Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 94 of 163
Found at i:30104325 original size:42 final size:43
Alignment explanation
Indices: 30104222--30104362 Score: 230
Period size: 43 Copynumber: 3.3 Consensus size: 43
30104212 TGTTTTTAAA
*
30104222 AAAAGCGCCGCTAAAGGTCATGGTTTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
* * * *
30104265 AAAAGCGTCGCAAAAGGTCTTGATCTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
30104308 -AAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
30104350 AAAAGCGCCGCTA
1 AAAAGCGCCGCTA
30104363 GGAGCCTGTT
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 38 0.43
43 50 0.57
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
Found at i:30105553 original size:29 final size:30
Alignment explanation
Indices: 30105496--30105553 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
30105486 GCTGGACCAT
* * *
30105496 TCCATACGGCTTGCACACACGATCGTGTGA
1 TCCACACGGCTTGCACACACGACCATGTGA
*
30105526 TCCACACGGGTTGC-CACACGACCATGTG
1 TCCACACGGCTTGCACACACGACCATGTG
30105554 GCAGACCGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.22, C:0.33, G:0.24, T:0.21
Consensus pattern (30 bp):
TCCACACGGCTTGCACACACGACCATGTGA
Found at i:30106675 original size:25 final size:25
Alignment explanation
Indices: 30106629--30106676 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
30106619 ATTTAACCAT
* * *
30106629 TTTTTATTTTATTTTAATATTCTTG
1 TTTTAATTTAATTTTAACATTCTTG
*
30106654 TTTTAATTTAATTTTTACATTCT
1 TTTTAATTTAATTTTAACATTCT
30106677 AATTTTTTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTTAATTTAATTTTAACATTCTTG
Found at i:30113496 original size:8 final size:8
Alignment explanation
Indices: 30113473--30113513 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
30113463 AAATAGTGAT
*
30113473 AAAAAAGA
1 AAAAAATA
*
30113481 AAATAATA
1 AAAAAATA
30113489 AAAAAATA
1 AAAAAATA
30113497 AAAAAAGTA
1 AAAAAA-TA
30113506 AAAAAATA
1 AAAAAATA
30113514 GTAGGTTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 21 0.72
9 8 0.28
ACGTcount: A:0.83, C:0.00, G:0.05, T:0.12
Consensus pattern (8 bp):
AAAAAATA
Found at i:30114284 original size:8 final size:8
Alignment explanation
Indices: 30114261--30114301 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
30114251 AAATAGTGAT
*
30114261 AAAAAAGA
1 AAAAAATA
*
30114269 AAATAATA
1 AAAAAATA
30114277 AAAAAATA
1 AAAAAATA
30114285 AAAAAAGTA
1 AAAAAA-TA
30114294 AAAAAATA
1 AAAAAATA
30114302 GTAGGTTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 21 0.72
9 8 0.28
ACGTcount: A:0.83, C:0.00, G:0.05, T:0.12
Consensus pattern (8 bp):
AAAAAATA
Found at i:30118596 original size:42 final size:42
Alignment explanation
Indices: 30118534--30118652 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
30118524 AGGAGCATAA
* * * * * * *
30118534 TCACTTAAGCTCGCATGGGGAGCTTCACTGGTGCATAGCTTG
1 TCACTTAAACTCTCGTGGGGAGCTTCACTGATACACAACTTG
* * * **
30118576 TCATTTAAATTCTTGTGGGGAGCTTCGTTGATACACAACTTG
1 TCACTTAAACTCTCGTGGGGAGCTTCACTGATACACAACTTG
*
30118618 TCACTTAAGCTCTCGTGGGGAGCTTCACTGATACA
1 TCACTTAAACTCTCGTGGGGAGCTTCACTGATACA
30118653 TGATCTATCA
Statistics
Matches: 59, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (42 bp):
TCACTTAAACTCTCGTGGGGAGCTTCACTGATACACAACTTG
Found at i:30124024 original size:12 final size:12
Alignment explanation
Indices: 30124005--30124034 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
30123995 CCTCACACAC
30124005 CCGTGTGCTAGG
1 CCGTGTGCTAGG
*
30124017 CTGTGTGCTAGG
1 CCGTGTGCTAGG
30124029 CCGTGT
1 CCGTGT
30124035 AAAAGCCTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.23, G:0.40, T:0.30
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:30125339 original size:24 final size:24
Alignment explanation
Indices: 30125263--30125341 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 24
30125253 TAGTCTCACA
30125263 AGCTAGAAATCGGTAAGCTCATATG
1 AGCT-GAAATCGGTAAGCTCATATG
* * *
30125288 AGTTGAGAATCAGTAAGCTC-TCACG
1 AGCTGA-AATCGGTAAGCTCAT-ATG
30125313 AGCTGAAATCGGTAAGCTCATATG
1 AGCTGAAATCGGTAAGCTCATATG
30125337 AGCTG
1 AGCTG
30125342 TGGTGTGTCC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
24 22 0.49
25 23 0.51
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (24 bp):
AGCTGAAATCGGTAAGCTCATATG
Found at i:30130907 original size:27 final size:27
Alignment explanation
Indices: 30130847--30130944 Score: 126
Period size: 27 Copynumber: 3.6 Consensus size: 27
30130837 ATACATAAAA
*
30130847 AAATGAAAGCCTTTGTGGC-GTATTTATG
1 AAATGGAAGCCTTTGTGGCAG--TTTATG
*
30130875 AAATGGAAGCCTTTGTGGCAGTTTATT
1 AAATGGAAGCCTTTGTGGCAGTTTATG
***
30130902 AAATGGAAGCCTTTGTGGCAACCTATG
1 AAATGGAAGCCTTTGTGGCAGTTTATG
30130929 AAATGGAAGCCTTTGT
1 AAATGGAAGCCTTTGT
30130945 AAAGGAACAC
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 44 0.70
28 18 0.29
29 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.33
Consensus pattern (27 bp):
AAATGGAAGCCTTTGTGGCAGTTTATG
Found at i:30146137 original size:21 final size:21
Alignment explanation
Indices: 30146111--30146167 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
30146101 TGAAGAGTGT
* * *
30146111 TGTGGATGCGTCTGATTTTGG
1 TGTGGATGCATCTGACTTTGC
*
30146132 TGTGGATGCATCTGGCTTTGC
1 TGTGGATGCATCTGACTTTGC
30146153 TGTGGATGCATCTGA
1 TGTGGATGCATCTGA
30146168 GTGTGTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.12, C:0.14, G:0.35, T:0.39
Consensus pattern (21 bp):
TGTGGATGCATCTGACTTTGC
Found at i:30153965 original size:19 final size:20
Alignment explanation
Indices: 30153938--30153976 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
30153928 TAAAATTTCT
* *
30153938 ATATGTTTA-AAATTATTAA
1 ATATCTTTATAAATAATTAA
30153957 ATATCTTTATAAATAATTAA
1 ATATCTTTATAAATAATTAA
30153977 TTGAAGATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (20 bp):
ATATCTTTATAAATAATTAA
Found at i:30154369 original size:24 final size:23
Alignment explanation
Indices: 30154341--30154386 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
30154331 TAGAACATAT
*
30154341 AATAAGATTGTTAAAAATATTTAA
1 AATAAGATTG-AAAAAATATTTAA
*
30154365 AATAATATTGAAAAAATATTTA
1 AATAAGATTGAAAAAATATTTA
30154387 GTTTATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (23 bp):
AATAAGATTGAAAAAATATTTAA
Found at i:30154373 original size:12 final size:11
Alignment explanation
Indices: 30154353--30154386 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
30154343 TAAGATTGTT
30154353 AAAAATATTTA
1 AAAAATATTTA
*
30154364 AAATAATATTGA
1 AAA-AATATTTA
30154376 AAAAATATTTA
1 AAAAATATTTA
30154387 GTTTATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (11 bp):
AAAAATATTTA
Found at i:30154437 original size:28 final size:28
Alignment explanation
Indices: 30154406--30154491 Score: 88
Period size: 28 Copynumber: 3.0 Consensus size: 28
30154396 AAAATTTATC
*
30154406 AAAAATTATCAATTTTAAAAATATATTT
1 AAAAAATATCAATTTTAAAAATATATTT
30154434 AAAAAAATAT-AA-TTTAAAACATAT-TTT
1 -AAAAAATATCAATTTTAAAA-ATATATTT
**
30154461 AAAACCTATCAATTTTAAAGAATATAATTT
1 AAAAAATATCAATTTTAAA-AATAT-ATTT
30154491 A
1 A
30154492 TTAAGGAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
26 7 0.15
27 12 0.25
28 16 0.33
29 9 0.19
30 4 0.08
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (28 bp):
AAAAAATATCAATTTTAAAAATATATTT
Found at i:30154440 original size:15 final size:15
Alignment explanation
Indices: 30154422--30154452 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
30154412 TATCAATTTT
30154422 AAAAATAT-ATTTAA
1 AAAAATATAATTTAA
30154436 AAAAATATAATTTAA
1 AAAAATATAATTTAA
30154451 AA
1 AA
30154453 CATATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAAATATAATTTAA
Found at i:30154441 original size:14 final size:14
Alignment explanation
Indices: 30154422--30154464 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
30154412 TATCAATTTT
30154422 AAAAATATATTTAA
1 AAAAATATATTTAA
30154436 AAAAATATAATTT-A
1 AAAAATAT-ATTTAA
*
30154450 AAACATAT-TTTAA
1 AAAAATATATTTAA
30154463 AA
1 AA
30154465 CCTATCAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 3 0.12
13 3 0.12
14 16 0.62
15 4 0.15
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAAATATATTTAA
Found at i:30154907 original size:22 final size:22
Alignment explanation
Indices: 30154882--30154924 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
30154872 AAAAAAATAA
* *
30154882 CAAAATAAAAAACCTGAAAATG
1 CAAAAAAAAAAAACTGAAAATG
*
30154904 CAAAAAAAAAAAAGTGAAAAT
1 CAAAAAAAAAAAACTGAAAAT
30154925 CTTTTATTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.12
Consensus pattern (22 bp):
CAAAAAAAAAAAACTGAAAATG
Found at i:30157949 original size:74 final size:74
Alignment explanation
Indices: 30157828--30157976 Score: 253
Period size: 74 Copynumber: 2.0 Consensus size: 74
30157818 ATTTAATTTT
* *
30157828 ATAAATTAAGAGCATTCTTAACCACACAAATTTTGGTTGACTTTTACCAACCTTGTTTTTAAATT
1 ATAAATTAAGAGCAATCTTAACCACACAAATTTTGGTTGACTTTTACCAACCTTATTTTTAAATT
30157893 GAATAAAAA
66 GAATAAAAA
* * *
30157902 ATAAATTAGGAGCAATCTTGACCACACAAATTTTGGTTGACTTTTACCAACTTTATTTTTAAATT
1 ATAAATTAAGAGCAATCTTAACCACACAAATTTTGGTTGACTTTTACCAACCTTATTTTTAAATT
30157967 GAATAAAAA
66 GAATAAAAA
30157976 A
1 A
30157977 GAAAAAGAGA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (74 bp):
ATAAATTAAGAGCAATCTTAACCACACAAATTTTGGTTGACTTTTACCAACCTTATTTTTAAATT
GAATAAAAA
Found at i:30173812 original size:69 final size:69
Alignment explanation
Indices: 30173718--30173869 Score: 200
Period size: 69 Copynumber: 2.2 Consensus size: 69
30173708 CGACCTATTA
* * * * *
30173718 TCTTACACCTCGTAATCCCTATGTTTAATGTCTTGGTGGACTATATTGGTTGCCATAG-CTGAGC
1 TCTTACACCTTGTAATCCCTATGTTTAATGTCCTGGCGGACTATATTGGTTGACATAGTC-AAGC
*
30173782 TATGG
65 TACGG
*
30173787 TCTTACACCTTGTAATGCCC-ATGTTTAATGTCCTGGCGGACTCTATTGGTTGACATAGTCAAGC
1 TCTTACACCTTGTAAT-CCCTATGTTTAATGTCCTGGCGGACTATATTGGTTGACATAGTCAAGC
30173851 TACGG
65 TACGG
*
30173856 TCTTACACCCTGTA
1 TCTTACACCTTGTA
30173870 CCTTTATTGA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
69 69 0.95
70 4 0.05
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (69 bp):
TCTTACACCTTGTAATCCCTATGTTTAATGTCCTGGCGGACTATATTGGTTGACATAGTCAAGCT
ACGG
Found at i:30176502 original size:25 final size:25
Alignment explanation
Indices: 30176474--30176556 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
30176464 CTATAATTCA
* *
30176474 CCACAATGGCATTACAGATAACTCG
1 CCACAAAGGCTTTACAGATAACTCG
*** * *
30176499 CCACAAAGGCTTTTTTGATAATTCA
1 CCACAAAGGCTTTACAGATAACTCG
*
30176524 CCACAAAGGCTTTACAGATAACTTG
1 CCACAAAGGCTTTACAGATAACTCG
30176549 CCACAAAG
1 CCACAAAG
30176557 CCTTGGATTG
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.24
Consensus pattern (25 bp):
CCACAAAGGCTTTACAGATAACTCG
Found at i:30177452 original size:33 final size:33
Alignment explanation
Indices: 30177410--30177475 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
30177400 AATCATTCTC
30177410 AGCTCTATCTTAACGAAGAAGAAAAGAACATTT
1 AGCTCTATCTTAACGAAGAAGAAAAGAACATTT
*
30177443 AGCTCTATCTTAACGAATAAGAAAAGAACATTT
1 AGCTCTATCTTAACGAAGAAGAAAAGAACATTT
30177476 CAATGGATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (33 bp):
AGCTCTATCTTAACGAAGAAGAAAAGAACATTT
Found at i:30184542 original size:18 final size:18
Alignment explanation
Indices: 30184505--30184542 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
30184495 TAAATGATGA
30184505 ATTTAAAATATTAGTTGTT
1 ATTTAAAATATTA-TTGTT
30184524 ATTTAAAAATATT-TTGTT
1 ATTT-AAAATATTATTGTT
30184542 A
1 A
30184543 AGCGATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (18 bp):
ATTTAAAATATTATTGTT
Found at i:30185177 original size:20 final size:20
Alignment explanation
Indices: 30185160--30185388 Score: 100
Period size: 20 Copynumber: 11.4 Consensus size: 20
30185150 GAAGTGCCAT
30185160 TGTTTGCACATCAGTGCCCC
1 TGTTTGCACATCAGTGCCCC
* * * *
30185180 TGTTTGTACTTCAATACCCC
1 TGTTTGCACATCAGTGCCCC
* *
30185200 TATTTGCACATCAGTGCCCT
1 TGTTTGCACATCAGTGCCCC
* * * * *
30185220 TGATTGTACTTC-GATACCAC
1 TGTTTGCACATCAG-TGCCCC
30185240 TGTTTGCACATCAGTGCCCC
1 TGTTTGCACATCAGTGCCCC
** ** * ** * *
30185260 TAATTATACTTTGGTACACC
1 TGTTTGCACATCAGTGCCCC
* * *
30185280 TATTTGCACATAAATGCCCC
1 TGTTTGCACATCAGTGCCCC
** * * * *
30185300 TAATTGTACTTCGGTACCCC
1 TGTTTGCACATCAGTGCCCC
30185320 TGTTTGCACATCAGTGCCCC
1 TGTTTGCACATCAGTGCCCC
* * * *
30185340 TGTTTGAACTTCGGTTCCCC
1 TGTTTGCACATCAGTGCCCC
*** *
30185360 TAAATGCACATCTGTGCCCC
1 TGTTTGCACATCAGTGCCCC
*
30185380 TATTTGCAC
1 TGTTTGCAC
30185389 TTTGGTGCCC
Statistics
Matches: 141, Mismatches: 66, Indels: 4
0.67 0.31 0.02
Matches are distributed among these distances:
19 1 0.01
20 139 0.99
21 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.15, T:0.34
Consensus pattern (20 bp):
TGTTTGCACATCAGTGCCCC
Found at i:30185217 original size:40 final size:40
Alignment explanation
Indices: 30185162--30185400 Score: 244
Period size: 40 Copynumber: 6.0 Consensus size: 40
30185152 AGTGCCATTG
** **
30185162 TTTGCACATCAGTGCCCCTGTTTGTACTTCAATACCCCTA
1 TTTGCACATCAGTGCCCCTAATTGTACTTCGGTACCCCTA
* * * * *
30185202 TTTGCACATCAGTGCCCTTGATTGTACTTCGATACCACTG
1 TTTGCACATCAGTGCCCCTAATTGTACTTCGGTACCCCTA
* * *
30185242 TTTGCACATCAGTGCCCCTAATTATACTTTGGTACACCTA
1 TTTGCACATCAGTGCCCCTAATTGTACTTCGGTACCCCTA
* * *
30185282 TTTGCACATAAATGCCCCTAATTGTACTTCGGTACCCCTG
1 TTTGCACATCAGTGCCCCTAATTGTACTTCGGTACCCCTA
** * *
30185322 TTTGCACATCAGTGCCCCTGTTTGAACTTCGGTTCCCCTA
1 TTTGCACATCAGTGCCCCTAATTGTACTTCGGTACCCCTA
** * * * * *
30185362 AATGCACATCTGTGCCCCTATTTGCACTTTGGTGCCCCT
1 TTTGCACATCAGTGCCCCTAATTGTACTTCGGTACCCCT
30185401 GATCGCACAT
Statistics
Matches: 166, Mismatches: 33, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 166 1.00
ACGTcount: A:0.20, C:0.31, G:0.15, T:0.34
Consensus pattern (40 bp):
TTTGCACATCAGTGCCCCTAATTGTACTTCGGTACCCCTA
Found at i:30185378 original size:80 final size:80
Alignment explanation
Indices: 30185160--30185410 Score: 279
Period size: 80 Copynumber: 3.1 Consensus size: 80
30185150 GAAGTGCCAT
* ** * *
30185160 TGTTTGCACATCAGTGCCCCTGTTTGTACTTCAATACCCCTATTTGCACATCAGTGCCCTTGATT
1 TGTTTGCACATCAGTGCCCCTGTTTGAACTTCGGTACCCCTATTTGCACATCAGTGCCCCTAATT
* *
30185225 GTACTTCGATACCAC
66 GTACTTCGGTACCCC
** * * * *
30185240 TGTTTGCACATCAGTGCCCCTAATT-ATACTTTGGTACACCTATTTGCACATAAATGCCCCTAAT
1 TGTTTGCACATCAGTGCCCCTGTTTGA-ACTTCGGTACCCCTATTTGCACATCAGTGCCCCTAAT
30185304 TGTACTTCGGTACCCC
65 TGTACTTCGGTACCCC
* ** * *
30185320 TGTTTGCACATCAGTGCCCCTGTTTGAACTTCGGTTCCCCTAAATGCACATCTGTGCCCCTATTT
1 TGTTTGCACATCAGTGCCCCTGTTTGAACTTCGGTACCCCTATTTGCACATCAGTGCCCCTAATT
* * *
30185385 GCACTTTGGTGCCCC
66 GTACTTCGGTACCCC
* *
30185400 TGATCGCACAT
1 TGTTTGCACAT
30185411 TCGTGCTCTT
Statistics
Matches: 140, Mismatches: 29, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
80 139 0.99
81 1 0.01
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (80 bp):
TGTTTGCACATCAGTGCCCCTGTTTGAACTTCGGTACCCCTATTTGCACATCAGTGCCCCTAATT
GTACTTCGGTACCCC
Found at i:30185391 original size:120 final size:120
Alignment explanation
Indices: 30185162--30185394 Score: 286
Period size: 120 Copynumber: 1.9 Consensus size: 120
30185152 AGTGCCATTG
* * ** * *
30185162 TTTGCACATCAGTGCCCCTGTTTGTACTTCAATACCCCTATTTGCACATCAGTGCCCTTGATTGT
1 TTTGCACATAAATGCCCCTAATTGTACTTCAATACCCCTATTTGCACATCAGTGCCCCTGATTGA
*** *
30185227 ACTTCGATACCACTGTTTGCACATCAGTGCCCCTAATTATACTTTGGTACACCTA
66 ACTTCGATACCACTAAATGCACATCAGTGCCCCTAATTACACTTTGGTACACCTA
** * *
30185282 TTTGCACATAAATGCCCCTAATTGTACTTCGGTACCCCTGTTTGCACATCAGTGCCCCTGTTTGA
1 TTTGCACATAAATGCCCCTAATTGTACTTCAATACCCCTATTTGCACATCAGTGCCCCTGATTGA
* * * * * *
30185347 ACTTCGGTTCCCCTAAATGCACATCTGTGCCCCTATTTGCACTTTGGT
66 ACTTCGATACCACTAAATGCACATCAGTGCCCCTAATTACACTTTGGT
30185395 GCCCCTGATC
Statistics
Matches: 93, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
120 93 1.00
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.35
Consensus pattern (120 bp):
TTTGCACATAAATGCCCCTAATTGTACTTCAATACCCCTATTTGCACATCAGTGCCCCTGATTGA
ACTTCGATACCACTAAATGCACATCAGTGCCCCTAATTACACTTTGGTACACCTA
Found at i:30185396 original size:20 final size:20
Alignment explanation
Indices: 30185253--30185458 Score: 90
Period size: 20 Copynumber: 10.3 Consensus size: 20
30185243 TTGCACATCA
**
30185253 GTGCCCCTAATTATACTTTG
1 GTGCCCCTAATTGCACTTTG
* * * * **
30185273 GTACACCTATTTGCACATAA
1 GTGCCCCTAATTGCACTTTG
* * *
30185293 ATGCCCCTAATTGTACTTCG
1 GTGCCCCTAATTGCACTTTG
* ** * **
30185313 GTACCCCTGTTTGCACATCA
1 GTGCCCCTAATTGCACTTTG
** * *
30185333 GTGCCCCTGTTTGAACTTCG
1 GTGCCCCTAATTGCACTTTG
* * *
30185353 GTTCCCCTAAATGCACATCT-
1 GTGCCCCTAATTGCAC-TTTG
*
30185373 GTGCCCCTATTTGCACTTTG
1 GTGCCCCTAATTGCACTTTG
* * * *
30185393 GTGCCCCTGATCGCACATTC
1 GTGCCCCTAATTGCACTTTG
* * *
30185413 GTGCTCTTGATTGCACTTTG
1 GTGCCCCTAATTGCACTTTG
* *
30185433 GTGCTCCTAATTGCATTTTG
1 GTGCCCCTAATTGCACTTTG
30185453 GTGCCC
1 GTGCCC
30185459 TGTTATGCAT
Statistics
Matches: 132, Mismatches: 52, Indels: 4
0.70 0.28 0.02
Matches are distributed among these distances:
19 2 0.02
20 129 0.98
21 1 0.01
ACGTcount: A:0.17, C:0.30, G:0.18, T:0.35
Consensus pattern (20 bp):
GTGCCCCTAATTGCACTTTG
Found at i:30191065 original size:6 final size:6
Alignment explanation
Indices: 30191044--30191089 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
30191034 TTAATAAAAC
*
30191044 AAAATA AACGAATA AAAATA AAAATA AAAATA AAAA-C AAAATA AAA
1 AAAATA AA--AATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
30191090 TTTAAAACAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 4 0.11
6 25 0.71
8 6 0.17
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:30191098 original size:17 final size:17
Alignment explanation
Indices: 30191039--30191089 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 17
30191029 TAAGATTAAT
30191039 AAAACAAAATAAACGAATA
1 AAAACAAAATAAA--AATA
*
30191058 AAAATAAAAATAAAAATA
1 AAAA-CAAAATAAAAATA
30191076 AAAACAAAATAAAA
1 AAAACAAAATAAAA
30191090 TTTAAAACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 9 0.31
18 8 0.28
19 4 0.14
20 8 0.28
ACGTcount: A:0.80, C:0.06, G:0.02, T:0.12
Consensus pattern (17 bp):
AAAACAAAATAAAAATA
Found at i:30197457 original size:16 final size:15
Alignment explanation
Indices: 30197433--30197462 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
30197423 TTTATTATTA
30197433 TTTTTTTCTTTTTTC
1 TTTTTTTCTTTTTTC
30197448 TTTTTCTTCTTTTTT
1 TTTTT-TTCTTTTTT
30197463 TTCTTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTTTCTTTTTTC
Found at i:30203474 original size:31 final size:31
Alignment explanation
Indices: 30203432--30203493 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
30203422 TATATAGCCA
*
30203432 AAGTTTGCACGGTATCTTAGTCCATATTAGC
1 AAGTTTCCACGGTATCTTAGTCCATATTAGC
*
30203463 AAGTTTCCACGGTCTCTTAGTCCATATTAGC
1 AAGTTTCCACGGTATCTTAGTCCATATTAGC
30203494 CAATCACTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (31 bp):
AAGTTTCCACGGTATCTTAGTCCATATTAGC
Found at i:30205830 original size:38 final size:39
Alignment explanation
Indices: 30205782--30205891 Score: 100
Period size: 38 Copynumber: 2.8 Consensus size: 39
30205772 TCGGATAGTT
* *
30205782 CGAAGCAAAGTTGACACCCAGTGTCTCATC-AGCCTAGT-
1 CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTA-TC
* * * * *
30205820 CGTAGTAAAGTT-ATACCCAATATCTCATCGAATCTATC
1 CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTATC
*
30205858 CGAAGTAAAATAGTGACACCCAGTGTCTCATCGA
1 CGAAGTAAAGT--TGACACCCAGTGTCTCATCGA
30205892 CTCGAGGTCG
Statistics
Matches: 55, Mismatches: 12, Indels: 7
0.74 0.16 0.09
Matches are distributed among these distances:
37 15 0.27
38 23 0.42
40 1 0.02
41 16 0.29
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (39 bp):
CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTATC
Found at i:30206029 original size:18 final size:17
Alignment explanation
Indices: 30205983--30206036 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 17
30205973 TTTCCAATTC
30205983 TCAATTCAAATTCACTT
1 TCAATTCAAATTCACTT
* *
30206000 TCATTTCAAAATTTACTT
1 TCAATTC-AAATTCACTT
30206018 TCAATATCAAATTCACTT
1 TCAAT-TCAAATTCACTT
30206036 T
1 T
30206037 TTCATTCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 6 0.19
18 23 0.74
19 2 0.06
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.44
Consensus pattern (17 bp):
TCAATTCAAATTCACTT
Found at i:30207945 original size:30 final size:30
Alignment explanation
Indices: 30207878--30207956 Score: 79
Period size: 33 Copynumber: 2.5 Consensus size: 30
30207868 GCTTATATAC
*
30207878 TAAATATAATAAAATAATAATAATATCTCAT
1 TAAATATAATAAAATAATAAT-ATATCTAAT
* *
30207909 TAAAATATTATTAAAATAATACT-TATCTAAT
1 T-AAATA-TAATAAAATAATAATATATCTAAT
*
30207940 TAAATAATCATAAAATA
1 TAAAT-ATAATAAAATA
30207957 TTATCAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
30 12 0.30
31 10 0.25
32 5 0.12
33 13 0.32
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (30 bp):
TAAATATAATAAAATAATAATATATCTAAT
Found at i:30208971 original size:17 final size:17
Alignment explanation
Indices: 30208941--30208978 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
30208931 ACATGAAATT
30208941 TAATCATTTTATTGAAA
1 TAATCATTTTATTGAAA
*
30208958 TAAT-ATTTTAATTGAGA
1 TAATCATTTT-ATTGAAA
30208975 TAAT
1 TAAT
30208979 TTTCATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (17 bp):
TAATCATTTTATTGAAA
Found at i:30209311 original size:31 final size:29
Alignment explanation
Indices: 30209275--30209346 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 29
30209265 GATTAAATCA
*
30209275 AAATTAAAGTTTTA-TGTATACATTTGAACC
1 AAATTAAAGTTTCACTGTATA-A-TTGAACC
* *
30209305 ACAATTAGAGTTTCACGTGTATAATTGCACC
1 A-AATTAAAGTTTCAC-TGTATAATTGAACC
30209336 AAATTAAAGTT
1 AAATTAAAGTT
30209347 CTTCTATACA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 10 0.29
31 18 0.51
32 1 0.03
33 6 0.17
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (29 bp):
AAATTAAAGTTTCACTGTATAATTGAACC
Found at i:30209549 original size:16 final size:17
Alignment explanation
Indices: 30209512--30209555 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
30209502 TCTAGAAACT
30209512 TGGTTGTTATAGCGAAA
1 TGGTTGTTATAGCGAAA
**
30209529 T-GTTGTTATAGC-ATG
1 TGGTTGTTATAGCGAAA
30209544 TGGTTGTTATAG
1 TGGTTGTTATAG
30209556 AGAGGGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 21 0.88
17 1 0.04
ACGTcount: A:0.23, C:0.05, G:0.30, T:0.43
Consensus pattern (17 bp):
TGGTTGTTATAGCGAAA
Found at i:30211643 original size:113 final size:113
Alignment explanation
Indices: 30211445--30211674 Score: 433
Period size: 113 Copynumber: 2.0 Consensus size: 113
30211435 CATTTGTTTA
*
30211445 GTAAAAGAAGATCAGCGGAAGGGGACTATACCAGAGCTATATCTGCGAGTGAGCTACTTGTCTAT
1 GTAAAAGAAGATCAGCGGAAGGGGACTATACCAGAGCTATATCGGCGAGTGAGCTACTTGTCTAT
30211510 TTTTGTATCATGCATGGCTATTTGGCGAATGACATATACAAACGTATT
66 TTTTGTATCATGCATGGCTATTTGGCGAATGACATATACAAACGTATT
*
30211558 GTAAAAGAATATCAGCGGAAGGGGACTATACCAGAGCTATATCGGCGAGTGAGCTACTTGTCTAT
1 GTAAAAGAAGATCAGCGGAAGGGGACTATACCAGAGCTATATCGGCGAGTGAGCTACTTGTCTAT
*
30211623 TTTTGTATCATGCATGGCTATTTGGCGAATGACATATACAAACGTCTT
66 TTTTGTATCATGCATGGCTATTTGGCGAATGACATATACAAACGTATT
30211671 GTAA
1 GTAA
30211675 TTAACTTTTG
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 114 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (113 bp):
GTAAAAGAAGATCAGCGGAAGGGGACTATACCAGAGCTATATCGGCGAGTGAGCTACTTGTCTAT
TTTTGTATCATGCATGGCTATTTGGCGAATGACATATACAAACGTATT
Found at i:30212756 original size:20 final size:20
Alignment explanation
Indices: 30212731--30212774 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
30212721 AAATATCATT
30212731 AAACCGTTTACTGATAACGG
1 AAACCGTTTACTGATAACGG
*
30212751 AAACCGTTTACTGGTAACGG
1 AAACCGTTTACTGATAACGG
30212771 AAAC
1 AAAC
30212775 AATGATTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
AAACCGTTTACTGATAACGG
Found at i:30213813 original size:3 final size:3
Alignment explanation
Indices: 30213805--30213843 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
30213795 GGAAAGAAAG
*
30213805 GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA -AA GAGA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA
30213844 AATAAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:30218818 original size:81 final size:82
Alignment explanation
Indices: 30218725--30218888 Score: 312
Period size: 81 Copynumber: 2.0 Consensus size: 82
30218715 TATAGATTGA
30218725 TATAATGATAGAAATATTTTATATGTATTATAAATATAATTATATTAATAAATTTATTTTTTTAT
1 TATAATGATAGAAATATTTTATATGTATTATAAATATAATTATATTAATAAATTTATTTTTTTAT
30218790 TGTT-AATATTAATAAT
66 TGTTAAATATTAATAAT
30218806 TATAATGATAGAAATATTTTATATGTATTATAAATATAATTATATTAATAAATTTATTTTTTTAT
1 TATAATGATAGAAATATTTTATATGTATTATAAATATAATTATATTAATAAATTTATTTTTTTAT
30218871 TGTTAAAATATTAATAAT
66 TGTT-AAATATTAATAAT
30218889 ACAAGAAATT
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
81 69 0.85
83 12 0.15
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (82 bp):
TATAATGATAGAAATATTTTATATGTATTATAAATATAATTATATTAATAAATTTATTTTTTTAT
TGTTAAATATTAATAAT
Found at i:30219930 original size:3 final size:3
Alignment explanation
Indices: 30219922--30219957 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
30219912 ATTAAGGGGA
30219922 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
30219958 TTGAGTTAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:30239799 original size:24 final size:24
Alignment explanation
Indices: 30239700--30239814 Score: 85
Period size: 24 Copynumber: 4.8 Consensus size: 24
30239690 GCTCTTCTTG
* * *
30239700 AGCTTCTCGTTAATGGCTCTCCGG
1 AGCTTCCCGTTAATGGCTCTTCGA
*
30239724 AGCTTCCCGAT-ATGGCTCGCTT-G-
1 AGCTTCCCGTTAATGGCT--CTTCGA
* * *
30239747 AGCTTCCTGATATATGGCTATTC-A
1 AGCTTCCCGTTA-ATGGCTCTTCGA
30239771 GAGCTTCCCGTTAATGGCTCTTCGA
1 -AGCTTCCCGTTAATGGCTCTTCGA
* *
30239796 AGCTACCCGTTATTGGCTC
1 AGCTTCCCGTTAATGGCTC
30239815 GCATGAGCTT
Statistics
Matches: 73, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
23 18 0.25
24 36 0.49
25 19 0.26
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.33
Consensus pattern (24 bp):
AGCTTCCCGTTAATGGCTCTTCGA
Found at i:30239847 original size:72 final size:73
Alignment explanation
Indices: 30239698--30239849 Score: 193
Period size: 72 Copynumber: 2.1 Consensus size: 73
30239688 AGGCTCTTCT
* * * *
30239698 TGAGCTTCTCGTTAATGGCTCTCCGGAGCTTCCCGATATGGCTCGCTTGAGCTTCCTGATATATG
1 TGAGCTTCCCGTTAATGGCTCTCCGAAGCTACCCGATATGGCTCGCATGAGCTTCCTGATATATG
*
30239763 GCTATTCA
66 ACTATTCA
* * *
30239771 -GAGCTTCCCGTTAATGGCTCTTCGAAGCTACCCGTTATTGGCTCGCATGAGCTTCTTGA-ATAT
1 TGAGCTTCCCGTTAATGGCTCTCCGAAGCTACCCGATA-TGGCTCGCATGAGCTTCCTGATATAT
*
30239834 GACTCTT-A
65 GACTATTCA
30239842 TGAGCTTC
1 TGAGCTTC
30239850 ATATTTTAGC
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
71 1 0.01
72 48 0.71
73 19 0.28
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (73 bp):
TGAGCTTCCCGTTAATGGCTCTCCGAAGCTACCCGATATGGCTCGCATGAGCTTCCTGATATATG
ACTATTCA
Found at i:30245802 original size:10 final size:10
Alignment explanation
Indices: 30245787--30245841 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
30245777 CATTAATATA
30245787 TTTTTATAAT
1 TTTTTATAAT
*
30245797 TTTTTAAAAAT
1 TTTTT-ATAAT
*
30245808 TTTATATAAT
1 TTTTTATAAT
30245818 TTTTT-T-AT
1 TTTTTATAAT
30245826 ATTTTTA-AAT
1 -TTTTTATAAT
30245836 TTTTTA
1 TTTTTA
30245842 AGTGATTATG
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
8 2 0.05
9 12 0.32
10 15 0.41
11 8 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:30247417 original size:4 final size:4
Alignment explanation
Indices: 30247408--30247543 Score: 272
Period size: 4 Copynumber: 34.0 Consensus size: 4
30247398 ACTATATTTC
30247408 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
30247456 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
30247504 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
30247544 CACTTATATT
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 132 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:30253733 original size:26 final size:27
Alignment explanation
Indices: 30253697--30253759 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 27
30253687 TATTAGGAAG
* *
30253697 GAAAAGCCTTTGTGGCGTAATATGAAA
1 GAAAAGCCTTTATGGCGCAATATGAAA
30253724 GAAAA-CCTTTATGGCGCAATATGAAA
1 GAAAAGCCTTTATGGCGCAATATGAAA
* *
30253750 TAAATGCCTT
1 GAAAAGCCTT
30253760 CAGGCCGTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 22 0.71
27 9 0.29
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (27 bp):
GAAAAGCCTTTATGGCGCAATATGAAA
Found at i:30262904 original size:122 final size:123
Alignment explanation
Indices: 30262687--30262931 Score: 483
Period size: 122 Copynumber: 2.0 Consensus size: 123
30262677 GTAAAAATAA
30262687 TCCTCTCCTATTGCCCATATTTAATCATTCCTATAGAGATTTAAGAAATCATACAAGAAGAAAGT
1 TCCTCTCCTATTGCCCATATTTAATCATTCCTATAGAGATTTAAGAAATCATACAAGAAGAAAGT
30262752 ACTAGAAAATGTAATGTGCTTGTTTACTTTTATAAATAAATAAAAAA-ATATATATAT
66 ACTAGAAAATGTAATGTGCTTGTTTACTTTTATAAATAAATAAAAAATATATATATAT
30262809 TCCTCTCCTATTGCCCATATTTAATCATTCCTATAGAGATTTAAGAAATCATACAAGAAGAAAGT
1 TCCTCTCCTATTGCCCATATTTAATCATTCCTATAGAGATTTAAGAAATCATACAAGAAGAAAGT
30262874 ACTAGAAAATGTAATGTGCTTGTTTACTTTTATAAATAAATAAAAAATATATATATAT
66 ACTAGAAAATGTAATGTGCTTGTTTACTTTTATAAATAAATAAAAAATATATATATAT
30262932 CAATTGGATT
Statistics
Matches: 122, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
122 112 0.92
123 10 0.08
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.36
Consensus pattern (123 bp):
TCCTCTCCTATTGCCCATATTTAATCATTCCTATAGAGATTTAAGAAATCATACAAGAAGAAAGT
ACTAGAAAATGTAATGTGCTTGTTTACTTTTATAAATAAATAAAAAATATATATATAT
Found at i:30269608 original size:21 final size:19
Alignment explanation
Indices: 30269570--30269612 Score: 68
Period size: 21 Copynumber: 2.2 Consensus size: 19
30269560 GCACCTAGGA
30269570 TGATTGTTTTGACATGTTT
1 TGATTGTTTTGACATGTTT
30269589 TGATTGTATTTGATCATGTTT
1 TGATTGT-TTTGA-CATGTTT
30269610 TGA
1 TGA
30269613 ACTGGTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 7 0.32
20 5 0.23
21 10 0.45
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.56
Consensus pattern (19 bp):
TGATTGTTTTGACATGTTT
Found at i:30273681 original size:16 final size:17
Alignment explanation
Indices: 30273651--30273683 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
30273641 TTGTTTATTA
*
30273651 TTTAATAAATGTAATAT
1 TTTAATAAATATAATAT
30273668 TTTAAT-AATATAATAT
1 TTTAATAAATATAATAT
30273684 AATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAAATATAATAT
Found at i:30279821 original size:23 final size:23
Alignment explanation
Indices: 30279795--30279893 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
30279785 ATAAGTGTGA
30279795 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
30279818 CACTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
30279841 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
30279864 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
30279887 CACTGAT
1 CACTGAT
30279894 CAATAACACT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:30282215 original size:11 final size:11
Alignment explanation
Indices: 30282195--30282224 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
30282185 AATCAATACA
30282195 TAAA-CATGTT
1 TAAATCATGTT
30282205 TAAATCATGTT
1 TAAATCATGTT
30282216 TAAATCATG
1 TAAATCATG
30282225 CCTAAACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (11 bp):
TAAATCATGTT
Found at i:30284092 original size:16 final size:17
Alignment explanation
Indices: 30284062--30284094 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
30284052 TTGTTTATTA
*
30284062 TTTAATAAATGTAATAT
1 TTTAATAAATATAATAT
30284079 TTTAAT-AATATAATAT
1 TTTAATAAATATAATAT
30284095 AATTATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAAATATAATAT
Found at i:30285459 original size:9 final size:9
Alignment explanation
Indices: 30285445--30285475 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
30285435 CATAGTGATT
30285445 AATTTTTAC
1 AATTTTTAC
30285454 AATTTTTAC
1 AATTTTTAC
*
30285463 AATATTTAC
1 AATTTTTAC
30285472 AATT
1 AATT
30285476 AGTCTTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (9 bp):
AATTTTTAC
Found at i:30296700 original size:17 final size:19
Alignment explanation
Indices: 30296664--30296702 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
30296654 AAAAAATAAT
30296664 AATAAATTATGAATTATTC
1 AATAAATTATGAATTATTC
*
30296683 AATAAATT-T-AATTTTTC
1 AATAAATTATGAATTATTC
30296700 AAT
1 AAT
30296703 GTTAGTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 1 0.05
19 8 0.42
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (19 bp):
AATAAATTATGAATTATTC
Found at i:30298377 original size:14 final size:14
Alignment explanation
Indices: 30298358--30298409 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
30298348 TTAGTTCCAA
30298358 ATAATTTAAATTAT
1 ATAATTTAAATTAT
*
30298372 ATAATTTAAAATTTTT
1 ATAATTT-AAA-TTAT
*
30298388 CTTAATTTAAATTAT
1 -ATAATTTAAATTAT
30298403 ATAATTT
1 ATAATTT
30298410 TAAAATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 13 0.42
15 6 0.19
16 6 0.19
17 6 0.19
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
ATAATTTAAATTAT
Found at i:30298397 original size:31 final size:32
Alignment explanation
Indices: 30298359--30298423 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 32
30298349 TAGTTCCAAA
30298359 TAATTTAAATTATATAA-TTTAAAATTTTTCT
1 TAATTTAAATTATATAATTTTAAAATTTTTCT
30298390 TAATTTAAATTATATAATTTTAAAATTTTTCT
1 TAATTTAAATTATATAATTTTAAAATTTTTCT
30298422 TA
1 TA
30298424 TGAATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 17 0.52
32 16 0.48
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (32 bp):
TAATTTAAATTATATAATTTTAAAATTTTTCT
Found at i:30303089 original size:49 final size:49
Alignment explanation
Indices: 30303000--30303094 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
30302990 CTATTTATAG
* * * * *
30303000 GTTGAAAAAACTTATTCTAATCATTGTCAAATAGATGAAGTGTAGTAAA
1 GTTGAAAAAACTGATTCTAATCAATGTCAAATAAAAGAAGTATAGTAAA
*
30303049 GTTGAAAAACCTGATTCTAATCAATGT-AAAGTAAAAGAAGTATAGT
1 GTTGAAAAAACTGATTCTAATCAATGTCAAA-TAAAAGAAGTATAGT
30303095 TCTATATGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 3 0.08
49 36 0.92
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (49 bp):
GTTGAAAAAACTGATTCTAATCAATGTCAAATAAAAGAAGTATAGTAAA
Found at i:30309375 original size:28 final size:27
Alignment explanation
Indices: 30309334--30309436 Score: 88
Period size: 28 Copynumber: 3.9 Consensus size: 27
30309324 TTTTATTTTC
*
30309334 TTAAAAATACTTTTTAACATCAATAGTT
1 TTAAAAACACTTTTTAACATCAATA-TT
*** *
30309362 TTAAAAACA-TTTTTTTTATC--T-TC
1 TTAAAAACACTTTTTAACATCAATATT
*
30309385 TTAAAAATACTTTTTAACATCAATAATT
1 TTAAAAACACTTTTTAACATCAAT-ATT
* *
30309413 TTAAAAACATTTTTTAACCTCAAT
1 TTAAAAACACTTTTTAACATCAAT
30309437 GGTGTAATAG
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
23 9 0.16
24 8 0.14
25 1 0.02
26 1 0.02
27 8 0.14
28 30 0.53
ACGTcount: A:0.41, C:0.13, G:0.01, T:0.46
Consensus pattern (27 bp):
TTAAAAACACTTTTTAACATCAATATT
Found at i:30309393 original size:51 final size:51
Alignment explanation
Indices: 30309324--30309427 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
30309314 AAAATAGAAA
* *
30309324 TTTTATTTTCTTAAAAATACTTTTTAACATCAATAGTTTTAAAAACATTTT
1 TTTTATCTTCTTAAAAATACTTTTTAACATCAATAATTTTAAAAACATTTT
30309375 TTTTATCTTCTTAAAAATACTTTTTAACATCAATAATTTTAAAAACATTTT
1 TTTTATCTTCTTAAAAATACTTTTTAACATCAATAATTTTAAAAACATTTT
30309426 TT
1 TT
30309428 AACCTCAATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.51
Consensus pattern (51 bp):
TTTTATCTTCTTAAAAATACTTTTTAACATCAATAATTTTAAAAACATTTT
Found at i:30309682 original size:3 final size:3
Alignment explanation
Indices: 30309674--30309737 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
30309664 AGTAGGTCTT
30309674 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30309721 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
30309738 TAAGATATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 58 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:30310426 original size:31 final size:31
Alignment explanation
Indices: 30310388--30310447 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
30310378 CCTTATGTAA
30310388 AAAAAAAAAAAAACATGTTGTTGTAAGATGT
1 AAAAAAAAAAAAACATGTTGTTGTAAGATGT
*
30310419 AAAAAAAAAAAACCATGTTGTTGTAAGAT
1 AAAAAAAAAAAAACATGTTGTTGTAAGAT
30310448 ATGAATCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (31 bp):
AAAAAAAAAAAAACATGTTGTTGTAAGATGT
Found at i:30314613 original size:47 final size:49
Alignment explanation
Indices: 30314544--30314652 Score: 109
Period size: 50 Copynumber: 2.2 Consensus size: 49
30314534 AAGAGAAGGA
* *
30314544 AAAGAAAAGAAG-AGAAGAAGAAGAAGAAG-GAGAGGGCAGGAAGGGAAAAAG
1 AAAGAAAAAAAGAAGAAGAAGAAGAA-AAGAGAGAGGGAAGG-A--GAAAAAG
* *
30314595 AAAGAAAAAAA-AAG-AGAAGGAGAAAAGAGAGAGGGAAGGAGAAATAG
1 AAAGAAAAAAAGAAGAAGAAGAAGAAAAGAGAGAGGGAAGGAGAAAAAG
*
30314642 AAGGAAAAAAA
1 AAAGAAAAAAA
30314653 TAAAAAAGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
47 16 0.31
49 4 0.08
50 19 0.37
51 12 0.24
ACGTcount: A:0.63, C:0.01, G:0.35, T:0.01
Consensus pattern (49 bp):
AAAGAAAAAAAGAAGAAGAAGAAGAAAAGAGAGAGGGAAGGAGAAAAAG
Found at i:30315141 original size:20 final size:22
Alignment explanation
Indices: 30315118--30315159 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
30315108 TGAATAAGAG
*
30315118 TTTATGTT-TT-TAAATTTTAT
1 TTTATGTTCTTATAAATATTAT
30315138 TTTATGTTCTTATAAATATTAT
1 TTTATGTTCTTATAAATATTAT
30315160 AAATGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTATGTTCTTATAAATATTAT
Found at i:30317347 original size:33 final size:33
Alignment explanation
Indices: 30317310--30317372 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
30317300 TATCCACCGC
*
30317310 AGTACAGCACTCCTCTTGGCCCGTATCCACTAT
1 AGTACAGCACTCCTCCTGGCCCGTATCCACTAT
** **
30317343 AGTACTTCACTCCTCCTGGGTCGTATCCAC
1 AGTACAGCACTCCTCCTGGCCCGTATCCAC
30317373 CGTAATATGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.19, C:0.37, G:0.16, T:0.29
Consensus pattern (33 bp):
AGTACAGCACTCCTCCTGGCCCGTATCCACTAT
Found at i:30317814 original size:62 final size:63
Alignment explanation
Indices: 30317660--30317830 Score: 186
Period size: 62 Copynumber: 2.7 Consensus size: 63
30317650 AATTAGATTA
** *
30317660 ATTACAACATTAAAACTTGGAACAAACTTTGTGGTCATAAATTAGATTAATTGCAACATTACAAC
1 ATTACAACATTAAAACTTGGAACAAACTTTGTAAT-ATAAATTAGATTAATT-CAACATTAAAAC
* * * **
30317725 ATTAAAACACTAAAACTTGTAACAAACTTTGTAATATAAATTTTATT-ATAT-AA-ATTAAATAC
1 ATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAGATTAAT-TCAACATTAAA-AC
* * *
30317787 ATTACAACATTAAAAGTTGGAATAAACTTTGTAATATTAATTAG
1 ATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAG
30317831 GTAGATTGGA
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
61 5 0.06
62 40 0.45
63 2 0.02
64 11 0.12
65 30 0.34
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (63 bp):
ATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAGATTAATTCAACATTAAAAC
Found at i:30320312 original size:27 final size:27
Alignment explanation
Indices: 30320241--30320312 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
30320231 ATATTAGGTG
* * * *
30320241 TGCCGCCTATCAAATAGACACCACCAG
1 TGCCGCCTATCAGATAGGCACAACCAA
*
30320268 TGCCGCCTATCAGATAGGCACAACTAA
1 TGCCGCCTATCAGATAGGCACAACCAA
30320295 TGCCGCCTATCAGATAGG
1 TGCCGCCTATCAGATAGG
30320313 GGTCGCTGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (27 bp):
TGCCGCCTATCAGATAGGCACAACCAA
Found at i:30328041 original size:31 final size:31
Alignment explanation
Indices: 30327972--30328047 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
30327962 TGTTGAAAAT
** *
30327972 TTTTCTTTACTTTTCATATTTTTAGATTAGG
1 TTTTCTTTTTTTTTCATATTTTTAAATTAGG
*
30328003 -TTTCTTTTTTTTTCTTATTTTTAAATTAGG
1 TTTTCTTTTTTTTTCATATTTTTAAATTAGG
30328033 TTTTCTTTTTCTTTT
1 TTTTCTTTTT-TTTT
30328048 TAGAATAGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 26 0.67
31 9 0.23
32 4 0.10
ACGTcount: A:0.14, C:0.09, G:0.07, T:0.70
Consensus pattern (31 bp):
TTTTCTTTTTTTTTCATATTTTTAAATTAGG
Found at i:30330007 original size:16 final size:17
Alignment explanation
Indices: 30329968--30330009 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
30329958 TTTCAGTTTC
30329968 TGTTC-TTAGTAAATTT
1 TGTTCTTTAGTAAATTT
*
30329984 T-ATCTTTA-TAAATTT
1 TGTTCTTTAGTAAATTT
30329999 TGTTCTTTAGT
1 TGTTCTTTAGT
30330010 TTTAGTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
15 10 0.48
16 10 0.48
17 1 0.05
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.60
Consensus pattern (17 bp):
TGTTCTTTAGTAAATTT
Found at i:30340630 original size:21 final size:22
Alignment explanation
Indices: 30340601--30340644 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
30340591 GCATCTACTC
* *
30340601 AGGGCAATTATAATCCACAACA
1 AGGGCAATTACAATCAACAACA
30340623 AGGG-AATTACAATCAACAACA
1 AGGGCAATTACAATCAACAACA
30340644 A
1 A
30340645 AACTACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.50, C:0.20, G:0.14, T:0.16
Consensus pattern (22 bp):
AGGGCAATTACAATCAACAACA
Found at i:30352316 original size:3 final size:3
Alignment explanation
Indices: 30352308--30352332 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30352298 GACGTTAACA
30352308 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
30352333 GGAGGAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:30352337 original size:3 final size:3
Alignment explanation
Indices: 30352331--30352363 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
30352321 TGATGATGAT
*
30352331 GAG GAG GAG GAA GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
30352364 ACCCCTATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:30353625 original size:4 final size:4
Alignment explanation
Indices: 30353585--30353643 Score: 50
Period size: 4 Copynumber: 14.8 Consensus size: 4
30353575 TCCTGATTGG
* * *
30353585 TTTA TTGA TTTA TTTCA TTTT TTTA -TT- TTTC TTTA TTTA TTTA TTATA
1 TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA
*
30353633 GTTA TTTA TTT
1 TTTA TTTA TTT
30353644 GGTTTTACCT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
3 4 0.09
4 33 0.75
5 7 0.16
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:30354057 original size:13 final size:13
Alignment explanation
Indices: 30354039--30354063 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30354029 AAGTTTTATG
30354039 TTTTTATTAATTA
1 TTTTTATTAATTA
30354052 TTTTTATTAATT
1 TTTTTATTAATT
30354064 TTTGTTTTGT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTATTAATTA
Found at i:30358945 original size:2 final size:2
Alignment explanation
Indices: 30358938--30358962 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30358928 TAAGATTTAG
30358938 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
30358963 TTGTGTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30361176 original size:17 final size:17
Alignment explanation
Indices: 30361141--30361204 Score: 76
Period size: 17 Copynumber: 3.8 Consensus size: 17
30361131 TCCTAATTGG
* *
30361141 TTTATTGATTTATTTTA
1 TTTATTTATTTTTTTTA
30361158 TTT-TTTATTTTTCTTTA
1 TTTATTTATTTTT-TTTA
* *
30361175 TTTATTTCTTTTTGTTA
1 TTTATTTATTTTTTTTA
30361192 TTTATTTATTTTT
1 TTTATTTATTTTT
30361205 ATCTCTTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
16 7 0.17
17 25 0.62
18 8 0.20
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTATTTATTTTTTTTA
Found at i:30361180 original size:21 final size:20
Alignment explanation
Indices: 30361148--30361204 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 20
30361138 TGGTTTATTG
*
30361148 ATTTATTTTATTTTTTATTTTT
1 ATTTA-TTTATTTTTT-TTGTT
*
30361170 CTTTATTTATTTCTTTTTGTT
1 ATTTATTTATTT-TTTTTGTT
30361191 ATTTATTTATTTTT
1 ATTTATTTATTTTT
30361205 ATCTCTTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 2 0.06
21 22 0.71
22 7 0.23
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.79
Consensus pattern (20 bp):
ATTTATTTATTTTTTTTGTT
Found at i:30367662 original size:20 final size:20
Alignment explanation
Indices: 30367637--30367677 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
30367627 AATAAAAGAG
30367637 TGTTGAAATATCTATATATT
1 TGTTGAAATATCTATATATT
30367657 TGTTGAAATATCTATATATT
1 TGTTGAAATATCTATATATT
30367677 T
1 T
30367678 TAAAGTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (20 bp):
TGTTGAAATATCTATATATT
Found at i:30371575 original size:29 final size:29
Alignment explanation
Indices: 30371510--30371616 Score: 105
Period size: 29 Copynumber: 3.7 Consensus size: 29
30371500 TTACAGATTT
* *
30371510 GCCACAAAGGCATCCA-A-ACACATAAATA
1 GCCATAAAGGCATCCACATA-ACATTAATA
*
30371538 GCCATAAAGGCATCCACATAATAGTT-ATA
1 GCCATAAAGGCATCCACATAACA-TTAATA
* *
30371567 GCCAAAAAGGC-TCTCATATAACATTAGATA
1 GCCATAAAGGCATC-CACATAACATTA-ATA
30371597 GCCATAAAGGCATCCACATA
1 GCCATAAAGGCATCCACATA
30371617 TAACAAACTT
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
28 19 0.30
29 23 0.36
30 20 0.31
31 2 0.03
ACGTcount: A:0.44, C:0.24, G:0.13, T:0.19
Consensus pattern (29 bp):
GCCATAAAGGCATCCACATAACATTAATA
Found at i:30371994 original size:10 final size:10
Alignment explanation
Indices: 30371979--30372005 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
30371969 GGTCTTTACT
30371979 TGCCATATGA
1 TGCCATATGA
30371989 TGCCATATGA
1 TGCCATATGA
30371999 TGCCATA
1 TGCCATA
30372006 CTACTAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (10 bp):
TGCCATATGA
Found at i:30383531 original size:141 final size:141
Alignment explanation
Indices: 30383277--30383562 Score: 482
Period size: 141 Copynumber: 2.0 Consensus size: 141
30383267 CTAATTCCGT
*
30383277 TAAAATCATAACGATTTTACCGTAAAAGAATCTATGAGAAATTATATTTAATATTTCTACATTAT
1 TAAAATCATAACGATTTTACCGTAAAAGAATCTATGAGAAAATATATTTAATATTTCTACATTAT
* *
30383342 AACATCTCGCCTAACGAAGCCCTAGTATTTGAGTGTTGTTTTAGAAGTAAGAATTTTGGAACGAG
66 AAAATCTCGCCTAACGAAGCCCTAGTATTCGAGTGTTGTTTTAGAAGTAAGAATTTTGGAACGAG
30383407 CCCTAGATAAG
131 CCCTAGATAAG
* * *
30383418 TAAAATCATAACGATTTTACCGTAAAATAATTTATGAGAAAATATATTTAATTTTTCTACATTAT
1 TAAAATCATAACGATTTTACCGTAAAAGAATCTATGAGAAAATATATTTAATATTTCTACATTAT
* *
30383483 AAAATCTCGCCTAGCGAAGCCTTAGTATTCGAGTGTTGTTTTAGAAGTAAGAATTTTGGAACGAG
66 AAAATCTCGCCTAACGAAGCCCTAGTATTCGAGTGTTGTTTTAGAAGTAAGAATTTTGGAACGAG
* *
30383548 CCTTGGATAAG
131 CCCTAGATAAG
30383559 TAAA
1 TAAA
30383563 GTGATGGATT
Statistics
Matches: 135, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
141 135 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (141 bp):
TAAAATCATAACGATTTTACCGTAAAAGAATCTATGAGAAAATATATTTAATATTTCTACATTAT
AAAATCTCGCCTAACGAAGCCCTAGTATTCGAGTGTTGTTTTAGAAGTAAGAATTTTGGAACGAG
CCCTAGATAAG
Found at i:30384613 original size:298 final size:289
Alignment explanation
Indices: 30384046--30384635 Score: 1027
Period size: 298 Copynumber: 2.0 Consensus size: 289
30384036 TGTTCTCTAA
*
30384046 CACACATATTCATGCATCGATTTTGACATTTCATATCAATGACAACTCTTTATCATCAATCAACT
1 CACACATATTCATGCATCGATTTTGACATTCCATATCAATGACAACTCTTTATCATCAATCAACT
*
30384111 ACATGTTAGTCTTAATGCATTATTGTTGTCCTATCCAACAATAATACTTGACTAAGGATCTTTTA
66 ACATGTTAGTCTTAATGCATTATTGTTGTCCTATCCAACAATAATACTTGACTAAGGACCTTTTA
30384176 AGAATAATCACATTATATTATTATAAAATAGTTTATTTATACATACAGAAAAGAAATTGAAATAA
131 AGAATAATCACATTATATTATTATAAAATAGTTTATTTATACATACAGAAAAGAAATTGAAATAA
30384241 TAATGGTAACGCCTTATATCAATAAACATGATAAATCAAGTATGTTATTACAACCATCTCATGAT
196 TAATGGTAACGCCTTATATCAATAAACATGATAAATCAAGTATGTTATTACAACCATCTCATGAT
30384306 TGATCTTTGGGCATACTCTAACAATCTCC
261 TGATCTTTGGGCATACTCTAACAATCTCC
30384335 CACACATATTCATGCATCGATTTTGACATTCCATATCAATGACAACTCTTTATCATCAATCAACT
1 CACACATATTCATGCATCGATTTTGACATTCCATATCAATGACAACTCTTTATCATCAATCAACT
* * *
30384400 ACATGTTAGTCTTAATGCATTATTTTTGTCCTATCCAACAATAATTCTTGATTAAGGACCTTTTA
66 ACATGTTAGTCTTAATGCATTATTGTTGTCCTATCCAACAATAATACTTGACTAAGGACCTTTTA
*
30384465 AGAATAATCATATTACTCTCAGGATATTATTATAAAATAGTTTATTTATACATACAGAAAAGAAA
131 AGAATAATC--A-CA-T-T----ATATTATTATAAAATAGTTTATTTATACATACAGAAAAGAAA
* *
30384530 TTGAAATAATAATGGTAACGTCTTATATTAATAAACATGATAAATCAAGTATGTTATTACAACCA
187 TTGAAATAATAATGGTAACGCCTTATATCAATAAACATGATAAATCAAGTATGTTATTACAACCA
30384595 TCTCATGATTGATCTTTGGGCATACTCTAACAATCTCC
252 TCTCATGATTGATCTTTGGGCATACTCTAACAATCTCC
30384633 CAC
1 CAC
30384636 TAGCAGTAAG
Statistics
Matches: 284, Mismatches: 8, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
289 134 0.47
291 1 0.00
292 1 0.00
293 1 0.00
294 1 0.00
298 146 0.51
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (289 bp):
CACACATATTCATGCATCGATTTTGACATTCCATATCAATGACAACTCTTTATCATCAATCAACT
ACATGTTAGTCTTAATGCATTATTGTTGTCCTATCCAACAATAATACTTGACTAAGGACCTTTTA
AGAATAATCACATTATATTATTATAAAATAGTTTATTTATACATACAGAAAAGAAATTGAAATAA
TAATGGTAACGCCTTATATCAATAAACATGATAAATCAAGTATGTTATTACAACCATCTCATGAT
TGATCTTTGGGCATACTCTAACAATCTCC
Found at i:30389341 original size:42 final size:42
Alignment explanation
Indices: 30389281--30389411 Score: 147
Period size: 43 Copynumber: 3.1 Consensus size: 42
30389271 TAGGGTCCCG
* *
30389281 ATATGTGATTTACGTGTAAGACCATGTCTGGGACATTGGCAAC
1 ATATATGA-TTACGTGTAAGACCATGTCTGGGACATTGGCATC
* * *
30389324 ATATATGATTACGTGTAAGACCCTGTCTGGCACAGTGGCATC
1 ATATATGATTACGTGTAAGACCATGTCTGGGACATTGGCATC
* * * *
30389366 GTTATTTGATTACATGTAAGACCACGTCTGGGA-AGTTGGCATC
1 -ATATATGATTACGTGTAAGACCATGTCTGGGACA-TTGGCATC
30389409 ATA
1 ATA
30389412 CGGGCTTTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
42 33 0.45
43 40 0.55
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (42 bp):
ATATATGATTACGTGTAAGACCATGTCTGGGACATTGGCATC
Found at i:30391223 original size:26 final size:27
Alignment explanation
Indices: 30391194--30391257 Score: 103
Period size: 26 Copynumber: 2.4 Consensus size: 27
30391184 CATATAAGTG
30391194 AGCCTTTGTGACTATCTCTA-AAAGGA
1 AGCCTTTGTGACTATCTCTATAAAGGA
*
30391220 AGCCTTTGTGACTGTCTCTATTAAAGGA
1 AGCCTTTGTGACTATCTCTA-TAAAGGA
30391248 AGCCTTTGTG
1 AGCCTTTGTG
30391258 GTGATCTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 19 0.54
28 16 0.46
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (27 bp):
AGCCTTTGTGACTATCTCTATAAAGGA
Found at i:30391254 original size:28 final size:29
Alignment explanation
Indices: 30391194--30391373 Score: 140
Period size: 29 Copynumber: 6.3 Consensus size: 29
30391184 CATATAAGTG
30391194 AGCCTTTGTGACT-ATCTCTA--AAAGGA
1 AGCCTTTGTGACTGATCTCTATTAAAGGA
30391220 AGCCTTTGTGACTG-TCTCTATTAAAGGA
1 AGCCTTTGTGACTGATCTCTATTAAAGGA
* * * *
30391248 AGCCTTTGTG-GTGATCTTTGTTAAATGAA
1 AGCCTTTGTGACTGATCTCTATTAAA-GGA
* **
30391277 AGCTTTTGTGACAAATCTCTATTATAAGGA
1 AGCCTTTGTGACTGATCTCTATTA-AAGGA
* * * * *
30391307 AGTCTTTGTGGC-GATCTTTGTTAAATGAA
1 AGCCTTTGTGACTGATCTCTATTAAA-GGA
* * *
30391336 AGTCTTTGTGGC-GATCTCTATTAAATGA
1 AGCCTTTGTGACTGATCTCTATTAAAGGA
30391364 ATGCCTTTGT
1 A-GCCTTTGT
30391374 TGTTGTTTTT
Statistics
Matches: 122, Mismatches: 23, Indels: 15
0.76 0.14 0.09
Matches are distributed among these distances:
26 19 0.16
27 2 0.02
28 29 0.24
29 51 0.42
30 19 0.16
31 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (29 bp):
AGCCTTTGTGACTGATCTCTATTAAAGGA
Found at i:30391314 original size:59 final size:57
Alignment explanation
Indices: 30391223--30391373 Score: 196
Period size: 59 Copynumber: 2.6 Consensus size: 57
30391213 AAAAGGAAGC
** *
30391223 CTTTGTGACTGTCTCTATTAAAGGAAGCCTTTGTGGTGATCTTTGTTAAATGAAAG-
1 CTTTGTGACAATCTCTATTAAAGGAAGCCTTTGTGGCGATCTTTGTTAAATGAAAGT
*
30391279 CTTTTGTGACAAATCTCTATTATAAGGAAGTCTTTGTGGCGATCTTTGTTAAATGAAAGT
1 C-TTTGTGAC-AATCTCTATTA-AAGGAAGCCTTTGTGGCGATCTTTGTTAAATGAAAGT
* * *
30391339 CTTTGTGGCGATCTCTATTAAATGAATGCCTTTGT
1 CTTTGTGACAATCTCTATTAAAGGAA-GCCTTTGT
30391374 TGTTGTTTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
56 1 0.01
57 13 0.16
58 26 0.32
59 41 0.50
60 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (57 bp):
CTTTGTGACAATCTCTATTAAAGGAAGCCTTTGTGGCGATCTTTGTTAAATGAAAGT
Found at i:30391429 original size:29 final size:28
Alignment explanation
Indices: 30391214--30391450 Score: 134
Period size: 29 Copynumber: 8.2 Consensus size: 28
30391204 ACTATCTCTA
* * * * *
30391214 AAAGGAAGCCTTTGTGACTGTCTCTATT
1 AAAGGAAGCCTTTGTGGCTATCTTTGTC
*
30391242 AAAGGAAGCCTTTGTGG-TGATCTTTGTT
1 AAAGGAAGCCTTTGTGGCT-ATCTTTGTC
* * * * * * *
30391270 AAATGAAAGCTTTTGTGACAAATCTCTATT
1 AAA-GGAAGCCTTTGTGGC-TATCTTTGTC
* * *
30391300 ATAAGGAAGTCTTTGTGGCGATCTTTGTT
1 A-AAGGAAGCCTTTGTGGCTATCTTTGTC
* * * * * *
30391329 AAATGAAAGTCTTTGTGGCGATCTCTATT
1 AAA-GGAAGCCTTTGTGGCTATCTTTGTC
* * * * *
30391358 AAATGAATGCCTTTGTTGTTGTTTTTGTC
1 AAAGGAA-GCCTTTGTGGCTATCTTTGTC
*
30391387 ATAGGAAGCCTTTGTGGCTATCTTTGTC
1 AAAGGAAGCCTTTGTGGCTATCTTTGTC
* *
30391415 AAAAGGATGCCTTTGTGGCTATCTTTGTT
1 -AAAGGAAGCCTTTGTGGCTATCTTTGTC
30391444 AAAGGAA
1 AAAGGAA
30391451 TGTCTTGTGG
Statistics
Matches: 160, Mismatches: 41, Indels: 16
0.74 0.19 0.07
Matches are distributed among these distances:
27 1 0.01
28 52 0.32
29 86 0.54
30 19 0.12
31 2 0.01
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (28 bp):
AAAGGAAGCCTTTGTGGCTATCTTTGTC
Found at i:30391450 original size:57 final size:57
Alignment explanation
Indices: 30391214--30391484 Score: 201
Period size: 57 Copynumber: 4.7 Consensus size: 57
30391204 ACTATCTCTA
*
30391214 AAAGGAAGCCTTTGTGACTGTCTCTATT-AAAGGAAGCCTTTGTGG-TGATCTTTGTT
1 AAAGGAAGCCTTTGTGACTATCTCTATTAAAAGGAAGCCTTTGTGGCT-ATCTTTGTT
* * * * * *
30391270 AAATGAAAGCTTTTGTGACAAATCTCTATTATAAGGAAGTCTTTGTGGCGATCTTTGTT
1 AAA-GGAAGCCTTTGTGAC-TATCTCTATTAAAAGGAAGCCTTTGTGGCTATCTTTGTT
* * * * * * * * * *
30391329 AAATGAAAGTCTTTGTGGCGATCTCTATT-AAATGAATGCCTTTGTTGTTGTTTTTGTC
1 AAA-GGAAGCCTTTGTGACTATCTCTATTAAAAGGAA-GCCTTTGTGGCTATCTTTGTT
* * * * * *
30391387 ATAGGAAGCCTTTGTGGCTATCTTTGTCAAAAGGATGCCTTTGTGGCTATCTTTGTT
1 AAAGGAAGCCTTTGTGACTATCTCTATTAAAAGGAAGCCTTTGTGGCTATCTTTGTT
* * * *
30391444 AAAGGAATGTC-TTGTGGCAAAT-TCTATTAAAAGGACGCCTT
1 AAAGGAA-GCCTTTGTGAC-TATCTCTATTAAAAGGAAGCCTT
30391485 GAAGACAACT
Statistics
Matches: 166, Mismatches: 41, Indels: 15
0.75 0.18 0.07
Matches are distributed among these distances:
56 3 0.02
57 81 0.49
58 42 0.25
59 40 0.24
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.39
Consensus pattern (57 bp):
AAAGGAAGCCTTTGTGACTATCTCTATTAAAAGGAAGCCTTTGTGGCTATCTTTGTT
Found at i:30400408 original size:23 final size:23
Alignment explanation
Indices: 30400364--30400414 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
30400354 TAATTTTTAA
* *
30400364 ATTTTAAATTATTTAATGATAAT
1 ATTTAAAATTATTTAAGGATAAT
30400387 ATTTAAAATTATTT-AGGAATAAT
1 ATTTAAAATTATTTAAGG-ATAAT
30400410 ATTTA
1 ATTTA
30400415 GGAAAAATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (23 bp):
ATTTAAAATTATTTAAGGATAAT
Found at i:30401981 original size:17 final size:17
Alignment explanation
Indices: 30401959--30401992 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30401949 CTGAAAGAGT
*
30401959 TCCACATGGTTTGTCTA
1 TCCACAGGGTTTGTCTA
30401976 TCCACAGGGTTTGTCTA
1 TCCACAGGGTTTGTCTA
30401993 AGCATGAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.38
Consensus pattern (17 bp):
TCCACAGGGTTTGTCTA
Found at i:30407018 original size:22 final size:22
Alignment explanation
Indices: 30406970--30407018 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
30406960 GGGAAACCAC
*
30406970 ATTTATTTTTATTTATTTATTT
1 ATTTATTTTTATATATTTATTT
30406992 ATTTATTTTTA-AT-TTTAGTTT
1 ATTTATTTTTATATATTTA-TTT
30407013 AGTTTA
1 A-TTTA
30407019 GGAATTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 4 0.17
21 5 0.21
22 15 0.62
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (22 bp):
ATTTATTTTTATATATTTATTT
Found at i:30408501 original size:23 final size:23
Alignment explanation
Indices: 30408475--30408526 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
30408465 TGATTTTTAA
*
30408475 ATTTTGAATCATTTAGTGATAAT
1 ATTTAGAATCATTTAGTGATAAT
*
30408498 ATTTAGAATTATTTAGTGATAAT
1 ATTTAGAATCATTTAGTGATAAT
30408521 ATTTAG
1 ATTTAG
30408527 GAAAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (23 bp):
ATTTAGAATCATTTAGTGATAAT
Found at i:30408503 original size:13 final size:13
Alignment explanation
Indices: 30408485--30408526 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
30408475 ATTTTGAATC
30408485 ATTTAGTGATAAT
1 ATTTAGTGATAAT
*
30408498 ATTTA--GA-ATT
1 ATTTAGTGATAAT
30408508 ATTTAGTGATAAT
1 ATTTAGTGATAAT
30408521 ATTTAG
1 ATTTAG
30408527 GAAAAATCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.29
11 2 0.08
12 2 0.08
13 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (13 bp):
ATTTAGTGATAAT
Found at i:30409391 original size:20 final size:20
Alignment explanation
Indices: 30409364--30409416 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
30409354 AAAAAAATAT
30409364 TTTA-TTTTATTTTCTT-AAA
1 TTTATTTTTATTTT-TTCAAA
* *
30409383 TTTATTTTTGTTTTTTCGAA
1 TTTATTTTTATTTTTTCAAA
*
30409403 TATATTTTTATTTT
1 TTTATTTTTATTTT
30409417 ATTTATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.72
Consensus pattern (20 bp):
TTTATTTTTATTTTTTCAAA
Found at i:30410227 original size:17 final size:17
Alignment explanation
Indices: 30410205--30410261 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
30410195 TAACAATAAT
30410205 ATTAAAAATTTCAAAAA
1 ATTAAAAATTTCAAAAA
*
30410222 ATTAAAAATATCAAAAA
1 ATTAAAAATTTCAAAAA
30410239 ATTAAAAA-TT--AAAA
1 ATTAAAAATTTCAAAAA
30410253 ATTAAAAAT
1 ATTAAAAAT
30410262 CATAAAATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
14 12 0.32
16 1 0.03
17 24 0.65
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (17 bp):
ATTAAAAATTTCAAAAA
Found at i:30410245 original size:6 final size:7
Alignment explanation
Indices: 30410218--30410261 Score: 61
Period size: 7 Copynumber: 5.9 Consensus size: 7
30410208 AAAAATTTCA
30410218 AAAAATT
1 AAAAATT
30410225 AAAAATAT
1 AAAAAT-T
30410233 CAAAAAATT
1 --AAAAATT
30410242 AAAAATT
1 AAAAATT
30410249 AAAAATT
1 AAAAATT
30410256 AAAAAT
1 AAAAAT
30410262 CATAAAATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 26 0.76
8 1 0.03
9 1 0.03
10 6 0.18
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAAATT
Found at i:30425635 original size:21 final size:20
Alignment explanation
Indices: 30425604--30425642 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
30425594 ATTTACTTAC
*
30425604 AAATATATTTTATTTTTTAT
1 AAATATATTTTATATTTTAT
30425624 AAATATATTTTTATATTTT
1 AAATATA-TTTTATATTTT
30425643 CAATTAGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
AAATATATTTTATATTTTAT
Found at i:30428171 original size:92 final size:91
Alignment explanation
Indices: 30428014--30428222 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 91
30428004 TTGATTTTAG
* * *
30428014 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
30428079 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
30428106 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
30428170 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
30428198 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
30428223 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:30428185 original size:24 final size:25
Alignment explanation
Indices: 30428150--30428197 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
30428140 TTATGAAATT
30428150 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
30428174 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
30428198 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:30428393 original size:16 final size:16
Alignment explanation
Indices: 30428372--30428413 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
30428362 TTATTAAATT
*
30428372 ATATATTTTAATTATA
1 ATATATTTTAATAATA
30428388 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
30428403 AT-TATGTTTAA
1 ATATAT-TTTAA
30428414 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:30428398 original size:15 final size:15
Alignment explanation
Indices: 30428363--30428404 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
30428353 TTAAGAATTT
*
30428363 TATTAAATTAT-ATA
1 TATTTAATTATAATA
30428377 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
30428391 TATTTAATAATAAT
1 TATTTAATTATAAT
30428405 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:30430511 original size:13 final size:13
Alignment explanation
Indices: 30430493--30430532 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
30430483 AGTTTGGCAA
30430493 TACTTTTGAAAAG
1 TACTTTTGAAAAG
30430506 TACTTTTGAAAAG
1 TACTTTTGAAAAG
*
30430519 TGCTTTTGAAAAG
1 TACTTTTGAAAAG
30430532 T
1 T
30430533 TTGGTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.40
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:30431998 original size:32 final size:32
Alignment explanation
Indices: 30431962--30432030 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
30431952 TGATATTGCG
* *
30431962 ATGTCTTTGATATGTGAGGATGGGTGTTTGTA
1 ATGTCTTTGATATGTGAGGATAGGTGATTGTA
30431994 ATGTCTTTGATATGTGAGGATAGGTGATTGTA
1 ATGTCTTTGATATGTGAGGATAGGTGATTGTA
30432026 ATGTC
1 ATGTC
30432031 AGTTTGGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.22, C:0.04, G:0.32, T:0.42
Consensus pattern (32 bp):
ATGTCTTTGATATGTGAGGATAGGTGATTGTA
Found at i:30437528 original size:14 final size:13
Alignment explanation
Indices: 30437500--30437532 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
30437490 TATATATAAA
30437500 TTGATG-AATTGG
1 TTGATGAAATTGG
30437512 TTGATGAAATGTGG
1 TTGATGAAAT-TGG
30437526 TTGATGA
1 TTGATGA
30437533 GTTATGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 3 0.16
14 10 0.53
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.39
Consensus pattern (13 bp):
TTGATGAAATTGG
Found at i:30439407 original size:9 final size:8
Alignment explanation
Indices: 30439376--30439405 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
30439366 ATTATTTTTA
30439376 TTTTTTCT
1 TTTTTTCT
30439384 TTTTTTCT
1 TTTTTTCT
30439392 TTTTTTCT
1 TTTTTTCT
30439400 TTTTTT
1 TTTTTT
30439406 TCCATCAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTCT
Found at i:30439488 original size:18 final size:18
Alignment explanation
Indices: 30439465--30439514 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
30439455 CCAAGCAAAG
*
30439465 GAAACAATTAATTTTTAT
1 GAAACAATTAATTTTCAT
*
30439483 GAAACAATCAATTTTCAT
1 GAAACAATTAATTTTCAT
30439501 GAAACAATCTAATT
1 GAAACAAT-TAATT
30439515 ACAATATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.36
Consensus pattern (18 bp):
GAAACAATTAATTTTCAT
Found at i:30440455 original size:18 final size:18
Alignment explanation
Indices: 30440432--30440467 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
30440422 TTCCTACAAA
30440432 GTATAGTTTGTAATTTAT
1 GTATAGTTTGTAATTTAT
30440450 GTATAGTTTGTAATTTAT
1 GTATAGTTTGTAATTTAT
30440468 CCTTTTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.56
Consensus pattern (18 bp):
GTATAGTTTGTAATTTAT
Found at i:30442895 original size:16 final size:16
Alignment explanation
Indices: 30442874--30442907 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
30442864 TTGAGATAAC
30442874 ATAAAT-AAATAATTAA
1 ATAAATCAAA-AATTAA
30442890 ATAAATCAAAAATTAA
1 ATAAATCAAAAATTAA
30442906 AT
1 AT
30442908 TCAAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAATCAAAAATTAA
Found at i:30444959 original size:12 final size:13
Alignment explanation
Indices: 30444934--30444964 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
30444924 TTCAAATGAA
30444934 TCATTTCTCATTT
1 TCATTTCTCATTT
30444947 TCATTTC-CATTT
1 TCATTTCTCATTT
30444959 TCATTT
1 TCATTT
30444965 TGAGAAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (13 bp):
TCATTTCTCATTT
Found at i:30454479 original size:18 final size:19
Alignment explanation
Indices: 30454453--30454498 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
30454443 GTGGTCCCTG
*
30454453 GCGGTGGCGTGGC-TCGGC
1 GCGGAGGCGTGGCTTCGGC
* *
30454471 TCGGAGGCGTGGCTTTGGC
1 GCGGAGGCGTGGCTTCGGC
30454490 GCGGAGGCG
1 GCGGAGGCG
30454499 CCACACGCGC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.04, C:0.24, G:0.54, T:0.17
Consensus pattern (19 bp):
GCGGAGGCGTGGCTTCGGC
Found at i:30459379 original size:14 final size:15
Alignment explanation
Indices: 30459352--30459383 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
30459342 GTTTGAAGCC
30459352 ATTTAGTCATTTTTA
1 ATTTAGTCATTTTTA
30459367 ATTTAGT-ATTTTTA
1 ATTTAGTCATTTTTA
30459381 ATT
1 ATT
30459384 CTACAGCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.62
Consensus pattern (15 bp):
ATTTAGTCATTTTTA
Found at i:30463181 original size:15 final size:15
Alignment explanation
Indices: 30463162--30463193 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30463152 TAGTGTTTTA
30463162 AAAAATAAATAAAAAT
1 AAAAA-AAATAAAAAT
30463178 AAAAAAAATAAAAAT
1 AAAAAAAATAAAAAT
30463193 A
1 A
30463194 GCCCCAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAAAAATAAAAAT
Found at i:30463184 original size:9 final size:9
Alignment explanation
Indices: 30463161--30463191 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
30463151 ATAGTGTTTT
30463161 AAAAAATAA
1 AAAAAATAA
30463170 ATAAAAATAA
1 A-AAAAATAA
30463180 AAAAAATAA
1 AAAAAATAA
30463189 AAA
1 AAA
30463192 TAGCCCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAAATAA
Found at i:30468177 original size:2 final size:2
Alignment explanation
Indices: 30468170--30468194 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30468160 TTTAAACATA
30468170 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
30468195 AACTCTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30477009 original size:16 final size:15
Alignment explanation
Indices: 30476979--30477015 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
30476969 CATTAAAAAA
30476979 ATAATAATAATAAAC
1 ATAATAATAATAAAC
*
30476994 ATAATAATGTATAAAC
1 ATAATAAT-AATAAAC
30477010 ATAATA
1 ATAATA
30477016 TATTAGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (15 bp):
ATAATAATAATAAAC
Found at i:30477311 original size:3 final size:3
Alignment explanation
Indices: 30477303--30477362 Score: 52
Period size: 3 Copynumber: 19.7 Consensus size: 3
30477293 TGCGGTAAGT
* * *
30477303 ATA ATA ATA AAA ATA TATA AT- ATA ATG ATA ATA A-A CTA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30477347 ATA CAGTA ATA ATA AT
1 ATA -A-TA ATA ATA AT
30477363 GTAATATATA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
2 3 0.07
3 36 0.78
4 5 0.11
5 2 0.04
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:30478220 original size:20 final size:21
Alignment explanation
Indices: 30478195--30478236 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
30478185 ACATGGCAGG
**
30478195 AAATGTTTTTTTTATAA-AAA
1 AAATGTTGATTTTATAACAAA
30478215 AAATGTTGATTTTATAACAAA
1 AAATGTTGATTTTATAACAAA
30478236 A
1 A
30478237 TTAAAACGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (21 bp):
AAATGTTGATTTTATAACAAA
Found at i:30481575 original size:19 final size:20
Alignment explanation
Indices: 30481535--30481577 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
30481525 TATTTTTGGA
*
30481535 AATTAATTTTCAAGTCAGAC
1 AATTAATTTTCAAGTCAAAC
*
30481555 AATTAA-TTTCAAGTTAAAC
1 AATTAATTTTCAAGTCAAAC
30481574 AATT
1 AATT
30481578 GAACCAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (20 bp):
AATTAATTTTCAAGTCAAAC
Found at i:30483703 original size:34 final size:34
Alignment explanation
Indices: 30483665--30483732 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
30483655 AAACATGAAA
30483665 TATTTGTT-AATCATTGGATAACCTAAGGAAGTGG
1 TATTT-TTCAATCATTGGATAACCTAAGGAAGTGG
* *
30483699 TATTTTTCTATCATTGGATAACCTAAGGTAGTGG
1 TATTTTTCAATCATTGGATAACCTAAGGAAGTGG
30483733 CAGTACCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 2 0.06
34 29 0.94
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.38
Consensus pattern (34 bp):
TATTTTTCAATCATTGGATAACCTAAGGAAGTGG
Found at i:30496578 original size:18 final size:17
Alignment explanation
Indices: 30496521--30496578 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
30496511 ATGTGAGAAG
30496521 TAAAAGTTTAGGGGAAAAA
1 TAAAAGTTTA-GGG-AAAA
* *
30496540 TAAAAAGTTT-TGGAGAA
1 T-AAAAGTTTAGGGAAAA
30496557 TAAAAGTTTGAGGGAAAA
1 TAAAAGTTT-AGGGAAAA
30496575 TAAA
1 TAAA
30496579 TAGGGGGAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
16 8 0.25
17 4 0.12
18 11 0.34
19 1 0.03
20 8 0.25
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
TAAAAGTTTAGGGAAAA
Done.