Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold202
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: 2706578
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 16 of 16
Found at i:2549233 original size:13 final size:13
Alignment explanation
Indices: 2549215--2549239 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2549205 ACAATACTTA
2549215 TGTATCGATACAT
1 TGTATCGATACAT
2549228 TGTATCGATACA
1 TGTATCGATACA
2549240 AAACTTATGT
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:2549237 original size:32 final size:32
Alignment explanation
Indices: 2549196--2549258 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2549186 TAGCTAATTA
*
2549196 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2549228 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2549259 AATCGTTGAA
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:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2549793 original size:55 final size:54
Alignment explanation
Indices: 2549701--2550673 Score: 1308
Period size: 55 Copynumber: 17.6 Consensus size: 54
2549691 AAGAGGAAAA
* * * * * * *
2549701 TAAAGTGTATCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTT
1 TAAAG-GTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
**
2549756 TGAAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
* *
2549811 TAAGAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTAGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
* ** *
2549866 TGAAA-ATAAAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTT
1 T-AAAGGT-----G--TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
** *
2549927 TAAAAGGTGTCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTATGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
* * *
2549982 TGAAAGGTGTCTTGCTCTTCGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
* *
2550037 TGAGAGGTGTCCTGCTCTTTGAGGACT-AGAAGGCGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTT
2550092 TAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTT
* * *
2550148 TGAGAGGTGTCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
* * *
2550203 TAAGAGGTGTCCTGCTCTTTGAAGACTGGAAA-ATGCCACCAACTTGGGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTT
*
2550258 TGAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
**
2550313 TAAGAGGTGTCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
2550368 TGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTT
*
2550423 TAAGAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
2550478 TAAGAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
2550533 TAAGAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
2550588 TAAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTT
2550643 TAAGAGGTGTCCTGCTCTTTGAGGACTGAAA
1 TAA-AGGTGTCCTGCTCTTTGAGGACTGAAA
2550674 AGCGGAAGGA
Statistics
Matches: 835, Mismatches: 55, Indels: 57
0.88 0.06 0.06
Matches are distributed among these distances:
54 24 0.03
55 689 0.83
56 72 0.09
57 3 0.00
59 1 0.00
61 45 0.05
62 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (54 bp):
TAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
Found at i:2551675 original size:8 final size:8
Alignment explanation
Indices: 2551652--2551699 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 8
2551642 CTTTTCTCTC
*
2551652 TTTTTCTT
1 TTTTTGTT
2551660 TGTTTTGTT
1 T-TTTTGTT
2551669 TTTTTGTTT
1 TTTTTG-TT
*
2551678 TTTTTTTT
1 TTTTTGTT
2551686 TTTTTGCTT
1 TTTTTG-TT
2551695 TTTTT
1 TTTTT
2551700 TTTGCTCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
8 13 0.38
9 21 0.62
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (8 bp):
TTTTTGTT
Found at i:2551684 original size:12 final size:12
Alignment explanation
Indices: 2551662--2551717 Score: 67
Period size: 12 Copynumber: 4.4 Consensus size: 12
2551652 TTTTTCTTTG
2551662 TTTTGTTTTTTT
1 TTTTGTTTTTTT
*
2551674 GTTTTTTTTTTTT
1 -TTTTGTTTTTTT
*
2551687 TTTTGCTTTTTT
1 TTTTGTTTTTTT
2551699 TTTTGCTCTTTTTT
1 TTTTG-T-TTTTTT
2551713 TTTTG
1 TTTTG
2551718 AAGAGAAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
12 15 0.41
13 11 0.30
14 11 0.30
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:2551697 original size:14 final size:14
Alignment explanation
Indices: 2551651--2551717 Score: 63
Period size: 12 Copynumber: 5.0 Consensus size: 14
2551641 TCTTTTCTCT
2551651 CTTTTTCTTTGTTTTG
1 CTTTTT-TTT-TTTTG
*
2551667 -TTTTTTTGTTTT-
1 CTTTTTTTTTTTTG
2551679 -TTTTTTTTTTTTG
1 CTTTTTTTTTTTTG
2551692 C--TTTTTTTTTTG
1 CTTTTTTTTTTTTG
*
2551704 CTCTTTTTTTTTTG
1 CTTTTTTTTTTTTG
2551718 AAGAGAAGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
12 23 0.51
13 4 0.09
14 13 0.29
15 5 0.11
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (14 bp):
CTTTTTTTTTTTTG
Found at i:2551701 original size:17 final size:17
Alignment explanation
Indices: 2551652--2551702 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
2551642 CTTTTCTCTC
*
2551652 TTTTT-CTTTGTTTTGTT
1 TTTTTGCTTT-TTTTTTT
*
2551669 TTTTTGTTTTTTTTTTT
1 TTTTTGCTTTTTTTTTT
2551686 TTTTTGCTTTTTTTTTT
1 TTTTTGCTTTTTTTTTT
2551703 GCTCTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 27 0.90
18 3 0.10
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (17 bp):
TTTTTGCTTTTTTTTTT
Found at i:2564326 original size:51 final size:51
Alignment explanation
Indices: 2564169--2564339 Score: 189
Period size: 51 Copynumber: 3.3 Consensus size: 51
2564159 GAAATAACGA
* * *
2564169 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * * *
2564221 AATTAGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
2564274 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
2564325 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
2564340 TCAGAAATAA
Statistics
Matches: 95, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
51 39 0.41
52 15 0.16
53 31 0.33
54 10 0.11
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:2564385 original size:27 final size:28
Alignment explanation
Indices: 2564322--2564397 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
2564312 AAAATAAAGT
*
2564322 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
2564350 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
2564377 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2564398 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2566904 original size:33 final size:33
Alignment explanation
Indices: 2566846--2566912 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2566836 AAAATTTCCA
***
2566846 AATGTATCGATACAAAGATCCATGTATCAATAC
1 AATGTATCGATACAAAGAAAAATGTATCAATAC
* *
2566879 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCAATAC
2566912 A
1 A
2566913 TTTCCTTGGC
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:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCAATAC
Found at i:2566956 original size:19 final size:18
Alignment explanation
Indices: 2566932--2566999 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2566922 CAGTAGCTAA
2566932 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2566951 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2566966 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2566983 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2567000 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2566972 original size:13 final size:13
Alignment explanation
Indices: 2566954--2566978 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2566944 ACAATACTTA
2566954 TGTATCGATACAT
1 TGTATCGATACAT
2566967 TGTATCGATACA
1 TGTATCGATACA
2566979 AAACTTATGT
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:2566976 original size:32 final size:32
Alignment explanation
Indices: 2566935--2566997 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2566925 TAGCTAATTA
*
2566935 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2566967 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2566998 AATCGTTGAA
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:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2567060 original size:20 final size:19
Alignment explanation
Indices: 2567035--2567095 Score: 77
Period size: 21 Copynumber: 3.1 Consensus size: 19
2567025 GTTGGGACCC
2567035 TGTATCGATACATTTGTGAA
1 TGTATCGATACATTTG-GAA
**
2567055 TGTATCGATACATTCTACAAA
1 TGTATCGATACATT-T-GGAA
2567076 TGTATCGATACATTTGGAA
1 TGTATCGATACATTTGGAA
2567095 T
1 T
2567096 TTTTTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 3 0.09
20 15 0.43
21 17 0.49
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATTTGGAA
Found at i:2568594 original size:28 final size:28
Alignment explanation
Indices: 2568554--2568625 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
2568544 TTTCACCATC
* * *
2568554 GGGGATACTCCAA-TCTCGTTATTTTTGA
1 GGGGATACTCCAACTCT-ATTACTTCTGA
2568582 GGGGATACTCCAACTCTATTACTTCTGA
1 GGGGATACTCCAACTCTATTACTTCTGA
*
2568610 GGGGATACTACAACTC
1 GGGGATACTCCAACTC
2568626 CATTTTTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 36 0.92
29 3 0.08
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (28 bp):
GGGGATACTCCAACTCTATTACTTCTGA
Found at i:2583933 original size:14 final size:15
Alignment explanation
Indices: 2583894--2583957 Score: 58
Period size: 17 Copynumber: 4.1 Consensus size: 15
2583884 ATTAAAAATC
*
2583894 AAATAAAAAATGGTAA
1 AAATAAAAAA-AGTAA
*
2583910 CAAGTAAAAAAA-TAA
1 -AAATAAAAAAAGTAA
2583925 AAATAAAAAAAGTAAAA
1 AAATAAAAAAAGT--AA
*
2583942 AAACAAAAAAAGTAA
1 AAATAAAAAAAGTAA
2583957 A
1 A
2583958 GAAGGCGTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
14 10 0.25
15 7 0.17
17 23 0.57
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.12
Consensus pattern (15 bp):
AAATAAAAAAAGTAA
Found at i:2583943 original size:17 final size:17
Alignment explanation
Indices: 2583923--2583957 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2583913 GTAAAAAAAT
*
2583923 AAAAATAAAAAAAGTAA
1 AAAAACAAAAAAAGTAA
2583940 AAAAACAAAAAAAGTAA
1 AAAAACAAAAAAAGTAA
2583957 A
1 A
2583958 GAAGGCGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.03, G:0.06, T:0.09
Consensus pattern (17 bp):
AAAAACAAAAAAAGTAA
Found at i:2584980 original size:14 final size:14
Alignment explanation
Indices: 2584957--2585016 Score: 95
Period size: 14 Copynumber: 4.4 Consensus size: 14
2584947 TATTAGACTT
*
2584957 CACATTATGCATTC
1 CACATCATGCATTC
2584971 CACATCATGCATTC
1 CACATCATGCATTC
*
2584985 CACATTATGCATTC
1 CACATCATGCATTC
2584999 CACATCATGCATT-
1 CACATCATGCATTC
2585012 CACAT
1 CACAT
2585017 TACCATCACA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
13 5 0.12
14 38 0.88
ACGTcount: A:0.30, C:0.32, G:0.07, T:0.32
Consensus pattern (14 bp):
CACATCATGCATTC
Found at i:2584990 original size:28 final size:27
Alignment explanation
Indices: 2584955--2585018 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 27
2584945 TATATTAGAC
2584955 TTCACATTATGCATTCCACATCATGCA
1 TTCACATTATGCATTCCACATCATGCA
2584982 TTCCACATTATGCATTCCACATCATGCA
1 TT-CACATTATGCATTCCACATCATGCA
2585010 TTCACATTA
1 TTCACATTA
2585019 CCATCACACA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 9 0.25
28 27 0.75
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (27 bp):
TTCACATTATGCATTCCACATCATGCA
Found at i:2585727 original size:31 final size:30
Alignment explanation
Indices: 2585690--2585780 Score: 123
Period size: 28 Copynumber: 3.1 Consensus size: 30
2585680 TCTCTTCTCA
2585690 AAGTCCACAACTCAGTGGCATCCCTCTTTTT
1 AAGTCCACAACTCAGTGGCA-CCCTCTTTTT
* *
2585721 AAGTCCACAACTCCGTGACA-CC-CTTTTT
1 AAGTCCACAACTCAGTGGCACCCTCTTTTT
* *
2585749 AAGTCCACAACTCTGTGGCACCCTTTTTTT
1 AAGTCCACAACTCAGTGGCACCCTCTTTTT
2585779 AA
1 AA
2585781 AAAAAGCCCA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
28 24 0.45
29 4 0.08
30 7 0.13
31 18 0.34
ACGTcount: A:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (30 bp):
AAGTCCACAACTCAGTGGCACCCTCTTTTT
Found at i:2585819 original size:32 final size:31
Alignment explanation
Indices: 2585783--2585964 Score: 159
Period size: 32 Copynumber: 5.7 Consensus size: 31
2585773 TTTTTTAAAA
*
2585783 AAAGCCCACATAAGTCGGTGGCAACCATTTCT
1 AAAGCCCACACAAGTCGGTGGCAACC-TTTCT
* * * *
2585815 AAAGCCCACACAAATTGGT-GTAACCTTTTTT
1 AAAGCCCACACAAGTCGGTGGCAACC-TTTCT
* * * *
2585846 AAAGCCCATACAAGTTGGTGGCAACCATTCCA
1 AAAGCCCACACAAGTCGGTGGCAACC-TTTCT
* *
2585878 AAAGCCCACACAAGTCGATGCCAACCTTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCTTTCT
* * *
2585909 AAAAGCCCACACAAGTCGGTGGTAATCCTCTCA
1 -AAAGCCCACACAAGTCGGTGGCAA-CCTTTCT
* * *
2585942 AAAGTCCACATAAGTCGGGGGCA
1 AAAGCCCACACAAGTCGGTGGCA
2585965 TCTTTTCTCA
Statistics
Matches: 119, Mismatches: 28, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
31 29 0.24
32 85 0.71
33 5 0.04
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (31 bp):
AAAGCCCACACAAGTCGGTGGCAACCTTTCT
Found at i:2585944 original size:64 final size:62
Alignment explanation
Indices: 2585782--2585958 Score: 185
Period size: 64 Copynumber: 2.8 Consensus size: 62
2585772 TTTTTTTAAA
* * * * * * *
2585782 AAAAGCCCACATAAGTCGGTGGCAACCATTTCTAAAGCCCACACAAATTGGTGTAACCTTTTT
1 AAAAGCCCACACAAGTCGGTGGCAACCA-TTCAAAAGCCCACACAAGTCGATGCAACCTTTCT
* * *
2585845 TAAAGCCCATACAAGTTGGTGGCAACCATTCCAAAAGCCCACACAAGTCGATGCCAACCTTTCT
1 AAAAGCCCACACAAGTCGGTGGCAACCATT-CAAAAGCCCACACAAGTCGATG-CAACCTTTCT
* * *
2585909 AAAAGCCCACACAAGTCGGTGGTAATCC-TCTCAAAAGTCCACATAAGTCG
1 AAAAGCCCACACAAGTCGGTGGCAA-CCAT-TCAAAAGCCCACACAAGTCG
2585959 GGGGCATCTT
Statistics
Matches: 94, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
62 2 0.02
63 42 0.45
64 47 0.50
65 3 0.03
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.21
Consensus pattern (62 bp):
AAAAGCCCACACAAGTCGGTGGCAACCATTCAAAAGCCCACACAAGTCGATGCAACCTTTCT
Found at i:2586126 original size:52 final size:52
Alignment explanation
Indices: 2586002--2586248 Score: 219
Period size: 52 Copynumber: 4.8 Consensus size: 52
2585992 ATGGCATTTC
* * * * * * *
2586002 TTTAAGTCCAATGTCGTTGGCATTGAATCAACATATTGGCACCTTTGTCATC
1 TTTAAGTCCAATGTCGCTAGCCTTGAATCAACACATTGGCACTTTTATCATT
* * * * * *
2586054 TTTAAATCCGATATCACTAGCCTTGAATCAGCATATTGGCACTTTTATCATT
1 TTTAAGTCCAATGTCGCTAGCCTTGAATCAACACATTGGCACTTTTATCATT
* * * * * *
2586106 TTTAAGCCCAATGTTGCTAGCTTTGAATCAACACATTAGTA-TTCTTACCATT
1 TTTAAGTCCAATGTCGCTAGCCTTGAATCAACACATTGGCACTT-TTATCATT
* *
2586158 TTTAAGCCCAATGTCGCTAGCCTTGAATTAACACATTGGCA-TTCTTATCATT
1 TTTAAGTCCAATGTCGCTAGCCTTGAATCAACACATTGGCACTT-TTATCATT
* ** * * *
2586210 CTTAAGTCCAATGTCATTGGCCTTAAATCAGCACATTGG
1 TTTAAGTCCAATGTCGCTAGCCTTGAATCAACACATTGG
2586249 TACTCTTCTC
Statistics
Matches: 157, Mismatches: 37, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
51 2 0.01
52 155 0.99
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (52 bp):
TTTAAGTCCAATGTCGCTAGCCTTGAATCAACACATTGGCACTTTTATCATT
Found at i:2586401 original size:61 final size:61
Alignment explanation
Indices: 2586197--2586401 Score: 209
Period size: 61 Copynumber: 3.4 Consensus size: 61
2586187 AACACATTGG
* * * *
2586197 CATTCTTATCATTCTTAAGTCCAATGTCATTGGCCTTAAATCAGCACATTGGTACTCTTCT
1 CATTCTTATCATTCTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACTCTTAT
* * * ** * *
2586258 CATCCTTATCATTGTTAAGTCCAATATTGCTGGTCTTGAATCAGCATATTGGCAC-CTTAT
1 CATTCTTATCATTCTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACTCTTAT
** * * *
2586318 CATTCTTCGCA-TCTTTAAGTCCAACGTCACTCGCCTTGAATCAACACATTGGCACTCTTAT
1 CATTCTTATCATTC-TTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACTCTTAT
* *
2586379 CCTTATTATCA-TCTTTAAGTCCA
1 CATTCTTATCATTC-TTAAGTCCA
2586402 GTGTTATAAG
Statistics
Matches: 115, Mismatches: 27, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
59 1 0.01
60 45 0.39
61 69 0.60
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.38
Consensus pattern (61 bp):
CATTCTTATCATTCTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACTCTTAT
Found at i:2586853 original size:19 final size:19
Alignment explanation
Indices: 2586829--2586893 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
2586819 TATTATTCCC
2586829 ATTTTTAAGTCATGTGCAT
1 ATTTTTAAGTCATGTGCAT
* * **
2586848 ATTTTTTGAAGGT-ATTATTCCC
1 A-TTTTT-AA-GTCA-TGTGCAT
2586870 ATTTTTAAGTCATGTGCAT
1 ATTTTTAAGTCATGTGCAT
2586889 ATTTT
1 ATTTT
2586894 CCTAGAAACT
Statistics
Matches: 33, Mismatches: 8, Indels: 10
0.65 0.16 0.20
Matches are distributed among these distances:
19 11 0.33
20 8 0.24
21 8 0.24
22 6 0.18
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.51
Consensus pattern (19 bp):
ATTTTTAAGTCATGTGCAT
Found at i:2586865 original size:41 final size:41
Alignment explanation
Indices: 2586815--2586893 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
2586805 CCTTTTTGTA
2586815 AAGGTATTATTCCCATTTTTAAGTCATGTGCATATTTTTTG
1 AAGGTATTATTCCCATTTTTAAGTCATGTGCATATTTTTTG
2586856 AAGGTATTATTCCCATTTTTAAGTCATGTGCATATTTT
1 AAGGTATTATTCCCATTTTTAAGTCATGTGCATATTTT
2586894 CCTAGAAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.48
Consensus pattern (41 bp):
AAGGTATTATTCCCATTTTTAAGTCATGTGCATATTTTTTG
Found at i:2587529 original size:79 final size:79
Alignment explanation
Indices: 2587428--2587685 Score: 231
Period size: 85 Copynumber: 3.2 Consensus size: 79
2587418 TATTCTGAGG
* * * *
2587428 GGATATTCTAACCCCATTTTTTATTTCCAAAATATAAAATTTTTTATTACGGGGATACTCCAACC
1 GGATACTCCAACCCCACTTTTTATTTCCAAAATATAAAATTTTTCATTACGGGGATACTCCAACC
* *
2587493 CCATTATTTTCGAAG
66 CC-TTATTTACGAAA
* * *
2587508 GGATACTCCAACCTCACTTTTATTAAAATTTTCAAAATATTAAAA-TTTTCATTACGAGGATACT
1 GGATACTCCAACCCCAC-TTT-TT---ATTTCCAAAATA-TAAAATTTTTCATTACGGGGATACT
*
2587572 CCAACCCCGTT-TAATACGAAA
60 CCAACCCC-TTAT-TTACGAAA
* * *
2587593 GGATACTCCAACCCCA-TTTTTATGTCTAAAATATTAAATTTTTCA-T-CGTGGAGATACTCCAA
1 GGATACTCCAACCCCACTTTTTATTTCCAAAATATAAAATTTTTCATTACG-GG-GATACTCCAA
*
2587655 CCCCTTATTT-CTAAAA
64 CCCCTTATTTAC-GAAA
*
2587671 AGATACTCCAACCCC
1 GGATACTCCAACCCC
2587686 CTATTTCTGA
Statistics
Matches: 146, Mismatches: 20, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
77 3 0.02
78 26 0.18
79 30 0.21
80 13 0.09
81 3 0.02
82 4 0.03
83 3 0.02
84 1 0.01
85 58 0.40
86 5 0.03
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (79 bp):
GGATACTCCAACCCCACTTTTTATTTCCAAAATATAAAATTTTTCATTACGGGGATACTCCAACC
CCTTATTTACGAAA
Found at i:2587674 original size:27 final size:27
Alignment explanation
Indices: 2587644--2587714 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
2587634 TTCATCGTGG
*
2587644 AGATACTCCAACCCCTTATTTCTAAAA
1 AGATACTCCAACCCCCTATTTCTAAAA
*
2587671 AGATACTCCAACCCCCTATTTCTGAAA
1 AGATACTCCAACCCCCTATTTCTAAAA
2587698 AGATACTCCAACCCCCT
1 AGATACTCCAACCCCCT
2587715 TTCTATTTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.34, C:0.35, G:0.06, T:0.25
Consensus pattern (27 bp):
AGATACTCCAACCCCCTATTTCTAAAA
Found at i:2598867 original size:70 final size:70
Alignment explanation
Indices: 2598793--2598960 Score: 185
Period size: 71 Copynumber: 2.4 Consensus size: 70
2598783 CGCTAATGGC
* * * *
2598793 ACCCTTTATCCTTTTTGTCTTAAAAGAATATG-ATGCCTTTTTCTTTTGAAAACTTACACAAGTT
1 ACCCTTTATCCTTTTTGTCTTCAAAGAATA-GAATACCTTTTTCTTTTGAAAACTCACACAAGCT
* *
2598857 GGTGGT
65 GGTCGA
* * * * * * *
2598863 ACCCTTTATCTTTTTTATTTCTCAAAGAGTAGAATACTTTTTTCTTTTGAAAACTCATACATGCT
1 ACCCTTTATCCTTTTTGTCT-TCAAAGAATAGAATACCTTTTTCTTTTGAAAACTCACACAAGCT
2598928 GGTCGA
65 GGTCGA
*
2598934 ACCCTTTATCCTTTTAGTCTTCAAAGA
1 ACCCTTTATCCTTTTTGTCTTCAAAGA
2598961 GCAAGATACT
Statistics
Matches: 79, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
70 25 0.32
71 54 0.68
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (70 bp):
ACCCTTTATCCTTTTTGTCTTCAAAGAATAGAATACCTTTTTCTTTTGAAAACTCACACAAGCTG
GTCGA
Found at i:2599089 original size:72 final size:72
Alignment explanation
Indices: 2599013--2599203 Score: 253
Period size: 72 Copynumber: 2.7 Consensus size: 72
2599003 CCTTTTATCA
* * * * * **
2599013 TTTTTAGCTATCAAAGAGCAGGACACCTTTTTCTTTTTAAAGCCTATATAAGCTAGTTGCACTCT
1 TTTTTAGCTCTCAAAGATCAAGACACCTTTTTCTTTTTAAAGCCCACATAAGCTAGTAACACTCT
2599078 TTATCTT
66 TTATCTT
*
2599085 TTTTTA-TTCCTCAAAGATCAAGACACCTTTTTCTTTTTAAAGCCCACATAAGCTAGTAACACTC
1 TTTTTAGCT-CTCAAAGATCAAGACACCTTTTTCTTTTTAAAGCCCACATAAGCTAGTAACACTC
2599149 TTTATCTT
65 TTTATCTT
*
2599157 TTTTTAGAC-CTCAAAAATCAAGA-ACCCTTTTTCTTTTTAAAGCCCAC
1 TTTTTAG-CTCTCAAAGATCAAGACA-CCTTTTTCTTTTTAAAGCCCAC
2599204 TGTCGTAACG
Statistics
Matches: 105, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
71 2 0.02
72 103 0.98
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.40
Consensus pattern (72 bp):
TTTTTAGCTCTCAAAGATCAAGACACCTTTTTCTTTTTAAAGCCCACATAAGCTAGTAACACTCT
TTATCTT
Found at i:2602490 original size:104 final size:104
Alignment explanation
Indices: 2602301--2602497 Score: 306
Period size: 104 Copynumber: 1.9 Consensus size: 104
2602291 ATATGAAAAG
* * *
2602301 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTACATGTA
***
2602366 TCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
66 TCGATACATAAGATAATGTATCGATACATCTGGGCAAAT
*
2602405 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCTACATGTA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTACATGTA
*
2602470 TCGATACA-AAGATCAGTGTATCGATACA
66 TCGATACATAAGAT-AATGTATCGATACA
2602498 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
103 2 0.02
104 82 0.98
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (104 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTACATGTA
TCGATACATAAGATAATGTATCGATACATCTGGGCAAAT
Found at i:2602497 original size:52 final size:52
Alignment explanation
Indices: 2602301--2602477 Score: 318
Period size: 52 Copynumber: 3.4 Consensus size: 52
2602291 ATATGAAAAG
* * *
2602301 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
2602353 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
2602405 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
*
2602457 TTGCCTACATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
2602478 AAGATCAGTG
Statistics
Matches: 121, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 121 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
Found at i:2602504 original size:13 final size:13
Alignment explanation
Indices: 2602486--2602510 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2602476 CAAAGATCAG
2602486 TGTATCGATACAA
1 TGTATCGATACAA
2602499 TGTATCGATACA
1 TGTATCGATACA
2602511 TGTGAGTAAT
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:2602593 original size:13 final size:13
Alignment explanation
Indices: 2602575--2602599 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2602565 CAAAAAAATA
2602575 TGTATCGATACAT
1 TGTATCGATACAT
2602588 TGTATCGATACA
1 TGTATCGATACA
2602600 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:2602595 original size:33 final size:33
Alignment explanation
Indices: 2602553--2602619 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2602543 AGTAGCTTAA
2602553 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2602586 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2602619 A
1 A
2602620 AATCGTTGAA
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:2603116 original size:72 final size:70
Alignment explanation
Indices: 2602936--2603112 Score: 216
Period size: 72 Copynumber: 2.5 Consensus size: 70
2602926 AATTTTATCC
* * * *
2602936 TTTTAGTCTTCAAAGAGTAGGACAC-CTTTTTTTTAAAGCACATACAAGCTGGTGACACCCTTTA
1 TTTTAGTCCTCAAAGAGTAGGACACTTTTTTTTTTAAAGCACACACAAGCTGGTGACACCCTTCA
2603000 TCTTT
66 TCTTT
* **
2603005 TTTTAGTCCTCAAAGAGTAGGACACATGTTTCTTTTTAAAGC-CTACACAAGCTGGTTG-CATTC
1 TTTTAGTCCTCAAAGAGTAGGACAC-T-TTTTTTTTTAAAGCAC-ACACAAGCTGG-TGACACCC
*
2603068 TTCATTTTT
62 TTCATCTTT
2603077 TTTTCAGTCCTCAAAGAGTAGGACACTTTTTTTTTT
1 TTTT-AGTCCTCAAAGAGTAGGACACTTTTTTTTTT
2603113 TAAAACCCAC
Statistics
Matches: 93, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
69 24 0.26
71 9 0.10
72 37 0.40
73 23 0.25
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (70 bp):
TTTTAGTCCTCAAAGAGTAGGACACTTTTTTTTTTAAAGCACACACAAGCTGGTGACACCCTTCA
TCTTT
Found at i:2610005 original size:22 final size:22
Alignment explanation
Indices: 2609962--2610005 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2609952 ACCTTTTATT
**
2609962 TTTAAAAATATTTTTATTTTAA
1 TTTAAAAATATTTAAATTTTAA
2609984 TTTAAAAATA-TTAAATTATTAA
1 TTTAAAAATATTTAAATT-TTAA
2610006 AATATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTAAAAATATTTAAATTTTAA
Found at i:2610257 original size:21 final size:21
Alignment explanation
Indices: 2610233--2610272 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2610223 ACTGTTAATT
* *
2610233 TTAATTTTATTATTATAATAA
1 TTAATTTTATCACTATAATAA
2610254 TTAATTTTATCACTATAAT
1 TTAATTTTATCACTATAAT
2610273 TATTTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAATTTTATCACTATAATAA
Found at i:2610587 original size:21 final size:20
Alignment explanation
Indices: 2610553--2610595 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
2610543 CTATCAATAA
2610553 ATATTATAATTATATAAATT
1 ATATTATAATTATATAAATT
*
2610573 ATATTATTTATTATATAAATT
1 ATATTA-TAATTATATAAATT
2610594 AT
1 AT
2610596 TATGATCGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTATAATTATATAAATT
Found at i:2611679 original size:21 final size:21
Alignment explanation
Indices: 2611648--2611704 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
2611638 GTAAAAAAAT
* *
2611648 TATAT-TTTTAATTTTATTAA
1 TATATATTTTAATATTACTAA
2611668 TATATATTTTAATATTACTAA
1 TATATATTTTAATATTACTAA
* *
2611689 TAAATATATT-ATATTA
1 TATATATTTTAATATTA
2611705 ATAAAAACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATATTTTAATATTACTAA
Found at i:2612459 original size:10 final size:10
Alignment explanation
Indices: 2612444--2612471 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2612434 AATAACAACT
2612444 ATTTTAAAAA
1 ATTTTAAAAA
2612454 ATTTTAAAAA
1 ATTTTAAAAA
2612464 ATTTTAAA
1 ATTTTAAA
2612472 TCCTCAACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:2616104 original size:25 final size:24
Alignment explanation
Indices: 2616049--2616110 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
2616039 TTTTTTAAAA
*
2616049 TAATTTTTATTAATAAATAATTTT
1 TAATTTTTATTAAAAAATAATTTT
* *
2616073 CATATTTTTATTAAAATAATTATTTT
1 TA-ATTTTTATTAAAA-AATAATTTT
*
2616099 TAATTTATATTA
1 TAATTTTTATTA
2616111 TTATTAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 1 0.03
25 21 0.68
26 9 0.29
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TAATTTTTATTAAAAAATAATTTT
Found at i:2616469 original size:2 final size:2
Alignment explanation
Indices: 2616462--2616495 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2616452 ATTTAAAGGA
2616462 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2616496 GCGTTATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2620670 original size:13 final size:13
Alignment explanation
Indices: 2620652--2620678 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2620642 ACATTATGCT
2620652 TTGTATCGATACA
1 TTGTATCGATACA
2620665 TTGTATCGATACA
1 TTGTATCGATACA
2620678 T
1 T
2620679 ATTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2620675 original size:33 final size:32
Alignment explanation
Indices: 2620633--2620697 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
2620623 CATATCCAAA
*
2620633 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACA-TATGCATTGTATCGATACAT
* *
2620666 TGTATCGATACATATTCATTGTATTGATACAT
1 TGTATCGATACATATGCATTGTATCGATACAT
2620698 GCATAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (32 bp):
TGTATCGATACATATGCATTGTATCGATACAT
Found at i:2620687 original size:19 final size:19
Alignment explanation
Indices: 2620663--2620717 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
2620653 TGTATCGATA
2620663 CATTGTATCGATACAT-ATT
1 CATTGTATCGATACATCA-T
*
2620682 CATTGTATTGATACATGCAT
1 CATTGTATCGATACAT-CAT
*
2620702 AATTGTATCGATACAT
1 CATTGTATCGATACAT
2620718 GAAACTGGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.48
20 15 0.48
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (19 bp):
CATTGTATCGATACATCAT
Found at i:2620785 original size:13 final size:13
Alignment explanation
Indices: 2620763--2620792 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2620753 TGATAATGGC
*
2620763 ACATTTTATCGAT
1 ACATTGTATCGAT
2620776 ACATTGTATCGAT
1 ACATTGTATCGAT
2620789 ACAT
1 ACAT
2620793 GGAGAATTGT
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:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:2622426 original size:15 final size:15
Alignment explanation
Indices: 2622403--2622433 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2622393 ATCAAAGATT
2622403 ATGAAGATAATGATG
1 ATGAAGATAATGATG
*
2622418 ATGATGATAATGATG
1 ATGAAGATAATGATG
2622433 A
1 A
2622434 AGTTGACTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (15 bp):
ATGAAGATAATGATG
Found at i:2626714 original size:20 final size:20
Alignment explanation
Indices: 2626661--2626715 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2626651 AAATTCCTAG
**
2626661 ATGTATCGATACAAAGATCA
1 ATGTATCGATACATTGATCA
2626681 ATGTATCGATACATTGAAT-A
1 ATGTATCGATACATTG-ATCA
2626701 ATGTATCGATACATT
1 ATGTATCGATACATT
2626716 TCCTTAGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGATCA
Found at i:2627715 original size:49 final size:49
Alignment explanation
Indices: 2627543--2628007 Score: 385
Period size: 43 Copynumber: 9.9 Consensus size: 49
2627533 GCTCGAAGAT
* * * *
2627543 ATGAAGAATGACAATGTGCTGATTCATA-GCCAGCGACATTAGACTTGAAG
1 ATGAAG-ATGCCAATATGCTGATTCA-AGGCCAGCGACATTGGACTTAAAG
* * * ** ** *
2627593 AAG-A-ATGCCAATGTGCTAAGACAAGGTTAGCGACATTGGGCTTAGGAATG
1 ATGAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA--AA-G
* * * * *
2627643 -TTAAGGATGCCAATATGCAGATTCAAGGCCAACGATATCGGACTTAAAG
1 ATGAA-GATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * *
2627692 ATGAAGATACCAATGTGCTGATTCAAGGCCGGCGACATTGGACTT-AA-
1 ATGAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
*
2627739 A-G--G-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 ATGAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* *
2627784 ATGAAGATGCCAATGTGCTGATTCAAGGCC-GATGACATTGGACTT-AA-
1 ATGAAGATGCCAATATGCTGATTCAAGGCCAG-CGACATTGGACTTAAAG
* *
2627831 A-G--G-TGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAG
1 ATGAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
** *
2627876 ATGAAGATGCCAATGCGCTGATTCAAGGTCAGCGACATTGGACTT-AA-
1 ATGAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
2627923 A-G--G-TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AA-
1 ATGAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * *
2627966 A-G--G-TGCCAATATGCTGATTCAAGGCTAGTGATATTGGACTTA
1 ATGAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
2628008 GAAAAAGATG
Statistics
Matches: 339, Mismatches: 53, Indels: 52
0.76 0.12 0.12
Matches are distributed among these distances:
43 141 0.42
44 8 0.02
45 2 0.01
46 6 0.02
47 32 0.09
48 9 0.03
49 103 0.30
50 9 0.03
52 29 0.09
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (49 bp):
ATGAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
Found at i:2627807 original size:92 final size:92
Alignment explanation
Indices: 2627645--2627967 Score: 538
Period size: 92 Copynumber: 3.5 Consensus size: 92
2627635 TAGGAATGTT
* * * *
2627645 AAGGATGCCAATATGCAGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGATACCAATGTGC
1 AAGG-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGC
2627710 TGATTCAAGGCCGGCGACATTGGACTTA
65 TGATTCAAGGCCGGCGACATTGGACTTA
2627738 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCT
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCT
**
2627803 GATTCAAGGCCGATGACATTGGACTTA
66 GATTCAAGGCCGGCGACATTGGACTTA
* *
2627830 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATGAAGATGCCAATGCGCT
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCT
* *
2627895 GATTCAAGGTCAGCGACATTGGACTTA
66 GATTCAAGGCCGGCGACATTGGACTTA
*
2627922 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
2627968 GTGCCAATAT
Statistics
Matches: 216, Mismatches: 14, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
92 212 0.98
93 4 0.02
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (92 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCT
GATTCAAGGCCGGCGACATTGGACTTA
Found at i:2627989 original size:21 final size:21
Alignment explanation
Indices: 2627922--2627989 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
2627912 ATTGGACTTA
2627922 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
* * *
2627943 AAGGCCAGCGACAT-TG--GACTTA
1 AAGG--TGCCA-ATATGCTGA-TTC
2627965 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
2627986 AAGG
1 AAGG
2627990 CTAGTGATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 12 0.35
22 8 0.24
23 5 0.15
24 2 0.06
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:2628071 original size:29 final size:30
Alignment explanation
Indices: 2628033--2628275 Score: 220
Period size: 29 Copynumber: 8.4 Consensus size: 30
2628023 AACTTATGTA
*
2628033 GGCTTTTGAAAGGGTTG-CACCAACTTGTG
1 GGCTTTTGAAAGGGTTGCCACCGACTTGTG
* **
2628062 TGCTTTTG-AA-GGTTGCCATTGACTTGTG
1 GGCTTTTGAAAGGGTTGCCACCGACTTGTG
* * * *
2628090 GGCTTTTGAAA-AGATACCACTGACTTGTG
1 GGCTTTTGAAAGGGTTGCCACCGACTTGTG
** * *
2628119 GGCTTTAAAAAGGG-TACCACTGACTTGTG
1 GGCTTTTGAAAGGGTTGCCACCGACTTGTG
*
2628148 GGC-TTTGAAAGGGGTGCCACCGACTTGTG
1 GGCTTTTGAAAGGGTTGCCACCGACTTGTG
2628177 GGC-TTTGAAAGAGG-TGCCACCGACTTGTG
1 GGCTTTTGAAAG-GGTTGCCACCGACTTGTG
**
2628206 GGCTTTTG-AA-GGTTGCCACTAACTTGTG
1 GGCTTTTGAAAGGGTTGCCACCGACTTGTG
* * * *
2628234 GGCTTTGGAAA-AGATGCCACTGACTTGTG
1 GGCTTTTGAAAGGGTTGCCACCGACTTGTG
*
2628263 GGTTTTTGAAAGG
1 GGCTTTTGAAAGG
2628276 TGAAGAATGT
Statistics
Matches: 180, Mismatches: 25, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
27 7 0.04
28 46 0.26
29 120 0.67
30 7 0.04
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (30 bp):
GGCTTTTGAAAGGGTTGCCACCGACTTGTG
Found at i:2628173 original size:58 final size:58
Alignment explanation
Indices: 2628033--2628275 Score: 246
Period size: 57 Copynumber: 4.2 Consensus size: 58
2628023 AACTTATGTA
* ** * *
2628033 GGCTTTTGAAAGGGTTG-CACCAACTTGTGTGCTTTTGAAGGTTGCCATTGACTTGTG
1 GGCTTTTGAAAGGGTTGCCACCAACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTG
* * * ** *
2628090 GGCTTTTGAAA-AGATACCACTGACTTGTGGGCTTTAAAAAGGGTACCACTGACTTGTG
1 GGCTTTTGAAAGGGTTGCCACCAACTTGTGGGCTTT-AAAAGGGTGCCACTGACTTGTG
* * * *
2628148 GGC-TTTGAAAGGGGTGCCACCGACTTGTGGGCTTTGAAAGAGGTGCCACCGACTTGTG
1 GGCTTTTGAAAGGGTTGCCACCAACTTGTGGGCTTTAAAAG-GGTGCCACTGACTTGTG
* *
2628206 GGCTTTTG-AA-GGTTGCCACTAACTTGTGGGCTTTGGAAAA-GATGCCACTGACTTGTG
1 GGCTTTTGAAAGGGTTGCCACCAACTTGTGGGCTTT--AAAAGGGTGCCACTGACTTGTG
*
2628263 GGTTTTTGAAAGG
1 GGCTTTTGAAAGG
2628276 TGAAGAATGT
Statistics
Matches: 152, Mismatches: 25, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
56 2 0.01
57 80 0.53
58 62 0.41
59 8 0.05
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (58 bp):
GGCTTTTGAAAGGGTTGCCACCAACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTG
Found at i:2629727 original size:1 final size:1
Alignment explanation
Indices: 2629723--2629788 Score: 60
Period size: 1 Copynumber: 66.0 Consensus size: 1
2629713 GTTGTTATTG
* * * * * * * *
2629723 TTTTTTTTTTGTTTTTTTTTGTTTGTTTGTTTTTTTTTTTGTTTGTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2629788 T
1 T
2629789 ACGAAGGACG
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (1 bp):
T
Found at i:2629734 original size:20 final size:18
Alignment explanation
Indices: 2629705--2629788 Score: 80
Period size: 20 Copynumber: 4.4 Consensus size: 18
2629695 ATTCGGACCC
*
2629705 TTTTTGTTGTTGTTATTGTT
1 TTTTTTTTGTT-TT-TTGTT
2629725 TTTTTTTTGTTTTTT-TT
1 TTTTTTTTGTTTTTTGTT
* *
2629742 TGTTTGTTTGTTTTTTTTT
1 T-TTTTTTTGTTTTTTGTT
2629761 TTGTTTGTTTGTTTTTTTGTT
1 TT-TTT-TTTG-TTTTTTGTT
2629782 TTTTTTT
1 TTTTTTT
2629789 ACGAAGGACG
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
17 3 0.05
18 16 0.29
19 9 0.16
20 17 0.31
21 10 0.18
ACGTcount: A:0.01, C:0.00, G:0.14, T:0.85
Consensus pattern (18 bp):
TTTTTTTTGTTTTTTGTT
Found at i:2629755 original size:16 final size:15
Alignment explanation
Indices: 2629720--2629788 Score: 97
Period size: 16 Copynumber: 4.6 Consensus size: 15
2629710 GTTGTTGTTA
2629720 TTGTTTTTTTTTTGT
1 TTGTTTTTTTTTTGT
*
2629735 TT-TTTTTTGTTTGT
1 TTGTTTTTTTTTTGT
2629749 TTGTTTTTTTTTTTGT
1 TTG-TTTTTTTTTTGT
2629765 TTGTTTGTTTTTTTGT
1 TTGTTT-TTTTTTTGT
2629781 TT-TTTTTT
1 TTGTTTTTT
2629789 ACGAAGGACG
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
14 16 0.33
15 8 0.16
16 25 0.51
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (15 bp):
TTGTTTTTTTTTTGT
Found at i:2629756 original size:28 final size:28
Alignment explanation
Indices: 2629720--2629788 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 28
2629710 GTTGTTGTTA
* *
2629720 TTGTTTTTTTTTTGTTTTTTTTTGTTTGT
1 TTGTTTTTTTTTT-TGTTTGTTTGTTTGT
*
2629749 TTGTTTTTTTTTTTGTTTGTTTGTTTTT
1 TTGTTTTTTTTTTTGTTTGTTTGTTTGT
2629777 TTGTTTTTTTTT
1 TTGTTTTTTTTT
2629789 ACGAAGGACG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 24 0.65
29 13 0.35
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (28 bp):
TTGTTTTTTTTTTTGTTTGTTTGTTTGT
Found at i:2643740 original size:13 final size:13
Alignment explanation
Indices: 2643722--2643747 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2643712 ACAAAGATCC
2643722 ATGTATCGATACA
1 ATGTATCGATACA
2643735 ATGTATCGATACA
1 ATGTATCGATACA
2643748 TTGAATAATG
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:2643964 original size:19 final size:19
Alignment explanation
Indices: 2643940--2644007 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
2643930 AATTCAACAA
2643940 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2643959 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2643974 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
* *
2643991 ATTATATCGATACATAA
1 TTTGTATCGATACATAA
2644008 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 27 0.64
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2643979 original size:13 final size:13
Alignment explanation
Indices: 2643961--2643985 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2643951 ACATAAGTTT
2643961 TGTATCGATACAA
1 TGTATCGATACAA
2643974 TGTATCGATACA
1 TGTATCGATACA
2643986 TAAGTATTAT
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:2643983 original size:32 final size:32
Alignment explanation
Indices: 2643942--2644004 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
2643932 TTCAACAATT
* *
2643942 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTATATCGATACAA
2643974 TGTATCGATACATAAGTATTATATCGATACA
1 TGTATCGATACATAAGTATTATATCGATACA
2644005 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTATATCGATACAA
Found at i:2644065 original size:13 final size:13
Alignment explanation
Indices: 2644047--2644072 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2644037 CATTTTTCTG
2644047 TGTATCGATACAT
1 TGTATCGATACAT
2644060 TGTATCGATACAT
1 TGTATCGATACAT
2644073 GGATCTTTGT
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:2644084 original size:33 final size:33
Alignment explanation
Indices: 2644027--2644093 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2644017 GCCAAGGAAA
*** *
2644027 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCAATACAT
*
2644060 TGTATCGATACATGGATCTTTGTATCAATACAT
1 TGTATCGATACATGGATCTGTGTATCAATACAT
2644093 T
1 T
2644094 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:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCAATACAT
Found at i:2644636 original size:11 final size:11
Alignment explanation
Indices: 2644606--2644636 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2644596 ATCCTTTAGC
*
2644606 AAAAAACAAAA
1 AAAAAACACAA
2644617 AAAAAACACAA
1 AAAAAACACAA
2644628 AAAAAACAC
1 AAAAAACAC
2644637 TATTCCATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAACACAA
Found at i:2646629 original size:31 final size:28
Alignment explanation
Indices: 2646547--2646615 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 28
2646537 TTCACAATCA
* ***
2646547 GGGATACTCCAACCCCGTTA-ATCATCG
1 GGGATACTCCAACCCCGTTATTTCCGAG
2646574 GGGATACTCCAACCCCGTTATTTCCGAG
1 GGGATACTCCAACCCCGTTATTTCCGAG
2646602 GGGATACTCCAACC
1 GGGATACTCCAACC
2646616 TCGACTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 20 0.54
28 17 0.46
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.22
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTCCGAG
Found at i:2646780 original size:53 final size:51
Alignment explanation
Indices: 2646601--2646823 Score: 189
Period size: 52 Copynumber: 4.3 Consensus size: 51
2646591 TTATTTCCGA
* * *** *
2646601 GGGGATACTCCAACCTCGACTTTATTTCCAAAATATTGATTTT-TCATAATC
1 GGGGATACTCCAACC-CGATTTTATTTCCAAAACACAAATTTTCCCATAATC
* * * * ** *
2646652 GGGGATACTCCAACCCCAGTTTTATTGCTAAAACACTAATTTTTTCACAATC
1 GGGGATACTCCAACCCGA-TTTTATTTCCAAAACACAAATTTTCCCATAATC
* * *
2646704 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACAAATTTTCCCTTTAATC
1 GGGGATACTCCAA-CCCGATTTTATTTCCAAAACACAAATTTTCCC-ATAATC
* * * *
2646757 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTT-TCACAATC
1 GGGGATACTCCAAC-CCGATTTTATTTCC-AAAACACAAATTTTCCCATAATC
*
2646809 GAGGATACTCCAACC
1 GGGGATACTCCAACC
2646824 TCGTTATTTC
Statistics
Matches: 140, Mismatches: 26, Indels: 12
0.79 0.15 0.07
Matches are distributed among these distances:
50 2 0.01
51 34 0.24
52 59 0.42
53 33 0.24
54 12 0.09
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCGATTTTATTTCCAAAACACAAATTTTCCCATAATC
Found at i:2646842 original size:28 final size:28
Alignment explanation
Indices: 2646806--2646882 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
2646796 ATTTTTCACA
* * *
2646806 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
2646834 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
2646862 --CGAAGGGATACTCCAACCCCG
1 ATCG--GGGATACTCCAACCCCG
2646883 GCTTTATTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 2 0.05
28 42 0.95
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:2646914 original size:264 final size:263
Alignment explanation
Indices: 2646434--2646933 Score: 792
Period size: 264 Copynumber: 1.9 Consensus size: 263
2646424 CTCAATTCTC
* * *
2646434 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATA
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACAAATTTTCTATAATCGGGGATA
*
2646499 CTCCAATTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAGGGATACTCCAACCCCG
66 CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAGGGATACTCCAACCCCG
* * * *
2646564 TTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCTCGACTTTATTTC
131 TTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAAGGGATACTCCAACCCCGACTTTATTCC
2646629 CAAAATATTGATTTTTCATAATCGGGGATACTCCAACCCCAGTTTTATTGCTAAAACACTAATTT
196 CAAAATATTGATTTTTCATAATCGGGGATACTCCAACCCCAGTTTTATTGCTAAAACACTAATTT
2646694 TTT
261 TTT
* *
2646697 CACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACAAATTTTCCCTTTAATCGGGGA
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACAAATTTT--CTATAATCGGGGA
*
2646762 TACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATC-GAGGATACTCCAACC
64 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAG-GGATACTCCAACC
* * *
2646824 TCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAAGGGATACTCCAACCCCGGCTTTA
128 CCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAAGGGATACTCCAACCCCGACTTTA
*
2646889 TTCCCAAAATATTG-TTTTCTCATAATTGGGGATACTCCAACCCCA
192 TTCCCAAAATATTGATTTT-TCATAATCGGGGATACTCCAACCCCA
2646934 TTATTTTCGA
Statistics
Matches: 217, Mismatches: 15, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
262 1 0.00
263 77 0.35
264 104 0.48
265 35 0.16
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (263 bp):
CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACAAATTTTCTATAATCGGGGATA
CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAGGGATACTCCAACCCCG
TTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAAGGGATACTCCAACCCCGACTTTATTCC
CAAAATATTGATTTTTCATAATCGGGGATACTCCAACCCCAGTTTTATTGCTAAAACACTAATTT
TTT
Found at i:2654226 original size:20 final size:19
Alignment explanation
Indices: 2654203--2654275 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
2654193 CATATCCAGA
*
2654203 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
2654223 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
2654242 TGTATCGATACATGCACAAT
1 TGTATCGATACATGTTC-AT
2654262 TGTATCGATACATG
1 TGTATCGATACATG
2654276 AAATTTGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 17 0.35
20 30 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:2656803 original size:13 final size:13
Alignment explanation
Indices: 2656785--2656811 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2656775 TACATGGCAT
2656785 AATGTATCGATAC
1 AATGTATCGATAC
2656798 AATGTATCGATAC
1 AATGTATCGATAC
2656811 A
1 A
2656812 TGAAGAATTA
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):
AATGTATCGATAC
Found at i:2656826 original size:33 final size:33
Alignment explanation
Indices: 2656767--2656831 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2656757 TACCACTGTT
* * *
2656767 TGTATCGATACATGGCATAATGTATCGATACAA
1 TGTATCGATACATGGAAGAATATATCGATACAA
2656800 TGTATCGATACAT-GAAGAATTATATCGATACA
1 TGTATCGATACATGGAAGAA-TATATCGATACA
2656832 TTGCCTCAAA
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:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (33 bp):
TGTATCGATACATGGAAGAATATATCGATACAA
Found at i:2658933 original size:13 final size:13
Alignment explanation
Indices: 2658915--2658939 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2658905 CAGTCCTAAC
2658915 TAATATTTAATTA
1 TAATATTTAATTA
2658928 TAATATTTAATT
1 TAATATTTAATT
2658940 CTTTAGAAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATATTTAATTA
Found at i:2665980 original size:18 final size:18
Alignment explanation
Indices: 2665959--2666014 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
2665949 ACATTTATTA
2665959 TTATTAATTAATTTTATC
1 TTATTAATTAATTTTATC
* * *
2665977 TTATTCATTAAATTTA-A
1 TTATTAATTAATTTTATC
* *
2665994 TAAATATATTAATTTTATC
1 TTATTA-ATTAATTTTATC
2666013 TT
1 TT
2666015 CACATATCTA
Statistics
Matches: 27, Mismatches: 9, Indels: 3
0.69 0.23 0.08
Matches are distributed among these distances:
17 3 0.11
18 23 0.85
19 1 0.04
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATTAATTAATTTTATC
Found at i:2666161 original size:45 final size:46
Alignment explanation
Indices: 2666063--2666161 Score: 155
Period size: 46 Copynumber: 2.2 Consensus size: 46
2666053 ATTATTAATT
* * *
2666063 AATTTTATCTCATTTACTGTTTATAATATAAAAATTATTGACAATA
1 AATTTTATCTCATTTACTGCTCATAATATAAAAATTATTAACAATA
*
2666109 AACTTTATCTCATTTACTGCTCATAATAT-AAAATTATTAACAATA
1 AATTTTATCTCATTTACTGCTCATAATATAAAAATTATTAACAATA
2666154 AATTTTAT
1 AATTTTAT
2666162 TTCTTTTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 22 0.46
46 26 0.54
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.44
Consensus pattern (46 bp):
AATTTTATCTCATTTACTGCTCATAATATAAAAATTATTAACAATA
Found at i:2666492 original size:201 final size:200
Alignment explanation
Indices: 2666178--2666692 Score: 603
Period size: 201 Copynumber: 2.6 Consensus size: 200
2666168 TATTAAATTT
* * * * *
2666178 AATAAATATATTAATTTTATCTTATT-AATAGTTTTGTATCTTGTTAATTGATTTTAATATAATA
1 AATAAATATATTAATTTTATCTTATTCAA-A-TTTTTTATCTTATTCATTAAATTTAATATAATA
* * * ** *
2666242 TATTAATAATTCAAAATCAATCTTAAATATTTTTTTGATTTTATTTTAACTTTTTTTAATA-ATA
64 TATTAATCATTCAACATCAATCTTAAATATTCTTCGGATTTTATTTTAACTTTTTCTAATAGA-A
* * *
2666306 TTTGAATGATTAAATTATTAAAAAC-ATAATCTAAAAATTATAAC-CATTTAATTTTAACTCATT
128 TTTAAATGATTAAATTATT-AAAACTATAATATAAAAATTATAACTAATTT-ATTTTAACTCATT
*
2666369 TATTGAGTGC
191 TATTGAATGC
*
2666379 AATACAATATATTAA-TTTATCTCATTCACAATTTTTTATCTTATTCATTAAATTTAATATAATA
1 AATA-AATATATTAATTTTATCTTATTCA-AATTTTTTATCTTATTCATTAAATTTAATATAATA
* * *
2666443 TATTAATCATTCAACATCAATCTTGAATGTTCTTCGGATTTTGTTTTAACTTTTTCTAATAGAAT
64 TATTAATCATTCAACATCAATCTTAAATATTCTTCGGATTTTATTTTAACTTTTTCTAATAGAAT
** * *
2666508 TTAAATGATTAAATTATTAAAACTATAATATAAAAATTATAACTAATTTATTTTATTTTATTTTT
129 TTAAATGATTAAATTATTAAAACTATAATATAAAAATTATAACTAATTTATTTTAACTCATTTAT
**
2666573 TGAATTT
194 TGAATGC
* * * *
2666580 AATATAATAAATTAATTTTATCTTATTCAAAGTTTTTATATCATTCATTAAATTTAATATAATAT
1 AATA-AATATATTAATTTTATCTTATTCAAATTTTTTATCTTATTCATTAAATTTAATATAATAT
* * * *
2666645 ATTAATCATTCAACATCGATTTTAAAT-TT-TTATGAATTTTATTTTAAC
65 ATTAATCATTCAACATCAATCTTAAATATTCTT-CGGATTTTATTTTAAC
2666693 ACTTTTTAAT
Statistics
Matches: 269, Mismatches: 37, Indels: 17
0.83 0.11 0.05
Matches are distributed among these distances:
199 2 0.01
200 20 0.07
201 217 0.81
202 29 0.11
203 1 0.00
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (200 bp):
AATAAATATATTAATTTTATCTTATTCAAATTTTTTATCTTATTCATTAAATTTAATATAATATA
TTAATCATTCAACATCAATCTTAAATATTCTTCGGATTTTATTTTAACTTTTTCTAATAGAATTT
AAATGATTAAATTATTAAAACTATAATATAAAAATTATAACTAATTTATTTTAACTCATTTATTG
AATGC
Found at i:2667059 original size:2 final size:2
Alignment explanation
Indices: 2667052--2667082 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2667042 TTTACTCATG
*
2667052 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2667083 GTTTTTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2672999 original size:8 final size:8
Alignment explanation
Indices: 2672975--2673023 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
2672965 CTGCCAACAT
*
2672975 TACATACA
1 TACATATA
*
2672983 TAAATATA
1 TACATATA
*
2672991 TATATATA
1 TACATATA
*
2672999 TACATACA
1 TACATATA
2673007 TACATATA
1 TACATATA
*
2673015 TATATATA
1 TACATATA
2673023 T
1 T
2673024 CAATGAGAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (8 bp):
TACATATA
Found at i:2673002 original size:24 final size:24
Alignment explanation
Indices: 2672975--2673023 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2672965 CTGCCAACAT
2672975 TACATACATAAATATATATATATA
1 TACATACATAAATATATATATATA
*
2672999 TACATACATACATATATATATATA
1 TACATACATAAATATATATATATA
2673023 T
1 T
2673024 CAATGAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (24 bp):
TACATACATAAATATATATATATA
Found at i:2673003 original size:20 final size:20
Alignment explanation
Indices: 2672978--2673020 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2672968 CCAACATTAC
*
2672978 ATACATAAATATATATATAT
1 ATACATAAATACATATATAT
*
2672998 ATACATACATACATATATAT
1 ATACATAAATACATATATAT
2673018 ATA
1 ATA
2673021 TATCAATGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (20 bp):
ATACATAAATACATATATAT
Found at i:2675810 original size:17 final size:18
Alignment explanation
Indices: 2675781--2675824 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
2675771 AATTTTTTTT
*
2675781 ATTAAA-AATATTTACTC
1 ATTAAATAATATTTAATC
*
2675798 ATTAAATAA-ATTTAATT
1 ATTAAATAATATTTAATC
2675815 ATTAAATAAT
1 ATTAAATAAT
2675825 CAATAACCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 21 0.91
18 2 0.09
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAAATAATATTTAATC
Found at i:2677193 original size:17 final size:19
Alignment explanation
Indices: 2677160--2677196 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2677150 ATTCTTGAAA
2677160 TTTATATACCGATAATTAT
1 TTTATATACCGATAATTAT
2677179 TTTATATACC-A-AATTAT
1 TTTATATACCGATAATTAT
2677196 T
1 T
2677197 GATAGGGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 1 0.06
19 10 0.56
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.49
Consensus pattern (19 bp):
TTTATATACCGATAATTAT
Found at i:2679885 original size:75 final size:75
Alignment explanation
Indices: 2679758--2679906 Score: 201
Period size: 75 Copynumber: 2.0 Consensus size: 75
2679748 GATGAAACGA
* * **
2679758 TAATCCAAGATCATCTGCATAATATTTACAATCAACAAATGTTTCAGCATATTTCACAGTACTAA
1 TAATCCAAGATAATCTGCACAATAACTACAATCAACAAATGTTTCAGCATATTTCACAGTACTAA
2679823 TATCAACAAT
66 TATCAACAAT
* * * *
2679833 TAATCCGAGATAATCTGCACAATAACTACAATCAACAAATGTTTC-TCTATATTTCACATTGCTA
1 TAATCCAAGATAATCTGCACAATAACTACAATCAACAAATGTTTCAGC-ATATTTCACAGTACTA
*
2679897 CTATCAACAA
65 ATATCAACAA
2679907 CTATAATTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
74 1 0.02
75 63 0.98
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.32
Consensus pattern (75 bp):
TAATCCAAGATAATCTGCACAATAACTACAATCAACAAATGTTTCAGCATATTTCACAGTACTAA
TATCAACAAT
Found at i:2680361 original size:15 final size:15
Alignment explanation
Indices: 2680339--2680379 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
2680329 TGGGTAAACA
2680339 GGTGGTGGATGCACG
1 GGTGGTGGATGCACG
*
2680354 GGTTGTGGATGCACG
1 GGTGGTGGATGCACG
2680369 GGTGGTGGATG
1 GGTGGTGGATG
2680380 GACAGGATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.12, C:0.10, G:0.54, T:0.24
Consensus pattern (15 bp):
GGTGGTGGATGCACG
Found at i:2685210 original size:7 final size:7
Alignment explanation
Indices: 2685185--2685222 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
2685175 AAATCCTAAA
2685185 CAATAA-
1 CAATAAT
2685191 CAA-AAT
1 CAATAAT
*
2685197 AAATAAT
1 CAATAAT
2685204 CAATAAT
1 CAATAAT
2685211 CAATAAT
1 CAATAAT
2685218 CAATA
1 CAATA
2685223 CAAATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 2 0.07
6 5 0.18
7 21 0.75
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.24
Consensus pattern (7 bp):
CAATAAT
Found at i:2685261 original size:15 final size:14
Alignment explanation
Indices: 2685241--2685280 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
2685231 TTATAGGCTT
2685241 TAAACTAATTACCCC
1 TAAACTAATTA-CCC
*
2685256 TAAACTAATTACGC
1 TAAACTAATTACCC
2685270 TAAACCTAATT
1 TAAA-CTAATT
2685281 TCACATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.42, C:0.25, G:0.03, T:0.30
Consensus pattern (14 bp):
TAAACTAATTACCC
Found at i:2685534 original size:21 final size:21
Alignment explanation
Indices: 2685494--2685534 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2685484 CGAACTTTAA
*
2685494 AATTTTAGAGAGAAGCGAGAG
1 AATTTTAGAGAGAAGAGAGAG
* *
2685515 AATTTTAGAGTGTAGAGAGA
1 AATTTTAGAGAGAAGAGAGA
2685535 AAGTGAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.02, G:0.32, T:0.24
Consensus pattern (21 bp):
AATTTTAGAGAGAAGAGAGAG
Found at i:2693185 original size:21 final size:22
Alignment explanation
Indices: 2693146--2693186 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2693136 AAGCTTATGC
2693146 AAATAAAGTAATTAAAAATTTA
1 AAATAAAGTAATTAAAAATTTA
*
2693168 AAATAAAG-AATTACAAATT
1 AAATAAAGTAATTAAAAATT
2693187 GGTGAATACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (22 bp):
AAATAAAGTAATTAAAAATTTA
Found at i:2695727 original size:12 final size:12
Alignment explanation
Indices: 2695712--2695736 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2695702 AAAGTATGCT
2695712 TAAAAATTATGA
1 TAAAAATTATGA
2695724 TAAAAATTATGA
1 TAAAAATTATGA
2695736 T
1 T
2695737 TTAAAAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TAAAAATTATGA
Found at i:2697468 original size:2 final size:2
Alignment explanation
Indices: 2697461--2697486 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2697451 CCTTACACCC
2697461 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
2697487 ATTCCCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2701552 original size:2 final size:2
Alignment explanation
Indices: 2701545--2701576 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2701535 TAGACAACTG
2701545 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2701577 GAGTGATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2703539 original size:87 final size:87
Alignment explanation
Indices: 2703392--2703550 Score: 264
Period size: 87 Copynumber: 1.8 Consensus size: 87
2703382 TGGCATTTTG
* * *
2703392 ATGCAATTTTAAGGAATAGGCACTACATTAGCTAAAATACCCATTTAGAATGCCTAAATACTCTC
1 ATGCAATTTTAAGAAATACGCACTACATTAGCCAAAATACCCATTTAGAATGCCTAAATACTCTC
2703457 TTAAAATATTCTCTTGGAATGC
66 TTAAAATATTCTCTTGGAATGC
* * *
2703479 ATGCAATTTTAAGAAATACGCACTATATTAGCCAAAATACTCATTTAGAATGCCTGAATACTCTC
1 ATGCAATTTTAAGAAATACGCACTACATTAGCCAAAATACCCATTTAGAATGCCTAAATACTCTC
2703544 TTAAAAT
66 TTAAAAT
2703551 GCTTAAATAC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 66 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.32
Consensus pattern (87 bp):
ATGCAATTTTAAGAAATACGCACTACATTAGCCAAAATACCCATTTAGAATGCCTAAATACTCTC
TTAAAATATTCTCTTGGAATGC
Found at i:2703559 original size:21 final size:21
Alignment explanation
Indices: 2703513--2703560 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2703503 ATATTAGCCA
*
2703513 AAATACTCATTTAGAATGCCT
1 AAATACTCATTTAAAATGCCT
* *
2703534 GAATACTC-TCTTAAAATGCTT
1 AAATACTCAT-TTAAAATGCCT
2703555 AAATAC
1 AAATAC
2703561 ACAATGCCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (21 bp):
AAATACTCATTTAAAATGCCT
Found at i:2705981 original size:15 final size:14
Alignment explanation
Indices: 2705951--2705998 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
2705941 TCTAGGTTCA
2705951 AGGTTTGGGGTTTG
1 AGGTTTGGGGTTTG
*
2705965 AGGTTTGTGGTTTTG
1 AGGTTTG-GGGTTTG
* *
2705980 AGTTTTAGGGTTT-
1 AGGTTTGGGGTTTG
2705993 AGGTTT
1 AGGTTT
2705999 CGAGGTTAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 5 0.18
14 12 0.43
15 11 0.39
ACGTcount: A:0.10, C:0.00, G:0.40, T:0.50
Consensus pattern (14 bp):
AGGTTTGGGGTTTG
Found at i:2706076 original size:8 final size:7
Alignment explanation
Indices: 2705983--2706269 Score: 137
Period size: 7 Copynumber: 41.0 Consensus size: 7
2705973 GGTTTTGAGT
2705983 TTTAGGG
1 TTTAGGG
2705990 TTTA-GG
1 TTTAGGG
*
2705996 TTTCGAGG
1 TTTAG-GG
*
2706004 TTAAGGG
1 TTTAGGG
*
2706011 TTT-GAG
1 TTTAGGG
2706017 TTTCA-GG
1 TTT-AGGG
*
2706024 -TTCGGG
1 TTTAGGG
**
2706030 TTCGGGG
1 TTTAGGG
**
2706037 TTTAAAG
1 TTTAGGG
2706044 TTTAGGG
1 TTTAGGG
*
2706051 TTTAAGG
1 TTTAGGG
*
2706058 TTTAAGG
1 TTTAGGG
2706065 TTTAGGGG
1 TTTA-GGG
2706073 TTTAGGG
1 TTTAGGG
*
2706080 TGTTAAGG
1 T-TTAGGG
*
2706088 TTAAAGGG
1 TT-TAGGG
* *
2706096 TTAAGGT
1 TTTAGGG
*
2706103 TTTAAGG
1 TTTAGGG
*
2706110 TTAAGGG
1 TTTAGGG
2706117 TTT-GGG
1 TTTAGGG
* *
2706123 GTTCGAGG
1 TTTAG-GG
2706131 TTT-GCGG
1 TTTAG-GG
2706138 TTT-GGG
1 TTTAGGG
2706144 TTTAGGG
1 TTTAGGG
2706151 TTTAGGG
1 TTTAGGG
*
2706158 GTTAGGGG
1 TTTA-GGG
*
2706166 TTTAGGA
1 TTTAGGG
* *
2706173 ATCAGGG
1 TTTAGGG
*
2706180 TTTAAGG
1 TTTAGGG
*
2706187 CTTAGGGG
1 TTTA-GGG
*
2706195 TTTGGGG
1 TTTAGGG
*
2706202 TTTTGGG
1 TTTAGGG
2706209 TTTAGGG
1 TTTAGGG
2706216 TTT--GG
1 TTTAGGG
*
2706221 TTTGGGG
1 TTTAGGG
2706228 TTTAGGG
1 TTTAGGG
2706235 TTTTA-GG
1 -TTTAGGG
2706242 -TTAGGGG
1 TTTA-GGG
*
2706249 TTTAAGG
1 TTTAGGG
*
2706256 TTTTGGG
1 TTTAGGG
2706263 TTTAGGG
1 TTTAGGG
2706270 GTATCGAGGT
Statistics
Matches: 210, Mismatches: 50, Indels: 40
0.70 0.17 0.13
Matches are distributed among these distances:
5 8 0.04
6 24 0.11
7 135 0.64
8 43 0.20
ACGTcount: A:0.16, C:0.03, G:0.41, T:0.40
Consensus pattern (7 bp):
TTTAGGG
Found at i:2706124 original size:7 final size:7
Alignment explanation
Indices: 2706114--2706291 Score: 74
Period size: 7 Copynumber: 25.3 Consensus size: 7
2706104 TTAAGGTTAA
2706114 GGGTTTG
1 GGGTTTG
*
2706121 GGGTTCG
1 GGGTTTG
*
2706128 AGGTTTG
1 GGGTTTG
*
2706135 CGGTTT-
1 GGGTTTG
*
2706141 GGGTTTA
1 GGGTTTG
2706148 GGGTTTAG
1 GGGTTT-G
*
2706156 GGGTTAG
1 GGGTTTG
*
2706163 GGGTTTA
1 GGGTTTG
** **
2706170 GGAATCA
1 GGGTTTG
*
2706177 GGGTTTAA
1 GGGTTT-G
* *
2706185 GGCTTAG
1 GGGTTTG
2706192 GGGTTTG
1 GGGTTTG
*
2706199 GGGTTTT
1 GGGTTTG
*
2706206 GGGTTTA
1 GGGTTTG
2706213 GGGTTT-
1 GGGTTTG
2706219 -GGTTTG
1 GGGTTTG
*
2706225 GGGTTTA
1 GGGTTTG
*
2706232 GGGTTTT
1 GGGTTTG
* *
2706239 AGGTTAG
1 GGGTTTG
*
2706246 GGGTTTA
1 GGGTTTG
* *
2706253 AGGTTTT
1 GGGTTTG
2706260 GGGTTTAG
1 GGGTTT-G
*
2706268 GGGTATCG
1 GGGT-TTG
* *
2706276 AGGTTCG
1 GGGTTTG
2706283 GGGTTTG
1 GGGTTTG
2706290 GG
1 GG
2706292 TTCAAGTTCT
Statistics
Matches: 126, Mismatches: 38, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
5 5 0.04
6 5 0.04
7 97 0.77
8 18 0.14
9 1 0.01
ACGTcount: A:0.11, C:0.03, G:0.46, T:0.39
Consensus pattern (7 bp):
GGGTTTG
Found at i:2706408 original size:8 final size:7
Alignment explanation
Indices: 2706389--2706473 Score: 80
Period size: 7 Copynumber: 12.0 Consensus size: 7
2706379 TGGGATAAGG
2706389 TTGGGGT
1 TTGGGGT
2706396 TTGGGGCT
1 TTGGGG-T
*
2706404 TTGGGGA
1 TTGGGGT
*
2706411 TTGGGGA
1 TTGGGGT
*
2706418 TTGGGGG
1 TTGGGGT
*
2706425 TTGGGGA
1 TTGGGGT
2706432 TTGGGGT
1 TTGGGGT
*
2706439 TGGGGGT
1 TTGGGGT
*
2706446 TGGGGGT
1 TTGGGGT
*
2706453 TCGGGGT
1 TTGGGGT
*
2706460 TCGGGGT
1 TTGGGGT
*
2706467 TAGGGGT
1 TTGGGGT
2706474 GGTTTTAGCG
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
7 63 0.90
8 7 0.10
ACGTcount: A:0.05, C:0.04, G:0.60, T:0.32
Consensus pattern (7 bp):
TTGGGGT
Found at i:2706430 original size:21 final size:20
Alignment explanation
Indices: 2706389--2706472 Score: 96
Period size: 21 Copynumber: 4.0 Consensus size: 20
2706379 TGGGATAAGG
*
2706389 TTGGGGTTTGGGGCTTTGGGGA
1 TTGGGG-TTGGGG-GTTGGGGA
2706411 TTGGGGATTGGGGGTTGGGGA
1 TTGGGG-TTGGGGGTTGGGGA
*
2706432 TTGGGGTTGGGGGTTGGGGG
1 TTGGGGTTGGGGGTTGGGGA
*
2706452 TTCGGGGTTCGGGGTTAGGGG
1 TT-GGGGTTGGGGGTT-GGGG
2706473 TGGTTTTAGC
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
20 15 0.27
21 25 0.45
22 16 0.29
ACGTcount: A:0.05, C:0.04, G:0.61, T:0.31
Consensus pattern (20 bp):
TTGGGGTTGGGGGTTGGGGA
Found at i:2706520 original size:15 final size:14
Alignment explanation
Indices: 2706387--2706524 Score: 77
Period size: 14 Copynumber: 9.8 Consensus size: 14
2706377 TTTGGGATAA
2706387 GGTT-GGGGTTTGGG
1 GGTTAGGGG-TTGGG
* *
2706401 GCTTTGGGGATTGGG
1 GGTTAGGGG-TTGGG
* *
2706416 GATTGGGGGTTGGG
1 GGTTAGGGGTTGGG
*
2706430 GATT-GGGGTTGGG
1 GGTTAGGGGTTGGG
* *
2706443 GGTTGGGGGTTCGG
1 GGTTAGGGGTTGGG
* *
2706457 GGTTCGGGGTTAGG
1 GGTTAGGGGTTGGG
**
2706471 GG-T-GGTTTTAGCGG
1 GGTTAGGGGTT-G-GG
** *
2706485 TTTTAGGGGGTGGG
1 GGTTAGGGGTTGGG
2706499 GGTTAGGGGTTGGG
1 GGTTAGGGGTTGGG
2706513 GCGTTAGGGGTT
1 G-GTTAGGGGTT
2706525 CGGGTTTCGG
Statistics
Matches: 98, Mismatches: 19, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
12 4 0.04
13 13 0.13
14 50 0.51
15 28 0.29
16 3 0.03
ACGTcount: A:0.06, C:0.04, G:0.59, T:0.32
Consensus pattern (14 bp):
GGTTAGGGGTTGGG
Done.