Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold324
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: 2336777
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 12 of 16
Found at i:1646191 original size:13 final size:13
Alignment explanation
Indices: 1646173--1646197 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1646163 TTATATAAAT
1646173 AAAATAAATTTAA
1 AAAATAAATTTAA
1646186 AAAATAAATTTA
1 AAAATAAATTTA
1646198 GATATATGGC
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATAAATTTAA
Found at i:1646449 original size:2 final size:2
Alignment explanation
Indices: 1646444--1646476 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1646434 TTCTTTTTTA
*
1646444 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1646477 ATCGATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1646680 original size:17 final size:18
Alignment explanation
Indices: 1646640--1646682 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1646630 CCGACCTTCC
*
1646640 ATAATTTTGAATTATTTG
1 ATAATTTTGAATTAATTG
*
1646658 AT-ATTTTTAATTAATT-
1 ATAATTTTGAATTAATTG
1646674 ATAATTTTG
1 ATAATTTTG
1646683 TTTTTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.10
17 17 0.81
18 2 0.10
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (18 bp):
ATAATTTTGAATTAATTG
Found at i:1646927 original size:27 final size:26
Alignment explanation
Indices: 1646889--1646952 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 26
1646879 TTATATAATT
1646889 ATATAATAAAAAATAATTA-AAATATA
1 ATATAATAAAAAAT-ATTATAAATATA
*
1646915 ATATAATATAAAAATATTATGAATATA
1 ATATAATA-AAAAATATTATAAATATA
1646942 ATATTAATAAA
1 ATA-TAATAAA
1646953 TTAAAATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 12 0.35
27 17 0.50
28 5 0.15
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (26 bp):
ATATAATAAAAAATATTATAAATATA
Found at i:1646939 original size:17 final size:17
Alignment explanation
Indices: 1646881--1646973 Score: 63
Period size: 16 Copynumber: 5.7 Consensus size: 17
1646871 TTTTAAATTT
* *
1646881 ATATAATTATATAATAAA
1 ATATAA-TATAAAATATA
*
1646899 AAATAAT-TAAAATATA
1 ATATAATATAAAATATA
1646915 ATATAATATAAAA-ATA
1 ATATAATATAAAATATA
* *
1646931 TTATGAATATAATAT-TA
1 ATAT-AATATAAAATATA
*
1646948 ATA-AAT-TAAAATTTA
1 ATATAATATAAAATATA
*
1646963 A-ATAACATAAA
1 ATATAATATAAA
1646974 TAATTAATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
14 6 0.10
15 8 0.13
16 23 0.38
17 18 0.30
18 5 0.08
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (17 bp):
ATATAATATAAAATATA
Found at i:1646955 original size:22 final size:20
Alignment explanation
Indices: 1646890--1646955 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
1646880 TATATAATTA
* * *
1646890 TATAATAAAAAATAATTAAAA
1 TATAATATAATATAA-TAAAT
*
1646911 TATAATATAATATAAAAATAT
1 TATAATATAATATAATAA-AT
1646932 TATGAATATAATATTAATAAAT
1 TAT-AATATAATA-TAATAAAT
1646954 TA
1 TA
1646956 AAATTTAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
20 2 0.05
21 17 0.46
22 13 0.35
23 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
TATAATATAATATAATAAAT
Found at i:1647056 original size:15 final size:14
Alignment explanation
Indices: 1646969--1647084 Score: 50
Period size: 14 Copynumber: 8.4 Consensus size: 14
1646959 TTTAAATAAC
1646969 ATAAATA-ATTAAT
1 ATAAATATATTAAT
*
1646982 ATATTAA-A-ATTTAT
1 ATA--AATATATTAAT
*
1646996 ATAAAAATATTAGAT
1 ATAAATATATTA-AT
* * *
1647011 CTTAAT-TATGAAT
1 ATAAATATATTAAT
1647024 AT-AATATATTAA-
1 ATAAATATATTAAT
*
1647036 AAAAATATATATAAT
1 ATAAATATAT-TAAT
* *
1647051 ATAAATATCTGAATT
1 ATAAATATATTAA-T
1647066 ATTAAATATA--AAT
1 A-TAAATATATTAAT
1647079 ATAAAT
1 ATAAAT
1647085 GGATAGGAGC
Statistics
Matches: 79, Mismatches: 13, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
12 11 0.14
13 21 0.27
14 23 0.29
15 17 0.22
16 7 0.09
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (14 bp):
ATAAATATATTAAT
Found at i:1647745 original size:4 final size:4
Alignment explanation
Indices: 1647736--1647761 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1647726 TTGCTTTGCC
1647736 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
1647762 CAAAACCAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:1648189 original size:21 final size:20
Alignment explanation
Indices: 1648155--1648195 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1648145 AAAAGATATG
* *
1648155 AATATAATTTTTTATTATTT
1 AATATAAATTTTTATAATTT
1648175 AATATTAAATTTTTATAATTT
1 AATA-TAAATTTTTATAATTT
1648196 TTTCATGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
AATATAAATTTTTATAATTT
Found at i:1648607 original size:20 final size:19
Alignment explanation
Indices: 1648556--1648632 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 19
1648546 AAATTTGAAC
*
1648556 TTAAATTTTATTTTTTAAAA
1 TTAAA-TTTAATTTTTAAAA
1648576 --AAATTTAAAATTTTTGAAAA
1 TTAAATTT--AATTTTT-AAAA
*
1648596 TTAAATTTAATTATTTAAAT
1 TTAAATTTAATT-TTTAAAA
*
1648616 TTAATTTTAATATTTTA
1 TTAAATTTAAT-TTTTA
1648633 TCATTCAGAC
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
17 3 0.06
18 3 0.06
19 6 0.13
20 25 0.53
21 4 0.09
22 6 0.13
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (19 bp):
TTAAATTTAATTTTTAAAA
Found at i:1651201 original size:181 final size:180
Alignment explanation
Indices: 1650842--1651201 Score: 446
Period size: 179 Copynumber: 2.0 Consensus size: 180
1650832 CATTCGGTTC
* * *
1650842 TTTCGAACTGTTGATTTTTTATTTTCGCAAGATGATCCCCTCGATCATATCACCAATTCCATCTC
1 TTTCGAACTGTTGATGTTTGATCTTCGCAAGATGATCCCCTCGATCATATCACCAATTCCA-CTC
* *
1650907 TCTTTTGGTCATTGTTTTTGCTTGTTGCAGTAAATTAATTAATTAATTTTAGCTGCAAAATTAAC
65 TCTTTTGATCATTGTTATTGCTTGTTGCAGTAAATTAATTAATTAA--TTAGCTGCAAAATTAAC
* * * * * *
1650972 ATTTAGTATATAATTATCTGTTAAGAGTAAACACTGTTCTGACTTTTTTCCTT
128 ATTTAGTAAAGAATTATATGCTAAAAGTAAACACTGTTCTAACTTTTTTCCTT
* * * *
1651025 TTTCG-ACTGTTGA-GTTTGATCTTCGCAAGATGATCCTCTTGTTCATATCGCCAATTCCA-TCT
1 TTTCGAACTGTTGATGTTTGATCTTCGCAAGATGATCCCCTCGATCATATCACCAATTCCACTCT
* *
1651087 CTTTTGATCATTGTTATTGTTTGTTGCAGTAAATTAATTAATT-A-TAGCTGC-AAATTAATATT
66 CTTTTGATCATTGTTATTGCTTGTTGCAGTAAATTAATTAATTAATTAGCTGCAAAATTAACATT
* * * *
1651149 TAGTAAAGAATTATAT-CTAAAATTATACACTGTTCTAACCTTTTCTCTTT
131 TAGTAAAGAATTATATGCTAAAAGTAAACACTGTTCTAA-CTTTTTTCCTT
1651199 TTT
1 TTT
1651202 TTTTTTTTCC
Statistics
Matches: 155, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
173 17 0.11
174 35 0.23
175 7 0.05
178 1 0.01
179 43 0.28
181 39 0.25
182 8 0.05
183 5 0.03
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (180 bp):
TTTCGAACTGTTGATGTTTGATCTTCGCAAGATGATCCCCTCGATCATATCACCAATTCCACTCT
CTTTTGATCATTGTTATTGCTTGTTGCAGTAAATTAATTAATTAATTAGCTGCAAAATTAACATT
TAGTAAAGAATTATATGCTAAAAGTAAACACTGTTCTAACTTTTTTCCTT
Found at i:1651622 original size:15 final size:16
Alignment explanation
Indices: 1651602--1651654 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
1651592 GGTTTTAATA
1651602 ATTA-TTTAAAATAAG
1 ATTATTTTAAAATAAG
1651617 ATTATTATTTTAAAATAAG
1 ---ATTATTTTAAAATAAG
1651636 ATTATTTTAAAAT-AG
1 ATTATTTTAAAATAAG
1651651 ATTA
1 ATTA
1651655 AAATAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.18
16 13 0.38
18 4 0.12
19 11 0.32
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
ATTATTTTAAAATAAG
Found at i:1651630 original size:19 final size:18
Alignment explanation
Indices: 1651602--1651654 Score: 76
Period size: 19 Copynumber: 3.1 Consensus size: 18
1651592 GGTTTTAATA
1651602 ATTATTTAAAATAAGATT
1 ATTATTTAAAATAAGATT
1651620 ATTATTTTAAAATAAGATT
1 ATTA-TTTAAAATAAGATT
1651639 A-T-TTTAAAAT-AGATT
1 ATTATTTAAAATAAGATT
1651654 A
1 A
1651655 AAATAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.18
16 8 0.24
18 5 0.15
19 15 0.44
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (18 bp):
ATTATTTAAAATAAGATT
Found at i:1652186 original size:21 final size:21
Alignment explanation
Indices: 1652162--1652209 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1652152 AATAGTTTTT
1652162 ATTTTTAATAAGATTTATT-AA
1 ATTTTTAATAA-ATTTATTAAA
* * *
1652183 ATTTATATTAATTTTATTAAA
1 ATTTTTAATAAATTTATTAAA
1652204 ATTTTT
1 ATTTTT
1652210 TATTAAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTTTTAATAAATTTATTAAA
Found at i:1652649 original size:19 final size:19
Alignment explanation
Indices: 1652622--1652675 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
1652612 TTATCTATTC
*
1652622 AAATTATTAAATGTAACAT
1 AAATTATTAAATATAACAT
* * *
1652641 AAGTTATTACATATATCAT
1 AAATTATTAAATATAACAT
1652660 AAATTATTAAATATAA
1 AAATTATTAAATATAA
1652676 AATGTTAATC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.39
Consensus pattern (19 bp):
AAATTATTAAATATAACAT
Found at i:1652718 original size:17 final size:17
Alignment explanation
Indices: 1652622--1652736 Score: 55
Period size: 17 Copynumber: 6.8 Consensus size: 17
1652612 TTATCTATTC
*
1652622 AAATTATTAAATGTAACAT
1 AAATTATTAAA--TAATAT
* *
1652641 AAGTTATTACATATATCAT
1 AAATTATTAAATA-AT-AT
1652660 AAATTATTAAAT-ATA-
1 AAATTATTAAATAATAT
* * *
1652675 AAA-TGTT-AATCAGAT
1 AAATTATTAAATAATAT
*
1652690 AAA-TATAAAAATAATAT
1 AAATTAT-TAAATAATAT
1652707 AAATTATTAAAT-ATATT
1 AAATTATTAAATAATA-T
1652724 AAAATT-TTAAATA
1 -AAATTATTAAATA
1652737 TAATTATATA
Statistics
Matches: 74, Mismatches: 12, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
13 3 0.04
14 5 0.07
15 8 0.11
16 4 0.05
17 24 0.32
18 9 0.12
19 21 0.28
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATTATTAAATAATAT
Found at i:1652750 original size:17 final size:18
Alignment explanation
Indices: 1652690--1652756 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 18
1652680 TTAATCAGAT
*
1652690 AAATA-TAAAAATAATATA
1 AAATATTAAATATAAT-TA
*
1652708 AATTATTAAATAT-ATTA
1 AAATATTAAATATAATTA
*
1652725 AAATTTTAAATATAATT-
1 AAATATTAAATATAATTA
*
1652742 ATATATTAAA-ATAAT
1 AAATATTAAATATAAT
1652757 ACGGTTATCT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
16 5 0.12
17 21 0.51
18 9 0.22
19 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATTAAATATAATTA
Found at i:1653420 original size:21 final size:21
Alignment explanation
Indices: 1653394--1653435 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1653384 TTAGTGAGGA
*
1653394 TTTATACTTTCTTTAAATTCT
1 TTTATACTTTATTTAAATTCT
1653415 TTTATACTTTATTTAAATTCT
1 TTTATACTTTATTTAAATTCT
1653436 CTTCTCTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATACTTTATTTAAATTCT
Found at i:1660758 original size:3 final size:3
Alignment explanation
Indices: 1660750--1660784 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1660740 AGCAACTTTT
1660750 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1660785 TCTTGGGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1664023 original size:9 final size:9
Alignment explanation
Indices: 1664009--1664033 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1663999 TCTGATCATA
1664009 TGAACCGAG
1 TGAACCGAG
1664018 TGAACCGAG
1 TGAACCGAG
1664027 TGAACCG
1 TGAACCG
1664034 GTTGTGTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.32, T:0.12
Consensus pattern (9 bp):
TGAACCGAG
Found at i:1664837 original size:20 final size:20
Alignment explanation
Indices: 1664812--1664852 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1664802 GAGCTTTATA
1664812 TAACTTTTTATGTTCATGTG
1 TAACTTTTTATGTTCATGTG
1664832 TAACTTTTTATGTTCATGTG
1 TAACTTTTTATGTTCATGTG
1664852 T
1 T
1664853 GCATGTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.56
Consensus pattern (20 bp):
TAACTTTTTATGTTCATGTG
Found at i:1665112 original size:17 final size:17
Alignment explanation
Indices: 1665092--1665135 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1665082 AGTATTTAAA
1665092 AAAATAATAAAAAACTT-
1 AAAA-AATAAAAAACTTG
* *
1665109 AAAAAATGAAGAACTTG
1 AAAAAATAAAAAACTTG
1665126 AAAAAATAAA
1 AAAAAATAAA
1665136 GTGTCTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.18
Consensus pattern (17 bp):
AAAAAATAAAAAACTTG
Found at i:1665173 original size:20 final size:20
Alignment explanation
Indices: 1665150--1665212 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
1665140 CTCAAAAGGC
1665150 AATGAAAAGTCTAAAAAAAT
1 AATGAAAAGTCTAAAAAAAT
1665170 AATGACAAA-TC-AAAAAAATT
1 AATGA-AAAGTCTAAAAAAA-T
* *
1665190 AAT-AACAAGCCTCAAAAAAT
1 AATGAA-AAGTCTAAAAAAAT
1665210 AAT
1 AAT
1665213 AATAAGCCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
18 1 0.03
19 10 0.28
20 16 0.44
21 9 0.25
ACGTcount: A:0.63, C:0.11, G:0.06, T:0.19
Consensus pattern (20 bp):
AATGAAAAGTCTAAAAAAAT
Found at i:1665213 original size:20 final size:21
Alignment explanation
Indices: 1665182--1665226 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
1665172 TGACAAATCA
1665182 AAAAAATTAATAACAAGCCTC
1 AAAAAATTAATAACAAGCCTC
* *
1665203 AAAAAA-TAATAATAAGCCTG
1 AAAAAATTAATAACAAGCCTC
1665223 AAAA
1 AAAA
1665227 GGCCAAGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.62, C:0.13, G:0.07, T:0.18
Consensus pattern (21 bp):
AAAAAATTAATAACAAGCCTC
Found at i:1668845 original size:12 final size:12
Alignment explanation
Indices: 1668820--1668861 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1668810 ATTTCATGTG
**
1668820 TATATATAAATA
1 TATATATATTTA
1668832 TATATATATTTA
1 TATATATATTTA
*
1668844 TATTTATATTTA
1 TATATATATTTA
1668856 TATATA
1 TATATA
1668862 CACACCATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATATATATTTA
Found at i:1669359 original size:13 final size:11
Alignment explanation
Indices: 1669332--1669356 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1669322 AATAATTAAG
1669332 TATTATAAATA
1 TATTATAAATA
1669343 TATTATAAATA
1 TATTATAAATA
1669354 TAT
1 TAT
1669357 ATTTATTTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TATTATAAATA
Found at i:1669881 original size:2 final size:2
Alignment explanation
Indices: 1669874--1669904 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1669864 ATTACCACAA
1669874 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 A
1669905 ATTACTCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1670330 original size:19 final size:19
Alignment explanation
Indices: 1670305--1670348 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1670295 AATATTTAAA
*
1670305 AAAATTTAAATAAAAATAT
1 AAAATTTAAACAAAAATAT
*
1670324 TAAATTTAAACAAAAATAT
1 AAAATTTAAACAAAAATAT
1670343 AAAATT
1 AAAATT
1670349 CTTTTTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATTTAAACAAAAATAT
Found at i:1670436 original size:26 final size:26
Alignment explanation
Indices: 1670389--1670444 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
1670379 TTCAGCACTC
*
1670389 ATTTTTAATTATATAATATATAT-TA
1 ATTTTAAATTATATAATATATATGTA
1670414 ATTTTAAATTTATATAA-ATTATATGTA
1 ATTTTAAA-TTATATAATA-TATATGTA
1670441 ATTT
1 ATTT
1670445 ATATCTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 8 0.30
26 13 0.48
27 6 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
ATTTTAAATTATATAATATATATGTA
Found at i:1672721 original size:29 final size:29
Alignment explanation
Indices: 1672685--1672778 Score: 108
Period size: 29 Copynumber: 3.3 Consensus size: 29
1672675 TCTTAATTAC
1672685 ATAATATAAATATAATA-TAAAATATAAT
1 ATAATATAAATATAATATTAAAATATAAT
* *
1672713 ATAGATATATATAT-ATATTAAAAT-TTAT
1 ATA-ATATAAATATAATATTAAAATATAAT
*
1672741 ATAATATTAATTATAATATTAAAATAT-AT
1 ATAATA-TAAATATAATATTAAAATATAAT
1672770 A-AATATAAA
1 ATAATATAAA
1672779 ATATGATTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
27 6 0.11
28 21 0.38
29 28 0.50
30 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (29 bp):
ATAATATAAATATAATATTAAAATATAAT
Found at i:1672758 original size:45 final size:44
Alignment explanation
Indices: 1672694--1672780 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 44
1672684 CATAATATAA
* *
1672694 ATATAATATAAAATATAATA-TAGATATATATATATATTAAAATTT
1 ATATAATATAAAATATAATATTA-AAATATATAAATA-TAAAATTT
* *
1672739 ATATAATATTAATTATAATATTAAAATATATAAATATAAAAT
1 ATATAATATAAAATATAATATTAAAATATATAAATATAAAAT
1672781 ATGATTAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 6 0.16
45 29 0.78
46 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (44 bp):
ATATAATATAAAATATAATATTAAAATATATAAATATAAAATTT
Found at i:1673519 original size:41 final size:42
Alignment explanation
Indices: 1673443--1673521 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 42
1673433 AAATTACCAC
* * **
1673443 ATGTTTTTTTAATTAATTTTTTTATAGTATCTTAATAAATAT
1 ATGTTATTTTAATTAATTTTCTTATAAAATCTTAATAAATAT
1673485 ATGTTATTTT-ATTAATTTTACTTATAAAAT-TTAATAA
1 ATGTTATTTTAATTAATTTT-CTTATAAAATCTTAATAA
1673522 TTCAACTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 16 0.50
42 16 0.50
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.57
Consensus pattern (42 bp):
ATGTTATTTTAATTAATTTTCTTATAAAATCTTAATAAATAT
Found at i:1675280 original size:11 final size:12
Alignment explanation
Indices: 1675260--1675301 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1675250 TATCTGTGTA
1675260 TTTATATTAT-T
1 TTTATATTATAT
*
1675271 TTTATCTTATAT
1 TTTATATTATAT
1675283 TTT-TAATTATAT
1 TTTAT-ATTATAT
1675295 TTTATAT
1 TTTATAT
1675302 AACATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 10 0.38
12 15 0.58
13 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:1676093 original size:4 final size:4
Alignment explanation
Indices: 1676076--1676105 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1676066 TGATTATGTA
*
1676076 TATG TATA TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
1676106 GTAAGAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:1676661 original size:12 final size:12
Alignment explanation
Indices: 1676643--1676696 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
1676633 ATACATAATT
*
1676643 AGAGAGGGCGAG
1 AGAGAGGGAGAG
*
1676655 GGAGAGGGAGAG
1 AGAGAGGGAGAG
*
1676667 AGAGAGAGAGAG
1 AGAGAGGGAGAG
*
1676679 AGAGAGAGAGAG
1 AGAGAGGGAGAG
1676691 AGAGAG
1 AGAGAG
1676697 AGAAGGGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.43, C:0.02, G:0.56, T:0.00
Consensus pattern (12 bp):
AGAGAGGGAGAG
Found at i:1676667 original size:2 final size:2
Alignment explanation
Indices: 1676656--1676699 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1676646 GAGGGCGAGG
*
1676656 GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1676698 GA
1 GA
1676700 AGGGAATTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1677041 original size:27 final size:27
Alignment explanation
Indices: 1677006--1677077 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
1676996 GGATTACACG
*
1677006 TTTAAATTATTTATTTGATTTAATAAA
1 TTTAAATTATTTATTTAATTTAATAAA
*
1677033 TTTTAATTATTTATTTAATTTAATAAA
1 TTTAAATTATTTATTTAATTTAATAAA
*
1677060 TTTAAATTATTAATTTAA
1 TTTAAATTATTTATTTAA
1677078 AAAAATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (27 bp):
TTTAAATTATTTATTTAATTTAATAAA
Found at i:1677072 original size:22 final size:24
Alignment explanation
Indices: 1677014--1677087 Score: 80
Period size: 27 Copynumber: 3.0 Consensus size: 24
1677004 CGTTTAAATT
*
1677014 ATTTATTTGATTTAATAAATTTTAA
1 ATTTATTTAATTTAATAAA-TTTAA
1677039 TTATTTATTTAATTTAATAAATTTAA
1 --ATTTATTTAATTTAATAAATTTAA
* *
1677065 A-TTA-TTAATTTAAAAAAATTAA
1 ATTTATTTAATTTAATAAATTTAA
1677087 A
1 A
1677088 ATTTTATGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
22 17 0.39
23 3 0.07
24 1 0.02
26 5 0.11
27 18 0.41
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (24 bp):
ATTTATTTAATTTAATAAATTTAA
Found at i:1677196 original size:22 final size:23
Alignment explanation
Indices: 1677169--1677211 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1677159 TAAATTTATT
1677169 TATAAAAATATATTT-ATATTAA
1 TATAAAAATATATTTAATATTAA
* *
1677191 TATAAAATTATTTTTAATATT
1 TATAAAAATATATTTAATATT
1677212 TTTTAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATAAAAATATATTTAATATTAA
Found at i:1677202 original size:20 final size:18
Alignment explanation
Indices: 1677162--1677203 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 18
1677152 TTTTATTTAA
1677162 ATTTATTTATAAAAATAT
1 ATTTATTTATAAAAATAT
1677180 ATTTATATTAATATAAAAT-T
1 ATTTAT-TT-ATA-AAAATAT
1677200 ATTT
1 ATTT
1677204 TTAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.29
19 2 0.10
20 8 0.38
21 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTATTTATAAAAATAT
Found at i:1678833 original size:16 final size:16
Alignment explanation
Indices: 1678814--1678846 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1678804 AGTATATTAA
1678814 AAATTAATT-AATAAAT
1 AAATT-ATTAAATAAAT
1678830 AAATTATTAAATAAAT
1 AAATTATTAAATAAAT
1678846 A
1 A
1678847 TGTGTCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATTATTAAATAAAT
Found at i:1679099 original size:3 final size:3
Alignment explanation
Indices: 1679091--1679115 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1679081 TTTTTTAATA
1679091 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1679116 TATGCATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1679678 original size:8 final size:8
Alignment explanation
Indices: 1679667--1679691 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1679657 TAAGTAGATT
1679667 TATGTATA
1 TATGTATA
1679675 TATGTATA
1 TATGTATA
1679683 TATGTATA
1 TATGTATA
1679691 T
1 T
1679692 GATAACTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (8 bp):
TATGTATA
Found at i:1680512 original size:16 final size:15
Alignment explanation
Indices: 1680477--1680535 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
1680467 GTTTAAATCG
*
1680477 AATTATTTTATATTT
1 AATTATTTTAAATTT
1680492 GAATTATTTTAAATTAT
1 -AATTATTTTAAATT-T
* * *
1680509 AATTTTTTTGAGTTT
1 AATTATTTTAAATTT
1680524 AGATTATTTTAA
1 A-ATTATTTTAA
1680536 TTAGAGATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 2 0.06
16 32 0.91
17 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (15 bp):
AATTATTTTAAATTT
Found at i:1680554 original size:31 final size:32
Alignment explanation
Indices: 1680494--1680554 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1680484 TTATATTTGA
* *
1680494 ATTATTTTAAATTATAATTTTTTTGAGTTTAG
1 ATTATTTTAAATTAGAATTATTTTGAGTTTAG
1680526 ATTATTTT-AATTAGAGATTATTTT-AGTTT
1 ATTATTTTAAATTAGA-ATTATTTTGAGTTT
1680555 TAAGAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (32 bp):
ATTATTTTAAATTAGAATTATTTTGAGTTTAG
Found at i:1681724 original size:2 final size:2
Alignment explanation
Indices: 1681711--1681742 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1681701 AGAATCTATT
*
1681711 TA TA TT 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 TA
1681743 ATAAAGAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1686870 original size:2 final size:2
Alignment explanation
Indices: 1686863--1686892 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1686853 GTGTTTTGAA
1686863 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
1686893 TAGGCCAAAC
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):
AT
Found at i:1690299 original size:31 final size:32
Alignment explanation
Indices: 1690258--1690318 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
1690248 AAAATTATAA
1690258 TATTAAATATATAAAT-ATTAATATTTATATT
1 TATTAAATATATAAATAATTAATATTTATATT
* * *
1690289 TATTTAATATATTAATAATTTATATTTATA
1 TATTAAATATATAAATAATTAATATTTATA
1690319 AATTTTGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
TATTAAATATATAAATAATTAATATTTATATT
Found at i:1690662 original size:14 final size:12
Alignment explanation
Indices: 1690643--1690681 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
1690633 TATAATTTAA
1690643 TAAAATTAATTCT
1 TAAAATTAATT-T
1690656 TATAAATTAATTT
1 TA-AAATTAATTT
*
1690669 TAAATTTAATTT
1 TAAAATTAATTT
1690681 T
1 T
1690682 TAATAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 10 0.42
13 5 0.21
14 9 0.38
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (12 bp):
TAAAATTAATTT
Found at i:1690704 original size:30 final size:30
Alignment explanation
Indices: 1690658--1690754 Score: 79
Period size: 35 Copynumber: 3.0 Consensus size: 30
1690648 TTAATTCTTA
1690658 TAAATTAATTTTAAATTTAATTTTTAATAATT
1 TAAATTAA--TTAAATTTAATTTTTAATAATT
*
1690690 TAAATTAATTAAATTATTTATATAATTTAATAATT
1 TAAATTAATT-AA--ATTTA-AT-TTTTAATAATT
* * *
1690725 TTAATTCATATAAA-TAAATTTTTAATAATT
1 TAAATTAAT-TAAATTTAATTTTTAATAATT
1690755 GGTTAATAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
30 12 0.22
31 4 0.07
32 10 0.19
33 6 0.11
34 2 0.04
35 19 0.35
36 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (30 bp):
TAAATTAATTAAATTTAATTTTTAATAATT
Found at i:1690727 original size:18 final size:18
Alignment explanation
Indices: 1690658--1690730 Score: 66
Period size: 17 Copynumber: 4.3 Consensus size: 18
1690648 TTAATTCTTA
*
1690658 TAAATTAATTTTA-AATT
1 TAAATTAATTTAATAATT
1690675 T-AATT--TTTAATAATT
1 TAAATTAATTTAATAATT
* *
1690690 TAAATTAATTAAATTATT
1 TAAATTAATTTAATAATT
*
1690708 TATA-TAATTTAATAATT
1 TAAATTAATTTAATAATT
*
1690725 TTAATT
1 TAAATT
1690731 CATATAAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
14 4 0.09
15 5 0.12
16 8 0.19
17 14 0.33
18 12 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAAATTAATTTAATAATT
Found at i:1690728 original size:27 final size:29
Alignment explanation
Indices: 1690663--1690728 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 29
1690653 TCTTATAAAT
*
1690663 TAATTTTAAATTTAATTTTTAATAATTTA
1 TAATTTTAAATTTAATTTATAATAATTTA
1690692 -AATTAATTAAA-TT-ATTTAT-ATAATTTAA
1 TAATT--TTAAATTTAATTTATAATAATTT-A
1690720 TAATTTTAA
1 TAATTTTAA
1690729 TTCATATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
27 11 0.34
28 10 0.31
29 6 0.19
30 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
TAATTTTAAATTTAATTTATAATAATTTA
Found at i:1690730 original size:26 final size:26
Alignment explanation
Indices: 1690626--1690730 Score: 92
Period size: 26 Copynumber: 4.1 Consensus size: 26
1690616 ACAAAATAAG
* *
1690626 TTATTCATATAATTTAATAAAATTAA
1 TTATTTATATAATTTAATAAATTTAA
* *
1690652 TTCTTATAAATTAATTT--TAAATTTAA
1 TTATT-TATA-TAATTTAATAAATTTAA
* *
1690678 TT-TTTA-ATAATTTAAATTAATTAAA
1 TTATTTATATAATTT-AATAAATTTAA
*
1690703 TTATTTATATAATTTAATAATTTTAA
1 TTATTTATATAATTTAATAAATTTAA
1690729 TT
1 TT
1690731 CATATAAATA
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
22 6 0.10
23 1 0.02
24 2 0.03
25 11 0.17
26 28 0.44
27 9 0.14
28 6 0.10
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
TTATTTATATAATTTAATAAATTTAA
Found at i:1690741 original size:27 final size:26
Alignment explanation
Indices: 1690634--1690741 Score: 80
Period size: 26 Copynumber: 4.2 Consensus size: 26
1690624 AGTTATTCAT
* *
1690634 ATAATTTAATAAAATTAATTCTTATAA
1 ATAATTTAATAAATTTAATT-ATATAA
*
1690661 ATTAATTT--TAAATTTAATT-T-TTA
1 A-TAATTTAATAAATTTAATTATATAA
* * * *
1690684 ATAATTTAAATTAATTAAATTATTTAT
1 ATAATTT-AATAAATTTAATTATATAA
*
1690711 ATAATTTAATAATTTTAATTCATATAA
1 ATAATTTAATAAATTTAATT-ATATAA
1690738 ATAA
1 ATAA
1690742 ATTTTTAATA
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
22 6 0.10
23 3 0.05
24 1 0.02
25 9 0.14
26 21 0.33
27 17 0.27
28 6 0.10
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
ATAATTTAATAAATTTAATTATATAA
Found at i:1691570 original size:18 final size:18
Alignment explanation
Indices: 1691536--1691570 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1691526 TTATTGGTAG
*
1691536 TTTTATTTTATATATATT
1 TTTTATTTTATAAATATT
*
1691554 TTTTATTTTTTAAATAT
1 TTTTATTTTATAAATAT
1691571 ATTATAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATTTTATAAATATT
Found at i:1691592 original size:13 final size:13
Alignment explanation
Indices: 1691576--1691609 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1691566 AATATATTAT
1691576 AATATAAAT-ATAA
1 AATA-AAATCATAA
1691589 AATAAAATCATAA
1 AATAAAATCATAA
1691602 AATAAAAT
1 AATAAAAT
1691610 TTTATAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (13 bp):
AATAAAATCATAA
Found at i:1692998 original size:60 final size:60
Alignment explanation
Indices: 1692896--1693014 Score: 188
Period size: 60 Copynumber: 2.0 Consensus size: 60
1692886 AACTATAAGT
*
1692896 AATCAAAGAACTAACTGAGAAAATGACAGTTTATGTTTTGTAATAATCAAAAACAACAAG
1 AATCAAAGAACTAAATGAGAAAATGACAGTTTATGTTTTGTAATAATCAAAAACAACAAG
*
1692956 AATCAAAGAACTGATAAT-AGAAAATGACAGTTTATG-TTTGTAATAATCCAAAACAACAA
1 AATCAAAGAACT-A-AATGAGAAAATGACAGTTTATGTTTTGTAATAATCAAAAACAACAA
1693015 AACATTTTGA
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
60 34 0.62
61 19 0.35
62 2 0.04
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (60 bp):
AATCAAAGAACTAAATGAGAAAATGACAGTTTATGTTTTGTAATAATCAAAAACAACAAG
Found at i:1694816 original size:2 final size:2
Alignment explanation
Indices: 1694811--1694851 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1694801 TACAGCTAAT
1694811 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1694852 TATCAGCACC
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:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1705964 original size:16 final size:16
Alignment explanation
Indices: 1705925--1705966 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1705915 TAAGTTTTCA
* *
1705925 TTATAATTTT-TAATT
1 TTATATTTTTATAAAT
*
1705940 TTATTTTTTTATAAAT
1 TTATATTTTTATAAAT
1705956 TTATATTTTTA
1 TTATATTTTTA
1705967 ATTTATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATATTTTTATAAAT
Found at i:1706795 original size:22 final size:22
Alignment explanation
Indices: 1706767--1706808 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1706757 TGTTCACAAC
1706767 AAATTTAGATAAATA-AAAATTG
1 AAATTTA-ATAAATATAAAATTG
*
1706789 AAATTTAATAACTATAAAAT
1 AAATTTAATAAATATAAAAT
1706809 AATAATAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
AAATTTAATAAATATAAAATTG
Found at i:1707752 original size:20 final size:20
Alignment explanation
Indices: 1707727--1707766 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1707717 AATAAAGGAA
1707727 GTAGAGTATCTCCTAAAGTT
1 GTAGAGTATCTCCTAAAGTT
1707747 GTAGAGTATCTCCTAAAGTT
1 GTAGAGTATCTCCTAAAGTT
1707767 TAAAGAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
GTAGAGTATCTCCTAAAGTT
Found at i:1714770 original size:6 final size:6
Alignment explanation
Indices: 1714759--1714831 Score: 71
Period size: 6 Copynumber: 12.3 Consensus size: 6
1714749 TTTTAATAGG
**
1714759 ATATTT ATATTT ATATTAT ATATTT ATAAAT ATATATT ATA-TT ATATTT
1 ATATTT ATATTT ATATT-T ATATTT ATATTT ATAT-TT ATATTT ATATTT
* *
1714808 -TAATT ATTTTT ATA-TT ATATTT AT
1 ATATTT ATATTT ATATTT ATATTT AT
1714832 TAATAGAATT
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
5 14 0.26
6 30 0.56
7 10 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
ATATTT
Found at i:1714779 original size:11 final size:11
Alignment explanation
Indices: 1714763--1714831 Score: 68
Period size: 11 Copynumber: 5.9 Consensus size: 11
1714753 AATAGGATAT
1714763 TTATATTTATA
1 TTATATTTATA
1714774 TTATATATTTATAA
1 -T-TATATTTAT-A
*
1714788 ATATATATTATA
1 TTATAT-TTATA
1714800 TTATATTT-TAA
1 TTATATTTAT-A
*
1714811 TTATTTTTATA
1 TTATATTTATA
1714822 TTATATTTAT
1 TTATATTTAT
1714832 TAATAGAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
10 1 0.02
11 20 0.42
12 13 0.27
13 13 0.27
14 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATATTTATA
Found at i:1714783 original size:19 final size:18
Alignment explanation
Indices: 1714760--1714833 Score: 66
Period size: 19 Copynumber: 4.1 Consensus size: 18
1714750 TTTAATAGGA
1714760 TATTTATATTTATATTAT
1 TATTTATATTTATATTAT
**
1714778 ATATTTATAAATATA-TAT
1 -TATTTATATTTATATTAT
1714796 TATATTATATTT-TAATTAT
1 TAT-TTATATTTAT-ATTAT
1714815 T-TTTATA-TTATATTTAT
1 TATTTATATTTATA-TTAT
1714832 TA
1 TA
1714834 ATAGAATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
16 3 0.07
17 15 0.33
18 11 0.24
19 16 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTATATTTATATTAT
Found at i:1716205 original size:3 final size:3
Alignment explanation
Indices: 1716197--1716225 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1716187 GGATTCACAA
1716197 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1716226 AACTAACAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1719115 original size:67 final size:67
Alignment explanation
Indices: 1719007--1719144 Score: 267
Period size: 67 Copynumber: 2.1 Consensus size: 67
1718997 GTGAATCATT
*
1719007 CATTAGCATGACAGGCAGAGTTACTTATCCAAAATTCTGTCTTTTAGAACTATAGAGATGGCATA
1 CATTAGCATGACAGGCAGAGTTACTTATCCAAAATTCTGTCTTTTAGAACTACAGAGATGGCATA
1719072 TG
66 TG
1719074 CATTAGCATGACAGGCAGAGTTACTTATCCAAAATTCTGTCTTTTAGAACTACAGAGATGGCATA
1 CATTAGCATGACAGGCAGAGTTACTTATCCAAAATTCTGTCTTTTAGAACTACAGAGATGGCATA
1719139 TG
66 TG
1719141 CATT
1 CATT
1719145 CAATAGAACC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (67 bp):
CATTAGCATGACAGGCAGAGTTACTTATCCAAAATTCTGTCTTTTAGAACTACAGAGATGGCATA
TG
Found at i:1722291 original size:32 final size:30
Alignment explanation
Indices: 1722250--1722308 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
1722240 TATTTAATTA
1722250 TTAAAAATTAAAATTAAAAGATATATAATTTT
1 TTAAAAATT-AAATTAAAAGA-ATATAATTTT
*
1722282 TTAAAAATTAAATTAAAATAATATAAT
1 TTAAAAATTAAATTAAAAGAATATAAT
1722309 ATGAACAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 7 0.27
31 10 0.38
32 9 0.35
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
TTAAAAATTAAATTAAAAGAATATAATTTT
Found at i:1722364 original size:6 final size:6
Alignment explanation
Indices: 1722355--1722405 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
1722345 TAAACATAAA
* *
1722355 TAAATT TAAA-T AAAATT TAAATT TATATTT TAAA-T TAAA-T TAAATT
1 TAAATT TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT
1722401 TAAAT
1 TAAAT
1722406 GAATATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
5 14 0.37
6 19 0.50
7 5 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:1725586 original size:17 final size:17
Alignment explanation
Indices: 1725566--1725601 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1725556 AAGGAAGATG
* *
1725566 AAGAAGAAAGAAAGAAA
1 AAGAAAAAAAAAAGAAA
1725583 AAGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
1725600 AA
1 AA
1725602 ATATGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:1728907 original size:38 final size:38
Alignment explanation
Indices: 1728856--1728928 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
1728846 TAAGCATCAA
1728856 AGAAGAATACTGTTTGCTACCTAGGCTGAGCTCATCTG
1 AGAAGAATACTGTTTGCTACCTAGGCTGAGCTCATCTG
* * *
1728894 AGAAGAATGCTGTTTGCTGCCTAGGCTTAGCTCAT
1 AGAAGAATACTGTTTGCTACCTAGGCTGAGCTCAT
1728929 TTGATTAGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (38 bp):
AGAAGAATACTGTTTGCTACCTAGGCTGAGCTCATCTG
Found at i:1732115 original size:12 final size:13
Alignment explanation
Indices: 1732092--1732133 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
1732082 TATTTTTCAA
1732092 AATATTTATATTT
1 AATATTTATATTT
1732105 AATATTT-TATTT
1 AATATTTATATTT
1732117 AATA--TATATTT
1 AATATTTATATTT
1732128 ATATAT
1 A-ATAT
1732134 AAATATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.04
11 6 0.23
12 12 0.46
13 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:1732139 original size:8 final size:8
Alignment explanation
Indices: 1732128--1732166 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
1732118 ATATATATTT
1732128 ATATATAA
1 ATATATAA
1732136 ATATA-AA
1 ATATATAA
1732143 A-ATATAA
1 ATATATAA
*
1732150 ATATTTAA
1 ATATATAA
1732158 ATATATAA
1 ATATATAA
1732166 A
1 A
1732167 AAAATTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 3 0.11
7 6 0.22
8 18 0.67
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATATAA
Found at i:1732139 original size:14 final size:14
Alignment explanation
Indices: 1732091--1732162 Score: 56
Period size: 14 Copynumber: 5.1 Consensus size: 14
1732081 ATATTTTTCA
1732091 AAATATTTATAT-T
1 AAATATTTATATAT
* *
1732104 TAATATTTTATTTAAT
1 AAATA-TTTATAT-AT
*
1732120 ATATATTTATATAT
1 AAATATTTATATAT
** *
1732134 AAATATAAAAATAT
1 AAATATTTATATAT
*
1732148 AAATATTTAAATAT
1 AAATATTTATATAT
1732162 A
1 A
1732163 TAAAAAAATT
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
13 4 0.09
14 31 0.69
15 6 0.13
16 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AAATATTTATATAT
Found at i:1732147 original size:16 final size:15
Alignment explanation
Indices: 1732128--1732166 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
1732118 ATATATATTT
1732128 ATATATAAATATAAA
1 ATATATAAATATAAA
*
1732143 A-ATATAAATATTTAA
1 ATATATAAATA-TAAA
1732158 ATATATAAA
1 ATATATAAA
1732167 AAAATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 9 0.43
15 5 0.24
16 7 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATATATAAATATAAA
Found at i:1733803 original size:2 final size:2
Alignment explanation
Indices: 1733796--1733833 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1733786 AGATTTCAAT
*
1733796 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1733834 TATAAAGTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1735364 original size:19 final size:20
Alignment explanation
Indices: 1735326--1735364 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1735316 TTAGATCGAT
*
1735326 TAAAATTATTATTTAATTAA
1 TAAAAATATTATTTAATTAA
*
1735346 TAAAAATATT-TTTATTTAA
1 TAAAAATATTATTTAATTAA
1735365 ATTTAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAAATATTATTTAATTAA
Found at i:1735390 original size:29 final size:29
Alignment explanation
Indices: 1735324--1735399 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
1735314 TGTTAGATCG
* *
1735324 ATTAAAATTATTATTTAATTAATAAAAAT
1 ATTAATATTAATATTTAATTAATAAAAAT
**
1735353 ATTTTTATTTAA-ATTTAATT-ATAAAATAT
1 ATTAATA-TTAATATTTAATTAATAAAA-AT
1735382 ATTAATATTAATATTTAA
1 ATTAATATTAATATTTAA
1735400 ATTTATTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 10 0.26
29 25 0.66
30 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTAATATTAATATTTAATTAATAAAAAT
Found at i:1736137 original size:34 final size:34
Alignment explanation
Indices: 1736094--1736162 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
1736084 AAATAATGAT
* *
1736094 TAAATTATATA-TTAAATCAATAAAATTAAAATAA
1 TAAATTATATATTTAAAT-AACAAAATAAAAATAA
*
1736128 TAAATTATATATTTAGATAACAAAATAAAAATAA
1 TAAATTATATATTTAAATAACAAAATAAAAATAA
1736162 T
1 T
1736163 TGTGAAGTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 26 0.84
35 5 0.16
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (34 bp):
TAAATTATATATTTAAATAACAAAATAAAAATAA
Found at i:1736361 original size:26 final size:25
Alignment explanation
Indices: 1736309--1736362 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
1736299 TGATTAATAA
* * **
1736309 TTTTTATATAATTATATAAATTTAT
1 TTTTTATATAAGTAAATAAATAAAT
1736334 TTTTTATATTAAGTAAATAAATAAAT
1 TTTTTATA-TAAGTAAATAAATAAAT
1736360 TTT
1 TTT
1736363 AAAATTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTTTATATAAGTAAATAAATAAAT
Found at i:1736389 original size:21 final size:21
Alignment explanation
Indices: 1736367--1736408 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1736357 AATTTTAAAA
1736367 TTTTAAATAAAAATTAAATAAT
1 TTTTAAA-AAAAATTAAATAAT
* *
1736389 TTTTAAAAATATTTAAATAA
1 TTTTAAAAAAAATTAAATAA
1736409 AAATAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTTAAAAAAAATTAAATAAT
Found at i:1736409 original size:32 final size:29
Alignment explanation
Indices: 1736348--1736416 Score: 102
Period size: 32 Copynumber: 2.3 Consensus size: 29
1736338 TATATTAAGT
1736348 AAATAAATAAATTTTAAAATTTTAAATAA
1 AAATAAATAAATTTTAAAATTTTAAATAA
*
1736377 AAATTAAATAATTTTTAAAAATATTTAAATAA
1 AAA-TAAATAAATTTT-AAAAT-TTTAAATAA
1736409 AAATAAAT
1 AAATAAAT
1736417 TAATAAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 3 0.08
30 11 0.31
31 10 0.28
32 12 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
AAATAAATAAATTTTAAAATTTTAAATAA
Found at i:1742246 original size:20 final size:21
Alignment explanation
Indices: 1742223--1742267 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1742213 ATCAATTTTT
*
1742223 TATTAAACT-TGAATATTTGA
1 TATTAAACTATAAATATTTGA
*
1742243 TATTAAATTATAAATATTTGA
1 TATTAAACTATAAATATTTGA
1742264 -ATTA
1 TATTA
1742268 GATTAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (21 bp):
TATTAAACTATAAATATTTGA
Found at i:1742272 original size:20 final size:21
Alignment explanation
Indices: 1742234--1742272 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1742224 ATTAAACTTG
1742234 AATATTTGATATTAAATTATA
1 AATATTTGATATTAAATTATA
*
1742255 AATATTTGA-ATTAGATTA
1 AATATTTGATATTAAATTA
1742273 AATCATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (21 bp):
AATATTTGATATTAAATTATA
Found at i:1743043 original size:24 final size:24
Alignment explanation
Indices: 1743013--1743060 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1743003 CCGGAGGTGT
1743013 TTATTATATAA-AT-ATGTTTAAATA
1 TTATTAT-TAATATGATG-TTAAATA
1743037 TTATTATTAATATGATGTTAAATA
1 TTATTATTAATATGATGTTAAATA
1743061 AAATATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 3 0.14
24 16 0.73
25 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (24 bp):
TTATTATTAATATGATGTTAAATA
Found at i:1743807 original size:21 final size:17
Alignment explanation
Indices: 1743742--1743796 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
1743732 AAAAAATCAG
* *
1743742 ATAAAAAAATTTAATTA
1 ATAAAAATATATAATTA
*
1743759 AAAATTAAATATATAATTA
1 ATAA--AAATATATAATTA
1743778 ATAAAAATATATAATTA
1 ATAAAAATATATAATTA
1743795 AT
1 AT
1743797 TTTATAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 18 0.56
19 14 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAAAATATATAATTA
Found at i:1744181 original size:19 final size:18
Alignment explanation
Indices: 1744143--1744186 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1744133 TATTTTTTTA
*
1744143 AAAATATTTAAATTTAAT
1 AAAATATTTAAATATAAT
1744161 AAAATATTTAAATATATAT
1 AAAATATTTAAATATA-AT
*
1744180 AATATAT
1 AAAATAT
1744187 AATTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATATTTAAATATAAT
Found at i:1747575 original size:2 final size:2
Alignment explanation
Indices: 1747568--1747592 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1747558 AACTACTTAA
1747568 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1747593 AAATAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1749133 original size:11 final size:11
Alignment explanation
Indices: 1749117--1749151 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1749107 TTATAATTTA
1749117 TATATTTATAT
1 TATATTTATAT
1749128 TATATTTATAT
1 TATATTTATAT
* *
1749139 CATATTTTTAT
1 TATATTTATAT
1749150 TA
1 TA
1749152 AAATATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1749173 original size:20 final size:22
Alignment explanation
Indices: 1749148--1749190 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
1749138 TCATATTTTT
*
1749148 ATTAAAATA-TAATATAA-ATA
1 ATTAAAATACGAATATAATATA
1749168 ATTAAAATACGAATATAATATA
1 ATTAAAATACGAATATAATATA
1749190 A
1 A
1749191 ATTATTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 7 0.35
22 4 0.20
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
ATTAAAATACGAATATAATATA
Found at i:1749491 original size:10 final size:10
Alignment explanation
Indices: 1749460--1749537 Score: 52
Period size: 10 Copynumber: 7.5 Consensus size: 10
1749450 TTTTAACGTA
1749460 TTTATT-TAT
1 TTTATTATAT
1749469 TTGTATTAT-T
1 TT-TATTATAT
*
1749479 TTTTTTATAT
1 TTTATTATAT
*
1749489 TTTATCATAT
1 TTTATTATAT
*
1749499 TTTAATTTTTAT
1 TTT-A-TTATAT
**
1749511 TAAATTATAT
1 TTTATTATAT
1749521 TTTAATTATTAT
1 TTT-ATTA-TAT
1749533 TTTAT
1 TTTAT
1749538 ATTATGTTCA
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
9 7 0.13
10 25 0.48
11 9 0.17
12 11 0.21
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (10 bp):
TTTATTATAT
Found at i:1749537 original size:19 final size:20
Alignment explanation
Indices: 1749486--1749540 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 20
1749476 ATTTTTTTTA
*
1749486 TATT-TTATCATATTTTAAT
1 TATTATTATTATATTTTAAT
*
1749505 TTTTATTAAATTATATTTTAAT
1 TATTATT--ATTATATTTTAAT
1749527 TATTATT-TTATATT
1 TATTATTATTATATT
1749541 ATGTTCAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 10 0.33
20 2 0.07
22 18 0.60
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTATTATTATATTTTAAT
Found at i:1750270 original size:26 final size:26
Alignment explanation
Indices: 1750236--1750285 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1750226 TTTATTTAAA
*
1750236 TTATTATTTAATTAATAAAA-ATATTT
1 TTATAATTTAATT-ATAAAATATATTT
1750262 TTATAATTTAATTATAAAATATAT
1 TTATAATTTAATTATAAAATATAT
1750286 AAATATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTATAATTTAATTATAAAATATATTT
Found at i:1750302 original size:21 final size:22
Alignment explanation
Indices: 1750269--1750309 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1750259 TTTTTATAAT
1750269 TTAATTATAAAATATATAAATA
1 TTAATTATAAAATATATAAATA
*
1750291 TTAATT-TAAAATATTTAAA
1 TTAATTATAAAATATATAAA
1750310 AAATATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAATTATAAAATATATAAATA
Found at i:1750319 original size:21 final size:21
Alignment explanation
Indices: 1750270--1750339 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 21
1750260 TTTTATAATT
* * *
1750270 TAATTATAAAATATATAAATAT
1 TAATT-TAAAATATTTAAAAAA
1750292 TAATTTAAAATATTTAAAAAA
1 TAATTTAAAATATTTAAAAAA
* *
1750313 TATTTTAATATACTTTTAAAATAA
1 TAATTTAAAATA--TTTAAAA-AA
1750337 TAA
1 TAA
1750340 AGTAATTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 23 0.59
22 5 0.13
23 7 0.18
24 4 0.10
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATTTAAAATATTTAAAAAA
Found at i:1751711 original size:2 final size:2
Alignment explanation
Indices: 1751704--1751738 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1751694 GGTTAGAAAT
1751704 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1751739 TTTCAAAGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1752118 original size:13 final size:13
Alignment explanation
Indices: 1752074--1752132 Score: 59
Period size: 13 Copynumber: 4.6 Consensus size: 13
1752064 GATTATAAAC
1752074 ATAATAAATATT-
1 ATAATAAATATTA
* * *
1752086 ATCACAATTAATTA
1 ATAATAAAT-ATTA
1752100 A-AATAAATATTA
1 ATAATAAATATTA
*
1752112 ATTATAAATATTA
1 ATAATAAATATTA
1752125 ATAATAAA
1 ATAATAAA
1752133 AAAAATTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
12 11 0.31
13 24 0.67
14 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAATAAATATTA
Found at i:1753112 original size:16 final size:15
Alignment explanation
Indices: 1753093--1753157 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 15
1753083 ATTATATTTA
1753093 AATTAATATATATCAT
1 AATTAATATATAT-AT
1753109 AATTAATA-ATA-AT
1 AATTAATATATATAT
*
1753122 AA-TAATATTTATTAT
1 AATTAATATATA-TAT
1753137 AATT-ATA-AT-TAT
1 AATTAATATATATAT
*
1753149 AATAAATAT
1 AATTAATAT
1753158 CATTCAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
12 11 0.28
13 9 0.22
14 1 0.03
15 10 0.25
16 9 0.22
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTAATATATATAT
Found at i:1753586 original size:14 final size:15
Alignment explanation
Indices: 1753569--1753628 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 15
1753559 TTTCATCACA
1753569 TTTTTAAATAT-ATT
1 TTTTTAAATATAATT
*
1753583 TTTTT-AATTTAATT
1 TTTTTAAATATAATT
* *
1753597 TTTTT-AATCTAAAT
1 TTTTTAAATATAATT
1753611 TTTTTAAAT-TAACTT
1 TTTTTAAATATAA-TT
1753626 TTT
1 TTT
1753629 AAGTTGTCGG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
13 4 0.10
14 28 0.72
15 7 0.18
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTAAATATAATT
Found at i:1753599 original size:15 final size:14
Alignment explanation
Indices: 1753580--1753628 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
1753570 TTTTAAATAT
1753580 ATTTTTTTAATTTA
1 ATTTTTTTAATTTA
*
1753594 ATTTTTTTAATCTA
1 ATTTTTTTAATTTA
* *
1753608 AATTTTTTAAATTA
1 ATTTTTTTAATTTA
1753622 ACTTTTT
1 A-TTTTT
1753629 AAGTTGTCGG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 25 0.86
15 4 0.14
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTTTTTAATTTA
Found at i:1753627 original size:13 final size:14
Alignment explanation
Indices: 1753569--1753630 Score: 56
Period size: 13 Copynumber: 4.5 Consensus size: 14
1753559 TTTCATCACA
1753569 TTTTTAAATAT-AT
1 TTTTTAAATATAAT
* *
1753582 TTTTTTAATTTAAT
1 TTTTTAAATATAAT
* *
1753596 TTTTTTAATCTAAAT
1 TTTTTAAATAT-AAT
*
1753611 TTTTTAAAT-TAAC
1 TTTTTAAATATAAT
1753624 TTTTTAA
1 TTTTTAA
1753631 GTTGTCGGTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 18 0.43
14 13 0.31
15 11 0.26
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTAAATATAAT
Found at i:1753741 original size:9 final size:10
Alignment explanation
Indices: 1753712--1753746 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
1753702 ATCAAGGCTT
1753712 ACAAATTTAA
1 ACAAATTTAA
1753722 ACAATATTTAA
1 ACAA-ATTTAA
1753733 A-AAATTTAA
1 ACAAATTTAA
1753742 ACAAA
1 ACAAA
1753747 AAATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 7 0.30
10 9 0.39
11 7 0.30
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (10 bp):
ACAAATTTAA
Found at i:1754734 original size:10 final size:10
Alignment explanation
Indices: 1754721--1754747 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1754711 TAAGTGTTAA
1754721 TAATAATTAT
1 TAATAATTAT
1754731 TAATAATTAT
1 TAATAATTAT
1754741 TAATAAT
1 TAATAAT
1754748 ATTTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TAATAATTAT
Found at i:1754822 original size:15 final size:16
Alignment explanation
Indices: 1754795--1754826 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1754785 GATATTTAAA
1754795 AATTTTAAAAATTTAT
1 AATTTTAAAAATTTAT
1754811 AATTTT-AAAATTTAT
1 AATTTTAAAAATTTAT
1754826 A
1 A
1754827 TTTATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTTAAAAATTTAT
Found at i:1754834 original size:15 final size:16
Alignment explanation
Indices: 1754798--1754834 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1754788 ATTTAAAAAT
1754798 TTTA-AAAATTTATAA
1 TTTATAAAATTTATAA
1754813 TTT-TAAAATTTAT-A
1 TTTATAAAATTTATAA
1754827 TTTATAAA
1 TTTATAAA
1754835 TAAACACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTATAAAATTTATAA
Found at i:1757810 original size:108 final size:108
Alignment explanation
Indices: 1757602--1757815 Score: 333
Period size: 108 Copynumber: 2.0 Consensus size: 108
1757592 TTATTGTTAA
* * *
1757602 ATTTAACAATATAATTGTATTCTTTGTTCACATAAAATTTTAAATTGATTGGATATATTTATCAT
1 ATTTAACAATATAATTGTATTCTTTGTGCACATAAAATTTTAAAGTGATCGGATATATTTATCAT
* *
1757667 ATGAATCGAGAATATTATTTTTTTTACATAAATTTAATGGTGG
66 ATGAATCGAGAATATTATCTATTTTACATAAATTTAATGGTGG
*
1757710 ATTTAACAATATAATTGTATTCTTTGTGCACATAAAATTTTGAAGTGATCGGATATATTTATCAT
1 ATTTAACAATATAATTGTATTCTTTGTGCACATAAAATTTTAAAGTGATCGGATATATTTATCAT
*
1757775 AT-AATTGAGAATATTATCTATTTTA-ATATATATTTAATGGT
66 ATGAATCGAGAATATTATCTATTTTACATA-A-ATTTAATGGT
1757816 TTAAATTTTT
Statistics
Matches: 97, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
106 3 0.03
107 21 0.22
108 73 0.75
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (108 bp):
ATTTAACAATATAATTGTATTCTTTGTGCACATAAAATTTTAAAGTGATCGGATATATTTATCAT
ATGAATCGAGAATATTATCTATTTTACATAAATTTAATGGTGG
Found at i:1758281 original size:17 final size:19
Alignment explanation
Indices: 1758256--1758296 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1758246 CAATATATAT
1758256 ATATAAAT-ATTTAAAA-A
1 ATATAAATAATTTAAAAGA
*
1758273 ATATTAATAAATTTAAAAGA
1 ATATAAAT-AATTTAAAAGA
1758293 ATAT
1 ATAT
1758297 GTCAAAACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 7 0.35
19 8 0.40
20 5 0.25
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
ATATAAATAATTTAAAAGA
Found at i:1760076 original size:19 final size:18
Alignment explanation
Indices: 1760043--1760081 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 18
1760033 AGCCTAATTT
1760043 ATATGTATAAATACG-AA
1 ATATGTATAAATACGTAA
1760060 ATATGTATATCAATACGTAA
1 ATATGTATA--AATACGTAA
1760080 AT
1 AT
1760082 TATTGTAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.47
19 6 0.32
20 4 0.21
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (18 bp):
ATATGTATAAATACGTAA
Found at i:1760819 original size:2 final size:2
Alignment explanation
Indices: 1760812--1760849 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1760802 TTTAGGATTT
*
1760812 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1760850 ATTCTAGCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1766178 original size:30 final size:30
Alignment explanation
Indices: 1766144--1766202 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1766134 ACAAACAAGC
*
1766144 AAAATAAATCAAATTTAAACTTTATATTTT
1 AAAATAAATCAAATTTAAACTTTAAATTTT
* **
1766174 AAAATATATTGAATTTAAACTTTAAATTT
1 AAAATAAATCAAATTTAAACTTTAAATTT
1766203 AACTTATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (30 bp):
AAAATAAATCAAATTTAAACTTTAAATTTT
Found at i:1766727 original size:19 final size:18
Alignment explanation
Indices: 1766703--1766761 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 18
1766693 ATTTATATAA
1766703 TATTAAT-TAATAATATTAT
1 TATTAATAT-ATAATATT-T
*
1766722 TATTAATATATAAAATTT
1 TATTAATATATAATATTT
1766740 TATATAAATATATAATATTT
1 TAT-T-AATATATAATATTT
1766760 TA
1 TA
1766762 AAAATAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 4 0.11
19 15 0.43
20 16 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTAATATATAATATTT
Found at i:1766766 original size:18 final size:18
Alignment explanation
Indices: 1766712--1766767 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
1766702 ATATTAATTA
**
1766712 ATAATATTATTATTAATAT
1 ATAATATT-TTAAAAATAT
*
1766731 ATAAAATTTTATATAAATAT
1 ATAATATTTTA-A-AAATAT
1766751 ATAATATTTTAAAAATA
1 ATAATATTTTAAAAATA
1766768 AATATAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 8 0.26
19 8 0.26
20 15 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAATATTTTAAAAATAT
Found at i:1768414 original size:136 final size:136
Alignment explanation
Indices: 1768264--1768536 Score: 528
Period size: 136 Copynumber: 2.0 Consensus size: 136
1768254 ATATGTTAAT
1768264 TAAGGAATGACTTTTGTTTGCAAGAAAAAAAAAACATGCATGCACTTATATTTTCATCGTTTAAC
1 TAAGGAATGACTTTTGTTTGCAAGAAAAAAAAAACATGCATGCACTTATATTTTCATCGTTTAAC
*
1768329 ATGCATAATAAATTTCTTGGCTTTTGCATATTCAAGTGCTGAAGTAATAGTTTTTATATTTTATT
66 ATGCATAATAAATTTCTTGGCTTTTGCATATTCAAGTGCTGAAGTAATAGTTATTATATTTTATT
1768394 TCAAAC
131 TCAAAC
1768400 TAAGGAATGACTTTTGTTTGCAAGAAAAAAAAAACATGCATGCACTTATATTTTCATCGTTTAAC
1 TAAGGAATGACTTTTGTTTGCAAGAAAAAAAAAACATGCATGCACTTATATTTTCATCGTTTAAC
*
1768465 ATGCATAATAAATTTCTTGGCTTTTGCATATTCAAGTGCTGAAGTAATCGTTATTATATTTTATT
66 ATGCATAATAAATTTCTTGGCTTTTGCATATTCAAGTGCTGAAGTAATAGTTATTATATTTTATT
1768530 TCAAAC
131 TCAAAC
1768536 T
1 T
1768537 TTTTAGGGAA
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 135 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (136 bp):
TAAGGAATGACTTTTGTTTGCAAGAAAAAAAAAACATGCATGCACTTATATTTTCATCGTTTAAC
ATGCATAATAAATTTCTTGGCTTTTGCATATTCAAGTGCTGAAGTAATAGTTATTATATTTTATT
TCAAAC
Found at i:1770374 original size:18 final size:18
Alignment explanation
Indices: 1770353--1770416 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
1770343 AAATTTAAGC
1770353 TTATTTTATTAATTATTG
1 TTATTTTATTAATTATTG
*
1770371 TTATTTTATT-TTTATTTG
1 TTATTTTATTAATTA-TTG
*
1770389 CTATATTTA--AAGTTATTG
1 TTAT-TTTATTAA-TTATTG
1770407 TTATTTTATT
1 TTATTTTATT
1770417 TTATTTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
17 7 0.19
18 22 0.61
19 7 0.19
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (18 bp):
TTATTTTATTAATTATTG
Found at i:1772615 original size:24 final size:26
Alignment explanation
Indices: 1772588--1772642 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
1772578 TTTATTGTAA
1772588 AAATTAATTTGA-TTAATAAAA-AAT
1 AAATTAATTTGAGTTAATAAAATAAT
* *
1772612 AAA-TAGTTTGAGTTAATAAAATATT
1 AAATTAATTTGAGTTAATAAAATAAT
1772637 AAATTA
1 AAATTA
1772643 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 7 0.27
24 12 0.46
25 5 0.19
26 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (26 bp):
AAATTAATTTGAGTTAATAAAATAAT
Found at i:1773813 original size:20 final size:19
Alignment explanation
Indices: 1773767--1773822 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
1773757 AAAACCCTTA
**
1773767 AATGTATCGATACACAATTC
1 AATGTATCGATACA-TGTTC
*
1773787 AAAGTATCGATACATGTTGC
1 AATGTATCGATACATGTT-C
1773807 AATGTATCGATACATG
1 AATGTATCGATACATG
1773823 AAAAAGATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (19 bp):
AATGTATCGATACATGTTC
Found at i:1773899 original size:13 final size:13
Alignment explanation
Indices: 1773881--1773906 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1773871 TACAGCAAGT
1773881 ATGTATCGATACA
1 ATGTATCGATACA
1773894 ATGTATCGATACA
1 ATGTATCGATACA
1773907 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:1776166 original size:21 final size:21
Alignment explanation
Indices: 1776133--1776182 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1776123 TTGCAAGTTG
*
1776133 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1776155 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
1776176 AAATAAA
1 AAATAAA
1776183 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1778001 original size:15 final size:15
Alignment explanation
Indices: 1777981--1778019 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1777971 TAAAAATGTC
*
1777981 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1777996 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
1778011 CCAAATGAA
1 CAAAATGAA
1778020 ATTGATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1780108 original size:13 final size:13
Alignment explanation
Indices: 1780090--1780128 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1780080 ACATTTTTCT
1780090 TTGTATCGATACA
1 TTGTATCGATACA
1780103 TTGTATCGATACA
1 TTGTATCGATACA
*
1780116 TTATATCGATACA
1 TTGTATCGATACA
1780129 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1782598 original size:20 final size:19
Alignment explanation
Indices: 1782552--1782607 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
1782542 AAAACCCTTA
**
1782552 AATGTATCGATACACAATTC
1 AATGTATCGATACA-TGTTC
*
1782572 AAAGTATCGATACATGTTGC
1 AATGTATCGATACATGTT-C
1782592 AATGTATCGATACATG
1 AATGTATCGATACATG
1782608 AAAAAGATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (19 bp):
AATGTATCGATACATGTTC
Done.