC
54578732 AAAAAAAATC
1 AAAAAAAATC
54578742 AAAAAAAAT-
1 AAAAAAAATC
54578751 AAAAAAAA
1 AAAAAAAA
54578759 GAGTGATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.86, C:0.05, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:54578739 original size:20 final size:19
Alignment explanation
Indices: 54578716--54578758 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
54578706 TATACAAGTT
54578716 AAAAAAAAAAAAAATCAAAA
1 AAAAAAAAAAAAAAT-AAAA
**
54578736 AAAATCAAAAAAAATAAAA
1 AAAAAAAAAAAAAATAAAA
54578755 AAAA
1 AAAA
54578759 GAGTGATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.88, C:0.05, G:0.00, T:0.07
Consensus pattern (19 bp):
AAAAAAAAAAAAAATAAAA
Found at i:54583988 original size:19 final size:19
Alignment explanation
Indices: 54583964--54584003 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54583954 AGCTCCCATG
54583964 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
54583983 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
54584002 TA
1 TA
54584004 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:54587163 original size:46 final size:46
Alignment explanation
Indices: 54587113--54587285 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
54587103 TGGTTGAGCA
54587113 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
54587159 TCCGAACTCGCTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
54587204 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54587252 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
54587286 GGGCGGGTTA
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 60 0.57
47 28 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54587269 original size:93 final size:93
Alignment explanation
Indices: 54587110--54587280 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
54587100 GGATGGTTGA
* *
54587110 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGCTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGCTGAGT
54587175 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
54587203 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGCTGAGT
54587268 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
54587281 ACTTAGGGCG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGCTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:54590272 original size:15 final size:15
Alignment explanation
Indices: 54590234--54590277 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
54590224 CATAGTATCG
* *
54590234 TATCTTGGGTTTCTT
1 TATCTTGGATTTCTC
54590249 TAT-TCTGGATTTCTC
1 TATCT-TGGATTTCTC
54590264 TATCTTGGATTTCT
1 TATCTTGGATTTCT
54590278 TTATTCGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (15 bp):
TATCTTGGATTTCTC
Found at i:54594768 original size:14 final size:14
Alignment explanation
Indices: 54594751--54594790 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
54594741 TATCTTTTTG
*
54594751 TTCCTACCCTTTCA
1 TTCCTACCCTTCCA
*
54594765 TTCCTACCATTCCA
1 TTCCTACCCTTCCA
*
54594779 TTCGTACCCTTC
1 TTCCTACCCTTC
54594791 TTCTACTTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.15, C:0.42, G:0.03, T:0.40
Consensus pattern (14 bp):
TTCCTACCCTTCCA
Found at i:54595099 original size:30 final size:31
Alignment explanation
Indices: 54595065--54595161 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
54595055 AGCTCACTCC
*
54595065 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
54595095 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
54595125 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
54595155 TAGCTCA
1 TAGCTCA
54595162 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:54599495 original size:9 final size:10
Alignment explanation
Indices: 54599488--54599544 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
54599478 AAGAGAAAAC
54599488 AAAGAAAAGA
1 AAAGAAAAGA
54599498 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
54599510 AAAGAAGA-A
1 AAAGAAAAGA
54599519 AAAGAAAATGA
1 AAAGAAAA-GA
54599530 AATA-AAAAGA
1 AA-AGAAAAGA
54599540 AAAGA
1 AAAGA
54599545 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:54599511 original size:21 final size:20
Alignment explanation
Indices: 54599477--54599544 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
54599467 ACATTCTTGT
54599477 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
54599498 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
54599519 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
54599540 AAAGA
1 AAAGA
54599545 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:54599512 original size:6 final size:5
Alignment explanation
Indices: 54599488--54599544 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
54599478 AAGAGAAAAC
*
54599488 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
54599535 AAAGA AAAGA
1 AAAGA AAAGA
54599545 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:54599519 original size:15 final size:14
Alignment explanation
Indices: 54599488--54599544 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
54599478 AAGAGAAAAC
54599488 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
54599504 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
54599519 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
54599535 AAAGAAAAGA
1 AAAGAAAAGA
54599545 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:54599621 original size:12 final size:12
Alignment explanation
Indices: 54599613--54599637 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54599603 TTTGAAAAGC
54599613 AAAAAGAAAATG
1 AAAAAGAAAATG
54599625 AAAAAGAAAATG
1 AAAAAGAAAATG
54599637 A
1 A
54599638 GATTAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:54599647 original size:30 final size:31
Alignment explanation
Indices: 54599613--54599694 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
54599603 TTTGAAAAGC
*
54599613 AAAAAGAAAATGAAAAAGAAA-ATGAGATTA
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTA
* * * *
54599643 AAAAAGAGAACG-AAAAGAAATCTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTA
*
54599673 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
54599695 TGAAACAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 8 0.19
30 25 0.60
31 9 0.21
ACGTcount: A:0.66, C:0.02, G:0.21, T:0.11
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTA
Found at i:54601828 original size:30 final size:31
Alignment explanation
Indices: 54601794--54601890 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
54601784 AGCTCACTCC
*
54601794 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
54601824 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
54601854 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
54601884 TAGCTCA
1 TAGCTCA
54601891 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:54606737 original size:10 final size:11
Alignment explanation
Indices: 54606722--54606791 Score: 85
Period size: 10 Copynumber: 6.6 Consensus size: 11
54606712 TAAATCACTT
54606722 TTTTTTTC-AA
1 TTTTTTTCGAA
*
54606732 TTTTTTTCAAA
1 TTTTTTTCGAA
54606743 TTTTTTTTCGAA
1 -TTTTTTTCGAA
*
54606755 TTTTTTT--TA
1 TTTTTTTCGAA
54606764 TTTTTTTCGAA
1 TTTTTTTCGAA
54606775 TTTTTTT-GAA
1 TTTTTTTCGAA
54606785 TTTTTTT
1 TTTTTTT
54606792 TTAACTTGTA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
9 8 0.15
10 18 0.34
11 17 0.32
12 10 0.19
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:54606737 original size:11 final size:12
Alignment explanation
Indices: 54606721--54606792 Score: 79
Period size: 12 Copynumber: 6.7 Consensus size: 12
54606711 ATAAATCACT
54606721 TTTTTTTTC-AA
1 TTTTTTTTCGAA
*
54606732 -TTTTTTTCAAA
1 TTTTTTTTCGAA
54606743 TTTTTTTTCGAA
1 TTTTTTTTCGAA
54606755 TTTTTTTT---A
1 TTTTTTTTCGAA
54606764 -TTTTTTTCGAA
1 TTTTTTTTCGAA
54606775 -TTTTTTT-GAA
1 TTTTTTTTCGAA
54606785 TTTTTTTT
1 TTTTTTTT
54606793 TAACTTGTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
8 7 0.13
9 1 0.02
10 11 0.20
11 17 0.31
12 18 0.33
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:54613771 original size:19 final size:19
Alignment explanation
Indices: 54613726--54613771 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
54613716 ATTAACACAC
*
54613726 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
54613745 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
54613763 AATTAATAA
1 AATTAATAA
54613772 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:54617865 original size:5 final size:5
Alignment explanation
Indices: 54617855--54617879 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54617845 TATTGGGGTT
54617855 GACAG GACAG GACAG GACAG GACAG
1 GACAG GACAG GACAG GACAG GACAG
54617880 AAATGAGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
GACAG
Found at i:54617977 original size:51 final size:46
Alignment explanation
Indices: 54617876--54617980 Score: 120
Period size: 46 Copynumber: 2.2 Consensus size: 46
54617866 ACAGGACAGG
* * * *
54617876 ACAGAAATGAGCCATGTAAGTCCATATCAGATATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGCCCATATCAGATATATGGCATTGGAA
*
54617922 ACAGGAATGAGCCATGTAAGCCCATATTAGATATATTATATGGCATTGGAA
1 ACAGGAATGAGCCATGTAAGCCCATATCAG----A-TATATGGCATTGGAA
54617973 ACAGGAAT
1 ACAGGAAT
54617981 AATTCATGTA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
46 27 0.55
50 1 0.02
51 21 0.43
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (46 bp):
ACAGGAATGAGCCATGTAAGCCCATATCAGATATATGGCATTGGAA
Found at i:54619739 original size:29 final size:29
Alignment explanation
Indices: 54619673--54619729 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
54619663 GATTCAAAGA
*
54619673 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
54619702 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
54619730 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:54623010 original size:30 final size:28
Alignment explanation
Indices: 54622957--54623012 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
54622947 TTCTTCCACG
* *
54622957 CTTTCTTTTTGCTCACTCTCTTTTTCAA
1 CTTTCTTTTTGCACACACTCTTTTTCAA
54622985 CTTTACTTTCTTGCACACACTCTTTTTC
1 CTTT-CTTT-TTGCACACACTCTTTTTC
54623013 TTTTTCGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (28 bp):
CTTTCTTTTTGCACACACTCTTTTTCAA
Found at i:54624392 original size:29 final size:29
Alignment explanation
Indices: 54624326--54624382 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
54624316 GATTCAAAGA
*
54624326 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
54624355 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
54624383 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:54628856 original size:30 final size:30
Alignment explanation
Indices: 54628822--54628918 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
54628812 TAAACTAAAA
54628822 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
54628852 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
54628882 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
54628912 TGAGCTA
1 TGAGCTA
54628919 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:54631111 original size:30 final size:30
Alignment explanation
Indices: 54631030--54631111 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
54631020 CTTTTGTTTC
* *
54631030 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTC-TTTTCATTTTCTTTTTCAATCTCA
* *
54631061 AATTTCTTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTCATTTTCTTTTTCAATCTCA
*
54631090 ATTTTCTTTTCATTTTGCTTTT
1 AATTTCTTTTCATTTT-CTTTT
54631112 CAAAGGCTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 13 0.30
30 24 0.56
31 6 0.14
ACGTcount: A:0.13, C:0.22, G:0.02, T:0.62
Consensus pattern (30 bp):
AATTTCTTTTCATTTTCTTTTTCAATCTCA
Found at i:54631184 original size:5 final size:5
Alignment explanation
Indices: 54631174--54631235 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
54631164 CTCTTGCCTC
* *
54631174 TCTTT TCTTT T-ATT TCATTT TCTTT T-TCT TCTTT TGCTTT TGCTTTT
1 TCTTT TCTTT TCTTT TC-TTT TCTTT TCTTT TCTTT T-CTTT T-C-TTT
54631221 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
54631236 GTTTTCTCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
4 6 0.12
5 26 0.54
6 12 0.25
7 4 0.08
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (5 bp):
TCTTT
Found at i:54631213 original size:15 final size:14
Alignment explanation
Indices: 54631174--54631247 Score: 51
Period size: 14 Copynumber: 4.9 Consensus size: 14
54631164 CTCTTGCCTC
54631174 TCTTTTCTTTTATT
1 TCTTTTCTTTTATT
54631188 TCATTTTCTTTT-TCT
1 TC-TTTTCTTTTAT-T
*
54631203 TCTTTTGCTTTTGCTTTT
1 TCTTTT-C-TTT--TATT
*
54631221 TCTTTTCTTTTCTT
1 TCTTTTCTTTTATT
*
54631235 TGTTTTCTCTTTA
1 TCTTTTCT-TTTA
54631248 CAAGAATGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 15
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.35
15 16 0.33
16 6 0.12
17 1 0.02
18 8 0.16
19 1 0.02
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.74
Consensus pattern (14 bp):
TCTTTTCTTTTATT
Found at i:54631236 original size:21 final size:22
Alignment explanation
Indices: 54631176--54631246 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 22
54631166 CTTGCCTCTC
* *
54631176 TTTTCTTTT-ATTTCATTTTCT
1 TTTTCTTTTCTTTTCATTTGCT
*
54631197 TTTTC--TTCTTTTGCTTTTGCT
1 TTTTCTTTTCTTTT-CATTTGCT
54631218 TTTTCTTTTCTTTTC-TTTG-T
1 TTTTCTTTTCTTTTCATTTGCT
54631238 TTTCTCTTT
1 TTT-TCTTT
54631247 ACAAGAATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
19 2 0.05
20 7 0.17
21 25 0.60
22 1 0.02
23 7 0.17
ACGTcount: A:0.03, C:0.17, G:0.04, T:0.76
Consensus pattern (22 bp):
TTTTCTTTTCTTTTCATTTGCT
Found at i:54633770 original size:30 final size:30
Alignment explanation
Indices: 54633736--54633832 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
54633726 TAAACTAAAA
54633736 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
54633766 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
54633796 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
54633826 TGAGCTA
1 TGAGCTA
54633833 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:54635955 original size:10 final size:10
Alignment explanation
Indices: 54635940--54635985 Score: 78
Period size: 10 Copynumber: 4.8 Consensus size: 10
54635930 TAAATCACTC
54635940 TTTTTTTT-A
1 TTTTTTTTGA
54635949 TTTTTTTTGA
1 TTTTTTTTGA
54635959 TTTTTTTTGA
1 TTTTTTTTGA
54635969 TTTTTTTT-A
1 TTTTTTTTGA
54635978 TTTTTTTT
1 TTTTTTTT
54635986 AACTTGTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
9 17 0.47
10 19 0.53
ACGTcount: A:0.09, C:0.00, G:0.04, T:0.87
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:54636382 original size:14 final size:14
Alignment explanation
Indices: 54636335--54636382 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
54636325 GTACGAATGG
*
54636335 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
54636349 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
54636363 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
54636377 ATTGGT
1 AATGGT
54636383 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:54640935 original size:24 final size:24
Alignment explanation
Indices: 54640899--54640951 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
54640889 TTTTTCTCTC
*
54640899 TCAAACTCTTTTTCATTCTCTTTT
1 TCAAACTCATTTTCATTCTCTTTT
* * * *
54640923 TCAATCTCATTTTCTTTTTGTTTT
1 TCAAACTCATTTTCATTCTCTTTT
54640947 TCAAA
1 TCAAA
54640952 GGCTTTTTCA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.19, C:0.21, G:0.02, T:0.58
Consensus pattern (24 bp):
TCAAACTCATTTTCATTCTCTTTT
Found at i:54640971 original size:13 final size:12
Alignment explanation
Indices: 54640943--54640974 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
54640933 TTTCTTTTTG
54640943 TTTTTCAAAGGC
1 TTTTTCAAAGGC
54640955 TTTTTCAAAGGC
1 TTTTTCAAAGGC
54640967 TTTTTCAA
1 TTTTTCAA
54640975 GTTCTCTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (12 bp):
TTTTTCAAAGGC
Found at i:54641032 original size:5 final size:5
Alignment explanation
Indices: 54641022--54641078 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
54641012 CTTTTGCCTC
*
54641022 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
54641069 TCTTT TCTTT
1 TCTTT TCTTT
54641079 GTTTTCTCGT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:54641062 original size:15 final size:14
Alignment explanation
Indices: 54641022--54641078 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
54641012 CTTTTGCCTC
*
54641022 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
54641037 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
54641052 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
54641069 TCTTTTCTTT
1 TCTTTTCTTT
54641079 GTTTTCTCGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:54641079 original size:21 final size:21
Alignment explanation
Indices: 54641022--54641083 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
54641012 CTTTTGCCTC
* *
54641022 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
54641043 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
54641064 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
54641084 CTCGTTACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 7 0.21
21 22 0.65
22 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:54642021 original size:11 final size:10
Alignment explanation
Indices: 54642001--54642044 Score: 61
Period size: 11 Copynumber: 4.2 Consensus size: 10
54641991 AAGTTTTCAC
54642001 TTCAATTTTT
1 TTCAATTTTT
54642011 TTCAGATTTTT
1 TTCA-ATTTTT
*
54642022 TTTAATTTTT
1 TTCAATTTTT
54642032 TTCGAATTTTT
1 TTC-AATTTTT
54642043 TT
1 TT
54642045 TAACTTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
10 12 0.40
11 18 0.60
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (10 bp):
TTCAATTTTT
Found at i:54642028 original size:21 final size:21
Alignment explanation
Indices: 54642004--54642047 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
54641994 TTTTCACTTC
54642004 AATTTTTTTC-AGATTTTTTTT
1 AATTTTTTTCGA-ATTTTTTTT
54642025 AATTTTTTTCGAATTTTTTTT
1 AATTTTTTTCGAATTTTTTTT
54642046 AA
1 AA
54642048 CTTGTATAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (21 bp):
AATTTTTTTCGAATTTTTTTT
Found at i:54644523 original size:10 final size:10
Alignment explanation
Indices: 54644508--54644553 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
54644498 TAAAAGAAAT
54644508 GAGCTAAAAC
1 GAGCTAAAAC
*
54644518 GAGCTAAATTC
1 GAGCTAAA-AC
*
54644529 GAGCTCAAAC
1 GAGCTAAAAC
*
54644539 GAGCTAAATC
1 GAGCTAAAAC
54644549 GAGCT
1 GAGCT
54644554 CAAGTGAGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (10 bp):
GAGCTAAAAC
Found at i:54644563 original size:20 final size:21
Alignment explanation
Indices: 54644508--54644556 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
54644498 TAAAAGAAAT
*
54644508 GAGCTAAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAATTC
54644529 GAGCTCAAACGAGCTAAA-TC
1 GAGCTCAAACGAGCTAAATTC
54644549 GAGCTCAA
1 GAGCTCAA
54644557 GTGAGCTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.16
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAATTC
Found at i:54647195 original size:20 final size:20
Alignment explanation
Indices: 54647170--54647207 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
54647160 CTTGAAGTCG
54647170 GCACAAATGTGAACAAACTT
1 GCACAAATGTGAACAAACTT
54647190 GCACAAATGTGAACAAAC
1 GCACAAATGTGAACAAAC
54647208 ATTCCAAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (20 bp):
GCACAAATGTGAACAAACTT
Found at i:54651983 original size:13 final size:13
Alignment explanation
Indices: 54651965--54651999 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
54651955 ATTATATGAA
*
54651965 TAATTATTTTATT
1 TAATTATGTTATT
54651978 TAATTATGTTATT
1 TAATTATGTTATT
54651991 TAATTATGT
1 TAATTATGT
54652000 AGGTTAGCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (13 bp):
TAATTATGTTATT
Found at i:54656716 original size:13 final size:13
Alignment explanation
Indices: 54656698--54656732 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
54656688 ATTATATGAA
*
54656698 TAATTATTTTATT
1 TAATTATGTTATT
54656711 TAATTATGTTATT
1 TAATTATGTTATT
54656724 TAATTATGT
1 TAATTATGT
54656733 AGGTTAGCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (13 bp):
TAATTATGTTATT
Found at i:54658032 original size:19 final size:19
Alignment explanation
Indices: 54658008--54658047 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
54657998 AGCTCCCATG
54658008 TAGCTC-CACACCAGCTCAT
1 TAGCTCGCA-ACCAGCTCAT
*
54658027 TAGCTCGGAACCAGCTCAT
1 TAGCTCGCAACCAGCTCAT
54658046 TA
1 TA
54658048 TCAGCTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCGCAACCAGCTCAT
Found at i:54659700 original size:46 final size:46
Alignment explanation
Indices: 54659633--54659804 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
54659623 AACCCGCCCC
* * **
54659633 TAAGTGAACTCGGTCTCAACTCAACAAACTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
54659679 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCA
* * * *
54659727 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
54659772 TAGGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
54659805 ATGCTCAACC
Statistics
Matches: 104, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 1 0.01
46 57 0.55
47 28 0.27
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
Found at i:54659746 original size:93 final size:93
Alignment explanation
Indices: 54659638--54659808 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
54659628 GCCCCTAAGT
* * *
54659638 GAACTCGGTCTCAACTCAACAAACTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54659703 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* ** *
54659731 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54659796 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54659809 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54660261 original size:30 final size:30
Alignment explanation
Indices: 54660227--54660283 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
54660217 ATTTAATACG
54660227 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
54660257 AACTTTTGCATAATTACACTTTTGCCC
1 AACTTTGGAAAAATTACACTTTTGCCC
54660284 TAGGCTCAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:54663223 original size:15 final size:15
Alignment explanation
Indices: 54663203--54663250 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
54663193 TCAAAGATGG
54663203 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
54663218 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
54663232 GTTTATGGATATAAA
1 GTTTATGGATATGAA
54663247 GTTT
1 GTTT
54663251 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:54663237 original size:14 final size:14
Alignment explanation
Indices: 54663197--54663240 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
54663187 AAGGATTCAA
54663197 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
54663211 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
54663226 AGATGGGTTTATGG
1 AGATGGGTTTATGG
54663240 A
1 A
54663241 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:54663266 original size:29 final size:29
Alignment explanation
Indices: 54663197--54663256 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
54663187 AAGGATTCAA
*
54663197 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
54663226 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
54663255 AG
1 AG
54663257 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:54666367 original size:30 final size:28
Alignment explanation
Indices: 54666314--54666369 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
54666304 TTCTTCCACG
* *
54666314 CTTTCTTTTTGCTCACTCTCTTTTTCAA
1 CTTTCTTTTTGCACACACTCTTTTTCAA
54666342 CTTTACTTTCTTGCACACACTCTTTTTC
1 CTTT-CTTT-TTGCACACACTCTTTTTC
54666370 TTTTTCGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (28 bp):
CTTTCTTTTTGCACACACTCTTTTTCAA
Found at i:54667460 original size:8 final size:9
Alignment explanation
Indices: 54667438--54667472 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
54667428 TTGTTTGAAA
*
54667438 TTTTTTTCAT
1 TTTTTTTC-G
54667448 TTTTTTTCG
1 TTTTTTTCG
54667457 TTTTTTTCG
1 TTTTTTTCG
54667466 TTTTTTT
1 TTTTTTT
54667473 TAAACTTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.03, C:0.09, G:0.06, T:0.83
Consensus pattern (9 bp):
TTTTTTTCG
Found at i:54673210 original size:47 final size:47
Alignment explanation
Indices: 54673096--54673265 Score: 169
Period size: 45 Copynumber: 3.7 Consensus size: 47
54673086 GCCCCTAAGT
* * * *
54673096 GAACTCGGACTCAACTCAACGAGCTCGG--G-CGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCC--AAGC
54673142 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACATCTC-A-C
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACATC-CAAGC
* *
54673189 GAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCATCCATAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCA-AGC
54673234 GAACTCGGACTCAACTCAACGAGTTCGGATGC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGC
54673266 TCAACCATCC
Statistics
Matches: 105, Mismatches: 6, Indels: 24
0.78 0.04 0.18
Matches are distributed among these distances:
42 3 0.03
43 5 0.05
44 2 0.02
45 29 0.28
46 27 0.26
47 29 0.28
48 2 0.02
49 1 0.01
50 4 0.04
51 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCAAGC
Found at i:54673265 original size:92 final size:93
Alignment explanation
Indices: 54673096--54673265 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
54673086 GCCCCTAAGT
* *
54673096 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54673161 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
54673189 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54673253 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54673266 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 35 0.47
93 39 0.53
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54673718 original size:30 final size:30
Alignment explanation
Indices: 54673684--54673743 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
54673674 ATTTAATACG
54673684 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
54673714 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
54673744 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:54675450 original size:30 final size:30
Alignment explanation
Indices: 54675416--54675512 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
54675406 AGCTCACTCC
54675416 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * *
54675446 TAGCTCAACTTCAGCAT-AGGAGTTTAATCT
1 TAGCTCAACTTCAGC-TCACGAGCTAAACCT
* * *
54675476 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
54675506 TAGCTCA
1 TAGCTCA
54675513 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
29 2 0.04
30 50 0.94
31 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:54678029 original size:6 final size:5
Alignment explanation
Indices: 54678005--54678067 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
54677995 AAGAGAAAAC
*
54678005 AAAGA AAAGA AAAGAA AAAGCA AAAGCA AAAGA AGA-A AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA
54678053 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
54678068 GAGGCAAGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 4 0.08
5 25 0.50
6 20 0.40
7 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:54678035 original size:12 final size:10
Alignment explanation
Indices: 54678005--54678067 Score: 58
Period size: 11 Copynumber: 6.0 Consensus size: 10
54677995 AAGAGAAAAC
54678005 AAAGAAAAGA
1 AAAGAAAAGA
54678015 AAAGAAAAAGCA
1 AAAG-AAAAG-A
54678027 AAAGCAAAAGA
1 AAAG-AAAAGA
*
54678038 AGA-AAAAGA
1 AAAGAAAAGA
54678047 AAATGAAATA-A
1 AAA-GAAA-AGA
54678058 AAAGAAAAGA
1 AAAGAAAAGA
54678068 GAGGCAAGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
9 9 0.20
10 9 0.20
11 15 0.34
12 11 0.25
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:54678137 original size:12 final size:12
Alignment explanation
Indices: 54678129--54678153 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54678119 TTTGAAAAGC
54678129 AAAAAGAAAATG
1 AAAAAGAAAATG
54678141 AAAAAGAAAATG
1 AAAAAGAAAATG
54678153 A
1 A
54678154 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:54678150 original size:18 final size:18
Alignment explanation
Indices: 54678123--54678178 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
54678113 AAAGCCTTTG
*
54678123 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAATGAAAATGA
* *
54678142 AAAAGAAAATGAGATTGA
1 AAAAGAAAATGAAAATGA
*
54678160 AAAAGAGAATGAAAA-GA
1 AAAAGAAAATGAAAATGA
54678177 AA
1 AA
54678179 TTTGAGAGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 4 0.13
18 22 0.71
19 5 0.16
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.09
Consensus pattern (18 bp):
AAAAGAAAATGAAAATGA
Found at i:54678163 original size:30 final size:31
Alignment explanation
Indices: 54678129--54678210 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
54678119 TTTGAAAAGC
**
54678129 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGAG
* *
54678159 AAAAAGAGAATG-AAAAGAAATTTGAGAGAG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGAG
**
54678189 AAAAAGAAGTTGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
54678211 TGAAAAAGAG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGAG
Found at i:54678205 original size:12 final size:12
Alignment explanation
Indices: 54678188--54678242 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
54678178 ATTTGAGAGA
*
54678188 GAAAAAGAAGTT
1 GAAAAAGAAATT
54678200 GAAAAAGAAATT
1 GAAAAAGAAATT
*
54678212 GAAAAAGAGATT
1 GAAAAAGAAATT
*
54678224 ACAGAGAAAGAAATT
1 ---GAAAAAGAAATT
54678239 GAAA
1 GAAA
54678243 TAAAAGAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 25 0.71
15 10 0.29
ACGTcount: A:0.62, C:0.02, G:0.22, T:0.15
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:54680414 original size:30 final size:30
Alignment explanation
Indices: 54680319--54680415 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
54680309 AGCTCACTCC
*
54680319 TAGCTCATA-TTCATCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAACTCACGAGCTAAACCT
* * * *
54680349 TAGCTCAACTTCAACAT-AGGAGTTTAATCT
1 TAGCTCAACTTCAAC-TCACGAGCTAAACCT
* * * *
54680379 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAACTCACGAGCTAAACCT
54680409 TAGCTCA
1 TAGCTCA
54680416 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 2 0.04
30 48 0.94
31 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAACTCACGAGCTAAACCT
Found at i:54684121 original size:19 final size:18
Alignment explanation
Indices: 54684099--54684137 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
54684089 AGCTATATTC
54684099 GAGCT-AAGTCTGAGCTCGA
1 GAGCTGAAGT-TGAGCT-GA
54684118 GAGCTGAAGTTGAGCTGA
1 GAGCTGAAGTTGAGCTGA
54684136 GA
1 GA
54684138 ACAAGCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 11 0.58
20 4 0.21
ACGTcount: A:0.28, C:0.15, G:0.36, T:0.21
Consensus pattern (18 bp):
GAGCTGAAGTTGAGCTGA
Found at i:54684870 original size:17 final size:17
Alignment explanation
Indices: 54684838--54684872 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
54684828 CCATCTTTGC
*
54684838 TACTAAATTGAACCTAT
1 TACTAAATTCAACCTAT
*
54684855 TACTAAATTCACCCTAT
1 TACTAAATTCAACCTAT
54684872 T
1 T
54684873 TGAAACCTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (17 bp):
TACTAAATTCAACCTAT
Found at i:54686147 original size:21 final size:21
Alignment explanation
Indices: 54686123--54686190 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
54686113 GATTTTGAAT
54686123 GAAATCGAGAGAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
***** *
54686144 GAAAAT-GAGAGAATCTTGAAT
1 G-AAATCGAGAGAAGAAACAAA
*
54686165 GAAATCGAGAAAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
54686186 GAAAT
1 GAAAT
54686191 GAAAGAAAAA
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.59, C:0.07, G:0.22, T:0.12
Consensus pattern (21 bp):
GAAATCGAGAGAAGAAACAAA
Found at i:54686148 original size:42 final size:42
Alignment explanation
Indices: 54686101--54686197 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
54686091 AGATTATGAG
* * *
54686101 AGAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
54686143 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
54686185 AG-AAATGAAAGAA
1 AGAAAATGAGAGAA
54686198 AAAGAAAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 10 0.20
42 41 0.80
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (42 bp):
AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
Found at i:54686224 original size:18 final size:18
Alignment explanation
Indices: 54686201--54686262 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
54686191 GAAAGAAAAA
*
54686201 GAAAAAGAGAGTGAGAGT
1 GAAAAAGAGAATGAGAGT
* * *
54686219 GAAAAAGAAAAAGAGAAT
1 GAAAAAGAGAATGAGAGT
** *
54686237 GAAAAAGAGTTTGAGAGA
1 GAAAAAGAGAATGAGAGT
54686255 GAAAAAGA
1 GAAAAAGA
54686263 ATGTGAACAA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.60, C:0.00, G:0.31, T:0.10
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:54686241 original size:36 final size:36
Alignment explanation
Indices: 54686192--54686263 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
54686182 CAAAGAAATG
*
54686192 AAAGAAAAAGAAAAAGAGAGTGAGAGTGAAAAAGAA
1 AAAGAAAAAGAAAAAGAGAGTGAGAGAGAAAAAGAA
* * **
54686228 AAAGAGAATGAAAAAGAGTTTGAGAGAGAAAAAGAA
1 AAAGAAAAAGAAAAAGAGAGTGAGAGAGAAAAAGAA
54686264 TGTGAACAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (36 bp):
AAAGAAAAAGAAAAAGAGAGTGAGAGAGAAAAAGAA
Found at i:54687905 original size:20 final size:20
Alignment explanation
Indices: 54687882--54687929 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
54687872 AGCTCCGTCC
54687882 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
**** *
54687902 AGCTTGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
54687922 AGCTCAAC
1 AGCTCAAC
54687930 CGAGCTTACT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:54692000 original size:13 final size:13
Alignment explanation
Indices: 54691982--54692010 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54691972 GATCACCTTT
54691982 TCGAGATTGATTC
1 TCGAGATTGATTC
54691995 TCGAGATTGATTC
1 TCGAGATTGATTC
54692008 TCG
1 TCG
54692011 GTGGACTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (13 bp):
TCGAGATTGATTC
Found at i:54694486 original size:13 final size:13
Alignment explanation
Indices: 54694468--54694492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54694458 AAAAATTTCG
54694468 AAAAAATTTGAAA
1 AAAAAATTTGAAA
54694481 AAAAAATTTGAA
1 AAAAAATTTGAA
54694493 GTGAAAACTT
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
AAAAAATTTGAAA
Found at i:54700066 original size:30 final size:30
Alignment explanation
Indices: 54700032--54700128 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
54700022 AGCTCACTCC
54700032 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
54700062 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
54700092 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
54700122 TAGCTCA
1 TAGCTCA
54700129 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:54706798 original size:31 final size:29
Alignment explanation
Indices: 54706759--54706844 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 29
54706749 TTCTTTTGTT
* *
54706759 TCAATTTCTTTTTCATCTTCTTTTTCACTC
1 TCAATTTCTTTTTCAT-TTCTTTTTAAATC
*
54706789 TCAAATTTC-TTTTCGTTCTCTTTTTTAAATC
1 TC-AATTTCTTTTTCATT-TC-TTTTTAAATC
*
54706820 TCATTTTCTTTTTCATTTTCTTTTT
1 TCAATTTCTTTTTCA-TTTCTTTTT
54706845 GCTTTTCAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
29 1 0.02
30 20 0.43
31 23 0.50
32 2 0.04
ACGTcount: A:0.14, C:0.21, G:0.01, T:0.64
Consensus pattern (29 bp):
TCAATTTCTTTTTCATTTCTTTTTAAATC
Found at i:54706851 original size:12 final size:12
Alignment explanation
Indices: 54706820--54706844 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54706810 TTTTTAAATC
54706820 TCATTTTCTTTT
1 TCATTTTCTTTT
54706832 TCATTTTCTTTT
1 TCATTTTCTTTT
54706844 T
1 T
54706845 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:54706923 original size:5 final size:5
Alignment explanation
Indices: 54706913--54706969 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
54706903 CTCTTGCCTC
*
54706913 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
54706960 TCTTT TCTTT
1 TCTTT TCTTT
54706970 ATTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:54706953 original size:15 final size:14
Alignment explanation
Indices: 54706913--54706969 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
54706903 CTCTTGCCTC
*
54706913 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
54706928 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
54706943 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
54706960 TCTTTTCTTT
1 TCTTTTCTTT
54706970 ATTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:54706979 original size:21 final size:20
Alignment explanation
Indices: 54706911--54706980 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
54706901 GCCTCTTGCC
54706911 TCTCTTTTCTTTTTATTTCATTT
1 TCTCTTTTC-TTTT-TTT-ATTT
**
54706934 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTT-TTTTTATTT
54706954 T-TCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTT-TTTATTT
54706974 TCTCTTT
1 TCTCTTT
54706981 AAATGTACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 3 0.08
20 17 0.44
21 9 0.23
22 7 0.18
23 3 0.08
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTATTT
Found at i:54710176 original size:40 final size:40
Alignment explanation
Indices: 54710126--54710242 Score: 164
Period size: 39 Copynumber: 3.0 Consensus size: 40
54710116 GTGCATTTGA
54710126 GGTACCAAAGTACAAAAAAGGGCACATATGTGCATTCAGG
1 GGTACCAAAGTACAAAAAAGGGCACATATGTGCATTCAGG
* * * *
54710166 GGTACTAAAGTATAAATAAGGG-ACGTATGTGCATTCAGG
1 GGTACCAAAGTACAAAAAAGGGCACATATGTGCATTCAGG
* * *
54710205 GGTACCAAAGTACAAACAGGGGCACATATGTGTATTCA
1 GGTACCAAAGTACAAAAAAGGGCACATATGTGCATTCA
54710243 TCAATAATTT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
39 34 0.52
40 32 0.48
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (40 bp):
GGTACCAAAGTACAAAAAAGGGCACATATGTGCATTCAGG
Found at i:54716333 original size:15 final size:15
Alignment explanation
Indices: 54716313--54716360 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
54716303 TCAAAGATGG
54716313 GTTTATGGATATAAA
1 GTTTATGGATATAAA
* * **
54716328 GTTTATGTAGATGGA
1 GTTTATGGATATAAA
54716343 -TTTATGGATATAAA
1 GTTTATGGATATAAA
54716357 GTTT
1 GTTT
54716361 TTGTAGGTTT
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATAAA
Found at i:54716339 original size:29 final size:29
Alignment explanation
Indices: 54716307--54716366 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
54716297 AAGGATTCAA
*
54716307 AGATGGGTTTATGGATATAAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
54716336 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
54716365 AG
1 AG
54716367 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.27, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:54729931 original size:10 final size:10
Alignment explanation
Indices: 54729916--54729941 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
54729906 GTATTCGGTC
54729916 ACTTTGTGGA
1 ACTTTGTGGA
54729926 ACTTTGTGGA
1 ACTTTGTGGA
54729936 ACTTTG
1 ACTTTG
54729942 AGCCATCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.27, T:0.42
Consensus pattern (10 bp):
ACTTTGTGGA
Found at i:54730339 original size:10 final size:10
Alignment explanation
Indices: 54730325--54730360 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
54730315 TAAGCTCGGT
54730325 TGAGCTCAAA
1 TGAGCTCAAA
* *
54730335 CGAGCTGAAA
1 TGAGCTCAAA
54730345 TGAGCTCAAA
1 TGAGCTCAAA
54730355 TGAGCT
1 TGAGCT
54730361 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.19
Consensus pattern (10 bp):
TGAGCTCAAA
Found at i:54730359 original size:30 final size:31
Alignment explanation
Indices: 54730302--54730360 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
54730292 TGAAATAAAG
***
54730302 AACGAGCTGAAAATAAGCTCGGTTGAGCTCA
1 AACGAGCTGAAAATAAGCTCAAATGAGCTCA
*
54730333 AACGAGCTG-AAATGAGCTCAAATGAGCT
1 AACGAGCTGAAAATAAGCTCAAATGAGCT
54730361 GAGTTGAGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (31 bp):
AACGAGCTGAAAATAAGCTCAAATGAGCTCA
Found at i:54730368 original size:20 final size:20
Alignment explanation
Indices: 54730323--54730370 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
54730313 AATAAGCTCG
54730323 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
** *
54730343 AATGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
54730363 GTTGAGCT
1 GTTGAGCT
54730371 GGACAGAGCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:54730399 original size:20 final size:20
Alignment explanation
Indices: 54730352--54730400 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
54730342 AAATGAGCTC
54730352 AAATGAGCTGAGTTGAGCTGG
1 AAATGAGCTGAG-TGAGCTGG
*
54730373 ACA-GAGCTCGAG-GAGCTGG
1 AAATGAGCT-GAGTGAGCTGG
54730392 AAATGAGCT
1 AAATGAGCT
54730401 AGGATCAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 9 0.38
20 10 0.42
21 5 0.21
ACGTcount: A:0.31, C:0.14, G:0.37, T:0.18
Consensus pattern (20 bp):
AAATGAGCTGAGTGAGCTGG
Found at i:54731751 original size:22 final size:21
Alignment explanation
Indices: 54731718--54731759 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
54731708 TCAAACCTAC
54731718 ACAAGCATGCAAAATTTACACA
1 ACAAGCATGCAAAA-TTACACA
*
54731740 ACAAGGCA-GCAACATTACAC
1 ACAA-GCATGCAAAATTACAC
54731760 CACTATCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 9 0.50
23 3 0.17
ACGTcount: A:0.48, C:0.26, G:0.12, T:0.14
Consensus pattern (21 bp):
ACAAGCATGCAAAATTACACA
Found at i:54732371 original size:6 final size:6
Alignment explanation
Indices: 54732350--54732422 Score: 56
Period size: 6 Copynumber: 11.5 Consensus size: 6
54732340 CTCGATCTCT
* * ** **
54732350 TTTTTC CTTCTC TTTTTC TTTTTC ACTTTC TTTTTC AATTTC ATTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC
54732399 TTTTTC TTATTCTC TTTTTGC TTT
1 TTTTTC TT-TT-TC TTTTT-C TTT
54732423 CTTTCACACT
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
6 35 0.69
7 12 0.24
8 4 0.08
ACGTcount: A:0.07, C:0.21, G:0.01, T:0.71
Consensus pattern (6 bp):
TTTTTC
Found at i:54732371 original size:18 final size:18
Alignment explanation
Indices: 54732350--54732406 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
54732340 CTCGATCTCT
54732350 TTTTTC-CTTCTCTTTTTC
1 TTTTTCACTT-TCTTTTTC
54732368 TTTTTCACTTTCTTTTTC
1 TTTTTCACTTTCTTTTTC
** *
54732386 AATTTCATTTTTCTTTTTC
1 TTTTTCA-CTTTCTTTTTC
54732405 TT
1 TT
54732407 ATTCTCTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 19 0.59
19 13 0.41
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTCACTTTCTTTTTC
Found at i:54732441 original size:35 final size:34
Alignment explanation
Indices: 54732397--54732462 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
54732387 ATTTCATTTT
54732397 TCTTTTTCTTATTCTCT-TTTTGCTTTCTTTCACAC
1 TCTTTTTCTT-TTCTCTCTTTTG-TTTCTTTCACAC
* *
54732432 TCTTTTTCTTTTGTTTCTTTTGTTTCTTTCA
1 TCTTTTTCTTTTCTCTCTTTTGTTTCTTTCA
54732463 AATTCTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 13 0.46
35 15 0.54
ACGTcount: A:0.06, C:0.21, G:0.05, T:0.68
Consensus pattern (34 bp):
TCTTTTTCTTTTCTCTCTTTTGTTTCTTTCACAC
Found at i:54732450 original size:9 final size:9
Alignment explanation
Indices: 54732436--54732460 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
54732426 TCACACTCTT
54732436 TTTCTTTTG
1 TTTCTTTTG
54732445 TTTCTTTTG
1 TTTCTTTTG
54732454 TTTCTTT
1 TTTCTTT
54732461 CAAATTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (9 bp):
TTTCTTTTG
Found at i:54732470 original size:34 final size:35
Alignment explanation
Indices: 54732396--54732470 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 35
54732386 AATTTCATTT
*
54732396 TTCTTTTTCTTATTCTCTTTTTGCTTTCTTTCACA
1 TTCTTTTTCTTATTCTCTTTTTGCTTTCTTTCAAA
* * *
54732431 CTCTTTTTCTT-TTGTTTCTTTTG-TTTCTTTCAAA
1 TTCTTTTTCTTATTCTCT-TTTTGCTTTCTTTCAAA
54732465 TTCTTT
1 TTCTTT
54732471 CTCACTTGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
34 19 0.56
35 15 0.44
ACGTcount: A:0.08, C:0.20, G:0.04, T:0.68
Consensus pattern (35 bp):
TTCTTTTTCTTATTCTCTTTTTGCTTTCTTTCAAA
Found at i:54734545 original size:10 final size:10
Alignment explanation
Indices: 54734530--54734555 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
54734520 GTATTCGGTC
54734530 ACTTTGTGGA
1 ACTTTGTGGA
54734540 ACTTTGTGGA
1 ACTTTGTGGA
54734550 ACTTTG
1 ACTTTG
54734556 AGCCATCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.27, T:0.42
Consensus pattern (10 bp):
ACTTTGTGGA
Found at i:54737479 original size:46 final size:46
Alignment explanation
Indices: 54737412--54737505 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
54737402 ATGCTCATGT
54737412 CAATTTCTTAAGCAATAAATATCATAGAATATACTCACATCATTAC
1 CAATTTCTTAAGCAATAAATATCATAGAATATACTCACATCATTAC
*
54737458 CAATTTCTTAAGCAATAAATATCATAGAATTTACTCACATCATTAC
1 CAATTTCTTAAGCAATAAATATCATAGAATATACTCACATCATTAC
54737504 CA
1 CA
54737506 CATACTTGTC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33
Consensus pattern (46 bp):
CAATTTCTTAAGCAATAAATATCATAGAATATACTCACATCATTAC
Found at i:54741030 original size:30 final size:31
Alignment explanation
Indices: 54740996--54741092 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
54740986 AGCTCACTCC
*
54740996 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
54741026 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
54741056 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
54741086 TAGCTCA
1 TAGCTCA
54741093 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Done.