Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold205
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: 1179939
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.30
Warning! 53951 characters in sequence are not A, C, G, or T
File 7 of 7
Found at i:1017478 original size:34 final size:35
Alignment explanation
Indices: 1017415--1017481 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1017405 CTAAGTGATT
1017415 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1017451 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1017482 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1020375 original size:13 final size:13
Alignment explanation
Indices: 1020357--1020381 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1020347 CATGCTGCTT
1020357 TGTATTGATACAA
1 TGTATTGATACAA
1020370 TGTATTGATACA
1 TGTATTGATACA
1020382 TGTTCAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
TGTATTGATACAA
Found at i:1021855 original size:20 final size:20
Alignment explanation
Indices: 1021794--1021865 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
1021784 ACCCTTGAAA
*
1021794 GTATCGATACACACCCAGA-T
1 GTATCGATACATACCCA-ATT
*
1021814 GTATCGATACATTATGCC--TT
1 GTATCGATACA-TA-CCCAATT
1021834 GTATCGATACATACCCAATT
1 GTATCGATACATACCCAATT
1021854 GTATCGATACAT
1 GTATCGATACAT
1021866 GAAACTAGCA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 37 0.84
21 1 0.02
22 2 0.05
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (20 bp):
GTATCGATACATACCCAATT
Found at i:1021922 original size:20 final size:20
Alignment explanation
Indices: 1021897--1021947 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1021887 AAGTGAAATA
*
1021897 TATCGATACAT-AGGATATTG
1 TATCGATACATGAAGA-ATTG
*
1021917 TATCGATACATGAAGAATTT
1 TATCGATACATGAAGAATTG
1021937 TATCGATACAT
1 TATCGATACAT
1021948 TGTGTCCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (20 bp):
TATCGATACATGAAGAATTG
Found at i:1030387 original size:19 final size:20
Alignment explanation
Indices: 1030363--1030414 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1030353 ATTATGCTTC
*
1030363 GTATCGATACATGCTC-ATT
1 GTATCGATACATGCCCAATT
*
1030382 GTATCGATACATACCCAATT
1 GTATCGATACATGCCCAATT
1030402 GTATCGATACATG
1 GTATCGATACATG
1030415 AAACTGGTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGCCCAATT
Found at i:1033235 original size:13 final size:13
Alignment explanation
Indices: 1033217--1033246 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1033207 ACAATTCATC
1033217 ATGTATCGATACA
1 ATGTATCGATACA
*
1033230 ATGTATCGATATA
1 ATGTATCGATACA
1033243 ATGT
1 ATGT
1033247 CCTATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1033235 original size:33 final size:33
Alignment explanation
Indices: 1033195--1033263 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1033185 CCGTTACAAG
1033195 CAATGTATCCATACAAT-TCATCATGTATCGATA
1 CAATGTATCCATACAATGTCAT-ATGTATCGATA
* * *
1033228 CAATGTATCGATATAATGTCCTATGTATCGATA
1 CAATGTATCCATACAATGTCATATGTATCGATA
1033261 CAA
1 CAA
1033264 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (33 bp):
CAATGTATCCATACAATGTCATATGTATCGATA
Found at i:1033336 original size:19 final size:19
Alignment explanation
Indices: 1033291--1033348 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
1033281 ACTGCCAGTT
*
1033291 TCATGTATCCATACAATTG
1 TCATGTATCGATACAATTG
1033310 TCCATGTATCGATACAA-TG
1 T-CATGTATCGATACAATTG
*
1033329 ATCATGTATTGATAC-ATTG
1 -TCATGTATCGATACAATTG
1033348 T
1 T
1033349 ATCGATACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 2 0.06
19 17 0.50
20 15 0.44
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (19 bp):
TCATGTATCGATACAATTG
Found at i:1033355 original size:32 final size:33
Alignment explanation
Indices: 1033314--1033376 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
1033304 CAATTGTCCA
* * *
1033314 TGTATCGATACAATG-ATCATGTATTGATACAT
1 TGTATCGATACAAAGCATAATGTATCGATACAT
1033346 TGTATCGATACAAAGCATAATGTATCGATAC
1 TGTATCGATACAAAGCATAATGTATCGATAC
1033377 TTCTGGGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (33 bp):
TGTATCGATACAAAGCATAATGTATCGATACAT
Found at i:1033980 original size:28 final size:28
Alignment explanation
Indices: 1033941--1034031 Score: 102
Period size: 28 Copynumber: 3.4 Consensus size: 28
1033931 AACAAAATTT
*
1033941 TTTTCTCTCCCTAAATCGGTTAACGAGA
1 TTTTCTCCCCCTAAATCGGTTAACGAGA
* ** *
1033969 TTTTCTCCCCCT--A---GATAAAAAAA
1 TTTTCTCCCCCTAAATCGGTTAACGAGA
1033992 TTTTCTCCCCCTAAATCGGTTAACGAGA
1 TTTTCTCCCCCTAAATCGGTTAACGAGA
1034020 TTTTCTCCCCCT
1 TTTTCTCCCCCT
1034032 TGATAAAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
23 18 0.37
25 1 0.02
26 1 0.02
28 29 0.59
ACGTcount: A:0.25, C:0.30, G:0.10, T:0.35
Consensus pattern (28 bp):
TTTTCTCCCCCTAAATCGGTTAACGAGA
Found at i:1034013 original size:51 final size:51
Alignment explanation
Indices: 1033941--1034055 Score: 203
Period size: 51 Copynumber: 2.2 Consensus size: 51
1033931 AACAAAATTT
*
1033941 TTTTCTCTCCCTAAATCGGTTAACGAGATTTTCTCCCCCTAGATAAAAAAA
1 TTTTCTCCCCCTAAATCGGTTAACGAGATTTTCTCCCCCTAGATAAAAAAA
*
1033992 TTTTCTCCCCCTAAATCGGTTAACGAGATTTTCTCCCCCTTGATAAAAAAA
1 TTTTCTCCCCCTAAATCGGTTAACGAGATTTTCTCCCCCTAGATAAAAAAA
1034043 TATTTCTCCCCCT
1 T-TTTCTCCCCCT
1034056 TCTCAAAGCA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 50 0.82
52 11 0.18
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.35
Consensus pattern (51 bp):
TTTTCTCCCCCTAAATCGGTTAACGAGATTTTCTCCCCCTAGATAAAAAAA
Found at i:1036769 original size:20 final size:20
Alignment explanation
Indices: 1036744--1036793 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1036734 CATGTATCAA
*
1036744 TATCGATACATGGTACTATG
1 TATCGATACATGGTACCATG
*
1036764 TATCGATACATTGTACCATG
1 TATCGATACATGGTACCATG
1036784 TATCGATACA
1 TATCGATACA
1036794 AACAGTGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (20 bp):
TATCGATACATGGTACCATG
Found at i:1036867 original size:19 final size:19
Alignment explanation
Indices: 1036823--1036878 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
1036813 CTACCAATTT
**
1036823 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
1036843 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1036862 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1036879 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1036881 original size:13 final size:13
Alignment explanation
Indices: 1036863--1036889 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1036853 TACAATGAAC
1036863 ATGTATCGATACA
1 ATGTATCGATACA
1036876 ATGTATCGATACA
1 ATGTATCGATACA
1036889 A
1 A
1036890 AGGATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1036905 original size:33 final size:32
Alignment explanation
Indices: 1036844--1036908 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
1036834 ACAATTGTCC
*
1036844 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAGGAACATGTATCGATACA
1036876 ATGTATCGATACAAAGGATA-ATGTATCGATACA
1 ATGTATCGATAC-AAGGA-ACATGTATCGATACA
1036909 TTTGGGTGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.40
33 17 0.57
34 1 0.03
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAAGGAACATGTATCGATACA
Found at i:1037510 original size:50 final size:50
Alignment explanation
Indices: 1037435--1037548 Score: 201
Period size: 50 Copynumber: 2.3 Consensus size: 50
1037425 AGTTTTCGTT
* *
1037435 TTTCTCCCCCTTAATTAATTAATGAGATTTTCTCATCCTAGATAAACATA
1 TTTCTCCCCTTTAATAAATTAATGAGATTTTCTCATCCTAGATAAACATA
1037485 TTTCTCCCCTTTAATAAATTAATGAGATTTTCTCATCCTAGATAAACATA
1 TTTCTCCCCTTTAATAAATTAATGAGATTTTCTCATCCTAGATAAACATA
1037535 TTTCTCCCCCTTTA
1 TTTCT-CCCCTTTA
1037549 TCAAAGCATT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
50 53 0.87
51 8 0.13
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (50 bp):
TTTCTCCCCTTTAATAAATTAATGAGATTTTCTCATCCTAGATAAACATA
Found at i:1037529 original size:28 final size:28
Alignment explanation
Indices: 1037451--1037530 Score: 68
Period size: 28 Copynumber: 3.1 Consensus size: 28
1037441 CCCCTTAATT
1037451 AATTAATGAGATTTTCTCATCCTAGATA
1 AATTAATGAGATTTTCTCATCCTAGATA
* *
1037479 AA--CAT---A-TTTCTC-CCCTTTA-ATA
1 AATTAATGAGATTTTCTCATCC--TAGATA
1037501 AATTAATGAGATTTTCTCATCCTAGATA
1 AATTAATGAGATTTTCTCATCCTAGATA
1037529 AA
1 AA
1037531 CATATTTCTC
Statistics
Matches: 38, Mismatches: 4, Indels: 20
0.61 0.06 0.32
Matches are distributed among these distances:
21 2 0.05
22 11 0.29
23 3 0.08
24 2 0.05
26 2 0.05
27 3 0.08
28 13 0.34
29 2 0.05
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.39
Consensus pattern (28 bp):
AATTAATGAGATTTTCTCATCCTAGATA
Found at i:1037559 original size:22 final size:22
Alignment explanation
Indices: 1037534--1037575 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1037524 AGATAAACAT
1037534 ATTTCTCCCCCTTTATCAAAGC
1 ATTTCTCCCCCTTTATCAAAGC
* *
1037556 ATTTCTCCCCTTTTGTCAAA
1 ATTTCTCCCCCTTTATCAAA
1037576 TCTTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.33, G:0.05, T:0.40
Consensus pattern (22 bp):
ATTTCTCCCCCTTTATCAAAGC
Found at i:1045680 original size:13 final size:13
Alignment explanation
Indices: 1045664--1045691 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1045654 ACAATTCATC
1045664 ATGTATCGATATA
1 ATGTATCGATATA
1045677 ATGTATCGATATA
1 ATGTATCGATATA
1045690 AT
1 AT
1045692 ATCCTATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (13 bp):
ATGTATCGATATA
Found at i:1045770 original size:20 final size:19
Alignment explanation
Indices: 1045747--1045791 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1045737 TTCATGCATT
*
1045747 GATACAATTGCCCATGTATC
1 GATACAA-TGACCATGTATC
*
1045767 GATACAATGATCATGTATC
1 GATACAATGACCATGTATC
1045786 GATACA
1 GATACA
1045792 TTGTAACGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (19 bp):
GATACAATGACCATGTATC
Found at i:1045819 original size:33 final size:32
Alignment explanation
Indices: 1045761--1045823 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
1045751 CAATTGCCCA
* * *
1045761 TGTATCGATACAATGATCATGTATCGATACAT
1 TGTAACGATACAAAGATAATGTATCGATACAT
1045793 TGTAACGATACAAAGCATAATGTATCGATAC
1 TGTAACGATACAAAG-ATAATGTATCGATAC
1045824 TTTTGGGCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (32 bp):
TGTAACGATACAAAGATAATGTATCGATACAT
Found at i:1048702 original size:20 final size:20
Alignment explanation
Indices: 1048659--1048732 Score: 123
Period size: 20 Copynumber: 3.8 Consensus size: 20
1048649 ACATTACGCT
**
1048659 TTGTATCGATACATGTTC-A
1 TTGTATCGATACATGGACAA
1048678 TTGTATCGATACATGGACAA
1 TTGTATCGATACATGGACAA
1048698 TTGTATCGATACATGGACAA
1 TTGTATCGATACATGGACAA
1048718 TTGTATCGATACATG
1 TTGTATCGATACATG
1048733 AAACTGGCAG
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
19 16 0.31
20 36 0.69
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:1051065 original size:21 final size:21
Alignment explanation
Indices: 1051041--1051080 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1051031 GATATTAAAA
* *
1051041 AATTGGCTAAGGAAAATAATG
1 AATTAGCTAAGAAAAATAATG
*
1051062 AATTAGCTAATAAAAATAA
1 AATTAGCTAAGAAAAATAA
1051081 AAACTTGCAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (21 bp):
AATTAGCTAAGAAAAATAATG
Found at i:1053360 original size:20 final size:21
Alignment explanation
Indices: 1053335--1053373 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1053325 TATTAATCCT
*
1053335 AATTTTC-TTGAAATTTTTGA
1 AATTTTCTTTAAAATTTTTGA
1053355 AATTTTCTTTAAAATTTTT
1 AATTTTCTTTAAAATTTTT
1053374 TTATTTGTTC
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:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
AATTTTCTTTAAAATTTTTGA
Found at i:1053731 original size:19 final size:19
Alignment explanation
Indices: 1053693--1053752 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 19
1053683 TTGGCAAGTG
1053693 GAGAAAAAAGAGAGCAAAAAAA
1 GAGAAAAAA-A-AG-AAAAAAA
*
1053715 AAGAAAGAAAAAGAAAAAAA
1 GAGAAA-AAAAAGAAAAAAA
*
1053735 GAGAAAAAATAGAAAAAA
1 GAGAAAAAAAAGAAAAAA
1053753 TAAGCTGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 11 0.32
20 12 0.35
21 2 0.06
22 6 0.18
23 3 0.09
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (19 bp):
GAGAAAAAAAAGAAAAAAA
Found at i:1053754 original size:9 final size:9
Alignment explanation
Indices: 1053709--1053752 Score: 61
Period size: 10 Copynumber: 4.7 Consensus size: 9
1053699 AAAGAGAGCA
1053709 AAAAAAAAG
1 AAAAAAAAG
1053718 AAAGAAAAAG
1 AAA-AAAAAG
1053728 AAAAAAAGAG
1 AAAAAAA-AG
*
1053738 AAAAAATAG
1 AAAAAAAAG
1053747 AAAAAA
1 AAAAAA
1053753 TAAGCTGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 15 0.47
10 17 0.53
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1055030 original size:13 final size:13
Alignment explanation
Indices: 1055008--1055037 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1054998 CAATTCTTCA
1055008 TGTATCGATACAT
1 TGTATCGATACAT
*
1055021 TGTATTGATACAT
1 TGTATCGATACAT
1055034 TGTA
1 TGTA
1055038 CCATGTATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1055031 original size:33 final size:33
Alignment explanation
Indices: 1054988--1055052 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1054978 TTTGAGGTAA
*
1054988 TGTATCGATACAATTCT-TCATGTATCGATACAT
1 TGTATCGATAC-ATTCTACCATGTATCGATACAT
* *
1055021 TGTATTGATACATTGTACCATGTATCGATACA
1 TGTATCGATACATTCTACCATGTATCGATACA
1055053 AACAGTGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 4 0.14
33 24 0.86
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (33 bp):
TGTATCGATACATTCTACCATGTATCGATACAT
Found at i:1056066 original size:33 final size:33
Alignment explanation
Indices: 1056024--1056092 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
1056014 TCAGTTAAGA
*
1056024 GAACTAAAGTTCTCATCCATGCGCTGCGAAAGT
1 GAACTAAAGTGCTCATCCATGCGCTGCGAAAGT
*
1056057 GAACTAAAGTGCTCATCCATGTGCTGCGAAAGT
1 GAACTAAAGTGCTCATCCATGCGCTGCGAAAGT
1056090 GAA
1 GAA
1056093 GTGATCAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (33 bp):
GAACTAAAGTGCTCATCCATGCGCTGCGAAAGT
Found at i:1060295 original size:13 final size:13
Alignment explanation
Indices: 1060277--1060316 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
1060267 CAGATGTTCT
1060277 TTGTATCGATACA
1 TTGTATCGATACA
*
1060290 TTGTATCGATATA
1 TTGTATCGATACA
*
1060303 ATGTATCGATACA
1 TTGTATCGATACA
1060316 T
1 T
1060317 AGGTTACAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1061788 original size:33 final size:33
Alignment explanation
Indices: 1061746--1061812 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1061736 CGAGAGTTGA
* *
1061746 TCACTTCACTTTCGTAGCACATGAATGAGCACT
1 TCACTTCACTCTCGTAGCACATGAATAAGCACT
* *
1061779 TCACTTCACTCTCGTAGCGCATGGATAAGCACT
1 TCACTTCACTCTCGTAGCACATGAATAAGCACT
1061812 T
1 T
1061813 TAGTTCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.30
Consensus pattern (33 bp):
TCACTTCACTCTCGTAGCACATGAATAAGCACT
Found at i:1062151 original size:22 final size:25
Alignment explanation
Indices: 1062099--1062151 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 25
1062089 GAGCATTTTT
1062099 GAAAATAAATTCTTGACAAAAGGGGA
1 GAAAATAAATTCTT-ACAAAAGGGGA
1062125 G-AAATAAATT-TT-C-AAAGGGGA
1 GAAAATAAATTCTTACAAAAGGGGA
1062146 GAAAAT
1 GAAAAT
1062152 TTTGAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 9 0.35
22 5 0.19
24 2 0.08
25 9 0.35
26 1 0.04
ACGTcount: A:0.51, C:0.06, G:0.23, T:0.21
Consensus pattern (25 bp):
GAAAATAAATTCTTACAAAAGGGGA
Found at i:1062771 original size:20 final size:20
Alignment explanation
Indices: 1062746--1062783 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1062736 GTATCAATAC
1062746 AATGTATCGATACATGAACA
1 AATGTATCGATACATGAACA
*
1062766 AATGTATTGATACATGAA
1 AATGTATCGATACATGAA
1062784 ACTGGCAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACATGAACA
Found at i:1069063 original size:32 final size:32
Alignment explanation
Indices: 1068989--1069236 Score: 269
Period size: 32 Copynumber: 7.8 Consensus size: 32
1068979 TGAAAAACGA
* *
1068989 TGCCACCAACTTGTGTGGGCTTTAAAAG-GGT
1 TGCCACCGACTTGTGTGGGCTTTGAAAGAGGT
* ** *
1069020 TCCCACCGACTTGTACGAGCTTTGAAAGAGGT
1 TGCCACCGACTTGTGTGGGCTTTGAAAGAGGT
* *
1069052 TCCCACTGACTTGTGTGGGCTTTGAAA-AGGGT
1 TGCCACCGACTTGTGTGGGCTTTGAAAGA-GGT
* *
1069084 TGCCACCAACTTGTGTGGGCTTAGAAA-AGGGT
1 TGCCACCGACTTGTGTGGGCTTTGAAAGA-GGT
1069116 TGCCACCGACTTGTGTGGGCTTTGAAATG-GGT
1 TGCCACCGACTTGTGTGGGCTTTGAAA-GAGGT
*
1069148 TGCCACTGACTTGTGTGGGCTTTGAAATGA-GT
1 TGCCACCGACTTGTGTGGGCTTTGAAA-GAGGT
* *
1069180 TGCCACCGAGTTGTATGGGCTTTGAAATGA-GT
1 TGCCACCGACTTGTGTGGGCTTTGAAA-GAGGT
*
1069212 TGCCACTGAC-T-TGTGGGCTTTGAAA
1 TGCCACCGACTTGTGTGGGCTTTGAAA
1069237 TGATGCCACG
Statistics
Matches: 189, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
30 13 0.07
31 24 0.13
32 152 0.80
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (32 bp):
TGCCACCGACTTGTGTGGGCTTTGAAAGAGGT
Found at i:1069127 original size:64 final size:64
Alignment explanation
Indices: 1068989--1069236 Score: 297
Period size: 64 Copynumber: 3.9 Consensus size: 64
1068979 TGAAAAACGA
* * ** *
1068989 TGCCACCAACTTGTGTGGGCTTT-AAAAGGGTTCCCACCGACTTGTACGAGCTTTG-AAAGAGGT
1 TGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAG-GGT
* * * *
1069052 TCCCACTGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGTGGGCTTAGAAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGT
* * * *
1069116 TGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGAGT
1 TGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGT
* * * * *
1069180 TGCCACCGAGTTGTATGGGCTTTGAAATGAGTTGCCACTGAC-T-TGTGGGCTTTGAAA
1 TGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAA
1069237 TGATGCCACG
Statistics
Matches: 163, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
62 14 0.09
63 21 0.13
64 124 0.76
65 4 0.02
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (64 bp):
TGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGT
Found at i:1069142 original size:96 final size:95
Alignment explanation
Indices: 1068989--1069238 Score: 326
Period size: 96 Copynumber: 2.6 Consensus size: 95
1068979 TGAAAAACGA
* * ** *
1068989 TGCCACCAACTTGTGTGGGCTTTAAAAGGGTTCCCACCGACTTGTACGAGCTTTGAAA-GAGGTT
1 TGCCACCAACTTGTGTGGGCTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATG-GGTT
*
1069053 CCCACTGACTTGTGTGGGCTTTGAAAAGGGT
65 CCCACTGACTTGTGTGGGCTTTGAAAAGAGT
1069084 TGCCACCAACTTGTGTGGGCTTAGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTT
1 TGCCACCAACTTGTGTGGGCTT-GAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTT
* *
1069149 GCCACTGACTTGTGTGGGCTTTGAAATGAGT
65 CCCACTGACTTGTGTGGGCTTTGAAAAGAGT
* * * * * *
1069180 TGCCACCGAGTTGTATGGGCTTTGAAATGAGTTGCCACTGAC-T-TGTGGGCTTTGAAATG
1 TGCCACCAACTTGTGTGGGC-TTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATG
1069239 ATGCCACGAA
Statistics
Matches: 138, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
94 16 0.12
95 23 0.17
96 96 0.70
97 3 0.02
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (95 bp):
TGCCACCAACTTGTGTGGGCTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTC
CCACTGACTTGTGTGGGCTTTGAAAAGAGT
Found at i:1069254 original size:28 final size:28
Alignment explanation
Indices: 1069129--1069400 Score: 321
Period size: 28 Copynumber: 9.4 Consensus size: 28
1069119 CACCGACTTG
*
1069129 TGTGGGCTTTGAAATGGGTTGCCACTGACTT
1 TGTGGGCTTTGAAAT--GATGCCACTGAC-T
* *
1069160 GTGTGGGCTTTGAAATGAGTTGCCACCGAGT
1 -TGTGGGCTTTGAAATGA--TGCCACTGACT
1069191 TGTATGGGCTTTGAAATGAGTTGCCACTGACT
1 TG--TGGGCTTTGAAATGA--TGCCACTGACT
*
1069223 TGTGGGCTTTGAAATGATGCCAC-GAACC
1 TGTGGGCTTTGAAATGATGCCACTG-ACT
* *
1069251 TGTGGGCTTTGAAATGATGCCATTAACT
1 TGTGGGCTTTGAAATGATGCCACTGACT
*
1069279 TGTGGGCTTCGAAATGATGCCACTGACT
1 TGTGGGCTTTGAAATGATGCCACTGACT
* *
1069307 TGTGGGCTTCGAAATGATGCCACAGACT
1 TGTGGGCTTTGAAATGATGCCACTGACT
* *
1069335 TGTAGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAATGATGCCACTGACT
*
1069363 TGTGGGCTTTGAAATAATGCCACTGACT
1 TGTGGGCTTTGAAATGATGCCACTGACT
*
1069391 TGTGGACTTT
1 TGTGGGCTTT
1069401 AAAGGGTGCC
Statistics
Matches: 213, Mismatches: 21, Indels: 16
0.85 0.08 0.06
Matches are distributed among these distances:
27 1 0.00
28 142 0.67
30 18 0.08
31 1 0.00
32 51 0.24
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (28 bp):
TGTGGGCTTTGAAATGATGCCACTGACT
Found at i:1069423 original size:27 final size:27
Alignment explanation
Indices: 1069380--1069880 Score: 486
Period size: 27 Copynumber: 18.2 Consensus size: 27
1069370 TTTGAAATAA
* * *
1069380 TGCCACTGACTTGTGGACTTTAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAGGG
* *
1069407 TGCCATAGAGTTATGGACTTAAATA-GG
1 TGCCACAGAGTTGTGGACTTAAA-AGGG
* * *
1069434 TGCCACGGAGTTGTGGACCTAAAAGGT
1 TGCCACAGAGTTGTGGACTTAAAAGGG
* **
1069461 TGCCACGGAGCGGTGGACTTTAAAAGGG
1 TGCCACAGAGTTGTGGAC-TTAAAAGGG
*
1069489 TGCCAC-GAAGTTGTGGACTTAAAAAGG
1 TGCCACAG-AGTTGTGGACTTAAAAGGG
*
1069516 TGCCACAAAGTTGTGGACTTTAAAAGGG
1 TGCCACAGAGTTGTGGAC-TTAAAAGGG
*
1069544 TGCCACAGAGTTGTGGAGTTAAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAGGG
*
1069571 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAGGG
*
1069598 TGCCACAGAGTTGTGGACTTTAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAGGG
* *
1069625 TGCCACGGAGTTGTGGGCTTAAAAAAGGG
1 TGCCACAGAGTTGTGGACTT--AAAAGGG
* *
1069654 TGCCGC-GAAGTTGTGGGCTTAAAAAGGGG
1 TGCCACAG-AGTTGTGGACTT-AAAA-GGG
** * *
1069683 TGCCATTGACTTGTGGGCTTAAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAGGG
* * *
1069710 ATGCCACAGAGTTCTAGACTTAAAAGGA
1 -TGCCACAGAGTTGTGGACTTAAAAGGG
* * *
1069738 TGCTACAAAGTTGTGGACTTAAAAGGA
1 TGCCACAGAGTTGTGGACTTAAAAGGG
* * *
1069765 TGCCATAGAGTTGTGGACTTTAATAGGA
1 TGCCACAGAGTTGTGGAC-TTAAAAGGG
** * *
1069793 TGCCAGGGAGTTATGGACTTTAAAAGGA
1 TGCCACAGAGTTGTGGAC-TTAAAAGGG
* *
1069821 TGCCACGGAGTTGTGGACTTAAAAGGA
1 TGCCACAGAGTTGTGGACTTAAAAGGG
* ** *
1069848 TGCTATGGAGTTGTGGACTTAAAAGGA
1 TGCCACAGAGTTGTGGACTTAAAAGGG
1069875 TGCCAC
1 TGCCAC
1069881 TGAATCATGG
Statistics
Matches: 404, Mismatches: 57, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
26 1 0.00
27 237 0.59
28 124 0.31
29 41 0.10
30 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (27 bp):
TGCCACAGAGTTGTGGACTTAAAAGGG
Found at i:1069505 original size:55 final size:55
Alignment explanation
Indices: 1069390--1069880 Score: 480
Period size: 55 Copynumber: 8.9 Consensus size: 55
1069380 TGCCACTGAC
* * ** *
1069390 TTGTGGACTTTAAAGGGTGCCATAGAGTTATGGACTTAAATA-GGTGCCACG-GAG
1 TTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAA-AGGGTGCCACGAGAG
* * **
1069444 TTGTGGACCTAAAAGGTTGCCACGGAGCGGTGGACTTTAAAAGGGTGCCACGA-AG
1 TTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGAGAG
**
1069499 TTGTGGACTTAAAAAGG-TGCCACAAAGTTGTGGACTTTAAAAGGGTGCCAC-AGAG
1 TTGTGGACTT-AAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGAGAG
* *
1069554 TTGTGGAGTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC-AGAG
1 TTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAGAG
* * * *
1069608 TTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGGCTTAAAAAAGGGTGCCGCGA-AG
1 TTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTT--AAAAGGGTGCCACGAGAG
* * ** * *
1069664 TTGTGGGCTTAAAAAGGGGTGCCATTGACTTGTGGGCTTAAAAGGGATGCCAC-AGAG
1 TTGTGGACTT-AAAA-GGATGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGAGAG
* * * ** * *
1069721 TTCTAGACTTAAAAGGATGCTACAAAGTTGTGGACTTAAAAGGATGCCA-TAGAG
1 TTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAGAG
* * * *
1069775 TTGTGGACTTTAATAGGATGCCAGGGAGTTATGGACTTTAAAAGGATGCCACG-GAG
1 TTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGAGAG
* * *
1069831 TTGTGGACTTAAAAGGATGCTATGGAGTTGTGGACTTAAAAGGATGCCAC
1 TTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
1069881 TGAATCATGG
Statistics
Matches: 370, Mismatches: 50, Indels: 34
0.81 0.11 0.07
Matches are distributed among these distances:
54 118 0.32
55 148 0.40
56 66 0.18
57 18 0.05
58 20 0.05
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (55 bp):
TTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAGAG
Found at i:1070505 original size:268 final size:269
Alignment explanation
Indices: 1070027--1070570 Score: 937
Period size: 268 Copynumber: 2.0 Consensus size: 269
1070017 TGGACCCTCT
*
1070027 TTTTTTTGGGGAAAAGATTTGGAGGATTGAGATTTGCTCCATTGGGGATTAATGAGAGCGAGATT
1 TTTTTTTGGGGAAAAGATTTGGAGGATTGAGATTTGCTCCATTAGGGATTAATGAGAGCGAGATT
* * *
1070092 GGCACAATGATGACAGGTGGAGATGATATGAATGTATGATGCAAGCAATGATGTTATTGATGTTA
66 GGCACAATGATGACAAGTGGAGATGATATGAATGCATGATGCAAGCAATGATGTTATTAATGTTA
* *
1070157 TGATGGCATGATCATAGCACAAAAACGTAATGCTGAGAATGACCATAGCCATAGCAAGTTAGCTA
131 TGATGGCATGATCATAGCACAAAAACCTAATGCTGAGAATGACCATAACCATAGCAAGTTAGCTA
*
1070222 GATCAACCTTGGGGATTATGATTTCCACAAAACTAGGGCCACCTGAGTCTTGGCATTACCAACAG
196 GATCAACCTTGGGGATTACGATTTCCACAAAACTAGGGCCACCTGAGTCTTGGCATTACCAACAG
*
1070287 CCTTGGGTG
261 CCTTAGGTG
1070296 TTTTTTTGGGGAAAAGATTTGGAGGATTGAGATTTGCTCCATTAGGGATTAATG-GAGCGAGATT
1 TTTTTTTGGGGAAAAGATTTGGAGGATTGAGATTTGCTCCATTAGGGATTAATGAGAGCGAGATT
* *
1070360 GGGACAATGATGACAAGTGGTGATGATATGAATGCATGATGCAAGCAATGATGTTATTAATGTTA
66 GGCACAATGATGACAAGTGGAGATGATATGAATGCATGATGCAAGCAATGATGTTATTAATGTTA
* * *
1070425 TGATGGCATGATTATAGCACAAAAGCCTAATGCTGAGAATGACCATAACCATAGCGAGTTAGCTA
131 TGATGGCATGATCATAGCACAAAAACCTAATGCTGAGAATGACCATAACCATAGCAAGTTAGCTA
* *
1070490 GATCAACCTTGGGGATTACGATTTCCACACAACTAGGGCCACCTGAGTCTTGGCATTGCCAACAG
196 GATCAACCTTGGGGATTACGATTTCCACAAAACTAGGGCCACCTGAGTCTTGGCATTACCAACAG
*
1070555 CTTTAGGTG
261 CCTTAGGTG
1070564 TTTTTTT
1 TTTTTTT
1070571 CACATGATGC
Statistics
Matches: 259, Mismatches: 16, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
268 206 0.80
269 53 0.20
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (269 bp):
TTTTTTTGGGGAAAAGATTTGGAGGATTGAGATTTGCTCCATTAGGGATTAATGAGAGCGAGATT
GGCACAATGATGACAAGTGGAGATGATATGAATGCATGATGCAAGCAATGATGTTATTAATGTTA
TGATGGCATGATCATAGCACAAAAACCTAATGCTGAGAATGACCATAACCATAGCAAGTTAGCTA
GATCAACCTTGGGGATTACGATTTCCACAAAACTAGGGCCACCTGAGTCTTGGCATTACCAACAG
CCTTAGGTG
Found at i:1078153 original size:33 final size:33
Alignment explanation
Indices: 1078116--1078182 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1078106 TTCAATGATT
1078116 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1078149 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1078182 T
1 T
1078183 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1078154 original size:13 final size:13
Alignment explanation
Indices: 1078136--1078160 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1078126 CATAAAATGT
1078136 TGTATCGATACAA
1 TGTATCGATACAA
1078149 TGTATCGATACA
1 TGTATCGATACA
1078161 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1078221 original size:13 final size:13
Alignment explanation
Indices: 1078203--1078227 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1078193 GCCAAAAAAA
1078203 TGTATCGATACAT
1 TGTATCGATACAT
1078216 TGTATCGATACA
1 TGTATCGATACA
1078228 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1078329 original size:52 final size:52
Alignment explanation
Indices: 1078236--1078359 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
1078226 CACTGATCTT
*
1078236 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
1078287 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
1078339 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
1078360 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 19 0.28
52 47 0.68
53 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:1085281 original size:7 final size:7
Alignment explanation
Indices: 1085269--1085316 Score: 71
Period size: 7 Copynumber: 7.0 Consensus size: 7
1085259 AAAAGTAAAC
1085269 ACAAAAA
1 ACAAAAA
1085276 ACAAAAA
1 ACAAAAA
*
1085283 AAAAAAA
1 ACAAAAA
1085290 ACAAAAA
1 ACAAAAA
*
1085297 ACAACAA
1 ACAAAAA
1085304 ACAAAAA
1 ACAAAAA
1085311 A-AAAAA
1 ACAAAAA
1085317 GTGCAAAGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
6 5 0.14
7 32 0.86
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
ACAAAAA
Found at i:1085575 original size:16 final size:16
Alignment explanation
Indices: 1085544--1085575 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1085534 TGTTCTTTTC
*
1085544 CAAAAAAGAAACAAAA
1 CAAAAAAGAAAAAAAA
1085560 CAAAAAAGAAAAAAAA
1 CAAAAAAGAAAAAAAA
1085576 AGAGAGAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.00
Consensus pattern (16 bp):
CAAAAAAGAAAAAAAA
Found at i:1086539 original size:31 final size:31
Alignment explanation
Indices: 1086501--1086645 Score: 206
Period size: 31 Copynumber: 4.7 Consensus size: 31
1086491 ATACCTTTTT
1086501 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
1086532 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
* *
1086563 AAAGTCCACGACTCAGTGGC-ATCTTTTCCTTT
1 AAAGTCCACGACTCAGTGGCAATCTCTT-C-TC
*
1086595 AAAGTCCACGACTCAGTGGC-AT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCT-TCTC
1086625 AAAGTCCACGACTCAGTGGCA
1 AAAGTCCACGACTCAGTGGCA
1086646 TTTTTTCTTC
Statistics
Matches: 105, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
30 26 0.25
31 55 0.52
32 24 0.23
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCAATCTCTTCTC
Found at i:1086639 original size:93 final size:93
Alignment explanation
Indices: 1086498--1086782 Score: 288
Period size: 93 Copynumber: 3.0 Consensus size: 93
1086488 CAAATACCTT
1086498 TTTAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGC-T
1 TTTAAAGTCCACGACTCAGTGGC-ATCTCTTCTCAAAGTCCACGACTCAGTGGC-ATCTCTGCTT
* * *
1086562 CAAAGTCCACGAC-TCAGTGGCATCTTTTCC
64 CAAAGCCCACAACTTC-GTGGCACCTTTTCC
* * * *
1086592 TTTAAAGTCCACGACTCAGTGGCAT-TTTGTCTCAAAGTCCACGACTCAGTGGCATTTTTTCTTC
1 TTTAAAGTCCACGACTCAGTGGCATCTCT-TCTCAAAGTCCACGACTCAGTGGCATCTCTGCTTC
1086656 AAAGCCCACAACTTCGTGGCACCTTTTCC
65 AAAGCCCACAACTTCGTGGCACCTTTTCC
* * * * * * * * * *
1086685 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTT
1 TTTAAAGTCCACGACTCAGTGGCA----TCTCTTCTCAAAGTCCACGACTCAGTGGCATC-TCTG
*
1086750 CTTTTAAAGCCCACAACTTCGTGGCACTCTTTT
61 C-TTCAAAGCCCACAACTTCGTGGCAC-CTTTT
1086783 TTCCTTTTCA
Statistics
Matches: 161, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
92 7 0.04
93 72 0.45
94 25 0.16
97 22 0.14
98 6 0.04
99 24 0.15
100 5 0.03
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (93 bp):
TTTAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTGCTTCA
AAGCCCACAACTTCGTGGCACCTTTTCC
Found at i:1086646 original size:62 final size:62
Alignment explanation
Indices: 1086501--1086664 Score: 226
Period size: 62 Copynumber: 2.6 Consensus size: 62
1086491 ATACCTTTTT
*
1086501 AAAGTCCACGACTCAGTGGCAATCTCTT-CTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTCCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
* *
1086563 AAAGTCCACGACTCAGTGGCATCTTTTCCTTTAAAGTCCACGACTCAGTGGC-AT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCATCTTTTCC-TCAAAGTCCACGACTCAGTGGCAATCTCTG-CTC
* * *
1086625 AAAGTCCACGACTCAGTGGCATTTTTTCTTCAAAGCCCAC
1 AAAGTCCACGACTCAGTGGCATCTTTTCCTCAAAGTCCAC
1086665 AACTTCGTGG
Statistics
Matches: 92, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
61 18 0.20
62 53 0.58
63 21 0.23
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (62 bp):
AAAGTCCACGACTCAGTGGCATCTTTTCCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
Found at i:1086731 original size:34 final size:33
Alignment explanation
Indices: 1086625--1087186 Score: 634
Period size: 34 Copynumber: 16.8 Consensus size: 33
1086615 ATTTTGTCTC
* * * * *
1086625 AAAGTCCACGACTCAGTGGCA-TTTTTTC-TTC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
* *
1086656 AAAGCCCACAACTTCGTGGCACC-TTTTCCTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
1086688 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
1086721 CAAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
1086755 AAAGCCCACAACTTCGTGGCACTCTTTTTTCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-C-TTTTT-CTTTT
1086791 CAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTT
1086826 AAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTT
1 AAAGCCCACAACTCCGTGGCAC-C-TTTT-TCTTTT
*
1086862 CAAAGCCCACGACTCCGTGGCA-C----TC-TTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
1086890 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTC-TTTT
1086924 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
1086957 AAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTT
*
1086993 CAAAGCCCACAACTCCGTGGCACCTTTTTTTGTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTT
1087028 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTT
*
1087064 CAAAGCCCACGACTCCGTGGCA-C----TC-TTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
1087092 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTC-TTTT
1087126 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTT
* * *
1087162 -AAGTCCACAACTTCGTGGCATCTTT
1 AAAGCCCACAACTCCGTGGCACCTTT
1087187 CTCCCTTCCT
Statistics
Matches: 467, Mismatches: 25, Indels: 75
0.82 0.04 0.13
Matches are distributed among these distances:
27 40 0.09
28 8 0.02
29 3 0.01
31 23 0.05
32 28 0.06
33 54 0.12
34 146 0.31
35 47 0.10
36 31 0.07
37 87 0.19
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (33 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
Found at i:1086925 original size:98 final size:97
Alignment explanation
Indices: 1086792--1087186 Score: 550
Period size: 98 Copynumber: 4.0 Consensus size: 97
1086782 TTTCCTTTTC
* * *
1086792 AAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
*
1086857 CTTTTCAAAGCCCACGACTCCGTGGCACTCTTT
66 CTTTT-AAAGCCCACAACTCCGTGGCACTCTTT
1086890 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT--
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
*
1086952 CTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTT
66 CTTTTAAAGCCCACAACTCCGTGGCA--C----T--C-TTT
*
1086993 CAAAGCCCACAACTCCGTGGCACCTT-TTTTTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 -AAAGCCCACAACTCCGTGGCACCTTCTTCTT-TTTAAAGCCCACAACTCCGTGGCACTCTTTTT
*
1087057 CCCTTTTCAAAGCCCACGACTCCGTGGCACTCTTT
64 CCCTTTT-AAAGCCCACAACTCCGTGGCACTCTTT
1087092 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
* *
1087157 CTTTT-AAGTCCACAACTTCGTGGCA-TCTTT
66 CTTTTAAAGCCCACAACTCCGTGGCACTCTTT
1087187 CTCCCTTCCT
Statistics
Matches: 270, Mismatches: 11, Indels: 35
0.85 0.03 0.11
Matches are distributed among these distances:
94 19 0.07
95 10 0.04
96 18 0.07
97 6 0.02
98 118 0.44
99 7 0.03
100 2 0.01
102 2 0.01
103 7 0.03
104 50 0.19
105 6 0.02
106 1 0.00
107 5 0.02
108 19 0.07
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (97 bp):
AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
CTTTTAAAGCCCACAACTCCGTGGCACTCTTT
Found at i:1087004 original size:202 final size:202
Alignment explanation
Indices: 1086684--1087206 Score: 892
Period size: 202 Copynumber: 2.6 Consensus size: 202
1086674 GCACCTTTTC
* * *
1086684 CTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCT
1 CTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTT
*
1086749 TCTTTTAAAGCCCACAACTTCGTGGCACTCTTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCAC
66 TCTTTTAAAGCCCACAACTTCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCAC
*
1086814 CTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCG
131 CTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACGACTCCG
1086879 TGGCACT
196 TGGCACT
1086886 CTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTT
1 CTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTT
1086951 TCTTTTAAAGCCCACAAC-TCTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCA
66 TCTTTTAAAGCCCACAACTTC-GTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCA
*
1087015 CCTTTTTTTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACGACTCC
130 CCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACGACTCC
1087080 GTGGCACT
195 GTGGCACT
1087088 CTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTT
1 CTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAACTCCGTGGCAC-CTTT
* * *
1087153 TTCCCTTTT-AAGTCCACAACTTCGTGGCA-TCTTTCTCCC-TTCCTAAAGCCCACA
65 TT--CTTTTAAAGCCCACAACTTCGTGGCACTCTTTTTCCCTTTTC-AAAGCCCACA
1087207 CAAGTAGGTG
Statistics
Matches: 306, Mismatches: 9, Indels: 11
0.94 0.03 0.03
Matches are distributed among these distances:
201 2 0.01
202 256 0.84
203 25 0.08
204 16 0.05
205 7 0.02
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.32
Consensus pattern (202 bp):
CTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTT
TCTTTTAAAGCCCACAACTTCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCAC
CTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACGACTCCG
TGGCACT
Found at i:1087234 original size:33 final size:35
Alignment explanation
Indices: 1087191--1087260 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 35
1087181 ATCTTTCTCC
1087191 CTTCCTAAAGCCCACACAAGTAGGTGGCAA-CCTT
1 CTTCCTAAAGCCCACACAAGTAGGTGGCAACCCTT
*
1087225 CTTCC-AAAGCCCACACAAGTCGGTGGCAACCCTT
1 CTTCCTAAAGCCCACACAAGTAGGTGGCAACCCTT
1087259 CT
1 CT
1087261 AAGCCCAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 23 0.68
34 11 0.32
ACGTcount: A:0.27, C:0.36, G:0.17, T:0.20
Consensus pattern (35 bp):
CTTCCTAAAGCCCACACAAGTAGGTGGCAACCCTT
Found at i:1087324 original size:49 final size:48
Alignment explanation
Indices: 1087260--1088436 Score: 1509
Period size: 49 Copynumber: 24.8 Consensus size: 48
1087250 GCAACCCTTC
* * *
1087260 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
1087309 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* * *
1087352 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
1087401 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* * * *
1087444 TAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
1087493 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* *
1087536 TAAGTCCAATATCA-CTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGT-AGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
*
1087585 TAAGTCTAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* * *
1087628 TAAGTCCAATATCA-CTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATGT-AGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
*
1087677 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
*
1087726 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
*
1087774 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* * *
1087822 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
* *
1087871 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
1087919 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* *
1087962 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C--TT-CATCTT
* * * * * *
1088014 TAAATCCAATGTAGCTGGTCTTGACTCAGCATATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
* * * *
1088063 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
* *
1088112 TAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
*
1088161 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
*
1088209 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
* *
1088258 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
1088306 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* * * *
1088349 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGTACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C--TT-CATCTT
* *
1088401 TGAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
1088437 ACATCCTTTT
Statistics
Matches: 1001, Mismatches: 79, Indels: 93
0.85 0.07 0.08
Matches are distributed among these distances:
43 230 0.23
44 2 0.00
45 6 0.01
47 4 0.00
48 232 0.23
49 449 0.45
50 4 0.00
52 74 0.07
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (48 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
Found at i:1087422 original size:92 final size:92
Alignment explanation
Indices: 1087255--1088379 Score: 1407
Period size: 92 Copynumber: 11.9 Consensus size: 92
1087245 CGGTGGCAAC
*
1087255 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1087320 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
*
1087348 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1087413 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
1087440 CCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1087505 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
1087532 CCTTTAAGTCCAATATCA-CTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCTAATG
1 CCTTTAAGTCCAATAT-AGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1087596 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
*
1087624 CCTTTAAGTCCAATATCA-CTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATG
1 CCTTTAAGTCCAATAT-AGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
*
1087688 TAGCTGGCCTTGACTCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
* * *
1087716 CCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTCATCTTTAAGTC
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTC
1087780 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
60 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
* *
1087813 CCTCATCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCC
1 ---C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCC
1087878 AATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCA
61 AATGTAGCTGGCCTTGAATCAGCACATTGG-----CA
* * *
1087915 CCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATAT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
*
1087974 AGCTGGCCTTGAATCAGCATATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * * * * * *
1088001 CCTTTTCCATCTTTAAATCCAATGTAGCTGGTCTTGACTCAGCATATTGGCACCTTCACCATTAA
1 -------C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAA
* * *
1088066 GCCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
57 GTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
* * * * *
1088102 CCTTTATCTTTAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTC
1 -C-----CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTC
1088167 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
60 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
* * * *
1088200 CCTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCC
1 ---C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCC
1088265 AATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCA
61 AATGTAGCTGGCCTTGAATCAGCACATTGG-----CA
* * *
1088302 CCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATAT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1088361 AGCTGGCCTTGAATCAGCA
66 AGCTGGCCTTGAATCAGCA
1088380 TATCGGTACC
Statistics
Matches: 951, Mismatches: 42, Indels: 80
0.89 0.04 0.07
Matches are distributed among these distances:
86 2 0.00
91 71 0.07
92 354 0.37
93 7 0.01
95 40 0.04
96 45 0.05
97 262 0.28
98 122 0.13
99 3 0.00
100 1 0.00
101 40 0.04
102 4 0.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (92 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:1089319 original size:33 final size:33
Alignment explanation
Indices: 1089282--1089348 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1089272 TTCAATGATT
*
1089282 TGTATTGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1089315 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1089348 T
1 T
1089349 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1089320 original size:13 final size:13
Alignment explanation
Indices: 1089302--1089326 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1089292 CATAAAATGT
1089302 TGTATCGATACAA
1 TGTATCGATACAA
1089315 TGTATCGATACA
1 TGTATCGATACA
1089327 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1089408 original size:13 final size:13
Alignment explanation
Indices: 1089390--1089414 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1089380 ATTACTCAAA
1089390 TGTATCGATACAT
1 TGTATCGATACAT
1089403 TGTATCGATACA
1 TGTATCGATACA
1089415 CTAATCTTTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1089464 original size:51 final size:50
Alignment explanation
Indices: 1089403--1089546 Score: 155
Period size: 52 Copynumber: 2.8 Consensus size: 50
1089393 ATCGATACAT
** *
1089403 TGTATCGATACACTAATCTTTATATCGATACATGCAGGC-AATTTGCCTAGA
1 TGTATCGATACACTAA--AATATATCGATACATGCAGGCAAATTTGCCCAGA
* *
1089454 TGTATCGATACAATTTAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATAC-A-CTAAAATATATCGATACATGCAGGCAAATTTGCCCAGA
* * *
1089506 TGGATCGATACACTATTAAATGTATCGATACATGCAAGCAA
1 TGTATCGATACACTA--AAATATATCGATACATGCAGGCAA
1089547 CTTTTCATAT
Statistics
Matches: 80, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
50 2 0.03
51 30 0.38
52 45 0.56
53 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (50 bp):
TGTATCGATACACTAAAATATATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:1089516 original size:52 final size:52
Alignment explanation
Indices: 1089425--1089546 Score: 185
Period size: 52 Copynumber: 2.4 Consensus size: 52
1089415 CTAATCTTTA
* *
1089425 TATCGATACATGCAGGC-AATTTGCCTAGATGTATCGATACAAT-TTAAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGGATCGATACAATATT-AAATG
*
1089476 TATCGATACATGCAGGCAAATTTGCCCAGATGGATCGATACACTATTAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGGATCGATACAATATTAAATG
*
1089528 TATCGATACATGCAAGCAA
1 TATCGATACATGCAGGCAA
1089547 CTTTTCATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 17 0.26
52 46 0.71
53 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TATCGATACATGCAGGCAAATTTGCCCAGATGGATCGATACAATATTAAATG
Found at i:1093605 original size:20 final size:20
Alignment explanation
Indices: 1093582--1093655 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1093572 ACAATTCAAA
1093582 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1093602 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1093623 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1093643 GTATCGATACATG
1 GTATCGATACATG
1093656 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1093626 original size:21 final size:21
Alignment explanation
Indices: 1093600--1093675 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1093590 ACATGTTGCA
1093600 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1093621 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
1093641 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
1093662 ATGTATCGATACAT
1 ATGTATCGATACAT
1093676 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1093633 original size:41 final size:41
Alignment explanation
Indices: 1093582--1093675 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
1093572 ACAATTCAAA
1093582 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1093623 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1093664 GTATCGATACAT
1 GTATCGATACAT
1093676 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:1093732 original size:13 final size:13
Alignment explanation
Indices: 1093714--1093739 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1093704 TACAGCAAGT
1093714 ATGTATCGATACA
1 ATGTATCGATACA
1093727 ATGTATCGATACA
1 ATGTATCGATACA
1093740 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1095986 original size:21 final size:21
Alignment explanation
Indices: 1095953--1095997 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1095943 TTGCAAGTTG
*
1095953 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1095975 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1095995 AAA
1 AAA
1095998 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1099924 original size:20 final size:20
Alignment explanation
Indices: 1099845--1099924 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1099835 AATGTCCAAA
*
1099845 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1099865 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1099890 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1099910 TTGTATCGATACATT
1 ATGTATCGATACATT
1099925 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1099928 original size:13 final size:13
Alignment explanation
Indices: 1099910--1099948 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1099900 ACATTTTTCT
1099910 TTGTATCGATACA
1 TTGTATCGATACA
1099923 TTGTATCGATACA
1 TTGTATCGATACA
*
1099936 CTGTATCGATACA
1 TTGTATCGATACA
1099949 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1102422 original size:20 final size:21
Alignment explanation
Indices: 1102399--1102492 Score: 111
Period size: 20 Copynumber: 4.6 Consensus size: 21
1102389 ACAATTCAAA
** *
1102399 GTATCGATACATGTTACA-AT
1 GTATCGATACATGAAAAAGAT
1102419 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGAAAAAGAT
****
1102440 GTATCGATACATGTTGCA-AT
1 GTATCGATACATGAAAAAGAT
1102460 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGAAAAAGAT
1102481 GTATCGATACAT
1 GTATCGATACAT
1102493 TTCTTGGTAG
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (21 bp):
GTATCGATACATGAAAAAGAT
Found at i:1102450 original size:41 final size:41
Alignment explanation
Indices: 1102399--1102492 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1102389 ACAATTCAAA
1102399 GTATCGATACATGTTACAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTACAATGTATCGATACATGAAAAAGAT
*
1102440 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTACAATGTATCGATACATGAAAAAGAT
1102481 GTATCGATACAT
1 GTATCGATACAT
1102493 TTCTTGGTAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTACAATGTATCGATACATGAAAAAGAT
Found at i:1102549 original size:13 final size:13
Alignment explanation
Indices: 1102531--1102556 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1102521 TACAGCAAGT
1102531 ATGTATCGATACA
1 ATGTATCGATACA
1102544 ATGTATCGATACA
1 ATGTATCGATACA
1102557 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1103963 original size:49 final size:51
Alignment explanation
Indices: 1103905--1104018 Score: 196
Period size: 50 Copynumber: 2.3 Consensus size: 51
1103895 TGAACAGTAC
*
1103905 ATGTATCGATACATTCTG-TTTTTTACCCAGATGTATCGATACGTT-TTCA
1 ATGTATCGATACATTCTGCTTTTTTACCCAGATGTATCGATACATTATTCA
1103954 ATGTATCGATACATTCTGCTTTTTTACCCAGATGTATCGATACATTATTCA
1 ATGTATCGATACATTCTGCTTTTTTACCCAGATGTATCGATACATTATTCA
*
1104005 ATATATCGATACAT
1 ATGTATCGATACAT
1104019 CTAGTTAATT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
49 18 0.30
50 26 0.43
51 17 0.28
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41
Consensus pattern (51 bp):
ATGTATCGATACATTCTGCTTTTTTACCCAGATGTATCGATACATTATTCA
Found at i:1106222 original size:27 final size:27
Alignment explanation
Indices: 1106192--1106256 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
1106182 TTTATCGGGA
* *
1106192 ATACTCCAACCCTATTCTTACGAGGGG
1 ATACTCCAACCCTATTCCTACAAGGGG
1106219 ATACTCCAACCCTATTCCTACAAGGGG
1 ATACTCCAACCCTATTCCTACAAGGGG
1106246 ATACTCCAACC
1 ATACTCCAACC
1106257 TCGCTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.29, C:0.34, G:0.14, T:0.23
Consensus pattern (27 bp):
ATACTCCAACCCTATTCCTACAAGGGG
Found at i:1117867 original size:17 final size:17
Alignment explanation
Indices: 1117844--1117886 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1117834 TCCTTCGTAC
*
1117844 CAAAAAAAATAAAAAAA
1 CAAAAAAAACAAAAAAA
* *
1117861 TAAAAAAAACAAAAAGA
1 CAAAAAAAACAAAAAAA
1117878 CAAAAAAAA
1 CAAAAAAAA
1117887 AGGGTCTAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.86, C:0.07, G:0.02, T:0.05
Consensus pattern (17 bp):
CAAAAAAAACAAAAAAA
Found at i:1119230 original size:55 final size:57
Alignment explanation
Indices: 1119104--1119259 Score: 183
Period size: 55 Copynumber: 2.7 Consensus size: 57
1119094 ATTCATCTCT
* ** * *
1119104 TCAAAGCCTA-AAGGTTAGTGGCATCTCTTCAAAAAACCCATAAGTCAGTGGCATCCTTC
1 TCAAAGCCCACAA-GTTAGTGGCATC-CTTCTCAAAGCCCACAAGTCAGTGGCATCC-TC
* * *
1119163 TCAAAGCGCACAAGTTAGTGGCATCCTTGTCAAAGCCCACAAGTTAGTGGCAT-C-C
1 TCAAAGCCCACAAGTTAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGCATCCTC
*
1119218 TCAAAGCCCACAAGTTAGTGGCATCCTTCTCAGAGCCCACAA
1 TCAAAGCCCACAAGTTAGTGGCATCCTTCTCAAAGCCCACAA
1119260 CACTATGGCA
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
55 40 0.47
57 1 0.01
58 22 0.26
59 20 0.24
60 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (57 bp):
TCAAAGCCCACAAGTTAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGCATCCTC
Found at i:1119269 original size:55 final size:55
Alignment explanation
Indices: 1119162--1119273 Score: 163
Period size: 55 Copynumber: 2.0 Consensus size: 55
1119152 TGGCATCCTT
* * **
1119162 CTCAAAGCGCACAAGTTAGTGGCATCCTTGTCAAAGCCCACAAGTTAGTGGCATC
1 CTCAAAGCCCACAAGTTAGTGGCATCCTTCTCAAAGCCCACAAACTAGTGGCATC
*
1119217 CTCAAAGCCCACAAGTTAGTGGCATCCTTCTCAGAGCCCACAACACTA-TGGCATC
1 CTCAAAGCCCACAAGTTAGTGGCATCCTTCTCAAAGCCCACAA-ACTAGTGGCATC
1119272 CT
1 CT
1119274 TTTAAAGTCC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 49 0.96
56 2 0.04
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (55 bp):
CTCAAAGCCCACAAGTTAGTGGCATCCTTCTCAAAGCCCACAAACTAGTGGCATC
Found at i:1119269 original size:84 final size:87
Alignment explanation
Indices: 1119103--1119287 Score: 211
Period size: 84 Copynumber: 2.2 Consensus size: 87
1119093 CATTCATCTC
* *
1119103 TTCAAAGCCTA-AAGGTTAGTGGCATCTCTTCAAAAAACCCATAAGTCAGTGGCATCCTTCTCAA
1 TTCAAAGCCCACAAGGTTAGTGGCATCTCTTC-AAAAACCCACAAGTCAGTGGCATCCTTCTCAA
* **
1119167 AGCGCACAAGTTAGTGGCATCCT
65 AGCCCACAAACTAGTGGCATCCT
* * *
1119190 TGTCAAAGCCCACAA-GTTAGTGGCATC-C-TC-AAAGCCCACAAGTTAGTGGCATCCTTCTCAG
1 T-TCAAAGCCCACAAGGTTAGTGGCATCTCTTCAAAAACCCACAAGTCAGTGGCATCCTTCTCAA
1119251 AGCCCACAACACTA-TGGCATCCT
65 AGCCCACAA-ACTAGTGGCATCCT
* *
1119274 TTTAAAGTCCACAA
1 TTCAAAGCCCACAA
1119288 CTCCGTGGAA
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
83 11 0.13
84 45 0.53
85 2 0.02
86 2 0.02
87 2 0.02
88 21 0.25
89 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (87 bp):
TTCAAAGCCCACAAGGTTAGTGGCATCTCTTCAAAAACCCACAAGTCAGTGGCATCCTTCTCAAA
GCCCACAAACTAGTGGCATCCT
Found at i:1119274 original size:29 final size:29
Alignment explanation
Indices: 1119104--1119259 Score: 185
Period size: 29 Copynumber: 5.4 Consensus size: 29
1119094 ATTCATCTCT
*
1119104 TCAAAGCCTA-AAGGTTAGTGGCATCTCTTC
1 TCAAAGCCCACAA-GTTAGTGGCATC-CTTC
** * * *
1119134 AAAAAACCCATAAGTCAGTGGCATCCTTC
1 TCAAAGCCCACAAGTTAGTGGCATCCTTC
* *
1119163 TCAAAGCGCACAAGTTAGTGGCATCCTTG
1 TCAAAGCCCACAAGTTAGTGGCATCCTTC
1119192 TCAAAGCCCACAAGTTAGTGGCAT-C--C
1 TCAAAGCCCACAAGTTAGTGGCATCCTTC
1119218 TCAAAGCCCACAAGTTAGTGGCATCCTTC
1 TCAAAGCCCACAAGTTAGTGGCATCCTTC
*
1119247 TCAGAGCCCACAA
1 TCAAAGCCCACAA
1119260 CACTATGGCA
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
26 24 0.22
27 1 0.01
28 1 0.01
29 62 0.58
30 17 0.16
31 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (29 bp):
TCAAAGCCCACAAGTTAGTGGCATCCTTC
Found at i:1119316 original size:27 final size:27
Alignment explanation
Indices: 1119265--1120152 Score: 971
Period size: 27 Copynumber: 32.4 Consensus size: 27
1119255 CACAACACTA
*
1119265 TGGCATCCTTTTAAAGTCCACAACTCCG
1 TGGCAACCTTTT-AAGTCCACAACTCCG
* *
1119293 TGGAAACCTTTTAAGTCCACAACTTCG
1 TGGCAACCTTTTAAGTCCACAACTCCG
*
1119320 TGGCAACCTTTTAAGTCCACAACTCCA
1 TGGCAACCTTTTAAGTCCACAACTCCG
*
1119347 TGGCAACCTTTTAAGTCCACAACTCTG
1 TGGCAACCTTTTAAGTCCACAACTCCG
1119374 TGGCAACCTTTTAAGTCCACAACT-CG
1 TGGCAACCTTTTAAGTCCACAACTCCG
* * **
1119400 TGGCACCCTTTTAAAATCCACAACTCTA
1 TGGCAACCTTTT-AAGTCCACAACTCCG
* *
1119428 TGGCATCCTTTTAAAGTCCACAACTCTG
1 TGGCAACCTTTT-AAGTCCACAACTCCG
1119456 TGGCAACCTTTTAAGTCCACAACTCCG
1 TGGCAACCTTTTAAGTCCACAACTCCG
1119483 TGGC-ACCTTTTTAAGTCCACAACTCCG
1 TGGCAACC-TTTTAAGTCCACAACTCCG
*
1119510 TGGCAACTTTTTAAAGTCCACAACTCCG
1 TGGCAACCTTTT-AAGTCCACAACTCCG
*
1119538 TGGCAACCTTTTAAGT-CACAACTCCA
1 TGGCAACCTTTTAAGTCCACAACTCCG
* **
1119564 TGGCACCCTTTTAAGTCCACAACTCTA
1 TGGCAACCTTTTAAGTCCACAACTCCG
* *
1119591 TAGC-ACACTTTTAAGTCCACAACTCTG
1 TGGCAAC-CTTTTAAGTCCACAACTCCG
* * *
1119618 TGGC-ACACTTTGAAGTCCACAGCTCCA
1 TGGCAAC-CTTTTAAGTCCACAACTCCG
*
1119645 TGGCAACCTTCTAAGTCCACAACTCCG
1 TGGCAACCTTTTAAGTCCACAACTCCG
* * *
1119672 TGGCAACCTTTTCAGTCTACAACTCCA
1 TGGCAACCTTTTAAGTCCACAACTCCG
* *
1119699 TGGAAACCTTTTAAAGTCCACAACTCTG
1 TGGCAACCTTTT-AAGTCCACAACTCCG
*
1119727 TGGCATCCTTTTAAAGTCCACAACTCCG
1 TGGCAACCTTTT-AAGTCCACAACTCCG
** *
1119755 TGGCATTCTTTTAAAGTCCACAACTCCA
1 TGGCAACCTTTT-AAGTCCACAACTCCG
* *
1119783 TGACACCCTTTTAATGTCCACAACTCCG
1 TGGCAACCTTTTAA-GTCCACAACTCCG
* *
1119811 TGGCATCCTTTTAAAGTCCACAACTCTG
1 TGGCAACCTTTT-AAGTCCACAACTCCG
* *
1119839 TGGCATCCTTTCAAAGTCCACAACTCCG
1 TGGCAACCTTT-TAAGTCCACAACTCCG
* * *
1119867 TGGTATCCTTTGAAAGTCCACAACTCCG
1 TGGCAACCTTT-TAAGTCCACAACTCCG
* * *
1119895 TGGCACCCTTTTAAGTCCACAGCTTCG
1 TGGCAACCTTTTAAGTCCACAACTCCG
*
1119922 TGGCAACCCTTTAAGTCCACAACTCCG
1 TGGCAACCTTTTAAGTCCACAACTCCG
* *
1119949 TAGCAACCTTTTAAGTCCACAACTCCA
1 TGGCAACCTTTTAAGTCCACAACTCCG
* *
1119976 TGG-AAGCCTTTTAAGTCCATAACTTCG
1 TGGCAA-CCTTTTAAGTCCACAACTCCG
* *
1120003 TGGCATCCTTTTAAAGTCCACAACTCTG
1 TGGCAACCTTTT-AAGTCCACAACTCCG
* *
1120031 TGGTATCCTTTTAAGTCCACAACTCCG
1 TGGCAACCTTTTAAGTCCACAACTCCG
* * **
1120058 TGGCATCCTTTTAAGTCCACAAGTTAG
1 TGGCAACCTTTTAAGTCCACAACTCCG
* ** * *
1120085 TGGCACCCTTCCAAAG-CCTACAAGTCAG
1 TGGCAACCTT-TTAAGTCC-ACAACTCCG
* * *
1120113 TGGCATCCTTTTAGAGTCCACAAGTCCA
1 TGGCAACCTTTTA-AGTCCACAACTCCG
*
1120141 TGGCATCCTTTT
1 TGGCAACCTTTT
1120153 CAAAGCCCAC
Statistics
Matches: 746, Mismatches: 95, Indels: 38
0.85 0.11 0.04
Matches are distributed among these distances:
26 42 0.06
27 394 0.53
28 306 0.41
29 4 0.01
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (27 bp):
TGGCAACCTTTTAAGTCCACAACTCCG
Found at i:1120190 original size:28 final size:28
Alignment explanation
Indices: 1119140--1120567 Score: 609
Period size: 28 Copynumber: 51.6 Consensus size: 28
1119130 CTTCAAAAAA
*
1119140 CCCATAAGTCAGTGGCATCCTTCTCAAAG
1 CCCACAAGTCAGTGGCATCCTT-TCAAAG
* *
1119169 CGCACAAGTTAGTGGCATCCTTGTCAAAG
1 CCCACAAGTCAGTGGCATCCTT-TCAAAG
*
1119198 CCCACAAGTTAGTGGCATCC--TCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* *
1119224 CCCACAAGTTAGTGGCATCCTTCTCAGAG
1 CCCACAAGTCAGTGGCATCCTT-TCAAAG
** *
1119253 CCCACAACACTA-TGGCATCCTTTTAAAG
1 CCCACAAGTC-AGTGGCATCCTTTCAAAG
* * * * * *
1119281 TCCACAACTCCGTGGAAACCTTT-TAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * * *
1119308 TCCACAACTTC-GTGGCAACCTTT-TAAG
1 CCCACAA-GTCAGTGGCATCCTTTCAAAG
* * * *
1119335 TCCACAACTCCA-TGGCAACCTTT-TAAG
1 CCCACAAGT-CAGTGGCATCCTTTCAAAG
* * * * *
1119362 TCCACAACTCTGTGGCAACCTTT-TAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * * * *
1119389 TCCACAACTC-GTGGCACCCTTTTAAAA
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * *
1119416 TCCACAACTCTA-TGGCATCCTTTTAAAG
1 CCCACAAGTC-AGTGGCATCCTTTCAAAG
* * * * *
1119444 TCCACAACTCTGTGGCAACCTTT-TAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * * **
1119471 TCCACAACTCCGTGGCA-CCTTTTTAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * * * * *
1119498 TCCACAACTCCGTGGCAACTTTTTAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * * * *
1119526 TCCACAACTCCGTGGCAACCTTT-TAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * * *
1119553 -TCACAACTCCA-TGGCACCCTTT-TAAG
1 CCCACAAGT-CAGTGGCATCCTTTCAAAG
* * * *
1119579 TCCACAACTCTA-TAGCA-CACTTT-TAAG
1 CCCACAAGTC-AGTGGCATC-CTTTCAAAG
* * * *
1119606 TCCACAACTCTGTGGCA-CACTTT-GAAG
1 CCCACAAGTCAGTGGCATC-CTTTCAAAG
* * *
1119633 TCCAC-AGCTCCA-TGGCAACC-TTCTAAG
1 CCCACAAG-T-CAGTGGCATCCTTTCAAAG
* * * *
1119660 TCCACAACTCCGTGGCAACCTTTTC--AG
1 CCCACAAGTCAGTGGCATCC-TTTCAAAG
* * * * * *
1119687 TCTACAACTCCA-TGGAAACCTTTTAAAG
1 CCCACAAGT-CAGTGGCATCCTTTCAAAG
* * * *
1119715 TCCACAACTCTGTGGCATCCTTTTAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * * * *
1119743 TCCACAACTCCGTGGCATTCTTTTAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * * * * *
1119771 TCCACAACTCCA-TGACACCCTTTTAATG
1 CCCACAAGT-CAGTGGCATCCTTTCAAAG
* * * *
1119799 TCCACAACTCCGTGGCATCCTTTTAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * *
1119827 TCCACAACTCTGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * * * *
1119855 TCCACAACTCCGTGGTATCCTTTGAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * * * *
1119883 TCCACAACTCCGTGGCACCCTTT-TAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* *
1119910 TCCAC-AGCTTC-GTGGCAACCCTTT--AAG
1 CCCACAAG--TCAGTGGC-ATCCTTTCAAAG
* * * * * *
1119937 TCCACAACTCCGTAGCAACCTTT-TAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * * * *
1119964 TCCACAACTCCA-TGGAAGCCTTT-TAAG
1 CCCACAAGT-CAGTGGCATCCTTTCAAAG
* * * *
1119991 TCCATAACTTC-GTGGCATCCTTTTAAAG
1 CCCACAA-GTCAGTGGCATCCTTTCAAAG
* * * * *
1120019 TCCACAACTCTGTGGTATCCTTT-TAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * * *
1120046 TCCACAACTCCGTGGCATCCTTT-TAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * * *
1120073 TCCACAAGTTAGTGGCACCCTTCCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * *
1120101 CCTACAAGTCAGTGGCATCCTTTTAGAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
*
1120129 TCCACAAGTCCA-TGGCATCCTTTTCAAAG
1 CCCACAAGT-CAGTGGCATCC-TTTCAAAG
*
1120158 CCCACGAA-TCAGTGGCACCCTTTCAAAG
1 CCCAC-AAGTCAGTGGCATCCTTTCAAAG
** *
1120186 CCCACAAGTCAGTGGCATATTTTCCAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
** * *
1120214 CCCACAAGTTTGTGGCATCTTTTCCAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* *
1120242 CCCACAAGTCAATGGCA-CCTTTTCATAG
1 CCCACAAGTCAGTGGCATCC-TTTCAAAG
* *
1120270 CCCACAAGTTAGTGGCA-CATTTTCAAAG
1 CCCACAAGTCAGTGGCATC-CTTTCAAAG
** * *
1120298 CCCATGAGTTAGTGGCA-CATTGTCAAAG
1 CCCACAAGTCAGTGGCATCCTT-TCAAAG
*
1120326 CCCACGAGTCAGTGG-ATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
1120353 CCCACAAGTCAGTGGCATCC-TTCTAAAG
1 CCCACAAGTCAGTGGCATCCTTTC-AAAG
* *
1120381 CCCACGAGTCGGTGGCAT-CTTTCCAAAG
1 CCCACAAGTCAGTGGCATCCTTT-CAAAG
*
1120409 CCCACGAGTCAGTGGCATCC-TTCTAAAG
1 CCCACAAGTCAGTGGCATCCTTTC-AAAG
* *
1120437 CCCACGAGTTAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
*
1120465 CCCATAAGTCAGTGGCAT-CTCTTCAAAG
1 CCCACAAGTCAGTGGCATCCT-TTCAAAG
* * *
1120493 CCCACAAGTCAGAGGCA-ACTTCTCAAAA
1 CCCACAAGTCAGTGGCATCCTT-TCAAAG
* *
1120521 CCCATAAGTCAGTGGCATCCTTTTAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
1120549 CCCACACAAGTCAGTGGCA
1 -CC-CACAAGTCAGTGGCA
1120568 ACTTTCTCTG
Statistics
Matches: 1179, Mismatches: 152, Indels: 135
0.80 0.10 0.09
Matches are distributed among these distances:
26 83 0.07
27 376 0.32
28 603 0.51
29 100 0.08
30 17 0.01
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (28 bp):
CCCACAAGTCAGTGGCATCCTTTCAAAG
Found at i:1121490 original size:49 final size:51
Alignment explanation
Indices: 1121432--1121545 Score: 198
Period size: 50 Copynumber: 2.3 Consensus size: 51
1121422 TGAACAGTAC
1121432 ATGTATCGATACATTCTG-TTTTTTA-CCTAGATGTATCGATACATT-TTCA
1 ATGTATCGATACATTCTGTTTTTTTATCC-AGATGTATCGATACATTATTCA
1121481 ATGTATCGATACATTCTGTTTTTTTATCCAGATGTATCGATACATTATTCA
1 ATGTATCGATACATTCTGTTTTTTTATCCAGATGTATCGATACATTATTCA
1121532 ATGTATCGATACAT
1 ATGTATCGATACAT
1121546 CTAGTTAATT
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
49 18 0.29
50 24 0.39
51 20 0.32
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (51 bp):
ATGTATCGATACATTCTGTTTTTTTATCCAGATGTATCGATACATTATTCA
Found at i:1127596 original size:13 final size:13
Alignment explanation
Indices: 1127578--1127602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1127568 ATATTGCTTA
1127578 GTATCGATACATT
1 GTATCGATACATT
1127591 GTATCGATACAT
1 GTATCGATACAT
1127603 GTTCATAGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1127617 original size:32 final size:33
Alignment explanation
Indices: 1127557--1127620 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1127547 TACACCCAGA
*
1127557 TGTATCGATACATATTGCTTAGTATCGATACAT
1 TGTATCGATACATATTGCATAGTATCGATACAT
*
1127590 TGTATCGATACATGTT-CATAGTATCGATACA
1 TGTATCGATACATATTGCATAGTATCGATACA
1127621 CCTTGAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (33 bp):
TGTATCGATACATATTGCATAGTATCGATACAT
Found at i:1131568 original size:166 final size:166
Alignment explanation
Indices: 1131096--1131587 Score: 545
Period size: 167 Copynumber: 3.0 Consensus size: 166
1131086 TTTTCAAATT
* * * ** *
1131096 ATGAGGTTTTCTTCTTCGTAAATTTTTCTCGAGAAGG-TTTTTCTTAATTTTTAATTTTTAAAAT
1 ATGATGTTTTCTACTTCGTAAATTTTTTTCGAG--GGATTTTTCTTGGTTTTCAATTTTTAAAAT
* * * *
1131160 TCATCAAATA-C-TTTTATTTATTTTATACTAATTCAGTTTTCAAAAATTCATTCATTTTCATGA
64 TCATCAAACATCATTAT-TTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGA
* *
1131223 GCTTTTGATTTTTTTTCCTTGAAATTCCCTTTTTTTCGAAAC
128 G-TTTTGA--TTTTTTCCTTGAAATTCTCTTTTTTCCGAAAC
* *
1131265 ATGATGTTTTCTACTTCGTAAA-TTTTTCCTGTA-GGATTTTTCTTGGTTTTCAA-TTTTAAAAC
1 ATGATGTTTTCTACTTCGTAAATTTTTTTC-G-AGGGATTTTTCTTGGTTTTCAATTTTTAAAAT
* * * *
1131327 ACATCAAACATTATTA-TTTATTTCTTATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAA
64 TCATCAAACATCATTATTTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAG
* * *
1131391 TATTTGATTTTTTCCTTGAAACTCTCTTTTTTCCTAAAT
129 T-TTTGATTTTTTCCTTGAAATTCTCTTTTTTCCGAAAC
* * * *
1131430 ATGGTGTTTTCTACTCCGTAAATTTTTTTCGAGCGGATTTTTCTCGGTTTTCAATTTTTAGAATT
1 ATGATGTTTTCTACTTCGTAAATTTTTTTCGAG-GGATTTTTCTTGGTTTTCAATTTTTAAAATT
* * *
1131495 CATCAAACATCATCATTTTA-TTCATATTAATTCA-TTTTAAAAAATTAATTCATTTTCATGAGT
65 CATCAAACATCATTATTTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGT
*
1131558 TTTGGATTTTTT-GTTGAAATTCCTCTTTTT
130 TTT-GATTTTTTCCTTGAAATT-CTCTTTTT
1131588 CAAGAAATCG
Statistics
Matches: 274, Mismatches: 36, Indels: 29
0.81 0.11 0.09
Matches are distributed among these distances:
164 1 0.00
165 58 0.21
166 68 0.25
167 100 0.36
168 23 0.08
169 23 0.08
170 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (166 bp):
ATGATGTTTTCTACTTCGTAAATTTTTTTCGAGGGATTTTTCTTGGTTTTCAATTTTTAAAATTC
ATCAAACATCATTATTTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGTT
TTGATTTTTTCCTTGAAATTCTCTTTTTTCCGAAAC
Found at i:1133311 original size:162 final size:160
Alignment explanation
Indices: 1133035--1133488 Score: 637
Period size: 162 Copynumber: 2.8 Consensus size: 160
1133025 TTTCCATATT
* *
1133035 TTTTTTCTAATCTTTTATATTCCTATGGGCATTTATGGGGGTATAAAAGATTTCAAAAACCTTTC
1 TTTTTTCTAATCTTTTATATTCCTATGGGCATCTATAGGGGTATAAAAGATTTCAAAAACCTTTC
* * * *
1133100 ATATT-TTTTCGGGCTTCCATTAGGGTACGAAATAGTA-TTTGAGAAAATAAATAAAATTAAATT
66 GTATTCTTTT-GGGCTTCTATTAGGGTACGGAATAGTATTTTCA-AAAATAAATAAAATTAAATT
1133163 AAATTGGTATTATTGGGATAAATTCTAATATTTA
129 AAATTGGTATTATTGGG--AAATTCTAATATTTA
* ** *
1133197 TTTTTTCTAATCTTTTATATTCCTATGGGCATCCATAAAGGTATAAAAGATTTCAAAAAGCTTTC
1 TTTTTTCTAATCTTTTATATTCCTATGGGCATCTATAGGGGTATAAAAGATTTCAAAAACCTTTC
** *
1133262 GTATTCTTTTGGGCTTCTATTATTGTACGGAATAGAATTTTCAAAAATAAATAAAATTAAATTAA
66 GTATTCTTTTGGGCTTCTATTAGGGTACGGAATAGTATTTTCAAAAATAAATAAAATTAAATTAA
1133327 ATTGGTATTATTGGGAAATTCTAATATTTA
131 ATTGGTATTATTGGGAAATTCTAATATTTA
* * *
1133357 TTTTTTCTAATCTTTTATATTCCTATAGGCATCTGTAGGGGTAT-AAAGATTTCAAAAACCTTTT
1 TTTTTTCTAATCTTTTATATTCCTATGGGCATCTATAGGGGTATAAAAGATTTCAAAAACCTTTC
* * * * * *
1133421 GTATCCTTTCGGGCTT-TCATTAGGGCATGGAATGGTATTTTCAAAAATAAATAAAATTAAATTG
66 GTATTCTTTTGGGCTTCT-ATTAGGGTACGGAATAGTATTTTCAAAAATAAATAAAATTAAATTA
1133485 AATT
130 AATT
1133489 AATACTTTCA
Statistics
Matches: 260, Mismatches: 29, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
158 1 0.00
159 75 0.29
160 54 0.21
162 122 0.47
163 8 0.03
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.41
Consensus pattern (160 bp):
TTTTTTCTAATCTTTTATATTCCTATGGGCATCTATAGGGGTATAAAAGATTTCAAAAACCTTTC
GTATTCTTTTGGGCTTCTATTAGGGTACGGAATAGTATTTTCAAAAATAAATAAAATTAAATTAA
ATTGGTATTATTGGGAAATTCTAATATTTA
Found at i:1134392 original size:155 final size:155
Alignment explanation
Indices: 1133699--1134380 Score: 635
Period size: 156 Copynumber: 4.4 Consensus size: 155
1133689 CATTGCCAAT
* * * *
1133699 TTTTTGAAGTCCTTTAGGGGTATTATGTACTTTTACATCTAAA-GTATCCCCTAAAGGCATTTTC
1 TTTTT-AAGTCCTTTAGGGGTATCAGGTACTTTTACATC-AAAGGTATCCCTTAAGGGCATTTTC
* * * * * * *
1133763 ATAATTTTTTAGAACCGAGGCCTAAGTTGTCACTAGGTCTAC-TTTATGTCGAAGATGGGTATTT
64 ATAATTTTTTAGAACCAAGTCCTAGGTTGTCACCAGGTCTACTTTTATGCCAAAGGTGGGTATTT
* * *
1133827 AGGATAGGTTCATCCCTTTTATTATCC
129 AGGATAGGTTCATCCCATTTGTAATCC
* * * ** *
1133854 TTTTTAAGTCCTTTAGGGGTACCGAGATA-TTTTCACGTTGAAGGTATCTCC-TAGGGGCATTTT
1 TTTTTAAGTCCTTTAGGGGTATC-AGGTACTTTT-ACATCAAAGGTATC-CCTTAAGGGCATTTT
* * * * *
1133917 CATAATTTTTTAGAACCAAGTCCTAGGTTATCACTAGGTTTGCTTTTGTGCCAAAGGTGGGTATT
63 CATAATTTTTTAGAACCAAGTCCTAGGTTGTCACCAGGTCTACTTTTATGCCAAAGGTGGGTATT
* * * *
1133982 TAGGATAGGTTTATCACATCTCTAAT-C
128 TAGGATAGGTTCATCCCATTTGTAATCC
* * * * *
1134009 TTTTTAAGTCCTTTAAGGTTACTC-GGATACTTTCACATCGAAA-GTATACCCATAAGGGTATTT
1 TTTTTAAGTCCTTTAGGGGTA-TCAGG-TACTTTTACATC-AAAGGTAT-CCCTTAAGGGCATTT
** * * ** *
1134072 TTGTAATTTTCTAGAACCAAGTCCTAGGTTGTCACCAGGTCCACTTCAATGCCAAATGTGGGTAT
62 TCATAATTTTTTAGAACCAAGTCCTAGGTTGTCACCAGGTCTACTTTTATGCCAAAGGTGGGTAT
* * *
1134137 ATAGGATAGGTTCATCCTATTTTGTTATCC
127 TTAGGATAGGTTCATCCCA-TTTGTAATCC
* * * * * * *
1134167 TTTTTAAGTCCTTTAGGGATATC-GAGCA-TTTATACATCGAAGATATCCTTTAGGGGCATTTTG
1 TTTTTAAGTCCTTTAGGGGTATCAG-GTACTTT-TACATCAAAGGTATCCCTTAAGGGCATTTTC
* * * * * *** *
1134230 ATAATTTTTTATAATCAAGTCTTAGGTTGTCACCAAGTCTGCTTTTATGTTGAAGGTGAGTATTT
64 ATAATTTTTTAGAACCAAGTCCTAGGTTGTCACCAGGTCTACTTTTATGCCAAAGGTGGGTATTT
1134295 AGGATAGGTTCATCCCATTTGTAATCC
129 AGGATAGGTTCATCCCATTTGTAATCC
* *
1134322 TTTTTAAGTCCTTTAGGGGTATCAGGTACTTTTACATCAAAGGTAACCCTTAAAGGCAT
1 TTTTTAAGTCCTTTAGGGGTATCAGGTACTTTTACATCAAAGGTATCCCTTAAGGGCAT
1134381 ATTTTTAATT
Statistics
Matches: 418, Mismatches: 91, Indels: 36
0.77 0.17 0.07
Matches are distributed among these distances:
154 23 0.06
155 148 0.35
156 209 0.50
157 17 0.04
158 21 0.05
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (155 bp):
TTTTTAAGTCCTTTAGGGGTATCAGGTACTTTTACATCAAAGGTATCCCTTAAGGGCATTTTCAT
AATTTTTTAGAACCAAGTCCTAGGTTGTCACCAGGTCTACTTTTATGCCAAAGGTGGGTATTTAG
GATAGGTTCATCCCATTTGTAATCC
Found at i:1136152 original size:13 final size:13
Alignment explanation
Indices: 1136134--1136159 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1136124 CAATTTTTTG
1136134 TGTATCGATACAT
1 TGTATCGATACAT
1136147 TGTATCGATACAT
1 TGTATCGATACAT
1136160 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1136898 original size:21 final size:21
Alignment explanation
Indices: 1136857--1136900 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1136847 CTCCCCTTTA
* *
1136857 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1136878 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1136899 TC
1 TC
1136901 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1140433 original size:19 final size:19
Alignment explanation
Indices: 1140409--1140495 Score: 123
Period size: 19 Copynumber: 4.9 Consensus size: 19
1140399 AATTCAACGA
1140409 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1140428 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1140447 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1140462 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1140479 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1140496 TTAGCTACTG
Statistics
Matches: 62, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
13 11 0.18
15 2 0.03
17 2 0.03
19 47 0.76
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1140466 original size:32 final size:32
Alignment explanation
Indices: 1140430--1140492 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1140420 ACATAAGTTT
*
1140430 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1140462 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1140493 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1140467 original size:13 final size:13
Alignment explanation
Indices: 1140449--1140473 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1140439 ACATAAGTTT
1140449 TGTATCGATACAA
1 TGTATCGATACAA
1140462 TGTATCGATACA
1 TGTATCGATACA
1140474 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1140572 original size:33 final size:33
Alignment explanation
Indices: 1140515--1140581 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1140505 GCCAAGGAAA
*** *
1140515 TGTATCGATACATTTTTCTGTGTATTGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1140548 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1140581 T
1 T
1140582 TGGAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1143105 original size:28 final size:27
Alignment explanation
Indices: 1143038--1143105 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
1143028 CTTCACAATC
*
1143038 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
1143065 GGGGATACTCCAACCCCGTTACTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
1143093 GGGGATACTCCAA
1 GGGGATACTCCAA
1143106 TCCTGATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 22 0.59
28 15 0.41
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:1149051 original size:13 final size:13
Alignment explanation
Indices: 1149033--1149058 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1149023 TACACCAAGT
1149033 ATGTATCGATACA
1 ATGTATCGATACA
1149046 ATGTATCGATACA
1 ATGTATCGATACA
1149059 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1149056 original size:32 final size:33
Alignment explanation
Indices: 1149015--1149078 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1149005 TAGCCAAACT
* **
1149015 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1149047 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1149079 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1149580 original size:34 final size:35
Alignment explanation
Indices: 1149517--1149583 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1149507 CTAAGTGATT
1149517 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1149553 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1149584 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1153631 original size:48 final size:48
Alignment explanation
Indices: 1153577--1153672 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
1153567 GGGGAGATAA
1153577 AGGAGAGAATGCATGAATTACCTTATTAAGGGGGAGAATGTACAAATT
1 AGGAGAGAATGCATGAATTACCTTATTAAGGGGGAGAATGTACAAATT
*
1153625 AGGAGAGAATGCGTGAATTACCTTATTAAGGGGGAGAATGTACAAATT
1 AGGAGAGAATGCATGAATTACCTTATTAAGGGGGAGAATGTACAAATT
1153673 CGTAAAATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25
Consensus pattern (48 bp):
AGGAGAGAATGCATGAATTACCTTATTAAGGGGGAGAATGTACAAATT
Found at i:1154331 original size:13 final size:13
Alignment explanation
Indices: 1154313--1154338 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1154303 TACACCAAGT
1154313 ATGTATCGATACA
1 ATGTATCGATACA
1154326 ATGTATCGATACA
1 ATGTATCGATACA
1154339 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1154336 original size:32 final size:33
Alignment explanation
Indices: 1154295--1154358 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1154285 TAGCCAAACT
* **
1154295 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1154327 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1154359 TTGATATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1154871 original size:48 final size:48
Alignment explanation
Indices: 1154816--1154911 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
1154806 AAATTTTACG
1154816 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
*
1154864 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCATGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1154912 TTATTGGGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.08, T:0.39
Consensus pattern (48 bp):
AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
Found at i:1155232 original size:20 final size:20
Alignment explanation
Indices: 1155209--1155281 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1155199 ACAATTCAAA
1155209 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1155229 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
1155250 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1155270 GTATCGATACAT
1 GTATCGATACAT
1155282 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1155252 original size:21 final size:21
Alignment explanation
Indices: 1155226--1155302 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
1155216 TACATGTTGC
1155226 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
1155247 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
1155267 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
*
1155287 GGATGTATCGATACAT
1 -AATGTATCGATACAT
1155303 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:1155260 original size:41 final size:41
Alignment explanation
Indices: 1155209--1155302 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
1155199 ACAATTCAAA
1155209 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-AAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAAT
*
1155250 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
1155291 GTATCGATACAT
1 GTATCGATACAT
1155303 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
Found at i:1155359 original size:13 final size:13
Alignment explanation
Indices: 1155341--1155366 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1155331 TACAGCAAGT
1155341 ATGTATCGATACA
1 ATGTATCGATACA
1155354 ATGTATCGATACA
1 ATGTATCGATACA
1155367 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1157614 original size:21 final size:21
Alignment explanation
Indices: 1157581--1157625 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1157571 TTGCAAGTTG
*
1157581 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1157603 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1157623 AAA
1 AAA
1157626 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1161415 original size:20 final size:19
Alignment explanation
Indices: 1161390--1161484 Score: 66
Period size: 20 Copynumber: 4.6 Consensus size: 19
1161380 ATGTCCAAAA
1161390 TGTATCGATACATGTTTCT
1 TGTATCGATACATGTTTCT
*
1161409 GTGTATCGATACATCTGGAAATTCT
1 -TGTATCGATACA--T-G--TTTCT
* *
1161434 ATGTATCAATACATTTTTCTT
1 -TGTATCGATACATGTTTC-T
* *
1161455 TGTATCGATACAT-TGTAT
1 TGTATCGATACATGTTTCT
1161473 TGTATCGATACA
1 TGTATCGATACA
1161485 CTGTATCGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
18 13 0.21
19 2 0.03
20 27 0.44
21 1 0.02
22 1 0.02
23 2 0.03
25 15 0.25
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATGTTTCT
Found at i:1161472 original size:13 final size:13
Alignment explanation
Indices: 1161473--1161497 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1161463 TACATTGTAT
1161473 TGTATCGATACAC
1 TGTATCGATACAC
1161486 TGTATCGATACA
1 TGTATCGATACA
1161498 GGGTGATTAT
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1161477 original size:18 final size:18
Alignment explanation
Indices: 1161454--1161490 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1161444 ACATTTTTCT
*
1161454 TTGTATCGATACATTGTA
1 TTGTATCGATACACTGTA
1161472 TTGTATCGATACACTGTA
1 TTGTATCGATACACTGTA
1161490 T
1 T
1161491 CGATACAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (18 bp):
TTGTATCGATACACTGTA
Found at i:1164050 original size:13 final size:13
Alignment explanation
Indices: 1164032--1164057 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1164022 TACAGCAAGT
1164032 ATGTATCGATACA
1 ATGTATCGATACA
1164045 ATGTATCGATACA
1 ATGTATCGATACA
1164058 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1165045 original size:13 final size:13
Alignment explanation
Indices: 1165027--1165052 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1165017 TACACCAAGT
1165027 ATGTATCGATACA
1 ATGTATCGATACA
1165040 ATGTATCGATACA
1 ATGTATCGATACA
1165053 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1165050 original size:32 final size:33
Alignment explanation
Indices: 1165009--1165072 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1164999 TAGCCAAACT
* **
1165009 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1165041 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1165073 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1165574 original size:34 final size:35
Alignment explanation
Indices: 1165511--1165577 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1165501 CTAAGTGATT
1165511 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1165547 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1165578 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1169236 original size:52 final size:52
Alignment explanation
Indices: 1169158--1169285 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
1169148 CGAAATATGA
1169158 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
1169210 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
1169262 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1169286 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
51 21 0.28
52 55 0.72
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:1169312 original size:13 final size:13
Alignment explanation
Indices: 1169294--1169318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1169284 CAAAGATCAG
1169294 TGTATCGATACAA
1 TGTATCGATACAA
1169307 TGTATCGATACA
1 TGTATCGATACA
1169319 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1169396 original size:33 final size:33
Alignment explanation
Indices: 1169359--1169425 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1169349 AGTAGCTTAA
1169359 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1169392 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1169425 A
1 A
1169426 GATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1169399 original size:13 final size:13
Alignment explanation
Indices: 1169381--1169405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1169371 CAAAAAAATA
1169381 TGTATCGATACAT
1 TGTATCGATACAT
1169394 TGTATCGATACA
1 TGTATCGATACA
1169406 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1176386 original size:1 final size:1
Alignment explanation
Indices: 1176380--1176433 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
1176370 CCTTCTCTTC
** * * * *
1176380 AAAAAAAAAAGCAAAAAAAAAAAAACAAAACAAAGAAAAAGAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1176434 TCTGCTTAAG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.89, C:0.06, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:1177569 original size:55 final size:55
Alignment explanation
Indices: 1177395--1177950 Score: 709
Period size: 55 Copynumber: 9.9 Consensus size: 55
1177385 CTCCTTCCGC
*
1177395 TTTT-CAGTCCCCAAAGAGCAGGACACCTTTC-AAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
1177448 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTC-AAGCCCACATAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1177502 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
1177557 TTTTCCAATCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
** * *
1177612 TTTTTTAGTCCTC-AAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
1177672 CCTTTT-CAGTCCTCAAA-AGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 --TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1177727 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
1177782 TTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
1177843 CCTTTT--AGTCCCCAAAGAGCAGGACACCTCTT-AAGAGCCCACACAAGTTGGTGGCA
1 --TTTTCCAGTCCTCAAAGAGCAGGACACCT-TTCAA-AGCCCACACAAGTTGGTGGCA
* * *
1177899 CCTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTG
1 -TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTG
1177951 CACTTTTAAC
Statistics
Matches: 448, Mismatches: 30, Indels: 48
0.85 0.06 0.09
Matches are distributed among these distances:
53 8 0.02
54 100 0.22
55 197 0.44
56 47 0.10
57 1 0.00
59 2 0.00
60 26 0.06
61 57 0.13
62 6 0.01
63 4 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (55 bp):
TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:1177701 original size:170 final size:172
Alignment explanation
Indices: 1177395--1177977 Score: 833
Period size: 170 Copynumber: 3.5 Consensus size: 172
1177385 CTCCTTCCGC
* * * *
1177395 TTTT-CAGTCCCCAAAGAGCAGGACACC-TTTCAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
1 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
* * *
1177458 CTCAAAGAGCAGGA--C----ACCTTTC-AAGCCCACATAAGTTGGTGGCA--TTTTCCAGTCCT
66 CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTT-CAGTCCT
1177514 CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
130 CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1177557 TTTTCCAATCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTTAGTC
1 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
1177622 CTC-AAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTCAGTCCTC
66 CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTCAGTCCTC
1177686 AAA-AGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
131 AAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1177727 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
1 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
*
1177792 CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTT-AGTCCCC
66 CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTCAGTCCTC
1177856 AAAGAGCAGGACACCTCTT-AAGAGCCCACACAAGTTGGTGGCA
131 AAAGAGCAGGACACCT-TTCAA-AGCCCACACAAGTTGGTGGCA
* * * * * *
1177899 CCTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACAC-GAGTTGGT-GCACTTTTAAC
1 -TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAG-GTTGGTGGCATTTTTCAG
* *
1177961 TCCTCAATGAGAAGGAT
64 TCCTCAAAGAGCAGGAT
1177978 ACACTTTATT
Statistics
Matches: 384, Mismatches: 20, Indels: 25
0.90 0.05 0.06
Matches are distributed among these distances:
162 4 0.01
163 31 0.08
164 35 0.09
165 1 0.00
169 5 0.01
170 134 0.35
171 102 0.27
172 69 0.18
173 3 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (172 bp):
TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTCAGTCCTC
AAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Done.