Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000572.1 Hibiscus syriacus cultivar Beakdansim tig00001120_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: 2399138
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:1112625 original size:16 final size:16
Alignment explanation
Indices: 1112606--1112646 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1112596 TTTTTTATCG
1112606 TTATTTTATATTATTA
1 TTATTTTATATTATTA
1112622 TTA-TTTATTATTATTA
1 TTATTTTA-TATTATTA
*
1112638 TTATATTAT
1 TTATTTTAT
1112647 TAATATCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.18
16 15 0.68
17 3 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTTATATTATTA
Found at i:1112763 original size:25 final size:25
Alignment explanation
Indices: 1112730--1112806 Score: 136
Period size: 25 Copynumber: 3.1 Consensus size: 25
1112720 CAATCAACCC
*
1112730 ATCATATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1112755 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
1112780 AACAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1112805 AT
1 AT
1112807 GTTCCAGCCG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:1125519 original size:21 final size:21
Alignment explanation
Indices: 1125502--1125560 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 21
1125492 ATAATTTGCA
1125502 CCGAAGTG-CCACATATTTGTC
1 CCGAA-TGACCACATATTTGTC
1125523 CCGAATGACCACATAGATTTGTC
1 CCGAATGACCACAT--ATTTGTC
1125546 CCGAATGACCACATA
1 CCGAATGACCACATA
1125561 GAACCCTCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.06
21 12 0.34
23 21 0.60
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (21 bp):
CCGAATGACCACATATTTGTC
Found at i:1125546 original size:23 final size:23
Alignment explanation
Indices: 1125516--1125562 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1125506 AGTGCCACAT
1125516 ATTTGTCCCGAATGACCACATAG
1 ATTTGTCCCGAATGACCACATAG
1125539 ATTTGTCCCGAATGACCACATAG
1 ATTTGTCCCGAATGACCACATAG
1125562 A
1 A
1125563 ACCCTCGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (23 bp):
ATTTGTCCCGAATGACCACATAG
Found at i:1127851 original size:26 final size:27
Alignment explanation
Indices: 1127822--1127878 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
1127812 TTATAATCAT
1127822 TTAAAAATAATTTTGAAAATA-AAAA-A
1 TTAAAAATAATTTT-AAAATATAAAATA
**
1127848 TT-AATTTAATTTTAAAATATAAAATA
1 TTAAAAATAATTTTAAAATATAAAATA
1127874 TTAAA
1 TTAAA
1127879 CTCATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 6 0.23
25 13 0.50
26 5 0.19
27 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
TTAAAAATAATTTTAAAATATAAAATA
Found at i:1127871 original size:25 final size:26
Alignment explanation
Indices: 1127829--1127877 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
1127819 CATTTAAAAA
1127829 TAATTTTGAAAATAAAAA-ATTAATT
1 TAATTTTGAAAATAAAAATATTAATT
1127854 TAATTTT-AAAATATAAAATATTAA
1 TAATTTTGAAAATA-AAAATATTAA
1127878 ACTCATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.27
25 11 0.50
26 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
TAATTTTGAAAATAAAAATATTAATT
Found at i:1127885 original size:26 final size:25
Alignment explanation
Indices: 1127829--1127886 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
1127819 CATTTAAAAA
**
1127829 TAATTTTGAAAATAAAAAATTAATT
1 TAATTTTGAAAATAAAAAATTAAAC
1127854 TAATTTT-AAAATATAAAATATTAAAC
1 TAATTTTGAAAATA-AAAA-ATTAAAC
*
1127880 TCATTTT
1 TAATTTT
1127887 TATTTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 6 0.21
25 11 0.39
26 11 0.39
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (25 bp):
TAATTTTGAAAATAAAAAATTAAAC
Found at i:1132452 original size:5 final size:5
Alignment explanation
Indices: 1132442--1132467 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1132432 TTTTATTTAC
1132442 ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA A
1132468 AAATAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:1138347 original size:24 final size:24
Alignment explanation
Indices: 1138320--1138370 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1138310 TTCAATTGCA
*
1138320 TAAAA-ATAATTTGATTCATAAATT
1 TAAAAGAT-ATTTGAATCATAAATT
* *
1138344 TAAAAGATATTTTAATCATACATT
1 TAAAAGATATTTGAATCATAAATT
1138368 TAA
1 TAA
1138371 GGAAGTGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (24 bp):
TAAAAGATATTTGAATCATAAATT
Found at i:1149544 original size:22 final size:22
Alignment explanation
Indices: 1149516--1149559 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1149506 AGATCTTGAC
1149516 CCATTTGATTAATAAGAAAACT
1 CCATTTGATTAATAAGAAAACT
1149538 CCATTTGATTAATAAGAAAACT
1 CCATTTGATTAATAAGAAAACT
1149560 TTCGGACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
CCATTTGATTAATAAGAAAACT
Found at i:1155699 original size:42 final size:42
Alignment explanation
Indices: 1155642--1155732 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
1155632 TGGATGCAGC
**
1155642 AGGAGACTCTGCGGAAGGTGTTTCGGTTGGCGGAGACACAGG
1 AGGAGACTCCACGGAAGGTGTTTCGGTTGGCGGAGACACAGG
* *
1155684 AGGAGACTCCACGGAAGGTGTTTTGGTTGGCGGAGACGCAGG
1 AGGAGACTCCACGGAAGGTGTTTCGGTTGGCGGAGACACAGG
1155726 AGGAGAC
1 AGGAGAC
1155733 AACGTAGAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.23, C:0.16, G:0.43, T:0.18
Consensus pattern (42 bp):
AGGAGACTCCACGGAAGGTGTTTCGGTTGGCGGAGACACAGG
Found at i:1155743 original size:42 final size:41
Alignment explanation
Indices: 1155653--1155745 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 41
1155643 GGAGACTCTG
*
1155653 CGGAAGGTGTTTCGGTTGGCGGAGACACAGGAGGAGACTCCA
1 CGGAAGGTGTTTCGGTTGGCGGAGACACAGGAGGAGAC-CAA
* *
1155695 CGGAAGGTGTTTTGGTTGGCGGAGACGCAGGAGGAGA-CAA
1 CGGAAGGTGTTTCGGTTGGCGGAGACACAGGAGGAGACCAA
1155735 CGTAGAAGGTG
1 CG--GAAGGTG
1155746 CCAGAGGTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
40 4 0.09
42 42 0.91
ACGTcount: A:0.25, C:0.15, G:0.43, T:0.17
Consensus pattern (41 bp):
CGGAAGGTGTTTCGGTTGGCGGAGACACAGGAGGAGACCAA
Found at i:1161809 original size:5 final size:5
Alignment explanation
Indices: 1161799--1161839 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
1161789 CAGCCCTTCT
1161799 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG T
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG T
1161840 GTGTGAGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
TTTTG
Found at i:1162595 original size:18 final size:19
Alignment explanation
Indices: 1162553--1162596 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1162543 TTTGGTTTAC
*
1162553 GGAATATAAGATTACCAATG
1 GGAATAAAAGATTACC-ATG
*
1162573 AGAATAAAAGATTACC-TG
1 GGAATAAAAGATTACCATG
1162591 GGAATA
1 GGAATA
1162597 GGATTACTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.23
Consensus pattern (19 bp):
GGAATAAAAGATTACCATG
Found at i:1162764 original size:15 final size:15
Alignment explanation
Indices: 1162746--1162776 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1162736 AAATTCTAAA
1162746 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1162761 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1162776 T
1 T
1162777 CTATATGTTA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:1165019 original size:84 final size:84
Alignment explanation
Indices: 1164878--1165039 Score: 315
Period size: 84 Copynumber: 1.9 Consensus size: 84
1164868 TGACTAACAA
*
1164878 TTAAAAAGAAAATTAACAAAAGCCCAAACATCCAACAAATTCAGATAAGAGATGTCAAAAGTAAA
1 TTAAAAAGAAAATTAACAAAAACCCAAACATCCAACAAATTCAGATAAGAGATGTCAAAAGTAAA
1164943 AGCCAGAAAAACAGTTTAT
66 AGCCAGAAAAACAGTTTAT
1164962 TTAAAAAGAAAATTAACAAAAACCCAAACATCCAACAAATTCAGATAAGAGATGTCAAAAGTAAA
1 TTAAAAAGAAAATTAACAAAAACCCAAACATCCAACAAATTCAGATAAGAGATGTCAAAAGTAAA
1165027 AGCCAGAAAAACA
66 AGCCAGAAAAACA
1165040 ATATATAAAC
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.57, C:0.16, G:0.11, T:0.16
Consensus pattern (84 bp):
TTAAAAAGAAAATTAACAAAAACCCAAACATCCAACAAATTCAGATAAGAGATGTCAAAAGTAAA
AGCCAGAAAAACAGTTTAT
Found at i:1165929 original size:24 final size:24
Alignment explanation
Indices: 1165897--1165944 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1165887 TTTCTGTCTA
1165897 TTTTTCTTGGATGGATGCTATAAC
1 TTTTTCTTGGATGGATGCTATAAC
*
1165921 TTTTTCTTGGATGGGTGCTATAAC
1 TTTTTCTTGGATGGATGCTATAAC
1165945 CAGTTACTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.46
Consensus pattern (24 bp):
TTTTTCTTGGATGGATGCTATAAC
Found at i:1168836 original size:22 final size:22
Alignment explanation
Indices: 1168800--1168854 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1168790 TATATATATA
*
1168800 TATATATAACATTTTATATTAAT
1 TATATATAA-TTTTTATATTAAT
1168823 TATATATAATTTTTATATTAAT
1 TATATATAATTTTTATATTAAT
1168845 TATATATAAT
1 TATATATAAT
1168855 ATTTCTGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 22 0.71
23 9 0.29
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TATATATAATTTTTATATTAAT
Found at i:1168839 original size:11 final size:11
Alignment explanation
Indices: 1168786--1168851 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 11
1168776 GCCCCGATTA
1168786 TATATATATATAT
1 TATATAT-TA-AT
*
1168799 ATATATATAACAT
1 -TATATATTA-AT
*
1168812 TTTATATTAAT
1 TATATATTAAT
1168823 TATATA-TAATT
1 TATATATTAA-T
*
1168834 TTTATATTAAT
1 TATATATTAAT
1168845 TATATAT
1 TATATAT
1168852 AATATTTCTG
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
10 3 0.07
11 20 0.47
12 10 0.23
13 3 0.07
14 7 0.16
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
TATATATTAAT
Found at i:1169099 original size:25 final size:25
Alignment explanation
Indices: 1169071--1169119 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1169061 AAAGATGACA
*
1169071 TATTCTGTAAACAAGCAATAAAATG
1 TATTCCGTAAACAAGCAATAAAATG
1169096 TATTCCGTAAACAAGCAATAAAAT
1 TATTCCGTAAACAAGCAATAAAAT
1169120 AACCGATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (25 bp):
TATTCCGTAAACAAGCAATAAAATG
Found at i:1170337 original size:33 final size:33
Alignment explanation
Indices: 1170268--1170337 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
1170258 GGTTGAGTAA
* *
1170268 ATATAAATATAATAAAAAATTTTAACACAATAT
1 ATATAAATATAATAAAAAATTATAACAAAATAT
* * *
1170301 ATATATATATATATAAAAAA-TATAATAAAATTT
1 ATATAAATATA-ATAAAAAATTATAACAAAATAT
1170334 ATAT
1 ATAT
1170338 TTAAGTTGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 23 0.74
34 8 0.26
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (33 bp):
ATATAAATATAATAAAAAATTATAACAAAATAT
Found at i:1173419 original size:26 final size:26
Alignment explanation
Indices: 1173385--1173435 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1173375 TTAGGATCAA
1173385 AATACACTA-AAATTACTAAATTATTC
1 AATACACTATAAATTACT-AATTATTC
1173411 AATACACTATAAATTACTAATTATT
1 AATACACTATAAATTACTAATTATT
1173436 TGAATTAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (26 bp):
AATACACTATAAATTACTAATTATTC
Found at i:1175246 original size:16 final size:17
Alignment explanation
Indices: 1175215--1175256 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1175205 TCATATTTCT
*
1175215 ATTATCTTGTTTATATG
1 ATTATCTTGTTCATATG
*
1175232 ATTAT-TTGTTCATATC
1 ATTATCTTGTTCATATG
1175248 ATATATCTT
1 AT-TATCTT
1175257 ATAACATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 11 0.52
17 8 0.38
18 2 0.10
ACGTcount: A:0.26, C:0.10, G:0.07, T:0.57
Consensus pattern (17 bp):
ATTATCTTGTTCATATG
Found at i:1185466 original size:28 final size:27
Alignment explanation
Indices: 1185413--1185471 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 27
1185403 ATGTTTCACT
1185413 TAATATTGATTTTACAAAATCAATAAA
1 TAATATTGATTTTACAAAATCAATAAA
*
1185440 CTAATATTGATTTTATAAAAT-ATATAAA
1 -TAATATTGATTTTACAAAATCA-ATAAA
1185468 TAAT
1 TAAT
1185472 TATTTAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 5 0.17
28 24 0.83
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (27 bp):
TAATATTGATTTTACAAAATCAATAAA
Found at i:1185523 original size:28 final size:31
Alignment explanation
Indices: 1185469--1185525 Score: 93
Period size: 28 Copynumber: 1.9 Consensus size: 31
1185459 ATATATAAAT
1185469 AATTATTTAATTGTCTTAAATTAAAATAAGA
1 AATTATTTAATTGTCTTAAATTAAAATAAGA
1185500 AATTATTTAA-T-T-TTAAATTAAAATAA
1 AATTATTTAATTGTCTTAAATTAAAATAA
1185526 ATTAAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 14 0.54
29 1 0.04
30 1 0.04
31 10 0.38
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (31 bp):
AATTATTTAATTGTCTTAAATTAAAATAAGA
Found at i:1187809 original size:228 final size:228
Alignment explanation
Indices: 1187419--1188296 Score: 1105
Period size: 228 Copynumber: 3.9 Consensus size: 228
1187409 GTGCAAAGTT
* * * ** * * *
1187419 GATTCCTTCTGGATGTTGTAGTCTG-CAAGGGTCCTCCCATCTTCAAGTTGCTTCCCAGCAAAGA
1 GATTCCTTCTGGATGTTGTAATCAGCCAA-GGTGCGGCCATCCTCGAGTTGCTTACCAGCAAAGA
* * * * * * *
1187483 TCAGCCTCTGCTGGTCTGGGGGGATTCCCTCCTTATCCTGGATCTTAGCCTTAACATTATCAATC
65 TCAACCTCTGCTGGTCTGGGGGGATACCCTCCTTGTCCTGAATCTTAGCCTTGACATTGTCAATG
* * * * * ** * * *
1187548 GTGTCCGAGCTCTCGACTTCCAGGGTGATGGTCTTTCCAGTCAGGGTCTTCACAAAAATCTGCAT
130 GTATCTGAACTCTCCACCTCCAATGTGATGGTCTTTCCAGTGAGGGTCTTAACAAAAATTTGCAT
* * * * *
1187613 CCCACCAC-GAAGGCGAAGCACCAAGTGGAGGGTG
195 ACCACCACTCAA-ACGAAGGACCAAGTGGAGTGTG
*
1187647 GACTCCTTCTGGATGTTGTAATCAGCCAAGGTGCGGCCATCCTCGAGTTGCTTACCAGCAAAGAT
1 GATTCCTTCTGGATGTTGTAATCAGCCAAGGTGCGGCCATCCTCGAGTTGCTTACCAGCAAAGAT
1187712 CAACCTCTGCTGGTCTGGGGGGATACCCTCCTTGTCCTGAATCTTAGCCTTGACATTGTCAATGG
66 CAACCTCTGCTGGTCTGGGGGGATACCCTCCTTGTCCTGAATCTTAGCCTTGACATTGTCAATGG
* * * * *
1187777 TATCTGAACTCTCCACCTCCAATGTAATGGTCTTTCCCGTGAGGGTCTTGACGAATATTTGCATA
131 TATCTGAACTCTCCACCTCCAATGTGATGGTCTTTCCAGTGAGGGTCTTAACAAAAATTTGCATA
* *
1187842 CCACCCCTCAATCGAAGGACCAAGTGGAGTGTG
196 CCACCACTCAAACGAAGGACCAAGTGGAGTGTG
*
1187875 GATTCCTTTTGGATGTTGTAATCAGCCAAGGTGCGGCCATCCTCGAGTTGCTTACCAGCAAAGAT
1 GATTCCTTCTGGATGTTGTAATCAGCCAAGGTGCGGCCATCCTCGAGTTGCTTACCAGCAAAGAT
1187940 CAACCTCTGCTGGTCTGGGGGGATACCCTCCTTGTCCTGAATCTTAGCCTTGACATTGTCAATGG
66 CAACCTCTGCTGGTCTGGGGGGATACCCTCCTTGTCCTGAATCTTAGCCTTGACATTGTCAATGG
* *
1188005 TATCTGAACTCTCCACCTCCAATGTGATGGTCTTTCCTGTGAGGGTCTTAACAAAAATTTGCATT
131 TATCTGAACTCTCCACCTCCAATGTGATGGTCTTTCCAGTGAGGGTCTTAACAAAAATTTGCATA
*
1188070 CCACCTCTCAAACGAAGGACCAAGTGGAGTGTG
196 CCACCACTCAAACGAAGGACCAAGTGGAGTGTG
* * * * * * *
1188103 GATTCCTTCTGGATGTTATAGTC-GGCAAGAGTACGGCCATCCTCCAGCTGTTTACCAGCAAAGA
1 GATTCCTTCTGGATGTTGTAATCAGCCAAG-GTGCGGCCATCCTCGAGTTGCTTACCAGCAAAGA
* * * * * * * * *
1188167 TCAATCTCTGTTGGTCTGGTGGGATTCCTTCCTTGTCTTGAATCTTGGCCTTTACATTGTCGATG
65 TCAACCTCTGCTGGTCTGGGGGGATACCCTCCTTGTCCTGAATCTTAGCCTTGACATTGTCAATG
* * * ** * * * *
1188232 GTATCAGAACTTTCCACCTCGAGGGTGATGGTCTTACCAGTGAGTGTTTTAACGAAAATTTGCAT
130 GTATCTGAACTCTCCACCTCCAATGTGATGGTCTTTCCAGTGAGGGTCTTAACAAAAATTTGCAT
1188297 CTATATTGAA
Statistics
Matches: 574, Mismatches: 73, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
227 5 0.01
228 564 0.98
229 5 0.01
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (228 bp):
GATTCCTTCTGGATGTTGTAATCAGCCAAGGTGCGGCCATCCTCGAGTTGCTTACCAGCAAAGAT
CAACCTCTGCTGGTCTGGGGGGATACCCTCCTTGTCCTGAATCTTAGCCTTGACATTGTCAATGG
TATCTGAACTCTCCACCTCCAATGTGATGGTCTTTCCAGTGAGGGTCTTAACAAAAATTTGCATA
CCACCACTCAAACGAAGGACCAAGTGGAGTGTG
Found at i:1189469 original size:29 final size:28
Alignment explanation
Indices: 1189420--1189479 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
1189410 AAAAATAAAT
* *
1189420 ATAAATGTGTAGATATTTTTTTAATA-A
1 ATAAATATGTAGATATTTTTTGAATAGA
1189447 ATAAATATGTAGATATTAGTTTTGAATAGA
1 ATAAATATGTAGATATT--TTTTGAATAGA
1189477 ATA
1 ATA
1189480 GAGCAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 16 0.57
29 8 0.29
30 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (28 bp):
ATAAATATGTAGATATTTTTTGAATAGA
Found at i:1203646 original size:21 final size:21
Alignment explanation
Indices: 1203622--1203674 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1203612 ATTATGACTA
*
1203622 TCGCATTGTGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1203643 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1203664 TCGCAATGCGA
1 TCGCATTGCGA
1203675 ATACGTAATC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1203739 original size:20 final size:20
Alignment explanation
Indices: 1203714--1203782 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
1203704 CGAATTTGGA
*
1203714 AAATCGCAATGCGATTACGT
1 AAATCGCAATGCGAATACGT
1203734 AAATCGCAATGCGAATACGT
1 AAATCGCAATGCGAATACGT
1203754 AAATCGCAATGCGAAT-CTGT
1 AAATCGCAATGCGAATAC-GT
1203774 AAATCGCAA
1 AAATCGCAA
1203783 CGAGATTCTG
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 1 0.02
20 46 0.98
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (20 bp):
AAATCGCAATGCGAATACGT
Found at i:1203792 original size:20 final size:19
Alignment explanation
Indices: 1203714--1203790 Score: 57
Period size: 20 Copynumber: 3.9 Consensus size: 19
1203704 CGAATTTGGA
* *
1203714 AAATCGCAATGCGATTACGT
1 AAATCGCAACGAGATT-CGT
*
1203734 AAATCGCAATGCGA-ATACGT
1 AAATCGCAA--CGAGATTCGT
* * *
1203754 AAATCGCAATGCGAATCTGT
1 AAATCGCAACGAGATTC-GT
1203774 AAATCGCAACGAGATTC
1 AAATCGCAACGAGATTC
1203791 TGACTATCGC
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
19 2 0.05
20 37 0.86
21 2 0.05
22 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGAGATTCGT
Found at i:1207133 original size:20 final size:20
Alignment explanation
Indices: 1207108--1207195 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
1207098 GACATTCATT
1207108 TGACTATCGCAACAC-GAACA
1 TGACTATCGCAACACGGAA-A
*
1207128 TGACTATTGCAACACGGAAA
1 TGACTATCGCAACACGGAAA
* *
1207148 TGACTATCGCAACGCGGAAT
1 TGACTATCGCAACACGGAAA
* *
1207168 TGACAATCGCAACGCGGAAA
1 TGACTATCGCAACACGGAAA
1207188 TGACTATC
1 TGACTATC
1207196 ACAATGAGAG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 57 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (20 bp):
TGACTATCGCAACACGGAAA
Found at i:1207393 original size:14 final size:14
Alignment explanation
Indices: 1207374--1207410 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1207364 CATCAATTAA
1207374 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1207388 ACAAATCATCTTTT
1 ACAAATCAACATTT
1207402 ACAAATCAA
1 ACAAATCAA
1207411 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1209429 original size:33 final size:34
Alignment explanation
Indices: 1209356--1209452 Score: 106
Period size: 33 Copynumber: 2.9 Consensus size: 34
1209346 TCTGAAACTT
** * *
1209356 AAAATCGCAACGCAAAAATGACTATCGCAACGAG
1 AAAATCGCAACGCAAAAATGAAAATCGCAACAAC
* * *
1209390 AGAATCGCAATGC-GAAATGAAAATCGCAACAAC
1 AAAATCGCAACGCAAAAATGAAAATCGCAACAAC
**
1209423 AAAATCGCAACGCAAAAATGACTATCGCAA
1 AAAATCGCAACGCAAAAATGAAAATCGCAA
1209453 TGCGAAAATG
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
33 26 0.52
34 24 0.48
ACGTcount: A:0.48, C:0.23, G:0.16, T:0.12
Consensus pattern (34 bp):
AAAATCGCAACGCAAAAATGAAAATCGCAACAAC
Found at i:1209473 original size:20 final size:20
Alignment explanation
Indices: 1209426--1209512 Score: 102
Period size: 20 Copynumber: 4.3 Consensus size: 20
1209416 CAACAACAAA
* *
1209426 ATCGCAACGCAAAAATGACT
1 ATCGCAATGCGAAAATGACT
1209446 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* **
1209466 ATCGCAATGTGAATTTGACT
1 ATCGCAATGCGAAAATGACT
* **
1209486 ATCGCAATGTGAATTTGACT
1 ATCGCAATGCGAAAATGACT
1209506 ATCGCAA
1 ATCGCAA
1209513 CGAGAGAATC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:1209549 original size:19 final size:19
Alignment explanation
Indices: 1209521--1209586 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
1209511 AACGAGAGAA
*
1209521 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1209540 TCGCATTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
**
1209556 TCG--TTGCGATAGTCATTT
1 TCGCATTGCGATTTTCA-TT
1209574 TCGCATTGCGATT
1 TCGCATTGCGATT
1209587 CTCTCATTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
14 6 0.16
16 7 0.18
17 3 0.08
18 5 0.13
19 10 0.26
20 7 0.18
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1209581 original size:34 final size:34
Alignment explanation
Indices: 1209538--1209653 Score: 214
Period size: 34 Copynumber: 3.4 Consensus size: 34
1209528 GCGATTTTCA
* *
1209538 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
1 TTTCGCATTGCGATTCTCTCATTGCGATAGTCAT
1209572 TTTCGCATTGCGATTCTCTCATTGCGATAGTCAT
1 TTTCGCATTGCGATTCTCTCATTGCGATAGTCAT
1209606 TTTCGCATTGCGATTCTCTCATTGCGATAGTCAT
1 TTTCGCATTGCGATTCTCTCATTGCGATAGTCAT
1209640 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1209654 AGTAAACTAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 80 1.00
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.42
Consensus pattern (34 bp):
TTTCGCATTGCGATTCTCTCATTGCGATAGTCAT
Found at i:1209584 original size:20 final size:20
Alignment explanation
Indices: 1209559--1209656 Score: 94
Period size: 20 Copynumber: 5.5 Consensus size: 20
1209549 GATTCTTTCG
1209559 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1209579 TTGCGAT--TC----TCTCA
1 TTGCGATAGTCATTTTCGCA
1209593 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1209613 TTGCGAT--TC----TCTCA
1 TTGCGATAGTCATTTTCGCA
1209627 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1209647 TTGCGATAGT
1 TTGCGATAGT
1209657 AAACTATTCT
Statistics
Matches: 62, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
14 22 0.35
16 4 0.06
18 4 0.06
20 32 0.52
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1209596 original size:14 final size:14
Alignment explanation
Indices: 1209577--1209633 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 14
1209567 GTCATTTTCG
1209577 CATTGCGATTCTCT
1 CATTGCGATTCTCT
*
1209591 CATTGCGATAGTCATTTTCG
1 CATTGCGAT--TC----TCT
1209611 CATTGCGATTCTCT
1 CATTGCGATTCTCT
1209625 CATTGCGAT
1 CATTGCGAT
1209634 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
18 2 0.06
20 11 0.31
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.40
Consensus pattern (14 bp):
CATTGCGATTCTCT
Found at i:1211556 original size:19 final size:20
Alignment explanation
Indices: 1211518--1211567 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1211508 CTGAAACTTT
*
1211518 AAATCGCAACACGAAAATGA
1 AAATCGCAACGCGAAAATGA
**
1211538 CTATCGCAACGCG-AAATGA
1 AAATCGCAACGCGAAAATGA
1211557 AAATCGCAACG
1 AAATCGCAACG
1211568 ACAGAATCGC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.46, C:0.24, G:0.18, T:0.12
Consensus pattern (20 bp):
AAATCGCAACGCGAAAATGA
Found at i:1211964 original size:22 final size:22
Alignment explanation
Indices: 1211903--1211964 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
1211893 TGACCGTGAA
*
1211903 TGATTTCG-CTGGAGATGGAGAC
1 TGATTTCGTC-GGAGATGGGGAC
*
1211925 TGATATCGTC---G-TGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
1211943 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
1211965 GGATGTCGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
18 15 0.47
19 1 0.03
21 1 0.03
22 14 0.44
23 1 0.03
ACGTcount: A:0.19, C:0.15, G:0.39, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:1212165 original size:20 final size:20
Alignment explanation
Indices: 1212137--1212174 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1212127 ATGGCGCTAT
*
1212137 GTAAACGCATTGCTATTTAC
1 GTAAACGCATTGCGATTTAC
*
1212157 GTAATCGCATTGCGATTT
1 GTAAACGCATTGCGATTT
1212175 TCCAAATTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (20 bp):
GTAAACGCATTGCGATTTAC
Found at i:1212210 original size:20 final size:20
Alignment explanation
Indices: 1212142--1212212 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
1212132 GCTATGTAAA
* *
1212142 CGCATTGCTATTTACGTAAT
1 CGCATTGCGATTTACGTATT
* **
1212162 CGCATTGCGATTTTCCAAATT
1 CGCATTGCGA-TTTACGTATT
* *
1212183 CGCGTTGCGATTTACGTGTT
1 CGCATTGCGATTTACGTATT
1212203 CGCATTGCGA
1 CGCATTGCGA
1212213 ATTTGGGAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 24 0.62
21 15 0.38
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
CGCATTGCGATTTACGTATT
Found at i:1216296 original size:16 final size:16
Alignment explanation
Indices: 1216275--1216328 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
1216265 TAGTGACCAA
1216275 AATATAATAAATCAAT
1 AATATAATAAATCAAT
*
1216291 AATATAA-ATGATCAA-
1 AATATAATA-AATCAAT
1216306 AATATAATAAATCAAT
1 AATATAATAAATCAAT
1216322 AATATAA
1 AATATAA
1216329 ATGACCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 13 0.39
16 20 0.61
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.30
Consensus pattern (16 bp):
AATATAATAAATCAAT
Found at i:1216307 original size:31 final size:31
Alignment explanation
Indices: 1216268--1216338 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
1216258 ATGTTTGTAG
1216268 TGACCAAAATATAATAAATCAATAATATAAA
1 TGACCAAAATATAATAAATCAATAATATAAA
*
1216299 TGATCAAAATATAATAAATCAATAATATAAA
1 TGACCAAAATATAATAAATCAATAATATAAA
1216330 TGACCAAAA
1 TGACCAAAA
1216339 CAAAAAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.61, C:0.10, G:0.04, T:0.25
Consensus pattern (31 bp):
TGACCAAAATATAATAAATCAATAATATAAA
Found at i:1217932 original size:98 final size:98
Alignment explanation
Indices: 1217763--1217944 Score: 364
Period size: 98 Copynumber: 1.9 Consensus size: 98
1217753 CAACAGATTA
1217763 TTTGACAGTTTTGAAAAGGTAAAAGAATCAATCTCTGAATCAATCTTTGCAGAAAAATGAACGTT
1 TTTGACAGTTTTGAAAAGGTAAAAGAATCAATCTCTGAATCAATCTTTGCAGAAAAATGAACGTT
1217828 TAATATCAGGCTAAGATTGCAAAAGAATCAATC
66 TAATATCAGGCTAAGATTGCAAAAGAATCAATC
1217861 TTTGACAGTTTTGAAAAGGTAAAAGAATCAATCTCTGAATCAATCTTTGCAGAAAAATGAACGTT
1 TTTGACAGTTTTGAAAAGGTAAAAGAATCAATCTCTGAATCAATCTTTGCAGAAAAATGAACGTT
1217926 TAATATCAGGCTAAGATTG
66 TAATATCAGGCTAAGATTG
1217945 TAAACGCTTT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 84 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (98 bp):
TTTGACAGTTTTGAAAAGGTAAAAGAATCAATCTCTGAATCAATCTTTGCAGAAAAATGAACGTT
TAATATCAGGCTAAGATTGCAAAAGAATCAATC
Found at i:1220808 original size:33 final size:33
Alignment explanation
Indices: 1220741--1220832 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 33
1220731 AGAAAGCAGC
**
1220741 GGTGCAGCACGAGGACCAGGAGAAGGAGGCGGT
1 GGTGCAGCACGAGGACCAGGAGAAGGAGAAGGT
* * * *
1220774 GGTGCAGCAGGAGGTCCAGGGGAAGGCGAAGGT
1 GGTGCAGCACGAGGACCAGGAGAAGGAGAAGGT
* * * *
1220807 GGTTCGGCAAGAGGACCTGGAGAAGG
1 GGTGCAGCACGAGGACCAGGAGAAGG
1220833 TGGTTCGGCA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.26, C:0.16, G:0.49, T:0.09
Consensus pattern (33 bp):
GGTGCAGCACGAGGACCAGGAGAAGGAGAAGGT
Found at i:1220839 original size:27 final size:27
Alignment explanation
Indices: 1220801--1221143 Score: 370
Period size: 27 Copynumber: 12.7 Consensus size: 27
1220791 AGGGGAAGGC
* * *
1220801 GAAGGTGGTTCGGCAAGAGGACCTGGA
1 GAAGGTGGTTCGGCACGAGGATCAGGA
* *
1220828 GAAGGTGGTTCGGCAAGAGGATCTGGA
1 GAAGGTGGTTCGGCACGAGGATCAGGA
* *
1220855 GAAGGTGATTCGGCACGAGGATCTGGA
1 GAAGGTGGTTCGGCACGAGGATCAGGA
* *
1220882 AAAGGT-GTTGCGGCAGGAGGATCAGGA
1 GAAGGTGGTT-CGGCACGAGGATCAGGA
*
1220909 GAAGGTGGTGCGGCACGAGGATCAGGA
1 GAAGGTGGTTCGGCACGAGGATCAGGA
* * ** *
1220936 AAAGGTGGTGCTACAGGAGGATCAGGA
1 GAAGGTGGTTCGGCACGAGGATCAGGA
* * *
1220963 GAAGGTGGTGT-AGCATGAGGATCAGGT
1 GAAGGTGGT-TCGGCACGAGGATCAGGA
1220990 GAAGGTGGTTCGGCACGAGGATCAGGA
1 GAAGGTGGTTCGGCACGAGGATCAGGA
*
1221017 AAAGGTGGTGT-GGCACGAGGATCAGGA
1 GAAGGTGGT-TCGGCACGAGGATCAGGA
* * * *
1221044 AAAGGTGGTGCGCCACGAGGATCAGGT
1 GAAGGTGGTTCGGCACGAGGATCAGGA
* *
1221071 GAAGGTGGTGCGCCACGAGGATCAGGA
1 GAAGGTGGTTCGGCACGAGGATCAGGA
*
1221098 AAAGGTGGTGT-GGCACGAGGATCAGGA
1 GAAGGTGGT-TCGGCACGAGGATCAGGA
* *
1221125 GAAGGTGGTGCAGCACGAG
1 GAAGGTGGTTCGGCACGAG
1221144 CACAGAGGTA
Statistics
Matches: 273, Mismatches: 35, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
26 3 0.01
27 267 0.98
28 3 0.01
ACGTcount: A:0.27, C:0.13, G:0.44, T:0.15
Consensus pattern (27 bp):
GAAGGTGGTTCGGCACGAGGATCAGGA
Found at i:1221142 original size:81 final size:81
Alignment explanation
Indices: 1220801--1221143 Score: 422
Period size: 81 Copynumber: 4.2 Consensus size: 81
1220791 AGGGGAAGGC
* * * * * * * * * *
1220801 GAAGGTGGTTCGGCAAGAGGACCTGGAGAAGGTGGTTCGGCAAGAGGATCTGGAGAAGGTGAT-T
1 GAAGGTGGTGCAGCACGAGGATCAGGAGAAGGTGGTGCGGCACGAGGATCAGGAAAAGGTGGTGT
*
1220865 CGGCACGAGGATCTGGA
66 -GGCACGAGGATCAGGA
* * * *
1220882 AAAGGTGTTGCGGCAGGAGGATCAGGAGAAGGTGGTGCGGCACGAGGATCAGGAAAAGGTGGTGC
1 GAAGGTGGTGCAGCACGAGGATCAGGAGAAGGTGGTGCGGCACGAGGATCAGGAAAAGGTGGTG-
* *
1220947 T-ACAGGAGGATCAGGA
65 TGGCACGAGGATCAGGA
* * * *
1220963 GAAGGTGGTGTAGCATGAGGATCAGGTGAAGGTGGTTCGGCACGAGGATCAGGAAAAGGTGGTGT
1 GAAGGTGGTGCAGCACGAGGATCAGGAGAAGGTGGTGCGGCACGAGGATCAGGAAAAGGTGGTGT
1221028 GGCACGAGGATCAGGA
66 GGCACGAGGATCAGGA
* * *
1221044 AAAGGTGGTGC-GCCACGAGGATCAGGTGAAGGTGGTGCGCCACGAGGATCAGGAAAAGGTGGTG
1 GAAGGTGGTGCAG-CACGAGGATCAGGAGAAGGTGGTGCGGCACGAGGATCAGGAAAAGGTGGTG
1221108 TGGCACGAGGATCAGGA
65 TGGCACGAGGATCAGGA
1221125 GAAGGTGGTGCAGCACGAG
1 GAAGGTGGTGCAGCACGAG
1221144 CACAGAGGTA
Statistics
Matches: 228, Mismatches: 29, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
80 2 0.01
81 224 0.98
82 1 0.00
83 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.44, T:0.15
Consensus pattern (81 bp):
GAAGGTGGTGCAGCACGAGGATCAGGAGAAGGTGGTGCGGCACGAGGATCAGGAAAAGGTGGTGT
GGCACGAGGATCAGGA
Found at i:1221421 original size:297 final size:307
Alignment explanation
Indices: 1221042--1221646 Score: 1122
Period size: 297 Copynumber: 2.0 Consensus size: 307
1221032 CGAGGATCAG
1221042 GAAAAGGTGGTGCGCCACGAGGATCAGGTGAAGGTGGTGCGCCACGAGGATCAGGAAAAGGTGGT
1 GAAAAGGTGGTGCGCCACGAGGATCAGGTGAAGGTGGTGCGCCACGAGGATCAGGAAAAGGTGGT
1221107 GTGGCACGAGGATCAGGAGAAGGTGGTGCAGCACGAG-CACAGAGGT-A-GATACATTGGACCCC
66 GTGGCACGAGGATCAGGAGAAGGTGGTGCAGCACGAGACACAGAGGTAATGATACATTGGACCCC
1221169 TGCTTTTTA-GTGGTGGCTTAATAGGGCAA-TTTT-ACCTC-TTGCACACCTTATCC-AAATAAC
131 TGCTTTTTAGGTGGTGGCTTAATAGGGCAATTTTTAACCTCTTTGCACACCTTATCCAAAATAAC
1221229 C-AAAAATCTCGAACAATGGAAAACAATCGCAAGCCCTCATCCTTTTTCACATTACCATGAAAGT
196 CAAAAAATCTCGAACAATGGAAAACAATCGCAAGCCCTCATCCTTTTTCACATTACCATGAAAGT
1221293 -ATCGCCGGTGCTCTTCACTAAATCCATTACTTTCTTCTCCTCCTCA
261 AATCGCCGGTGCTCTTCACTAAATCCATTACTTTCTTCTCCTCCTCA
1221339 GAAAAGGTGGTGCGCCACGAGGATCAGGTGAAGGTGGTGCGCCACGAGGATCAGGAAAAGGTGGT
1 GAAAAGGTGGTGCGCCACGAGGATCAGGTGAAGGTGGTGCGCCACGAGGATCAGGAAAAGGTGGT
*
1221404 GTGGCACGAGGATCAGGAGAAGGTGGTGCAGCACGAGACTCAGAGGTAGATGATACATTGGACCC
66 GTGGCACGAGGATCAGGAGAAGGTGGTGCAGCACGAGACACAGAGGTA-ATGATACATTGGACCC
1221469 CTGCTTTTTAGGTGGTGGCTTAATAGGGCAATTTTTAACCTCTTTGCACACCTTATCCAAAATAA
130 CTGCTTTTTAGGTGGTGGCTTAATAGGGCAATTTTTAACCTCTTTGCACACCTTATCCAAAATAA
1221534 CCAAAAAATCTCGAACAATGGAAAACAATCGCAAGCCCTCATCCTTTTTCACATTACCATGAAAG
195 CCAAAAAATCTCGAACAATGGAAAACAATCGCAAGCCCTCATCCTTTTTCACATTACCATGAAAG
1221599 TAATCGCCGGTGCTCTTCACTAAATCCATTACTTTCTTCTCCTCCTCA
260 TAATCGCCGGTGCTCTTCACTAAATCCATTACTTTCTTCTCCTCCTCA
1221647 AGCAACGACA
Statistics
Matches: 296, Mismatches: 1, Indels: 11
0.96 0.00 0.04
Matches are distributed among these distances:
297 102 0.34
298 8 0.03
300 1 0.00
301 24 0.08
302 20 0.07
303 4 0.01
304 5 0.02
305 15 0.05
306 8 0.03
307 63 0.21
308 46 0.16
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (307 bp):
GAAAAGGTGGTGCGCCACGAGGATCAGGTGAAGGTGGTGCGCCACGAGGATCAGGAAAAGGTGGT
GTGGCACGAGGATCAGGAGAAGGTGGTGCAGCACGAGACACAGAGGTAATGATACATTGGACCCC
TGCTTTTTAGGTGGTGGCTTAATAGGGCAATTTTTAACCTCTTTGCACACCTTATCCAAAATAAC
CAAAAAATCTCGAACAATGGAAAACAATCGCAAGCCCTCATCCTTTTTCACATTACCATGAAAGT
AATCGCCGGTGCTCTTCACTAAATCCATTACTTTCTTCTCCTCCTCA
Found at i:1221446 original size:27 final size:27
Alignment explanation
Indices: 1221342--1221440 Score: 146
Period size: 27 Copynumber: 3.7 Consensus size: 27
1221332 CTCCTCAGAA
*
1221342 AAGGTGGTGCGCCACGAGGATCAGGTG
1 AAGGTGGTGCGCCACGAGGATCAGGAG
*
1221369 AAGGTGGTGCGCCACGAGGATCAGGAA
1 AAGGTGGTGCGCCACGAGGATCAGGAG
* *
1221396 AAGGTGGTGTGGCACGAGGATCAGGAG
1 AAGGTGGTGCGCCACGAGGATCAGGAG
1221423 AAGGTGGTGCAG-CACGAG
1 AAGGTGGTGC-GCCACGAG
1221441 ACTCAGAGGT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 64 0.98
28 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.44, T:0.13
Consensus pattern (27 bp):
AAGGTGGTGCGCCACGAGGATCAGGAG
Found at i:1223182 original size:36 final size:34
Alignment explanation
Indices: 1223126--1223195 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 34
1223116 CCCTGAGCCA
*
1223126 CACCAGCACACCTTTGGAGGAGGTGGTGGAGGAG
1 CACCAGCACACCTTTGGAGGAGGAGGTGGAGGAG
*
1223160 CACCAGCACCACCTTTTGGAGGAGGAGGTGGTGGAG
1 CACCAGCA-CACC-TTTGGAGGAGGAGGTGGAGGAG
1223196 GACCTGGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 8 0.25
35 4 0.12
36 20 0.62
ACGTcount: A:0.23, C:0.21, G:0.40, T:0.16
Consensus pattern (34 bp):
CACCAGCACACCTTTGGAGGAGGAGGTGGAGGAG
Found at i:1226305 original size:14 final size:14
Alignment explanation
Indices: 1226286--1226316 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1226276 AGAGCCTTAC
1226286 ACTCTATCAACTGA
1 ACTCTATCAACTGA
1226300 ACTCTATCAACTGA
1 ACTCTATCAACTGA
1226314 ACT
1 ACT
1226317 GAACGGACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29
Consensus pattern (14 bp):
ACTCTATCAACTGA
Found at i:1228725 original size:17 final size:17
Alignment explanation
Indices: 1228692--1228731 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
1228682 ATCTGAAAAT
1228692 TTTTAATTTATTATATA
1 TTTTAATTTATTATATA
*
1228709 TTTTATATTTTTCTATATA
1 TTTTA-ATTTAT-TATATA
1228728 TTTT
1 TTTT
1228732 CTTTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 5 0.25
19 10 0.50
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTAATTTATTATATA
Found at i:1229566 original size:13 final size:13
Alignment explanation
Indices: 1229548--1229577 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1229538 CCTTTTATGA
1229548 TTTTTTTAATAAT
1 TTTTTTTAATAAT
1229561 TTTTTTTAATAAT
1 TTTTTTTAATAAT
1229574 TTTT
1 TTTT
1229578 AATATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTTTTAATAAT
Found at i:1230402 original size:6 final size:6
Alignment explanation
Indices: 1230393--1230417 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1230383 GGGATGATAA
1230393 ACGGGG ACGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG A
1230418 AAACCCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.64, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:1230517 original size:12 final size:13
Alignment explanation
Indices: 1230481--1230524 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
1230471 GCCCCGATTA
1230481 CCCGATTACCCGC
1 CCCGATTACCCGC
1230494 CCCGATTACCCGC
1 CCCGATTACCCGC
*
1230507 CCCGA-TACCCGA
1 CCCGATTACCCGC
1230519 CCCGAT
1 CCCGAT
1230525 AAATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.18, C:0.52, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:1230578 original size:32 final size:32
Alignment explanation
Indices: 1230526--1230622 Score: 101
Period size: 32 Copynumber: 3.0 Consensus size: 32
1230516 CGACCCGATA
*
1230526 AATATTAA-AAATAATT-ATTTATATATATATAT
1 AATATTAATAAAT--TTAATTTAAATATATATAT
* *
1230558 AATATTAATAAATTTAATTTAAATA-AAAAAT
1 AATATTAATAAATTTAATTTAAATATATATAT
* *
1230589 ATATATTTATATATTTAATTTAAATATATATAT
1 A-ATATTAATAAATTTAATTTAAATATATATAT
1230622 A
1 A
1230623 TACCCGACCC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
31 7 0.13
32 38 0.70
33 9 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
AATATTAATAAATTTAATTTAAATATATATAT
Found at i:1230654 original size:24 final size:24
Alignment explanation
Indices: 1230622--1230676 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
1230612 ATATATATAT
* * *
1230622 ATACCCGACCCGATTCTCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
1230646 ATACCCGACCCAATACCCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
1230670 ATACCCG
1 ATACCCG
1230677 TTTAAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.47, G:0.15, T:0.13
Consensus pattern (24 bp):
ATACCCGACCCAATACCCGGCCCA
Found at i:1230659 original size:12 final size:12
Alignment explanation
Indices: 1230622--1230676 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
1230612 ATATATATAT
*
1230622 ATACCCGACCCG
1 ATACCCGACCCA
* * *
1230634 ATTCTCGGCCCA
1 ATACCCGACCCA
1230646 ATACCCGACCCA
1 ATACCCGACCCA
*
1230658 ATACCCGGCCCA
1 ATACCCGACCCA
1230670 ATACCCG
1 ATACCCG
1230677 TTTAAATAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.25, C:0.47, G:0.15, T:0.13
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:1235480 original size:24 final size:25
Alignment explanation
Indices: 1235431--1235480 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 25
1235421 AATAAAAATA
* *
1235431 AAAAATAAATTAAAATTTCTATAAT
1 AAAAATAAATTAAAATTTATAGAAT
1235456 AAAAAT-AA-TAAAATTTATACGAAT
1 AAAAATAAATTAAAATTTATA-GAAT
1235480 A
1 A
1235481 CCCAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 10 0.45
24 6 0.27
25 6 0.27
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (25 bp):
AAAAATAAATTAAAATTTATAGAAT
Found at i:1240088 original size:17 final size:17
Alignment explanation
Indices: 1240029--1240139 Score: 61
Period size: 17 Copynumber: 6.4 Consensus size: 17
1240019 CATTTTTGGA
* *
1240029 TTAAATGATTTAATTAT
1 TTAAATAATTTGATTAT
* * *
1240046 TTAAATTAGAGTCGAATAT
1 TTAAA-TA-ATTTGATTAT
1240065 ATTAAATAATTTGATTAT
1 -TTAAATAATTTGATTAT
*
1240083 TTAAATATAAATTG--TAT
1 TT-AA-ATAATTTGATTAT
*
1240100 TTAATTGAA-TT-A-TAT
1 TTAAAT-AATTTGATTAT
1240115 ATTAAATAATTTGATTAT
1 -TTAAATAATTTGATTAT
1240133 TTAAATA
1 TTAAATA
1240140 TAAGTACCTA
Statistics
Matches: 72, Mismatches: 11, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
15 8 0.11
16 11 0.15
17 20 0.28
18 13 0.18
19 15 0.21
20 5 0.07
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (17 bp):
TTAAATAATTTGATTAT
Found at i:1240888 original size:29 final size:29
Alignment explanation
Indices: 1240855--1240917 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1240845 CTAAATGAGT
1240855 TTACACCTAAATTAA-TTTGATGTCATTGC
1 TTACACC-AAATTAATTTTGATGTCATTGC
* *
1240884 TTACATCAATTTAATTTTGATGTCATTGC
1 TTACACCAAATTAATTTTGATGTCATTGC
1240913 TTACA
1 TTACA
1240918 TCAATTTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 6 0.19
29 25 0.81
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (29 bp):
TTACACCAAATTAATTTTGATGTCATTGC
Found at i:1240918 original size:29 final size:28
Alignment explanation
Indices: 1240866--1240925 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 28
1240856 TACACCTAAA
1240866 TTAATTTGATGTCATTGCTTACATCAAT
1 TTAATTTGATGTCATTGCTTACATCAAT
1240894 TTAATTTTGATGTCATTGCTTACATCAAT
1 TTAA-TTTGATGTCATTGCTTACATCAAT
1240923 TTA
1 TTA
1240926 GTTAGGTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.48
Consensus pattern (28 bp):
TTAATTTGATGTCATTGCTTACATCAAT
Found at i:1243116 original size:12 final size:12
Alignment explanation
Indices: 1243101--1243131 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1243091 GTTATTTAAA
1243101 CGGGTATTGGGC
1 CGGGTATTGGGC
1243113 CGGGTATTGGGC
1 CGGGTATTGGGC
*
1243125 CGAGTAT
1 CGGGTAT
1243132 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.16, G:0.45, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:1243172 original size:27 final size:27
Alignment explanation
Indices: 1243134--1243189 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
1243124 CCGAGTATAT
*
1243134 ATATATATATATATATTTTTAAATTAA
1 ATATATAAATATATATTTTTAAATTAA
* *
1243161 ATATATAAATATATATTTTTTATTTAA
1 ATATATAAATATATATTTTTAAATTAA
1243188 AT
1 AT
1243190 TAAATTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATATATAAATATATATTTTTAAATTAA
Found at i:1243265 original size:13 final size:13
Alignment explanation
Indices: 1243235--1243283 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
1243225 TTTAATATTT
*
1243235 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
1243247 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
*
1243260 ATCGGGTCGGGTA
1 ATCGGGGCGGGTA
1243273 ATCGGGGCGGG
1 ATCGGGGCGGG
1243284 GATTACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
12 11 0.33
13 22 0.67
ACGTcount: A:0.12, C:0.16, G:0.53, T:0.18
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:1243269 original size:25 final size:26
Alignment explanation
Indices: 1243235--1243283 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
1243225 TTTAATATTT
1243235 ATCGGGTCGGGT-ATCGGGGCGGGTA
1 ATCGGGTCGGGTAATCGGGGCGGGTA
1243260 ATCGGGTCGGGTAATCGGGGCGGG
1 ATCGGGTCGGGTAATCGGGGCGGG
1243284 GATTACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.12, C:0.16, G:0.53, T:0.18
Consensus pattern (26 bp):
ATCGGGTCGGGTAATCGGGGCGGGTA
Found at i:1246113 original size:29 final size:29
Alignment explanation
Indices: 1246079--1246137 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1246069 CCTAAATTAA
1246079 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
*
1246108 TTTGATGTTATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1246137 T
1 T
1246138 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1251598 original size:20 final size:21
Alignment explanation
Indices: 1251575--1251627 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1251565 GATAGTTAAA
1251575 TTAATTTAAAAT-ATAATTTT
1 TTAATTTAAAATCATAATTTT
* * *
1251595 TTAATATGAGATCATAATTTT
1 TTAATTTAAAATCATAATTTT
*
1251616 ATATATTTAAAA
1 TTA-ATTTAAAA
1251628 GTAATTATTA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 9 0.38
21 10 0.42
22 5 0.21
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (21 bp):
TTAATTTAAAATCATAATTTT
Found at i:1256169 original size:18 final size:18
Alignment explanation
Indices: 1256148--1256182 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1256138 TAAAGATTTT
*
1256148 ATTTATTTAGACATATTC
1 ATTTATTTAGAAATATTC
*
1256166 ATTTTTTTAGAAATATT
1 ATTTATTTAGAAATATT
1256183 TTAAAATTAT
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:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (18 bp):
ATTTATTTAGAAATATTC
Found at i:1256516 original size:19 final size:18
Alignment explanation
Indices: 1256483--1256519 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1256473 AAGGGAAAAA
*
1256483 CCAATTGATAAAATGCAG
1 CCAATAGATAAAATGCAG
1256501 CCAATAGATGAAAATGCAG
1 CCAATAGAT-AAAATGCAG
1256520 ATGCAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.19
Consensus pattern (18 bp):
CCAATAGATAAAATGCAG
Found at i:1268263 original size:138 final size:138
Alignment explanation
Indices: 1268014--1268291 Score: 502
Period size: 138 Copynumber: 2.0 Consensus size: 138
1268004 TTATCCATGA
*
1268014 AACAGTTGACCTCTTAGCTTCATAACCAGAAAATGAAGATGATCCCACGCTAGACTTGCTGGAGG
1 AACAGTTGACCTCTTAGCTTCATAACCAGAAAATGAAGATGATCCCACGCTAGACTTGCCGGAGG
*
1268079 AAGATTTACGGTCTGTTGATTCCGTCCTATTACTCCTATCATCATTAATCTCAACCCTTGATGCT
66 AAGATTTACGGTCTGTTGATTCCGTCCTATTACTCCTATCAGCATTAATCTCAACCCTTGATGCT
1268144 GGTCTCGT
131 GGTCTCGT
** *
1268152 AACAGTTGACCTCTTAGCTTCATAGGCAGAAAATGAAGATGATCCCACTCTAGACTTGCCGGAGG
1 AACAGTTGACCTCTTAGCTTCATAACCAGAAAATGAAGATGATCCCACGCTAGACTTGCCGGAGG
1268217 AAGATTTACGGTCTGTTGATTCCGTCCTATTACTCCTATCAGCATTAATCTCAACCCTTGATGCT
66 AAGATTTACGGTCTGTTGATTCCGTCCTATTACTCCTATCAGCATTAATCTCAACCCTTGATGCT
*
1268282 GGTCTTGT
131 GGTCTCGT
1268290 AA
1 AA
1268292 TAAAACTTTT
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 134 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (138 bp):
AACAGTTGACCTCTTAGCTTCATAACCAGAAAATGAAGATGATCCCACGCTAGACTTGCCGGAGG
AAGATTTACGGTCTGTTGATTCCGTCCTATTACTCCTATCAGCATTAATCTCAACCCTTGATGCT
GGTCTCGT
Found at i:1270176 original size:20 final size:20
Alignment explanation
Indices: 1270151--1270347 Score: 232
Period size: 20 Copynumber: 9.8 Consensus size: 20
1270141 CACTATCGCA
1270151 AATTCGCGTTGCGATTTTCC
1 AATTCGCGTTGCGATTTTCC
1270171 AATTCGCGTTGCGATTTTCC
1 AATTCGCGTTGCGATTTTCC
*
1270191 ATTTCGCGTTGCGATTTTCC
1 AATTCGCGTTGCGATTTTCC
* * **
1270211 AGTTCGCGTTGCGATAGTTGA
1 AATTCGCGTTGCGAT-TTTCC
* *
1270232 AAATCACGTTGCGATTTTCC
1 AATTCGCGTTGCGATTTTCC
* * **
1270252 ATTTCGCGTTGCGATAGTTGA
1 AATTCGCGTTGCGAT-TTTCC
*
1270273 AAATCGCGTTGCGATTTTCC
1 AATTCGCGTTGCGATTTTCC
* *
1270293 ATTTCGCGTTGCGATTTTTC
1 AATTCGCGTTGCGATTTTCC
*
1270313 ATTTCGCGTTGCGATTTTCC
1 AATTCGCGTTGCGATTTTCC
*
1270333 AGTTCGCGTTGCGAT
1 AATTCGCGTTGCGAT
1270348 AGTCTACAGT
Statistics
Matches: 148, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
20 119 0.80
21 29 0.20
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.40
Consensus pattern (20 bp):
AATTCGCGTTGCGATTTTCC
Found at i:1270243 original size:21 final size:21
Alignment explanation
Indices: 1270214--1270287 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
1270204 ATTTTCCAGT
1270214 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
1270235 TCACGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
1270255 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
1270276 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1270288 TTTCCATTTC
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:1270251 original size:41 final size:41
Alignment explanation
Indices: 1270154--1270350 Score: 254
Period size: 41 Copynumber: 4.9 Consensus size: 41
1270144 TATCGCAAAT
* * ** **
1270154 TCGCGTTGCGATTTTCCAATTCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
1270194 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
* *
1270235 TCACGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
* * ** **
1270276 TCGCGTTGCGATTTTCCATTTCGCGTTGCGAT-TTTTCATT
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
1270316 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGT
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGT
1270351 CTACAGTTGT
Statistics
Matches: 139, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
40 65 0.47
41 74 0.53
ACGTcount: A:0.15, C:0.22, G:0.23, T:0.40
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
Found at i:1270364 original size:22 final size:21
Alignment explanation
Indices: 1270339--1270451 Score: 99
Period size: 22 Copynumber: 5.4 Consensus size: 21
1270329 TTCCAGTTCG
1270339 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTT-T
* * **
1270361 CGTTGCGAT--TTTCCAAATT
1 CGTTGCGATAGTCTACAGTTT
1270380 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTT-T
* * **
1270402 CGTTGCGAT--TTTCCAAATT
1 CGTTGCGATAGTCTACAGTTT
1270421 CGTTGCGATAGTCTACAGTTAT
1 CGTTGCGATAGTCTACAGTT-T
1270443 CGTTGCGAT
1 CGTTGCGAT
1270452 TTTCCAAATT
Statistics
Matches: 69, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
19 20 0.29
20 10 0.14
21 10 0.14
22 29 0.42
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTTT
Found at i:1270373 original size:61 final size:60
Alignment explanation
Indices: 1270153--1270375 Score: 243
Period size: 61 Copynumber: 3.6 Consensus size: 60
1270143 CTATCGCAAA
* *
1270153 TTCGCGTTGCGAT-TTTCCAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAG
1 TTCGCGTTGCGATAGTTACAATT-GCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAG
* ** * ** *
1270213 TTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTT-ACAATTGCGTTGCGATTTTCCATTTCGCGTTGCGAT-TTTCCAG
* * * * *
1270275 ATCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATTTTTCATTTCGCGTTGCGATTTTCCAG
1 TTCGCGTTGCGATAGTTACAATT-GCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAG
*
1270335 TTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCA
1 TTCGCGTTGCGATAGT-TACAATTG-CGTTGCGATTTTCCA
1270376 AATTCGTTGC
Statistics
Matches: 130, Mismatches: 26, Indels: 12
0.77 0.15 0.07
Matches are distributed among these distances:
60 30 0.23
61 63 0.48
62 37 0.28
ACGTcount: A:0.15, C:0.22, G:0.23, T:0.40
Consensus pattern (60 bp):
TTCGCGTTGCGATAGTTACAATTGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAG
Found at i:1270384 original size:19 final size:19
Alignment explanation
Indices: 1270360--1270469 Score: 94
Period size: 19 Copynumber: 5.5 Consensus size: 19
1270350 TCTACAGTTG
1270360 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
1270379 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
1270400 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
* * **
1270420 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
1270441 ATCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
1270461 TCGTTGCGA
1 TCGTTGCGA
1270470 AAATTCGTTG
Statistics
Matches: 69, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
19 29 0.42
20 10 0.14
21 10 0.14
22 20 0.29
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:1270384 original size:122 final size:121
Alignment explanation
Indices: 1270154--1270429 Score: 364
Period size: 122 Copynumber: 2.3 Consensus size: 121
1270144 TATCGCAAAT
1270154 TCGCGTTGCGATTTTCCAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCG
1 TCGCGTTGCGATTTTCCAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCG
*
1270219 TTGCGATAGTTGAAAATCACGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
66 TTGCGATAGTTGAAAATCACGTTGCGATTTTCCAATTC-CGTTGCGATAGTTGAAAA
* *
1270276 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTTCATTTCGCGTTGCGATTTTCCAGTTCGCG
1 TCGCGTTGCGATTTTCCAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCG
** ** * *
1270341 TTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT-CGTTGCGATAGTCT-ACAG
66 TTGCGATAGT-TGA-AAATCACGTTGCGATTTTCC-AATTCCGTTGCGATAGT-TGAAAA
*
1270398 TTGTCGTTGCGATTTTCCAAATT--CGTTGCGAT
1 TCG-CGTTGCGATTTTCC-AATTCGCGTTGCGAT
1270430 AGTCTACAGT
Statistics
Matches: 137, Mismatches: 11, Indels: 12
0.86 0.07 0.08
Matches are distributed among these distances:
122 99 0.72
123 32 0.23
124 6 0.04
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.39
Consensus pattern (121 bp):
TCGCGTTGCGATTTTCCAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCG
TTGCGATAGTTGAAAATCACGTTGCGATTTTCCAATTCCGTTGCGATAGTTGAAAA
Found at i:1270394 original size:41 final size:41
Alignment explanation
Indices: 1270319--1270469 Score: 259
Period size: 41 Copynumber: 3.7 Consensus size: 41
1270309 TTTCATTTCG
*
1270319 CGTTGCGATTTTCC-AGTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
1270361 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
*
1270402 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTAT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1270443 CGTTGCGATTTTCCAAATTCGTTGCGA
1 CGTTGCGATTTTCCAAATTCGTTGCGA
1270470 AAATTCGTTG
Statistics
Matches: 106, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
41 89 0.84
42 14 0.13
43 3 0.03
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:1270573 original size:6 final size:6
Alignment explanation
Indices: 1270562--1270603 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
1270552 GACACGTATT
1270562 ACCACG ACCACG ACCACG ACCACG A-CACG A-CACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1270604 CGAGACGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 15 0.43
6 20 0.57
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1270611 original size:15 final size:16
Alignment explanation
Indices: 1270562--1270602 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
1270552 GACACGTATT
1270562 ACCACGACCACGACCACG
1 ACCACGA-CACGA-CACG
1270580 ACCACGACACGACACG
1 ACCACGACACGACACG
1270596 ACC-CGAC
1 ACCACGAC
1270603 CCGAGACGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.17
16 7 0.30
17 5 0.22
18 7 0.30
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (16 bp):
ACCACGACACGACACG
Found at i:1271109 original size:6 final size:6
Alignment explanation
Indices: 1271098--1271136 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
1271088 GTCCGTCTCG
1271098 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1271137 AATACGTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1271330 original size:41 final size:41
Alignment explanation
Indices: 1271285--1271381 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 41
1271275 ACGAATTTGG
* *
1271285 AAAATCGCAACGAC-ATTGTAC-ACTATCGCAATGCGAAATGA
1 AAAATCGCAACG-CGATT-TACAACTATAGCAACGCGAAATGA
* *
1271326 AAAATCGCAACGCGATTTTCAACTATAGCAACGCGAAATGG
1 AAAATCGCAACGCGATTTACAACTATAGCAACGCGAAATGA
1271367 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1271382 AAAATCGCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 3 0.06
41 47 0.94
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.18
Consensus pattern (41 bp):
AAAATCGCAACGCGATTTACAACTATAGCAACGCGAAATGA
Found at i:1271387 original size:15 final size:15
Alignment explanation
Indices: 1271367--1271396 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1271357 CGCGAAATGG
1271367 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1271382 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1271397 TTTTCAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.27, G:0.20, T:0.07
Consensus pattern (15 bp):
AAAATCGCAACGCGA
Found at i:1271392 original size:56 final size:56
Alignment explanation
Indices: 1271324--1271437 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
1271314 AATGCGAAAT
1271324 GAAAAATCGCAACGCGATTTTCAACTATAGCAACGCGAAATGGAAAATCGCAACGC
1 GAAAAATCGCAACGCGATTTTCAACTATAGCAACGCGAAATGGAAAATCGCAACGC
* *
1271380 GAAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAACATCGCAACGC
1 GAAAAATCGCAACGCGATTTTCAACTATAGCAACGCGAAATGGAAAATCGCAACGC
1271436 GA
1 GA
1271438 TTTTCAACTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (56 bp):
GAAAAATCGCAACGCGATTTTCAACTATAGCAACGCGAAATGGAAAATCGCAACGC
Found at i:1271409 original size:97 final size:97
Alignment explanation
Indices: 1271285--1271478 Score: 295
Period size: 97 Copynumber: 2.0 Consensus size: 97
1271275 ACGAATTTGG
*
1271285 AAAATCGCAACGACATTGTACACTATCGCAATGCGAAATGAAAAATCGCAACGCGATTTTCAACT
1 AAAATCGCAACGACATTGTACACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACT
*
1271350 AT-AGCAACGCGAAATGGAAAATCGCAACGCGA
66 ATCA-CAACGCAAAATGGAAAATCGCAACGCGA
* * *
1271382 AAAATCGCAACG-CGATT-TTCAACTATCGCAACGCGAAATGGAACATCGCAACGCGATTTTCAA
1 AAAATCGCAACGAC-ATTGTAC-ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAA
1271445 CTATCACAACGCAAAATGGAAAATCGCAACGCGA
64 CTATCACAACGCAAAATGGAAAATCGCAACGCGA
1271479 TTTCCAACTA
Statistics
Matches: 89, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
96 3 0.03
97 85 0.96
98 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (97 bp):
AAAATCGCAACGACATTGTACACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACT
ATCACAACGCAAAATGGAAAATCGCAACGCGA
Found at i:1271411 original size:21 final size:21
Alignment explanation
Indices: 1271385--1271499 Score: 108
Period size: 21 Copynumber: 5.6 Consensus size: 21
1271375 AACGCGAAAA
*
1271385 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTGCAACT
** *
1271406 ATCGCAACGCGAAATGGAAC-
1 ATCGCAACGCGATTTGCAACT
*
1271426 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTGCAACT
* * ** * *
1271447 ATCACAACGCAAAATGGAA-A
1 ATCGCAACGCGATTTGCAACT
*
1271467 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTGCAACT
1271488 ATCGCAACGCGA
1 ATCGCAACGCGA
1271500 AATGCAACGC
Statistics
Matches: 70, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 29 0.41
21 41 0.59
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGATTTGCAACT
Found at i:1271442 original size:41 final size:41
Alignment explanation
Indices: 1271382--1271503 Score: 208
Period size: 41 Copynumber: 3.0 Consensus size: 41
1271372 CGCAACGCGA
1271382 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGG
1 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGG
* * *
1271423 AACATCGCAACGCGATTTTCAACTATCACAACGCAAAATGG
1 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGG
*
1271464 AAAATCGCAACGCGATTTCCAACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
1271504 CAACGCGAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGG
Found at i:1271520 original size:41 final size:39
Alignment explanation
Indices: 1271370--1271512 Score: 152
Period size: 41 Copynumber: 3.6 Consensus size: 39
1271360 GAAATGGAAA
*
1271370 ATCGCAACGCGAAA--AATCGC-AACGCGATTTTCAACT
1 ATCGCAACGCGAAATGAAACGCGAACGCGATTTTCAACT
1271406 ATCGCAACGCGAAATGGAACATCGC-AACGCGATTTTCAACT
1 ATCGCAACGCGAAAT-GAA-A-CGCGAACGCGATTTTCAACT
* * *
1271447 ATCACAACGCAAAATGGAAAATCGC-AACGCGATTTCCAACT
1 ATCGCAACGCGAAAT-G-AAA-CGCGAACGCGATTTTCAACT
*
1271488 ATCGCAACGCGAAATGCAACGCGAA
1 ATCGCAACGCGAAATGAAACGCGAA
1271513 TTTGCGATAG
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
36 14 0.15
38 3 0.03
39 6 0.06
40 1 0.01
41 67 0.72
42 2 0.02
ACGTcount: A:0.38, C:0.27, G:0.18, T:0.17
Consensus pattern (39 bp):
ATCGCAACGCGAAATGAAACGCGAACGCGATTTTCAACT
Found at i:1272053 original size:10 final size:10
Alignment explanation
Indices: 1272038--1272234 Score: 78
Period size: 10 Copynumber: 20.1 Consensus size: 10
1272028 AAAAATGAAG
1272038 AATAAAAATA
1 AATAAAAATA
1272048 AAT-AAAATA
1 AATAAAAATA
**
1272057 AATAAAAGGA
1 AATAAAAATA
*
1272067 AAGGAAAAATA
1 AA-TAAAAATA
1272078 AAT--AAATA
1 AATAAAAATA
1272086 AAT--AAATA
1 AATAAAAATA
*
1272094 AATGAAATATTTA
1 AAT-AAA-A-ATA
* *
1272107 AATATATATA
1 AATAAAAATA
* * *
1272117 TATATATATA
1 AATAAAAATA
* * *
1272127 TATATATATA
1 AATAAAAATA
* *
1272137 TATATAAATA
1 AATAAAAATA
1272147 AAT-AAAATA
1 AATAAAAATA
1272156 GAA-AAAAATA
1 -AATAAAAATA
1272166 TAATAATAAA-A
1 -AATAA-AAATA
1272177 AATAAAAA-A
1 AATAAAAATA
1272186 AA-AAAAA-A
1 AATAAAAATA
*
1272194 AAAAAAAAT-
1 AATAAAAATA
1272203 AATAAAAATA
1 AATAAAAATA
1272213 TAA-AAAATATA
1 -AATAAAA-ATA
*
1272224 AATATAAATA
1 AATAAAAATA
1272234 A
1 A
1272235 TTAGCTTATT
Statistics
Matches: 153, Mismatches: 17, Indels: 34
0.75 0.08 0.17
Matches are distributed among these distances:
8 24 0.16
9 33 0.22
10 66 0.43
11 19 0.12
12 6 0.04
13 5 0.03
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (10 bp):
AATAAAAATA
Found at i:1272080 original size:4 final size:4
Alignment explanation
Indices: 1272073--1272227 Score: 72
Period size: 4 Copynumber: 39.2 Consensus size: 4
1272063 AGGAAAGGAA
** * * *
1272073 AAAT AAAT AAAT AAAT AAAT AAAT GAAAT ATTT AAAT ATAT ATAT ATAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT
* * * * * *
1272122 ATAT ATAT ATAT ATAT ATAT AAAT AAAT AAAAT AGA- AAA- AAAT ATAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT A-AAT
* * * *
1272170 -AAT AAA- AAAT AAA- AAAA AAAA AAAA AAAA AAAT -AAT AAA- AATAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT
*
1272214 AAAA AATAT AAAT A
1 AAAT AA-AT AAAT A
1272228 TAAATAATTA
Statistics
Matches: 129, Mismatches: 11, Indels: 22
0.80 0.07 0.14
Matches are distributed among these distances:
3 19 0.15
4 94 0.73
5 16 0.12
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:1272115 original size:2 final size:2
Alignment explanation
Indices: 1272108--1272142 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1272098 AAATATTTAA
1272108 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1272143 AATAAATAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1272175 original size:23 final size:25
Alignment explanation
Indices: 1272138--1272221 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 25
1272128 ATATATATAT
*
1272138 ATATAAATAAATAAAATAGAAAAAA
1 ATATAAATAAATAAAAAAGAAAAAA
*
1272163 ATAT-AAT-AATAAAAAATAAAAAA
1 ATATAAATAAATAAAAAAGAAAAAA
* * *
1272186 A-A-AAAAAAAAAAAAAATAATAAAA
1 ATATAAATAAATAAAAAAGAA-AAAA
1272210 ATATAAA-AAATA
1 ATATAAATAAATA
1272222 TAAATATAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
22 3 0.06
23 26 0.53
24 8 0.16
25 9 0.18
26 3 0.06
ACGTcount: A:0.81, C:0.00, G:0.01, T:0.18
Consensus pattern (25 bp):
ATATAAATAAATAAAAAAGAAAAAA
Found at i:1272194 original size:33 final size:33
Alignment explanation
Indices: 1272142--1272219 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
1272132 ATATATATAT
* * * *
1272142 AAATAAATAAAATAGAAAAAAATATAATAATAAA
1 AAATAAA-AAAAAAAAAAAAAAAAAAATAATAAA
1272176 AAATAAAAAAAAAAAAAAAAAAAAAATAATAAA
1 AAATAAAAAAAAAAAAAAAAAAAAAATAATAAA
1272209 AATATAAAAAA
1 AA-ATAAAAAA
1272220 TATAAATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 24 0.62
34 15 0.38
ACGTcount: A:0.83, C:0.00, G:0.01, T:0.15
Consensus pattern (33 bp):
AAATAAAAAAAAAAAAAAAAAAAAAATAATAAA
Found at i:1272341 original size:11 final size:12
Alignment explanation
Indices: 1272313--1272459 Score: 71
Period size: 12 Copynumber: 12.6 Consensus size: 12
1272303 GATAATTACA
1272313 ATATA-TAT-AT
1 ATATAGTATAAT
1272323 ATATAGTATAAT
1 ATATAGTATAAT
*
1272335 ATA-AGTAAAAT
1 ATATAGTATAAT
* * ** *
1272346 AAAAAAAAAAAT
1 ATATAGTATAAT
1272358 ATATA-TATATAT
1 ATATAGTATA-AT
*
1272370 ATATATATATAAT
1 ATATA-GTATAAT
* *
1272383 ATATATATATAAA
1 ATATA-GTATAAT
* *
1272396 AAATAATA-AAT
1 ATATAGTATAAT
1272407 ATATA-TATAA-
1 ATATAGTATAAT
1272417 ATATA-TATATAT
1 ATATAGTATA-AT
1272429 ATATA-TATATAT
1 ATATAGTATA-AT
1272441 ATATA-TATATAT
1 ATATAGTATA-AT
1272453 ATATAGT
1 ATATAGT
1272460 GTAAAAAAAT
Statistics
Matches: 115, Mismatches: 12, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
10 16 0.14
11 23 0.20
12 53 0.46
13 19 0.17
14 4 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
ATATAGTATAAT
Found at i:1272361 original size:2 final size:2
Alignment explanation
Indices: 1272356--1272457 Score: 147
Period size: 2 Copynumber: 52.5 Consensus size: 2
1272346 AAAAAAAAAA
*
1272356 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT A- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1272396 AA AT A- AT AA AT AT AT AT AT AA 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
1272437 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
1272458 GTGTAAAAAA
Statistics
Matches: 92, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
1 3 0.03
2 89 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1272973 original size:37 final size:37
Alignment explanation
Indices: 1272932--1273033 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
1272922 TTTGTGGATT
* *
1272932 ATATTTTTAGGAGTTTAAATCATAGTAGAACTCTATC
1 ATATTTTTAGGAGTTTGAATCCTAGTAGAACTCTATC
* * * *
1272969 ATATTTTTAGGAGTTTGAATCCTAGCAAAATTTTATC
1 ATATTTTTAGGAGTTTGAATCCTAGTAGAACTCTATC
*
1273006 CTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATATTTTTAGGAGTTTGAATCCTAGTAG
1273034 GACGAAAAAG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (37 bp):
ATATTTTTAGGAGTTTGAATCCTAGTAGAACTCTATC
Found at i:1274081 original size:106 final size:106
Alignment explanation
Indices: 1273763--1274907 Score: 1525
Period size: 106 Copynumber: 11.0 Consensus size: 106
1273753 GCATTGTTCT
* * ** *
1273763 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * * * *
1273827 ACCAGCCGTTCCTTCATTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1273869 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * ** ***
1273928 TCAGCTGCCCCTTCGTCGTGAAGTTGAGGTTGTACTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * *
1273970 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
1274034 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
1274075 GAGTCCAATATCCTAGGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
1274140 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1274181 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1274246 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1274287 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
1274352 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1274393 GAGTCAAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
1274458 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1274499 GAGTGCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1274564 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1274605 GAGTCCAATATCCTTCG-T-T---G-TG-AA---G-T-TTAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
1274658 CCAGCGGTCTCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1274699 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
1274764 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1274805 GAGTCCAATA----TC-CT-TGAAGTTGAAATTGGCTCCGAAATTGGAAAATT-ATTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * * *
1274863 CCAACTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1274904 GAGT
1 GAGT
1274908 GGCACGATAT
Statistics
Matches: 936, Mismatches: 82, Indels: 49
0.88 0.08 0.05
Matches are distributed among these distances:
94 81 0.09
95 2 0.00
96 2 0.00
99 53 0.06
100 109 0.12
101 10 0.01
102 7 0.01
104 5 0.01
105 7 0.01
106 659 0.70
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1275760 original size:22 final size:22
Alignment explanation
Indices: 1275734--1275807 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
1275724 TATGTTTTAT
*
1275734 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
1275756 TCAAAGGTTTGACA--T--TGC
1 TCAAAGGTTTGACATTTGATGC
*
1275774 TCATAGGTTT-ACCATTTGATGC
1 TCAAAGGTTTGA-CATTTGATGC
*
1275796 TCAACGGTTTGA
1 TCAAAGGTTTGA
1275808 TGGGGTAGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
17 1 0.02
18 14 0.33
20 2 0.05
22 24 0.57
23 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:1276454 original size:13 final size:12
Alignment explanation
Indices: 1276438--1276500 Score: 58
Period size: 13 Copynumber: 5.2 Consensus size: 12
1276428 TTTCTTTCGA
1276438 TTTTTGTTCTTT
1 TTTTTGTTCTTT
1276450 CTTTTTGTTCTTT
1 -TTTTTGTTCTTT
* *
1276463 TGTTT-TTC-CT
1 TTTTTGTTCTTT
1276473 TTTTTGCTTCTTT
1 TTTTTG-TTCTTT
*
1276486 TCTTTTTTTCTTT
1 T-TTTTGTTCTTT
1276499 TT
1 TT
1276501 GCCCTTTTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
10 5 0.12
11 3 0.07
12 8 0.20
13 21 0.51
14 4 0.10
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.79
Consensus pattern (12 bp):
TTTTTGTTCTTT
Found at i:1276455 original size:35 final size:37
Alignment explanation
Indices: 1276416--1276501 Score: 88
Period size: 35 Copynumber: 2.4 Consensus size: 37
1276406 TTGCATGTGT
*
1276416 TTTTTGTCCCTTTT-TCTTTCGATTTTTG-TTC-TTTC
1 TTTTTGT-CCTTTTGTCTTTCCATTTTTGCTTCTTTTC
* * *
1276451 TTTTTGTTCTTTTGTTTTTCCTTTTTTGCTTCTTTTC
1 TTTTTGTCCTTTTGTCTTTCCATTTTTGCTTCTTTTC
* *
1276488 TTTTTTTCTTTTTG
1 TTTTTGTCCTTTTG
1276502 CCCTTTTTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
34 5 0.12
35 18 0.44
36 3 0.07
37 15 0.37
ACGTcount: A:0.01, C:0.16, G:0.08, T:0.74
Consensus pattern (37 bp):
TTTTTGTCCTTTTGTCTTTCCATTTTTGCTTCTTTTC
Found at i:1276499 original size:23 final size:22
Alignment explanation
Indices: 1276439--1276502 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
1276429 TTCTTTCGAT
*
1276439 TTTTGTTCTTTCTTTTTG-TTC
1 TTTTGTTTTTTCTTTTTGCTTC
*
1276460 TTTTGTTTTTCCTTTTTTGCTTC
1 TTTTGTTTTTTC-TTTTTGCTTC
*
1276483 TTTTCTTTTTTTCTTTTTGC
1 TTTT-GTTTTTTCTTTTTGC
1276503 CCTTTTTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.28
22 6 0.17
23 14 0.39
24 6 0.17
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.77
Consensus pattern (22 bp):
TTTTGTTTTTTCTTTTTGCTTC
Found at i:1279543 original size:16 final size:17
Alignment explanation
Indices: 1279508--1279593 Score: 61
Period size: 17 Copynumber: 5.1 Consensus size: 17
1279498 TGTTAGAGGG
*
1279508 AAAAAATGAATAAATGA
1 AAAAAATGAATAAATAA
*
1279525 AAAAAATGAA-GAATAA
1 AAAAAATGAATAAATAA
* *
1279541 AAATAAGTAAATAAAATAA
1 AAA-AAATGAAT-AAATAA
*
1279560 AATAAAAAGAA-AAAT-A
1 AA-AAAATGAATAAATAA
* *
1279576 AATAAATAAATAAATAA
1 AAAAAATGAATAAATAA
1279593 A
1 A
1279594 TGAAATATAT
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
15 5 0.10
16 14 0.27
17 21 0.40
19 11 0.21
20 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (17 bp):
AAAAAATGAATAAATAA
Found at i:1279543 original size:30 final size:27
Alignment explanation
Indices: 1279509--1279637 Score: 80
Period size: 30 Copynumber: 4.4 Consensus size: 27
1279499 GTTAGAGGGA
* *
1279509 AAAAATGAATAAATGAAAAAAATGAAGAAT
1 AAAAAT-AATAAAT-AAAAAAAT-AAAAAG
1279539 AAAAATAAGTAAATAAAATAAAATAAAAAG
1 AAAAATAA-TAAAT-AAA-AAAATAAAAAG
* *
1279569 AAAAATAAATAAATAAATAAAT-AAATG
1 AAAAAT-AATAAATAAAAAAATAAAAAG
* ** *
1279596 AAATATATATATATATAAATGAGTAAAATAG
1 AAA-A-ATA-ATAAATAAAAAAATAAAA-AG
1279627 AAAAATAATAA
1 AAAAATAATAA
1279638 TTATAACAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
27 7 0.09
28 9 0.11
29 21 0.26
30 33 0.41
31 11 0.14
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (27 bp):
AAAAATAATAAATAAAAAAATAAAAAG
Found at i:1279580 original size:4 final size:4
Alignment explanation
Indices: 1279541--1279615 Score: 62
Period size: 4 Copynumber: 18.0 Consensus size: 4
1279531 TGAAGAATAA
* *
1279541 AAAT AAGT AAAT AAAAT AAAAT AAA- AAGAA AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT -AAAT -AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT
* * *
1279591 AAAT GAAAT ATAT ATAT ATAT AAAT
1 AAAT -AAAT AAAT AAAT AAAT AAAT
1279616 GAGTAAAATA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
3 2 0.03
4 45 0.73
5 15 0.24
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:1279599 original size:21 final size:21
Alignment explanation
Indices: 1279511--1279617 Score: 69
Period size: 21 Copynumber: 5.0 Consensus size: 21
1279501 TAGAGGGAAA
* *
1279511 AAATGAATAAATGAAAAAAATG
1 AAATAAATAAAT-AAATAAATG
* *
1279533 AAGA-ATAA-AAATAAGTAAATA
1 AA-ATA-AATAAATAAATAAATG
*
1279554 AAATAAAATAAA-AAGAAAAAT-
1 AAAT-AAATAAATAA-ATAAATG
1279575 AAATAAATAAATAAATAAATG
1 AAATAAATAAATAAATAAATG
* * *
1279596 AAATATATATATATATAAATG
1 AAATAAATAAATAAATAAATG
1279617 A
1 A
1279618 GTAAAATAGA
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
20 13 0.19
21 37 0.55
22 14 0.21
23 3 0.04
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (21 bp):
AAATAAATAAATAAATAAATG
Found at i:1279711 original size:29 final size:30
Alignment explanation
Indices: 1279678--1279735 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
1279668 ACAATATAAT
*
1279678 ATAAACAAATAAAAAAATCAAA-ATAAAAA
1 ATAAACAAATAAAAAAACCAAATATAAAAA
* * *
1279707 ATAAATAAATATATAAACCAAATATAAAA
1 ATAAACAAATAAAAAAACCAAATATAAAA
1279736 GTATACATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (30 bp):
ATAAACAAATAAAAAAACCAAATATAAAAA
Found at i:1280443 original size:37 final size:37
Alignment explanation
Indices: 1280402--1280498 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
1280392 GGATCCTATA
*
1280402 TTTAGGAGTTTAAATCATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTGAATCATAGTAGAACTCTATCATATT
* * * * *
1280439 TTTAGGAGTTTGAATCGTAGCAAAATTCTATCTTATT
1 TTTAGGAGTTTGAATCATAGTAGAACTCTATCATATT
1280476 TTTAGGAGTTTGAATCATAGTAG
1 TTTAGGAGTTTGAATCATAGTAG
1280499 GACGAAAAGG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCATAGTAGAACTCTATCATATT
Found at i:1281835 original size:63 final size:60
Alignment explanation
Indices: 1281576--1281836 Score: 360
Period size: 60 Copynumber: 4.3 Consensus size: 60
1281566 TTTTTTCTTC
* ** *** *
1281576 TTTTCCTGTTCATTTTGCATCTTCACCTCGCACTGTTGTAATTGTTCCCGTAATGCGGCA
1 TTTTCCTGTTCTTTTTGCATCTTGGCCTCATTCTGTTGTAATTGTTCCCGTAATGTGGCA
* *
1281636 CTTTCCTGTTCTTTTTGCATCTTGGCCTCATTCTGTTGTGATTGTTCCCGTAATGTGGCA
1 TTTTCCTGTTCTTTTTGCATCTTGGCCTCATTCTGTTGTAATTGTTCCCGTAATGTGGCA
*
1281696 TTTTCCAGTTCTTTTTGCATCTTGGCCTCATTCTGTTGTAATTGTTCCCGTAATGTGGCA
1 TTTTCCTGTTCTTTTTGCATCTTGGCCTCATTCTGTTGTAATTGTTCCCGTAATGTGGCA
* * **
1281756 TTTTCCAGTTCTTTTTGCATCTTGGCCTCATCATACTGTTGTAATTGTTCCCGCAGCGTGGCA
1 TTTTCCTGTTCTTTTTGCATCTTGGCCTCAT--T-CTGTTGTAATTGTTCCCGTAATGTGGCA
*
1281819 TTTTCCTGTTCCTTTTGC
1 TTTTCCTGTTCTTTTTGC
1281837 CCCAAAGTCG
Statistics
Matches: 181, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
60 139 0.77
62 1 0.01
63 41 0.23
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (60 bp):
TTTTCCTGTTCTTTTTGCATCTTGGCCTCATTCTGTTGTAATTGTTCCCGTAATGTGGCA
Found at i:1282359 original size:33 final size:33
Alignment explanation
Indices: 1282312--1282397 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
1282302 ATTGAGAACC
1282312 AGATGCCGAGTAGCTACTTGCCCCCTCATTTGT
1 AGATGCCGAGTAGCTACTTGCCCCCTCATTTGT
* * *
1282345 AGATCCCGAGTAGCTACTTGCCTCCTCCTTTGT
1 AGATGCCGAGTAGCTACTTGCCCCCTCATTTGT
* *
1282378 AGATGCTGAGTAGCTTCTTG
1 AGATGCCGAGTAGCTACTTG
1282398 ACTCATTAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (33 bp):
AGATGCCGAGTAGCTACTTGCCCCCTCATTTGT
Found at i:1295669 original size:23 final size:23
Alignment explanation
Indices: 1295639--1295690 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
1295629 AAATTTATTA
1295639 AACAAATAGTTAAGATTCATACC
1 AACAAATAGTTAAGATTCATACC
1295662 AACAAATAGTTAAGATTCATACC
1 AACAAATAGTTAAGATTCATACC
*
1295685 GACAAA
1 AACAAA
1295691 ACTCGGCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.23
Consensus pattern (23 bp):
AACAAATAGTTAAGATTCATACC
Found at i:1299012 original size:65 final size:62
Alignment explanation
Indices: 1298904--1299033 Score: 197
Period size: 65 Copynumber: 2.0 Consensus size: 62
1298894 ATTTATACAG
*
1298904 AAAACTCCACTTTATTAAGACAGATTTTATTTTAGGTACTCCCTTAGTTGCTATTGTGATGTGC
1 AAAACTCCACTTTATTAAGACAGATTTTATTTTAGGTACTCCCTTAGTTGCTA--GTGATATGC
* * *
1298968 AAAAGCTCCATTTTATTAAGACAGTTTTTATTTTAGGTACTCCCTTATTTGCTAGTGATATGC
1 AAAA-CTCCACTTTATTAAGACAGATTTTATTTTAGGTACTCCCTTAGTTGCTAGTGATATGC
1299031 AAA
1 AAA
1299034 TCTTCTTTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
63 11 0.18
64 4 0.07
65 46 0.75
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (62 bp):
AAAACTCCACTTTATTAAGACAGATTTTATTTTAGGTACTCCCTTAGTTGCTAGTGATATGC
Found at i:1310937 original size:138 final size:138
Alignment explanation
Indices: 1310679--1310942 Score: 302
Period size: 138 Copynumber: 1.9 Consensus size: 138
1310669 GGTCTGAGCC
* * * * *
1310679 AGATTTTGATGGGTTCAAGCCAATTGTTGATGGGTATGCGCCTGTTGCTGGTGAGTCAGGCCGTA
1 AGATTTTGATGGGTTCAAGCCAACTGTTGATGGGTATGAGCCTGGTGCAGGTGAATCAGGCCGTA
* * **
1310744 CAGTGAAGGTAGAAGAAGACGAGTCAAAACCAGAAGTGGAGTTGGGTTTCTCTATTGAGGAGTCA
66 CAGTGAAGGTAGAAGAAGACGAGTCAAAACCAGAAGTGGAATCGACTTTCTCTATTGAGGAGTCA
1310809 AAGCCAGA
131 AAGCCAGA
* * * *
1310817 AGATTTTTATGTGTTCAAGCCAACTGTTTG-TGGGTCTGAGCC-GGTGCGAGGTGAATCAGGCTG
1 AGATTTTGATGGGTTCAAGCCAACTG-TTGATGGGTATGAGCCTGGTGC-AGGTGAATCAGGCCG
* * * **
1310880 TACAGTGGAGGTGGAAGAAGAGGAGTTTAAACCAGAAG-GGAATCCGACTTTAC-CTATTGAGGA
64 TACAGTGAAGGTAGAAGAAGACGAGTCAAAACCAGAAGTGGAAT-CGACTTT-CTCTATTGAGGA
1310943 AGTGATTGAG
Statistics
Matches: 104, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
137 8 0.08
138 92 0.88
139 4 0.04
ACGTcount: A:0.27, C:0.14, G:0.33, T:0.26
Consensus pattern (138 bp):
AGATTTTGATGGGTTCAAGCCAACTGTTGATGGGTATGAGCCTGGTGCAGGTGAATCAGGCCGTA
CAGTGAAGGTAGAAGAAGACGAGTCAAAACCAGAAGTGGAATCGACTTTCTCTATTGAGGAGTCA
AAGCCAGA
Found at i:1322464 original size:26 final size:26
Alignment explanation
Indices: 1322434--1322485 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1322424 ATTATAATGA
1322434 AGTATTTTCTCCAGTTGTAAAACATT
1 AGTATTTTCTCCAGTTGTAAAACATT
1322460 AGTATTTTCTCCAGTTGTAAAACATT
1 AGTATTTTCTCCAGTTGTAAAACATT
1322486 CCTCCATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (26 bp):
AGTATTTTCTCCAGTTGTAAAACATT
Found at i:1325451 original size:23 final size:23
Alignment explanation
Indices: 1325392--1325451 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
1325382 TTTATATGGA
* *
1325392 ACTTCGGTGCAATTCTACGTGGC
1 ACTTCGGTGCATTTCTACGCGGC
*
1325415 ACTACGGT-CTATTTCTACGCGGC
1 ACTTCGGTGC-ATTTCTACGCGGC
1325438 ACTTCGGTGCATTT
1 ACTTCGGTGCATTT
1325452 ATACAAGCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 29 0.94
24 1 0.03
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.33
Consensus pattern (23 bp):
ACTTCGGTGCATTTCTACGCGGC
Found at i:1327171 original size:21 final size:21
Alignment explanation
Indices: 1327138--1327178 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1327128 TTCTGGGCAA
* *
1327138 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
1327159 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
1327179 ACGAACAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:1328767 original size:149 final size:149
Alignment explanation
Indices: 1328587--1328901 Score: 580
Period size: 149 Copynumber: 2.1 Consensus size: 149
1328577 GAGTCGAGGG
*
1328587 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
1328652 A-TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATT
66 ACT-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
1328716 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTGCAAT
1328736 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1328801 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1328866 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1328885 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1328902 TGCAATTATA
Statistics
Matches: 162, Mismatches: 2, Indels: 4
0.96 0.01 0.02
Matches are distributed among these distances:
148 1 0.01
149 160 0.99
150 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1328902 original size:23 final size:23
Alignment explanation
Indices: 1328869--1328913 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1328859 ATCATTATAT
*
1328869 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
1328892 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
1328914 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1332207 original size:21 final size:21
Alignment explanation
Indices: 1332174--1332214 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1332164 TTCTGGGCAA
* *
1332174 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
1332195 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
1332215 ACGAACAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Done.