Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009343.1 Hibiscus syriacus cultivar Beakdansim tig00113123_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: 2141224
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1224455 original size:22 final size:22
Alignment explanation
Indices: 1224430--1224480 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1224420 TCAATCGGTC
1224430 GAACCGGTCCGACCGGTCGGAA
1 GAACCGGTCCGACCGGTCGGAA
1224452 GAACCGGTCCGACCGGTCGGAA
1 GAACCGGTCCGACCGGTCGGAA
1224474 GAACCGG
1 GAACCGG
1224481 ACGACGTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.24, C:0.31, G:0.37, T:0.08
Consensus pattern (22 bp):
GAACCGGTCCGACCGGTCGGAA
Found at i:1224576 original size:19 final size:20
Alignment explanation
Indices: 1224536--1224577 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
1224526 ATTTAATAAA
1224536 AAATAATTTTTTATATCACAT
1 AAATAATTTTTTATAT-ACAT
1224557 AAATAATTTTTTATAT-CAT
1 AAATAATTTTTTATATACAT
1224576 AA
1 AA
1224578 GTTATATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.24
21 16 0.76
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATAATTTTTTATATACAT
Found at i:1226001 original size:14 final size:14
Alignment explanation
Indices: 1225982--1226022 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1225972 TTTAGATTTT
1225982 TTAAAATTACATTA
1 TTAAAATTACATTA
*
1225996 TTAAAATTATATTA
1 TTAAAATTACATTA
1226010 --AAAATT-CATTA
1 TTAAAATTACATTA
1226021 TT
1 TT
1226023 GATAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 4 0.17
12 6 0.26
14 13 0.57
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAAAATTACATTA
Found at i:1226065 original size:30 final size:30
Alignment explanation
Indices: 1226029--1226085 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1226019 TATTGATAAT
* *
1226029 TATAAAATTTTAAAAATATATTAAAAATTC
1 TATAAAATTTTAAAAACATAATAAAAATTC
1226059 TATAAAATTTTAAAAACATAATAAAAA
1 TATAAAATTTTAAAAACATAATAAAAA
1226086 ATATATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (30 bp):
TATAAAATTTTAAAAACATAATAAAAATTC
Found at i:1226093 original size:30 final size:30
Alignment explanation
Indices: 1226029--1226093 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
1226019 TATTGATAAT
* * * *
1226029 TATAAAATTTTAAAAATATATTAAAAATTC
1 TATAAAATTTTAAAAACATAATAAAAAATA
1226059 TATAAAATTTTAAAAACATAATAAAAAATA
1 TATAAAATTTTAAAAACATAATAAAAAATA
1226089 TATAA
1 TATAA
1226094 TTCAATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (30 bp):
TATAAAATTTTAAAAACATAATAAAAAATA
Found at i:1226560 original size:7 final size:7
Alignment explanation
Indices: 1226550--1226623 Score: 53
Period size: 7 Copynumber: 10.7 Consensus size: 7
1226540 ACCCTAAATG
1226550 CTAAACA
1 CTAAACA
*
1226557 CTAAACT
1 CTAAACA
1226564 CTAAATC-
1 CTAAA-CA
* *
1226571 TTAAACC
1 CTAAACA
1226578 CTAAACA
1 CTAAACA
*
1226585 TTAAACA
1 CTAAACA
*
1226592 TTAAAC-
1 CTAAACA
*
1226598 CTAAACC
1 CTAAACA
*
1226605 CTAAACC
1 CTAAACA
*
1226612 CTAAATA
1 CTAAACA
1226619 CTAAA
1 CTAAA
1226624 ACATAAAACA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
6 6 0.11
7 49 0.88
8 1 0.02
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (7 bp):
CTAAACA
Found at i:1226567 original size:21 final size:21
Alignment explanation
Indices: 1226543--1226623 Score: 62
Period size: 21 Copynumber: 3.9 Consensus size: 21
1226533 GCCATGAACC
1226543 CTAAATGC-TAAACACTAAACT
1 CTAAAT-CTTAAACACTAAACT
*
1226564 CTAAATCTTAAACCCTAAACAT
1 CTAAATCTTAAACACTAAAC-T
*
1226586 -TAAA-CATTAAAC-CTAAACC
1 CTAAATC-TTAAACACTAAACT
* * *
1226605 CTAAACCCTAAATACTAAA
1 CTAAATCTTAAACACTAAA
1226624 ACATAAAACA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
20 16 0.32
21 33 0.66
22 1 0.02
ACGTcount: A:0.49, C:0.26, G:0.01, T:0.23
Consensus pattern (21 bp):
CTAAATCTTAAACACTAAACT
Found at i:1226630 original size:21 final size:21
Alignment explanation
Indices: 1226606--1226655 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1226596 ACCTAAACCC
1226606 TAAACCCTAAATACTAAAACA
1 TAAACCCTAAATACTAAAACA
* * * *
1226627 TAAAACATAAATTCTAAACCA
1 TAAACCCTAAATACTAAAACA
1226648 TAAACCCT
1 TAAACCCT
1226656 TAATCCGATA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAACCCTAAATACTAAAACA
Found at i:1226751 original size:25 final size:25
Alignment explanation
Indices: 1226723--1226796 Score: 139
Period size: 25 Copynumber: 3.0 Consensus size: 25
1226713 CAAAATTATG
1226723 TTATGTGACTCCTAAATAAATCATA
1 TTATGTGACTCCTAAATAAATCATA
*
1226748 TTATGTGACTCCTAAATAAATCATG
1 TTATGTGACTCCTAAATAAATCATA
1226773 TTATGTGACTCCTAAATAAATCAT
1 TTATGTGACTCCTAAATAAATCAT
1226797 TCGCATACTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (25 bp):
TTATGTGACTCCTAAATAAATCATA
Found at i:1226788 original size:21 final size:22
Alignment explanation
Indices: 1226715--1226789 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 22
1226705 AAATTATGCA
*
1226715 AAATTATGTTATGTGACTCCTAAAT
1 AAATCATGTTATGTGACTCC---AT
*
1226740 AAATCATATTATGTGACTCCTAAAT
1 AAATCATGTTATGTGACTCC---AT
1226765 AAATCATGTTATGTGACTCC-T
1 AAATCATGTTATGTGACTCCAT
1226786 AAAT
1 AAAT
1226790 AAATCATTCG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
21 5 0.11
25 42 0.89
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (22 bp):
AAATCATGTTATGTGACTCCAT
Found at i:1227232 original size:16 final size:16
Alignment explanation
Indices: 1227211--1227243 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1227201 TAAAAAATAA
1227211 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1227227 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1227243 A
1 A
1227244 ATTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1227321 original size:10 final size:10
Alignment explanation
Indices: 1227308--1227336 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1227298 TTCATTTAAT
1227308 ACATAAACGA
1 ACATAAACGA
1227318 ACATAAACGA
1 ACATAAACGA
1227328 ACATAAACG
1 ACATAAACG
1227337 TTGGAGACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.59, C:0.21, G:0.10, T:0.10
Consensus pattern (10 bp):
ACATAAACGA
Found at i:1228431 original size:14 final size:15
Alignment explanation
Indices: 1228405--1228434 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1228395 AGAAGATTGG
1228405 ATTAAACATAAATGA
1 ATTAAACATAAATGA
1228420 ATTAAA-ATAAATGA
1 ATTAAACATAAATGA
1228434 A
1 A
1228435 CATAACCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.63, C:0.03, G:0.07, T:0.27
Consensus pattern (15 bp):
ATTAAACATAAATGA
Found at i:1228449 original size:14 final size:14
Alignment explanation
Indices: 1228432--1228477 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
1228422 TAAAATAAAT
1228432 GAACATAACCGAAC
1 GAACATAACCGAAC
1228446 GAACAT-A---AAC
1 GAACATAACCGAAC
1228456 GAACATAACCGAAC
1 GAACATAACCGAAC
1228470 GAACATAA
1 GAACATAA
1228478 ACAGACATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.32
11 1 0.04
13 1 0.04
14 17 0.61
ACGTcount: A:0.54, C:0.24, G:0.13, T:0.09
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:1228453 original size:24 final size:24
Alignment explanation
Indices: 1228426--1228494 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
1228416 ATGAATTAAA
*
1228426 ATAAATGAACATAACCGAACGAAC
1 ATAAACGAACATAACCGAACGAAC
1228450 ATAAACGAACATAACCGAACGAAC
1 ATAAACGAACATAACCGAACGAAC
*
1228474 ATAAAC-AGACATAACAGAACG
1 ATAAACGA-ACATAACCGAACG
1228495 TTCACAAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
23 1 0.02
24 41 0.98
ACGTcount: A:0.55, C:0.22, G:0.13, T:0.10
Consensus pattern (24 bp):
ATAAACGAACATAACCGAACGAAC
Found at i:1229570 original size:12 final size:12
Alignment explanation
Indices: 1229553--1229619 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
1229543 AATTAACCCG
1229553 AATCGAGCTTAA
1 AATCGAGCTTAA
1229565 AATCGAG-TTCAA
1 AATCGAGCTT-AA
* *
1229577 AATTGAGCTT-G
1 AATCGAGCTTAA
1229588 AATCGAG-TTCAA
1 AATCGAGCTT-AA
*
1229600 AATCGAGCTT-C
1 AATCGAGCTTAA
1229611 AATCGAGCT
1 AATCGAGCT
1229620 CTAGTTTCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
10 2 0.04
11 17 0.38
12 22 0.49
13 4 0.09
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (12 bp):
AATCGAGCTTAA
Found at i:1229593 original size:23 final size:23
Alignment explanation
Indices: 1229553--1229617 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
1229543 AATTAACCCG
*
1229553 AATCGAGCTTAAAATCGAGTTCAA
1 AATCGAGCTT-CAATCGAGTTCAA
* *
1229577 AATTGAGCTTGAATCGAGTTCAA
1 AATCGAGCTTCAATCGAGTTCAA
1229600 AATCGAGCTTCAATCGAG
1 AATCGAGCTTCAATCGAG
1229618 CTCTAGTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 28 0.76
24 9 0.24
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (23 bp):
AATCGAGCTTCAATCGAGTTCAA
Found at i:1229635 original size:24 final size:24
Alignment explanation
Indices: 1229602--1229691 Score: 153
Period size: 24 Copynumber: 3.8 Consensus size: 24
1229592 GAGTTCAAAA
1229602 TCGAGCTTCAATCGAGCTCTAGTT
1 TCGAGCTTCAATCGAGCTCTAGTT
*
1229626 TCAAGCTTCAATCGAGCTCTAGTT
1 TCGAGCTTCAATCGAGCTCTAGTT
*
1229650 TCGAGCTTCAATCGAGCTCGAGTT
1 TCGAGCTTCAATCGAGCTCTAGTT
*
1229674 TCGAGCTTTAATCGAGCT
1 TCGAGCTTCAATCGAGCT
1229692 TGAGGTTTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.32
Consensus pattern (24 bp):
TCGAGCTTCAATCGAGCTCTAGTT
Found at i:1241413 original size:19 final size:21
Alignment explanation
Indices: 1241376--1241418 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1241366 TAACTTTTTC
1241376 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
1241396 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
1241416 TTT
1 TTT
1241419 ACGTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:1248157 original size:15 final size:15
Alignment explanation
Indices: 1248137--1248166 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1248127 TTGAGACCTT
*
1248137 ACCCGCCCCGCATCC
1 ACCCGCCCCACATCC
1248152 ACCCGCCCCACATCC
1 ACCCGCCCCACATCC
1248167 GCCAGCCCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.67, G:0.10, T:0.07
Consensus pattern (15 bp):
ACCCGCCCCACATCC
Found at i:1248393 original size:18 final size:18
Alignment explanation
Indices: 1248370--1248421 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
1248360 CAGATATAAA
*
1248370 TGGGTATGAGATGGATGG
1 TGGGTATGAGATGGATAG
* *
1248388 TGGGTATCAGTTGG-TAG
1 TGGGTATGAGATGGATAG
*
1248405 TGGGTGTGAGGATGGAT
1 TGGGTATGA-GATGGAT
1248422 TTGAGAATGT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
17 9 0.35
18 16 0.62
19 1 0.04
ACGTcount: A:0.19, C:0.02, G:0.48, T:0.31
Consensus pattern (18 bp):
TGGGTATGAGATGGATAG
Found at i:1253311 original size:30 final size:28
Alignment explanation
Indices: 1253247--1253314 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 28
1253237 ATTCATTAAT
1253247 AGGACTAAAATAGAAATACATAAACATA
1 AGGACTAAAATAGAAATACATAAACATA
*
1253275 ATGGACTAAAATA-AAATAACCATATACATA
1 A-GGACTAAAATAGAAAT-A-CATAAACATA
1253305 GAGGACTAAA
1 -AGGACTAAA
1253315 CAATAATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
28 5 0.14
29 12 0.34
30 17 0.49
31 1 0.03
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.19
Consensus pattern (28 bp):
AGGACTAAAATAGAAATACATAAACATA
Found at i:1255168 original size:40 final size:39
Alignment explanation
Indices: 1255091--1255168 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 39
1255081 TGGTTATCTA
* *
1255091 GGGGTGACACGGCTCATACGTGATGATGAGATTTGGTCG
1 GGGGTGACACGGCTCATACATGATGAAGAGATTTGGTCG
1255130 GGGGATGACACGGCTCATACATGATGAAGAG-TTCTGGTC
1 GGGG-TGACACGGCTCATACATGATGAAGAGATT-TGGTC
1255169 ATCTATAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
39 6 0.17
40 29 0.83
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.24
Consensus pattern (39 bp):
GGGGTGACACGGCTCATACATGATGAAGAGATTTGGTCG
Found at i:1255170 original size:134 final size:133
Alignment explanation
Indices: 1254977--1255300 Score: 459
Period size: 134 Copynumber: 2.4 Consensus size: 133
1254967 CGGATCCTAC
** *
1254977 ATGATGAGAATATCTGGTCGGGGATGACATTGCTCATATATGATGAAGAGTTCTGGTCATCTATA
1 ATGATGAG-AT-T-TGGTCGGGGATGACACGGCTCATACATGATGAAGAGTTCTGGTCATCTATA
* * *
1255042 GGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTGGTTATCTAGGGGTGACACGGCTCA
63 GAAAGGGCGATAACACGGTTCCTACGCGATGAGGACGGCTGGTTATCTAGGGGTGACACGGCTCA
1255107 TACGTG
128 TACGTG
1255113 ATGATGAGATTTGGTCGGGGGATGACACGGCTCATACATGATGAAGAGTTCTGGTCATCTATAGA
1 ATGATGAGATTTGGTC-GGGGATGACACGGCTCATACATGATGAAGAGTTCTGGTCATCTATAGA
* * * *
1255178 AAGGGCGATAACACGGTTCCTACGTGATGAGGACGTCTGGTTATCTAGGGGTGACATGGCTCCTA
65 AAGGGCGATAACACGGTTCCTACGCGATGAGGACGGCTGGTTATCTAGGGGTGACACGGCTCATA
1255243 CGTG
130 CGTG
* * * * * *
1255247 ATGAAGAGATCTGGTCAGGAGATGACACGACTTATACGTGATGAAGAGTTCTGG
1 ATGATGAGATTTGGTC-GGGGATGACACGGCTCATACATGATGAAGAGTTCTGG
1255301 CTATCTTTAG
Statistics
Matches: 170, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
133 5 0.03
134 155 0.91
135 2 0.01
136 8 0.05
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (133 bp):
ATGATGAGATTTGGTCGGGGATGACACGGCTCATACATGATGAAGAGTTCTGGTCATCTATAGAA
AGGGCGATAACACGGTTCCTACGCGATGAGGACGGCTGGTTATCTAGGGGTGACACGGCTCATAC
GTG
Found at i:1255355 original size:29 final size:30
Alignment explanation
Indices: 1255312--1255370 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
1255302 TATCTTTAGG
*
1255312 GATGATGATTTCAAAAGAAACCGACTCAAA
1 GATGATGATTTCAAAAGAAACAGACTCAAA
*
1255342 GATGATG-TTTCAAAAGAAACATACTCAAA
1 GATGATGATTTCAAAAGAAACAGACTCAAA
1255371 TATTTTTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.22
Consensus pattern (30 bp):
GATGATGATTTCAAAAGAAACAGACTCAAA
Found at i:1255462 original size:29 final size:30
Alignment explanation
Indices: 1255413--1255614 Score: 108
Period size: 29 Copynumber: 6.9 Consensus size: 30
1255403 ACAAAACTTT
1255413 GTTTCAAAAGAAACAAACTCAAAGATTTTG
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
**
1255443 GTTTCAAAAGAAA-TGACTCAAAGA-TTT-
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
* *
1255470 -TTTCACGAAATTGTCTTAAGAGAAA--CAAA-ACTTTG
1 GTTTCA--AAA--G----AA-ACAAACTCAAAGATTTTG
* *
1255505 G-TTCAAAAGAAACATACTCAAAGA-ATT-
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
*
1255532 -TTTCAAAAGAAAC-AACTCAAAGATTTTT
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
* *
1255560 ATTTCAAAAGAAAC-AACTCACAGACTTTT-
1 GTTTCAAAAGAAACAAACTCAAAGA-TTTTG
* * *
1255589 GTGTCAAGAGAAACAAGCTCAAAGAT
1 GTTTCAAAAGAAACAAACTCAAAGAT
1255615 AGGTAAATTT
Statistics
Matches: 135, Mismatches: 15, Indels: 45
0.69 0.08 0.23
Matches are distributed among these distances:
26 17 0.13
27 16 0.12
28 12 0.09
29 44 0.33
30 26 0.19
31 1 0.01
33 4 0.03
34 9 0.07
35 5 0.04
36 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.27
Consensus pattern (30 bp):
GTTTCAAAAGAAACAAACTCAAAGATTTTG
Found at i:1255559 original size:26 final size:27
Alignment explanation
Indices: 1255506--1255614 Score: 121
Period size: 29 Copynumber: 3.9 Consensus size: 27
1255496 AAAACTTTGG
*
1255506 TTCAAAAGAAACATACTCAAAGA-ATTT
1 TTCAAAAGAAACA-ACTCAAAGATTTTT
1255533 TTCAAAAGAAACAACTCAAAGATTTTTAT
1 TTCAAAAGAAACAACTCAAAGA-TTTT-T
*
1255562 TTCAAAAGAAACAACTCACAGACTTTTGT
1 TTCAAAAGAAACAACTCAAAGA-TTTT-T
* *
1255591 GTCAAGAGAAACAAGCTCAAAGAT
1 TTCAAAAGAAACAA-CTCAAAGAT
1255615 AGGTAAATTT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
26 9 0.13
27 13 0.18
28 2 0.03
29 40 0.56
30 7 0.10
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.25
Consensus pattern (27 bp):
TTCAAAAGAAACAACTCAAAGATTTTT
Found at i:1255565 original size:91 final size:91
Alignment explanation
Indices: 1255321--1255559 Score: 286
Period size: 91 Copynumber: 2.6 Consensus size: 91
1255311 GGATGATGAT
** * * *
1255321 TTCAAAAGAAACCGACTCAAAGATGATGTTTCAAAAGAAACATACTCAAATATTTTTCTCAAGAA
1 TTCAAAAGAAACAAACTCAAAGAT-ATTTTTCAAAAGAAACA-ACTCAAAGATTTTTTTCAAG-A
* *
1255386 AAACTGTCTCAAGAGAGACAAAACTTTGT
63 AAACTGTCTCAAGAGAAACAAAACTTTGG
* ** *
1255415 TTCAAAAGAAACAAACTCAAAGATTTTGGTTTCAAAAGAAATGACTCAAAGA-TTTTTTCACG-A
1 TTCAAAAGAAACAAACTCAAAGATATT--TTTCAAAAGAAACAACTCAAAGATTTTTTTCAAGAA
* *
1255478 AATTGTCTTAAGAGAAACAAAACTTTGG
64 AACTGTCTCAAGAGAAACAAAACTTTGG
*
1255506 TTCAAAAGAAACATACTCAAAGA-ATTTTTCAAAAGAAACAACTCAAAGATTTTT
1 TTCAAAAGAAACAAACTCAAAGATATTTTTCAAAAGAAACAACTCAAAGATTTTT
1255560 ATTTCAAAAG
Statistics
Matches: 125, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
88 21 0.17
89 4 0.03
90 2 0.02
91 47 0.38
93 9 0.07
94 30 0.24
95 12 0.10
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (91 bp):
TTCAAAAGAAACAAACTCAAAGATATTTTTCAAAAGAAACAACTCAAAGATTTTTTTCAAGAAAA
CTGTCTCAAGAGAAACAAAACTTTGG
Found at i:1255688 original size:65 final size:63
Alignment explanation
Indices: 1255619--1255757 Score: 197
Period size: 65 Copynumber: 2.2 Consensus size: 63
1255609 AAAGATAGGT
* *
1255619 AAATTTTGTTTCCAAGGAAACAGACTCAAAGATTTTTCTTAAAAGAAATTGTCTCCGAAGAGACA
1 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTC--AAAAGAAATTGTCTCAGAAGAGACA
* * * *
1255684 AAATTTTGTTTCCAAAGAAACATATTCAATGATTTTTCAAAAGAAATTGTCTCAGGAGAGACA
1 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCAAAAGAAATTGTCTCAGAAGAGACA
*
1255747 AAACTTTGTTT
1 AAATTTTGTTT
1255758 TTCAGAAAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 33 0.49
65 34 0.51
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (63 bp):
AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCAAAAGAAATTGTCTCAGAAGAGACA
Found at i:1255755 original size:63 final size:64
Alignment explanation
Indices: 1255623--1255757 Score: 191
Period size: 63 Copynumber: 2.1 Consensus size: 64
1255613 ATAGGTAAAT
* * *
1255623 TTTGTTTCCAAGGAAACAGACTCAAAGATTTTTCTTAAAAGAAATTGTCTCCGAAGAGACAAAAT
1 TTTGTTTCCAAAGAAACAGACTCAAAGATTTTTC-TAAAAGAAATTGTCTCAGAAGAGACAAAAC
* * * *
1255688 TTTGTTTCCAAAGAAACATATTCAATGATTTTTC-AAAAGAAATTGTCTCAGGAGAGACAAAAC
1 TTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCTAAAAGAAATTGTCTCAGAAGAGACAAAAC
1255751 TTTGTTT
1 TTTGTTT
1255758 TTCAGAAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
63 33 0.52
65 30 0.48
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.33
Consensus pattern (64 bp):
TTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCTAAAAGAAATTGTCTCAGAAGAGACAAAAC
Found at i:1255891 original size:36 final size:36
Alignment explanation
Indices: 1255851--1255921 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
1255841 AAGAGACAAA
1255851 ATTTTGTTATGAAAGAAACATG-CTCAAAGATTTTTT
1 ATTTTGTTATGAAAGAAACA-GACTCAAAGATTTTTT
* * **
1255887 ATTTTGTTTTTAGTGAAACAGACTCAAAGATTTTT
1 ATTTTGTTATGAAAGAAACAGACTCAAAGATTTTT
1255922 CAATAAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 1 0.03
36 29 0.97
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (36 bp):
ATTTTGTTATGAAAGAAACAGACTCAAAGATTTTTT
Found at i:1256421 original size:107 final size:107
Alignment explanation
Indices: 1256226--1256418 Score: 325
Period size: 107 Copynumber: 1.8 Consensus size: 107
1256216 CGGTTTTGAA
*
1256226 AATCTCAAGTGAGATTACTTTTGTCTCAAGTGAATCAAATTCAAAATTTGTATATCAAAGGAAAA
1 AATCTCAAGTGAGATTAATTTTGTCTCAAGTGAATCAAATTCAAAATTTGTATATCAAAGGAAAA
1256291 AAATATCTCAAACGAGACGAAATTTGTTTTGAAATAAATAAC
66 AAATATCTCAAACGAGACGAAATTTGTTTTGAAATAAATAAC
* * *
1256333 AATCTCAAGTGAGATTAATTTTGTTTCAAGTGAATCAAATTCGAAATTTGTATCTCAAA-GAAAA
1 AATCTCAAGTGAGATTAATTTTGTCTCAAGTGAATCAAATTCAAAATTTGTATATCAAAGGAAAA
* *
1256397 AAATGTCTCAAGCGAGACGAAA
66 AAATATCTCAAACGAGACGAAA
1256419 ATTATTTTTA
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
106 25 0.31
107 55 0.69
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (107 bp):
AATCTCAAGTGAGATTAATTTTGTCTCAAGTGAATCAAATTCAAAATTTGTATATCAAAGGAAAA
AAATATCTCAAACGAGACGAAATTTGTTTTGAAATAAATAAC
Found at i:1256824 original size:4 final size:4
Alignment explanation
Indices: 1256817--1256958 Score: 236
Period size: 4 Copynumber: 36.0 Consensus size: 4
1256807 TTTATATATA
* *
1256817 ATGT ATGT ATG- -TGT ATAT ATGT TTGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1256863 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1256911 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT-T GATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT -ATGT ATGT
1256959 TTTTCTCGAT
Statistics
Matches: 130, Mismatches: 4, Indels: 8
0.92 0.03 0.06
Matches are distributed among these distances:
2 2 0.02
3 1 0.01
4 126 0.97
5 1 0.01
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
ATGT
Found at i:1257264 original size:24 final size:23
Alignment explanation
Indices: 1257234--1257289 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
1257224 TTCAAAAGTC
1257234 TAAAAATATCT-ATCAAAAGAGTTT
1 TAAAAATATCTAATC-AAAGA-TTT
* *
1257258 TAAAAATGTTTAATCAAAGATTT
1 TAAAAATATCTAATCAAAGATTT
*
1257281 TGAAAATAT
1 TAAAAATAT
1257290 TGCCCCTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 10 0.37
24 14 0.52
25 3 0.11
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (23 bp):
TAAAAATATCTAATCAAAGATTT
Found at i:1258166 original size:11 final size:11
Alignment explanation
Indices: 1258152--1258194 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
1258142 CCTCTTTTTG
1258152 TTCTTTGCTTT
1 TTCTTTGCTTT
1258163 TTCTTTGCTCTT
1 TTCTTTGCT-TT
1258175 TTCTTTG-TTT
1 TTCTTTGCTTT
1258185 TTGCTTTGCT
1 TT-CTTTGCT
1258195 ATTCTTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.14
11 15 0.52
12 10 0.34
ACGTcount: A:0.00, C:0.19, G:0.12, T:0.70
Consensus pattern (11 bp):
TTCTTTGCTTT
Found at i:1258169 original size:18 final size:18
Alignment explanation
Indices: 1258148--1258209 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 18
1258138 TTGTCCTCTT
1258148 TTTGTTCTTTGCTTTTTC
1 TTTGTTCTTTGCTTTTTC
* *
1258166 TTTGCTCTTTTCTTTGTT-
1 TTTGTTCTTTGCTTT-TTC
*
1258184 TTTG--CTTTGC-TATTC
1 TTTGTTCTTTGCTTTTTC
1258199 TTTGTTTCTTT
1 TTTG-TTCTTT
1258210 TTTCTTATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 2 0.06
15 5 0.14
16 5 0.14
18 21 0.60
19 2 0.06
ACGTcount: A:0.02, C:0.16, G:0.11, T:0.71
Consensus pattern (18 bp):
TTTGTTCTTTGCTTTTTC
Found at i:1258169 original size:29 final size:29
Alignment explanation
Indices: 1258135--1258191 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1258125 TTGTTTGTGC
1258135 TCTTTG-TCCTCTT-TTTGTTCTTTGCTTTT
1 TCTTTGCT-CTCTTCTTTGTT-TTTGCTTTT
*
1258164 TCTTTGCTCTTTTCTTTGTTTTTGCTTT
1 TCTTTGCTCTCTTCTTTGTTTTTGCTTT
1258192 GCTATTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.00, C:0.19, G:0.11, T:0.70
Consensus pattern (29 bp):
TCTTTGCTCTCTTCTTTGTTTTTGCTTTT
Found at i:1261525 original size:19 final size:20
Alignment explanation
Indices: 1261491--1261528 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1261481 ATATACAATT
*
1261491 AAATTATGATTCATTTGTTG
1 AAATTATGATTAATTTGTTG
1261511 AAATT-TGATTAATTTGTT
1 AAATTATGATTAATTTGTT
1261529 TCGTATTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.53
Consensus pattern (20 bp):
AAATTATGATTAATTTGTTG
Found at i:1262235 original size:30 final size:28
Alignment explanation
Indices: 1262171--1262238 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 28
1262161 ATATATTAAT
1262171 AGGACTAAAATAGAAATACATAAACATA
1 AGGACTAAAATAGAAATACATAAACATA
*
1262199 ATGGACTAAAATA-AAATAACCATATACATA
1 A-GGACTAAAATAGAAAT-A-CATAAACATA
1262229 GAGGACTAAA
1 -AGGACTAAA
1262239 CAATAATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
28 5 0.14
29 12 0.34
30 17 0.49
31 1 0.03
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.19
Consensus pattern (28 bp):
AGGACTAAAATAGAAATACATAAACATA
Found at i:1263545 original size:21 final size:21
Alignment explanation
Indices: 1263519--1263567 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1263509 GGCCTGAACC
1263519 GGGTCTGGGCTCCAACTTGTT
1 GGGTCTGGGCTCCAACTTGTT
*
1263540 GGGTCTGGGCTCCAGCTTGTT
1 GGGTCTGGGCTCCAACTTGTT
1263561 GGGTCTG
1 GGGTCTG
1263568 CTGCTGGTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.06, C:0.22, G:0.39, T:0.33
Consensus pattern (21 bp):
GGGTCTGGGCTCCAACTTGTT
Found at i:1267327 original size:21 final size:22
Alignment explanation
Indices: 1267295--1267349 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
1267285 TCATCAACTA
*
1267295 ATATATAT-TTTAATA-TACTTT
1 ATAT-TATGTTTAATATTACGTT
*
1267316 ATATTATGTTTAATATTTCGTT
1 ATATTATGTTTAATATTACGTT
1267338 AT-TTATGTTTAA
1 ATATTATGTTTAA
1267350 CAAGTAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 3 0.10
21 21 0.70
22 6 0.20
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (22 bp):
ATATTATGTTTAATATTACGTT
Found at i:1276856 original size:19 final size:20
Alignment explanation
Indices: 1276801--1276864 Score: 78
Period size: 19 Copynumber: 3.2 Consensus size: 20
1276791 GTAAAAAAAG
*
1276801 ATAAAACAAACAATAAA-AA
1 ATAAAATAAACAATAAACAA
* *
1276820 ATTAAATAAGATAATAAACAA
1 ATAAAATAA-ACAATAAACAA
1276841 ATAAAATAAA-AATAAACAA
1 ATAAAATAAACAATAAACAA
1276860 ATAAA
1 ATAAA
1276865 CAAGAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 21 0.54
20 8 0.21
21 10 0.26
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.17
Consensus pattern (20 bp):
ATAAAATAAACAATAAACAA
Found at i:1276872 original size:19 final size:18
Alignment explanation
Indices: 1276812--1276880 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 18
1276802 TAAAACAAAC
1276812 AATAAA-AAATTAAATAAGA
1 AATAAACAAA-TAAA-AAGA
*
1276831 TAATAAACAAATAAAATAAA
1 -AATAAACAAATAAAA-AGA
1276851 AATAAACAAATAAACAAGA
1 AATAAACAAATAAA-AAGA
1276870 AATAAACAAAT
1 AATAAACAAAT
1276881 TAGAAAAATC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
19 28 0.64
20 13 0.30
21 3 0.07
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (18 bp):
AATAAACAAATAAAAAGA
Found at i:1276962 original size:19 final size:20
Alignment explanation
Indices: 1276917--1276964 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1276907 TGAAAATACA
*
1276917 AATACAAATATTAAGTAAAAT
1 AATA-AAATAGTAAGTAAAAT
*
1276938 AA-AAAATAGTAA-TAACAT
1 AATAAAATAGTAAGTAAAAT
1276956 AATAAAATA
1 AATAAAATA
1276965 TGAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 7 0.29
19 14 0.58
20 1 0.04
21 2 0.08
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (20 bp):
AATAAAATAGTAAGTAAAAT
Found at i:1277316 original size:15 final size:16
Alignment explanation
Indices: 1277296--1277332 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1277286 AATAATAAAT
1277296 AAAGAAAAAG-AATAA
1 AAAGAAAAAGAAATAA
*
1277311 AAAG-AAAAGAAATTA
1 AAAGAAAAAGAAATAA
1277326 AAAGAAA
1 AAAGAAA
1277333 TTAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 5 0.26
15 12 0.63
16 2 0.11
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (16 bp):
AAAGAAAAAGAAATAA
Found at i:1277328 original size:10 final size:10
Alignment explanation
Indices: 1277315--1277342 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1277305 GAATAAAAAG
1277315 AAAAGAAATT
1 AAAAGAAATT
1277325 AAAAGAAATT
1 AAAAGAAATT
1277335 AAAAGAAA
1 AAAAGAAA
1277343 GAAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (10 bp):
AAAAGAAATT
Found at i:1277328 original size:24 final size:24
Alignment explanation
Indices: 1277301--1277346 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1277291 TAAATAAAGA
1277301 AAAAG-AATAAAAAGAAAAGAAATT
1 AAAAGAAATAAAAAG-AAAGAAATT
*
1277325 AAAAGAAATTAAAAGAAAGAAA
1 AAAAGAAATAAAAAGAAAGAAA
1277347 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (24 bp):
AAAAGAAATAAAAAGAAAGAAATT
Found at i:1277328 original size:25 final size:27
Alignment explanation
Indices: 1277300--1277355 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
1277290 ATAAATAAAG
1277300 AAAAAG-AATAAAAAGAAA-AGAAAT-T
1 AAAAAGAAATAAAAAGAAAGA-AAATAT
*
1277325 -AAAAGAAATTAAAAGAAAGAAAATAT
1 AAAAAGAAATAAAAAGAAAGAAAATAT
1277351 AAAAA
1 AAAAA
1277356 ACGTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 5 0.19
25 15 0.58
26 2 0.08
27 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.12
Consensus pattern (27 bp):
AAAAAGAAATAAAAAGAAAGAAAATAT
Found at i:1277405 original size:18 final size:18
Alignment explanation
Indices: 1277384--1277450 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
1277374 ATAGATAAGT
1277384 AAAAAAATAGTAATAATA
1 AAAAAAATAGTAATAATA
* *
1277402 AAAATAATAAG-GATAATA
1 AAAAAAAT-AGTAATAATA
* * *
1277420 TAAAGAATAATAATAA-A
1 AAAAAAATAGTAATAATA
1277437 AATAAAAATAGTAA
1 AA-AAAAATAGTAA
1277451 AAGAGTATAA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
17 3 0.08
18 32 0.86
19 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (18 bp):
AAAAAAATAGTAATAATA
Found at i:1277411 original size:12 final size:12
Alignment explanation
Indices: 1277386--1277536 Score: 56
Period size: 12 Copynumber: 11.4 Consensus size: 12
1277376 AGATAAGTAA
*
1277386 AAAAATAGTAAT
1 AAAAATAATAAT
1277398 AATAAA-AATAAT
1 AA-AAATAATAAT
**
1277410 AAGGATAAT-AT
1 AAAAATAATAAT
1277421 AAAGAATAATAAT
1 AAA-AATAATAAT
*
1277434 AAAAATAAAAAT
1 AAAAATAATAAT
* *
1277446 AGTAAAAGAGT-AT
1 A--AAAATAATAAT
*
1277459 AAAAAGAAATAAGT
1 AAAAA-TAATAA-T
1277473 AAATATATATATATAT
1 AAA-A-ATA-ATA-AT
1277489 ACATATAATAATAAT
1 A-A-A-AATAATAAT
*
1277504 AATATATATATAAT
1 AA-AAATA-ATAAT
1277518 AAAACATAATATAT
1 AAAA-ATAATA-AT
1277532 AAAAA
1 AAAAA
1277537 AGATTTAAAA
Statistics
Matches: 107, Mismatches: 14, Indels: 35
0.69 0.09 0.22
Matches are distributed among these distances:
11 9 0.08
12 28 0.26
13 20 0.19
14 28 0.26
15 5 0.05
16 9 0.08
17 5 0.05
18 3 0.03
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:1277516 original size:14 final size:14
Alignment explanation
Indices: 1277474--1277519 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 14
1277464 GAAATAAGTA
1277474 AATATATATATATAT
1 AATATATATATA-AT
1277489 ACATATA-ATAATAAT
1 A-ATATATAT-ATAAT
1277504 AATATATATATAAT
1 AATATATATATAAT
1277518 AA
1 AA
1277520 AACATAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 12 0.43
15 8 0.29
16 8 0.29
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
AATATATATATAAT
Found at i:1279238 original size:106 final size:106
Alignment explanation
Indices: 1279049--1279245 Score: 297
Period size: 106 Copynumber: 1.9 Consensus size: 106
1279039 AATTTAACAA
* * * *
1279049 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCTTTCACTGTGAA
1 TCAGCCGCCCCTTCCTCGTGAAGTTGAGCTTGTGCTATCTTGGGTCCAATATCCTTCACTGTGAA
*
1279114 GTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACAG
66 GTTGAAATTGACTATGAAATTGGGAAATTGTTTGTTGACAG
**
1279155 TCAGCCGCCCCTTCACT-GTGAAGTTGAGCTTGTGCTATCTTGGGTCCAATATCCTTCGTTGTGA
1 TCAGCCGCCCCTTC-CTCGTGAAGTTGAGCTTGTGCTATCTTGGGTCCAATATCCTTCACTGTGA
* *
1279219 AGTTGAATTTGGCTATGAAATTGGGAA
65 AGTTGAAATTGACTATGAAATTGGGAA
1279246 GCCCCTTCGT
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
106 80 0.99
107 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (106 bp):
TCAGCCGCCCCTTCCTCGTGAAGTTGAGCTTGTGCTATCTTGGGTCCAATATCCTTCACTGTGAA
GTTGAAATTGACTATGAAATTGGGAAATTGTTTGTTGACAG
Found at i:1280324 original size:12 final size:11
Alignment explanation
Indices: 1280307--1280359 Score: 61
Period size: 11 Copynumber: 4.5 Consensus size: 11
1280297 ACCCACCTTA
1280307 TTTTTCTTTTCT
1 TTTTTCTTTT-T
1280319 TTTTTCTCTTGTT
1 TTTTTCT-TT-TT
*
1280332 CTTTTTCTCTTT
1 -TTTTTCTTTTT
1280344 TTTTTCTTTTT
1 TTTTTCTTTTT
1280355 TTTTT
1 TTTTT
1280360 TCAATTTAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
11 15 0.42
12 9 0.25
13 4 0.11
14 8 0.22
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:1280336 original size:14 final size:14
Alignment explanation
Indices: 1280307--1280348 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1280297 ACCCACCTTA
1280307 TTTT-TCTTTTCTT
1 TTTTCTCTTTTCTT
1280320 TTTTCTCTTGTTC-T
1 TTTTCTCTT-TTCTT
1280334 TTTTCTCTTTT-TT
1 TTTTCTCTTTTCTT
1280347 TT
1 TT
1280349 CTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 9 0.35
14 14 0.54
15 3 0.12
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (14 bp):
TTTTCTCTTTTCTT
Found at i:1280346 original size:23 final size:23
Alignment explanation
Indices: 1280316--1280361 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1280306 ATTTTTCTTT
1280316 TCTTTTTTCTCTTGTTCTTTTTC
1 TCTTTTTTCTCTTGTTCTTTTTC
* * *
1280339 TCTTTTTTTTCTTTTTTTTTTTC
1 TCTTTTTTCTCTTGTTCTTTTTC
1280362 AATTTAGGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (23 bp):
TCTTTTTTCTCTTGTTCTTTTTC
Found at i:1280358 original size:14 final size:14
Alignment explanation
Indices: 1280307--1280360 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
1280297 ACCCACCTTA
*
1280307 TTTT-TCTTTTCTT
1 TTTTCTCTTTTTTT
* *
1280320 TTTTCTCTTGTTCT
1 TTTTCTCTTTTTTT
1280334 TTTTCTCTTTTTTT
1 TTTTCTCTTTTTTT
1280348 TCTTT-T-TTTTTTT
1 T-TTTCTCTTTTTTT
1280361 CAATTTAGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
13 11 0.32
14 20 0.59
15 3 0.09
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (14 bp):
TTTTCTCTTTTTTT
Found at i:1280360 original size:12 final size:12
Alignment explanation
Indices: 1280307--1280361 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
1280297 ACCCACCTTA
1280307 TTTTTCTTTTCTT
1 TTTTTCTTTT-TT
* *
1280320 TTTTCTCTTGTTC
1 TTTT-TCTTTTTT
*
1280333 TTTTTC-TCTTT
1 TTTTTCTTTTTT
1280344 TTTTTCTTTTTT
1 TTTTTCTTTTTT
1280356 TTTTTC
1 TTTTTC
1280362 AATTTAGGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 9 0.26
12 12 0.34
13 9 0.26
14 5 0.14
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:1280435 original size:16 final size:15
Alignment explanation
Indices: 1280398--1280436 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1280388 ACCATAAACG
*
1280398 TTTTTCTCCTTTTTT
1 TTTTTTTCCTTTTTT
1280413 TTCTTTTTCCTTTTTT
1 TT-TTTTTCCTTTTTT
*
1280429 CTTTTTTC
1 TTTTTTTC
1280437 AACTTAGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTCCTTTTTT
Found at i:1290326 original size:19 final size:19
Alignment explanation
Indices: 1290304--1290387 Score: 84
Period size: 19 Copynumber: 4.3 Consensus size: 19
1290294 GTAAAAAAAG
1290304 ATAAAACAAACAATAAA-AA
1 ATAAAACAAA-AATAAACAA
*
1290323 ATAAATA-AGATAATAAACAA
1 ATAAA-ACA-AAAATAAACAA
*
1290343 ATAAAATAAAAATAAACAA
1 ATAAAACAAAAATAAACAA
1290362 AT-AAACAAGAAATAAACAA
1 ATAAAACAA-AAATAAACAA
1290381 ATTAAAA
1 A-TAAAA
1290388 AACCAAATGA
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
18 5 0.09
19 36 0.65
20 11 0.20
21 3 0.05
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.15
Consensus pattern (19 bp):
ATAAAACAAAAATAAACAA
Found at i:1290348 original size:39 final size:38
Alignment explanation
Indices: 1290304--1290387 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 38
1290294 GTAAAAAAAG
*
1290304 ATAAAACAAACAATAAA-AAATAAATAAGATAATAAACAA
1 ATAAAACAAA-AATAAACAAATAAACAAGA-AATAAACAA
*
1290343 ATAAAATAAAAATAAACAAATAAACAAGAAATAAACAA
1 ATAAAACAAAAATAAACAAATAAACAAGAAATAAACAA
1290381 ATTAAAA
1 A-TAAAA
1290388 AACCAAATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
38 16 0.39
39 25 0.61
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.15
Consensus pattern (38 bp):
ATAAAACAAAAATAAACAAATAAACAAGAAATAAACAA
Found at i:1290450 original size:19 final size:20
Alignment explanation
Indices: 1290405--1290452 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1290395 TGAAAATACA
*
1290405 AATACAAATATTAAGTAAAAT
1 AATA-AAATAGTAAGTAAAAT
*
1290426 AA-AAAATAGTAA-TAACAT
1 AATAAAATAGTAAGTAAAAT
1290444 AATAAAATA
1 AATAAAATA
1290453 TGAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 7 0.29
19 14 0.58
20 1 0.04
21 2 0.08
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (20 bp):
AATAAAATAGTAAGTAAAAT
Found at i:1290677 original size:2 final size:2
Alignment explanation
Indices: 1290670--1290730 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1290660 AAATATGTAA
1290670 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1290712 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1290731 GTTAAAAACA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1290847 original size:15 final size:16
Alignment explanation
Indices: 1290827--1290861 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1290817 TAAATAAAGA
1290827 AAAAGAA-AAAAAATT
1 AAAAGAAGAAAAAATT
*
1290842 AAAAGAAGAAAATATT
1 AAAAGAAGAAAAAATT
1290858 AAAA
1 AAAA
1290862 ACGTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (16 bp):
AAAAGAAGAAAAAATT
Found at i:1290914 original size:18 final size:18
Alignment explanation
Indices: 1290886--1290959 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
1290876 ATACACATAG
1290886 ATAAGTAAAAAAAATAGTA
1 ATAA-TAAAAAAAATAGTA
* *
1290905 ATAATAAAAATAATAAG-C
1 ATAATAAAAAAAAT-AGTA
* * *
1290923 ATAATATAAAGAATAATA
1 ATAATAAAAAAAATAGTA
1290941 ATAA-AAATAAAAATAGTA
1 ATAATAAA-AAAAATAGTA
1290959 A
1 A
1290960 AAGAGTATAA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
17 3 0.07
18 34 0.79
19 6 0.14
ACGTcount: A:0.69, C:0.01, G:0.07, T:0.23
Consensus pattern (18 bp):
ATAATAAAAAAAATAGTA
Found at i:1290918 original size:12 final size:12
Alignment explanation
Indices: 1290895--1290955 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
1290885 GATAAGTAAA
*
1290895 AAAAATAGTAAT
1 AAAAATAATAAT
1290907 AATAAA-AATAAT
1 AA-AAATAATAAT
**
1290919 AAGCATAAT-AT
1 AAAAATAATAAT
1290930 AAAGAATAATAAT
1 AAA-AATAATAAT
*
1290943 AAAAATAAAAAT
1 AAAAATAATAAT
1290955 A
1 A
1290956 GTAAAAGAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
11 5 0.13
12 26 0.67
13 8 0.21
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:1291029 original size:2 final size:2
Alignment explanation
Indices: 1290984--1291012 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1290974 AAATAAGTAA
1290984 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 A
1291013 ATAAAACGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1298811 original size:20 final size:20
Alignment explanation
Indices: 1298774--1298811 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1298764 GACCAAAATA
*
1298774 TGAGTAAATCGAACATTTGG
1 TGAGTAAATCGAAAATTTGG
*
1298794 TGAGTAAATTGAAAATTT
1 TGAGTAAATCGAAAATTT
1298812 ATAAACTTCA
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:0.39, C:0.05, G:0.21, T:0.34
Consensus pattern (20 bp):
TGAGTAAATCGAAAATTTGG
Found at i:1301424 original size:19 final size:15
Alignment explanation
Indices: 1301386--1301415 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1301376 CCTTAAGAAT
1301386 CAAGAAAGAATCCCA
1 CAAGAAAGAATCCCA
1301401 CAAGAAAGAATCCCA
1 CAAGAAAGAATCCCA
1301416 ACAATAAGAT
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:0.53, C:0.27, G:0.13, T:0.07
Consensus pattern (15 bp):
CAAGAAAGAATCCCA
Found at i:1305695 original size:43 final size:41
Alignment explanation
Indices: 1305638--1305731 Score: 143
Period size: 43 Copynumber: 2.2 Consensus size: 41
1305628 CCTCCAACCA
* *
1305638 AACACACTAAATGTGTAGGTTTCCCAGAACCATACACCCACC
1 AACACACCAAATGTGTAGGTTCCCCAGAACCATA-ACCCACC
1305680 AACACACCATAATGTGTAGGTTCCCCAGAACCATAACCCACC
1 AACACACCA-AATGTGTAGGTTCCCCAGAACCATAACCCACC
*
1305722 AATACACCAA
1 AACACACCAA
1305732 GTAAGGCCCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
41 1 0.02
42 23 0.48
43 24 0.50
ACGTcount: A:0.38, C:0.34, G:0.11, T:0.17
Consensus pattern (41 bp):
AACACACCAAATGTGTAGGTTCCCCAGAACCATAACCCACC
Found at i:1305704 original size:42 final size:42
Alignment explanation
Indices: 1305638--1305731 Score: 138
Period size: 42 Copynumber: 2.2 Consensus size: 42
1305628 CCTCCAACCA
*
1305638 AACACACTAAATGTGTAGGTTT-CCCAGAACCATACACCCACC
1 AACACACCAAATGTGTAGGTTTCCCCAGAACCATA-ACCCACC
1305680 AACACACCATAATGTGTAGG-TTCCCCAGAACCATAACCCACC
1 AACACACCA-AATGTGTAGGTTTCCCCAGAACCATAACCCACC
*
1305722 AATACACCAA
1 AACACACCAA
1305732 GTAAGGCCCC
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
41 1 0.02
42 25 0.52
43 22 0.46
ACGTcount: A:0.38, C:0.34, G:0.11, T:0.17
Consensus pattern (42 bp):
AACACACCAAATGTGTAGGTTTCCCCAGAACCATAACCCACC
Found at i:1308345 original size:13 final size:13
Alignment explanation
Indices: 1308329--1308362 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1308319 CAATAGGTCT
*
1308329 GGTCGGGTCAACG
1 GGTCGGGTAAACG
1308342 GGTCGGGTAAACG
1 GGTCGGGTAAACG
1308355 GGTCGGGT
1 GGTCGGGT
1308363 TAGGACCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.18, G:0.50, T:0.18
Consensus pattern (13 bp):
GGTCGGGTAAACG
Found at i:1315712 original size:9 final size:9
Alignment explanation
Indices: 1315695--1315724 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1315685 ATTTTCCTTG
1315695 TCTTTTTCT
1 TCTTTTTCT
*
1315704 TCTTCTTCT
1 TCTTTTTCT
1315713 TCTTTTTCT
1 TCTTTTTCT
1315722 TCT
1 TCT
1315725 CGTTAGTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (9 bp):
TCTTTTTCT
Found at i:1316328 original size:21 final size:19
Alignment explanation
Indices: 1316304--1316345 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
1316294 ATCATGATAG
1316304 TATCAATACTAGGGGTATCGA
1 TATCAATA--AGGGGTATCGA
*
1316325 TATCAATAGGGGGTATCGA
1 TATCAATAAGGGGTATCGA
1316344 TA
1 TA
1316346 CCAGGAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
21 8 0.40
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (19 bp):
TATCAATAAGGGGTATCGA
Found at i:1317304 original size:21 final size:21
Alignment explanation
Indices: 1317271--1317311 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1317261 ATATATGTTA
1317271 TATGTAGTCATTCGGAACATC
1 TATGTAGTCATTCGGAACATC
* * *
1317292 TATGTGGTTATTCGGGACAT
1 TATGTAGTCATTCGGAACAT
1317312 TTCTACGTGG
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:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (21 bp):
TATGTAGTCATTCGGAACATC
Found at i:1319266 original size:65 final size:65
Alignment explanation
Indices: 1319158--1319311 Score: 197
Period size: 65 Copynumber: 2.4 Consensus size: 65
1319148 AGAGTTGAAC
*
1319158 CGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATACATGGCT-GGTGTA
1 CGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATACATGG-TAGGTGCA
1319221 T
65 T
* * * *
1319222 CGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTGAGTGCATCGATGCATGGTATGTGCA
1 CGATGCATAAAATGCATTCGATGTTTTCA-AAATAGCCTGAGTGCATCGATACATGGTAGGTGCA
1319286 T
65 T
** *
1319287 AAATGCATGAAATGCATTCGATGTT
1 CGATGCATAAAATGCATTCGATGTT
1319312 CAATTTATTC
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 23 0.29
65 53 0.67
66 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (65 bp):
CGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATACATGGTAGGTGCAT
Found at i:1327993 original size:65 final size:64
Alignment explanation
Indices: 1327860--1328060 Score: 212
Period size: 65 Copynumber: 3.1 Consensus size: 64
1327850 GAGTGCATCG
* **
1327860 ATGCATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTGGTGCATCG
1 ATGCATAAAATGCATTCGATGTTTCAAAATACCCTGAGTGCATCGATGCATGGCTGGTGCATAA
* *
1327924 ATGCATCAAATGCATTCGATGTGTTCATAAA-ACCCTGAGTGCATCGATGCATGG-TATGTGCAT
1 ATGCATAAAATGCATTCGATGT-TTCA-AAATACCCTGAGTGCATCGATGCATGGCT-GGTGCAT
1327987 AA
63 AA
* * * * *
1327989 ATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGGTTGGTGCAT
1 ATGCATAAAATGCATTCGATGTTTCAA--AATACCCTGAGTGCATCGATGCAT-GGCTGGTGCAT
**
1328052 CG
63 AA
1328054 ATGCATA
1 ATGCATA
1328061 GGTTGGTGCA
Statistics
Matches: 116, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 37 0.32
65 70 0.60
66 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (64 bp):
ATGCATAAAATGCATTCGATGTTTCAAAATACCCTGAGTGCATCGATGCATGGCTGGTGCATAA
Found at i:1328049 original size:20 final size:20
Alignment explanation
Indices: 1328024--1328093 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
1328014 ATTTATTCCA
1328024 TGGTGCATCGATGCATGGGT
1 TGGTGCATCGATGCATGGGT
*
1328044 TGGTGCATCGATGCATAGGT
1 TGGTGCATCGATGCATGGGT
1328064 TGGTGCATCGATGCATGGGT
1 TGGTGCATCGATGCATGGGT
1328084 TGGTGCATCG
1 TGGTGCATCG
1328094 GTACATCACT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.16, C:0.16, G:0.39, T:0.30
Consensus pattern (20 bp):
TGGTGCATCGATGCATGGGT
Found at i:1334447 original size:13 final size:13
Alignment explanation
Indices: 1334429--1334457 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1334419 ATAAAAACAA
1334429 TTAAATACAAACG
1 TTAAATACAAACG
1334442 TTAAATACAAACG
1 TTAAATACAAACG
1334455 TTA
1 TTA
1334458 CAATTTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (13 bp):
TTAAATACAAACG
Found at i:1334489 original size:24 final size:25
Alignment explanation
Indices: 1334472--1334553 Score: 70
Period size: 25 Copynumber: 3.5 Consensus size: 25
1334462 TTAAACAATT
1334472 AAAT-AATAAAAATATTAAGAAATA
1 AAATAAATAAAAATATTAAGAAATA
* * *
1334496 AAATAAATAAAAATGTCCATG--AT-
1 AAATAAATAAAAATAT-TAAGAAATA
*
1334519 ---TAAATAAAAACATTAAGAAATA
1 AAATAAATAAAAATATTAAGAAATA
1334541 AAATAAATAAAAA
1 AAATAAATAAAAA
1334554 GTCCATAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 15
0.66 0.11 0.23
Matches are distributed among these distances:
19 2 0.05
20 11 0.26
21 2 0.05
24 6 0.14
25 20 0.47
26 2 0.05
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.23
Consensus pattern (25 bp):
AAATAAATAAAAATATTAAGAAATA
Found at i:1334573 original size:44 final size:45
Alignment explanation
Indices: 1334476--1334598 Score: 203
Period size: 44 Copynumber: 2.8 Consensus size: 45
1334466 ACAATTAAAT
* * *
1334476 AATAAAAATATTAAGAAATAAAATAAATAAAAATGTCCATGATTA
1 AATAAAAACATTAAGAAATAAAATAAATAAAAATGTCCATAAGTA
1334521 AATAAAAACATTAAGAAATAAAATAAATAAAAA-GTCCATAAGTA
1 AATAAAAACATTAAGAAATAAAATAAATAAAAATGTCCATAAGTA
*
1334565 AATAAAAACATTAAGAAACAAAATAAATAAAAAT
1 AATAAAAACATTAAGAAATAAAATAAATAAAAAT
1334599 AAGTCTATCG
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 41 0.56
45 32 0.44
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.22
Consensus pattern (45 bp):
AATAAAAACATTAAGAAATAAAATAAATAAAAATGTCCATAAGTA
Found at i:1338623 original size:24 final size:20
Alignment explanation
Indices: 1338575--1338629 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 20
1338565 AAAATTGTAA
1338575 TTTTTAAAAATATTTTTACT
1 TTTTTAAAAATATTTTTACT
*
1338595 GTTTTAAAAATAAATTTTTCACAT
1 TTTTTAAAAAT--ATTTTT-AC-T
*
1338619 TTTTTACAAAT
1 TTTTTAAAAAT
1338630 TCTCTGATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 10 0.36
22 6 0.21
23 2 0.07
24 10 0.36
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTTTAAAAATATTTTTACT
Found at i:1339156 original size:15 final size:15
Alignment explanation
Indices: 1339138--1339166 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1339128 ATTTCCCCCG
1339138 ACGCCATATCCACCA
1 ACGCCATATCCACCA
1339153 ACGCCATATCCACC
1 ACGCCATATCCACC
1339167 GGCACCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.48, G:0.07, T:0.14
Consensus pattern (15 bp):
ACGCCATATCCACCA
Found at i:1344294 original size:2 final size:2
Alignment explanation
Indices: 1344287--1344320 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1344277 ATGGTCCTCA
1344287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1344321 TTATGTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1345274 original size:51 final size:51
Alignment explanation
Indices: 1345191--1345287 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
1345181 CTTACCCGGT
* *
1345191 TGGGCTCCTTGTTGGACCTCTATTGGACTGTTGGATTTATTAGACCCCTGC
1 TGGGCTCCTTGTTGGACCTCTATTAGACTGTTGGACTTATTAGACCCCTGC
* *
1345242 TGGGCTCCTTGTTGGACCT-T-TTCAAGATTGTTGGACTTATTGGACC
1 TGGGCTCCTTGTTGGACCTCTATT--AGACTGTTGGACTTATTAGACC
1345288 TTAAAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
49 2 0.05
50 1 0.03
51 37 0.93
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.38
Consensus pattern (51 bp):
TGGGCTCCTTGTTGGACCTCTATTAGACTGTTGGACTTATTAGACCCCTGC
Found at i:1345326 original size:12 final size:13
Alignment explanation
Indices: 1345302--1345346 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 13
1345292 AAAAAAGAAA
*
1345302 AATA-ATATTAAT
1 AATATATATAAAT
1345314 AATATA-ATAAAT
1 AATATATATAAAT
*
1345326 AATATATATATAT
1 AATATATATAAAT
1345339 -ATATATAT
1 AATATATAT
1345347 TATGTATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 23 0.79
13 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATATATATAAAT
Found at i:1345593 original size:73 final size:72
Alignment explanation
Indices: 1345402--1345707 Score: 339
Period size: 71 Copynumber: 4.2 Consensus size: 72
1345392 ATATACTATA
* **
1345402 TGTTTTTAAAAATATTTTAAAAAAACTATATATTATACATTTTCAAGAAAATTATTTTAAAAACT
1 TGTTTTCAAAAATATTTTTTAAAAACTATATATTATACATTTTC-A-AAAA-TATTTTAAAAACT
1345467 ATATATTATA
63 ATATATTATA
* ** * ** *
1345477 TGTTTTCAAAGATATTTTAAAAAAACTATATATTAAATGTTTTCAAAAATA-TTAAAAAACTATA
1 TGTTTTCAAAAATATTTTTTAAAAACTATATATTATACATTTTCAAAAATATTTTAAAAACTATA
1345541 TATTATA
66 TATTATA
* * *
1345548 CGTTTTCAAAAAGTATTTTTTTTAAAACTATATATTATACATTTTCAAAGATATTTTAAAAACTA
1 TGTTTTCAAAAA-TA-TTTTTTAAAAACTATATATTATACATTTTCAAAAATATTTTAAAAACTA
1345613 TATATTATA
64 TATATTATA
* * * * *
1345622 TGTTTTCAAAAA-ATATTTTCAAAACCATATATTATACGTTTTCAAAAATACGTTTTCAAAA-TA
1 TGTTTTCAAAAATATTTTTTAAAAACTATATATTATACATTTTCAAAAATA--TTTTAAAAACTA
*
1345685 TATACTATA
64 TATATTATA
**
1345694 TACTTTCAAAAATA
1 TGTTTTCAAAAATA
1345708 ACGTTTGAAA
Statistics
Matches: 199, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
71 61 0.31
72 25 0.13
73 43 0.22
74 31 0.16
75 39 0.20
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (72 bp):
TGTTTTCAAAAATATTTTTTAAAAACTATATATTATACATTTTCAAAAATATTTTAAAAACTATA
TATTATA
Found at i:1345598 original size:110 final size:107
Alignment explanation
Indices: 1345392--1345669 Score: 378
Period size: 110 Copynumber: 2.5 Consensus size: 107
1345382 TTTTAAAGCC
* * *
1345392 ATATACTATATGTTTTTAAAAATATTTTAAAAAAACTATATATTATACATTTTCAAGAAAATTAT
1 ATATATTATATGTTTTCAAAAATA-TTT-AAAAAACTATATATTATACGTTTTCAA-AAAATTAT
**
1345457 TTTAAAAACTATATATTATATGTTTTCAAAGATATTTTAAAAAAACT
63 TTTAAAAACTATATATTATACATTTTCAAAGATATTTT--AAAAACT
* *
1345504 ATATATTAAATGTTTTCAAAAATA-TTAAAAAACTATATATTATACGTTTTCAAAAAGTATTTTT
1 ATATATTATATGTTTTCAAAAATATTTAAAAAACTATATATTATACGTTTTCAAAAA--ATTATT
*
1345568 TTTAAAACTATATATTATACATTTTCAAAGATATTTTAAAAACT
64 TTAAAAACTATATATTATACATTTTCAAAGATATTTTAAAAACT
** *
1345612 ATATATTATATGTTTTCAAAAAATATTTTCAAAACCATATATTATACGTTTTCAAAAA
1 ATATATTATATGTTTTC-AAAAATATTTAAAAAACTATATATTATACGTTTTCAAAAA
1345670 TACGTTTTCA
Statistics
Matches: 150, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
108 26 0.17
109 33 0.22
110 70 0.47
112 21 0.14
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (107 bp):
ATATATTATATGTTTTCAAAAATATTTAAAAAACTATATATTATACGTTTTCAAAAAATTATTTT
AAAAACTATATATTATACATTTTCAAAGATATTTTAAAAACT
Found at i:1345684 original size:13 final size:14
Alignment explanation
Indices: 1345655--1345682 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1345645 ACCATATATT
1345655 ATACGTTTTCAAAA
1 ATACGTTTTCAAAA
1345669 ATACGTTTTCAAAA
1 ATACGTTTTCAAAA
1345683 TATATACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
ATACGTTTTCAAAA
Found at i:1345688 original size:36 final size:35
Alignment explanation
Indices: 1345375--1345707 Score: 316
Period size: 37 Copynumber: 9.2 Consensus size: 35
1345365 TTTAAAATAT
* * * * * *
1345375 AAAAACATTTT-AAAGCCATATACTATATGTTTTT
1 AAAAATATTTTAAAAACTATATATTATACGTTTTC
*
1345409 AAAAATATTTTAAAAAAACTATATATTATACATTTTC
1 AAAAATATTTT--AAAAACTATATATTATACGTTTTC
*
1345446 AAGAAAATTATTTTAAAAACTATATATTATATGTTTTC
1 -A-AAAA-TATTTTAAAAACTATATATTATACGTTTTC
* * *
1345484 AAAGATATTTTAAAAAAACTATATATTAAATGTTTTC
1 AAAAATATTTT--AAAAACTATATATTATACGTTTTC
*
1345521 AAAAATA-TTAAAAAACTATATATTATACGTTTTC
1 AAAAATATTTTAAAAACTATATATTATACGTTTTC
* *
1345555 AAAAAGTATTTTTTTTAAAACTATATATTATACATTTTC
1 AAAAA-TA---TTTTAAAAACTATATATTATACGTTTTC
* *
1345594 AAAGATATTTTAAAAACTATATATTATATGTTTTC
1 AAAAATATTTTAAAAACTATATATTATACGTTTTC
* *
1345629 AAAAAATATTTTCAAAACCATATATTATACGTTTTC
1 -AAAAATATTTTAAAAACTATATATTATACGTTTTC
*
1345665 AAAAATACGTTTTCAAAA-TATATACTATATAC--TTTC
1 AAAAATA--TTTTAAAAACTATATA-T-TATACGTTTTC
1345701 AAAAATA
1 AAAAATA
1345708 ACGTTTGAAA
Statistics
Matches: 254, Mismatches: 27, Indels: 34
0.81 0.09 0.11
Matches are distributed among these distances:
34 37 0.15
35 40 0.16
36 52 0.20
37 57 0.22
38 30 0.12
39 32 0.13
40 6 0.02
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (35 bp):
AAAAATATTTTAAAAACTATATATTATACGTTTTC
Found at i:1345730 original size:36 final size:36
Alignment explanation
Indices: 1345566--1345713 Score: 101
Period size: 36 Copynumber: 4.1 Consensus size: 36
1345556 AAAAGTATTT
* * * * *
1345566 TTTTTAAAACTATATATTATACATTTTCAAAGATA--
1 TTTTCAAAA-TATATACTATATACTTTCAAAAATACG
* * **
1345601 TTTTAAAAACTATATATTATATGTTTTCAAAAAATA--
1 TTTTCAAAA-TATATACTATATACTTTC-AAAAATACG
*
1345637 TTTTCAAAACCATATA-T-TATACGTTTTCAAAAATACG
1 TTTTCAAAA-TATATACTATATAC--TTTCAAAAATACG
1345674 TTTTCAAAATATATACTATATACTTTCAAAAATAACG
1 TTTTCAAAATATATACTATATACTTTCAAAAAT-ACG
1345711 TTT
1 TTT
1345714 GAAATTATTA
Statistics
Matches: 96, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
34 3 0.03
35 33 0.34
36 39 0.41
37 16 0.17
38 5 0.05
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (36 bp):
TTTTCAAAATATATACTATATACTTTCAAAAATACG
Found at i:1352125 original size:54 final size:54
Alignment explanation
Indices: 1352051--1352386 Score: 381
Period size: 54 Copynumber: 6.2 Consensus size: 54
1352041 ATTATCGATG
* * * *
1352051 CTAAGTGTCCAACCCACGGAATTCATAATAAGTTTATGAACGACCATATCGACA
1 CTAAGTGTGCAACCTACAGAATTCATAATAAGTTTATGAACGACCGTATCGACA
* * * * **
1352105 CTAAGTGTGCAACC-ATCGGAATTCATATTAATTTTATGAACAACCGTATCGGTA
1 CTAAGTGTGCAACCTA-CAGAATTCATAATAAGTTTATGAACGACCGTATCGACA
* * * * *
1352159 CTAAGTGTGGAACCTACAAAATTCATAATAAGTTTATGAACGACCATATTGGCA
1 CTAAGTGTGCAACCTACAGAATTCATAATAAGTTTATGAACGACCGTATCGACA
* **
1352213 CTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACCGTATCGACA
1 CTAAGTGTGCAACCTACAGAATTCATAATAAGTTTATGAACGACCGTATCGACA
*
1352267 CTAAGTGTGCAACCTACATAATTCATAATAAGTTTATGAACGACCGTATCAGTAC-
1 CTAAGTGTGCAACCTACAGAATTCATAATAAGTTTATGAACGACCGTATC-G-ACA
* * * * * *
1352322 C-AAGTGTGCAACCTACATAATTCATAATAAGGTTTACGAATGACGGTATAGGCA
1 CTAAGTGTGCAACCTACAGAATTCATAATAA-GTTTATGAACGACCGTATCGACA
*
1352376 CTACGTGTGCA
1 CTAAGTGTGCA
1352387 CCCCATGAAA
Statistics
Matches: 241, Mismatches: 34, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
53 2 0.01
54 211 0.88
55 26 0.11
56 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (54 bp):
CTAAGTGTGCAACCTACAGAATTCATAATAAGTTTATGAACGACCGTATCGACA
Found at i:1352329 original size:162 final size:163
Alignment explanation
Indices: 1352051--1352393 Score: 492
Period size: 162 Copynumber: 2.1 Consensus size: 163
1352041 ATTATCGATG
* *
1352051 CTAAGTGTCCAACCCACGGAATTCATAATAAGTTTATGAACGACCATATCGACACTAAGTGTGCA
1 CTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACCATATCGACACTAAGTGTGCA
* * * * * *
1352116 ACCATCGGAATTCATATTAATTTTATGAACAACCGTATCGGTACTAAGTGTGGAACCTACAAAAT
66 ACCATCAGAATTCATAATAAGTTTATGAACAACCGTATCAGTACCAAGTGTGCAACCTACAAAAT
* *
1352181 TCATAATAA-GTTTATGAACGACCATATTGGCA
131 TCATAATAAGGTTTACGAACGACCATATAGGCA
*
1352213 CTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACCGTATCGACACTAAGTGTGCA
1 CTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACCATATCGACACTAAGTGTGCA
* * *
1352278 ACC-TACATAATTCATAATAAGTTTATGAACGACCGTATCAGTACCAAGTGTGCAACCTACATAA
66 ACCAT-CAGAATTCATAATAAGTTTATGAACAACCGTATCAGTACCAAGTGTGCAACCTACAAAA
* **
1352342 TTCATAATAAGGTTTACGAATGACGGTATAGGCA
130 TTCATAATAAGGTTTACGAACGACCATATAGGCA
* *
1352376 CTACGTGTGCACCCCATG
1 CTAAGTGTGCAACCCATG
1352394 AAACTTCTAA
Statistics
Matches: 160, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
161 1 0.01
162 125 0.78
163 34 0.21
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (163 bp):
CTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACCATATCGACACTAAGTGTGCA
ACCATCAGAATTCATAATAAGTTTATGAACAACCGTATCAGTACCAAGTGTGCAACCTACAAAAT
TCATAATAAGGTTTACGAACGACCATATAGGCA
Found at i:1353492 original size:10 final size:9
Alignment explanation
Indices: 1353477--1353745 Score: 126
Period size: 10 Copynumber: 29.6 Consensus size: 9
1353467 GTTTATTTTC
1353477 ATTATATCAT
1 ATTATAT-AT
1353487 ATTATATATT
1 ATTATATA-T
1353497 ATT-T-TAT
1 ATTATATAT
*
1353504 ATAATATAT
1 ATTATATAT
*
1353513 ATTATATGGT
1 ATTATAT-AT
1353523 A-T-TATAT
1 ATTATATAT
1353530 A-TATATAT
1 ATTATATAT
1353538 ATTATA-AT
1 ATTATATAT
1353546 ATT-TATAT
1 ATTATATAT
*
1353554 AGTATATAT
1 ATTATATAT
1353563 CATTATATAGT
1 -ATTATATA-T
1353574 -TATATAGTAT
1 AT-TATA-TAT
1353584 ATTATTATAGT
1 ATTA-TATA-T
1353595 ATTATA-AT
1 ATTATATAT
*
1353603 ATATATTATGT
1 AT-TA-TATAT
*
1353614 ATTAGAT-T
1 ATTATATAT
1353622 ATATATTATAT
1 AT-TA-TATAT
1353633 ATTATAGTAT
1 ATTATA-TAT
1353643 A-TATATAT
1 ATTATATAT
*
1353651 ATAATCATACT
1 ATTAT-ATA-T
1353662 A-TATATAT
1 ATTATATAT
1353670 ATTAGTATATT
1 ATTA-TATA-T
*
1353681 ATAATATAT
1 ATTATATAT
1353690 ATTACGTAT-T
1 ATTA--TATAT
1353700 AGTTAT-T-T
1 A-TTATATAT
1353708 ATTATAGTAT
1 ATTATA-TAT
**
1353718 ATGGTAT-T
1 ATTATATAT
1353726 ATT-TATAT
1 ATTATATAT
1353734 -TTAT-TAT
1 ATTATATAT
1353741 ATTAT
1 ATTAT
1353746 TTTTATTTCC
Statistics
Matches: 206, Mismatches: 16, Indels: 76
0.69 0.05 0.26
Matches are distributed among these distances:
7 20 0.10
8 45 0.22
9 49 0.24
10 63 0.31
11 29 0.14
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (9 bp):
ATTATATAT
Found at i:1353506 original size:2 final size:2
Alignment explanation
Indices: 1353479--1353691 Score: 121
Period size: 2 Copynumber: 112.5 Consensus size: 2
1353469 TTATTTTCAT
*
1353479 TA TA TCA TA T- TA TA TA T- TA T- TT TA TA TA -A TA TA TA T- TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1353517 TA TGG TA T- TA TA TA TA TA TA TA T- TA TA -A TA TT TA TA TA GTA
1 TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
1353558 TA TA TCA T- TA TA TA GT- TA TA TA GTA TA T- TA T- TA TA GTA T-
1 TA TA T-A TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* *
1353597 TA TA -A TA TA TA T- TA TG TA T- TA GA T- TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1353634 T- TA TA GTA TA TA TA TA TA TA -A TCA TA CTA TA TA TA TA T- TA
1 TA TA TA -TA TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA TA TA
1353674 GTA TA T- TA TA -A TA TA TA T
1 -TA TA TA TA TA TA TA TA TA T
1353692 TACGTATTAG
Statistics
Matches: 168, Mismatches: 9, Indels: 68
0.69 0.04 0.28
Matches are distributed among these distances:
1 23 0.14
2 125 0.74
3 20 0.12
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1353537 original size:23 final size:23
Alignment explanation
Indices: 1353477--1353653 Score: 124
Period size: 23 Copynumber: 7.6 Consensus size: 23
1353467 GTTTATTTTC
1353477 ATTATATCATAT-TATATATTAT-T
1 ATTATAT-ATATATAT-TATTATGT
1353500 -TTATATAATATATATTA-TATGGT
1 ATTATAT-ATATATATTATTAT-GT
*
1353523 ATTATATATATATA-TATTATAAT
1 ATTATATATATATATTATTAT-GT
* *
1353546 ATTTATATAGTATATATCATTATAT
1 A-TTATATA-TATATATTATTATGT
*
1353571 AGTTATATA-GTATATTATTATAGT
1 A-TTATATATATATATTATTAT-GT
1353595 ATTATA-ATATATATTATGTAT-T
1 ATTATATATATATATTAT-TATGT
1353617 AGATTATATAT-TATA-TATTATAGT
1 --ATTATATATATATATTATTAT-GT
1353641 A-TATATATATATA
1 ATTATATATATATA
1353654 ATCATACTAT
Statistics
Matches: 128, Mismatches: 9, Indels: 35
0.74 0.05 0.20
Matches are distributed among these distances:
21 10 0.08
22 24 0.19
23 42 0.33
24 29 0.23
25 18 0.14
26 5 0.04
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (23 bp):
ATTATATATATATATTATTATGT
Found at i:1353699 original size:19 final size:19
Alignment explanation
Indices: 1353489--1353700 Score: 114
Period size: 19 Copynumber: 10.8 Consensus size: 19
1353479 TATATCATAT
*
1353489 TATATATTAT-TTTATATAA
1 TATATATTATGTAT-TATAA
* ** *
1353508 TATATATTATATGGTATTA
1 TATATATTATGTATTATAA
*
1353527 TATATA-TATATATTATAA
1 TATATATTATGTATTATAA
* *
1353545 TATTTA-TATAGTATATATCA
1 TATATATTAT-GTAT-TATAA
*
1353565 T-TATA-TA-GT-TATATAG
1 TATATATTATGTAT-TATAA
1353581 TATATTATTATAGTATTATAA
1 TATA-TATTAT-GTATTATAA
* *
1353602 TATATATTATGTATTAGAT
1 TATATATTATGTATTATAA
* *
1353621 TATATATTATATATTATAG
1 TATATATTATGTATTATAA
*
1353640 TATATATATATATAATCATACTATA
1 TATATAT-TATGT-AT--TA-TA-A
*
1353665 TATATATTAGTATATTATAA
1 TATATATTA-TGTATTATAA
*
1353685 TATATATTACGTATTA
1 TATATATTATGTATTA
1353701 GTTATTTATT
Statistics
Matches: 156, Mismatches: 21, Indels: 32
0.75 0.10 0.15
Matches are distributed among these distances:
16 6 0.04
17 4 0.03
18 19 0.12
19 65 0.42
20 27 0.17
21 14 0.09
22 3 0.02
23 2 0.01
24 6 0.04
25 10 0.06
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (19 bp):
TATATATTATGTATTATAA
Found at i:1354055 original size:20 final size:21
Alignment explanation
Indices: 1354030--1354072 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1354020 ATAACAGGGT
* *
1354030 AATAACCCGAA-ATGCTCGAA
1 AATAACCCCAAGATACTCGAA
1354050 AATAACCCCAAGATACTCGAA
1 AATAACCCCAAGATACTCGAA
1354071 AA
1 AA
1354073 CCACCACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.49, C:0.26, G:0.12, T:0.14
Consensus pattern (21 bp):
AATAACCCCAAGATACTCGAA
Found at i:1354460 original size:13 final size:13
Alignment explanation
Indices: 1354428--1354452 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1354418 TTGTTTAGGG
1354428 GATTTGGGGTTTA
1 GATTTGGGGTTTA
1354441 GATTTGGGGTTT
1 GATTTGGGGTTT
1354453 GGTTTTGGTG
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:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (13 bp):
GATTTGGGGTTTA
Found at i:1359314 original size:29 final size:29
Alignment explanation
Indices: 1359264--1359324 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
1359254 TATTTTAACA
* *
1359264 AAAGTCTTTCATATAAATTTTATGTTTT-T
1 AAAGTATTTAATATAAATTTTAT-TTTTAT
1359293 AAAGTATTTAATAT-AATATTTATTTTTAT
1 AAAGTATTTAATATAAAT-TTTATTTTTAT
1359322 AAA
1 AAA
1359325 ATAGATAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.52
Consensus pattern (29 bp):
AAAGTATTTAATATAAATTTTATTTTTAT
Found at i:1371038 original size:41 final size:39
Alignment explanation
Indices: 1370948--1371059 Score: 111
Period size: 40 Copynumber: 2.8 Consensus size: 39
1370938 TTTTTATATT
* **
1370948 ATTA-AAATATATTATTTGATTAT-TAAAATATAAAAATA
1 ATTATAAATATATTATTTCAAAATAT-AAATATAAAAATA
* * *
1370986 TTTTTAAATATATTTATTTCACAATATAAATATAATAAATA
1 ATTATAAATATA-TTATTTCAAAATATAAATATAA-AAATA
* *
1371027 ATTATAAATATATTATTTTAAAATATTAATATA
1 ATTATAAATATATTATTTCAAAATATAAATATA
1371060 TCAGGTATAG
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.03
39 7 0.12
40 35 0.58
41 16 0.27
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.46
Consensus pattern (39 bp):
ATTATAAATATATTATTTCAAAATATAAATATAAAAATA
Found at i:1372000 original size:9 final size:9
Alignment explanation
Indices: 1371983--1372021 Score: 55
Period size: 8 Copynumber: 4.4 Consensus size: 9
1371973 ACCCTTTTTA
1371983 TTTTT-ATT
1 TTTTTCATT
1371991 TTTTTCATT
1 TTTTTCATT
1372000 TTTTTCCATT
1 TTTTT-CATT
1372010 TTTTTC-TT
1 TTTTTCATT
1372018 TTTT
1 TTTT
1372022 CAAATATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 11 0.38
9 9 0.31
10 9 0.31
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTCATT
Found at i:1378926 original size:30 final size:30
Alignment explanation
Indices: 1378890--1379047 Score: 155
Period size: 30 Copynumber: 5.3 Consensus size: 30
1378880 GTACCCAAAA
* * **
1378890 AGAATCAGGACATGTAATGAAGTCCCATGC
1 AGAATCAGGACAGGGAACAAAGTCCCATGC
1378920 AGAATCAGGAC--GGATAGCAAAGTCCCATGC
1 AGAATCAGGACAGGGA-A-CAAAGTCCCATGC
* *
1378950 AGAATCAGGAC-GAAGAACGAAGTCCCATGC
1 AGAATCAGGACAG-GGAACAAAGTCCCATGC
* *
1378980 AAAAACAGGAC-GTGGAACAAAGTCCCATGC
1 AGAATCAGGACAG-GGAACAAAGTCCCATGC
*
1379010 AGAAAT-AGGACGGGGAACAAAGTCCCATGC
1 AG-AATCAGGACAGGGAACAAAGTCCCATGC
1379040 AGAATCAG
1 AGAATCAG
1379048 AAATGTACAA
Statistics
Matches: 109, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
28 2 0.02
29 4 0.04
30 97 0.89
31 4 0.04
32 2 0.02
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.13
Consensus pattern (30 bp):
AGAATCAGGACAGGGAACAAAGTCCCATGC
Found at i:1378989 original size:60 final size:59
Alignment explanation
Indices: 1378890--1379040 Score: 173
Period size: 60 Copynumber: 2.5 Consensus size: 59
1378880 GTACCCAAAA
* * * *
1378890 AGAATCAGGAC-ATGTAATGAAGTCCCATGCAGAATCAGGAC-GGATAGCAAAGTCCCATGC
1 AGAATCAGGACGAAG-AACGAAGTCCCATGCAAAAACAGGACGGGA-A-CAAAGTCCCATGC
1378950 AGAATCAGGACGAAGAACGAAGTCCCATGCAAAAACAGGACGTGGAACAAAGTCCCATGC
1 AGAATCAGGACGAAGAACGAAGTCCCATGCAAAAACAGGACG-GGAACAAAGTCCCATGC
** *
1379010 AGAAAT-AGGACGGGGAACAAAGTCCCATGCA
1 AG-AATCAGGACGAAGAACGAAGTCCCATGCA
1379041 GAATCAGAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
60 71 0.89
61 6 0.08
62 3 0.04
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.13
Consensus pattern (59 bp):
AGAATCAGGACGAAGAACGAAGTCCCATGCAAAAACAGGACGGGAACAAAGTCCCATGC
Found at i:1381924 original size:13 final size:14
Alignment explanation
Indices: 1381902--1381936 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1381892 CCTATTACCA
1381902 TGCACTATATATTT
1 TGCACTATATATTT
1381916 TGCAC-ATATATTT
1 TGCACTATATATTT
*
1381929 TGAACTAT
1 TGCACTAT
1381937 TTGTGCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (14 bp):
TGCACTATATATTT
Found at i:1382308 original size:3 final size:3
Alignment explanation
Indices: 1382302--1382361 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
1382292 TTTTTTTTTA
* * * *
1382302 TAT TAT TAT TAT TAT T-T TAA TAT TAA TAT TAA TAT TAT TATT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
1382347 TAA TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
1382362 AGGCCCGATA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1383412 original size:29 final size:30
Alignment explanation
Indices: 1383380--1383437 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
1383370 ATCACTAAAA
* *
1383380 TCAAGTTTTT-GTTTATTTTAATTTAGTCT
1 TCAAATTTTTAGTTTATTATAATTTAGTCT
* *
1383409 TCAAATTTTTATTTTATTATATTTTAGTC
1 TCAAATTTTTAGTTTATTATAATTTAGTC
1383438 CCTACCATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (30 bp):
TCAAATTTTTAGTTTATTATAATTTAGTCT
Found at i:1383753 original size:2 final size:2
Alignment explanation
Indices: 1383746--1383793 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1383736 AGTCACATTA
1383746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1383788 AT AT AT
1 AT AT AT
1383794 GAAAATTCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1387207 original size:39 final size:39
Alignment explanation
Indices: 1387164--1387241 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
1387154 GATAACATAG
*
1387164 ATTAAAGCAACAATAATCTACATAACATAGATTAAAACA
1 ATTAAAACAACAATAATCTACATAACATAGATTAAAACA
* * * *
1387203 ATTAAAATAGCAATAATCTAGATAATATAGATTAAAACA
1 ATTAAAACAACAATAATCTACATAACATAGATTAAAACA
1387242 GGACTATTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (39 bp):
ATTAAAACAACAATAATCTACATAACATAGATTAAAACA
Found at i:1393699 original size:18 final size:18
Alignment explanation
Indices: 1393676--1393711 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1393666 TGAAGATAGA
1393676 ATGATATAT-AAATATATG
1 ATGATATATGAAA-ATATG
1393694 ATGATATATGAAAATATG
1 ATGATATATGAAAATATG
1393712 TATTATAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (18 bp):
ATGATATATGAAAATATG
Found at i:1397011 original size:3 final size:3
Alignment explanation
Indices: 1396998--1397049 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
1396988 GGCCTACAAA
1396998 AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AA-
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1397042 AAT -AT AAT
1 AAT AAT AAT
1397050 GTTTTTGTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.13
3 36 0.80
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1398293 original size:15 final size:15
Alignment explanation
Indices: 1398273--1398303 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1398263 CAAAATAATC
1398273 ATTCCTTTTGTATAT
1 ATTCCTTTTGTATAT
*
1398288 ATTCCTTTTGTTTAT
1 ATTCCTTTTGTATAT
1398303 A
1 A
1398304 ATTACACGTG
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:0.19, C:0.13, G:0.06, T:0.61
Consensus pattern (15 bp):
ATTCCTTTTGTATAT
Found at i:1398680 original size:46 final size:47
Alignment explanation
Indices: 1398602--1398692 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 47
1398592 TGTAACAATT
* * *
1398602 AACACATACTTATATCGGTGTAAGTATATACATCTCTCAGCCTAAAA
1 AACACATACTTACATCGGTGTAAGTATATACATCTCCCAACCTAAAA
*
1398649 AACACATACTTACAT-GGTGTAAGTATGTACATCTCCCAACCTAA
1 AACACATACTTACATCGGTGTAAGTATATACATCTCCCAACCTAA
1398693 CAATAAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 26 0.65
47 14 0.35
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (47 bp):
AACACATACTTACATCGGTGTAAGTATATACATCTCCCAACCTAAAA
Found at i:1402072 original size:18 final size:19
Alignment explanation
Indices: 1402049--1402085 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
1402039 TGAAGAGAGA
1402049 ATGATATAT-AAATATATG
1 ATGATATATAAAATATATG
1402067 ATGATATATGAAAATATAT
1 ATGATATAT-AAAATATAT
1402086 ATTATAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
ATGATATATAAAATATATG
Found at i:1402403 original size:3 final size:3
Alignment explanation
Indices: 1402397--1402495 Score: 134
Period size: 3 Copynumber: 34.0 Consensus size: 3
1402387 TTTTTTATCT
1402397 TTA TTA TTA TTA TT- TTA TTA -TA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1402442 TTA TTA -TA TTA TTA TTA TTA TTA TTTA TTT TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
*
1402487 TTA TCA TTA
1 TTA TTA TTA
1402496 CAAACAGGCC
Statistics
Matches: 85, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
2 8 0.09
3 74 0.87
4 3 0.04
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1402431 original size:25 final size:26
Alignment explanation
Indices: 1402397--1402490 Score: 133
Period size: 25 Copynumber: 3.7 Consensus size: 26
1402387 TTTTTTATCT
1402397 TTATTATTATTATT-TTATTATATTA
1 TTATTATTATTATTATTATTATATTA
1402422 TTATTATTATTA-TATTATTATTATTA
1 TTATTATTATTATTATTATTA-TATTA
*
1402448 -TATTATTATTATTATTATT-TATTT
1 TTATTATTATTATTATTATTATATTA
*
1402472 TTATTATTAATATTATTAT
1 TTATTATTATTATTATTAT
1402491 CATTACAAAC
Statistics
Matches: 63, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
24 5 0.08
25 46 0.73
26 12 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
TTATTATTATTATTATTATTATATTA
Found at i:1405211 original size:15 final size:15
Alignment explanation
Indices: 1405191--1405221 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1405181 CAAAATAATC
1405191 ATTCCTTTTGTATAT
1 ATTCCTTTTGTATAT
*
1405206 ATTCCTTTTGTTTAT
1 ATTCCTTTTGTATAT
1405221 A
1 A
1405222 ATTACACGTG
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:0.19, C:0.13, G:0.06, T:0.61
Consensus pattern (15 bp):
ATTCCTTTTGTATAT
Found at i:1405617 original size:48 final size:50
Alignment explanation
Indices: 1405521--1405617 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 50
1405511 GTAACAATTA
* *
1405521 ACATACTTATATCGGTGTAAGTATATACAACTCTCAGCCTAAAAATAAAC
1 ACATACTTACATCGGTGTAAGTATATACAACTCTCAACCTAAAAATAAAC
* * *
1405571 ACATACTTACAT-GGTGTAAGTATGTACATCTC-CAACCTAACAATAAA
1 ACATACTTACATCGGTGTAAGTATATACAACTCTCAACCTAAAAATAAA
1405618 TATACTTACA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 13 0.31
49 18 0.43
50 11 0.26
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (50 bp):
ACATACTTACATCGGTGTAAGTATATACAACTCTCAACCTAAAAATAAAC
Found at i:1405697 original size:16 final size:16
Alignment explanation
Indices: 1405676--1405711 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1405666 TATAAATTTT
1405676 ATTAAAA-AATAATAAA
1 ATTAAAATAATAA-AAA
1405692 ATTAAAATAATAAAAA
1 ATTAAAATAATAAAAA
1405708 ATTA
1 ATTA
1405712 TATTTCTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
ATTAAAATAATAAAAA
Found at i:1409351 original size:16 final size:17
Alignment explanation
Indices: 1409333--1409372 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1409323 GTTTACAATT
1409333 AAATAATAA-AAAAACTA
1 AAATAATAATAAAAA-TA
1409350 AAATAA-AATAAAAATA
1 AAATAATAATAAAAATA
1409366 AAATAAT
1 AAATAAT
1409373 TAATTACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (17 bp):
AAATAATAATAAAAATA
Found at i:1414024 original size:17 final size:17
Alignment explanation
Indices: 1414002--1414035 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1413992 CACCGGTCAA
1414002 CGGTCAACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
1414019 CGGTCAACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
1414036 AAACGGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
CGGTCAACGGGTCGGGT
Done.