Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008338.1 Hibiscus syriacus cultivar Beakdansim tig00111059_pilon, whole genome shotgun sequence
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: 2210178
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 12
Found at i:1615660 original size:21 final size:22
Alignment explanation
Indices: 1615636--1615691 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
1615626 ATTAATTGTG
**
1615636 AAAATAAAGATAAAT-GATTAAA
1 AAAATAAA-ATAAATGGAACAAA
1615658 AAAATAAACA-AAATGGAAC-AA
1 AAAATAAA-ATAAATGGAACAAA
1615679 AAAATAAAATAAA
1 AAAATAAAATAAA
1615692 AGAAAATGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.03
21 17 0.59
22 11 0.38
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (22 bp):
AAAATAAAATAAATGGAACAAA
Found at i:1617818 original size:85 final size:85
Alignment explanation
Indices: 1617675--1617972 Score: 461
Period size: 85 Copynumber: 3.5 Consensus size: 85
1617665 GCTGTCATCT
* *
1617675 AGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCT
1 AGCTGAATGAAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATACT
1617740 ATAAATTTGATATGCCCTTG
66 ATAAATTTGATATGCCCTTG
* ** *
1617760 AGCTGAATGAAATCAAACTCGAAGGTTTTTGTTGACAGATAGCTTTTCTCGCCTTGAGCTATACT
1 AGCTGAATGAAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATACT
*
1617825 GTAAATTTGATATGCCCTTG
66 ATAAATTTGATATGCCCTTG
* * *
1617845 AGTTGAATGAAATCGAACTCGAAGGTTTTTGTTTACAGATAACCCTTCTCACCTTGAGCTATACT
1 AGCTGAATGAAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATACT
*
1617910 TTAAATTTGATATGCCCTTG
66 ATAAATTTGATATGCCCTTG
* * *
1617930 AGCTGAATGTAATCGAACTCGAAGGTTATTGGTTGAGAGATAG
1 AGCTGAATGAAATCGAACTCGAAGGTT-TTTGTTGACAGATAG
1617973 TTCATTTTTG
Statistics
Matches: 191, Mismatches: 21, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
85 180 0.94
86 11 0.06
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (85 bp):
AGCTGAATGAAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATACT
ATAAATTTGATATGCCCTTG
Found at i:1618530 original size:163 final size:164
Alignment explanation
Indices: 1618260--1618587 Score: 649
Period size: 163 Copynumber: 2.0 Consensus size: 164
1618250 TATTCTTTCA
1618260 TGTGGTTCCCCTTCATGGGTCTAAACCAAGTGAAATGATCTTTGGACAACTCCTCTTCACGGGAA
1 TGTGGTTCCCCTTCATGGGTCTAAACCAAGTGAAATGATCTTTGGACAACTCCTCTTCACGGGAA
1618325 AATCATGTGAGATGTTATTCGAGTGAAATTGAAATATGGCTTGAAAACTTTAGTTGGAAACTAGC
66 AATCATGTGAGATGTTATTCGAGTGAAATTGAAATATGGCTTGAAAACTTTAGTTGGAAACTAGC
1618390 CACTCG-CGTTGAGTTAAACTGAATCGGATTCGT
131 CACTCGACGTTGAGTTAAACTGAATCGGATTCGT
1618423 TGTGGTTCCCCTTCATGGGTCTAAACCAAGTGAAATGATCTTTGGACAACTCCTCTTCACGGGAA
1 TGTGGTTCCCCTTCATGGGTCTAAACCAAGTGAAATGATCTTTGGACAACTCCTCTTCACGGGAA
1618488 AATCATGTGAGATGTTATTCGAGTGAAATTGAAATATGGCTTGAAAACTTTAGTTGGAAACTAGC
66 AATCATGTGAGATGTTATTCGAGTGAAATTGAAATATGGCTTGAAAACTTTAGTTGGAAACTAGC
1618553 CACTCGACGTTGAGTTAAACTGAATCGGATTCGT
131 CACTCGACGTTGAGTTAAACTGAATCGGATTCGT
1618587 T
1 T
1618588 TTGAATTGGC
Statistics
Matches: 164, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
163 136 0.83
164 28 0.17
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (164 bp):
TGTGGTTCCCCTTCATGGGTCTAAACCAAGTGAAATGATCTTTGGACAACTCCTCTTCACGGGAA
AATCATGTGAGATGTTATTCGAGTGAAATTGAAATATGGCTTGAAAACTTTAGTTGGAAACTAGC
CACTCGACGTTGAGTTAAACTGAATCGGATTCGT
Found at i:1619831 original size:99 final size:99
Alignment explanation
Indices: 1619660--1619844 Score: 259
Period size: 99 Copynumber: 1.9 Consensus size: 99
1619650 TTGTAATTTT
1619660 CCTTTATCAAGCTAGCTAAATCTTATCCATAAAGCCGAGGTGATTAACCAATTGCTCTAGAGGCA
1 CCTTTATCAAGCTAGCTAAATCTTATCCATAAAGCCGAGGTGATTAACCAATTGCTCTAGAGGCA
1619725 CAACTCAAGCTTTATTGTATATGTATTATAATCA
66 CAACTCAAGCTTTATTGTATATGTATTATAATCA
** * * * *
1619759 CCTTTATCTGGCTAGCTGAATCTTATCCATAAAGTCG-GG-GCATTTAATCAATTGCTTTAGAGG
1 CCTTTATCAAGCTAGCTAAATCTTATCCATAAAGCCGAGGTG-A-TTAACCAATTGCTCTAGAGG
*
1619822 GA-AAGCTCAAGCTTTATTGTATA
64 CACAA-CTCAAGCTTTATTGTATA
1619845 CATATAATAT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
97 1 0.01
98 5 0.07
99 70 0.92
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (99 bp):
CCTTTATCAAGCTAGCTAAATCTTATCCATAAAGCCGAGGTGATTAACCAATTGCTCTAGAGGCA
CAACTCAAGCTTTATTGTATATGTATTATAATCA
Found at i:1620400 original size:36 final size:36
Alignment explanation
Indices: 1620355--1620440 Score: 115
Period size: 36 Copynumber: 2.4 Consensus size: 36
1620345 TTAAATACCC
*
1620355 TTACAAAAAGAAATATGA-GAAATTTCAAAAAATAAG
1 TTACAAAAAGAAATAT-ATGAAAGTTCAAAAAATAAG
*
1620391 TTACAAAAAGATATATATGAAAGTTCAAAAAATAAG
1 TTACAAAAAGAAATATATGAAAGTTCAAAAAATAAG
*
1620427 TT-CAAACA-AAATAT
1 TTACAAAAAGAAATAT
1620441 TGTAAAATGG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
34 5 0.11
35 6 0.13
36 34 0.76
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.24
Consensus pattern (36 bp):
TTACAAAAAGAAATATATGAAAGTTCAAAAAATAAG
Found at i:1623952 original size:20 final size:20
Alignment explanation
Indices: 1623927--1623964 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1623917 TTCCCATTGA
*
1623927 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
1623947 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
1623965 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1627749 original size:5 final size:5
Alignment explanation
Indices: 1627739--1627796 Score: 80
Period size: 5 Copynumber: 10.8 Consensus size: 5
1627729 AATAATATTT
1627739 TTTTA TTTTA TTTTA TTTTA TTTTA TTATTA TTATAATA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TT-T--TA TTTTA TTTTA
1627788 TTTTA TTTT
1 TTTTA TTTT
1627797 GTTTCATTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
5 38 0.76
6 7 0.14
7 1 0.02
8 4 0.08
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:1632671 original size:37 final size:36
Alignment explanation
Indices: 1632624--1632731 Score: 173
Period size: 35 Copynumber: 3.0 Consensus size: 36
1632614 TTTTTCAATT
*
1632624 AACATCTACCAAACTTTGAAAAACTATTTTTCAAAGA
1 AACATTTACCAAACTTTG-AAAACTATTTTTCAAAGA
*
1632661 AACATTTACCAAACTTTGAAAACCA-TTTTCAAAGA
1 AACATTTACCAAACTTTGAAAACTATTTTTCAAAGA
1632696 AACATTTACCAAACTTTGAAAACTATTTTTTCAAAG
1 AACATTTACCAAACTTTGAAAACTA-TTTTTCAAAG
1632732 TTGGTTACCA
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
35 34 0.52
36 6 0.09
37 26 0.39
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (36 bp):
AACATTTACCAAACTTTGAAAACTATTTTTCAAAGA
Found at i:1632687 original size:21 final size:21
Alignment explanation
Indices: 1632663--1632723 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1632653 TTCAAAGAAA
1632663 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
1632684 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
1632698 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
1632719 TATTT
1 CATTT
1632724 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 9 0.30
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:1635958 original size:21 final size:22
Alignment explanation
Indices: 1635929--1635970 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1635919 GAATTTTACA
1635929 CATAGTGTACCGATGCACCAGC
1 CATAGTGTACCGATGCACCAGC
*
1635951 CATA-TGTATCGATGCACCAG
1 CATAGTGTACCGATGCACCAG
1635971 ACGCTCCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (22 bp):
CATAGTGTACCGATGCACCAGC
Found at i:1643514 original size:65 final size:64
Alignment explanation
Indices: 1643415--1643557 Score: 171
Period size: 65 Copynumber: 2.2 Consensus size: 64
1643405 TGCACTATAT
** * * ** **
1643415 CATGCATCGATGCACTCCTAATTAAATTGAACATCGAATGCACTT-AGTGCACCGATGCACCCAC
1 CATGCATCGATGCACTCCTAAACAAATAGAACATCGAATGCA-TTCAATGCACAAATGCACAAAC
* *
1643479 TATGCATCGATGCACTCTTAAACAAATAGAAACATCGAATGCATTCAATGCACAAATGCACAAAC
1 CATGCATCGATGCACTCCTAAACAAATAG-AACATCGAATGCATTCAATGCACAAATGCACAAAC
1643544 CATGCATCGATGCA
1 CATGCATCGATGCA
1643558 TCCATGCTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
64 26 0.39
65 40 0.61
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (64 bp):
CATGCATCGATGCACTCCTAAACAAATAGAACATCGAATGCATTCAATGCACAAATGCACAAAC
Found at i:1644380 original size:20 final size:19
Alignment explanation
Indices: 1644336--1644387 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
1644326 AGTTTTGAAA
1644336 TGGTATCGATACCTTCCCTT
1 TGGTATCGATACC-TCCCTT
*
1644356 CGGTATCGATACAC-CCCTTT
1 TGGTATCGATAC-CTCCC-TT
*
1644376 TGGTATTGATAC
1 TGGTATCGATAC
1644388 TGATTGAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.11
20 23 0.85
21 1 0.04
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (19 bp):
TGGTATCGATACCTCCCTT
Found at i:1649698 original size:23 final size:22
Alignment explanation
Indices: 1649670--1649714 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1649660 AACAAAGTGC
*
1649670 CATAAATAACATAAAATAAAATA
1 CATAAATAAC-CAAAATAAAATA
*
1649693 CATAAATGACCAAAATAAAATA
1 CATAAATAACCAAAATAAAATA
1649715 AAACATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.67, C:0.11, G:0.02, T:0.20
Consensus pattern (22 bp):
CATAAATAACCAAAATAAAATA
Found at i:1650864 original size:16 final size:17
Alignment explanation
Indices: 1650839--1650872 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1650829 CTGAGGTGTC
1650839 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
1650855 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
1650872 A
1 A
1650873 GAATGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:1651984 original size:25 final size:24
Alignment explanation
Indices: 1651956--1652003 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1651946 TTCTCTTATA
*
1651956 TTCAAATAAATCATATAAACATATT
1 TTCAAATAAATAATAT-AACATATT
* *
1651981 TTCACATAGATAATATAACATAT
1 TTCAAATAAATAATATAACATAT
1652004 GCAATACATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.35
Consensus pattern (24 bp):
TTCAAATAAATAATATAACATATT
Found at i:1661424 original size:18 final size:18
Alignment explanation
Indices: 1661380--1661433 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
1661370 TCTTCTTATT
1661380 TTTACTTTAAT-TACTTTTA
1 TTTA-TTTAATAT-CTTTTA
*
1661399 TTTATTTAATCTCTTTTA
1 TTTATTTAATATCTTTTA
1661417 TTGT-TTTAATATCTTTT
1 TT-TATTTAATATCTTTT
1661434 TACCAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 26 0.81
19 6 0.19
ACGTcount: A:0.22, C:0.09, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTTAATATCTTTTA
Found at i:1666946 original size:6 final size:6
Alignment explanation
Indices: 1666935--1666976 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
1666925 ATTCCATTAC
*
1666935 ATTTTT ATTTTT ATTTTT ATTTTT TTGTTTT ATTTTT CATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT AT-TTTT ATTTTT -ATTT
1666977 CGATCAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
6 23 0.72
7 9 0.28
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:1667920 original size:33 final size:33
Alignment explanation
Indices: 1667881--1667954 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
1667871 AGTTGAATGC
* **
1667881 GAAAAAAAACAGCAGTTCGAACGAAAAAAGAAAA
1 GAAAAAAAA-GGCAGTTCGAAAAAAAAAAGAAAA
** *
1667915 GAAAAAAAAGGTTGTTCGAAAAAAAAAAGAAGA
1 GAAAAAAAAGGCAGTTCGAAAAAAAAAAGAAAA
1667948 GAAAAAA
1 GAAAAAA
1667955 TATGTGAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 25 0.74
34 9 0.26
ACGTcount: A:0.66, C:0.07, G:0.19, T:0.08
Consensus pattern (33 bp):
GAAAAAAAAGGCAGTTCGAAAAAAAAAAGAAAA
Found at i:1668229 original size:20 final size:20
Alignment explanation
Indices: 1668204--1668248 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
1668194 ACTTGCAGGC
1668204 TTCTGGTAATACCATGTCGA
1 TTCTGGTAATACCATGTCGA
1668224 TTCTGGTAATACCATGTCGA
1 TTCTGGTAATACCATGTCGA
1668244 TTCTG
1 TTCTG
1668249 ACTTCGAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TTCTGGTAATACCATGTCGA
Found at i:1670593 original size:17 final size:17
Alignment explanation
Indices: 1670573--1670628 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
1670563 CTTTCATGTC
1670573 TTTTTTTTTGAACAGTT
1 TTTTTTTTTGAACAGTT
* * *
1670590 TTTTTTTTCGAACTGCT
1 TTTTTTTTTGAACAGTT
* *
1670607 ATTTTTTTTCAACA-TT
1 TTTTTTTTTGAACAGTT
1670623 TTTTTT
1 TTTTTT
1670629 GTGATGGAGA
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
16 6 0.20
17 24 0.80
ACGTcount: A:0.16, C:0.11, G:0.07, T:0.66
Consensus pattern (17 bp):
TTTTTTTTTGAACAGTT
Found at i:1686612 original size:21 final size:20
Alignment explanation
Indices: 1686586--1686630 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1686576 ATCTATATAT
1686586 ATATAATTTAAATT-AGGAAAA
1 ATATAA-TT-AATTAAGGAAAA
*
1686607 ATATAATTAATTAAGTAAAA
1 ATATAATTAATTAAGGAAAA
1686627 ATAT
1 ATAT
1686631 CTTGCGAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 12 0.55
21 6 0.27
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (20 bp):
ATATAATTAATTAAGGAAAA
Found at i:1695392 original size:22 final size:23
Alignment explanation
Indices: 1695367--1695415 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
1695357 CATTTATCGA
*
1695367 TACAGGGGTATCGATA-CCTTGC
1 TACAGGGGTACCGATACCCTTGC
*
1695389 TACA-GTGTACCGATACCCTTGC
1 TACAGGGGTACCGATACCCTTGC
1695411 TACAG
1 TACAG
1695416 TAATTTCGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (23 bp):
TACAGGGGTACCGATACCCTTGC
Found at i:1706354 original size:21 final size:21
Alignment explanation
Indices: 1706330--1706381 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
1706320 CACTTAGGGA
1706330 ACCGATTCCCTATAAGGGGGT
1 ACCGATTCCCTATAAGGGGGT
1706351 ACCGATTCCCTATAAGGGGGT
1 ACCGATTCCCTATAAGGGGGT
1706372 ACCGATTCCC
1 ACCGATTCCC
1706382 CCCACGCTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (21 bp):
ACCGATTCCCTATAAGGGGGT
Found at i:1711711 original size:22 final size:22
Alignment explanation
Indices: 1711685--1711744 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
1711675 TTAGTACAGA
* *
1711685 GGGAATCGATACCCTCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
1711707 GGGAACCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
1711729 GGGAACCGATACCCCC
1 GGGAACCGATACCCCC
1711745 CACGGGTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.27, C:0.32, G:0.27, T:0.15
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:1715455 original size:18 final size:18
Alignment explanation
Indices: 1715432--1715468 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1715422 CCCACATAGT
1715432 ATTGGAAACACTATTGGG
1 ATTGGAAACACTATTGGG
1715450 ATTGGAAACACTATTGGG
1 ATTGGAAACACTATTGGG
1715468 A
1 A
1715469 ATGGGTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (18 bp):
ATTGGAAACACTATTGGG
Found at i:1716714 original size:19 final size:21
Alignment explanation
Indices: 1716692--1716730 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1716682 TACAATAATA
*
1716692 TCCTT-CTTTTTC-AATTAAG
1 TCCTTACTTTGTCGAATTAAG
1716711 TCCTTACTTTGTCGAATTAA
1 TCCTTACTTTGTCGAATTAA
1716731 AATGAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.23, C:0.21, G:0.08, T:0.49
Consensus pattern (21 bp):
TCCTTACTTTGTCGAATTAAG
Found at i:1717191 original size:6 final size:6
Alignment explanation
Indices: 1717180--1717207 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1717170 AAGAGCGCAG
1717180 GATGAA GATGAA GATGAA GATGAA GATG
1 GATGAA GATGAA GATGAA GATGAA GATG
1717208 GATTTTCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.36, T:0.18
Consensus pattern (6 bp):
GATGAA
Found at i:1722888 original size:18 final size:18
Alignment explanation
Indices: 1722865--1722899 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1722855 GGTAATTCGA
*
1722865 TTAACCGATCGAACCGAT
1 TTAACCGACCGAACCGAT
1722883 TTAACCGACCGAACCGA
1 TTAACCGACCGAACCGA
1722900 ATTACCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.31, G:0.17, T:0.17
Consensus pattern (18 bp):
TTAACCGACCGAACCGAT
Found at i:1729775 original size:20 final size:18
Alignment explanation
Indices: 1729744--1729787 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
1729734 AAATAAAGTG
1729744 AAAATTCAAAAAAAATAA
1 AAAATTCAAAAAAAATAA
* *
1729762 AAAATTGCATAAAAACATCA
1 AAAATT-CA-AAAAAAATAA
1729782 AAAATT
1 AAAATT
1729788 TAAGATTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 2 0.09
20 14 0.64
ACGTcount: A:0.68, C:0.09, G:0.02, T:0.20
Consensus pattern (18 bp):
AAAATTCAAAAAAAATAA
Found at i:1731565 original size:2 final size:2
Alignment explanation
Indices: 1731558--1731583 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1731548 GTTTATATCA
1731558 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
1731584 TGAAAGCTTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1739070 original size:31 final size:30
Alignment explanation
Indices: 1738977--1739070 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 30
1738967 ATAGTAGACC
*
1738977 CATAATAATAAATATTATAAAAAAATTAAACT
1 CATAATAATAAATA-T-TAAAAAAATTAAATT
* *
1739009 CATAATAATAAATATTGAGAAAAATAAAATT
1 CATAATAATAAATATT-AAAAAAATTAAATT
**
1739040 TTTAATGAA-AAATATTAAAAATAATTAAATT
1 CATAAT-AATAAATATTAAAAA-AATTAAATT
1739071 ATATAACTGA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
30 5 0.10
31 31 0.60
32 16 0.31
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (30 bp):
CATAATAATAAATATTAAAAAAATTAAATT
Found at i:1739579 original size:21 final size:21
Alignment explanation
Indices: 1739538--1739580 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1739528 TTTTTAAAAG
*
1739538 TAAATAAGTTATGTTTCATTT
1 TAAATAAATTATGTTTCATTT
*
1739559 TAAATAAATGTAT-TTTTATTT
1 TAAATAAAT-TATGTTTCATTT
1739580 T
1 T
1739581 TTCATATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (21 bp):
TAAATAAATTATGTTTCATTT
Found at i:1746464 original size:21 final size:21
Alignment explanation
Indices: 1746438--1746507 Score: 122
Period size: 21 Copynumber: 3.3 Consensus size: 21
1746428 GGTGCTTATG
1746438 TGACAGTTCACTATGTTGACA
1 TGACAGTTCACTATGTTGACA
1746459 TGACAGTTCACTATGTTGACA
1 TGACAGTTCACTATGTTGACA
* *
1746480 TGACAGTCCACTATGTCGACA
1 TGACAGTTCACTATGTTGACA
1746501 TGACAGT
1 TGACAGT
1746508 CCACAATACT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (21 bp):
TGACAGTTCACTATGTTGACA
Found at i:1754904 original size:2 final size:2
Alignment explanation
Indices: 1754897--1754926 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1754887 ATCAACGAGT
1754897 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1754927 AACAATATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1756997 original size:26 final size:26
Alignment explanation
Indices: 1756961--1757011 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1756951 TTTCACTCGT
* *
1756961 CTTCTAGAAGTTGCTGACTGGATCGC
1 CTTCTAGAAGTTACTGACTAGATCGC
1756987 CTTCTAGAAGTTACTGACTAGATCG
1 CTTCTAGAAGTTACTGACTAGATCG
1757012 TTGAAGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (26 bp):
CTTCTAGAAGTTACTGACTAGATCGC
Found at i:1758518 original size:22 final size:23
Alignment explanation
Indices: 1758490--1758537 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1758480 ACACACACAA
* *
1758490 AAAAAGAGAG-AGAAAGGGGGAG
1 AAAAAGAGAGAAAAAAGAGGGAG
1758512 AAAAAGAGAGAAAAAAGAGGGAG
1 AAAAAGAGAGAAAAAAGAGGGAG
1758535 AAA
1 AAA
1758538 GAGTCATCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (23 bp):
AAAAAGAGAGAAAAAAGAGGGAG
Found at i:1759806 original size:20 final size:20
Alignment explanation
Indices: 1759777--1759829 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
1759767 GTAAGTTTAG
*
1759777 ATTTTAATTTATTTTTGATC
1 ATTTTTATTTATTTTTGATC
** *
1759797 ATTTTTATTTACCTTTGATT
1 ATTTTTATTTATTTTTGATC
1759817 A-TTTTATTT-TTTT
1 ATTTTTATTTATTTT
1759830 AAATAAATAG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 2 0.07
19 8 0.30
20 17 0.63
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.70
Consensus pattern (20 bp):
ATTTTTATTTATTTTTGATC
Found at i:1764280 original size:74 final size:73
Alignment explanation
Indices: 1764173--1764503 Score: 361
Period size: 70 Copynumber: 4.6 Consensus size: 73
1764163 ATTAGACAAT
* * * * *
1764173 TTTCTTTTGAAACAAATTTTTTTATCTCACTTGAGGTAATTTTCCACAAAAAGAATTTTCGTCTC
1 TTTCTCTTGAAACAAA--ATTTTATCTCACTTGAGATAATTTTCCTCAAAAA-AATTTTCATCTC
*
1764238 ACTCGAGATAG
63 ACTCGAGACAG
* * *
1764249 TTTCTCTCGAAACAAAATTTTATCTTACTTGAGATAATTTTCCTCAAAAACATTTTTCATCTCAC
1 TTTCTCTTGAAACAAAATTTTATCTCACTTGAGATAATTTTCCTCAAAAA-AATTTTCATCTCAC
1764314 TCGAGACAG
65 TCGAGACAG
* * * * * *
1764323 TTTCTCTTGAAA-TAAATTTTATCTCACTTGAGATATTTTTTCT-TAAAATA-TTACATCTCACT
1 TTTCTCTTGAAACAAAATTTTATCTCACTTGAGATAATTTTCCTCAAAAAAATTTTCATCTCACT
*
1764385 CGAGATAG
66 CGAGACAG
* **
1764393 TTTC-CTTTGAAAC-AAATTTTATCTCACTTGATAT-ATTTT-CTCTTAAAAATTTTCATCTCAC
1 TTTCTC-TTGAAACAAAATTTTATCTCACTTGAGATAATTTTCCTCAAAAAAATTTTCATCTCAC
1764454 TCGAGACAG
65 TCGAGACAG
* ** *
1764463 TTTCTTTTGAAACAAAATTACATCTCACTTGAGATATTTTT
1 TTTCTCTTGAAACAAAATTTTATCTCACTTGAGATAATTTT
1764504 TTCTTGAAAA
Statistics
Matches: 217, Mismatches: 31, Indels: 18
0.82 0.12 0.07
Matches are distributed among these distances:
68 2 0.01
69 10 0.05
70 77 0.35
71 18 0.08
72 8 0.04
73 27 0.12
74 61 0.28
76 14 0.06
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (73 bp):
TTTCTCTTGAAACAAAATTTTATCTCACTTGAGATAATTTTCCTCAAAAAAATTTTCATCTCACT
CGAGACAG
Found at i:1764300 original size:38 final size:37
Alignment explanation
Indices: 1764192--1764362 Score: 118
Period size: 37 Copynumber: 4.6 Consensus size: 37
1764182 AAACAAATTT
* * *
1764192 TTTTATCTCACTTGAGGTAATTTTCCACAAAA-AGAA
1 TTTTATCTCACTTGAGATAATTTTCCTCAAAACAAAA
* * * *
1764228 TTTTCGTCTCACTCGAGAT-AGTTTCTCTCGAAACAAAA
1 TTTT-ATCTCACTTGAGATAATTTTC-CTCAAAACAAAA
* * *
1764266 TTTTATCTTACTTGAGATAATTTTCCTCAAAA-ACAT
1 TTTTATCTCACTTGAGATAATTTTCCTCAAAACAAAA
* * * ** *
1764302 TTTTCATCTCACTCGAGA-CAGTTTCTCTTGAAA-TAAA
1 TTTT-ATCTCACTTGAGATAATTTTC-CTCAAAACAAAA
*
1764339 TTTTATCTCACTTGAGATATTTTT
1 TTTTATCTCACTTGAGATAATTTT
1764363 TCTTAAAATA
Statistics
Matches: 101, Mismatches: 27, Indels: 13
0.72 0.19 0.09
Matches are distributed among these distances:
36 32 0.32
37 57 0.56
38 12 0.12
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (37 bp):
TTTTATCTCACTTGAGATAATTTTCCTCAAAACAAAA
Found at i:1764349 original size:36 final size:35
Alignment explanation
Indices: 1764234--1764536 Score: 224
Period size: 34 Copynumber: 8.5 Consensus size: 35
1764224 AGAATTTTCG
*
1764234 TCTCACTCGAGATAGTTTCTCTCGAAACAAAATTTTA
1 TCTCACTCGAGATAGTTTCTCTTG-AA-AAAATTTTA
* * * * *
1764271 TCTTACTTGAGATAATTT-TCCTCAAAAACATTTTTCA
1 TCTCACTCGAGATAGTTTCTCTTGAAAAA-A-TTTT-A
*
1764308 TCTCACTCGAGACAGTTTCTCTTGAAATAAATTTTA
1 TCTCACTCGAGATAGTTTCTCTTGAAA-AAATTTTA
* * * * **
1764344 TCTCACTTGAGATATTTTTTCTT-AAAATATTACA
1 TCTCACTCGAGATAGTTTCTCTTGAAAAAATTTTA
1764378 TCTCACTCGAGATAGTTTC-CTTTGAAACAAATTTTA
1 TCTCACTCGAGATAGTTTCTC-TTGAAA-AAATTTTA
* * *
1764414 TCTCACTTGATATATTTTCTCTT--AAAAATTTTCA
1 TCTCACTCGAGATAGTTTCTCTTGAAAAAATTTT-A
* * **
1764448 TCTCACTCGAGACAGTTTCTTTTGAAACAAAATTACA
1 TCTCACTCGAGATAGTTTCTCTTG-AA-AAAATTTTA
* * * * *
1764485 TCTCACTTGAGATATTTTTTTCTTG--AAAATATCA
1 TCTCACTCGAGATA-GTTTCTCTTGAAAAAATTTTA
1764519 TCTCACTCGAGATAGTTT
1 TCTCACTCGAGATAGTTT
1764537 TTCCACATGA
Statistics
Matches: 207, Mismatches: 44, Indels: 34
0.73 0.15 0.12
Matches are distributed among these distances:
33 11 0.05
34 67 0.32
35 9 0.04
36 49 0.24
37 49 0.24
38 20 0.10
39 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (35 bp):
TCTCACTCGAGATAGTTTCTCTTGAAAAAATTTTA
Found at i:1764403 original size:70 final size:71
Alignment explanation
Indices: 1764229--1764536 Score: 367
Period size: 70 Copynumber: 4.3 Consensus size: 71
1764219 CAAAAAGAAT
* * *
1764229 TTTCGTCTCACTCGAGATAGTTTCTCTCGAAACAAAATTTTATCTTACTTGAGATAATTTTCCTC
1 TTTCATCTCACTCGAGATAGTTTCTCTTGAAACAAAATTTTATCTCACTTGAGAT-ATTTT-CTC
** *
1764294 AAAAACATT
64 TTAAA-ATA
* * *
1764303 TTTCATCTCACTCGAGACAGTTTCTCTTGAAA-TAAATTTTATCTCACTTGAGATATTTTTTCTT
1 TTTCATCTCACTCGAGATAGTTTCTCTTGAAACAAAATTTTATCTCACTTGAGATATTTTCTCTT
1764367 AAAATA
66 AAAATA
* *
1764373 TTACATCTCACTCGAGATAGTTTC-CTTTGAAAC-AAATTTTATCTCACTTGATATATTTTCTCT
1 TTTCATCTCACTCGAGATAGTTTCTC-TTGAAACAAAATTTTATCTCACTTGAGATATTTTCTCT
1764436 TAAAA-A
65 TAAAATA
* * ** *
1764442 TTTTCATCTCACTCGAGACAGTTTCTTTTGAAACAAAATTACATCTCACTTGAGATATTTTTTTC
1 -TTTCATCTCACTCGAGATAGTTTCTCTTGAAACAAAATTTTATCTCACTTGAGATA-TTTTCTC
1764507 TTGAAAATA
64 TT-AAAATA
1764516 --TCATCTCACTCGAGATAGTTT
1 TTTCATCTCACTCGAGATAGTTT
1764537 TTCCACATGA
Statistics
Matches: 205, Mismatches: 21, Indels: 19
0.84 0.09 0.08
Matches are distributed among these distances:
69 2 0.01
70 92 0.45
71 44 0.21
72 13 0.06
73 24 0.12
74 30 0.15
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.42
Consensus pattern (71 bp):
TTTCATCTCACTCGAGATAGTTTCTCTTGAAACAAAATTTTATCTCACTTGAGATATTTTCTCTT
AAAATA
Found at i:1764522 original size:141 final size:144
Alignment explanation
Indices: 1764234--1764536 Score: 433
Period size: 141 Copynumber: 2.1 Consensus size: 144
1764224 AGAATTTTCG
*
1764234 TCTCACTCGAGATAGTTTCTCTCGAAACAAAATTTTATCTTACTTGAGATAATTTTCCTCAAAAA
1 TCTCACTCGAGATAGTTTCTCTCGAAACAAAATTTTATCTCACTTGAGATAATTTTCCTCAAAAA
* **
1764299 CATTTTTCATCTCACTCGAGACAGTTTCTCTTGAAATAAATTTTATCTCACTTGAGATATTTTTT
66 CATTTTTCATCTCACTCGAGACAGTTTCTCTTGAAAAAAATTACATCTCACTTGAGATATTTTTT
1764364 CTTAAAATATTACA
131 CTTAAAATATTACA
* * *
1764378 TCTCACTCGAGATAGTTTC-CTTTGAAAC-AAATTTTATCTCACTTGATAT-ATTTT-CTCTTAA
1 TCTCACTCGAGATAGTTTCTC-TCGAAACAAAATTTTATCTCACTTGAGATAATTTTCCTC-AAA
*
1764439 AA-A-TTTTCATCTCACTCGAGACAGTTTCTTTTGAAACAAAATTACATCTCACTTGAGATATTT
64 AACATTTTTCATCTCACTCGAGACAGTTTCTCTTGAAA-AAAATTACATCTCACTTGAGATA-TT
1764502 TTTTCTTGAAAATA-T-CA
127 TTTTCTT-AAAATATTACA
1764519 TCTCACTCGAGATAGTTT
1 TCTCACTCGAGATAGTTT
1764537 TTCCACATGA
Statistics
Matches: 146, Mismatches: 8, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
140 32 0.22
141 44 0.30
142 19 0.13
143 26 0.18
144 25 0.17
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (144 bp):
TCTCACTCGAGATAGTTTCTCTCGAAACAAAATTTTATCTCACTTGAGATAATTTTCCTCAAAAA
CATTTTTCATCTCACTCGAGACAGTTTCTCTTGAAAAAAATTACATCTCACTTGAGATATTTTTT
CTTAAAATATTACA
Found at i:1770410 original size:36 final size:36
Alignment explanation
Indices: 1770364--1770567 Score: 153
Period size: 36 Copynumber: 5.5 Consensus size: 36
1770354 TCGAGACGAG
* * *
1770364 TTTTCGTAAAAACAAATTTTGTCTCACTTGAGACAA
1 TTTTCTTAAAAACAAATTTCGTCTCACTTGAGATAA
* *
1770400 TTTTCTTAAAAACAAAGTTCGTCTCACTGGAGATAA
1 TTTTCTTAAAAACAAATTTCGTCTCACTTGAGATAA
* ** * **
1770436 TTTTCCTT-AAAACAAAATTAATCTCACTTAAGATTG
1 TTTT-CTTAAAAACAAATTTCGTCTCACTTGAGATAA
* * * *
1770472 TTTTCCCTTAAAAACAACTTTTGTCTTACTTGAGA-CA
1 TTTT--CTTAAAAACAAATTTCGTCTCACTTGAGATAA
* *
1770509 TCTTTCTCTCAAAACAAATTACGTCTCA-TTGGAGATAGA
1 T-TTTCT-TAAAAACAAATTTCGTCTCACTT-GAGATA-A
1770548 TTTTCTTTAAAATACAAATT
1 TTTTC-TTAAAA-ACAAATT
1770568 CTGAAATTTG
Statistics
Matches: 131, Mismatches: 27, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
36 64 0.49
37 27 0.21
38 30 0.23
39 10 0.08
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (36 bp):
TTTTCTTAAAAACAAATTTCGTCTCACTTGAGATAA
Found at i:1770704 original size:77 final size:74
Alignment explanation
Indices: 1770608--1770917 Score: 315
Period size: 74 Copynumber: 4.1 Consensus size: 74
1770598 ATAAACTTTG
* * * * * ** *
1770608 AGATTGTTTCTCTTGAAACAGGTTTTATCTCGCTTAAGATTTTTTTTCACTCGAAACCGAAGATT
1 AGATTGTTTTTCTTAAAACAGATTTTGTCTCGCTTGAGA-AATTTTT-ACTCGAAA-CGAACATT
* * **
1770673 TTATCTCACTTG
63 TCATTTCACTCA
* * * * *
1770685 AGATTGTTTTTCTTAAAACAGACTTTGTCTCGCTTGAGACAGTTTTACTCGAAAGGATTCATTTC
1 AGATTGTTTTTCTTAAAACAGATTTTGTCTCGCTTGAGAAATTTTTACTCGAAACGA-ACATTTC
1770750 ATTTCACTCA
65 ATTTCACTCA
*
1770760 AGATTGTTTTTCTTAAAACA-ATATTTGTCTCGCTTGAGACAGTTTTTACTC-AAACGAACATTT
1 AGATTGTTTTTCTTAAAACAGAT-TTTGTCTCGCTTGAGA-AATTTTTACTCGAAACGAACATTT
1770823 CATTTCACTCA
64 CATTTCACTCA
* * *
1770834 AGATTGTTTTTCTTAAAACA-ATATTTGTCTCGCTTGAGATAGTTTTTACTC-AAAAGAATATTT
1 AGATTGTTTTTCTTAAAACAGAT-TTTGTCTCGCTTGAGA-AATTTTTACTCGAAACGAACATTT
1770897 -ATTTCACTCA
64 CATTTCACTCA
*
1770907 AGATTATTTTT
1 AGATTGTTTTT
1770918 AAAGAAGATT
Statistics
Matches: 204, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
73 20 0.10
74 79 0.39
75 60 0.29
76 12 0.06
77 33 0.16
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (74 bp):
AGATTGTTTTTCTTAAAACAGATTTTGTCTCGCTTGAGAAATTTTTACTCGAAACGAACATTTCA
TTTCACTCA
Found at i:1770805 original size:36 final size:37
Alignment explanation
Indices: 1770760--1770896 Score: 127
Period size: 36 Copynumber: 3.7 Consensus size: 37
1770750 ATTTCACTCA
*
1770760 AGATTGTTTTT-CTTAAAACAATATTTGTCTCGCTTG
1 AGATAGTTTTTACTTAAAACAATATTTGTCTCGCTTG
* * * * * * **
1770796 AGACAGTTTTTAC-TCAAACGAACATTTCATTTCACTCA
1 AGATAGTTTTTACTTAAAAC-AATATTT-GTCTCGCTTG
*
1770834 AGATTGTTTTT-CTTAAAACAATATTTGTCTCGCTTG
1 AGATAGTTTTTACTTAAAACAATATTTGTCTCGCTTG
* *
1770870 AGATAGTTTTTACTCAAAAGAATATTT
1 AGATAGTTTTTACTTAAAACAATATTT
1770897 ATTTCACTCA
Statistics
Matches: 75, Mismatches: 21, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
36 29 0.39
37 27 0.36
38 19 0.25
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (37 bp):
AGATAGTTTTTACTTAAAACAATATTTGTCTCGCTTG
Found at i:1770854 original size:74 final size:74
Alignment explanation
Indices: 1770685--1770917 Score: 355
Period size: 74 Copynumber: 3.1 Consensus size: 74
1770675 ATCTCACTTG
* * *
1770685 AGATTGTTTTTCTTAAAACAGA-CTTTGTCTCGCTTGAGACAG-TTTTACTCGAAAGGATTCATT
1 AGATTGTTTTTCTTAAAACA-ATATTTGTCTCGCTTGAGACAGTTTTTACTC-AAAAGA-ACATT
1770748 TCATTTCACTCA
63 TCATTTCACTCA
*
1770760 AGATTGTTTTTCTTAAAACAATATTTGTCTCGCTTGAGACAGTTTTTACTCAAACGAACATTTCA
1 AGATTGTTTTTCTTAAAACAATATTTGTCTCGCTTGAGACAGTTTTTACTCAAAAGAACATTTCA
1770825 TTTCACTCA
66 TTTCACTCA
* *
1770834 AGATTGTTTTTCTTAAAACAATATTTGTCTCGCTTGAGATAGTTTTTACTCAAAAGAATATTT-A
1 AGATTGTTTTTCTTAAAACAATATTTGTCTCGCTTGAGACAGTTTTTACTCAAAAGAACATTTCA
1770898 TTTCACTCA
66 TTTCACTCA
*
1770907 AGATTATTTTT
1 AGATTGTTTTT
1770918 AAAGAAGATT
Statistics
Matches: 149, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
73 20 0.13
74 77 0.52
75 44 0.30
76 8 0.05
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.42
Consensus pattern (74 bp):
AGATTGTTTTTCTTAAAACAATATTTGTCTCGCTTGAGACAGTTTTTACTCAAAAGAACATTTCA
TTTCACTCA
Found at i:1770917 original size:37 final size:37
Alignment explanation
Indices: 1770727--1770918 Score: 113
Period size: 37 Copynumber: 5.1 Consensus size: 37
1770717 CTTGAGACAG
* * *
1770727 TTTTACTCGAAAGGATTCATTTCATTTCACTCAAGATTGT
1 TTTTACTC-AAAAGAAT-ATTT-ATTTCACTCAAGATTAT
* * * * * ** *
1770767 TTTT-CTTAAAACAATATTTGTCTCGCTTGAGA-CAGT
1 TTTTACTCAAAAGAATATTTATTTCACTCAAGATTA-T
* * *
1770803 TTTTACTCAAACGAACATTTCATTTCACTCAAGATTGT
1 TTTTACTCAAAAGAATATTT-ATTTCACTCAAGATTAT
* * * * * **
1770841 TTTT-CTTAAAACAATATTTGTCTCGCTTGAGA-TAGT
1 TTTTACTCAAAAGAATATTTATTTCACTCAAGATTA-T
1770877 TTTTACTCAAAAGAATATTTATTTCACTCAAGATTAT
1 TTTTACTCAAAAGAATATTTATTTCACTCAAGATTAT
1770914 TTTTA
1 TTTTA
1770919 AAGAAGATTT
Statistics
Matches: 106, Mismatches: 39, Indels: 17
0.65 0.24 0.10
Matches are distributed among these distances:
35 1 0.01
36 26 0.25
37 53 0.50
38 20 0.19
39 2 0.02
40 4 0.04
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.43
Consensus pattern (37 bp):
TTTTACTCAAAAGAATATTTATTTCACTCAAGATTAT
Found at i:1770979 original size:39 final size:38
Alignment explanation
Indices: 1770921--1771015 Score: 104
Period size: 39 Copynumber: 2.5 Consensus size: 38
1770911 TATTTTTAAA
* **
1770921 GAAGATTTTATCTCACTTGAGATGGTTTCACTCGAAAC
1 GAAGATTTTGTCTCACTTGAGATAATTTCACTCGAAAC
* * *
1770959 TGAAGATTTTGTCTCGCTTGAGATAATTTCCCTTGAAAC
1 -GAAGATTTTGTCTCACTTGAGATAATTTCACTCGAAAC
*
1770998 -AA-ATTTTGTCTCCCTTGA
1 GAAGATTTTGTCTCACTTGA
1771016 AACTAGTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 15 0.31
37 2 0.04
39 32 0.65
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (38 bp):
GAAGATTTTGTCTCACTTGAGATAATTTCACTCGAAAC
Found at i:1771013 original size:21 final size:21
Alignment explanation
Indices: 1770987--1771180 Score: 103
Period size: 21 Copynumber: 10.4 Consensus size: 21
1770977 TGAGATAATT
1770987 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
* *
1771008 TCCCTTGAAACTAGTTTTGTC
1 TCCCTTGAAACAAATTTTGTC
*
1771029 TCCCTTGAGAC-AA---T-T-
1 TCCCTTGAAACAAATTTTGTC
*
1771044 TACCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
* * *
1771065 TCCCTTG----AGA--TAGTT
1 TCCCTTGAAACAAATTTTGTC
*
1771080 TCCCTTGAAACAAGTTTTGTC
1 TCCCTTGAAACAAATTTTGTC
* *
1771101 TCCCTTGAGAC--A----GTT
1 TCCCTTGAAACAAATTTTGTC
* *
1771116 TCACTTGAAACAAATTTTGTT
1 TCCCTTGAAACAAATTTTGTC
*
1771137 TCCCTTGAGAC-AA---T-T-
1 TCCCTTGAAACAAATTTTGTC
1771152 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
1771173 TCCCTTGA
1 TCCCTTGA
1771181 GATAGTTTCC
Statistics
Matches: 127, Mismatches: 22, Indels: 48
0.64 0.11 0.24
Matches are distributed among these distances:
15 40 0.31
16 6 0.05
17 5 0.04
19 3 0.02
20 5 0.04
21 68 0.54
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:1771036 original size:57 final size:56
Alignment explanation
Indices: 1770965--1771080 Score: 187
Period size: 57 Copynumber: 2.1 Consensus size: 56
1770955 AAACTGAAGA
* * *
1770965 TTTTGTCTCGCTTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAAACTAG
1 TTTTGTCTCCCTTGAGACAATTTACCTTGAAACAAATTTTGTCTCCCTTGAAA-TAG
*
1771022 TTTTGTCTCCCTTGAGACAATTTACCTTGAAACAAATTTTGTCTCCCTTGAGATAG
1 TTTTGTCTCCCTTGAGACAATTTACCTTGAAACAAATTTTGTCTCCCTTGAAATAG
1771078 TTT
1 TTT
1771081 CCCTTGAAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
56 6 0.11
57 49 0.89
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (56 bp):
TTTTGTCTCCCTTGAGACAATTTACCTTGAAACAAATTTTGTCTCCCTTGAAATAG
Found at i:1771155 original size:15 final size:15
Alignment explanation
Indices: 1771135--1771164 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1771125 ACAAATTTTG
*
1771135 TTTCCCTTGAGACAA
1 TTTCCCTTGAAACAA
1771150 TTTCCCTTGAAACAA
1 TTTCCCTTGAAACAA
1771165 ATTTTGTCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (15 bp):
TTTCCCTTGAAACAA
Found at i:1771561 original size:39 final size:39
Alignment explanation
Indices: 1771022--1771559 Score: 605
Period size: 39 Copynumber: 14.1 Consensus size: 39
1771012 TTGAAACTAG
* * * * *
1771022 TTTTGTCTCCCTTGAGACAATTTACCTTGAAAC--AA-A
1 TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA
* *
1771058 TTTTGTCTCCCTTGAGATAGTTTCCCTTGAAAC--AAG-
1 TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA
* * * *
1771094 TTTTGTCTCCCTTGAGACAGTTTCACTTGAAAC--AA-A
1 TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA
* * * * *
1771130 TTTTGTTTCCCTTGAGACAATTTCCCTTGAAAC--AA-A
1 TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA
* *
1771166 TTTTGTCTCCCTTGAGATAGTTTCCCTCGAAATAGAAGA
1 TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA
* * *
1771205 TTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAAAATA
1 TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA
* * * * *
1771244 TTTTATCACGCTTGAGAGAGTTTACCTCGAAACAGAATA
1 TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA
* * * *
1771283 TTTTGTCTCGCTTGAGATAGTTTCTCTTGAAACAAAATA
1 TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA
* * *
1771322 TTTTATCTCACTTGAGATAGTTTCACTCGAAACAGAAGA
1 TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA
* * *
1771361 TTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAAAATA
1 TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA
* *
1771400 TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA
1 TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA
1771439 TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA
1 TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA
* *
1771478 TTTTGTCTTGTTTGAGATAGTTTCCCTCGAAACAGAAGA
1 TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA
* * *
1771517 TTTTATCTCGCTTGAGATAGTTTCTCTCGAAACAAAAGA
1 TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA
1771556 TTTT
1 TTTT
1771560 ATAAGAAACT
Statistics
Matches: 440, Mismatches: 57, Indels: 7
0.87 0.11 0.01
Matches are distributed among these distances:
36 126 0.29
38 2 0.00
39 312 0.71
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (39 bp):
TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA
Found at i:1773454 original size:12 final size:12
Alignment explanation
Indices: 1773439--1773463 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1773429 TCTTTTAAAA
1773439 GAACATTTTTGG
1 GAACATTTTTGG
1773451 GAACATTTTTGG
1 GAACATTTTTGG
1773463 G
1 G
1773464 TGTTCGACCT
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:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (12 bp):
GAACATTTTTGG
Found at i:1775207 original size:30 final size:30
Alignment explanation
Indices: 1775147--1775207 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
1775137 TTTAAAAATT
* * *
1775147 AATTTGACATTTTTTCTTTATTTTGCTTTA
1 AATTAGACATTTTTTCTTTAGTTTACTTTA
*
1775177 AATTAGAC-TTTTTTCATTTAGTTTATTTTA
1 AATTAGACATTTTTTC-TTTAGTTTACTTTA
1775207 A
1 A
1775208 CCCTTTATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.25, C:0.08, G:0.07, T:0.61
Consensus pattern (30 bp):
AATTAGACATTTTTTCTTTAGTTTACTTTA
Found at i:1782895 original size:111 final size:111
Alignment explanation
Indices: 1782726--1782927 Score: 262
Period size: 111 Copynumber: 1.8 Consensus size: 111
1782716 AATGATGTTG
* * * * * * * *
1782726 CTGAGCAAACTGAAATTTTTGAGGGTATTCATGCTGTAGAGGAAGTAAGTACTGATATGGCCGA-
1 CTGAGCAAACTGAAAATATGGAGGATATTCATGATGTAGAGGAAGCAAGTACGGATATGGACGAG
*
1782790 GCCAGAGGAGGACCCTGTGATGGAAGAAAATATGGTGAATAGTGTGC
66 GCC-GAGGAGGACCCTGTAATGGAAGAAAATATGGTGAATAGTGTGC
* * * *
1782837 CTGAGCAAACTGAAAATATGGAGGATATTCATGATGTAGGGGCAGCAGGTACGGATATGGATGAG
1 CTGAGCAAACTGAAAATATGGAGGATATTCATGATGTAGAGGAAGCAAGTACGGATATGGACGAG
*
1782902 GCCGAGGAGGACCCTGTAATTGAAGA
66 GCCGAGGAGGACCCTGTAATGGAAGA
1782928 GGAAATGGAT
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
111 73 0.96
112 3 0.04
ACGTcount: A:0.32, C:0.13, G:0.33, T:0.22
Consensus pattern (111 bp):
CTGAGCAAACTGAAAATATGGAGGATATTCATGATGTAGAGGAAGCAAGTACGGATATGGACGAG
GCCGAGGAGGACCCTGTAATGGAAGAAAATATGGTGAATAGTGTGC
Found at i:1784142 original size:264 final size:257
Alignment explanation
Indices: 1783624--1784147 Score: 969
Period size: 264 Copynumber: 2.0 Consensus size: 257
1783614 GGAACATGAG
1783624 CACCGAAATTTTGAACTCTGACATCCCTTTCTCCTTTCGCATTCAATTGCACCATTATTGAAGTT
1 CACCGAAATTTTGAACTCTGACATCCCTTTCTCCTTTCGCATTCAATTGCACCATTATTGAAGTT
1783689 GTTACTTCTTATTTGCAAACGTCGGTTTGATGTAAATGACAGTGAAAACTTGCTGGAGTGGGCTT
66 GTTACTTCTTATTTGCAAACGTCGGTTTGATGTAAATGACAGTGAAAACTTGCTGGAGTGGGCTT
1783754 TCTGAAGGCACTGGAAGTTCAGTGTTAGTTTTTCCCAGCACCATTAAGTTTGCATTCTCCTCAAA
131 TCTGAAGGCACTGGAAGTTCAGTGTTAGTTTTTCCCAGCACCATTAAGTTTGCATTCTCCTCAAA
1783819 TTGGTTTAATGGCGCTCAAAAGAACATTTGAAGTGTAGTATCTCTCTGTAGCAATTAGGATT
196 TTGGTTTAATGGCGCTCAAAAGAACATTTGAAGTGTAGTATCTCTCTGTAGCAATTAGGATT
1783881 CACCGAAATTTTGAACTCTGACATCCCTTTCTCCTTTCGCATTCAATTGCACCATTATTGAAGTT
1 CACCGAAATTTTGAACTCTGACATCCCTTTCTCCTTTCGCATTCAATTGCACCATTATTGAAGTT
1783946 GTTACTTCTTATCTTTGCAAAACGTCGGTTTGATGTAAATGACAGTG-AAACTTGCTGGAGTGGG
66 GTTACTTCTTA--TTTGC-AAACGTCGGTTTGATGTAAATGACAGTGAAAACTTGCTGGAGTGGG
1784010 CTTTTCTGAAGGCACTGGAAGTTCAGTGTTTAGTTTTTCCCAGCACACCATTAAGTTTTGCATTC
128 C-TTTCTGAAGGCACTGGAAGTTCAGTG-TTAGTTTTTCCCAG--CACCATTAAG-TTTGCATTC
1784075 TCCTCAAATTGGTTTAATGGCGCTCAAAAGAACATTTGAAGTGTAGTATCTCTCTGTAGCAATTA
188 TCCTCAAATTGGTTTAATGGCGCTCAAAAGAACATTTGAAGTGTAGTATCTCTCTGTAGCAATTA
1784140 GGATT
253 GGATT
1784145 CAC
1 CAC
1784148 TTATCATTCC
Statistics
Matches: 259, Mismatches: 0, Indels: 9
0.97 0.00 0.03
Matches are distributed among these distances:
257 76 0.29
259 23 0.09
260 54 0.21
261 14 0.05
263 10 0.04
264 82 0.32
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (257 bp):
CACCGAAATTTTGAACTCTGACATCCCTTTCTCCTTTCGCATTCAATTGCACCATTATTGAAGTT
GTTACTTCTTATTTGCAAACGTCGGTTTGATGTAAATGACAGTGAAAACTTGCTGGAGTGGGCTT
TCTGAAGGCACTGGAAGTTCAGTGTTAGTTTTTCCCAGCACCATTAAGTTTGCATTCTCCTCAAA
TTGGTTTAATGGCGCTCAAAAGAACATTTGAAGTGTAGTATCTCTCTGTAGCAATTAGGATT
Found at i:1785392 original size:60 final size:60
Alignment explanation
Indices: 1785299--1785418 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
1785289 GTTCATAAGC
1785299 TTTTAGAATTCTTTATGCAAGTGTTCTTGTTCAAGATGTGGAATGTGCATTCAGGAATGT
1 TTTTAGAATTCTTTATGCAAGTGTTCTTGTTCAAGATGTGGAATGTGCATTCAGGAATGT
1785359 TTTTAGAATTCTTTATGCAAGTGTTCTTGTTCAAGATGTGGAATGTGCATTCAGGAATGT
1 TTTTAGAATTCTTTATGCAAGTGTTCTTGTTCAAGATGTGGAATGTGCATTCAGGAATGT
1785419 CTTCTTGTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (60 bp):
TTTTAGAATTCTTTATGCAAGTGTTCTTGTTCAAGATGTGGAATGTGCATTCAGGAATGT
Found at i:1793119 original size:18 final size:18
Alignment explanation
Indices: 1793096--1793130 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1793086 CACTTAAACT
1793096 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1793114 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1793131 CCTTAAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1793229 original size:21 final size:21
Alignment explanation
Indices: 1793182--1793230 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1793172 TACCGAAGTG
* *
1793182 CCACATATATGTTCCAAATGA
1 CCACATATATGTCCCAAAGGA
**
1793203 TTACATATATGTCCCAAAGGA
1 CCACATATATGTCCCAAAGGA
1793224 CCACATA
1 CCACATA
1793231 GAACCCTCGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (21 bp):
CCACATATATGTCCCAAAGGA
Found at i:1800246 original size:21 final size:21
Alignment explanation
Indices: 1800220--1800259 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1800210 CAGAACCCCA
*
1800220 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1800241 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1800260 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1800294 original size:20 final size:21
Alignment explanation
Indices: 1800240--1800302 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
1800230 GATTCCCCTG
1800240 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
1800264 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
1800284 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
1800303 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:1809755 original size:21 final size:21
Alignment explanation
Indices: 1809711--1809756 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1809701 CGAAGTATCG
* **
1809711 CATATATGTTCCAAAGGATTA
1 CATATATGTCCCAAAGGACCA
*
1809732 CATATATGTCCCGAAGGACCA
1 CATATATGTCCCAAAGGACCA
1809753 CATA
1 CATA
1809757 GAACCCTAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (21 bp):
CATATATGTCCCAAAGGACCA
Found at i:1820926 original size:289 final size:289
Alignment explanation
Indices: 1820407--1820992 Score: 1127
Period size: 289 Copynumber: 2.0 Consensus size: 289
1820397 ATTACATTTA
1820407 TTAATTAATATTTTATTACACTCAAAACTCATCCCATGTCACGTATCACTATCTAGTTGGAGGAT
1 TTAATTAATATTTTATTACACTCAAAACTCATCCCATGTCACGTATCACTATCTAGTTGGAGGAT
*
1820472 TAATTTTATTTTAATATAATATATTTATTTTTACCAATCAAAGAGTGACATGTGTCATCCTTTAA
66 TAACTTTATTTTAATATAATATATTTATTTTTACCAATCAAAGAGTGACATGTGTCATCCTTTAA
1820537 TTGAAAGAAAACAAAAGAAAGTAAATTATGTTAAAATTTATTTAAAAATATGATTAAATTGAGAG
131 TTGAAAGAAAACAAAAGAAAGTAAATTATGTTAAAATTTATTTAAAAATATGATTAAATTGAGAG
*
1820602 AATATGTAAATAATAGAGATTGAATGTGTGATTATACCTATTACTATCACGTCACATTAATTATT
196 AATATGTAAATAATAGAGATTAAATGTGTGATTATACCTATTACTATCACGTCACATTAATTATT
1820667 AACAACAATTAATCCGTAATTACTACGTC
261 AACAACAATTAATCCGTAATTACTACGTC
*
1820696 TTAATTAATATTTTATTACACTCAAAGCTCATCCCATGTCACGTATCACTATCTAGTTGGAGGAT
1 TTAATTAATATTTTATTACACTCAAAACTCATCCCATGTCACGTATCACTATCTAGTTGGAGGAT
*
1820761 TAACTTTATTTTAATATAATATATTTATTTTTACCAATCAAAGAGTGACATGTGTCATCCTTTAG
66 TAACTTTATTTTAATATAATATATTTATTTTTACCAATCAAAGAGTGACATGTGTCATCCTTTAA
*
1820826 TTGAAAGAAAACAAAAGAAAGTAAATTATGTTAAAATTTATTTAAAAATATGATTAAATTGTGAG
131 TTGAAAGAAAACAAAAGAAAGTAAATTATGTTAAAATTTATTTAAAAATATGATTAAATTGAGAG
1820891 AATATGTAAATAATAGAGATTAAATGTGTGATTATACCTATTACTATCACGTCACATTAATTATT
196 AATATGTAAATAATAGAGATTAAATGTGTGATTATACCTATTACTATCACGTCACATTAATTATT
1820956 AACAACAATTAATCCGTAATTACTACGTC
261 AACAACAATTAATCCGTAATTACTACGTC
1820985 TTAATTAA
1 TTAATTAA
1820993 ATAAAAACAA
Statistics
Matches: 292, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
289 292 1.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (289 bp):
TTAATTAATATTTTATTACACTCAAAACTCATCCCATGTCACGTATCACTATCTAGTTGGAGGAT
TAACTTTATTTTAATATAATATATTTATTTTTACCAATCAAAGAGTGACATGTGTCATCCTTTAA
TTGAAAGAAAACAAAAGAAAGTAAATTATGTTAAAATTTATTTAAAAATATGATTAAATTGAGAG
AATATGTAAATAATAGAGATTAAATGTGTGATTATACCTATTACTATCACGTCACATTAATTATT
AACAACAATTAATCCGTAATTACTACGTC
Found at i:1825417 original size:17 final size:18
Alignment explanation
Indices: 1825389--1825424 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1825379 AAAAAATTCA
1825389 AATAAGAAATATAATTAT
1 AATAAGAAATATAATTAT
*
1825407 AATAA-AAATATATTTAT
1 AATAAGAAATATAATTAT
1825424 A
1 A
1825425 TAATTCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AATAAGAAATATAATTAT
Found at i:1827391 original size:20 final size:21
Alignment explanation
Indices: 1827366--1827409 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
1827356 TAGTGAAAAA
1827366 TTACCTAAAACATT-ATTTTT
1 TTACCTAAAACATTAATTTTT
1827386 TTACCTAAAACATTAATTTTT
1 TTACCTAAAACATTAATTTTT
1827407 TTA
1 TTA
1827410 ACATTTCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (21 bp):
TTACCTAAAACATTAATTTTT
Found at i:1838140 original size:41 final size:42
Alignment explanation
Indices: 1838034--1838147 Score: 137
Period size: 41 Copynumber: 2.8 Consensus size: 42
1838024 TTTTTATCTA
1838034 ATTATTATTATTATTAAAATTATTA-TATTA-TTTATACTTTT
1 ATTATTATTATTATTAAAATTATTATTATTATTTTATAC-TTT
* *
1838075 ATTATTATTATTATTATATTTATTATTATTATTATTATA-TTT
1 ATTATTATTATTATTAAAATTATTATTATTATT-TTATACTTT
* * *
1838117 -TTATTATTAATAATAAAAATATTATTATTAT
1 ATTATTATTATTATTAAAATTATTATTATTAT
1838148 ATTTCTGGCC
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
41 49 0.78
42 8 0.13
43 1 0.02
44 5 0.08
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.61
Consensus pattern (42 bp):
ATTATTATTATTATTAAAATTATTATTATTATTTTATACTTT
Found at i:1838145 original size:3 final size:3
Alignment explanation
Indices: 1838034--1838125 Score: 95
Period size: 3 Copynumber: 31.3 Consensus size: 3
1838024 TTTTTATCTA
**
1838034 ATT ATT ATT ATT ATT AAA ATT ATT A-T ATT ATT -TAT ACTT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T A-TT ATT ATT
*
1838078 ATT ATT ATT ATT A-T ATTT ATT ATT ATT ATT ATT A-T ATT TTT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1838122 ATT A
1 ATT A
1838126 ATAATAAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 16
0.77 0.06 0.16
Matches are distributed among these distances:
2 9 0.12
3 62 0.83
4 3 0.04
5 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1847505 original size:23 final size:23
Alignment explanation
Indices: 1847479--1847529 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1847469 TTATACCTTA
1847479 CATTTTTTTTACATT-TTTACATT
1 CATTTTTTTT-CATTCTTTACATT
* *
1847502 CATTATTTTTCATTCTTTATATT
1 CATTTTTTTTCATTCTTTACATT
*
1847525 TATTT
1 CATTT
1847530 CATAAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.67
Consensus pattern (23 bp):
CATTTTTTTTCATTCTTTACATT
Found at i:1851097 original size:16 final size:15
Alignment explanation
Indices: 1851056--1851098 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1851046 AATAAAGGAA
*
1851056 AAAAATGAAGAAAAG
1 AAAAATGATGAAAAG
**
1851071 AAAAAAAATGAAAATG
1 AAAAATGATGAAAA-G
1851087 AAAAATGATGAA
1 AAAAATGATGAA
1851099 TATATATATA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (15 bp):
AAAAATGATGAAAAG
Found at i:1851105 original size:2 final size:2
Alignment explanation
Indices: 1851098--1851142 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1851088 AAAATGATGA
1851098 AT AT AT AT 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 AT AT AT AT
1851140 AT A
1 AT A
1851143 GAAAAAGAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1852894 original size:122 final size:123
Alignment explanation
Indices: 1852714--1853146 Score: 651
Period size: 122 Copynumber: 3.5 Consensus size: 123
1852704 TTCCGGAAAA
*
1852714 GTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
* *
1852779 ACCTTTTGCTCGATTCTATCAAAGAAAGGGATAGATCAGCATCAAAATTTCCAGAAGT
66 ACCTTTTGCTCGATTCTATCAAAGAAAGAGATAGATCAACATCAAAATTTCCAGAAGT
1852837 GTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
* **
1852901 ACCTTTTGCTCAATTCTATCAAAGAAAGAGATAGATCAACATCAAAATTTATAGAAGT
66 ACCTTTTGCTCGATTCTATCAAAGAAAGAGATAGATCAACATCAAAATTTCCAGAAGT
* * *
1852959 GTTCATAATGAGAAGAACTCATCTGAAG-ATGAAGAATAAGTTCATAATAAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
* * ** * *
1853023 ACCTTTTGCAT-GACTCTATCACAA-AAAGAGATATATCATTATCAACATTTCCAGAAAGA
66 ACCTTTTGC-TCGATTCTATCA-AAGAAAGAGATAGATCAACATCAAAATTTCCAG-AAGT
* *
1853082 GTTCATAATAAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1853146 A
66 A
1853147 TCTTACTTTA
Statistics
Matches: 283, Mismatches: 23, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
122 191 0.67
123 90 0.32
124 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (123 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
ACCTTTTGCTCGATTCTATCAAAGAAAGAGATAGATCAACATCAAAATTTCCAGAAGT
Found at i:1853618 original size:3 final size:3
Alignment explanation
Indices: 1853516--1853598 Score: 93
Period size: 3 Copynumber: 28.0 Consensus size: 3
1853506 TATCCATTTG
**
1853516 TTA TTA TTA TTA AAA TTA TTA TTA TTA -TA TTA TT- TATA CTT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA
1853560 TTA TTA TTA -TA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
1853599 ATAAAAAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
2 7 0.10
3 58 0.84
4 3 0.04
5 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1860043 original size:3 final size:3
Alignment explanation
Indices: 1860037--1860062 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1860027 TCTTCTCTGT
1860037 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
1860063 TGTTTCTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:1860116 original size:11 final size:11
Alignment explanation
Indices: 1860100--1860124 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1860090 TTGGGTGCCA
1860100 GTTTCTTCTCC
1 GTTTCTTCTCC
1860111 GTTTCTTCTCC
1 GTTTCTTCTCC
1860122 GTT
1 GTT
1860125 GGGTTACAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.32, G:0.12, T:0.56
Consensus pattern (11 bp):
GTTTCTTCTCC
Found at i:1868231 original size:15 final size:15
Alignment explanation
Indices: 1868211--1868241 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1868201 CAACAAATAG
1868211 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1868226 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1868241 A
1 A
1868242 TTTAGAATTT
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:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1874753 original size:29 final size:29
Alignment explanation
Indices: 1874711--1874790 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
1874701 AAACTAAATT
* *
1874711 GATGTTATTGCTTACATCAATTAGATGTA
1 GATGTCATTGCTTACATCAATTAGATGAA
1874740 GATGTCATTGCTTACATCAATTAGATGAA
1 GATGTCATTGCTTACATCAATTAGATGAA
*
1874769 GATGTCATTGCATACATCAATT
1 GATGTCATTGCTTACATCAATT
1874791 TAGTTAGGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (29 bp):
GATGTCATTGCTTACATCAATTAGATGAA
Found at i:1881538 original size:20 final size:20
Alignment explanation
Indices: 1881515--1881578 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
1881505 AAAATATAAT
*
1881515 ATTATCAGTGGAAATAAAAG
1 ATTATCAGTGGGAATAAAAG
*
1881535 ATTATTAGTGGGAATAAAAG
1 ATTATCAGTGGGAATAAAAG
*
1881555 ATTACCAGTGGGAATAAAAG
1 ATTATCAGTGGGAATAAAAG
1881575 ATTA
1 ATTA
1881579 CTAGGGAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.47, C:0.05, G:0.22, T:0.27
Consensus pattern (20 bp):
ATTATCAGTGGGAATAAAAG
Found at i:1881782 original size:35 final size:35
Alignment explanation
Indices: 1881738--1881810 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 35
1881728 GTTGAAAAAT
* *
1881738 ATTTATATATTTTCTTTTA-AAAATTTAAATTCATAAA
1 ATTTATATA-TAT-TTTTACAAAATTTAAAAT-ATAAA
1881775 ATTTATATATATTTTTACAAAATTTAAAATATAAA
1 ATTTATATATATTTTTACAAAATTTAAAATATAAA
1881810 A
1 A
1881811 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 11 0.33
36 13 0.39
37 9 0.27
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (35 bp):
ATTTATATATATTTTTACAAAATTTAAAATATAAA
Found at i:1889445 original size:25 final size:25
Alignment explanation
Indices: 1889417--1889479 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
1889407 TCACTTATCT
*
1889417 AAGAGAAGAATTACTCATCATCACA
1 AAGAGAAGAACTACTCATCATCACA
1889442 AAGAGAAGAACTACTCATCATCACA
1 AAGAGAAGAACTACTCATCATCACA
1889467 AAGAGAAGAACTA
1 AAGAGAAGAACTA
1889480 ATCTCGCTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (25 bp):
AAGAGAAGAACTACTCATCATCACA
Found at i:1904582 original size:20 final size:20
Alignment explanation
Indices: 1904553--1904611 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1904543 AATATCAAAT
1904553 AAAAATTAAATTTAAAAAAG
1 AAAAATTAAATTTAAAAAAG
* * *
1904573 AAAAAATAAA-TCAAAGAAGG
1 AAAAATTAAATTTAAA-AAAG
*
1904593 AAATATTAAATTTAAAAAA
1 AAAAATTAAATTTAAAAAA
1904612 AATGTTATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 4 0.13
20 22 0.73
21 4 0.13
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (20 bp):
AAAAATTAAATTTAAAAAAG
Found at i:1904688 original size:62 final size:59
Alignment explanation
Indices: 1904573--1904688 Score: 128
Period size: 62 Copynumber: 1.9 Consensus size: 59
1904563 TTTAAAAAAG
* * *
1904573 AAAAAATAAATCAAAGAAGGAAATATTAAATTTAAAAAAAATGTTATATAAAAACTATTTT
1 AAAAAATAAATCAAAGAAGAAAATATTAAATTTAAAAAAAA--TAATAAAAAAACTATTTT
1904634 AAAAAATAAAAT-AAATGAAGAAAATATTAAATTTCAGAAAAGAAA-AATAAAAAAA
1 AAAAAAT-AAATCAAA-GAAGAAAATATTAAATTT-A-AAAA-AAATAATAAAAAAA
1904689 TATAAAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
61 10 0.21
62 29 0.62
63 1 0.02
64 4 0.09
65 3 0.06
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.24
Consensus pattern (59 bp):
AAAAAATAAATCAAAGAAGAAAATATTAAATTTAAAAAAAATAATAAAAAAACTATTTT
Found at i:1904830 original size:18 final size:18
Alignment explanation
Indices: 1904809--1904851 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1904799 GTTATTTTTA
* *
1904809 AAATAAAATATAAGAATT
1 AAATAAAAGAAAAGAATT
*
1904827 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
1904845 AAATAAA
1 AAATAAA
1904852 TAATCTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:1905453 original size:12 final size:13
Alignment explanation
Indices: 1905436--1905464 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1905426 AAAGATAAAA
1905436 TAAAATAATAT-T
1 TAAAATAATATCT
1905448 TAAAATAATATCT
1 TAAAATAATATCT
1905461 TAAA
1 TAAA
1905465 TCCTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATAATATCT
Found at i:1906382 original size:200 final size:200
Alignment explanation
Indices: 1905752--1906515 Score: 978
Period size: 200 Copynumber: 3.8 Consensus size: 200
1905742 TCATCGTAGT
* * ** * * *
1905752 CAACCTTGGTATTCTTCTCGGTTTAAAGACCTCGGTTTAAAAATTCAACCGGAAAGTAGTTCCTT
1 CAACCTAGGTATTCTTCTTGACTTAAAGACCACAGTTT-AAAATTCAACCAGAAAGTAGTTCCTT
* ** * * * *
1905817 GATGCTACCATAAGGTTGATATG-TTATCGAGTTGAATGTAATCAAACTCGAATGTTTTTGTTGA
65 GTTGCTACCATGTGGTTGATATGCCT-TCGAGCTGAATGGAATCAAACTCGAAAG-TTTTGTTGA
* * *
1905881 CAGATAACCCTTCTCGTCTTGAGCTATGTTGTAAATTCGGTTGGGAGATAGTTCCTTGTTGCTAA
128 CAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTCGGCTGGGAGATAGTTCCTTGTTGCTAA
*
1905946 ATCGCAGC
193 ATAGCAGC
** * * *
1905954 CAACCTAGGTATTCTTCTTGACTTAAAGACCTTAGTTTAAACTTCAACCGGAAAGTAGTACCTTG
1 CAACCTAGGTATTCTTCTTGACTTAAAGACCACAGTTTAAAATTCAACCAGAAAGTAGTTCCTTG
*
1906019 TTGCTACCATGTGGTTGATATGCCTTCGAGCTGAATGGAATCGAAC-CGAAAGTTTTGTTGACAG
66 TTGCTACCATGTGGTTGATATGCCTTCGAGCTGAATGGAATCAAACTCGAAAGTTTTGTTGACAG
* * * * * *
1906083 ATAACCCTTTTCGCCTTGTGTTATTCTGTAAATTCGGCCGGGAGATAATT-CTTCGTTGCTAAAT
131 ATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTCGGCTGGGAGATAGTTCCTT-GTTGCTAAAT
*
1906147 TGCAGC
195 AGCAGC
* *
1906153 CAACCTAGGTATTCTTCTTGACTTAAAGACCACAGTTTAAAATTCAACCAGAAATTAGTTCCTCG
1 CAACCTAGGTATTCTTCTTGACTTAAAGACCACAGTTTAAAATTCAACCAGAAAGTAGTTCCTTG
* * * * *
1906218 TTGCTACCATGCGGTTGATATGCCTTCGAACTGAATGAAATCGAACTTGAAAGTTTTGTTGACAG
66 TTGCTACCATGTGGTTGATATGCCTTCGAGCTGAATGGAATCAAACTCGAAAGTTTTGTTGACAG
* * * * *
1906283 ATATCACTTTTCACCTTGAGCTATACTGTAAATTCGGCTGGGAGATAGTTCCTTGTTGCTAAATA
131 ATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTCGGCTGGGAGATAGTTCCTTGTTGCTAAATA
1906348 GCAGC
196 GCAGC
* * * * * *
1906353 TAAACTAGGTCTTCTTCTTGACTTAAAGACCACGGTTTAAACTTCAACCAGAAAGTAGTTCCTGG
1 CAACCTAGGTATTCTTCTTGACTTAAAGACCACAGTTTAAAATTCAACCAGAAAGTAGTTCCTTG
* *
1906418 TTGCTACCATGTGGTTGATATGCCTTCGAGCTGAATGGAATCAAACTCGAAAGTTTTTTTGATAG
66 TTGCTACCATGTGGTTGATATGCCTTCGAGCTGAATGGAATCAAACTCGAAAGTTTTGTTGACAG
* *
1906483 A-AAGTCCTTCTCGCCTTGAGTTATGCTGTAAAT
131 ATAA-CCCTTCTCGCCTTGAGCTATGCTGTAAAT
1906516 GGTTCCTCTA
Statistics
Matches: 490, Mismatches: 67, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
198 3 0.01
199 170 0.35
200 219 0.45
201 65 0.13
202 33 0.07
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (200 bp):
CAACCTAGGTATTCTTCTTGACTTAAAGACCACAGTTTAAAATTCAACCAGAAAGTAGTTCCTTG
TTGCTACCATGTGGTTGATATGCCTTCGAGCTGAATGGAATCAAACTCGAAAGTTTTGTTGACAG
ATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTCGGCTGGGAGATAGTTCCTTGTTGCTAAATA
GCAGC
Found at i:1906873 original size:86 final size:86
Alignment explanation
Indices: 1906577--1906862 Score: 392
Period size: 86 Copynumber: 3.3 Consensus size: 86
1906567 TTTCTTTAGT
** * * *
1906577 TGACTCCCCTTCACGGGAAAACCAAGTGGTATTTTCTTCAGGTGGTTCCCCTTCACAAGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCAAGTCTGAA
* * *
1906642 CCAGATGATATAATCTTTGGA
66 CCAGGTGAGATTATCTTTGGA
** * *
1906663 TGACTCCCCTTCTTGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTTGCATGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCAAGTCTGAA
*
1906728 CCAGGTGAGATTATCTTTAGA
66 CCAGGTGAGATTATCTTTGGA
** ***
1906749 TGACTCCCCTTCACGGGAATTTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGTGGGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCAAGTCTGAA
1906814 CCAGGTGAGATTATCTTTGGA
66 CCAGGTGAGATTATCTTTGGA
* *
1906835 TGACTCTCCTTCAGGGGAAAGTCATGTG
1 TGACTCCCCTTCACGGGAAAGTCATGTG
1906863 AGATGTTCTT
Statistics
Matches: 174, Mismatches: 26, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 174 1.00
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.33
Consensus pattern (86 bp):
TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCAAGTCTGAA
CCAGGTGAGATTATCTTTGGA
Found at i:1907710 original size:44 final size:45
Alignment explanation
Indices: 1907625--1907719 Score: 165
Period size: 45 Copynumber: 2.1 Consensus size: 45
1907615 TTCCTTCCTT
1907625 TTTTTTGCTGTTCGAAACAGTGAACAATTTGTTCATTTTTTTCGA
1 TTTTTTGCTGTTCGAAACAGTGAACAATTTGTTCATTTTTTTCGA
* *
1907670 TTTTTTGTTGTTTGAAACAGTGAACAATTTGTTC-TTTTTTTCGA
1 TTTTTTGCTGTTCGAAACAGTGAACAATTTGTTCATTTTTTTCGA
1907714 TTTTTT
1 TTTTTT
1907720 AAACAACGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 16 0.33
45 32 0.67
ACGTcount: A:0.20, C:0.11, G:0.15, T:0.55
Consensus pattern (45 bp):
TTTTTTGCTGTTCGAAACAGTGAACAATTTGTTCATTTTTTTCGA
Found at i:1912137 original size:15 final size:16
Alignment explanation
Indices: 1912102--1912136 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1912092 AAAAAAGAAG
1912102 AAAATATTAAATTAAA
1 AAAATATTAAATTAAA
1912118 AAAATATTAAATTAAA
1 AAAATATTAAATTAAA
1912134 AAA
1 AAA
1912137 TTCTTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATTAAATTAAA
Found at i:1912276 original size:20 final size:20
Alignment explanation
Indices: 1912253--1912291 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1912243 AAAACAAAAC
1912253 AAAA-CAAAATAATAATAAAT
1 AAAAGCAAAAT-ATAATAAAT
*
1912273 AAAAGGAAAATATAATAAA
1 AAAAGCAAAATATAATAAA
1912292 ATAATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAAGCAAAATATAATAAAT
Found at i:1912971 original size:12 final size:13
Alignment explanation
Indices: 1912954--1912982 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1912944 AAAGATAAAA
1912954 TAAAATAATATT-
1 TAAAATAATATTC
1912966 TAAAATAATATTC
1 TAAAATAATATTC
1912979 TAAA
1 TAAA
1912983 TCTTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATAATATTC
Found at i:1915375 original size:32 final size:32
Alignment explanation
Indices: 1915338--1915400 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1915328 TGTTTGGGAA
1915338 GTTGAGG-GATGAAATTCACAACTAAGCCATAC
1 GTTGAGGAG-TGAAATTCACAACTAAGCCATAC
1915370 GTTGAGGAGTGAAATTCACAACTAAGCCATA
1 GTTGAGGAGTGAAATTCACAACTAAGCCATA
1915401 AGCAAGAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 29 0.97
33 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.22
Consensus pattern (32 bp):
GTTGAGGAGTGAAATTCACAACTAAGCCATAC
Found at i:1920312 original size:55 final size:54
Alignment explanation
Indices: 1919899--1920310 Score: 444
Period size: 55 Copynumber: 7.6 Consensus size: 54
1919889 TGACGAGCCT
* * * **
1919899 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATAAAATGTGTAT
1 GCTCCCTATTCCTTCAGAG-AGTATAGGACTCGAACAATCTTCA-AAAACGGGTCC
* * * *
1919954 GCTCTCTATTCATTCAAAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAA-AAACGGGTCC
*
1920009 GCTCTCTATTCCTTCAGAGAGTATA-GATCTCGAACAATCTTCATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGA-CTCGAACAATCTTCA-AAAACGGGTCC
* * * *
1920064 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAGATGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAA-AAACGGGTCC
* *
1920119 GCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
1 GCTCCCTATTCC-TTCAGAGAGTATAGGACTCGAACAATCTTCA-AAAACGGGTCC
* * * * *
1920174 GCTCCCTA-TCCGTTCAGGGAGTATAAGACT----CTATCTTCAATAAACGTGTCT
1 GCTCCCTATTCC-TTCAGAGAGTATAGGACTCGAACAATCTTCAA-AAACGGGTCC
* * **
1920225 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAA-AAACGGGTCC
1920280 GCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTC
1920311 AATCTTCAAC
Statistics
Matches: 312, Mismatches: 31, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
50 1 0.00
51 40 0.13
52 3 0.01
54 6 0.02
55 258 0.83
56 4 0.01
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (54 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAAAAACGGGTCC
Found at i:1921557 original size:20 final size:20
Alignment explanation
Indices: 1921532--1921617 Score: 72
Period size: 20 Copynumber: 4.4 Consensus size: 20
1921522 ATATTTTTCA
1921532 TTTTTCTTCATTTTTCTCTT
1 TTTTTCTTCATTTTTCTCTT
** *
1921552 TTTTTCACCATTTTTCATTTT
1 TTTTTCTTCATTTTTC-TCTT
*
1921573 TTTTTC-TCA-TTTT-TCAT
1 TTTTTCTTCATTTTTCTCTT
* *
1921590 TTTCT-TTCATTTTTCCTCCT
1 TTTTTCTTCATTTTT-CTCTT
1921610 TTTTTCTT
1 TTTTTCTT
1921618 TTTCTTTTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
17 9 0.18
18 4 0.08
19 4 0.08
20 23 0.45
21 11 0.22
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTCTTCATTTTTCTCTT
Found at i:1921577 original size:66 final size:67
Alignment explanation
Indices: 1921478--1921620 Score: 154
Period size: 66 Copynumber: 2.2 Consensus size: 67
1921468 CCTCCTTTTA
* * *
1921478 TTTCTCTTTTTTTCATTTTTCTCTTTTTGTTTTTCAT-ACGTTTT-ATATT-TTTCATTTTTCTT
1 TTTCTCTTTTTTTCAATTTTCTCATTTTGTTTTTC-TCA-GTTTTCATATTCTTTCATTTTTCCT
1921540 CATT
64 CATT
* *
1921544 TTTCTCTTTTTTTCACCATTTT-TCATTTT-TTTTTCTCATTTTTCATTTTCTTTCATTTTTCCT
1 TTTCTCTTTTTTTCA--ATTTTCTCATTTTGTTTTTCTCAGTTTTCATATTCTTTCATTTTTCCT
*
1921607 CCTT
64 CATT
1921611 TTT-TCTTTTT
1 TTTCTCTTTTT
1921621 CTTTTTTTCT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
65 5 0.08
66 33 0.50
67 24 0.36
68 4 0.06
ACGTcount: A:0.09, C:0.18, G:0.01, T:0.71
Consensus pattern (67 bp):
TTTCTCTTTTTTTCAATTTTCTCATTTTGTTTTTCTCAGTTTTCATATTCTTTCATTTTTCCTCA
TT
Found at i:1921643 original size:57 final size:55
Alignment explanation
Indices: 1921524--1921655 Score: 144
Period size: 57 Copynumber: 2.3 Consensus size: 55
1921514 TACGTTTTAT
*
1921524 ATTTTTCATTTTTCTTCATTTTTCTCTTTTTTTCACCATTTTTCATTTTTTTTTCTC
1 ATTTTTCATTTTTCTTCATTTTTCTCCTTTTTT--CCATTTTTCATTTTTTTTTCTC
*
1921581 ATTTTTCA-TTTTCTTTCATTTTTCCTCCTTTTTT-C-TTTTTCTTTTTTTCTTTCTC
1 ATTTTTCATTTTTC-TTCATTTTT-CTCCTTTTTTCCATTTTTCATTTTTT-TTTCTC
* *
1921636 TTTTTTTTATTTCTTCTTCA
1 -ATTTTTCATTT-TTCTTCA
1921656 AGCGAAATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
54 12 0.18
55 7 0.11
56 11 0.17
57 23 0.35
58 12 0.18
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (55 bp):
ATTTTTCATTTTTCTTCATTTTTCTCCTTTTTTCCATTTTTCATTTTTTTTTCTC
Found at i:1921650 original size:13 final size:12
Alignment explanation
Indices: 1921562--1921650 Score: 52
Period size: 13 Copynumber: 6.7 Consensus size: 12
1921552 TTTTTCACCA
1921562 TTTTTCATTTTTT
1 TTTTTC-TTTTTT
* *
1921575 TTTCTCATTTTTC
1 TTTTTC-TTTTTT
*
1921588 ATTTTCTTTCATTT
1 TTTTTCTTT--TTT
* *
1921602 TTCCTCCTTTTTT
1 TT-TTTCTTTTTT
1921615 CTTTTTCTTTTTT
1 -TTTTTCTTTTTT
1921628 TCTTTCTCTTTTTT
1 T-TTT-TCTTTTTT
1921642 TTATTTCTT
1 TT-TTTCTT
1921651 CTTCAAGCGA
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
12 4 0.07
13 34 0.58
14 16 0.27
15 5 0.08
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:1921653 original size:22 final size:20
Alignment explanation
Indices: 1921614--1921650 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1921604 CCTCCTTTTT
*
1921614 TCTTTTTCTTTTTTTCTTTC
1 TCTTTTTCTTTATTTCTTTC
1921634 TCTTTTT-TTTATTTCTT
1 TCTTTTTCTTTATTTCTT
1921651 CTTCAAGCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (20 bp):
TCTTTTTCTTTATTTCTTTC
Found at i:1930575 original size:45 final size:45
Alignment explanation
Indices: 1930508--1930633 Score: 189
Period size: 45 Copynumber: 2.8 Consensus size: 45
1930498 TGTTATCCAC
* * *
1930508 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATACTTATTCA
1 AAAAATAAA-CCTAACCACATGATATCTAGTTCGCATACTTATTCA
* * *
1930554 AAAAATAAACCTAACCACATGATATCTAGTTCGCATGCTTGTTCG
1 AAAAATAAACCTAACCACATGATATCTAGTTCGCATACTTATTCA
1930599 AAAAATAAACCTAACCACATGATATCTAGTTCGCA
1 AAAAATAAACCTAACCACATGATATCTAGTTCGCA
1930634 AGCATTTATT
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
45 66 0.89
46 8 0.11
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.27
Consensus pattern (45 bp):
AAAAATAAACCTAACCACATGATATCTAGTTCGCATACTTATTCA
Found at i:1939511 original size:28 final size:27
Alignment explanation
Indices: 1939445--1939511 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
1939435 CATATAACTT
*
1939445 TTTTTTTCATTGCACAATCTCTCTTTC
1 TTTTTTTCTTTGCACAATCTCTCTTTC
* *
1939472 TTTATTTCCTTTGCACAAT-TTTGCTTCTC
1 TTT-TTTTCTTTGCACAATCTCT-CTT-TC
1939501 TTTTTTTCTTT
1 TTTTTTTCTTT
1939512 TTTTTCAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
27 5 0.15
28 23 0.70
29 5 0.15
ACGTcount: A:0.12, C:0.22, G:0.04, T:0.61
Consensus pattern (27 bp):
TTTTTTTCTTTGCACAATCTCTCTTTC
Found at i:1944446 original size:12 final size:12
Alignment explanation
Indices: 1944429--1944462 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1944419 GAAAATTAAG
1944429 AAAACTTAATGT
1 AAAACTTAATGT
*
1944441 AAAACTTGATGT
1 AAAACTTAATGT
1944453 AAAAC-TAATG
1 AAAACTTAATG
1944463 GCCCTAGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (12 bp):
AAAACTTAATGT
Found at i:1947781 original size:15 final size:15
Alignment explanation
Indices: 1947758--1947801 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
1947748 GTATCGAGAA
*
1947758 GCCAGTTTCGGACAT
1 GCCATTTTCGGACAT
1947773 GCCATTTTCGGACAT
1 GCCATTTTCGGACAT
1947788 GCCATTTTC-GACAT
1 GCCATTTTCGGACAT
1947802 AAAGAATTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 5 0.18
15 23 0.82
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.32
Consensus pattern (15 bp):
GCCATTTTCGGACAT
Found at i:1952092 original size:2 final size:2
Alignment explanation
Indices: 1952079--1952139 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
1952069 ATGGTAAAGA
* *
1952079 AT AT AC AT AT AT AT AT AT AT AT AT AC 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 AT AT AT AT
1952121 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1952140 ATTTTCATCA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1954087 original size:13 final size:12
Alignment explanation
Indices: 1954052--1954090 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1954042 CTACAACAGA
1954052 AAAAAGAAATCG
1 AAAAAGAAATCG
* *
1954064 AACATGAAATCTG
1 AAAAAGAAATC-G
1954077 AAAAAGAAATCG
1 AAAAAGAAATCG
1954089 AA
1 AA
1954091 CACGGATGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.13
Consensus pattern (12 bp):
AAAAAGAAATCG
Found at i:1959801 original size:27 final size:25
Alignment explanation
Indices: 1959771--1959848 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 25
1959761 AATGATTATG
*
1959771 ATACAATGGATATGTGAAATGACCAAA
1 ATACAATAG-TATG-GAAATGACCAAA
**
1959798 ATACCCCTAGTATGGAAATGACCAAA
1 ATA-CAATAGTATGGAAATGACCAAA
** *
1959824 ATACCTCTAGTATGCAAATGACCAA
1 ATA-CAATAGTATGGAAATGACCAA
1959849 GAATTTCACC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
26 35 0.78
27 7 0.16
28 3 0.07
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (25 bp):
ATACAATAGTATGGAAATGACCAAA
Found at i:1959819 original size:26 final size:26
Alignment explanation
Indices: 1959781--1959848 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
1959771 ATACAATGGA
1959781 TATGTGAAATGACCAAAATACCCCTAG
1 TATG-GAAATGACCAAAATACCCCTAG
*
1959808 TATGGAAATGACCAAAATACCTCTAG
1 TATGGAAATGACCAAAATACCCCTAG
*
1959834 TATGCAAATGACCAA
1 TATGGAAATGACCAA
1959849 GAATTTCACC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 35 0.90
27 4 0.10
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.22
Consensus pattern (26 bp):
TATGGAAATGACCAAAATACCCCTAG
Found at i:1965360 original size:178 final size:179
Alignment explanation
Indices: 1965054--1965411 Score: 709
Period size: 178 Copynumber: 2.0 Consensus size: 179
1965044 CTTCTTGGTA
1965054 ACATAGTTTTAAAGAGTACAAAATTAACTTACTTGTCTCTCGGTGTATTACTTCCTTGGAGTGAC
1 ACATAGTTTTAAAGAGTACAAAATTAACTTACTTGTCTCTCGGTGTATTACTTCCTTGGAGTGAC
1965119 TTGTGAGATTTCTTTCTTTTTATTATTTTTTTTCTTTTTCCGTTTTACATTGTTTTTTTAGTGTT
66 TTGTGAGATTTCTTTCTTTTTATTATTTTTTTTCTTTTTCCGTTTTACATTGTTTTTTTAGTGTT
1965184 GTGATTTTCAGAATATTCAAGCCAAAGATACCATGATCAAGCATTCCAT
131 GTGATTTTCAGAATATTCAAGCCAAAGATACCATGATCAAGCATTCCAT
1965233 ACATAG-TTTAAAGAGTACAAAATTAACTTACTTGTCTCTCGGTGTATTACTTCCTTGGAGTGAC
1 ACATAGTTTTAAAGAGTACAAAATTAACTTACTTGTCTCTCGGTGTATTACTTCCTTGGAGTGAC
1965297 TTGTGAGATTTCTTTCTTTTTATTATTTTTTTTCTTTTTCCGTTTTACATTGTTTTTTTAGTGTT
66 TTGTGAGATTTCTTTCTTTTTATTATTTTTTTTCTTTTTCCGTTTTACATTGTTTTTTTAGTGTT
1965362 GTGATTTTCAGAATATTCAAGCCAAAGATACCATGATCAAGCATTCCAT
131 GTGATTTTCAGAATATTCAAGCCAAAGATACCATGATCAAGCATTCCAT
1965411 A
1 A
1965412 ATTCTATGGT
Statistics
Matches: 179, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
178 173 0.97
179 6 0.03
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (179 bp):
ACATAGTTTTAAAGAGTACAAAATTAACTTACTTGTCTCTCGGTGTATTACTTCCTTGGAGTGAC
TTGTGAGATTTCTTTCTTTTTATTATTTTTTTTCTTTTTCCGTTTTACATTGTTTTTTTAGTGTT
GTGATTTTCAGAATATTCAAGCCAAAGATACCATGATCAAGCATTCCAT
Found at i:1967816 original size:20 final size:19
Alignment explanation
Indices: 1967789--1967866 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 19
1967779 TTTTCTGACT
*
1967789 CAAAGGATTGATCCCTTAG
1 CAAAGGATCGATCCCTTAG
*
1967808 CAGAAGGATCGATCCCTTCGAC
1 CA-AAGGATCGATCCCTT--AG
*
1967830 CAAAGGATTGATCCCCTT-G
1 CAAAGGATCGAT-CCCTTAG
*
1967849 AAAAAGGATCGATCCCTT
1 -CAAAGGATCGATCCCTT
1967867 GGATTCCAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
19 7 0.15
20 24 0.50
21 9 0.19
22 8 0.17
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (19 bp):
CAAAGGATCGATCCCTTAG
Found at i:1967856 original size:41 final size:41
Alignment explanation
Indices: 1967789--1967866 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
1967779 TTTTCTGACT
* *
1967789 CAAAGGATTGATCCCTTAGCAGAAGGATCGATCCCTTCGAC
1 CAAAGGATTGATCCCTTAGAAAAAGGATCGATCCCTTCGAC
1967830 CAAAGGATTGATCCCCTT-GAAAAAGGATCGATCCCTT
1 CAAAGGATTGAT-CCCTTAGAAAAAGGATCGATCCCTT
1967867 GGATTCCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
41 29 0.85
42 5 0.15
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (41 bp):
CAAAGGATTGATCCCTTAGAAAAAGGATCGATCCCTTCGAC
Found at i:1975100 original size:16 final size:16
Alignment explanation
Indices: 1975079--1975118 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
1975069 CCATTAAAAA
1975079 GCCCAAAAAAATAGAG
1 GCCCAAAAAAATAGAG
*
1975095 GCCC-AAAAAATAGGG
1 GCCCAAAAAAATAGAG
1975110 GCCCCAAAA
1 G-CCCAAAA
1975119 TCGAGTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 11 0.52
16 7 0.33
17 3 0.14
ACGTcount: A:0.50, C:0.25, G:0.20, T:0.05
Consensus pattern (16 bp):
GCCCAAAAAAATAGAG
Found at i:1976471 original size:91 final size:91
Alignment explanation
Indices: 1976316--1976497 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
1976306 GGGGGTCATT
1976316 TTTCAAAACAATTTTTGAAAGAGTTTGTTGACCATGTTTTATAATGTTTTGATATAAAAAATTAA
1 TTTCAAAACAATTTTTGAAAGAGTTTGTTGACCATGTTTTATAATGTTTTGATATAAAAAATTAA
1976381 GGTAAAATGTTTTCGGACTTGAATTG
66 GGTAAAATGTTTTCGGACTTGAATTG
1976407 TTTCAAAACAATTTTTGAAAGAGTTTGTTGACCATGTTTTATAATGTTTTGATATAAAAAATTAA
1 TTTCAAAACAATTTTTGAAAGAGTTTGTTGACCATGTTTTATAATGTTTTGATATAAAAAATTAA
1976472 GGTAAAATGTTTTCGGACTTGAATTG
66 GGTAAAATGTTTTCGGACTTGAATTG
1976498 AATTTGTCCA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (91 bp):
TTTCAAAACAATTTTTGAAAGAGTTTGTTGACCATGTTTTATAATGTTTTGATATAAAAAATTAA
GGTAAAATGTTTTCGGACTTGAATTG
Found at i:1980064 original size:181 final size:182
Alignment explanation
Indices: 1979747--1980102 Score: 556
Period size: 181 Copynumber: 2.0 Consensus size: 182
1979737 ATTCAATTTC
* *
1979747 TCAATAAAAAAGTGGGAGCTTTAATATTTTCCAAATTATATCATTTTTTCATTAAATGTTTTATT
1 TCAATAAAAAAGTGGGAGCTTTAATATTTTCCAAAATATATCATTTTTTCATTAAATATTTTATT
* * * *
1979812 AAGGGGGAGTTTTGCCGAAAATAATTTTTCAAATGTTTTGTTATATAAAAAATGAGAAGATTGTT
66 AAGGGGGAGTTTTGCCAAAAACAAATTTTCAAATGTTTTGTTATATAAAAAAGGAGAAGATTGTT
*
1979877 GAACCATGTTTTATAATGTTTTGATATAACAAAATAAGGCAAAATGGTTTTT
131 GAACCATGTTTTATAATGTTTTGATATAACAAAATAAGGAAAAATGGTTTTT
* *
1979929 TCAATGAAAAAG-GGGAGCTTTAATATTTTCCAAAATATATC-TCTTTTTTATTAAATATTTTAT
1 TCAATAAAAAAGTGGGAGCTTTAATATTTTCCAAAATATATCAT-TTTTTCATTAAATATTTTAT
* * *
1979992 TATGGGGGAGTTTTGCCAAAAACAAATTTTCAAATGTTTTGTTATATAAAAAAGGGGGAGATTAG
65 TAAGGGGGAGTTTTGCCAAAAACAAATTTTCAAATGTTTTGTTATATAAAAAAGGAGAAGATT-G
*
1980057 -TGAACCATGTTTTATAATGTTTTGATATAACAAATTAAGGAAAAAT
129 TTGAACCATGTTTTATAATGTTTTGATATAACAAAATAAGGAAAAAT
1980103 ATTTTTGGAC
Statistics
Matches: 159, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
180 1 0.01
181 146 0.92
182 12 0.08
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (182 bp):
TCAATAAAAAAGTGGGAGCTTTAATATTTTCCAAAATATATCATTTTTTCATTAAATATTTTATT
AAGGGGGAGTTTTGCCAAAAACAAATTTTCAAATGTTTTGTTATATAAAAAAGGAGAAGATTGTT
GAACCATGTTTTATAATGTTTTGATATAACAAAATAAGGAAAAATGGTTTTT
Found at i:1981408 original size:21 final size:21
Alignment explanation
Indices: 1981379--1981434 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
1981369 TTACAAAAGG
**
1981379 GATCGATCCCTTGAGGAAAAA
1 GATCGATCCCTTGACCAAAAA
* *
1981400 GATTGATCCCTTCACCAAAAA
1 GATCGATCCCTTGACCAAAAA
1981421 GATCGATCCCTTGA
1 GATCGATCCCTTGA
1981435 TAAAAATGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (21 bp):
GATCGATCCCTTGACCAAAAA
Found at i:1981432 original size:42 final size:42
Alignment explanation
Indices: 1981379--1981474 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
1981369 TTACAAAAGG
* *
1981379 GATCGATCCCTTGAGGAAAAA-GATTGATCCCTTCACCAAAAA
1 GATCGATCCCTTGA-GAAAAATGATAGATCCATTCACCAAAAA
* * * **
1981421 GATCGATCCCTTGATAAAAATGATAGATCTATTCTCTTAAAA
1 GATCGATCCCTTGAGAAAAATGATAGATCCATTCACCAAAAA
1981463 GATCGATCCCTT
1 GATCGATCCCTT
1981475 TCTTACAACG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
41 5 0.11
42 41 0.89
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (42 bp):
GATCGATCCCTTGAGAAAAATGATAGATCCATTCACCAAAAA
Found at i:1981440 original size:21 final size:21
Alignment explanation
Indices: 1981379--1981449 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
1981369 TTACAAAAGG
**
1981379 GATCGATCCCTTGAGGAAAAA
1 GATCGATCCCTTGACAAAAAA
* * *
1981400 GATTGATCCCTTCACCAAAAA
1 GATCGATCCCTTGACAAAAAA
* *
1981421 GATCGATCCCTTGATAAAAAT
1 GATCGATCCCTTGACAAAAAA
*
1981442 GATAGATC
1 GATCGATC
1981450 TATTCTCTTA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (21 bp):
GATCGATCCCTTGACAAAAAA
Found at i:1983086 original size:21 final size:20
Alignment explanation
Indices: 1983000--1983157 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
1982990 AAATGACCAA
**
1983000 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1983019 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1983039 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1983059 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1983080 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1983101 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
1983121 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1983142 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1983158 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1983186 original size:20 final size:20
Alignment explanation
Indices: 1983125--1983317 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1983115 GATTTTCCAG
* ** *
1983125 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1983145 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1983165 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1983185 AATCGCAACATGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1983205 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1983225 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1983245 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* ***
1983265 AATCGCAACG-ATAATATATAA
1 AATCGCAACGCGT-ATCCGT-A
1983286 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1983306 AATCGCAACGCG
1 AATCGCAACGCG
1983318 ATATTTAAAG
Statistics
Matches: 145, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.87
21 16 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1983735 original size:33 final size:33
Alignment explanation
Indices: 1983696--1983766 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1983686 TTCACTTAGA
1983696 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1983729 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1983762 TTTCA
1 TTTCA
1983767 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1983903 original size:41 final size:41
Alignment explanation
Indices: 1983845--1983922 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1983835 TTGCAGAAGA
*
1983845 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
1983886 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1983923 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:1983919 original size:21 final size:21
Alignment explanation
Indices: 1983846--1983921 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1983836 TGCAGAAGAG
*
1983846 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
1983867 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
1983887 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
1983908 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1983922 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:1983963 original size:19 final size:19
Alignment explanation
Indices: 1983941--1984068 Score: 78
Period size: 19 Copynumber: 7.1 Consensus size: 19
1983931 GAAACCAAAA
*
1983941 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1983960 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1983974 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1983993 TCACGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1984007 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
1984027 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
1984047 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1984067 TC
1 TC
1984069 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1983982 original size:14 final size:14
Alignment explanation
Indices: 1983963--1984019 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1983953 TTTCATTTCG
1983963 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1983977 CGTTGCGATTTTCATTTCA
1 CGTTGCGA--TTC---TCT
1983996 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1984010 CGTTGCGATT
1 CGTTGCGATT
1984020 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Done.