Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold29
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: 5511024
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 57772 characters in sequence are not A, C, G, or T
File 10 of 34
Found at i:1439558 original size:13 final size:13
Alignment explanation
Indices: 1439540--1439564 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1439530 ACTGAAGTAA
1439540 TGTATCGATACAT
1 TGTATCGATACAT
1439553 TGTATCGATACA
1 TGTATCGATACA
1439565 ATCTGGAAAA
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:1441640 original size:10 final size:10
Alignment explanation
Indices: 1441621--1441651 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1441611 GTATCGATAC
*
1441621 ATGAACAGTG
1 ATGAATAGTG
1441631 ATGAATAGTG
1 ATGAATAGTG
1441641 ATGAATAGTG
1 ATGAATAGTG
1441651 A
1 A
1441652 AAATGAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.29, T:0.26
Consensus pattern (10 bp):
ATGAATAGTG
Found at i:1441739 original size:53 final size:53
Alignment explanation
Indices: 1441675--1441811 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
1441665 CTACTTCCAA
*
1441675 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACT
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
1441728 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1441781 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
1441812 TATGCAATTT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 66 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:1441844 original size:20 final size:20
Alignment explanation
Indices: 1441781--1441851 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1441771 GCCAATGTCC
**
1441781 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
1441801 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
1441821 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
1441841 TGTATCGATAC
1 TGTATCGATAC
1441852 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:1441917 original size:21 final size:21
Alignment explanation
Indices: 1441891--1441931 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1441881 GTCAACCTTG
1441891 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
1441912 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
1441932 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:1447718 original size:18 final size:20
Alignment explanation
Indices: 1447695--1447736 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1447685 TTTGATGTTT
1447695 ATTATG-TTGTGTGA-ATGA
1 ATTATGCTTGTGTGATATGA
*
1447713 ATTATGCTTGTTTGATATGA
1 ATTATGCTTGTGTGATATGA
1447733 ATTA
1 ATTA
1447737 GGGTCTATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 7 0.33
20 8 0.38
ACGTcount: A:0.29, C:0.02, G:0.21, T:0.48
Consensus pattern (20 bp):
ATTATGCTTGTGTGATATGA
Found at i:1449792 original size:17 final size:17
Alignment explanation
Indices: 1449756--1449789 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1449746 AAATAAATTG
1449756 TTTATAAGGGGAGAAAA
1 TTTATAAGGGGAGAAAA
1449773 TTTATTAAGGGGAGAAA
1 TTTA-TAAGGGGAGAAA
1449790 TTTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.26
Consensus pattern (17 bp):
TTTATAAGGGGAGAAAA
Found at i:1451600 original size:3 final size:3
Alignment explanation
Indices: 1451586--1451637 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
1451576 CATCAAAGAC
*
1451586 GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1451634 GAT G
1 GAT G
1451638 TTGACTCGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:1456150 original size:22 final size:23
Alignment explanation
Indices: 1456122--1456176 Score: 82
Period size: 20 Copynumber: 2.6 Consensus size: 23
1456112 TTTTTCAGAA
1456122 TGTATCGATACATCAA-ATTCTT
1 TGTATCGATACATCAATATTCTT
1456144 TGTATCGA-A-A-CAATATTCTT
1 TGTATCGATACATCAATATTCTT
1456164 TGTATCGATACAT
1 TGTATCGATACAT
1456177 TGTATCGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.10
20 15 0.52
21 2 0.07
22 9 0.31
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (23 bp):
TGTATCGATACATCAATATTCTT
Found at i:1456181 original size:13 final size:13
Alignment explanation
Indices: 1456163--1456188 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1456153 ACAATATTCT
1456163 TTGTATCGATACA
1 TTGTATCGATACA
1456176 TTGTATCGATACA
1 TTGTATCGATACA
1456189 AGGGTTACTA
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):
TTGTATCGATACA
Found at i:1457479 original size:31 final size:32
Alignment explanation
Indices: 1457441--1457502 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
1457431 AATAAATTTG
1457441 TATCAAGGGGGAGAAAATCTTTTTAA-CCAAT
1 TATCAAGGGGGAGAAAATCTTTTTAATCCAAT
* *
1457472 TATCAAGGGGGAGAAATTTTTTTTAATCCAA
1 TATCAAGGGGGAGAAAATCTTTTTAATCCAA
1457503 GGAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.32
Consensus pattern (32 bp):
TATCAAGGGGGAGAAAATCTTTTTAATCCAAT
Found at i:1458181 original size:33 final size:32
Alignment explanation
Indices: 1458144--1458208 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
1458134 TACCACTGTT
1458144 TGTATCGATACATG-GCACATTGTATCGATACAA
1 TGTATCGATACATGAG-A-ATTGTATCGATACAA
1458177 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCGATACATGA-GAATTGTATCGATACA
1458209 TTGCTTCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATGAGAATTGTATCGATACAA
Found at i:1458182 original size:13 final size:13
Alignment explanation
Indices: 1458164--1458188 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1458154 CATGGCACAT
1458164 TGTATCGATACAA
1 TGTATCGATACAA
1458177 TGTATCGATACA
1 TGTATCGATACA
1458189 TGATGAATTG
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:1461268 original size:2 final size:2
Alignment explanation
Indices: 1461261--1461301 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1461251 AATGGCGAAA
1461261 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1461302 GGCTAATGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1465649 original size:21 final size:21
Alignment explanation
Indices: 1465611--1465650 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1465601 AACTAACTAC
*
1465611 AAATAATAATAATAAATATAT
1 AAATAATAATAACAAATATAT
1465632 AAATAAT-ATAACATAATAT
1 AAATAATAATAACA-AATAT
1465651 TTCATCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAATAATAACAAATATAT
Found at i:1465893 original size:4 final size:4
Alignment explanation
Indices: 1465884--1465918 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1465874 GGAGAATTCC
* *
1465884 CTTT CTTT CTTT CTTT CTGT CTTT CTTT CTCT CTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT
1465919 CTGAAAAAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.69
Consensus pattern (4 bp):
CTTT
Found at i:1472496 original size:32 final size:33
Alignment explanation
Indices: 1472459--1472522 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
1472449 GATGGATTAA
*
1472459 GGAAAAATG-AATGGGAAAGAAATAAGAATGTG
1 GGAAAAATGAAAAGGGAAAGAAATAAGAATGTG
1472491 GGAAAAATGAAAAGGGAAAGAAATAAGAATGT
1 GGAAAAATGAAAAGGGAAAGAAATAAGAATGT
1472523 TTACCGCCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 9 0.30
33 21 0.70
ACGTcount: A:0.56, C:0.00, G:0.30, T:0.14
Consensus pattern (33 bp):
GGAAAAATGAAAAGGGAAAGAAATAAGAATGTG
Found at i:1475979 original size:35 final size:36
Alignment explanation
Indices: 1475911--1475980 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 36
1475901 CCAAATTCTT
1475911 AAGTATTTTCACTCAAGTTTACACACAACCTTACTTG
1 AAGTATTTTCACTCAAGTTTA-ACACAACCTTACTTG
1475948 AAGTATTTTCACTCAAGTTT-ACACAACCTTACT
1 AAGTATTTTCACTCAAGTTTAACACAACCTTACT
1475981 AGATGTGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 13 0.39
37 20 0.61
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (36 bp):
AAGTATTTTCACTCAAGTTTAACACAACCTTACTTG
Found at i:1476383 original size:20 final size:19
Alignment explanation
Indices: 1476358--1476430 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
1476348 GTTGAACTCA
1476358 ATGTATCGATACATTTATGG
1 ATGTATCGATACATTTAT-G
*
1476378 ATGTATCAATACAATTTAT-
1 ATGTATCGATAC-ATTTATG
*
1476397 ATTGTATCGATATATTTTCATG
1 A-TGTATCGATACA-TTT-ATG
1476419 -TGTATCGATACA
1 ATGTATCGATACA
1476431 AATGAGGGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
19 2 0.05
20 34 0.77
21 8 0.18
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (19 bp):
ATGTATCGATACATTTATG
Found at i:1478962 original size:13 final size:13
Alignment explanation
Indices: 1478944--1478968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1478934 TACCAAGAAC
1478944 ATGTATCGATACA
1 ATGTATCGATACA
1478957 ATGTATCGATAC
1 ATGTATCGATAC
1478969 TAAGCAATAT
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):
ATGTATCGATACA
Found at i:1478967 original size:32 final size:33
Alignment explanation
Indices: 1478926--1478988 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
1478916 CAATTCTATG
1478926 TGTATCGATACCAAG-AACATGTATCGATACAA
1 TGTATCGATACCAAGCAACATGTATCGATACAA
* *
1478958 TGTATCGATACTAAGCAATATGTATCGATAC
1 TGTATCGATACCAAGCAACATGTATCGATAC
1478989 TTTCTAAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (33 bp):
TGTATCGATACCAAGCAACATGTATCGATACAA
Found at i:1480113 original size:21 final size:21
Alignment explanation
Indices: 1480089--1480133 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1480079 GCTATTGACT
* *
1480089 CATCGTATCTAAGTGCTGGTC
1 CATCATATCTAAGCGCTGGTC
*
1480110 CATCATGTCTAAGCGCTGGTC
1 CATCATATCTAAGCGCTGGTC
1480131 CAT
1 CAT
1480134 TGTGTTAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (21 bp):
CATCATATCTAAGCGCTGGTC
Found at i:1487877 original size:32 final size:33
Alignment explanation
Indices: 1487838--1487901 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1487828 CAATTCAATG
1487838 TGTATCGATACCAAG-AACATGTATCGATATAA
1 TGTATCGATACCAAGCAACATGTATCGATATAA
* *
1487870 TGTATCGATACTAAGCAATATGTATCGATATA
1 TGTATCGATACCAAGCAACATGTATCGATATA
1487902 TCTGGGTGTG
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:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (33 bp):
TGTATCGATACCAAGCAACATGTATCGATATAA
Found at i:1489859 original size:79 final size:80
Alignment explanation
Indices: 1489767--1489940 Score: 208
Period size: 79 Copynumber: 2.2 Consensus size: 80
1489757 GATAAAAACA
* **
1489767 GGGTTAGAGTATCCTC-TCGAAAAAAACGAGGTTGGAGTATCCCTAATGGTGAAAAATCAATGTT
1 GGGTTAGAGTATCCTCTTCGAAAAAAACGAGGTTGGAGTATCCCCAATGAAGAAAAATCAATGTT
* *
1489831 TTGGAAATAAAATTG
66 TTAGAAATAAAACTG
* * * * * * * *
1489846 GGGTTGGAGTATCC-CTTCGGAAATAACGGGGTTGGAGTATCCCCGATTAAGGAAAATCGATGTT
1 GGGTTAGAGTATCCTCTTCGAAAAAAACGAGGTTGGAGTATCCCCAATGAAGAAAAATCAATGTT
*
1489910 TTAGAAATAAAGCTG
66 TTAGAAATAAAACTG
1489925 GGGTTAGAGTATCCTC
1 GGGTTAGAGTATCCTC
1489941 GATTGTGAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
78 1 0.01
79 76 0.97
80 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (80 bp):
GGGTTAGAGTATCCTCTTCGAAAAAAACGAGGTTGGAGTATCCCCAATGAAGAAAAATCAATGTT
TTAGAAATAAAACTG
Found at i:1489938 original size:51 final size:52
Alignment explanation
Indices: 1489873--1489988 Score: 162
Period size: 51 Copynumber: 2.2 Consensus size: 52
1489863 CGGAAATAAC
* *
1489873 GGGGTTGGAGTATCCCCGATTAAGGAAAATCGATGTTTTAGAAAT-AAAGCT
1 GGGGTTAGAGTATCCCCGATTAAGAAAAATCGATGTTTTAGAAATAAAAGCT
* ** *
1489924 GGGGTTAGAGTATCCTCGATTGTGAAAAATCGGTGTTTTAGAAATAAAAGCT
1 GGGGTTAGAGTATCCCCGATTAAGAAAAATCGATGTTTTAGAAATAAAAGCT
*
1489976 GAGGTTAGAGTAT
1 GGGGTTAGAGTAT
1489989 TCTGTCAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
51 39 0.68
52 18 0.32
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.29
Consensus pattern (52 bp):
GGGGTTAGAGTATCCCCGATTAAGAAAAATCGATGTTTTAGAAATAAAAGCT
Found at i:1490108 original size:79 final size:79
Alignment explanation
Indices: 1489925--1490291 Score: 282
Period size: 79 Copynumber: 4.6 Consensus size: 79
1489915 AATAAAGCTG
* *
1489925 GGGTTAGAGTATCCTCGATTGTGAAAAATCGGTGTTTTAGAAATAAAAGCTGAGGTTAGAGTATT
1 GGGTTAGAGTATCCTCGATTGTGAAAAATCGGTGTTTTAGAAATAAAACCAG-GGTTAGAGTATT
** *
1489990 CTGTCAAAAATAACG
65 CCCTCAAAAATAACA
* * * * *
1490005 GGGTTGGAGTATCCTCGATGGTGAAAAATCAGTGTTTTAAAAAAAAAACCAGGGTTAGAGTATTC
1 GGGTTAGAGTATCCTCGATTGTGAAAAATCGGTGTTTTAGAAATAAAACCAGGGTTAGAGTATTC
*
1490070 CCTCAGAAATAACA
66 CCTCAAAAATAACA
* * * * * * *
1490084 TGGTTAGAGT-TACTCCGATTGTGAAAAATCGGTGTTCTGGAAATAAAACCGGGGTTGGAGTATC
1 GGGTTAGAGTATCCT-CGATTGTGAAAAATCGGTGTTTTAGAAATAAAACCAGGGTTAGAGTATT
**
1490148 CCCGATTGTGGAAAAT-ACA
65 CCC-----TCAAAAATAACA
* * * * * *
1490167 -GGTTGGAGTATCC-CTGATTGTGGAAAAT-TGTGTTTT-GAAAATAAAACCGGGGTTGGAATA-
1 GGGTTAGAGTATCCTC-GATTGTGAAAAATCGGTGTTTTAG-AAATAAAACCAGGGTTAGAGTAT
*
1490227 TCCGCTCAGAAATAAC-
64 TCC-CTCAAAAATAACA
* * * * * *
1490243 GAGTTTGGAGTATCTTGGATGGTGAAAAATCGGTATTTTAGAAATAAAA
1 G-GGTTAGAGTATCCTCGATTGTGAAAAATCGGTGTTTTAGAAATAAAA
1490292 ACATGAATAA
Statistics
Matches: 228, Mismatches: 43, Indels: 33
0.75 0.14 0.11
Matches are distributed among these distances:
76 5 0.02
77 2 0.01
78 25 0.11
79 88 0.39
80 49 0.21
81 29 0.13
82 20 0.09
83 5 0.02
84 5 0.02
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.29
Consensus pattern (79 bp):
GGGTTAGAGTATCCTCGATTGTGAAAAATCGGTGTTTTAGAAATAAAACCAGGGTTAGAGTATTC
CCTCAAAAATAACA
Found at i:1490114 original size:210 final size:210
Alignment explanation
Indices: 1489768--1490163 Score: 476
Period size: 210 Copynumber: 1.9 Consensus size: 210
1489758 ATAAAAACAG
1489768 GGTTAGAGTATCCTCTCGAAAAAAACGAGGTTGGAGTATCCCTAATGGTGAAAAATCAATGTTTT
1 GGTTAGAGTATCCTCTCGAAAAAAACGAGGTTGGAGTATCCCTAATGGTGAAAAATCAATGTTTT
** * *** * * * * *
1489833 GGAAATAAAATTGGGGTTGGAGTATCCCTTCGGAAATAACGGGGTTGGAGTATCCCCGATTAAGG
66 AAAAAAAAAACCAGGGTTAGAGTATCCCTTCAGAAATAACAGGGTTAGAGTATCCCCGATTAAGA
* * * *
1489898 AAAATCGATGTTTTAGAAATAAAGCTGGGGTTAGAGTATCCTCGATTGTGAAAAATCGGTGTTTT
131 AAAATCGATGTTCTAGAAATAAAACCGGGGTTAGAGTATCCCCGATTGTGAAAAATCGGTGTTTT
1489963 AGAAATAAAAGCTGA
196 AGAAATAAAAGCTGA
* * * * *
1489978 GGTTAGAGTATTCTGTC-AAAAATAACGGGGTTGGAGTAT-CCTCGATGGTGAAAAATCAGTGTT
1 GGTTAGAGTATCCTCTCGAAAAA-AACGAGGTTGGAGTATCCCT-AATGGTGAAAAATCAATGTT
* *
1490041 TTAAAAAAAAAACCAGGGTTAGAGTATTCCC-TCAGAAATAACATGGTTAGAGT-TACTCCGATT
64 TTAAAAAAAAAACCAGGGTTAGAGTA-TCCCTTCAGAAATAACAGGGTTAGAGTAT-CCCCGATT
** * * * *
1490104 GTGAAAAATCGGTGTTCTGGAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAT
127 AAGAAAAATCGATGTTCTAGAAATAAAACCGGGGTTAGAGTATCCCCGATTGTGAAAAAT
1490164 ACAGGTTGGA
Statistics
Matches: 154, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
209 9 0.06
210 141 0.92
211 4 0.03
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.28
Consensus pattern (210 bp):
GGTTAGAGTATCCTCTCGAAAAAAACGAGGTTGGAGTATCCCTAATGGTGAAAAATCAATGTTTT
AAAAAAAAAACCAGGGTTAGAGTATCCCTTCAGAAATAACAGGGTTAGAGTATCCCCGATTAAGA
AAAATCGATGTTCTAGAAATAAAACCGGGGTTAGAGTATCCCCGATTGTGAAAAATCGGTGTTTT
AGAAATAAAAGCTGA
Found at i:1490172 original size:31 final size:31
Alignment explanation
Indices: 1490136--1490194 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1490126 ATAAAACCGG
1490136 GGTTGGAGTATCCCCGATTGTGGAAAATACA
1 GGTTGGAGTATCCCCGATTGTGGAAAATACA
*
1490167 GGTTGGAGTATCCCTGATTGTGGAAAAT
1 GGTTGGAGTATCCCCGATTGTGGAAAAT
1490195 TGTGTTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.29
Consensus pattern (31 bp):
GGTTGGAGTATCCCCGATTGTGGAAAATACA
Found at i:1492263 original size:13 final size:13
Alignment explanation
Indices: 1492245--1492269 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1492235 AGATTGCACA
1492245 GTATCGATACATT
1 GTATCGATACATT
1492258 GTATCGATACAT
1 GTATCGATACAT
1492270 GACCAAATGT
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:1492392 original size:32 final size:33
Alignment explanation
Indices: 1492351--1492414 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1492341 ATTAACTGTT
*
1492351 TGTATCGATACA-CCCAATATATATCGATACAA
1 TGTATCGATACATCCCAAAATATATCGATACAA
*
1492383 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACATCCCAAAATATATCGATACA
1492415 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (33 bp):
TGTATCGATACATCCCAAAATATATCGATACAA
Found at i:1507604 original size:8 final size:8
Alignment explanation
Indices: 1507587--1507617 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
1507577 ATTCTTTTTC
1507587 AAAC-AAA
1 AAACAAAA
1507594 AAACAAAA
1 AAACAAAA
1507602 AAACAAAA
1 AAACAAAA
1507610 AAACAAAA
1 AAACAAAA
1507618 TAAAGACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.17
8 19 0.83
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (8 bp):
AAACAAAA
Found at i:1508719 original size:55 final size:55
Alignment explanation
Indices: 1508630--1509243 Score: 781
Period size: 55 Copynumber: 10.9 Consensus size: 55
1508620 GACGCATTTT
* *
1508630 CCTTTCAAAGCCCATACAAGTTGGTGGCATCTTT-CAGTCCTCAAAAAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCAT-TTTCCAGTCCTCAAAGAGCAGGACG
* *
1508685 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACG
* * *
1508740 CCTTTCAAATCCCACACAAGTTGGTGCCATTTTCCAGTCCTCAAAGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
*
1508795 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* *
1508850 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCTTC-AA-AG-AGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* * *
1508902 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* * *
1508957 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* *
1509012 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
*
1509067 CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATG
1 C-----C-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
** * *
1509128 CCTTTTCTTTCAAAGCATACACAAGTTGGTGGAATTTTCCAGTCCTCAAAGAGTAGGACG
1 -C----CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* *
1509188 CCTTCTCCTTTTAAAGCCCACACAAGTTAGTGGCA-CTTCCTAGTCCTCAAAGAGCA
1 CCTT-T-C----AAAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCA
1509244 CGACACTCTC
Statistics
Matches: 501, Mismatches: 39, Indels: 32
0.88 0.07 0.06
Matches are distributed among these distances:
52 45 0.09
53 4 0.01
54 7 0.01
55 298 0.59
56 1 0.00
57 1 0.00
59 1 0.00
60 53 0.11
61 90 0.18
62 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
Found at i:1508800 original size:28 final size:28
Alignment explanation
Indices: 1508764--1508854 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 28
1508754 CACAAGTTGG
1508764 TGCCATTTTCCAGTCCTCAAAGAGCAGGA
1 TGCC-TTTTCCAGTCCTCAAAGAGCAGGA
** * * * **
1508793 TGCCTTTTAAAGCCCACACA-AGTTGG-
1 TGCCTTTTCCAGTCCTCAAAGAGCAGGA
*
1508819 TGGCATTTTCCAGTCCTCAAAGAGCAGGA
1 T-GCCTTTTCCAGTCCTCAAAGAGCAGGA
*
1508848 CGCCTTT
1 TGCCTTT
1508855 CAAAGCCCAC
Statistics
Matches: 42, Mismatches: 17, Indels: 7
0.64 0.26 0.11
Matches are distributed among these distances:
26 1 0.02
27 17 0.40
28 20 0.48
29 4 0.10
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (28 bp):
TGCCTTTTCCAGTCCTCAAAGAGCAGGA
Found at i:1509008 original size:217 final size:219
Alignment explanation
Indices: 1508630--1509243 Score: 822
Period size: 217 Copynumber: 2.7 Consensus size: 219
1508620 GACGCATTTT
* * *
1508630 CCTTTCAAAGCCCATACAAGTTGGTGGCATCTTTCAGTCCTCAAAAAGCAGGACGCCTTTCAAAG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTC-AAAAGCAGGACGCCTTTTAAAG
* * * *
1508695 CCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAATCCCACACAA
65 CCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGTAGGACACCTTTTAAAGCCCACACAA
* *
1508759 GTTGGTGCCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCA
129 GTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
1508824 TTTTCCAGTCCTCAAAGAGCAGGACG
194 CTTTCCAGTCCTCAAAGAGCAGGACG
*
1508850 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCTTC-AAAG-AGGACGCCTTTTAAAGC
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAAGCAGGACGCCTTTTAAAGC
1508913 CCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACACCTTTTAAAGCCCACACAAGT
66 CCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACACCTTTTAAAGCCCACACAAGT
*
1508978 TGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACT
131 TGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACT
*
1509043 TTCCAGTCCTCAAAGAGCAGGATG
196 TTCCAGTCCTCAAAGAGCAGGACG
* *
1509067 CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTT
1 C-----C-TTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAA-AGCAGGACGCC--
** * *
1509132 TTCTTTCAAAGCATACACAAGTTGGTGGAATTTTCCAGTCCTCAAAGAGTAGGACGCCTTCTCCT
57 -T-TTT-AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGA------CACCT
* *
1509197 TTTAAAGCCCACACAAGTTAGTGGCA-CTTCCTAGTCCTCAAAGAGCA
113 TTTAAAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCA
1509244 CGACACTCTC
Statistics
Matches: 349, Mismatches: 23, Indels: 27
0.87 0.06 0.07
Matches are distributed among these distances:
216 3 0.01
217 158 0.45
218 4 0.01
220 39 0.11
222 1 0.00
223 38 0.11
224 2 0.01
225 2 0.01
226 7 0.02
229 1 0.00
230 3 0.01
231 44 0.13
236 3 0.01
237 44 0.13
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (219 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAAGCAGGACGCCTTTTAAAGC
CCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACACCTTTTAAAGCCCACACAAGT
TGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACT
TTCCAGTCCTCAAAGAGCAGGACG
Found at i:1509455 original size:145 final size:148
Alignment explanation
Indices: 1509109--1509524 Score: 523
Period size: 145 Copynumber: 2.8 Consensus size: 148
1509099 GCATTTTCCA
** * * **
1509109 GTCCTCAAAGAGCAGGATGCCTTTTCTTTCAAAGCATACACAAGTTGGTGGAATTTTCCAGTCCT
1 GTCCTCAAAGAGCAGGATGCC---T-TTT-AAAGCCCACACAAGCTGGTGGCACCTT-CAGTCCT
* *
1509174 CAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTAGTGGCACTTCCTAGTCCTCAAA
60 CAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA----CT--TCCTCAAA
*
1509239 GAGCACGACACTCTCTCCTTTCGTATTTTT
119 GAGCACGACACTCTCTCCTTTCGCATTTTT
* * * * *
1509269 GTCCTCAAAGAGCAGGATACCTTTTAAAGCCCATACGAGCTGGTGGCACCTTCAGTCATCAAA-T
1 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGA
* * * * *
1509333 GCAGGACACCTTCTCCTTTTAAAGCCC-TACAAGTTGGTGGCACTTCCT-AAAGAGTAGGACGCT
66 GCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTCAAAGAGCACGACACT
*
1509396 CTCTCCTTTCGCCTTTTT
131 CTCTCCTTTCGCATTTTT
1509414 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGA
1 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGA
1509479 GCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTT
66 GCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTT
1509525 TTCAGTCCTC
Statistics
Matches: 227, Mismatches: 27, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
145 87 0.38
146 30 0.13
147 17 0.07
148 2 0.01
152 13 0.06
153 25 0.11
154 10 0.04
155 19 0.08
156 3 0.01
157 1 0.00
160 20 0.09
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (148 bp):
GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGA
GCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTCAAAGAGCACGACACT
CTCTCCTTTCGCATTTTT
Found at i:1509564 original size:61 final size:61
Alignment explanation
Indices: 1509435--1509659 Score: 307
Period size: 61 Copynumber: 3.7 Consensus size: 61
1509425 GCAGGATGCC
* * * *
1509435 TTTT-AAAGCCCACACAAGCTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGACGCCTTCTCC
1 TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGGGCAGGACGCCTT-TCT
*
1509495 TTTT-AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGGGCAGGATG-CTTTCT
1 TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGGGCAGGACGCCTTTCT
* * *
1509554 TTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGGGTAGGACGCCTTT-T
1 TTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGGGCAGGACGCCTTTCT
*
1509615 CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAA
1 -TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAA
1509660 AAGTAGGACA
Statistics
Matches: 148, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
59 6 0.04
60 30 0.20
61 104 0.70
62 8 0.05
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (61 bp):
TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGGGCAGGACGCCTTTCT
Found at i:1509630 original size:122 final size:121
Alignment explanation
Indices: 1509439--1509659 Score: 372
Period size: 122 Copynumber: 1.8 Consensus size: 121
1509429 GATGCCTTTT
1509439 AAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGC
1 AAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGC
1509504 CCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGGGCAGGATGCTTTCTTTTTGC
66 CCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGGGCAGGATGCTTTCTTTTTGC
* * * *
1509560 AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGGGTAGGACGCCTT-TTCTTTTCAAA
1 AAAGCCCACACAAGCTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTT-AAA
*
1509624 GCCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAA
64 GCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAA
1509660 AAGTAGGACA
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
121 32 0.34
122 61 0.66
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.25
Consensus pattern (121 bp):
AAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGC
CCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGGGCAGGATGCTTTCTTTTTGC
Found at i:1509774 original size:42 final size:42
Alignment explanation
Indices: 1509682--1509785 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
1509672 CTTCCTTCCC
* *
1509682 TTCTTTTCTCTTTTGTCCTCAAAGAGTAGGATGTACTTTATT
1 TTCTTTTTTCTTTTGTCCTCAAAGAGCAGGATGTACTTTATT
* *
1509724 TTCCTTTTTCTTTTATCCT-AAGAGAGCAGGATGTA-TTTCA-T
1 TTCTTTTTTCTTTTGTCCTCAA-AGAGCAGGATGTACTTT-ATT
*
1509765 TTCTTTTTTTCCTTTGTCCTC
1 TTC-TTTTTTCTTTTGTCCTC
1509786 GAAAAATGGG
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
41 9 0.18
42 42 0.82
ACGTcount: A:0.16, C:0.19, G:0.12, T:0.52
Consensus pattern (42 bp):
TTCTTTTTTCTTTTGTCCTCAAAGAGCAGGATGTACTTTATT
Found at i:1510736 original size:20 final size:19
Alignment explanation
Indices: 1510711--1510784 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 19
1510701 TTTACCCAGA
1510711 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
1510731 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
*
1510751 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
1510771 TGTATCGATACATT
1 TGTATCGATACATT
1510785 CAGGCATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:1512620 original size:51 final size:51
Alignment explanation
Indices: 1512559--1512803 Score: 287
Period size: 51 Copynumber: 4.8 Consensus size: 51
1512549 CCTGGTTTTG
* *
1512559 TTTCTAAAACACTAATTTTTCACAATTAGGGATACTCTAACTCCGATTTTAT
1 TTTC-AAAACACTAATTTTTCACAATTGGGGATACTCCAACTCCGATTTTAT
* * * * * * *
1512611 TTTCGAAACACCAATTTTCCACAACTGGGAATACTCC-ACCCCGGTTTTAT
1 TTTCAAAACACTAATTTTTCACAATTGGGGATACTCCAACTCCGATTTTAT
* * *
1512661 TTTCAAAACACTAATTTTTTATAATCGGGGATACTCCAACTCCGATTTTAT
1 TTTCAAAACACTAATTTTTCACAATTGGGGATACTCCAACTCCGATTTTAT
* * * * *
1512712 TTCCAAAACACCAA-TTTTCTATAATCGAGGATACTCCAACTCCGATTTTAT
1 TTTCAAAACACTAATTTTTC-ACAATTGGGGATACTCCAACTCCGATTTTAT
*
1512763 TTTCAAAAACACTAATTTTTCACAATCGGGGATACTCCAAC
1 TTTC-AAAACACTAATTTTTCACAATTGGGGATACTCCAAC
1512804 CCCGTTAATC
Statistics
Matches: 162, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
50 44 0.27
51 82 0.51
52 31 0.19
53 5 0.03
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (51 bp):
TTTCAAAACACTAATTTTTCACAATTGGGGATACTCCAACTCCGATTTTAT
Found at i:1512678 original size:101 final size:103
Alignment explanation
Indices: 1512540--1512803 Score: 349
Period size: 101 Copynumber: 2.6 Consensus size: 103
1512530 TCATAGGGGG
* * * ** *
1512540 TACTCCAACCCTGGTTTT-GTTTCTAAAACACTAATTTTTCACAATTAGGGATACTCTAACTCCG
1 TACTCCAACCCCGGTTTTATTTTCAAAAACACTAATTTTTCACAATCGGGGATACTCCAACTCCG
* *
1512604 ATTTTATTTTCGAAACACCAATTTTCCACAA-CTG-GGAA
66 ATTTTATTTCCAAAACACCAATTTTCCACAATC-GAGG-A
* *
1512642 TACTCC-ACCCCGGTTTTATTTTC-AAAACACTAATTTTTTATAATCGGGGATACTCCAACTCCG
1 TACTCCAACCCCGGTTTTATTTTCAAAAACACTAATTTTTCACAATCGGGGATACTCCAACTCCG
* *
1512705 ATTTTATTTCCAAAACACCAATTTTCTATAATCGAGGA
66 ATTTTATTTCCAAAACACCAATTTTCCACAATCGAGGA
* *
1512743 TACTCCAACTCCGATTTTATTTTCAAAAACACTAATTTTTCACAATCGGGGATACTCCAAC
1 TACTCCAACCCCGGTTTTATTTTCAAAAACACTAATTTTTCACAATCGGGGATACTCCAAC
1512804 CCCGTTAATC
Statistics
Matches: 142, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
101 80 0.56
102 28 0.20
103 34 0.24
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (103 bp):
TACTCCAACCCCGGTTTTATTTTCAAAAACACTAATTTTTCACAATCGGGGATACTCCAACTCCG
ATTTTATTTCCAAAACACCAATTTTCCACAATCGAGGA
Found at i:1512856 original size:28 final size:28
Alignment explanation
Indices: 1512790--1512860 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
1512780 TTTCACAATC
1512790 GGGGATACTCCAACCCCGTTAATCATCA
1 GGGGATACTCCAACCCCGTTAATCATCA
* * *
1512818 -GGGATACTCCAATCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCATCA
1512845 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
1512861 TGGCTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTAATCATCA
Found at i:1513166 original size:79 final size:78
Alignment explanation
Indices: 1512818--1513158 Score: 493
Period size: 79 Copynumber: 4.3 Consensus size: 78
1512808 TTAATCATCA
* *
1512818 GGGATACTCCAATCCCGTTATTTCTGAGGGGATACTCCAACCCTGGCTTTATTCCTAAAATATTA
1 GGGATACTCCAA-CCCGTTATTTCCGAGGGGATACTCCAACCCTGGCTTTATTCCTAAAATATTG
*
1512883 ATTTCTAATAATCG
65 ATTTCTCATAATCG
* *
1512897 GGGATACTCCAACCCCGTTATTTCCGAGAGGATACTCTAACCCTGGCTTTATTCCTAAAATATTG
1 GGGATACTCCAA-CCCGTTATTTCCGAGGGGATACTCCAACCCTGGCTTTATTCCTAAAATATTG
*
1512962 ATTTCTCATAATCA
65 ATTTCTCATAATCG
* *
1512976 GGGATACTCCAACTCCGTTATTTCCGAGGGGATACTCCAACCTTGGCTTTATTTCTAAAATATTG
1 GGGATACTCCAAC-CCGTTATTTCCGAGGGGATACTCCAACCCTGGCTTTATTCCTAAAATATTG
*
1513041 ATTTCTCACAATCG
65 ATTTCTCATAATCG
* ** * * *
1513055 GGAATACTTTAACCCTGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTG
1 GGGATACTCCAACCC-GTTATTTCCGAGGGGATACTCCAACCCTGGCTTTATTCCTAAAATATTG
*
1513120 ATTTTTCATAATCG
65 ATTTCTCATAATCG
1513134 GGGATACTCCAATCCCGTTATTTCC
1 GGGATACTCCAA-CCCGTTATTTCC
1513159 AAAGGGATCT
Statistics
Matches: 235, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
78 3 0.01
79 229 0.97
80 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (78 bp):
GGGATACTCCAACCCGTTATTTCCGAGGGGATACTCCAACCCTGGCTTTATTCCTAAAATATTGA
TTTCTCATAATCG
Found at i:1513194 original size:158 final size:157
Alignment explanation
Indices: 1512814--1513199 Score: 424
Period size: 158 Copynumber: 2.4 Consensus size: 157
1512804 CCCGTTAATC
** * * *
1512814 ATCAGGGATACTCCAA-TCCCGTTATTTCTGAGGGGATACTCCAACCCTGGCTTTATTC-CTAAA
1 ATCAGGGATACTCCAACT-CCGTTATTTCCAAAGGGATACTCCAACCTTGGC-TTA-TCACCAAA
* * * *
1512877 ATATTAATTTCTAATAATCGGGGATACTCCAACCCCGTTATTTCCGAGAGGATACTCTAACCCTG
63 ATATTAATTTCTAACAATCGGGAATACTCCAACCCCGTTATTTCCGAGAGGATACTCCAACCCCG
1512942 GCTTTATTCCTAAAATATTGATTTCTCATA
128 GCTTTATTCCTAAAATATTGATTTCTCATA
* * ** *
1512972 ATCAGGGATACTCCAACTCCGTTATTTCCGAGGGGATACTCCAACCTTGGCTTTATTTCTAAAAT
1 ATCAGGGATACTCCAACTCCGTTATTTCCAAAGGGATACTCCAACCTTGGC-TTATCACCAAAAT
* * ** * * *
1513037 ATTGATTTCTCACAATCGGGAATACTTTAACCCTGTTATTTCCGAGGGGATACTCCAACCCCGGT
65 ATTAATTTCTAACAATCGGGAATACTCCAACCCCGTTATTTCCGAGAGGATACTCCAACCCCGGC
* *
1513102 TTTATTTCTAAAATATTGATTTTTCATA
130 TTTATTCCTAAAATATTGATTTCTCATA
* *
1513130 ATCGGGGATACTCCAA-TCCCGTTATTTCCAAAGGGAT-CTTCCAGCCCCATT-G-TTATCACCA
1 ATCAGGGATACTCCAACT-CCGTTATTTCCAAAGGGATAC-TCCA--ACC-TTGGCTTATCACCA
1513191 AAATATTAA
61 AAATATTAA
1513200 ATTTTCGTCG
Statistics
Matches: 197, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
157 3 0.02
158 188 0.95
159 1 0.01
160 3 0.02
161 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.34
Consensus pattern (157 bp):
ATCAGGGATACTCCAACTCCGTTATTTCCAAAGGGATACTCCAACCTTGGCTTATCACCAAAATA
TTAATTTCTAACAATCGGGAATACTCCAACCCCGTTATTTCCGAGAGGATACTCCAACCCCGGCT
TTATTCCTAAAATATTGATTTCTCATA
Found at i:1514890 original size:31 final size:31
Alignment explanation
Indices: 1514848--1514939 Score: 103
Period size: 34 Copynumber: 2.9 Consensus size: 31
1514838 TTGGACTTAA
1514848 GTGCCACCAGCTTGTGTGGGCTTTGACTCAG
1 GTGCCACCAGCTTGTGTGGGCTTTGACTCAG
** * *
1514879 GTGCTGCCAGCTTGTGTAGGCTACTTAGACTTAG
1 GTGCCACCAGCTTGTGTGGGCT--TT-GACTCAG
* *
1514913 GTGCCACTAGCTCGTGTGGGCTTTGAC
1 GTGCCACCAGCTTGTGTGGGCTTTGAC
1514940 ATTCTAAGGC
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
31 22 0.45
32 2 0.04
33 2 0.04
34 23 0.47
ACGTcount: A:0.14, C:0.24, G:0.32, T:0.30
Consensus pattern (31 bp):
GTGCCACCAGCTTGTGTGGGCTTTGACTCAG
Found at i:1514915 original size:34 final size:33
Alignment explanation
Indices: 1514836--1514934 Score: 94
Period size: 31 Copynumber: 3.0 Consensus size: 33
1514826 TGTGGACTTG
* *
1514836 ACTTGGACTTAAGTGCCACCAGCTTGTGTGGGCT
1 ACTT-GACTTAGGTGCCACCAGCTTGTGTAGGCT
* **
1514870 --TTGACTCAGGTGCTGCCAGCTTGTGTAGGCT
1 ACTTGACTTAGGTGCCACCAGCTTGTGTAGGCT
* * *
1514901 ACTTAGACTTAGGTGCCACTAGCTCGTGTGGGCT
1 ACTT-GACTTAGGTGCCACCAGCTTGTGTAGGCT
1514935 TTGACATTCT
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
31 24 0.47
32 2 0.04
33 2 0.04
34 23 0.45
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.30
Consensus pattern (33 bp):
ACTTGACTTAGGTGCCACCAGCTTGTGTAGGCT
Found at i:1515116 original size:126 final size:126
Alignment explanation
Indices: 1514965--1515222 Score: 347
Period size: 126 Copynumber: 2.0 Consensus size: 126
1514955 CTCCAAAGGC
* ** * *
1514965 AGGTGCCAACTAATTTCGACTTGACTTGAACTTAGGTGCTACCAGCTTGTGTTGGCTTTGAATTA
1 AGGTGCCAACTAATTTAGACTTGACTCAAACTTAGGTGCCACCAGCTTGTGTGGGCTTTGAATTA
* * * * *
1515030 GGTGCCGCCAACTCGTGC-AGGCTTAGACTCGAGTGCTGCCAGCTTGTGCGAGCTTTGACTA
66 GGTGCCACCAAATCGTGCGA-GCTTAGACTCGAGTGCCGCCAGCTTGTACAAGCTTTGACTA
*
1515091 AGGTGCCAACTAATTTAGACTTGACTCAAAGTTAGGTGCCACCAGCTTGTGTGGGCTTTGAATTA
1 AGGTGCCAACTAATTTAGACTTGACTCAAACTTAGGTGCCACCAGCTTGTGTGGGCTTTGAATTA
** * * *
1515156 GGTGTTACCAAATTGTGCGAGCTTGGACTCGAGTGCCGCTAGCTTGTACAAGCTTTGACTA
66 GGTGCCACCAAATCGTGCGAGCTTAGACTCGAGTGCCGCCAGCTTGTACAAGCTTTGACTA
*
1515217 GGGTGC
1 AGGTGC
1515223 TACCAACTCA
Statistics
Matches: 114, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
126 113 0.99
127 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (126 bp):
AGGTGCCAACTAATTTAGACTTGACTCAAACTTAGGTGCCACCAGCTTGTGTGGGCTTTGAATTA
GGTGCCACCAAATCGTGCGAGCTTAGACTCGAGTGCCGCCAGCTTGTACAAGCTTTGACTA
Found at i:1515320 original size:180 final size:180
Alignment explanation
Indices: 1515091--1515601 Score: 668
Period size: 180 Copynumber: 2.8 Consensus size: 180
1515081 GCTTTGACTA
* * *
1515091 AGGTGCCAACTAATTTAGACTTGACTCAAAGTTAGGTGCCACCAGCTTGTGTGGGCTTTGAATTA
1 AGGTGCCAACTAATTTGGACTTGACTCAAACTTAGGTGCCACTAGCTTGTGTGGGCTTTGAATTA
** * * * *
1515156 GGTGTTACCAAATTGTGCGAGCTTGGACTCGAGTGCCGCTAGCTTGTACAAGCTTTGACTAGGGT
66 GGTGTCGCCAACTTGTGCGGGCTTAGACTCGAGTGCCGCTAGCTTGTGCAAGCTTTGACTAGGGT
* * *
1515221 GCTACCAACTCATGTGGGTTTTGACATTCTAAGGCTTGACCTCCTGAGAC
131 GCCACCAACTCATGTGGGCTTTGACATTCTAAGGCTTAACCTCCTGAGAC
* * *
1515271 AGGTGCCTACTAATTTGGACTTGACTCGAACTTAGGTGCCACTAGCTTGTGTAGGCTTT-AACTT
1 AGGTGCCAACTAATTTGGACTTGACTCAAACTTAGGTGCCACTAGCTTGTGTGGGCTTTGAA-TT
* * ** * * * * ** *
1515335 CGGTGCCGTTAACTTATGCGGGCTTAGACTCGGGTGCCACCAGCTTGTGCGGGCTTTGACTAAGG
65 AGGTGTCGCCAACTTGTGCGGGCTTAGACTCGAGTGCCGCTAGCTTGTGCAAGCTTTGACTAGGG
* **
1515400 TGCCACCAACTCGTGTGGGCTTTGACATTCTAAGGCTTAACCTCCTTTGAC
130 TGCCACCAACTCATGTGGGCTTTGACATTCTAAGGCTTAACCTCCTGAGAC
* *
1515451 AGGTGCCAACTAATTTGGACTTGACTCAAACTTAGGTGCCA-TCAACTTGTGTGGGCTTTGACTT
1 AGGTGCCAACTAATTTGGACTTGACTCAAACTTAGGTGCCACT-AGCTTGTGTGGGCTTTGAATT
* *
1515515 CA-GTGTCGCCAACTCGTGCGGGCTTAGACTCGAGTGCCGCTAGCTAGTGCAAGCTTTGACTAGG
65 -AGGTGTCGCCAACTTGTGCGGGCTTAGACTCGAGTGCCGCTAGCTTGTGCAAGCTTTGACTAGG
*
1515579 GTGCCACCAACTCATGTAGGCTT
129 GTGCCACCAACTCATGTGGGCTT
1515602 ATAGAAGAGG
Statistics
Matches: 278, Mismatches: 49, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
179 3 0.01
180 274 0.99
181 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (180 bp):
AGGTGCCAACTAATTTGGACTTGACTCAAACTTAGGTGCCACTAGCTTGTGTGGGCTTTGAATTA
GGTGTCGCCAACTTGTGCGGGCTTAGACTCGAGTGCCGCTAGCTTGTGCAAGCTTTGACTAGGGT
GCCACCAACTCATGTGGGCTTTGACATTCTAAGGCTTAACCTCCTGAGAC
Found at i:1515422 original size:31 final size:31
Alignment explanation
Indices: 1515351--1515425 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
1515341 CGTTAACTTA
* ** * *
1515351 TGCGGGCTTAGACTCGGGTGCCACCAGCTTG
1 TGCGGGCTTTGACTAAGGTGCCACCAACTCG
1515382 TGCGGGCTTTGACTAAGGTGCCACCAACTCG
1 TGCGGGCTTTGACTAAGGTGCCACCAACTCG
*
1515413 TGTGGGCTTTGAC
1 TGCGGGCTTTGAC
1515426 ATTCTAAGGC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.15, C:0.27, G:0.33, T:0.25
Consensus pattern (31 bp):
TGCGGGCTTTGACTAAGGTGCCACCAACTCG
Found at i:1526863 original size:13 final size:13
Alignment explanation
Indices: 1526845--1526875 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1526835 ACTTTTCACT
*
1526845 ATGTATCAATACA
1 ATGTATAAATACA
1526858 ATGTATAAATACA
1 ATGTATAAATACA
1526871 ATGTA
1 ATGTA
1526876 CTATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (13 bp):
ATGTATAAATACA
Found at i:1526978 original size:13 final size:13
Alignment explanation
Indices: 1526960--1526984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1526950 ACCAAGATCA
1526960 TGTATCGATACAG
1 TGTATCGATACAG
1526973 TGTATCGATACA
1 TGTATCGATACA
1526985 AAGCAATATG
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1527539 original size:55 final size:54
Alignment explanation
Indices: 1527463--1527574 Score: 161
Period size: 55 Copynumber: 2.1 Consensus size: 54
1527453 TCATAACCTG
*
1527463 TAATATGATATACACAACTCAAGAAACACATTAGAAAAGTTCATTTGATATTCAA
1 TAATATGATATACACAACTCAAGAAACACATTAGAAAAGTT-ATTTGATAATCAA
* * * * *
1527518 TAATCTGATATCCACGACTCAAGAAACATATTAGAAAAGTTTTTTGATAATCAA
1 TAATATGATATACACAACTCAAGAAACACATTAGAAAAGTTATTTGATAATCAA
1527572 TAA
1 TAA
1527575 AGTCTCGAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
54 14 0.27
55 37 0.73
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (54 bp):
TAATATGATATACACAACTCAAGAAACACATTAGAAAAGTTATTTGATAATCAA
Found at i:1532257 original size:33 final size:33
Alignment explanation
Indices: 1532220--1532289 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 33
1532210 GCCATTTGAA
1532220 ACAATGTATCGATAC-ATGGTA-CATTGTATCGAT
1 ACAATGTATCGATACAAT-GTACCA-TGTATCGAT
1532253 ACAATGTATCGATACAATGTACCATGTATCGAT
1 ACAATGTATCGATACAATGTACCATGTATCGAT
1532286 ACAA
1 ACAA
1532290 ATAGTGGTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
33 31 0.89
34 4 0.11
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (33 bp):
ACAATGTATCGATACAATGTACCATGTATCGAT
Found at i:1532260 original size:13 final size:13
Alignment explanation
Indices: 1532239--1532273 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1532229 CGATACATGG
*
1532239 TACATTGTATCGA
1 TACAATGTATCGA
1532252 TACAATGTATCGA
1 TACAATGTATCGA
1532265 TACAATGTA
1 TACAATGTA
1532274 CCATGTATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:1532363 original size:19 final size:19
Alignment explanation
Indices: 1532318--1532370 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
1532308 CTGCCAGTTT
* * *
1532318 CATGTATTGATACAATTAT
1 CATGTATCGATACAATGAA
1532337 CTATGTATCGATACAATGAA
1 C-ATGTATCGATACAATGAA
1532357 CATGTATCGATACA
1 CATGTATCGATACA
1532371 TTGTATCGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1532377 original size:13 final size:13
Alignment explanation
Indices: 1532359--1532383 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1532349 ACAATGAACA
1532359 TGTATCGATACAT
1 TGTATCGATACAT
1532372 TGTATCGATACA
1 TGTATCGATACA
1532384 AAGCATAATG
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:1532400 original size:33 final size:32
Alignment explanation
Indices: 1532340--1532404 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
1532330 CAATTATCTA
*
1532340 TGTATCGATACAATGAACATGTATCGATACAT
1 TGTATCGATACAAAGAACATGTATCGATACAT
1532372 TGTATCGATACAAAGCATA-ATGTATCGATACAT
1 TGTATCGATACAAAG-A-ACATGTATCGATACAT
1532405 CTGGGTGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.47
33 15 0.50
34 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATGTATCGATACAT
Found at i:1532978 original size:20 final size:22
Alignment explanation
Indices: 1532955--1532996 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
1532945 TAAGGCTCTC
1532955 AAAAAAAATTT-TCC-CTTTGA
1 AAAAAAAATTTCTCCTCTTTGA
1532975 AAAAAAAATTTCTCCTCTTTGA
1 AAAAAAAATTTCTCCTCTTTGA
1532997 TAATCGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 3 0.15
22 6 0.30
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
AAAAAAAATTTCTCCTCTTTGA
Found at i:1534748 original size:22 final size:21
Alignment explanation
Indices: 1534713--1534762 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1534703 TTTGTTGTTG
*
1534713 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
1534733 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
1534754 AATTTGAAG
1 ATTTTGAAG
1534763 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:1534759 original size:21 final size:22
Alignment explanation
Indices: 1534720--1534762 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1534710 TTGATTTTGA
* *
1534720 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1534742 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1534763 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:1534891 original size:13 final size:13
Alignment explanation
Indices: 1534873--1534909 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1534863 GTAACCCTTG
1534873 TATCGATATAATA
1 TATCGATATAATA
* *
1534886 TATCGATACAATG
1 TATCGATATAATA
1534899 TATCGATATAA
1 TATCGATATAA
1534910 AGAATATTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (13 bp):
TATCGATATAATA
Found at i:1543587 original size:13 final size:12
Alignment explanation
Indices: 1543568--1543628 Score: 58
Period size: 13 Copynumber: 5.2 Consensus size: 12
1543558 TACATTTCTT
1543568 CATGTATCGATA
1 CATGTATCGATA
1543580 CAATGTATCGATA
1 C-ATGTATCGATA
*
1543593 CAT-T-TC--TT
1 CATGTATCGATA
1543601 CATGTATCGATA
1 CATGTATCGATA
*
1543613 CAATGTATCGACA
1 C-ATGTATCGATA
1543626 CAT
1 CAT
1543629 TGTACCATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
8 4 0.10
9 1 0.03
10 4 0.10
11 1 0.03
12 7 0.17
13 23 0.57
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (12 bp):
CATGTATCGATA
Found at i:1543587 original size:33 final size:33
Alignment explanation
Indices: 1543549--1543652 Score: 149
Period size: 33 Copynumber: 3.2 Consensus size: 33
1543539 GTTACAAGCT
*
1543549 ATGTATTGATACATTTCTTCATGTATCGATACA
1 ATGTATCGATACATTTCTTCATGTATCGATACA
1543582 ATGTATCGATACATTTCTTCATGTATCGATACA
1 ATGTATCGATACATTTCTTCATGTATCGATACA
*
1543615 ATGTATCGACACATTGTAC--CATGTATCGATACA
1 ATGTATCGATACATT-T-CTTCATGTATCGATACA
*
1543648 TTGTA
1 ATGTA
1543653 CCATGTATCG
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
33 64 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (33 bp):
ATGTATCGATACATTTCTTCATGTATCGATACA
Found at i:1543607 original size:20 final size:20
Alignment explanation
Indices: 1543549--1543614 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1543539 GTTACAAGCT
*
1543549 ATGTATTGATACATTTCTTC
1 ATGTATCGATACATTTCTTC
1543569 ATGTATCGATACA-------
1 ATGTATCGATACATTTCTTC
1543582 ATGTATCGATACATTTCTTC
1 ATGTATCGATACATTTCTTC
1543602 ATGTATCGATACA
1 ATGTATCGATACA
1543615 ATGTATCGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
13 13 0.34
20 25 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTCTTC
Found at i:1543664 original size:20 final size:20
Alignment explanation
Indices: 1543615--1543667 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1543605 TATCGATACA
*
1543615 ATGTATCGACACATTGTACC
1 ATGTATCGATACATTGTACC
1543635 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
1543655 ATGTATCGATACA
1 ATGTATCGATACA
1543668 AATAGTGATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACATTGTACC
Found at i:1543736 original size:13 final size:13
Alignment explanation
Indices: 1543718--1543742 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1543708 ACAATTGTCC
1543718 ATGTATCGATACA
1 ATGTATCGATACA
1543731 ATGTATCGATAC
1 ATGTATCGATAC
1543743 TATTAGGATT
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):
ATGTATCGATACA
Found at i:1544072 original size:13 final size:13
Alignment explanation
Indices: 1544054--1544078 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1544044 AGATTGCACA
1544054 GTATCGATACATT
1 GTATCGATACATT
1544067 GTATCGATACAT
1 GTATCGATACAT
1544079 GACCAAATGT
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:1547542 original size:80 final size:80
Alignment explanation
Indices: 1547409--1547570 Score: 324
Period size: 80 Copynumber: 2.0 Consensus size: 80
1547399 AGGTAAGCAT
1547409 AAAAGAAATTCTTTTAAACCTGTAAACATTGTCACGACTTCTAAAGTTCTGCAACTAGTTCACAT
1 AAAAGAAATTCTTTTAAACCTGTAAACATTGTCACGACTTCTAAAGTTCTGCAACTAGTTCACAT
1547474 GGATCTCTTTGGTCC
66 GGATCTCTTTGGTCC
1547489 AAAAGAAATTCTTTTAAACCTGTAAACATTGTCACGACTTCTAAAGTTCTGCAACTAGTTCACAT
1 AAAAGAAATTCTTTTAAACCTGTAAACATTGTCACGACTTCTAAAGTTCTGCAACTAGTTCACAT
1547554 GGATCTCTTTGGTCC
66 GGATCTCTTTGGTCC
1547569 AA
1 AA
1547571 CTAGAACACA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (80 bp):
AAAAGAAATTCTTTTAAACCTGTAAACATTGTCACGACTTCTAAAGTTCTGCAACTAGTTCACAT
GGATCTCTTTGGTCC
Found at i:1552554 original size:21 final size:21
Alignment explanation
Indices: 1552521--1552561 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1552511 ATGCAAGTTT
*
1552521 TTATTCTTCTTAGCTAATTTA
1 TTATTCTTCTTAGCCAATTTA
1552542 TTATT-TTCATTAGCCAATTT
1 TTATTCTTC-TTAGCCAATTT
1552562 TTTAATATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (21 bp):
TTATTCTTCTTAGCCAATTTA
Found at i:1554785 original size:21 final size:26
Alignment explanation
Indices: 1554757--1554818 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 26
1554747 CCGTTACAAG
1554757 CAATGTATCGATACAA-GT-TC-AT-
1 CAATGTATCGATACAATGTATCGATA
*
1554779 C-ATGTATTGATACAATGTATCGATA
1 CAATGTATCGATACAATGTATCGATA
1554804 CAATGTATCGATACA
1 CAATGTATCGATACA
1554819 TTGTCCCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 13 0.39
22 3 0.09
23 2 0.06
24 2 0.06
25 1 0.03
26 12 0.36
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (26 bp):
CAATGTATCGATACAATGTATCGATA
Found at i:1554798 original size:13 final size:13
Alignment explanation
Indices: 1554757--1554818 Score: 80
Period size: 13 Copynumber: 5.2 Consensus size: 13
1554747 CCGTTACAAG
1554757 CAATGTATCGATA
1 CAATGTATCGATA
1554770 CAA-GT-TC-AT-
1 CAATGTATCGATA
*
1554779 C-ATGTATTGATA
1 CAATGTATCGATA
1554791 CAATGTATCGATA
1 CAATGTATCGATA
1554804 CAATGTATCGATA
1 CAATGTATCGATA
1554817 CA
1 CA
1554819 TTGTCCCATG
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
8 1 0.02
9 3 0.07
10 3 0.07
11 4 0.10
12 3 0.07
13 28 0.67
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1555238 original size:13 final size:13
Alignment explanation
Indices: 1555220--1555245 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1555210 TACAGCAAGT
1555220 ATGTATCGATACA
1 ATGTATCGATACA
1555233 ATGTATCGATACA
1 ATGTATCGATACA
1555246 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:1557496 original size:21 final size:21
Alignment explanation
Indices: 1557463--1557507 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1557453 TTGCAAGTTG
*
1557463 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1557485 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1557505 AAA
1 AAA
1557508 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:1559331 original size:15 final size:15
Alignment explanation
Indices: 1559311--1559341 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1559301 TAAAAATGTC
*
1559311 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1559326 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1559341 C
1 C
1559342 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1561439 original size:13 final size:13
Alignment explanation
Indices: 1561421--1561485 Score: 112
Period size: 13 Copynumber: 5.0 Consensus size: 13
1561411 ACATTTTTTT
1561421 TTGTATCGATACA
1 TTGTATCGATACA
1561434 TTGTATCGATACA
1 TTGTATCGATACA
*
1561447 CTGTATCGATACA
1 TTGTATCGATACA
1561460 TTGTATCGATACA
1 TTGTATCGATACA
*
1561473 CTGTATCGATACA
1 TTGTATCGATACA
1561486 GGGTGATTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1561458 original size:26 final size:26
Alignment explanation
Indices: 1561422--1561485 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
1561412 CATTTTTTTT
1561422 TGTATCGATACATTGTATCGATACAC
1 TGTATCGATACATTGTATCGATACAC
1561448 TGTATCGATACATTGTATCGATACAC
1 TGTATCGATACATTGTATCGATACAC
1561474 TGTATCGATACA
1 TGTATCGATACA
1561486 GGGTGATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (26 bp):
TGTATCGATACATTGTATCGATACAC
Found at i:1561630 original size:21 final size:21
Alignment explanation
Indices: 1561606--1561652 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1561596 AAATCTTTTG
1561606 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
1561627 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
1561647 CAAAAT
1 CAAAAT
1561653 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:1561649 original size:20 final size:19
Alignment explanation
Indices: 1561608--1561650 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1561598 ATCTTTTGCA
1561608 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
1561628 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1561648 AAA
1 AAA
1561651 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:1564052 original size:13 final size:13
Alignment explanation
Indices: 1564034--1564059 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1564024 TACAGCAAGT
1564034 ATGTATCGATACA
1 ATGTATCGATACA
1564047 ATGTATCGATACA
1 ATGTATCGATACA
1564060 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:1564890 original size:19 final size:19
Alignment explanation
Indices: 1564836--1564890 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1564826 CTGCCAGTTT
*
1564836 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAC
*
1564856 CATGTAT-GATACAATGAG
1 CATGTATCGATACAATGAC
1564874 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1564891 TATCGATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 9 0.28
19 16 0.50
20 7 0.22
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:1564893 original size:13 final size:13
Alignment explanation
Indices: 1564875--1564901 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1564865 TACAATGAGC
1564875 ATGTATCGATACA
1 ATGTATCGATACA
1564888 ATGTATCGATACA
1 ATGTATCGATACA
1564901 A
1 A
1564902 AGCTGAATGT
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:1566668 original size:80 final size:80
Alignment explanation
Indices: 1566584--1567123 Score: 380
Period size: 80 Copynumber: 6.8 Consensus size: 80
1566574 CAAAAAAAGG
* * * *
1566584 TACTCCAACCTTGTTTTTACTTCCAAAACATCAAAAT-TTTCATTTCTGGGGATACTCTAACCCT
1 TACTCCAACCTTGTTTTTACTTCTAAAACA-CTAAATATTTCATCTCTGGGGATACTCCAACCCT
* ** **
1566648 ATCATCTTTGAAAAGA
65 ACCATCTCCGAAGGGA
* *** *
1566664 TACTCCACCCCTT-TTTTTACTTCTAAAATGTTAAAT-TTT-AT-T-T-GCGATACTCCAACACC
1 TACTCCA-ACCTTGTTTTTACTTCTAAAACACTAAATATTTCATCTCTGGGGATACTCCAAC-CC
**
1566723 -ATTATCTCCGAAGGGA
64 TACCATCTCCGAAGGGA
* ** * * * ** * *
1566739 TGCTCTTACCCTGTTTTTACTTCCAAAACACCAAATATTTCATCTCTAAGGAAACTCCAACCCTG
1 TACTCCAACCTTGTTTTTACTTCTAAAACACTAAATATTTCATCTCTGGGGATACTCCAACCCTA
1566804 CCATCTCCGAAGGGA
66 CCATCTCCGAAGGGA
* * *
1566819 TAATCCAACCTTGTTTTTACTTCTAAAACACTTAATATTTCATCTCTGGGGATACTCCAACCCCA
1 TACTCCAACCTTGTTTTTACTTCTAAAACACTAAATATTTCATCTCTGGGGATACTCCAACCCTA
* *
1566884 CCATCTCTGATGGGA
66 CCATCTCCGAAGGGA
* * * * *** * * * *
1566899 TGCTCCAACCTCGTTTTCACTTCTAAAACGTCGATTTTTTTTTTATCTTTAGGGATACTCCAACC
1 TACTCCAACCTTGTTTTTACTTCTAAAAC-AC--TAAATATTTCATCTCTGGGGATACTCCAACC
* *
1566964 CTACTATCTCTGAAGGGA
63 CTACCATCTCCGAAGGGA
** *** * * * *
1566982 TACTTTAACCCCATTTTTACTTCCAAAACACCAAATATTTCATCTCTAGGGATACTCCAACCCCA
1 TACTCCAACCTTGTTTTTACTTCTAAAACACTAAATATTTCATCTCTGGGGATACTCCAACCCTA
* *
1567047 CCATTTCCGAGGGGA
66 CCATCTCCGAAGGGA
* *** * * * *
1567062 TACTTCAACC-CCATTTTCCTTCTAAAAC-GTCAAATTTTTCATCTCTAGGGATACTCCAACCC
1 TACTCCAACCTTGTTTTTACTTCTAAAACACT-AAATATTTCATCTCTGGGGATACTCCAACCC
1567124 CATTATCTCT
Statistics
Matches: 361, Mismatches: 86, Indels: 27
0.76 0.18 0.06
Matches are distributed among these distances:
74 3 0.01
75 44 0.12
76 6 0.02
77 3 0.01
78 3 0.01
79 54 0.15
80 180 0.50
81 5 0.01
82 1 0.00
83 62 0.17
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (80 bp):
TACTCCAACCTTGTTTTTACTTCTAAAACACTAAATATTTCATCTCTGGGGATACTCCAACCCTA
CCATCTCCGAAGGGA
Found at i:1566983 original size:163 final size:159
Alignment explanation
Indices: 1566770--1567142 Score: 431
Period size: 163 Copynumber: 2.3 Consensus size: 159
1566760 TCCAAAACAC
* * * * * * ***
1566770 CAAATATTTCATCTCTAAGGAAACTCCAACCCTGCCATCTCCGAAGGGATAATCCAACCTTGTTT
1 CAAATTTTTCATCTCTAGGGATACTCCAACCCTACTATCTCTGAAGGGATAATCCAACCCCATTT
* ** * * *
1566835 TTACTTCTAAAACACTTAATATTTCATCTCTGGGGATACTCCAACCCCACCATCTCTGATGGGAT
66 TTACTTCCAAAACACCAAATATTTCATCTCTAGGGATACTCCAACCCCACCATCTCCGAGGGGAT
* * *
1566900 GCTCCAACCTCGTTTTCACTTCTAAAACGT
131 ACTCCAACCCCATTTTC-CTTCTAAAACGT
** * * * **
1566930 CGATTTTTTTTTTATCTTTAGGGATACTCCAACCCTACTATCTCTGAAGGGATACTTTAACCCCA
1 C-A--AATTTTTCATCTCTAGGGATACTCCAACCCTACTATCTCTGAAGGGATAATCCAACCCCA
*
1566995 TTTTTACTTCCAAAACACCAAATATTTCATCTCTAGGGATACTCCAACCCCACCATTTCCGAGGG
63 TTTTTACTTCCAAAACACCAAATATTTCATCTCTAGGGATACTCCAACCCCACCATCTCCGAGGG
*
1567060 GATACTTCAACCCCATTTTCCTTCTAAAACGT
128 GATACTCCAACCCCATTTTCCTTCTAAAACGT
* * * *
1567092 CAAATTTTTCATCTCTAGGGATACTCCAACCCCATTATCTCTAAATGGATA
1 CAAATTTTTCATCTCTAGGGATACTCCAACCCTACTATCTCTGAAGGGATA
1567143 TTTTAACCCT
Statistics
Matches: 175, Mismatches: 35, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
159 41 0.23
160 1 0.01
161 2 0.01
162 13 0.07
163 118 0.67
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.32
Consensus pattern (159 bp):
CAAATTTTTCATCTCTAGGGATACTCCAACCCTACTATCTCTGAAGGGATAATCCAACCCCATTT
TTACTTCCAAAACACCAAATATTTCATCTCTAGGGATACTCCAACCCCACCATCTCCGAGGGGAT
ACTCCAACCCCATTTTCCTTCTAAAACGT
Found at i:1570825 original size:20 final size:19
Alignment explanation
Indices: 1570796--1570834 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1570786 AGGTCAAAAC
1570796 CCTTAAATGTATCGATACA
1 CCTTAAATGTATCGATACA
1570815 CCTTCAAATGTATCGATACA
1 CCTT-AAATGTATCGATACA
1570835 TAATGCACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (19 bp):
CCTTAAATGTATCGATACA
Found at i:1570881 original size:20 final size:21
Alignment explanation
Indices: 1570856--1570908 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1570846 GTCGATACAT
*
1570856 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGCA-AAGAA
*
1570876 TGTATCGATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
1570897 TGTATCGATACA
1 TGTATCGATACA
1570909 GGTGATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:1570976 original size:13 final size:13
Alignment explanation
Indices: 1570958--1570983 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1570948 ACACATAATA
1570958 TGTATCGATACAT
1 TGTATCGATACAT
1570971 TGTATCGATACAT
1 TGTATCGATACAT
1570984 CCCAAAATGT
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:1577039 original size:19 final size:19
Alignment explanation
Indices: 1577015--1577054 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1577005 AAAGTTCCAG
*
1577015 AATGTATCGATACATTTGA
1 AATGTATCGATACATCTGA
1577034 AATGTATCGATACATCTGA
1 AATGTATCGATACATCTGA
1577053 AA
1 AA
1577055 AACTCAGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATCTGA
Found at i:1577101 original size:13 final size:13
Alignment explanation
Indices: 1577083--1577107 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1577073 CAGTATTCTC
1577083 TGTATCGATACAG
1 TGTATCGATACAG
1577096 TGTATCGATACA
1 TGTATCGATACA
1577108 AAGGGTTTAT
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1577574 original size:20 final size:22
Alignment explanation
Indices: 1577549--1577593 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
1577539 GCAACACTCA
*
1577549 CCAGGTCGCGATC-GGCA-CCC
1 CCAGGTCGCAATCGGGCAGCCC
*
1577569 CCAGGTTGCAATCGGGCAGCCC
1 CCAGGTCGCAATCGGGCAGCCC
1577591 CCA
1 CCA
1577594 CACTCACAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 4 0.19
22 6 0.29
ACGTcount: A:0.18, C:0.42, G:0.29, T:0.11
Consensus pattern (22 bp):
CCAGGTCGCAATCGGGCAGCCC
Found at i:1578986 original size:22 final size:22
Alignment explanation
Indices: 1578961--1579005 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1578951 AGTTATTGTT
1578961 AAATTGCCTT-ATTAAGGGGGAG
1 AAATT-CCTTGATTAAGGGGGAG
**
1578983 AAATTTTTTGATTAAGGGGGAG
1 AAATTCCTTGATTAAGGGGGAG
1579005 A
1 A
1579006 GAAAAGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.31
Consensus pattern (22 bp):
AAATTCCTTGATTAAGGGGGAG
Found at i:1579532 original size:20 final size:19
Alignment explanation
Indices: 1579503--1579541 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1579493 AGGTCAAAAC
1579503 CCTTAAATGTATCGATACA
1 CCTTAAATGTATCGATACA
1579522 CCTTCAAATGTATCGATACA
1 CCTT-AAATGTATCGATACA
1579542 AAATGCACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (19 bp):
CCTTAAATGTATCGATACA
Found at i:1579570 original size:13 final size:13
Alignment explanation
Indices: 1579552--1579576 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1579542 AAATGCACTA
1579552 GTATCGATACATT
1 GTATCGATACATT
1579565 GTATCGATACAT
1 GTATCGATACAT
1579577 GACCAAATGT
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:1579589 original size:20 final size:21
Alignment explanation
Indices: 1579564--1579616 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1579554 ATCGATACAT
**
1579564 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
1579584 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
1579605 TGTATCGATACA
1 TGTATCGATACA
1579617 GGTGATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:1579698 original size:32 final size:33
Alignment explanation
Indices: 1579657--1579724 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1579647 CCTTAACTGT
* *
1579657 TTGTATCGATACA-CACAATATGTATCGATATA
1 TTGTATCGATACATCACAAAATGTATCGATACA
*
1579689 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
1579722 TTG
1 TTG
1579725 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATCACAAAATGTATCGATACA
Found at i:1580933 original size:154 final size:154
Alignment explanation
Indices: 1580636--1580939 Score: 332
Period size: 154 Copynumber: 2.0 Consensus size: 154
1580626 ACATCTGGGT
* * *
1580636 ATACCTTTGACATAAAAGTATCTCGTTAACCCTAGAGGACTAAAAAATGATTATAAAAAGGTGAA
1 ATACCTTCGACATAAAAGTATCTAGTTAACCCTAAAGGACTAAAAAATGATTATAAAAAGGTGAA
* * * * * *
1580701 CCTATCATAAATGCATAACTTTGGCATAAAAGCATCCCGATGACTATATCAAACTCGATTTTTAA
66 CCTATCATAAATCCACAACTTTAGCATAAAAGCAT-CCGATGACTACATCAAACTCGAATTCTAA
**
1580766 AAAATTATTAAAATACCTTTAGGGC
130 AAAATTACAAAAATACCTTTAGGGC
* **
1580791 ATACCTTCGACAT-AAAGTATCCTAG-TAACCTTAAAGGACTCGAAAATGATCT-T-AAAAGGAT
1 ATACCTTCGACATAAAAGTAT-CTAGTTAACCCTAAAGGACTAAAAAATGAT-TATAAAAAGG-T
* * **
1580852 GAACCTATCCTAAATCCACACCTTTAGCATAAAAGCAT-CGTAGTGACTACATCGGACTC-AATT
63 GAACCTATCATAAATCCACAACTTTAGCATAAAAGCATCCG-A-TGACTACATCAAACTCGAATT
*
1580915 CTAAAAAATTACCAAAAATGCCTTT
126 CTAAAAAATTA-CAAAAATACCTTT
1580940 GGGGACTACT
Statistics
Matches: 124, Mismatches: 19, Indels: 13
0.79 0.12 0.08
Matches are distributed among these distances:
152 2 0.02
153 20 0.16
154 86 0.69
155 16 0.13
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (154 bp):
ATACCTTCGACATAAAAGTATCTAGTTAACCCTAAAGGACTAAAAAATGATTATAAAAAGGTGAA
CCTATCATAAATCCACAACTTTAGCATAAAAGCATCCGATGACTACATCAAACTCGAATTCTAAA
AAATTACAAAAATACCTTTAGGGC
Found at i:1582401 original size:13 final size:13
Alignment explanation
Indices: 1582383--1582408 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1582373 CAATTTTTTG
1582383 TGTATCGATACAT
1 TGTATCGATACAT
1582396 TGTATCGATACAT
1 TGTATCGATACAT
1582409 ACTTTGGTGT
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:1582407 original size:33 final size:33
Alignment explanation
Indices: 1582363--1582427 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1582353 TACAAGCCAA
* *
1582363 TGTATCAATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCAATACATA-CTTTGGTGTATCGATACAT
*
1582396 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCAATACATACTTTGGTGTATCGATACA
1582428 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCAATACATACTTTGGTGTATCGATACAT
Found at i:1584981 original size:13 final size:13
Alignment explanation
Indices: 1584963--1584987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1584953 ATAATTCCCC
1584963 TGTATCGATACAT
1 TGTATCGATACAT
1584976 TGTATCGATACA
1 TGTATCGATACA
1584988 AAGAAAAATG
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:1591196 original size:19 final size:19
Alignment explanation
Indices: 1591139--1591197 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
1591129 TACAAGCCAA
* *
1591139 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA-CTTTGG
1591159 TGTATCGATACATACTTTGG
1 TGTATCGATACA-ACTTTGG
* *
1591179 TGTCTCGATACAAGTTTGG
1 TGTATCGATACAACTTTGG
1591198 CTACTGCCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 6 0.18
20 27 0.79
21 1 0.03
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (19 bp):
TGTATCGATACAACTTTGG
Found at i:1591701 original size:21 final size:19
Alignment explanation
Indices: 1591677--1591719 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1591667 TATTATAACG
1591677 AAAATCAACACAAATACAACA
1 AAAATCAA-ACAAATA-AACA
*
1591698 AAAATCAAATAAATAAACA
1 AAAATCAAACAAATAAACA
1591717 AAA
1 AAA
1591720 TTCATAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 6 0.29
21 8 0.38
ACGTcount: A:0.72, C:0.16, G:0.00, T:0.12
Consensus pattern (19 bp):
AAAATCAAACAAATAAACA
Found at i:1592854 original size:7 final size:7
Alignment explanation
Indices: 1592842--1592905 Score: 51
Period size: 7 Copynumber: 9.4 Consensus size: 7
1592832 TTTCCTATCT
1592842 TTTTTTA
1 TTTTTTA
1592849 TTTTTTA
1 TTTTTTA
1592856 -TTTTTA
1 TTTTTTA
* *
1592862 TTTATTC
1 TTTTTTA
*
1592869 TTTTAT-
1 TTTTTTA
1592875 TTTTTTA
1 TTTTTTA
*
1592882 ATTTTTA
1 TTTTTTA
*
1592889 CTTTTTA
1 TTTTTTA
* *
1592896 ATTTTGA
1 TTTTTTA
1592903 TTT
1 TTT
1592906 GATTTAAATT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
6 11 0.24
7 34 0.76
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (7 bp):
TTTTTTA
Found at i:1592854 original size:8 final size:8
Alignment explanation
Indices: 1592841--1592900 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
1592831 TTTTCCTATC
1592841 TTTTTTTA
1 TTTTTTTA
1592849 -TTTTTTA
1 TTTTTTTA
1592856 TTTTTATTTA
1 -TTTT-TTTA
*
1592866 TTCTTTTA
1 TTTTTTTA
1592874 TTTTTTTA
1 TTTTTTTA
*
1592882 -ATTTTTA
1 TTTTTTTA
* *
1592889 CTTTTTAA
1 TTTTTTTA
1592897 TTTT
1 TTTT
1592901 GATTTGATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
7 13 0.31
8 19 0.45
9 6 0.14
10 4 0.10
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1592859 original size:13 final size:13
Alignment explanation
Indices: 1592843--1592905 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
1592833 TTCCTATCTT
1592843 TTTTTATTTTTTA
1 TTTTTATTTTTTA
*
1592856 TTTTTATTTATT-
1 TTTTTATTTTTTA
*
1592868 CTTTTATTTTTTTAA
1 TTTTTA-TTTTTT-A
*
1592883 TTTTTACTTTTTAA
1 TTTTTA-TTTTTTA
*
1592897 TTTTGATTT
1 TTTTTATTT
1592906 GATTTAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
12 5 0.12
13 19 0.47
14 6 0.15
15 10 0.25
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:1599079 original size:6 final size:6
Alignment explanation
Indices: 1599068--1599101 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
1599058 ATTTCTAGCA
1599068 TTTCTT TTTCTT TTTCTT TTTCTT TTTCCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT-CTT TTT
1599102 TTAATTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:1599134 original size:15 final size:14
Alignment explanation
Indices: 1599107--1599151 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 14
1599097 TTTTTTTAAT
*
1599107 TTTGATCTA-TTTA
1 TTTGATTTATTTTA
1599120 TTTGATTTGATTTTA
1 TTTGATTT-ATTTTA
*
1599135 TTTGATTTTTTTTA
1 TTTGATTTATTTTA
1599149 TTT
1 TTT
1599152 TTGTAATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 7 0.25
14 9 0.32
15 12 0.43
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.71
Consensus pattern (14 bp):
TTTGATTTATTTTA
Found at i:1599930 original size:13 final size:13
Alignment explanation
Indices: 1599889--1599937 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
1599879 TCGTTACAAG
1599889 CAATGTATCGATA
1 CAATGTATCGATA
1599902 CAAT-T-TC-AT-
1 CAATGTATCGATA
1599911 C-ATGTATCGATA
1 CAATGTATCGATA
1599923 CAATGTATCGATA
1 CAATGTATCGATA
1599936 CA
1 CA
1599938 TTGTCCCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 4 0.13
11 4 0.13
12 2 0.06
13 17 0.55
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1599953 original size:33 final size:34
Alignment explanation
Indices: 1599889--1599958 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
1599879 TCGTTACAAG
*
1599889 CAATGTATCGATACAATTTCATCATGTATCGATA
1 CAATGTATCGATACAATTTCACCATGTATCGATA
1599923 CAATGTATCGATAC-ATTGTC-CCATGTATCGATA
1 CAATGTATCGATACAATT-TCACCATGTATCGATA
1599956 CAA
1 CAA
1599959 ATAGTGATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 18 0.53
34 16 0.47
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (34 bp):
CAATGTATCGATACAATTTCACCATGTATCGATA
Found at i:1600031 original size:19 final size:20
Alignment explanation
Indices: 1599987--1600040 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
1599977 CTGCTAGTTT
* *
1599987 CATGCATCGATACAATTGTC
1 CATGTATCGATACAATTGAC
*
1600007 CATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGAC
1600026 CATGTATCGATACAA
1 CATGTATCGATACAA
1600041 AGCAGTATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (20 bp):
CATGTATCGATACAATTGAC
Found at i:1600052 original size:20 final size:19
Alignment explanation
Indices: 1600007--1600053 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
1599997 TACAATTGTC
*
1600007 CATGTATCGATACAATGAG
1 CATGTATCGATACAAAGAG
1600026 CATGTATCGATACAAAGCAG
1 CATGTATCGATACAAAG-AG
*
1600046 TATGTATC
1 CATGTATC
1600054 AAAACATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (19 bp):
CATGTATCGATACAAAGAG
Found at i:1600611 original size:22 final size:22
Alignment explanation
Indices: 1600581--1600655 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
1600571 CAAGTTTTCG
1600581 TTTTACTCCCCCTTAATTAAAGA
1 TTTT-CTCCCCCTTAATTAAAGA
*
1600604 TTTTCT-CCTCTT--TTAAA-A
1 TTTTCTCCCCCTTAATTAAAGA
* *
1600622 -ATTCTCCCCCTTAATCAAAGA
1 TTTTCTCCCCCTTAATTAAAGA
*
1600643 ATTTCTCCCCCTT
1 TTTTCTCCCCCTT
1600656 TGTCAAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
17 4 0.10
18 6 0.14
19 5 0.12
20 4 0.10
21 6 0.14
22 13 0.31
23 4 0.10
ACGTcount: A:0.25, C:0.31, G:0.03, T:0.41
Consensus pattern (22 bp):
TTTTCTCCCCCTTAATTAAAGA
Found at i:1607378 original size:13 final size:13
Alignment explanation
Indices: 1607360--1607388 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1607350 ACATTTGGTC
1607360 ATGTATCGATACA
1 ATGTATCGATACA
1607373 ATGTATCGATACA
1 ATGTATCGATACA
1607386 ATG
1 ATG
1607389 CAATCTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1609291 original size:21 final size:21
Alignment explanation
Indices: 1609260--1609311 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
1609250 GCTACTAGTG
* *
1609260 TGGGGGTTGCCCGGTTGCGACC
1 TGGGGG-TGCCCAGTCGCGACC
1609282 TGGGGGTG-CCAGTCGCGACC
1 TGGGGGTGCCCAGTCGCGACC
1609302 TGGTGGGTGC
1 TGG-GGGTGC
1609312 TACCTAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 13 0.50
21 7 0.27
22 6 0.23
ACGTcount: A:0.06, C:0.25, G:0.48, T:0.21
Consensus pattern (21 bp):
TGGGGGTGCCCAGTCGCGACC
Found at i:1611019 original size:13 final size:13
Alignment explanation
Indices: 1611001--1611026 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1610991 CAATTTTTTG
1611001 TGTATCGATACAT
1 TGTATCGATACAT
1611014 TGTATCGATACAT
1 TGTATCGATACAT
1611027 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:1613586 original size:13 final size:13
Alignment explanation
Indices: 1613568--1613606 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1613558 ATAATCCTCC
*
1613568 TGTATCGATACAG
1 TGTATCGATACAA
1613581 TGTATCGATACAA
1 TGTATCGATACAA
1613594 TGTATCGATACAA
1 TGTATCGATACAA
1613607 AGAAAAATGT
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:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1617551 original size:21 final size:21
Alignment explanation
Indices: 1617522--1617566 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1617512 AAGTTTTCAT
*
1617522 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1617542 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1617564 TTT
1 TTT
1617567 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1619803 original size:13 final size:13
Alignment explanation
Indices: 1619785--1619810 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1619775 CAATTTTTTA
1619785 TGTATCGATACAT
1 TGTATCGATACAT
1619798 TGTATCGATACAT
1 TGTATCGATACAT
1619811 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:1623134 original size:28 final size:29
Alignment explanation
Indices: 1623100--1623174 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 29
1623090 TTTTGGAGAT
1623100 AATAACGGGGTTGGAGTGTTCCCTC-A-GA
1 AATAACGGGGTTGGAGTGTTCCC-CGATGA
* *
1623128 AGTAACGGGGTTGGAGT-ATCCCCGATGA
1 AATAACGGGGTTGGAGTGTTCCCCGATGA
*
1623156 AATAACGAGGTTGGAGTGT
1 AATAACGGGGTTGGAGTGT
1623175 CCTTGATTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
26 1 0.03
27 5 0.13
28 33 0.85
ACGTcount: A:0.27, C:0.15, G:0.35, T:0.24
Consensus pattern (29 bp):
AATAACGGGGTTGGAGTGTTCCCCGATGA
Found at i:1623254 original size:52 final size:50
Alignment explanation
Indices: 1623185--1623333 Score: 172
Period size: 51 Copynumber: 2.9 Consensus size: 50
1623175 CCTTGATTGT
1623185 GAAAAATTGGTATTTTTGGAAATAAAATCGGTGTTGGAGTATCCCCGATTAAA
1 GAAAAATTGGTA-TTTTGGAAATAAAATCGG-GTTGGAGTATCCCCGATT-AA
* * * * *
1623238 GGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTAT
1 GAAAAATTGGTATTTTGGAAATAAAATC-GGGTTGGAGTATCCCCGATTAA
*** *
1623289 GAAAAATCAATATTTTGGAAATAAAGTCGAGGTTGGAGTATCCCC
1 GAAAAATTGGTATTTTGGAAATAAAATCG-GGTTGGAGTATCCCC
1623334 TCGGAAATAA
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
50 1 0.01
51 36 0.44
52 32 0.40
53 12 0.15
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (50 bp):
GAAAAATTGGTATTTTGGAAATAAAATCGGGTTGGAGTATCCCCGATTAA
Found at i:1623323 original size:51 final size:51
Alignment explanation
Indices: 1623161--1623333 Score: 186
Period size: 52 Copynumber: 3.4 Consensus size: 51
1623151 GATGAAATAA
* ** *
1623161 CGAGGTTGGAGTGTCCTTGATTGTGAAAAATTGGTATTTTTGGAAATAAAAT
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGGAAATAAAAT
* * * * *
1623213 CG-GTGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAAC
1 CGAG-GTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTGGAAATAAAAT
* *** *
1623265 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGT
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAAT
1623316 CGAGGTTGGAGTATCCCC
1 CGAGGTTGGAGTATCCCC
1623334 TCGGAAATAA
Statistics
Matches: 99, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
51 38 0.38
52 50 0.51
53 11 0.11
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.31
Consensus pattern (51 bp):
CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAAT
Found at i:1623354 original size:28 final size:28
Alignment explanation
Indices: 1623319--1623416 Score: 144
Period size: 28 Copynumber: 3.5 Consensus size: 28
1623309 ATAAAGTCGA
1623319 GGTTGGAGTATCCCCTCGGAAATAACGG
1 GGTTGGAGTATCCCCTCGGAAATAACGG
1623347 GGTTGGAGTATCCCCTCGGAAATAACGG
1 GGTTGGAGTATCCCCTCGGAAATAACGG
*** *
1623375 GGTTGGAGTATCCCCGATG-ATTAACGG
1 GGTTGGAGTATCCCCTCGGAAATAACGG
*
1623402 GGTTGGAGTGTCCCC
1 GGTTGGAGTATCCCC
1623417 AATTGTGAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
27 21 0.32
28 44 0.68
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.23
Consensus pattern (28 bp):
GGTTGGAGTATCCCCTCGGAAATAACGG
Done.