Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 4 of 373
Found at i:1009986 original size:116 final size:116
Alignment explanation
Indices: 1009811--1010077 Score: 462
Period size: 116 Copynumber: 2.3 Consensus size: 116
1009801 TTTATATTTT
* * *
1009811 ATTACTTGAAATAATATAAAAATATTCAAAATGTTGCTTTATTTAAAATAATTTTCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
*
1009876 AAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACATTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACATTTTATCTA
1009927 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
* *
1009992 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAATAACCTTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACATTTTATCTA
* *
1010043 ATTACATGAAATAATATAAAAAAATTTAAAATGTT
1 ATTACATGAAATAATATAAAAATATTCAAAATGTT
1010078 TGTACAAATA
Statistics
Matches: 143, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 143 1.00
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (116 bp):
ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACATTTTATCTA
Found at i:1010488 original size:18 final size:18
Alignment explanation
Indices: 1010462--1010504 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1010452 GACTAGAAAA
* *
1010462 AGGAAACATATAAGGGCT
1 AGGATACATAAAAGGGCT
1010480 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
1010498 AGGATAC
1 AGGATAC
1010505 GTACCTGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.44, C:0.12, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:1012311 original size:22 final size:22
Alignment explanation
Indices: 1012299--1012348 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
1012289 TAACGAGAGT
1012299 TTTGAGAGGAATTTAAGAGAAA
1 TTTGAGAGGAATTTAAGAGAAA
* *
1012321 TTTGAGA-G-ATTTGAGAGGAA
1 TTTGAGAGGAATTTAAGAGAAA
1012341 TTTGAGAG
1 TTTGAGAG
1012349 AATATTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 17 0.68
21 1 0.04
22 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (22 bp):
TTTGAGAGGAATTTAAGAGAAA
Found at i:1012356 original size:11 final size:10
Alignment explanation
Indices: 1012299--1012356 Score: 64
Period size: 11 Copynumber: 5.5 Consensus size: 10
1012289 TAACGAGAGT
1012299 TTTGAGAGGAA
1 TTTGAGA-GAA
*
1012310 TTTAAGAGAAA
1 TTTGAGAG-AA
1012321 TTTGAGAG-A
1 TTTGAGAGAA
1012330 TTTGAGAGGAA
1 TTTGAGA-GAA
1012341 TTTGAGAGAA
1 TTTGAGAGAA
1012351 TATTGA
1 T-TTGA
1012357 AAGATTGAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 8 0.20
10 6 0.15
11 27 0.66
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (10 bp):
TTTGAGAGAA
Found at i:1012362 original size:31 final size:31
Alignment explanation
Indices: 1012299--1012362 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1012289 TAACGAGAGT
*
1012299 TTTGAGAGGAATTTAAGAGAAATTTGAGAGA
1 TTTGAGAGGAATTTAAGAGAAATTTGAAAGA
*
1012330 TTTGAGAGGAATTTGAGAG-AATATTGAAAGA
1 TTTGAGAGGAATTTAAGAGAAAT-TTGAAAGA
1012361 TT
1 TT
1012363 GAAGATTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 3 0.10
31 27 0.90
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (31 bp):
TTTGAGAGGAATTTAAGAGAAATTTGAAAGA
Found at i:1012830 original size:67 final size:68
Alignment explanation
Indices: 1012743--1012878 Score: 247
Period size: 67 Copynumber: 2.0 Consensus size: 68
1012733 AAGTAGGAAA
*
1012743 AATGTTCTCTTTGTATTGTTTTTATAGTCTCTTCAGTGCAATGATAAGTCATATATATGACATAT
1 AATGTTCTCTTTGTATTGTTTTTATAGTCTCTTCAGTGCAATGATAAATCATATATATGACATAT
1012808 CAC
66 CAC
*
1012811 AATGTTCTC-TTGTATTGTTTTTATAGTCTCTTCAGTGCAATGATAAATCATATATATGACATCT
1 AATGTTCTCTTTGTATTGTTTTTATAGTCTCTTCAGTGCAATGATAAATCATATATATGACATAT
1012875 CAC
66 CAC
1012878 A
1 A
1012879 TGTCATGACC
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 57 0.86
68 9 0.14
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.43
Consensus pattern (68 bp):
AATGTTCTCTTTGTATTGTTTTTATAGTCTCTTCAGTGCAATGATAAATCATATATATGACATAT
CAC
Found at i:1013672 original size:46 final size:46
Alignment explanation
Indices: 1013566--1013886 Score: 444
Period size: 46 Copynumber: 7.0 Consensus size: 46
1013556 TTTGACATGA
* * * * ** * * *
1013566 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGC
** * *
1013613 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*** *** * *
1013659 TGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1013705 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1013751 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1013797 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1013843 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1013887 AGAGCACACT
Statistics
Matches: 253, Mismatches: 21, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
46 224 0.89
47 29 0.11
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
Found at i:1016060 original size:18 final size:20
Alignment explanation
Indices: 1016045--1016081 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1016035 TAATAATAAA
*
1016045 ATATCTCATTAAAATAATAT
1 ATATCTAATTAAAATAATAT
1016065 ATATCTAATT-AAATAAT
1 ATATCTAATTAAAATAAT
1016082 CATAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATCTAATTAAAATAATAT
Found at i:1017718 original size:30 final size:29
Alignment explanation
Indices: 1017654--1017720 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
1017644 ATAGGGATTT
*
1017654 GATCAAATTAGCCCTTCAACTATTAAATA
1 GATCAAATTAGCCCTTCAACTATTAAAAA
* *
1017683 GATCAATTTAGTCCCTT-TACTATTAAAAA
1 GATCAAATTAG-CCCTTCAACTATTAAAAA
1017712 GAATCAAAT
1 G-ATCAAAT
1017721 AAGACCAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 21 0.66
30 11 0.34
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (29 bp):
GATCAAATTAGCCCTTCAACTATTAAAAA
Found at i:1025349 original size:16 final size:17
Alignment explanation
Indices: 1025319--1025351 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1025309 AATCATTTTA
1025319 ATTAAAAAATCATTAAAT
1 ATTAAAAAA-CATTAAAT
1025337 ATTAAAAAA-ATTAAA
1 ATTAAAAAACATTAAA
1025352 AATATCAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
ATTAAAAAACATTAAAT
Found at i:1026791 original size:19 final size:19
Alignment explanation
Indices: 1026767--1026805 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1026757 GACAAAAAAA
1026767 TTATTTAATTATTGTTGGT
1 TTATTTAATTATTGTTGGT
1026786 TTATTTAATTATTGTTGGT
1 TTATTTAATTATTGTTGGT
1026805 T
1 T
1026806 CGGTAGTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (19 bp):
TTATTTAATTATTGTTGGT
Found at i:1026831 original size:9 final size:9
Alignment explanation
Indices: 1026814--1026843 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1026804 TTCGGTAGTC
1026814 GAACCAATT
1 GAACCAATT
*
1026823 GAACTAATT
1 GAACCAATT
1026832 GAACCAATT
1 GAACCAATT
1026841 GAA
1 GAA
1026844 TCGAAATCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (9 bp):
GAACCAATT
Found at i:1028870 original size:20 final size:20
Alignment explanation
Indices: 1028827--1028870 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1028817 TTTTTGTCTT
* * *
1028827 AAATCCATAAAATCTTACTT
1 AAATCCATAAAACCTAACTA
*
1028847 AAATCGATAAAACCTAACTA
1 AAATCCATAAAACCTAACTA
1028867 AAAT
1 AAAT
1028871 AAAACCCAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.18, G:0.02, T:0.27
Consensus pattern (20 bp):
AAATCCATAAAACCTAACTA
Found at i:1038001 original size:38 final size:38
Alignment explanation
Indices: 1037950--1038027 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
1037940 CACCGGTGTC
* *
1037950 CTATGCATATTTGGACGTATGTACCGAGATATGACTCT
1 CTATGCATATTTGGACATATGTACCAAGATATGACTCT
* *
1037988 CTATGTATATTTGGCCATATGTACCAAGATATGACTCT
1 CTATGCATATTTGGACATATGTACCAAGATATGACTCT
1038026 CT
1 CT
1038028 GAGGACTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (38 bp):
CTATGCATATTTGGACATATGTACCAAGATATGACTCT
Found at i:1041555 original size:38 final size:38
Alignment explanation
Indices: 1041512--1041590 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 38
1041502 GAATCAAATT
* * **
1041512 AGACCAACCAAATTAAAAGTCAATCGATGTAATGGTCG
1 AGACCAACCAAATCAAAAATCAATCGACATAATGGTCG
* * *
1041550 AGACCAACTAGATCAAAAATCAGTCGACATAATGGTCG
1 AGACCAACCAAATCAAAAATCAATCGACATAATGGTCG
1041588 AGA
1 AGA
1041591 GAAAGATATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (38 bp):
AGACCAACCAAATCAAAAATCAATCGACATAATGGTCG
Found at i:1059500 original size:3 final size:3
Alignment explanation
Indices: 1059492--1059519 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1059482 TTTAAAATTA
1059492 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1059520 CAATAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1059959 original size:6 final size:6
Alignment explanation
Indices: 1059948--1059972 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1059938 GAAAGGAAAG
1059948 AGATGA AGATGA AGATGA AGATGA A
1 AGATGA AGATGA AGATGA AGATGA A
1059973 ACGACTGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (6 bp):
AGATGA
Found at i:1068223 original size:21 final size:21
Alignment explanation
Indices: 1068199--1068242 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1068189 GAAATGAACA
1068199 TAGTTTTGGTCGTATAATGTT
1 TAGTTTTGGTCGTATAATGTT
1068220 TAGTTTTGGTCGTATAATGTT
1 TAGTTTTGGTCGTATAATGTT
1068241 TA
1 TA
1068243 TTGTTATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.05, G:0.23, T:0.52
Consensus pattern (21 bp):
TAGTTTTGGTCGTATAATGTT
Found at i:1076583 original size:25 final size:25
Alignment explanation
Indices: 1076554--1076601 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1076544 CCAAATATTT
1076554 ATTTTAAAAAAAAT-AGTAATTTAAA
1 ATTTTAAAAAAAATAAG-AATTTAAA
**
1076579 ATTTTTTAAAAAATAAGAATTTA
1 ATTTTAAAAAAAATAAGAATTTA
1076602 TTCAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTTTAAAAAAAATAAGAATTTAAA
Found at i:1082898 original size:16 final size:17
Alignment explanation
Indices: 1082877--1082914 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1082867 CATTTTAGTG
*
1082877 TTTATTTTTAT-ATTTA
1 TTTATTTATATAATTTA
*
1082893 TTTATTTATATAATTTT
1 TTTATTTATATAATTTA
1082910 TTTAT
1 TTTAT
1082915 ACTAGCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTATATAATTTA
Found at i:1083126 original size:14 final size:14
Alignment explanation
Indices: 1083109--1083142 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1083099 GGGTTCTGAG
1083109 TTTAGGGTTCAAGA
1 TTTAGGGTTCAAGA
*
1083123 TTTAAGGTTCAAGA
1 TTTAGGGTTCAAGA
1083137 TTTAGG
1 TTTAGG
1083143 TTTTAGGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.38
Consensus pattern (14 bp):
TTTAGGGTTCAAGA
Found at i:1083149 original size:7 final size:7
Alignment explanation
Indices: 1083137--1083165 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1083127 AGGTTCAAGA
1083137 TTTAGGT
1 TTTAGGT
1083144 TTTAGGT
1 TTTAGGT
1083151 TTTAGGT
1 TTTAGGT
1083158 TTTAGGT
1 TTTAGGT
1083165 T
1 T
1083166 CAAAGTTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.59
Consensus pattern (7 bp):
TTTAGGT
Found at i:1084689 original size:22 final size:22
Alignment explanation
Indices: 1084658--1084716 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
1084648 AAATTTTTAA
1084658 TAAATAAAAAATAA-AAAAATAT
1 TAAAT-AAAAATAATAAAAATAT
* *
1084680 TAAATTAAAATAATATAAATAT
1 TAAATAAAAATAATAAAAATAT
***
1084702 TTTTTAAAAATAATA
1 TAAATAAAAATAATA
1084717 TGGACGAGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 7 0.23
22 23 0.77
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAATAAAAATAATAAAAATAT
Found at i:1085379 original size:275 final size:275
Alignment explanation
Indices: 1084888--1085437 Score: 1100
Period size: 275 Copynumber: 2.0 Consensus size: 275
1084878 CCATGAACAC
1084888 CTCTACTCCTGAATATGGGCAAAAAAAAATATTATCAAATTTAGTTGAATTGTAATTAGGGTTGA
1 CTCTACTCCTGAATATGGGCAAAAAAAAATATTATCAAATTTAGTTGAATTGTAATTAGGGTTGA
1084953 AAATTCATTGAACTAAAACATTTTGGTCAAAATCTAATTCAAAGGTTCAACCCCTAATTTTAATT
66 AAATTCATTGAACTAAAACATTTTGGTCAAAATCTAATTCAAAGGTTCAACCCCTAATTTTAATT
1085018 CAAAACAAAGTGTATCAAAGTCAAATTTCCCCTTTTTATCCATTGCTCACATGATTTTTGTTTCA
131 CAAAACAAAGTGTATCAAAGTCAAATTTCCCCTTTTTATCCATTGCTCACATGATTTTTGTTTCA
1085083 ATTTATTAAAAAAAGTTATTTTATGTTTTGTAGTGTTTGATTTTGAGTTTGGAGGTTCATATGCA
196 ATTTATTAAAAAAAGTTATTTTATGTTTTGTAGTGTTTGATTTTGAGTTTGGAGGTTCATATGCA
1085148 ATGTGGCCCACTAAT
261 ATGTGGCCCACTAAT
1085163 CTCTACTCCTGAATATGGGCAAAAAAAAATATTATCAAATTTAGTTGAATTGTAATTAGGGTTGA
1 CTCTACTCCTGAATATGGGCAAAAAAAAATATTATCAAATTTAGTTGAATTGTAATTAGGGTTGA
1085228 AAATTCATTGAACTAAAACATTTTGGTCAAAATCTAATTCAAAGGTTCAACCCCTAATTTTAATT
66 AAATTCATTGAACTAAAACATTTTGGTCAAAATCTAATTCAAAGGTTCAACCCCTAATTTTAATT
1085293 CAAAACAAAGTGTATCAAAGTCAAATTTCCCCTTTTTATCCATTGCTCACATGATTTTTGTTTCA
131 CAAAACAAAGTGTATCAAAGTCAAATTTCCCCTTTTTATCCATTGCTCACATGATTTTTGTTTCA
1085358 ATTTATTAAAAAAAGTTATTTTATGTTTTGTAGTGTTTGATTTTGAGTTTGGAGGTTCATATGCA
196 ATTTATTAAAAAAAGTTATTTTATGTTTTGTAGTGTTTGATTTTGAGTTTGGAGGTTCATATGCA
1085423 ATGTGGCCCACTAAT
261 ATGTGGCCCACTAAT
1085438 AAATTTTGAA
Statistics
Matches: 275, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
275 275 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (275 bp):
CTCTACTCCTGAATATGGGCAAAAAAAAATATTATCAAATTTAGTTGAATTGTAATTAGGGTTGA
AAATTCATTGAACTAAAACATTTTGGTCAAAATCTAATTCAAAGGTTCAACCCCTAATTTTAATT
CAAAACAAAGTGTATCAAAGTCAAATTTCCCCTTTTTATCCATTGCTCACATGATTTTTGTTTCA
ATTTATTAAAAAAAGTTATTTTATGTTTTGTAGTGTTTGATTTTGAGTTTGGAGGTTCATATGCA
ATGTGGCCCACTAAT
Found at i:1095671 original size:14 final size:13
Alignment explanation
Indices: 1095634--1095676 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
1095624 GATATATAAA
1095634 TTATTATTTTAAT
1 TTATTATTTTAAT
1095647 CTCTATT-TTTTAAT
1 -T-TATTATTTTAAT
1095661 TTATTTATTTTAAT
1 TTA-TTATTTTAAT
1095675 TT
1 TT
1095677 TTCATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 2 0.08
13 3 0.12
14 17 0.65
15 4 0.15
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTATTTTAAT
Found at i:1097757 original size:2 final size:2
Alignment explanation
Indices: 1097750--1097774 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1097740 CTTTTTATTC
1097750 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
1097775 AATTAGTAGC
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:1099365 original size:23 final size:22
Alignment explanation
Indices: 1099322--1099368 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
1099312 TATTCTTTAG
* *
1099322 ATTTTACATATATATTTTTAAA
1 ATTTTACATATATAATCTTAAA
*
1099344 ATTTTACATGTTATAATCTTAAA
1 ATTTTACAT-ATATAATCTTAAA
1099367 AT
1 AT
1099369 ACCATGTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTTTACATATATAATCTTAAA
Found at i:1108145 original size:22 final size:22
Alignment explanation
Indices: 1108111--1108153 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1108101 ATTGAAACAA
*
1108111 AAAAAAATTAAATATCAAATTG
1 AAAAAAATCAAATATCAAATTG
*
1108133 AAAAAACTCAAATATCAAATT
1 AAAAAAATCAAATATCAAATT
1108154 TAATATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAAAAATCAAATATCAAATTG
Found at i:1108177 original size:31 final size:32
Alignment explanation
Indices: 1108135--1108199 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
1108125 TCAAATTGAA
* * *
1108135 AAAACTCAAATA-TCAAATTTAATATT-AAATC
1 AAAACTAAAATACT-AAATTAAACATTAAAATC
1108166 AAAACTAAAATACTAAATTAAACATTAAAATC
1 AAAACTAAAATACTAAATTAAACATTAAAATC
1108198 AA
1 AA
1108200 CATAAATACC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 21 0.72
32 8 0.28
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (32 bp):
AAAACTAAAATACTAAATTAAACATTAAAATC
Found at i:1108243 original size:16 final size:16
Alignment explanation
Indices: 1108222--1108253 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1108212 ATCCTTATTA
1108222 AAATTATTTTTAATTT
1 AAATTATTTTTAATTT
1108238 AAATTATTTTTAATTT
1 AAATTATTTTTAATTT
1108254 GCATAAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AAATTATTTTTAATTT
Found at i:1115852 original size:19 final size:21
Alignment explanation
Indices: 1115820--1115859 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
1115810 ATATATAATT
1115820 AAAAGATTATAAAAATAAAAA
1 AAAAGATTATAAAAATAAAAA
1115841 AAAAG-TTA-AAAAATAAAAA
1 AAAAGATTATAAAAATAAAAA
1115860 TATTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.58
20 3 0.16
21 5 0.26
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (21 bp):
AAAAGATTATAAAAATAAAAA
Found at i:1116879 original size:23 final size:24
Alignment explanation
Indices: 1116853--1116907 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
1116843 AAGCCTACCC
* *
1116853 ATATTAATTTTA-ATTTTTTTAAG
1 ATATTAATATTATATTATTTTAAG
* *
1116876 ATATTTATATTATATTATTTTAAT
1 ATATTAATATTATATTATTTTAAG
1116900 AT-TTAATA
1 ATATTAATA
1116908 AGTCTATACA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
ATATTAATATTATATTATTTTAAG
Found at i:1125404 original size:15 final size:15
Alignment explanation
Indices: 1125384--1125413 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1125374 AGATGAAGGA
1125384 GGTGAAACTTCTTCC
1 GGTGAAACTTCTTCC
1125399 GGTGAAACTTCTTCC
1 GGTGAAACTTCTTCC
1125414 TCAAGACAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (15 bp):
GGTGAAACTTCTTCC
Found at i:1127301 original size:21 final size:22
Alignment explanation
Indices: 1127271--1127311 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1127261 ACACCAAGAA
*
1127271 AAAATCCAAATTCTAAAATATG
1 AAAATCCAAATACTAAAATATG
1127293 AAAA-CCAAATACTAAAATA
1 AAAATCCAAATACTAAAATA
1127312 CCCAGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.61, C:0.15, G:0.02, T:0.22
Consensus pattern (22 bp):
AAAATCCAAATACTAAAATATG
Found at i:1133384 original size:82 final size:82
Alignment explanation
Indices: 1133247--1133413 Score: 334
Period size: 82 Copynumber: 2.0 Consensus size: 82
1133237 AATTTGTTTC
1133247 ATATACACCTTGTTCTAGTAGTAGAAAAATAACAGTAGCTGATGGTTCTGTGATCACAGTGGCCG
1 ATATACACCTTGTTCTAGTAGTAGAAAAATAACAGTAGCTGATGGTTCTGTGATCACAGTGGCCG
1133312 GTCAAGGTGATATTGTT
66 GTCAAGGTGATATTGTT
1133329 ATATACACCTTGTTCTAGTAGTAGAAAAATAACAGTAGCTGATGGTTCTGTGATCACAGTGGCCG
1 ATATACACCTTGTTCTAGTAGTAGAAAAATAACAGTAGCTGATGGTTCTGTGATCACAGTGGCCG
1133394 GTCAAGGTGATATTGTT
66 GTCAAGGTGATATTGTT
1133411 ATA
1 ATA
1133414 AACAAAAACC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 85 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (82 bp):
ATATACACCTTGTTCTAGTAGTAGAAAAATAACAGTAGCTGATGGTTCTGTGATCACAGTGGCCG
GTCAAGGTGATATTGTT
Found at i:1134682 original size:21 final size:21
Alignment explanation
Indices: 1134656--1134696 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1134646 TCCAGCAACC
*
1134656 AAACACTCTCATTCCAGCTCT
1 AAACACTCCCATTCCAGCTCT
*
1134677 AAACACTCCCATTCCGGCTC
1 AAACACTCCCATTCCAGCTC
1134697 CTGTCCAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.41, G:0.07, T:0.24
Consensus pattern (21 bp):
AAACACTCCCATTCCAGCTCT
Found at i:1143180 original size:33 final size:33
Alignment explanation
Indices: 1143142--1143208 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1143132 TGGTCAAAGC
*
1143142 TAACGACACAATTTTCACACCATCATCAGATGT
1 TAACGACACAATTCTCACACCATCATCAGATGT
1143175 TAACGACACAATTCTCACACCATCATCAGATGT
1 TAACGACACAATTCTCACACCATCATCAGATGT
1143208 T
1 T
1143209 CTTAAAGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.28, G:0.09, T:0.27
Consensus pattern (33 bp):
TAACGACACAATTCTCACACCATCATCAGATGT
Found at i:1164565 original size:19 final size:20
Alignment explanation
Indices: 1164530--1164575 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
1164520 AATTTTTATT
*
1164530 AAAAATATATAATACAT-AA
1 AAAAATATATAAAACATCAA
1164549 AAAAATACTA-AAAACATCAA
1 AAAAATA-TATAAAACATCAA
1164569 AATAAAT
1 AA-AAAT
1164576 GTTTCCTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 13 0.57
20 6 0.26
21 4 0.17
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAAATATATAAAACATCAA
Found at i:1181119 original size:10 final size:9
Alignment explanation
Indices: 1181094--1181118 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1181084 TTTTAAAAGG
1181094 AAAAAAATT
1 AAAAAAATT
1181103 AAAAAAATT
1 AAAAAAATT
1181112 AAAAAAA
1 AAAAAAA
1181119 AAAGGAAAAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAAAATT
Found at i:1190154 original size:8 final size:8
Alignment explanation
Indices: 1190141--1190218 Score: 60
Period size: 8 Copynumber: 10.0 Consensus size: 8
1190131 TTATGTTTAA
1190141 TATATTAT
1 TATATTAT
1190149 TATATTAT
1 TATATTAT
1190157 TATATTAT
1 TATATTAT
*
1190165 TATATAATAAA
1 TATAT--T-AT
1190176 TATATT-T
1 TATATTAT
*
1190183 TATGTT-T
1 TATATTAT
1190190 TA-ATTA-
1 TATATTAT
1190196 TAT-TATAT
1 TATAT-TAT
1190204 TATATTA-
1 TATATTAT
1190211 TATATTAT
1 TATATTAT
1190219 ATTATATAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
6 5 0.09
7 17 0.30
8 26 0.46
9 2 0.04
10 1 0.02
11 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (8 bp):
TATATTAT
Found at i:1190156 original size:5 final size:5
Alignment explanation
Indices: 1190146--1190225 Score: 51
Period size: 5 Copynumber: 15.6 Consensus size: 5
1190136 TTTAATATAT
* * *
1190146 TATTA TATTA T-TATA TTATTA TATAA TAAATA TATTT TATGT- T-TTA
1 TATTA TATTA TAT-TA -TATTA TATTA T-ATTA TATTA TAT-TA TATTA
1190192 -ATTA TATTA TATTA TATTATA TATTA TATTA TAT
1 TATTA TATTA TATTA TA-T-TA TATTA TATTA TAT
1190226 AAATAAGTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
3 1 0.02
4 5 0.08
5 40 0.67
6 9 0.15
7 5 0.08
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:1190217 original size:51 final size:53
Alignment explanation
Indices: 1190129--1190230 Score: 142
Period size: 51 Copynumber: 2.0 Consensus size: 53
1190119 TTAAGATTTT
1190129 TTTTATGTTTAATATATTATTATATTATTATATTATTATA-TA-ATAAATATA
1 TTTTATGTTTAATATATTATTATATTATTATATTATTATATTATATAAATATA
1190180 TTTTATGTTTTAAT-TA-TATTATATTA-TATTATATATTATATTATATAAATA
1 TTTTATG-TTTAATATATTATTATATTATTA-TAT-TATTATATTATATAAATA
1190231 AGTAAAGAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
49 2 0.04
50 13 0.28
51 16 0.35
52 8 0.17
53 7 0.15
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (53 bp):
TTTTATGTTTAATATATTATTATATTATTATATTATTATATTATATAAATATA
Found at i:1191519 original size:15 final size:15
Alignment explanation
Indices: 1191499--1191574 Score: 93
Period size: 15 Copynumber: 5.1 Consensus size: 15
1191489 TATGCGATGA
*
1191499 ATTTATTGAATTTAT
1 ATTTATTGAAATTAT
1191514 ATTTATTGAAATTAT
1 ATTTATTGAAATTAT
*
1191529 ATTGATTGAAATTAT
1 ATTTATTGAAATTAT
*
1191544 -TTTGATTGAATTTAT
1 ATTT-ATTGAAATTAT
*
1191559 ATTGATTG-AATTAT
1 ATTTATTGAAATTAT
1191573 AT
1 AT
1191575 AATATATATG
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
14 9 0.17
15 42 0.79
16 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.54
Consensus pattern (15 bp):
ATTTATTGAAATTAT
Found at i:1191552 original size:30 final size:30
Alignment explanation
Indices: 1191503--1191574 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
1191493 CGATGAATTT
*
1191503 ATTGAATTTATATTTATTGAAATTATATTG
1 ATTGAAATTATATTTATTGAAATTATATTG
*
1191533 ATTGAAATTAT-TTTGATTGAATTTATATTG
1 ATTGAAATTATATTT-ATTGAAATTATATTG
1191563 ATTG-AATTATAT
1 ATTGAAATTATAT
1191575 AATATATATG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 9 0.24
30 29 0.76
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (30 bp):
ATTGAAATTATATTTATTGAAATTATATTG
Found at i:1191987 original size:23 final size:23
Alignment explanation
Indices: 1191961--1192035 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 23
1191951 AGGCACTTTA
1191961 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
1191984 TGTGTCGTA--TCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
* **
1192005 TGTGTCGT-TTT-AGGCACTTTA
1 TGTGTCGTATTTCAGGCACCTCG
1192026 TGTGTCGTAT
1 TGTGTCGTAT
1192036 ACTGATCAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
21 35 0.76
22 2 0.04
23 9 0.20
ACGTcount: A:0.13, C:0.21, G:0.27, T:0.39
Consensus pattern (23 bp):
TGTGTCGTATTTCAGGCACCTCG
Found at i:1194858 original size:18 final size:19
Alignment explanation
Indices: 1194830--1194870 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
1194820 GATATAGGCC
1194830 CCTTTT-TTTTTT-CTTTT
1 CCTTTTCTTTTTTCCTTTT
1194847 -CTTTTCTTTTTTCCTTTT
1 CCTTTTCTTTTTTCCTTTT
1194865 CCTTTT
1 CCTTTT
1194871 TTCTTACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.24
17 6 0.29
18 5 0.24
19 5 0.24
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (19 bp):
CCTTTTCTTTTTTCCTTTT
Found at i:1195418 original size:29 final size:28
Alignment explanation
Indices: 1195385--1195455 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 28
1195375 AAACCGTAAA
* *
1195385 AAAATATTAAAAACAGTAAAAAGTATTTT
1 AAAATATTAAAAACAGTAAAAAATA-ATT
**
1195414 AAAATATATAAAAATTGTAAAAAATAATT
1 AAAATAT-TAAAAACAGTAAAAAATAATT
*
1195443 AAATTATTAAAAA
1 AAAATATTAAAAA
1195456 AGCAAATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 6 0.17
29 15 0.42
30 15 0.42
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (28 bp):
AAAATATTAAAAACAGTAAAAAATAATT
Found at i:1195437 original size:20 final size:20
Alignment explanation
Indices: 1195414--1195587 Score: 67
Period size: 20 Copynumber: 8.9 Consensus size: 20
1195404 AAAGTATTTT
1195414 AAAATATATAAAAATTGTAA
1 AAAATATATAAAAATTGTAA
* * *
1195434 AAAATA-AT-TAAATTATTA
1 AAAATATATAAAAATTGTAA
** * *
1195452 AAAA-A-GCAAATATTGTTA
1 AAAATATATAAAAATTGTAA
* * *
1195470 ACAATATTTTAAAATTGTAA
1 AAAATATATAAAAATTGTAA
*
1195490 AAAA-ATATTAAAAATTATAA
1 AAAATATA-TAAAAATTGTAA
* **
1195510 AATAT-TAATTAAATTTTGTAA
1 AAAATAT-A-TAAAAATTGTAA
* *
1195531 AAATTAT-TAAAAATTGCAA
1 AAAATATATAAAAATTGTAA
* *
1195550 ATAAT-TATTAAAAGTTGTAA
1 AAAATATA-TAAAAATTGTAA
* * *
1195570 AAATTATTTCAAAATTGT
1 AAAATATATAAAAATTGT
1195588 GAACCAATAG
Statistics
Matches: 108, Mismatches: 36, Indels: 20
0.66 0.22 0.12
Matches are distributed among these distances:
17 1 0.01
18 22 0.20
19 17 0.16
20 52 0.48
21 15 0.14
22 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (20 bp):
AAAATATATAAAAATTGTAA
Found at i:1195522 original size:21 final size:19
Alignment explanation
Indices: 1195489--1195577 Score: 79
Period size: 19 Copynumber: 4.5 Consensus size: 19
1195479 TAAAATTGTA
*
1195489 AAAAAATATTAAAAATTAT
1 AAAAATTATTAAAAATTAT
** *
1195508 AAAATATTAATTAAATTTTGT
1 AAAA-ATT-ATTAAAAATTAT
**
1195529 AAAAATTATTAAAAATTGC
1 AAAAATTATTAAAAATTAT
* *
1195548 AAATAATTATTAAAAGTTGT
1 AAA-AATTATTAAAAATTAT
1195568 AAAAATTATT
1 AAAAATTATT
1195578 TCAAAATTGT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
19 23 0.40
20 22 0.38
21 13 0.22
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (19 bp):
AAAAATTATTAAAAATTAT
Found at i:1195534 original size:11 final size:10
Alignment explanation
Indices: 1195489--1195577 Score: 53
Period size: 10 Copynumber: 9.0 Consensus size: 10
1195479 TAAAATTGTA
*
1195489 AAAAAATATT
1 AAAAATTATT
1195499 AAAAATTA-T
1 AAAAATTATT
1195508 -AAAA-TATT
1 AAAAATTATT
*
1195516 AATTAAATTTTGT
1 AA--AAATTAT-T
1195529 AAAAATTATT
1 AAAAATTATT
**
1195539 AAAAATT-GC
1 AAAAATTATT
1195548 AAATAATTATT
1 AAA-AATTATT
* *
1195559 AAAAGTT-GT
1 AAAAATTATT
1195568 AAAAATTATT
1 AAAAATTATT
1195578 TCAAAATTGT
Statistics
Matches: 59, Mismatches: 11, Indels: 18
0.67 0.12 0.20
Matches are distributed among these distances:
7 2 0.03
8 5 0.08
9 12 0.20
10 23 0.39
11 12 0.20
12 2 0.03
13 3 0.05
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (10 bp):
AAAAATTATT
Found at i:1195552 original size:39 final size:39
Alignment explanation
Indices: 1195478--1195586 Score: 114
Period size: 40 Copynumber: 2.7 Consensus size: 39
1195468 TAACAATATT
* *
1195478 TTAAAA-TTGTAAAAAAATATTAAAAATTATAAAAT-ATTAA
1 TTAAAAGTTGT-AAAAATTATTAAAAATT-GAAAATAATT-A
** *
1195518 TTAAATTTTGTAAAAATTATTAAAAATTGCAAATAATTA
1 TTAAAAGTTGTAAAAATTATTAAAAATTGAAAATAATTA
*
1195557 TTAAAAGTTGTAAAAATTATTTCAAAATTG
1 TTAAAAGTTGTAAAAATTA-TTAAAAATTG
1195587 TGAACCAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 22 0.37
40 33 0.56
41 4 0.07
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.39
Consensus pattern (39 bp):
TTAAAAGTTGTAAAAATTATTAAAAATTGAAAATAATTA
Found at i:1201642 original size:25 final size:25
Alignment explanation
Indices: 1201609--1201660 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1201599 TGATAAACAT
*
1201609 ATTCAAATACTT-AAAAAAATTATAA
1 ATTCAAATAATTCAAAAAAA-TATAA
*
1201634 ATTCGAATAATTCAAAAAAATATAA
1 ATTCAAATAATTCAAAAAAATATAA
1201659 AT
1 AT
1201661 ATTTGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.31
Consensus pattern (25 bp):
ATTCAAATAATTCAAAAAAATATAA
Found at i:1202259 original size:19 final size:19
Alignment explanation
Indices: 1202235--1202274 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1202225 ACATTAGGTA
1202235 AAACATAAAAAGATGTGTT
1 AAACATAAAAAGATGTGTT
1202254 AAACATAAAAAGATGTGTT
1 AAACATAAAAAGATGTGTT
1202273 AA
1 AA
1202275 GTGGTCTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (19 bp):
AAACATAAAAAGATGTGTT
Found at i:1207766 original size:39 final size:40
Alignment explanation
Indices: 1207723--1207801 Score: 151
Period size: 39 Copynumber: 2.0 Consensus size: 40
1207713 TTAAAACTCA
1207723 TTTTGTAGGTCTAACATTTTTATCCACA-CTTCGAACTTG
1 TTTTGTAGGTCTAACATTTTTATCCACACCTTCGAACTTG
1207762 TTTTGTAGGTCTAACATTTTTATCCACACCTTCGAACTTG
1 TTTTGTAGGTCTAACATTTTTATCCACACCTTCGAACTTG
1207802 GATAAATAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
39 28 0.72
40 11 0.28
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.43
Consensus pattern (40 bp):
TTTTGTAGGTCTAACATTTTTATCCACACCTTCGAACTTG
Found at i:1208269 original size:7 final size:7
Alignment explanation
Indices: 1208257--1208291 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
1208247 TGCTTTACTG
1208257 CTCACCA
1 CTCACCA
1208264 CTCACCA
1 CTCACCA
1208271 CTCACCA
1 CTCACCA
1208278 CTCACCA
1 CTCACCA
1208285 CTCACCA
1 CTCACCA
1208292 TATATTCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.57, G:0.00, T:0.14
Consensus pattern (7 bp):
CTCACCA
Found at i:1208307 original size:3 final size:3
Alignment explanation
Indices: 1208299--1208326 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1208289 CCATATATTC
1208299 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1208327 AGAAGCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1209808 original size:29 final size:29
Alignment explanation
Indices: 1209738--1209810 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 29
1209728 ACATTTTATT
1209738 TTTTTATTAAAAAAATAGATAAATTAATC
1 TTTTTATTAAAAAAATAGATAAATTAATC
* *
1209767 TTTGTATATTAAATATAA-A-ATAAATTGATC
1 TTT-T-TATTAAA-AAAATAGATAAATTAATC
1209797 ATTTTTATTAAAAA
1 -TTTTTATTAAAAA
1209811 TTTCATCCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
28 1 0.03
29 10 0.27
30 12 0.32
31 11 0.30
32 3 0.08
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (29 bp):
TTTTTATTAAAAAAATAGATAAATTAATC
Found at i:1212545 original size:15 final size:15
Alignment explanation
Indices: 1212525--1212558 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1212515 TTTGAACCAG
* *
1212525 ATTTTTTATATTTTT
1 ATTTTTTAAATATTT
1212540 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
1212555 ATTT
1 ATTT
1212559 AATCAAACCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTTTAAATATTT
Found at i:1214421 original size:5 final size:5
Alignment explanation
Indices: 1214413--1214453 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
1214403 ATTACATGAC
1214413 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
1214454 ACTTAGAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:1223380 original size:18 final size:18
Alignment explanation
Indices: 1223357--1223394 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1223347 ACATCAATAT
1223357 TTTCTACATCAAACCCAG
1 TTTCTACATCAAACCCAG
*
1223375 TTTCTACATCGAACCCAG
1 TTTCTACATCAAACCCAG
1223393 TT
1 TT
1223395 CCAACCGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.32, G:0.08, T:0.32
Consensus pattern (18 bp):
TTTCTACATCAAACCCAG
Found at i:1231267 original size:29 final size:29
Alignment explanation
Indices: 1231213--1231277 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
1231203 TGAATTTTAA
* * * *
1231213 TTTTAATATAATTTGGACTCATTTAATTT
1 TTTTAATATAATGTGGACTAAATTAATCT
1231242 TTTTAATA-ATATGTGGACTAAATTAATCT
1 TTTTAATATA-ATGTGGACTAAATTAATCT
*
1231271 ATTTAAT
1 TTTTAAT
1231278 TATCCAATCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 1 0.03
29 29 0.97
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (29 bp):
TTTTAATATAATGTGGACTAAATTAATCT
Found at i:1237666 original size:7 final size:7
Alignment explanation
Indices: 1237630--1237654 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1237620 TTTAATTTCC
1237630 TTTTAAA
1 TTTTAAA
1237637 TTTTAAA
1 TTTTAAA
1237644 TTTTAAA
1 TTTTAAA
1237651 TTTT
1 TTTT
1237655 CATTTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:1239511 original size:39 final size:39
Alignment explanation
Indices: 1239401--1239538 Score: 104
Period size: 39 Copynumber: 3.5 Consensus size: 39
1239391 GACCTCGAGT
* *
1239401 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT-
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCT--ATTC
** * **
1239442 CGATGAGGTACAGGGTACCAACT-TTACTTCGGCTATTC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTATTC
* *
1239480 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTATTC
* *
1239519 CGATGAGGCACTGAGTGTCA
1 CGATGAGACACTGGGTGTCA
1239539 TTTGGTGTGT
Statistics
Matches: 77, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
37 3 0.04
38 18 0.23
39 36 0.47
40 4 0.05
41 14 0.18
42 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTATTC
Found at i:1240242 original size:20 final size:20
Alignment explanation
Indices: 1240219--1240256 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1240209 GTTATTAAAT
1240219 TAAAAATTATGTTA-ATGATA
1 TAAAAATTA-GTTATATGATA
*
1240239 TAAATATTAGTTATATGA
1 TAAAAATTAGTTATATGA
1240257 ATGTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAAATTAGTTATATGATA
Found at i:1241329 original size:6 final size:6
Alignment explanation
Indices: 1241288--1241326 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
1241278 AATAATAATT
*
1241288 TTATAA TTATAA TTATAA -T-TAA TTATAA TTATAT TTATA
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTATA
1241327 TTTTTATCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
4 3 0.10
5 2 0.07
6 25 0.83
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:1241521 original size:9 final size:9
Alignment explanation
Indices: 1241507--1241531 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1241497 AGAAAACTTT
1241507 TTTAGTGCA
1 TTTAGTGCA
1241516 TTTAGTGCA
1 TTTAGTGCA
1241525 TTTAGTG
1 TTTAGTG
1241532 TATTATATAT
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:0.20, C:0.08, G:0.24, T:0.48
Consensus pattern (9 bp):
TTTAGTGCA
Found at i:1244467 original size:15 final size:15
Alignment explanation
Indices: 1244444--1244482 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
1244434 TATATTTACC
1244444 AAATAAATTTTC-AT
1 AAATAAATTTTCAAT
1244458 AAATTAAATTTTCAAT
1 AAA-TAAATTTTCAAT
1244474 AAATAAATT
1 AAATAAATT
1244483 ATTATTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.13
15 15 0.65
16 5 0.22
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATAAATTTTCAAT
Found at i:1249745 original size:15 final size:15
Alignment explanation
Indices: 1249725--1249772 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
1249715 AAATTCAACA
1249725 ATTAATTATTAAAAT
1 ATTAATTATTAAAAT
* *
1249740 ATTAATTATAAAAAA
1 ATTAATTATTAAAAT
*
1249755 ATTAATATATTTAAAT
1 ATTAAT-TATTAAAAT
1249771 AT
1 AT
1249773 CATCTCAAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 19 0.70
16 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAATTATTAAAAT
Found at i:1251091 original size:18 final size:18
Alignment explanation
Indices: 1251054--1251092 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1251044 TTCTAAATAT
* *
1251054 AATTAATTAATTAATTAA
1 AATTAATTAATCAATAAA
*
1251072 AATTAATTAATCGATAAA
1 AATTAATTAATCAATAAA
1251090 AAT
1 AAT
1251093 AGTAGCAGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
AATTAATTAATCAATAAA
Found at i:1254901 original size:174 final size:174
Alignment explanation
Indices: 1254611--1254958 Score: 696
Period size: 174 Copynumber: 2.0 Consensus size: 174
1254601 ATTAGTTGAA
1254611 AAAATCTATTAAAACAGAAGTTGGTGTTGTGGGGCTTTAATTAGTGTCAAATTTCTCTAATTATT
1 AAAATCTATTAAAACAGAAGTTGGTGTTGTGGGGCTTTAATTAGTGTCAAATTTCTCTAATTATT
1254676 TAATTAATCACAAATTTTTCTCTATCATTTGGATAGCACCTAGTCTTACTTAAAACTATATTTAT
66 TAATTAATCACAAATTTTTCTCTATCATTTGGATAGCACCTAGTCTTACTTAAAACTATATTTAT
1254741 CTGGGATTTTTTTTGAAAAGTTCTCACTCCAATGCTTCCCCCCC
131 CTGGGATTTTTTTTGAAAAGTTCTCACTCCAATGCTTCCCCCCC
1254785 AAAATCTATTAAAACAGAAGTTGGTGTTGTGGGGCTTTAATTAGTGTCAAATTTCTCTAATTATT
1 AAAATCTATTAAAACAGAAGTTGGTGTTGTGGGGCTTTAATTAGTGTCAAATTTCTCTAATTATT
1254850 TAATTAATCACAAATTTTTCTCTATCATTTGGATAGCACCTAGTCTTACTTAAAACTATATTTAT
66 TAATTAATCACAAATTTTTCTCTATCATTTGGATAGCACCTAGTCTTACTTAAAACTATATTTAT
1254915 CTGGGATTTTTTTTGAAAAGTTCTCACTCCAATGCTTCCCCCCC
131 CTGGGATTTTTTTTGAAAAGTTCTCACTCCAATGCTTCCCCCCC
1254959 CCCCCAAAAT
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 174 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (174 bp):
AAAATCTATTAAAACAGAAGTTGGTGTTGTGGGGCTTTAATTAGTGTCAAATTTCTCTAATTATT
TAATTAATCACAAATTTTTCTCTATCATTTGGATAGCACCTAGTCTTACTTAAAACTATATTTAT
CTGGGATTTTTTTTGAAAAGTTCTCACTCCAATGCTTCCCCCCC
Found at i:1255244 original size:22 final size:22
Alignment explanation
Indices: 1255216--1255260 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1255206 ATTATATTTC
1255216 AGTTCTATGGTTCAAAAAATTA
1 AGTTCTATGGTTCAAAAAATTA
1255238 AGTTCTATGGTTCAAAAAATTA
1 AGTTCTATGGTTCAAAAAATTA
1255260 A
1 A
1255261 ATGTAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (22 bp):
AGTTCTATGGTTCAAAAAATTA
Found at i:1258864 original size:24 final size:24
Alignment explanation
Indices: 1258832--1258879 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1258822 AACAATATAT
1258832 ATGTATGAAATCTATTCTAAATTC
1 ATGTATGAAATCTATTCTAAATTC
1258856 ATGTATGAAATCTATTCTAAATTC
1 ATGTATGAAATCTATTCTAAATTC
1258880 CCATAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (24 bp):
ATGTATGAAATCTATTCTAAATTC
Found at i:1258935 original size:3 final size:3
Alignment explanation
Indices: 1258927--1258951 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1258917 ACTTGGGAAC
1258927 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1258952 CTACTACTTA
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:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1264804 original size:15 final size:16
Alignment explanation
Indices: 1264784--1264820 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1264774 ACGCGCTGCC
1264784 ATAAAAA-TAT-ATTA
1 ATAAAAATTATAATTA
1264798 TATAAAAATTATAATTA
1 -ATAAAAATTATAATTA
1264815 ATAAAA
1 ATAAAA
1264821 GGTTAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
16 9 0.45
17 4 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAAAATTATAATTA
Found at i:1266769 original size:3 final size:3
Alignment explanation
Indices: 1266756--1266801 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
1266746 TATTCATTTA
*
1266756 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1266802 CCCATCAACT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1269098 original size:16 final size:16
Alignment explanation
Indices: 1269077--1269145 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
1269067 TTTGGTTCGC
1269077 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1269093 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1269109 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
1269126 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1269142 TGTA
1 TGTA
1269146 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:1269123 original size:33 final size:32
Alignment explanation
Indices: 1269077--1269145 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
1269067 TTTGGTTCGC
1269077 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1269109 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
1269142 TGTA
1 TGTA
1269146 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:1269210 original size:44 final size:45
Alignment explanation
Indices: 1269126--1269216 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
1269116 GGATTAGAGG
* * *
1269126 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
1269171 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
1269215 TG
1 TG
1269217 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:1269402 original size:18 final size:17
Alignment explanation
Indices: 1269381--1269415 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1269371 TTATTATTAA
*
1269381 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1269399 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1269416 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1269522 original size:18 final size:17
Alignment explanation
Indices: 1269501--1269535 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1269491 TTATTATTAA
*
1269501 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1269519 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1269536 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1269577 original size:120 final size:120
Alignment explanation
Indices: 1269364--1269589 Score: 443
Period size: 120 Copynumber: 1.9 Consensus size: 120
1269354 ATCATATTTA
1269364 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
1269429 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATAATACTGTAAAATATAAATT
1269484 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1269549 TATTCTTATATTAATTTACTGAAATCATAATATATAATACT
66 TATTCTTATATTAATTTACTGAAATCATAATATATAATACT
1269590 ACAATACTTA
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 105 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATAATACTGTAAAATATAAATT
Found at i:1269711 original size:14 final size:15
Alignment explanation
Indices: 1269692--1269724 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1269682 CTTTATTCTT
*
1269692 AAAATTCAAAAA-TA
1 AAAATTAAAAAACTA
1269706 AAAATTAAAAAACTA
1 AAAATTAAAAAACTA
1269721 AAAA
1 AAAA
1269725 ATTTAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATTAAAAAACTA
Found at i:1270191 original size:58 final size:58
Alignment explanation
Indices: 1270068--1270206 Score: 197
Period size: 59 Copynumber: 2.4 Consensus size: 58
1270058 AAAGTTGCTA
* * *
1270068 TGTTTTGGCACTAAAAGCAACCGCAAGCCACAACTACCAGCATGTCAAGGATTAAATT
1 TGTTTTGGCACTAAAAGAAACCACAAGCCACAACAACCAGCATGTCAAGGATTAAATT
* * *
1270126 TGTTTTGGCACTAAAAGTAAACCACAAGTCACAAGAACCAGCATGTCAAGGATTGAATT
1 TGTTTTGGCACTAAAAG-AAACCACAAGCCACAACAACCAGCATGTCAAGGATTAAATT
* *
1270185 TGTTTGGGCACTAAAAGCAACC
1 TGTTTTGGCACTAAAAGAAACC
1270207 GCAATCGCAA
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
58 21 0.29
59 51 0.71
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (58 bp):
TGTTTTGGCACTAAAAGAAACCACAAGCCACAACAACCAGCATGTCAAGGATTAAATT
Found at i:1274050 original size:26 final size:25
Alignment explanation
Indices: 1274020--1274079 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
1274010 ATTGAAATGG
*
1274020 TTTATTTTATTGATAAAA-ATAATATA
1 TTTATTTTATT-ATAAAAGAT-ATAAA
*
1274046 TTTATTTGATTATAAAAGATATAAA
1 TTTATTTTATTATAAAAGATATAAA
1274071 TATTATTTT
1 T-TTATTTT
1274080 TAAATAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 11 0.38
26 18 0.62
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (25 bp):
TTTATTTTATTATAAAAGATATAAA
Found at i:1278425 original size:13 final size:14
Alignment explanation
Indices: 1278407--1278436 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1278397 TAAGGGTTCC
1278407 TTAAAATTA-TTTT
1 TTAAAATTACTTTT
1278420 TTAAAATTACTTTT
1 TTAAAATTACTTTT
1278434 TTA
1 TTA
1278437 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (14 bp):
TTAAAATTACTTTT
Found at i:1283396 original size:84 final size:84
Alignment explanation
Indices: 1283283--1283484 Score: 404
Period size: 84 Copynumber: 2.4 Consensus size: 84
1283273 TTGGAATAGA
1283283 TTTGGGTGTTCATCGTTGCTTAATTTGATTTGAATACTGTACATCGTTGTGGGAACTTTTATGTA
1 TTTGGGTGTTCATCGTTGCTTAATTTGATTTGAATACTGTACATCGTTGTGGGAACTTTTATGTA
1283348 ATGTACTTCGTTGCTTAAT
66 ATGTACTTCGTTGCTTAAT
1283367 TTTGGGTGTTCATCGTTGCTTAATTTGATTTGAATACTGTACATCGTTGTGGGAACTTTTATGTA
1 TTTGGGTGTTCATCGTTGCTTAATTTGATTTGAATACTGTACATCGTTGTGGGAACTTTTATGTA
1283432 ATGTACTTCGTTGCTTAAT
66 ATGTACTTCGTTGCTTAAT
1283451 TTTGGGTGTTCATCGTTGCTTAATTTGATTTGAA
1 TTTGGGTGTTCATCGTTGCTTAATTTGATTTGAA
1283485 ATCCTAATTC
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 118 1.00
ACGTcount: A:0.20, C:0.11, G:0.22, T:0.47
Consensus pattern (84 bp):
TTTGGGTGTTCATCGTTGCTTAATTTGATTTGAATACTGTACATCGTTGTGGGAACTTTTATGTA
ATGTACTTCGTTGCTTAAT
Found at i:1316192 original size:21 final size:20
Alignment explanation
Indices: 1316166--1316218 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
1316156 AAATATGTAA
1316166 TTATATAATAAAAAATAAATT
1 TTATATAATAAAAAAT-AATT
* **
1316187 TTATATATTTTAAAATAATT
1 TTATATAATAAAAAATAATT
1316207 TTA-ATTAATAAA
1 TTATA-TAATAAA
1316219 GTTTTTATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
19 1 0.04
20 11 0.44
21 13 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTATATAATAAAAAATAATT
Found at i:1316277 original size:89 final size:89
Alignment explanation
Indices: 1316116--1316285 Score: 229
Period size: 89 Copynumber: 1.9 Consensus size: 89
1316106 TAATTCATCT
1316116 TTTTAATTAATAACTCTTTTATTTATATAAATAAAATAATAAATATGTAATTATATAATAAAAAA
1 TTTTAATTAATAACTCTTTTATTTATATAAATAAAATAATAAATATGTAATTATATAATAAAAAA
1316181 TAAA-TTTTATATATTTTAAAATAA
66 TAAATTTTTA-ATATTTTAAAATAA
* * * * *
1316205 TTTTAATTAATAAAGT-TTTTATTTATATATA-AAAATAATAATTATGTAATTATGTAATGAAAT
1 TTTTAATTAAT-AACTCTTTTATTTATATAAATAAAATAATAAATATGTAATTATATAAT-AAAA
* *
1316268 TATATATTTTTAATATTT
64 AATAAATTTTTAATATTT
1316286 ATAATTATGT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
88 25 0.35
89 38 0.54
90 8 0.11
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (89 bp):
TTTTAATTAATAACTCTTTTATTTATATAAATAAAATAATAAATATGTAATTATATAATAAAAAA
TAAATTTTTAATATTTTAAAATAA
Found at i:1322159 original size:12 final size:12
Alignment explanation
Indices: 1322142--1322174 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1322132 TCGCCTGTCC
1322142 ATATTAATTTTT
1 ATATTAATTTTT
1322154 ATATT-ATTTTT
1 ATATTAATTTTT
1322165 ATA-TAATTTT
1 ATATTAATTTT
1322175 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:1322329 original size:29 final size:30
Alignment explanation
Indices: 1322296--1322355 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1322286 CAATTTAACA
*
1322296 AGCAAATGCCTCT-AAATAATAACAAAATT
1 AGCAAATGCCTCTAAAATAATAAAAAAATT
* *
1322325 AGCAAATGTCTTTAAAATAATAAAAAAATT
1 AGCAAATGCCTCTAAAATAATAAAAAAATT
1322355 A
1 A
1322356 ACAATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.27
Consensus pattern (30 bp):
AGCAAATGCCTCTAAAATAATAAAAAAATT
Found at i:1322414 original size:22 final size:22
Alignment explanation
Indices: 1322389--1322431 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1322379 TATCCAAATA
1322389 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
1322411 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
1322432 AATAGGAAGA
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:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:1322435 original size:11 final size:11
Alignment explanation
Indices: 1322396--1322436 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1322386 ATAATAACAA
1322396 CAAAATAGTAG
1 CAAAATAGTAG
* *
1322407 CAACATAATAG
1 CAAAATAGTAG
*
1322418 TAAAATAGTAG
1 CAAAATAGTAG
1322429 CAAAATAG
1 CAAAATAG
1322437 GAAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:1324021 original size:43 final size:43
Alignment explanation
Indices: 1323973--1324084 Score: 206
Period size: 43 Copynumber: 2.6 Consensus size: 43
1323963 CCGGTATTAC
1323973 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
1324016 GCCTGCTAGGCATGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1324059 GCCTGCTAGGCACGAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
1324085 TAATACCAGC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.29, C:0.32, G:0.27, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:1324125 original size:38 final size:38
Alignment explanation
Indices: 1324077--1324430 Score: 582
Period size: 38 Copynumber: 9.3 Consensus size: 38
1324067 GGCACGAAGG
* * * *
1324077 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1324115 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
** * *
1324153 CCCGGATATTTTACCAGCACGAAGCCTGTGGGTCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGG-ATTTAA
1324192 GCCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 -CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1324231 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
1324269 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1324307 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* * *
1324345 CCCAGATATATTACCAGCACGAAGCCTGTGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1324383 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1324421 CCCGGATATA
1 CCCGGATATA
1324431 CATCGAATAT
Statistics
Matches: 294, Mismatches: 20, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
38 255 0.87
39 10 0.03
40 29 0.10
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:1338265 original size:13 final size:13
Alignment explanation
Indices: 1338236--1338277 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1338226 GATTGTCCTA
1338236 TTAATTGATTTGA-
1 TTAATTGATTT-AT
*
1338249 TTAATTGATTTTT
1 TTAATTGATTTAT
1338262 TTAATTG-TTTAT
1 TTAATTGATTTAT
1338274 TTAA
1 TTAA
1338278 CGGTGAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TTAATTGATTTAT
Found at i:1338670 original size:20 final size:21
Alignment explanation
Indices: 1338634--1338680 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1338624 AATTTCAACA
1338634 TTAA-TAATAATTTTAAT-TT
1 TTAATTAATAATTTTAATATT
1338653 TTAATTAAT-ATTTCTAATATT
1 TTAATTAATAATTT-TAATATT
1338674 TT-ATTAA
1 TTAATTAA
1338681 AAATGGCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 8 0.32
20 13 0.52
21 4 0.16
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATTAATAATTTTAATATT
Found at i:1339737 original size:20 final size:21
Alignment explanation
Indices: 1339714--1339800 Score: 78
Period size: 20 Copynumber: 4.3 Consensus size: 21
1339704 TCTAAAATGC
1339714 ATTT-TTTTCTCCAAAAATCA
1 ATTTATTTTCTCCAAAAATCA
* * *
1339734 ATTTATTTTTTATCTAAAATGC-
1 ATTTATTTTCT-CCAAAAAT-CA
1339756 ATTT-TTTTCTCCAAAAATCA
1 ATTTATTTTCTCCAAAAATCA
*
1339776 ATTTATTTT-T-TAAAAA-CA
1 ATTTATTTTCTCCAAAAATCA
1339794 ATTTATT
1 ATTTATT
1339801 CAAAGAAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
18 9 0.16
19 6 0.11
20 15 0.27
21 14 0.25
22 10 0.18
23 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.01, T:0.51
Consensus pattern (21 bp):
ATTTATTTTCTCCAAAAATCA
Found at i:1339749 original size:42 final size:42
Alignment explanation
Indices: 1339703--1339787 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
1339693 ACTCATAATA
1339703 ATCTAAAATGCATTTTTTTCTCCAAAAATCAATTTATTTTTT
1 ATCTAAAATGCATTTTTTTCTCCAAAAATCAATTTATTTTTT
1339745 ATCTAAAATGCATTTTTTTCTCCAAAAATCAATTTATTTTTT
1 ATCTAAAATGCATTTTTTTCTCCAAAAATCAATTTATTTTTT
1339787 A
1 A
1339788 AAAACAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.49
Consensus pattern (42 bp):
ATCTAAAATGCATTTTTTTCTCCAAAAATCAATTTATTTTTT
Found at i:1339752 original size:23 final size:23
Alignment explanation
Indices: 1339716--1339787 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
1339706 TAAAATGCAT
*
1339716 TTTTTTCTCCAAAAATCAATTTA
1 TTTTTTATCCAAAAATCAATTTA
*
1339739 TTTTTTAT-CTAAAATGC-A--T-
1 TTTTTTATCCAAAAAT-CAATTTA
*
1339758 TTTTTTCTCCAAAAATCAATTTA
1 TTTTTTATCCAAAAATCAATTTA
1339781 TTTTTTA
1 TTTTTTA
1339788 AAAACAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
19 8 0.21
20 8 0.21
22 8 0.21
23 14 0.37
ACGTcount: A:0.32, C:0.14, G:0.01, T:0.53
Consensus pattern (23 bp):
TTTTTTATCCAAAAATCAATTTA
Found at i:1343745 original size:27 final size:27
Alignment explanation
Indices: 1343693--1343746 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1343683 AAAGAAGTCG
**
1343693 GGTTCACAAAGTCGGGAGCATGGTGGT
1 GGTTCACAAAGTCGGGAGCAACGTGGT
1343720 GGTTCACAAAGTCGGGAGCAACGTGGT
1 GGTTCACAAAGTCGGGAGCAACGTGGT
1343747 TGATGGACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.24, C:0.17, G:0.39, T:0.20
Consensus pattern (27 bp):
GGTTCACAAAGTCGGGAGCAACGTGGT
Found at i:1346563 original size:30 final size:27
Alignment explanation
Indices: 1346510--1346569 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 27
1346500 ATTTAACAAG
*
1346510 TAAATATTTTTAAAATAATAAAATTAA
1 TAAATATTTTTAAAATAACAAAATTAA
1346537 TAAATATTTTTTAAATAATAACAAAATTAA
1 TAAATA-TTTTT-AA-AATAACAAAATTAA
1346567 TAA
1 TAA
1346570 TAAAATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 6 0.21
28 5 0.17
29 2 0.07
30 16 0.55
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (27 bp):
TAAATATTTTTAAAATAACAAAATTAA
Found at i:1346646 original size:22 final size:22
Alignment explanation
Indices: 1346598--1346646 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1346588 ATATCTAATC
* * *
1346598 AATAATATTAAAATAGTGATAA
1 AATAATAGTAAAATAGTAACAA
* *
1346620 TATAATAGTAAAATTGTAACAA
1 AATAATAGTAAAATAGTAACAA
1346642 AATAA
1 AATAA
1346647 AAAGAAAATA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (22 bp):
AATAATAGTAAAATAGTAACAA
Found at i:1347151 original size:19 final size:19
Alignment explanation
Indices: 1347123--1347159 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1347113 CGTAAAATTT
* *
1347123 AAATACTATTAAATTAATA
1 AAATAATATTAAAATAATA
1347142 AAATAATATTAAAATAAT
1 AAATAATATTAAAATAAT
1347160 TATCAACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATAATATTAAAATAATA
Found at i:1349156 original size:11 final size:11
Alignment explanation
Indices: 1349142--1349182 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1349132 TGTTTTCTCC
1349142 CTATTTTGCTA
1 CTATTTTGCTA
*
1349153 CTATTTTACTA
1 CTATTTTGCTA
* *
1349164 TTATGTTGCTA
1 CTATTTTGCTA
1349175 CTATTTTG
1 CTATTTTG
1349183 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:1349255 original size:30 final size:31
Alignment explanation
Indices: 1349219--1349282 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
1349209 ACTTATTTTA
*
1349219 TTGTTAATT-TTGTTATTATTTTAAAGGCAT
1 TTGTTAATTATTATTATTATTTTAAAGGCAT
*
1349249 TTGTTAATTATTATTATTATTTTAGAGGCAT
1 TTGTTAATTATTATTATTATTTTAAAGGCAT
1349280 TTG
1 TTG
1349283 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.27, C:0.03, G:0.14, T:0.56
Consensus pattern (31 bp):
TTGTTAATTATTATTATTATTTTAAAGGCAT
Found at i:1350609 original size:92 final size:92
Alignment explanation
Indices: 1350452--1350954 Score: 810
Period size: 92 Copynumber: 5.5 Consensus size: 92
1350442 TTTGACATGA
* * * * * *
1350452 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATATCACGTTGCCATGGTATCTTTCAA
** * * * *
1350516 CCATGGTCTTATTCTTTTCTTGTCACGT
65 CCATGGTCTTACACATTTCATATCAGGT
1350544 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAAC
1350609 CATGGTCTTACACATTTCATATCAGGT
66 CATGGTCTTACACATTTCATATCAGGT
*
1350636 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATAGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAAC
1350701 CATGGTCTTACACATTTCATATCAGGT
66 CATGGTCTTACACATTTCATATCAGGT
* *
1350728 TGCAATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGATATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAAC
*
1350793 TATGGTCTTACACATTTCATATCAGGT
66 CATGGTCTTACACATTTCATATCAGGT
*
1350820 TGCCATGGTATCTTTCAACCATGGCCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAAC
1350885 CATGGTCTTACACATTTCATATCAGGT
66 CATGGTCTTACACATTTCATATCAGGT
* **
1350912 TGCCATGGTATCTTTCAACCATGATCTTAGACATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCA
1350955 GAGAGCACAC
Statistics
Matches: 385, Mismatches: 25, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
91 4 0.01
92 381 0.99
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCAGGT
Found at i:1350955 original size:46 final size:46
Alignment explanation
Indices: 1350452--1350954 Score: 729
Period size: 46 Copynumber: 10.9 Consensus size: 46
1350442 TTTGACATGA
* * * * *
1350452 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGT
* * * *
1350498 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCTTGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
*
1350544 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* *
1350590 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
*
1350636 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* * *
1350682 TGCCATAGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* *
1350728 TGCAATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* * * *
1350774 TGCCATGATATCTTTCAACTATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* *
1350820 TGCCATGGTATCTTTCAACCATGGCCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* *
1350866 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* **
1350912 TGCCATGGTATCTTTCAACCATGATCTTAGACATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCA
1350955 GAGAGCACAC
Statistics
Matches: 414, Mismatches: 42, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
45 4 0.01
46 410 0.99
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
Found at i:1353153 original size:31 final size:31
Alignment explanation
Indices: 1353091--1353167 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
1353081 CTAATAAAAT
* * *
1353091 AATAAAAAAAAAATAATAATATATCTTATTAA
1 AATAATAATAAAATAATAATATATCTAATT-A
* *
1353123 AATACTAATAAAATAAT-ATTTATCTAATTA
1 AATAATAATAAAATAATAATATATCTAATTA
*
1353153 AATAATTATAAAATA
1 AATAATAATAAAATA
1353168 TCAAAATATC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 14 0.37
31 10 0.26
32 14 0.37
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (31 bp):
AATAATAATAAAATAATAATATATCTAATTA
Found at i:1356386 original size:7 final size:7
Alignment explanation
Indices: 1356374--1356399 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1356364 ATATAATTAA
1356374 ATTATTT
1 ATTATTT
1356381 ATTATTT
1 ATTATTT
1356388 ATTATTT
1 ATTATTT
1356395 ATTAT
1 ATTAT
1356400 ACAATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
ATTATTT
Found at i:1356578 original size:15 final size:16
Alignment explanation
Indices: 1356546--1356579 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1356536 AAAGACAAGA
1356546 ATTTTATTACAGTTCT
1 ATTTTATTACAGTTCT
*
1356562 ATTTTATTTCA-TTCT
1 ATTTTATTACAGTTCT
1356577 ATT
1 ATT
1356580 CAACCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.62
Consensus pattern (16 bp):
ATTTTATTACAGTTCT
Found at i:1373411 original size:16 final size:17
Alignment explanation
Indices: 1373390--1373423 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1373380 TAAATTTTAA
*
1373390 TTTAATATATAA-TAGG
1 TTTAATACATAATTAGG
1373406 TTTAATACATAATTAGG
1 TTTAATACATAATTAGG
1373423 T
1 T
1373424 ACCTAAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTAATACATAATTAGG
Found at i:1380773 original size:12 final size:12
Alignment explanation
Indices: 1380758--1380792 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1380748 CGAAGTGTTA
* *
1380758 GTGGAAGTGGAT
1 GTGGAGGTGGAG
1380770 GTGGAGGTGGAG
1 GTGGAGGTGGAG
1380782 GTGGAGGTGGA
1 GTGGAGGTGGA
1380793 AGCGCGGCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.60, T:0.20
Consensus pattern (12 bp):
GTGGAGGTGGAG
Found at i:1380785 original size:18 final size:18
Alignment explanation
Indices: 1380758--1380792 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1380748 CGAAGTGTTA
*
1380758 GTGGAAGTGGATGTGGAG
1 GTGGAAGTGGAGGTGGAG
*
1380776 GTGGAGGTGGAGGTGGA
1 GTGGAAGTGGAGGTGGA
1380793 AGCGCGGCGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.60, T:0.20
Consensus pattern (18 bp):
GTGGAAGTGGAGGTGGAG
Found at i:1381419 original size:86 final size:86
Alignment explanation
Indices: 1381321--1381503 Score: 226
Period size: 86 Copynumber: 2.1 Consensus size: 86
1381311 CTGTGGTAGA
* *
1381321 AAAGTGGT-TAAAAAACATATAAGAGGTACATAAATTATTGTTTTTATGCAA-ATTTTTATTTTA
1 AAAGT-GTATAAAAAACATATAAAAGGTACATAAATTATTGCTTTTATGCAATA-TTTTATTTTA
* * *
1381384 TATTCTTCTACATAATTAATTAT
64 AATTCTTCCACACAATTAATTAT
* * * * *
1381407 AAAGTGTATAAAAATCGTATAAAAGGTGCGTGAATTATTGCTTTTATGCAATATTTTATTTTAAA
1 AAAGTGTATAAAAAACATATAAAAGGTACATAAATTATTGCTTTTATGCAATATTTTATTTTAAA
*
1381472 TTCTTCCACACGATTAATTAT
66 TTCTTCCACACAATTAATTAT
*
1381493 AAAGTTTATAA
1 AAAGTGTATAA
1381504 GTTTATGATG
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
85 2 0.02
86 80 0.96
87 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (86 bp):
AAAGTGTATAAAAAACATATAAAAGGTACATAAATTATTGCTTTTATGCAATATTTTATTTTAAA
TTCTTCCACACAATTAATTAT
Found at i:1382396 original size:20 final size:20
Alignment explanation
Indices: 1382371--1382414 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1382361 AATTTAGAAT
* * *
1382371 TTTAATATTATTTATTTTAA
1 TTTAATATAATTAATTTCAA
1382391 TTTAATATAATTAATTTCAA
1 TTTAATATAATTAATTTCAA
1382411 TTTA
1 TTTA
1382415 TCAGTTTACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAATATAATTAATTTCAA
Found at i:1382890 original size:37 final size:37
Alignment explanation
Indices: 1382849--1382922 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
1382839 ATTTACCTAA
1382849 GCCCAAAGGTTAACATGATATTTTAAAAGATTTGTAC
1 GCCCAAAGGTTAACATGATATTTTAAAAGATTTGTAC
1382886 GCCCAAAGGTTAACATGATATTTTAAAAGATTTGTAC
1 GCCCAAAGGTTAACATGATATTTTAAAAGATTTGTAC
1382923 AAAAATTAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (37 bp):
GCCCAAAGGTTAACATGATATTTTAAAAGATTTGTAC
Found at i:1383193 original size:22 final size:21
Alignment explanation
Indices: 1383157--1383204 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
1383147 AAAAGTTGGA
*
1383157 TTTTTTTACTGTTTTCTTGCT
1 TTTTTTTACTGTTTTATTGCT
*
1383178 TTTTTTTAACTTTTTTATTGCT
1 TTTTTTT-ACTGTTTTATTGCT
*
1383200 ATTTT
1 TTTTT
1383205 CTTGTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.73
Consensus pattern (21 bp):
TTTTTTTACTGTTTTATTGCT
Found at i:1383460 original size:14 final size:14
Alignment explanation
Indices: 1383434--1383472 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1383424 ATATATGTTT
1383434 AAAAATT-ATATAA
1 AAAAATTAATATAA
1383447 AAATAA-TAATATAA
1 AAA-AATTAATATAA
1383461 AAAAATTAATAT
1 AAAAATTAATAT
1383473 GGGCAGGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAATTAATATAA
Found at i:1389311 original size:22 final size:22
Alignment explanation
Indices: 1389269--1389310 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1389259 TTTTTAATTC
1389269 ATTAAACCTTTTCAAAATTTTA
1 ATTAAACCTTTTCAAAATTTTA
* *
1389291 ATTAAAGC-TTTCAGAATTTT
1 ATTAAACCTTTTCAAAATTTT
1389311 TTGAAAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (22 bp):
ATTAAACCTTTTCAAAATTTTA
Found at i:1391729 original size:20 final size:20
Alignment explanation
Indices: 1391678--1391719 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1391668 TGTTTACATT
1391678 ATTATTATTTATTTATTTTG
1 ATTATTATTTATTTATTTTG
1391698 AATT-TTATTTATTTA-TTTG
1 -ATTATTATTTATTTATTTTG
1391717 ATT
1 ATT
1391720 TTGTTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.19
20 11 0.52
21 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (20 bp):
ATTATTATTTATTTATTTTG
Done.