Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 96 of 182
Found at i:31375565 original size:52 final size:52
Alignment explanation
Indices: 31375487--31375779 Score: 326
Period size: 52 Copynumber: 5.7 Consensus size: 52
31375477 AATGAAAAGT
* * * *
31375487 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTAACTGTCATCGTGAGTATATGAATCCTTTATGGATTAAGA
* *
31375539 GGTCCGATGACTAAATGTCATTGTGAGTATATGAAATCCTTTATGGATTTAA-A
1 GGTCCGATGACTAACTGTCATCGTGAGTATATG-AATCCTTTATGGA-TTAAGA
*
31375592 GGTCTGATGACTAACTGTCATCGTGAGTATAT-AGATCCTTTATGGATTAAGA
1 GGTCCGATGACTAACTGTCATCGTGAGTATATGA-ATCCTTTATGGATTAAGA
*** *
31375644 GGTCCGATGACTCTGTGTCATCGTGAGTATATGGATCCTTTATGGATTAAGA
1 GGTCCGATGACTAACTGTCATCGTGAGTATATGAATCCTTTATGGATTAAGA
* * * * **
31375696 GGTTCGATGACT--CTGTCATTGTGAGTATACGAATCCCTCGTGGATTATA-A
1 GGTCCGATGACTAACTGTCATCGTGAGTATATGAATCCTTTATGGATTA-AGA
* * **
31375746 GGTCCGGTGGCTATGTGTCATCGTGAGTATATGA
1 GGTCCGATGACTAACTGTCATCGTGAGTATATGA
31375780 CTGAAGTGAA
Statistics
Matches: 206, Mismatches: 27, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
50 38 0.18
51 6 0.03
52 117 0.57
53 42 0.20
54 3 0.01
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (52 bp):
GGTCCGATGACTAACTGTCATCGTGAGTATATGAATCCTTTATGGATTAAGA
Found at i:31375674 original size:105 final size:105
Alignment explanation
Indices: 31375487--31375779 Score: 348
Period size: 105 Copynumber: 2.8 Consensus size: 105
31375477 AATGAAAAGT
* * * * *
31375487 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGAGGTCCGATGACTA
1 GGTCTGATGACTAACTGTCATCGTGAGTATATGAATCCTTTATGGATTAAGAGGTCCGATGACTA
** *
31375552 AATGTCATTGTGAGTATATGAAATCCTTTATGGATTTAA-A
66 TGTGTCATCGTGAGTATATGAAATCCTTTATGGA-TTAAGA
31375592 GGTCTGATGACTAACTGTCATCGTGAGTATAT-AGATCCTTTATGGATTAAGAGGTCCGATGACT
1 GGTCTGATGACTAACTGTCATCGTGAGTATATGA-ATCCTTTATGGATTAAGAGGTCCGATGACT
* *
31375656 CTGTGTCATCGTGAGTATATG-GATCCTTTATGGATTAAGA
65 ATGTGTCATCGTGAGTATATGAAATCCTTTATGGATTAAGA
* * * ** * *
31375696 GGT-TCGATGACT--CTGTCATTGTGAGTATACGAATCCCTCGTGGATTATA-AGGTCCGGTGGC
1 GGTCT-GATGACTAACTGTCATCGTGAGTATATGAATCCTTTATGGATTA-AGAGGTCCGATGAC
31375757 TATGTGTCATCGTGAGTATATGA
64 TATGTGTCATCGTGAGTATATGA
31375780 CTGAAGTGAA
Statistics
Matches: 164, Mismatches: 18, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
102 59 0.36
103 7 0.04
104 24 0.15
105 74 0.45
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (105 bp):
GGTCTGATGACTAACTGTCATCGTGAGTATATGAATCCTTTATGGATTAAGAGGTCCGATGACTA
TGTGTCATCGTGAGTATATGAAATCCTTTATGGATTAAGA
Found at i:31380853 original size:3 final size:3
Alignment explanation
Indices: 31380845--31380872 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
31380835 ATGTTTAGAT
31380845 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
31380873 AAGTTAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31383034 original size:27 final size:28
Alignment explanation
Indices: 31382996--31383050 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
31382986 CAAAATTGTA
31382996 TCTTTGTTATTTTGG-TTTGGTTTAATG
1 TCTTTGTTATTTTGGTTTTGGTTTAATG
31383023 TCTTTGTTATTTTGGTTTTGGTTTAATG
1 TCTTTGTTATTTTGGTTTTGGTTTAATG
31383051 CGTAAGTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 15 0.56
28 12 0.44
ACGTcount: A:0.11, C:0.04, G:0.22, T:0.64
Consensus pattern (28 bp):
TCTTTGTTATTTTGGTTTTGGTTTAATG
Found at i:31387267 original size:40 final size:40
Alignment explanation
Indices: 31387222--31387311 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
31387212 TGTTTTTCGA
***
31387222 TGAGTGATCGGTAACTGTTGGTTTATGGTTTTTAAAGATG
1 TGAGTGATCGGTAACTGTCAATTTATGGTTTTTAAAGATG
* *
31387262 TGAGTGATCAGTAACTGTCAATTTATGGTTTTTAAATATG
1 TGAGTGATCGGTAACTGTCAATTTATGGTTTTTAAAGATG
31387302 TGAGTGATCG
1 TGAGTGATCG
31387312 AGTTCTGATA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.26, C:0.07, G:0.27, T:0.41
Consensus pattern (40 bp):
TGAGTGATCGGTAACTGTCAATTTATGGTTTTTAAAGATG
Found at i:31388108 original size:110 final size:109
Alignment explanation
Indices: 31387883--31388151 Score: 306
Period size: 110 Copynumber: 2.5 Consensus size: 109
31387873 CTCACTTTGT
* * * * * * * * * ** **
31387883 GTGCTCCTCTACTAGCTAGGTTGGATTATATCCAATGAGACAAGGTTTATGATTTGCTCCATATT
1 GTGCTCCTCTGCGAGCTAGGTTAGATTATATCCAACGAGACAAAGCTTCTGGTTTTCTCTTTAGA
* * *
31387948 GAGCATAGCTCTTATGCGAGCTAATGTGATTTGTCTCATTCTGC
66 GAGCATAGCTCTTATGCGAGCTAATGTGATTCGTCTCACTCTAC
* * *
31387992 GTGCTCCTTTGCGAGCTAGGTTAGATTGTATCCAACGAGTCAAAGCTTCTGGTTTTCTCTTTAGA
1 GTGCTCCTCTGCGAGCTAGGTTAGATTATATCCAACGAGACAAAGCTTCTGGTTTTCTCTTTAGA
* * *
31388057 GAGCCTAGCTCTTTATGTGAGCTAATGTG-TTACGTCTCACTCTAT
66 GAGCATAGCTC-TTATGCGAGCTAATGTGATT-CGTCTCACTCTAC
*
31388102 GTGCTCCTCTGCGAGCTAGGTTGGATTATATCCAACGAGACAAAGCTTCT
1 GTGCTCCTCTGCGAGCTAGGTTAGATTATATCCAACGAGACAAAGCTTCT
31388152 ATTTGACGAA
Statistics
Matches: 132, Mismatches: 26, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
109 61 0.46
110 71 0.54
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (109 bp):
GTGCTCCTCTGCGAGCTAGGTTAGATTATATCCAACGAGACAAAGCTTCTGGTTTTCTCTTTAGA
GAGCATAGCTCTTATGCGAGCTAATGTGATTCGTCTCACTCTAC
Found at i:31389010 original size:9 final size:9
Alignment explanation
Indices: 31388996--31389094 Score: 73
Period size: 9 Copynumber: 11.2 Consensus size: 9
31388986 AATAACATCC
31388996 AAACAACAA
1 AAACAACAA
31389005 AAACAACAA
1 AAACAACAA
31389014 AAACAAC--
1 AAACAACAA
*
31389021 AATCAA-AA
1 AAACAACAA
* *
31389029 CAACAGCAA
1 AAACAACAA
*
31389038 ACAATAACAA
1 A-AACAACAA
31389048 AAACAACAA
1 AAACAACAA
*
31389057 AAATAACAGA
1 AAACAACA-A
31389067 AAA-AACAA
1 AAACAACAA
*
31389075 TAACAA-AA
1 AAACAACAA
*
31389083 ATAACAAGAA
1 A-AACAACAA
31389093 AA
1 AA
31389095 GTAACACCAA
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
7 5 0.07
8 8 0.11
9 44 0.62
10 14 0.20
ACGTcount: A:0.74, C:0.18, G:0.03, T:0.05
Consensus pattern (9 bp):
AAACAACAA
Found at i:31389012 original size:3 final size:3
Alignment explanation
Indices: 31388997--31389056 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
31388987 ATAACATCCA
* * * *
31388997 AAC AAC AAA AAC AAC AAA AAC AAC AATC AA- AAC AAC AGC AAAC AAT
1 AAC AAC AAC AAC AAC AAC AAC AAC AA-C AAC AAC AAC AAC -AAC AAC
*
31389043 AAC AAA AAC AAC AA
1 AAC AAC AAC AAC AA
31389057 AAATAACAGA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
2 2 0.05
3 37 0.84
4 5 0.11
ACGTcount: A:0.72, C:0.23, G:0.02, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:31389021 original size:12 final size:12
Alignment explanation
Indices: 31388997--31389094 Score: 59
Period size: 12 Copynumber: 8.6 Consensus size: 12
31388987 ATAACATCCA
31388997 AACAACAAA-AAC
1 AACAA-AAACAAC
31389009 AACAAAAACAAC
1 AACAAAAACAAC
31389021 AATC-AAAACAAC
1 AA-CAAAAACAAC
* *
31389033 AGC--AAACAAT
1 AACAAAAACAAC
31389043 AACAAAAACAAC
1 AACAAAAACAAC
31389055 AA-AAATAAC-A-
1 AACAAA-AACAAC
* *
31389065 GA-AAAAACAAT
1 AACAAAAACAAC
*
31389076 AACAAAAATAAC
1 AACAAAAACAAC
*
31389088 AAGAAAA
1 AACAAAA
31389095 GTAACACCAA
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
9 3 0.04
10 13 0.19
11 9 0.13
12 43 0.62
13 1 0.01
ACGTcount: A:0.73, C:0.18, G:0.03, T:0.05
Consensus pattern (12 bp):
AACAAAAACAAC
Found at i:31389047 original size:43 final size:42
Alignment explanation
Indices: 31389000--31389089 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 42
31388990 ACATCCAAAC
* *
31389000 AACAAAAACAACAAAAACAACA-ATCAAAACAACAGCAAACAAT
1 AACAAAAACAACAAAAACAACAGA-AAAAACAACAACAAA-AAT
* *
31389043 AACAAAAACAACAAAAATAACAGAAAAAACAATAACAAAAAT
1 AACAAAAACAACAAAAACAACAGAAAAAACAACAACAAAAAT
31389085 AACAA
1 AACAA
31389090 GAAAAGTAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 8 0.19
43 33 0.79
44 1 0.02
ACGTcount: A:0.73, C:0.19, G:0.02, T:0.06
Consensus pattern (42 bp):
AACAAAAACAACAAAAACAACAGAAAAAACAACAACAAAAAT
Found at i:31389123 original size:22 final size:22
Alignment explanation
Indices: 31389098--31389140 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
31389088 AAGAAAAGTA
*
31389098 ACACCA-AAACAATAGAAAAAAC
1 ACACCAGAAACAACA-AAAAAAC
*
31389120 ACACTAGAAACAACAAAAAAA
1 ACACCAGAAACAACAAAAAAA
31389141 TAACAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.70, C:0.21, G:0.05, T:0.05
Consensus pattern (22 bp):
ACACCAGAAACAACAAAAAAAC
Found at i:31393203 original size:9 final size:9
Alignment explanation
Indices: 31393189--31393245 Score: 57
Period size: 9 Copynumber: 6.2 Consensus size: 9
31393179 TTTTGAAATA
31393189 TAAAATTAT
1 TAAAATTAT
31393198 TAAAATTAT
1 TAAAATTAT
31393207 TATATTATATT-T
1 TA-A--A-ATTAT
31393219 TAAAA-TA-
1 TAAAATTAT
31393226 TAAAATTAT
1 TAAAATTAT
31393235 TAAAATTAT
1 TAAAATTAT
31393244 TA
1 TA
31393246 TATTAAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
7 6 0.15
8 3 0.07
9 23 0.56
10 1 0.02
11 1 0.02
12 4 0.10
13 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TAAAATTAT
Found at i:31393232 original size:37 final size:38
Alignment explanation
Indices: 31393154--31393250 Score: 144
Period size: 37 Copynumber: 2.6 Consensus size: 38
31393144 ATTAGCAAAT
* * *
31393154 AATT-TTAAAATTATTAAATTTATTTTTTTGAAATATAA
1 AATTATTAAAATTATTATA-TTATTATTTTAAAATATAA
31393192 AATTATTAAAATTATTATATTA-TATTTTAAAATATAA
1 AATTATTAAAATTATTATATTATTATTTTAAAATATAA
31393229 AATTATTAAAATTATTATATTA
1 AATTATTAAAATTATTATATTA
31393251 AAATATATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
37 35 0.64
38 7 0.13
39 13 0.24
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (38 bp):
AATTATTAAAATTATTATATTATTATTTTAAAATATAA
Found at i:31393247 original size:20 final size:20
Alignment explanation
Indices: 31393187--31393247 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
31393177 TTTTTTGAAA
31393187 TATAAAATTATTAAAATTAT
1 TATAAAATTATTAAAATTAT
*
31393207 TATATTATATT-TT-AAA--A-
1 TATA--AAATTATTAAAATTAT
31393224 TATAAAATTATTAAAATTAT
1 TATAAAATTATTAAAATTAT
31393244 TATA
1 TATA
31393248 TTAAAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
15 4 0.12
16 2 0.06
17 7 0.22
18 1 0.03
19 1 0.03
20 11 0.34
21 2 0.06
22 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATAAAATTATTAAAATTAT
Found at i:31393251 original size:14 final size:15
Alignment explanation
Indices: 31393207--31393259 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 15
31393197 TTAAAATTAT
31393207 TATATTATATTTTAAAA
1 TATATTATA--TTAAAA
**
31393224 TATAAAATTATTAAAA
1 TATATTA-TATTAAAA
31393240 T-TATTATATTAAAA
1 TATATTATATTAAAA
31393254 TATATT
1 TATATT
31393260 TTAAGGTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 9 0.30
15 7 0.23
16 7 0.23
17 5 0.17
18 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATTATATTAAAA
Found at i:31393252 original size:30 final size:28
Alignment explanation
Indices: 31393189--31393257 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 28
31393179 TTTTGAAATA
* *
31393189 TAAAATTATTAAAATTATTATATTATATTT
1 TAAAA-TA-TAAAATTATTAAATTATATAT
31393219 TAAAATATAAAATTATTAAAATTATTATAT
1 TAAAATATAAAATTATT-AAATTA-TATAT
31393249 TAAAATATA
1 TAAAATATA
31393258 TTTTAAGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 10 0.29
29 7 0.20
30 18 0.51
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TAAAATATAAAATTATTAAATTATATAT
Found at i:31393666 original size:18 final size:18
Alignment explanation
Indices: 31393630--31393667 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
31393620 TGAATTTTCG
* *
31393630 AATTCGAATAACTCGAAT
1 AATTCGAATAAATCAAAT
31393648 AATTCGAATAAATCAAAT
1 AATTCGAATAAATCAAAT
31393666 AA
1 AA
31393668 AACTTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.13, G:0.08, T:0.26
Consensus pattern (18 bp):
AATTCGAATAAATCAAAT
Found at i:31394550 original size:23 final size:23
Alignment explanation
Indices: 31394524--31394573 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
31394514 GACCACCCAA
31394524 AACCCAAAATCCCCAAATTCAAC
1 AACCCAAAATCCCCAAATTCAAC
* * *
31394547 AACCTAAAATCTCCAAATTCGAC
1 AACCCAAAATCCCCAAATTCAAC
31394570 AACC
1 AACC
31394574 ATAAACAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.46, C:0.36, G:0.02, T:0.16
Consensus pattern (23 bp):
AACCCAAAATCCCCAAATTCAAC
Found at i:31395010 original size:18 final size:17
Alignment explanation
Indices: 31394974--31395013 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
31394964 TAAACTATTG
* *
31394974 TTTTTTAATTTTAATTA
1 TTTTTTAATTTAAAATA
31394991 TTTTTTAACTTTAAAATA
1 TTTTTTAA-TTTAAAATA
31395009 TTTTT
1 TTTTT
31395014 GTTGATGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTTAATTTAAAATA
Found at i:31404531 original size:18 final size:18
Alignment explanation
Indices: 31404502--31404545 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
31404492 AAATGTACTA
*
31404502 ACAAAT-AAAATGCAGTG
1 ACAAATAAAAATGCAATG
31404519 ACAAATAAAAATGCAATG
1 ACAAATAAAAATGCAATG
*
31404537 ACAACTAAA
1 ACAAATAAA
31404546 TGAGATGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.59, C:0.14, G:0.11, T:0.16
Consensus pattern (18 bp):
ACAAATAAAAATGCAATG
Found at i:31404969 original size:15 final size:16
Alignment explanation
Indices: 31404949--31404985 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
31404939 CACCTTCCTT
31404949 CTCTTCATTC-TTCTC
1 CTCTTCATTCTTTCTC
31404964 CTCTTC-TTCTTTCTC
1 CTCTTCATTCTTTCTC
*
31404979 TTCTTCA
1 CTCTTCA
31404986 GTGTCCTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57
Consensus pattern (16 bp):
CTCTTCATTCTTTCTC
Found at i:31404979 original size:12 final size:12
Alignment explanation
Indices: 31404942--31404984 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
31404932 ATCGGGGCAC
*
31404942 CTTCCTTCTCTT
1 CTTCTTTCTCTT
31404954 CATTCTTCTCCTCTT
1 C-TTCTT-T-CTCTT
31404969 CTTCTTTCTCTT
1 CTTCTTTCTCTT
31404981 CTTC
1 CTTC
31404985 AGTGTCCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 10 0.37
13 5 0.19
14 6 0.22
15 6 0.22
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.58
Consensus pattern (12 bp):
CTTCTTTCTCTT
Found at i:31419312 original size:19 final size:18
Alignment explanation
Indices: 31419281--31419327 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
31419271 AATATATATA
31419281 TTTTTTTCTTTTCTCTTTT
1 TTTTTTTCTTTTCT-TTTT
31419300 TTTTTTTGC-TTTCTTTTT
1 TTTTTTT-CTTTTCTTTTT
*
31419318 CTTCTTTTCT
1 -TTTTTTTCT
31419328 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 5 0.21
19 18 0.75
20 1 0.04
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTTTTCTTTTCTTTTT
Found at i:31419939 original size:18 final size:17
Alignment explanation
Indices: 31419900--31419936 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
31419890 ACTACAATGC
31419900 AAATGTACTAACAAATA
1 AAATGTACTAACAAATA
* *
31419917 AAATGTAGTGACAAATA
1 AAATGTACTAACAAATA
31419934 AAA
1 AAA
31419937 ATGCAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.08, G:0.11, T:0.22
Consensus pattern (17 bp):
AAATGTACTAACAAATA
Found at i:31420088 original size:19 final size:19
Alignment explanation
Indices: 31420048--31420090 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
31420038 TCTTTGGGCG
* *
31420048 TTCTTCTTTGTGCTTCTTT
1 TTCTTCTTTGTCCTTCTCT
31420067 TTCTT-TTTGTCCTTACTCT
1 TTCTTCTTTGTCCTT-CTCT
31420086 TTCTT
1 TTCTT
31420091 ATCTTATCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.02, C:0.23, G:0.07, T:0.67
Consensus pattern (19 bp):
TTCTTCTTTGTCCTTCTCT
Found at i:31451411 original size:40 final size:40
Alignment explanation
Indices: 31451362--31451475 Score: 138
Period size: 40 Copynumber: 2.9 Consensus size: 40
31451352 AGACATCTTC
* * *
31451362 AGGGGTTTGTCGCGACATAAACATGCTGTGTTGTGACATA
1 AGGGGTTTGTCGCAACATAAACATGCTATGTTGCGACATA
* *
31451402 AGGGGTTTGTCGCAACATAGACATTCTATGTTGCGACATA
1 AGGGGTTTGTCGCAACATAAACATGCTATGTTGCGACATA
* * * * *
31451442 GGGGGTTTGTTGCAATATAGACATTCTATGTTGC
1 AGGGGTTTGTCGCAACATAAACATGCTATGTTGC
31451476 AACAAAGAAG
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (40 bp):
AGGGGTTTGTCGCAACATAAACATGCTATGTTGCGACATA
Found at i:31452733 original size:20 final size:20
Alignment explanation
Indices: 31452704--31452786 Score: 62
Period size: 20 Copynumber: 4.2 Consensus size: 20
31452694 AAATCTAGTT
* *
31452704 AAAATTATTTTAAACATGTC
1 AAAATAATTTTAAACAAGTC
*
31452724 AAAATAA-TTTGAACTAAGTC
1 AAAATAATTTTAAAC-AAGTC
* **
31452744 AAAATCATTTT-AACACTTC
1 AAAATAATTTTAAACAAGTC
**
31452763 AAAATGTTTTTCAAACAAGTC
1 AAAATAATTTT-AAACAAGTC
31452784 AAA
1 AAA
31452787 TAGCTTAAGG
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
19 18 0.37
20 19 0.39
21 12 0.24
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (20 bp):
AAAATAATTTTAAACAAGTC
Found at i:31467796 original size:3 final size:3
Alignment explanation
Indices: 31467788--31467813 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31467778 AAACATGTCA
31467788 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
31467814 GATATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:31468015 original size:23 final size:22
Alignment explanation
Indices: 31467969--31468022 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
31467959 AACTGATGAT
*
31467969 TAATTTAA-A-AATTATAAATA
1 TAATTTAATATAAATATAAATA
*
31467989 TAATTTAATATAAATATAAAGTC
1 TAATTTAATATAAATATAAA-TA
*
31468012 TAATTCAATAT
1 TAATTTAATAT
31468023 TATCTATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.29
21 1 0.04
22 8 0.29
23 11 0.39
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (22 bp):
TAATTTAATATAAATATAAATA
Found at i:31476956 original size:21 final size:21
Alignment explanation
Indices: 31476924--31476995 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 21
31476914 TATATTGTTG
31476924 TTTTGG-TGCTTTTTTTACTA
1 TTTTGGTTGCTTTTTTTACTA
* *
31476944 TTTTGGTTGCTTTTTTTGCTG
1 TTTTGGTTGCTTTTTTTACTA
*
31476965 TTTTGATAT--TTTTTTTA-TA
1 TTTTGGT-TGCTTTTTTTACTA
31476984 GTTTTGGTTGCT
1 -TTTTGGTTGCT
31476996 GTTTAGTGCT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
19 2 0.05
20 19 0.46
21 19 0.46
22 1 0.02
ACGTcount: A:0.08, C:0.07, G:0.18, T:0.67
Consensus pattern (21 bp):
TTTTGGTTGCTTTTTTTACTA
Found at i:31477047 original size:51 final size:51
Alignment explanation
Indices: 31476951--31477054 Score: 124
Period size: 51 Copynumber: 2.0 Consensus size: 51
31476941 CTATTTTGGT
* *
31476951 TGCTTTTTTTGCTGTTTTGATATTTTTTTTATAGTTTTGGTTGCTG-TTTAG
1 TGCTTTTTTTACTGTTTTGATATTTTTTTTATA-TTTTGGCTGCTGCTTTAG
*
31477002 TGCTTTTTTTACTGTTTTGATGTTTTTAATGTTAT-TTTT-GCTGCTGCTTTAG
1 TGCTTTTTTTACTGTTTTGATATTTTT--T-TTATATTTTGGCTGCTGCTTTAG
31477054 T
1 T
31477055 TGTTTTGATG
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
51 31 0.67
52 10 0.22
53 1 0.02
54 4 0.09
ACGTcount: A:0.11, C:0.08, G:0.18, T:0.63
Consensus pattern (51 bp):
TGCTTTTTTTACTGTTTTGATATTTTTTTTATATTTTGGCTGCTGCTTTAG
Found at i:31479633 original size:7 final size:7
Alignment explanation
Indices: 31479621--31479656 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
31479611 CGCCATCTTG
31479621 TGCTCTC
1 TGCTCTC
31479628 TGCTCTC
1 TGCTCTC
31479635 TGCTCTC
1 TGCTCTC
* *
31479642 TGCTTTT
1 TGCTCTC
31479649 TGCTCTC
1 TGCTCTC
31479656 T
1 T
31479657 TCCGATGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.14, T:0.50
Consensus pattern (7 bp):
TGCTCTC
Found at i:31497559 original size:13 final size:12
Alignment explanation
Indices: 31497540--31497573 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
31497530 TCCTTTATTA
31497540 TTATTTTTAATT
1 TTATTTTTAATT
*
31497552 TATATTTTAAATT
1 T-TATTTTTAATT
31497565 TTATTTTTA
1 TTATTTTTA
31497574 TGTCAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTTTTAATT
Found at i:31497879 original size:23 final size:24
Alignment explanation
Indices: 31497850--31497911 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 24
31497840 ACCATTATTA
* **
31497850 TTATTACTTTTATTTTGTTTA-TG
1 TTATTACTTTTATTATCATTAGTG
*
31497873 TTATTACTTGTATTATCATTAGTG
1 TTATTACTTTTATTATCATTAGTG
31497897 TTATTA-TTTTATTAT
1 TTATTACTTTTATTAT
31497912 TTATGTGTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 25 0.76
24 8 0.24
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.65
Consensus pattern (24 bp):
TTATTACTTTTATTATCATTAGTG
Found at i:31499453 original size:10 final size:10
Alignment explanation
Indices: 31499440--31499484 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
31499430 AGATAAAAAA
31499440 AGAAAAGAAT
1 AGAAAAGAAT
*
31499450 AGAATAGAAT
1 AGAAAAGAAT
31499460 AGAAAA-AA-
1 AGAAAAGAAT
*
31499468 AGAAAA-AAG
1 AGAAAAGAAT
31499477 AGAAAAGA
1 AGAAAAGA
31499485 GAAAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 8 0.26
9 8 0.26
10 15 0.48
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (10 bp):
AGAAAAGAAT
Found at i:31499466 original size:27 final size:27
Alignment explanation
Indices: 31499434--31499505 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 27
31499424 AAAAAAAGAT
* * *
31499434 AAAAAAAGAAAAGAATAGAATAGA-ATAG
1 AAAAAAAGAAAA-AAGAGAAAAGAGA-AA
31499462 AAAAAAAGAAAAAAGAGAAAAGAG-AA
1 AAAAAAAGAAAAAAGAGAAAAGAGAAA
*
31499488 AAAAAAAGAAAAAGGAGA
1 AAAAAAAGAAAAAAGAGA
31499506 GGTCGAGATG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 18 0.46
27 9 0.23
28 12 0.31
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.04
Consensus pattern (27 bp):
AAAAAAAGAAAAAAGAGAAAAGAGAAA
Found at i:31499492 original size:10 final size:9
Alignment explanation
Indices: 31499423--31499500 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 9
31499413 AATTTCACCA
31499423 AAAAAAAAG
1 AAAAAAAAG
31499432 ATAAAAAAAG
1 A-AAAAAAAG
*
31499442 AAAAGAATAG
1 AAAA-AAAAG
* *
31499452 AATAGAATAG
1 AA-AAAAAAG
31499462 -AAAAAAAG
1 AAAAAAAAG
*
31499470 AAAAAAGAG
1 AAAAAAAAG
* *
31499479 AAAAGAGA-
1 AAAAAAAAG
31499487 AAAAAAAAG
1 AAAAAAAAG
31499496 AAAAA
1 AAAAA
31499501 GGAGAGGTCG
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
8 11 0.20
9 24 0.43
10 20 0.36
11 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:31500599 original size:50 final size:49
Alignment explanation
Indices: 31500540--31500701 Score: 134
Period size: 50 Copynumber: 3.2 Consensus size: 49
31500530 TATCTCTCTA
*
31500540 AAGTTGTAGTAGAGCAAGATGAAGCTACAACACCAAATCCTATACCTTTG
1 AAGTTGTAGT-GAGCAAGATGAAGCTACAACACCAAATCATATACCTTTG
* * * * *
31500590 AAGTTGTAGTGGGTC-AGATTGAAGCTATAGA-AGCAAAT-ATTTATCTCTCT-
1 AAGTTGTAGTGAG-CAAGA-TGAAGCTACA-ACACCAAATCATATA-C-CTTTG
* * * *
31500640 AAGGTTGCAGTGGAGCAAAATGAAGCTACAACATCAAATCATATACCCTTG
1 AA-GTTGTAGT-GAGCAAGATGAAGCTACAACACCAAATCATATACCTTTG
31500691 AAGTTGTAGTG
1 AAGTTGTAGTG
31500702 GGACAGATTG
Statistics
Matches: 86, Mismatches: 15, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
49 9 0.10
50 39 0.45
51 30 0.35
52 8 0.09
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (49 bp):
AAGTTGTAGTGAGCAAGATGAAGCTACAACACCAAATCATATACCTTTG
Found at i:31500663 original size:101 final size:97
Alignment explanation
Indices: 31500520--31500802 Score: 334
Period size: 101 Copynumber: 2.8 Consensus size: 97
31500510 AAATTACAGT
* *
31500520 AGCAAATCTTTATCTCTCTAAAGTTGTAGTAGAGCAAGATGAAGCTACAACACCAAATCCTATAC
1 AGCAAAT-TTTATCTCTCT-AAGTTGAAGT-GAGCAAAATGAAGCTACAACACCAAATCCTATAC
*
31500585 CTTTGAAGTTGTAGTGGGTCAGATTGAAGCTATAGA
63 C-TTGAAGTTGTAGTGGGACAGATTGAAGCTATAGA
* * *
31500621 AGCAAATATTTATCTCTCTAAGGTTGCAGTGGAGCAAAATGAAGCTACAACATCAAATCATATAC
1 AGCAAAT-TTTATCTCTCTAA-GTTGAAGT-GAGCAAAATGAAGCTACAACACCAAATCCTATA-
31500686 CCTTGAAGTTGTAGTGGGACAGATTGAAGCTATAGA
62 CCTTGAAGTTGTAGTGGGACAGATTGAAGCTATAGA
* * * * *
31500722 AGTAAATCTTATCTC-CTTGAAGATGAAGTGAGGCAGAATGAAGTTACAACACCAAATCCTATAT
1 AGCAAATTTTATCTCTC-T-AAGTTGAAGTGA-GCAAAATGAAGCTACAACACCAAATCCTATA-
* *
31500786 CCTTGAATTTATAGTGG
62 CCTTGAAGTTGTAGTGG
31500803 ATCGAATTAA
Statistics
Matches: 159, Mismatches: 18, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
99 3 0.02
100 58 0.36
101 96 0.60
102 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (97 bp):
AGCAAATTTTATCTCTCTAAGTTGAAGTGAGCAAAATGAAGCTACAACACCAAATCCTATACCTT
GAAGTTGTAGTGGGACAGATTGAAGCTATAGA
Found at i:31500678 original size:51 final size:49
Alignment explanation
Indices: 31500522--31500678 Score: 122
Period size: 51 Copynumber: 3.1 Consensus size: 49
31500512 ATTACAGTAG
* *
31500522 CAAATCTTTATCTCTCTAAAGTTGTAGTAGAGCAAGATGAAGCTACAACAC
1 CAAAT-TTTATCTCTCT-AAGTTGTAGTGGAGCAAAATGAAGCTACAACAC
** * * * * *
31500573 CAAATCCTATAC-CTTTGAAGTTGTAGTGG-GTCAGATTGAAGCTATAGA-AG
1 CAAATTTTAT-CTCTCT-AAGTTGTAGTGGAG-CAAAATGAAGCTACA-ACAC
* *
31500623 CAAATATTTATCTCTCTAAGGTTGCAGTGGAGCAAAATGAAGCTACAACAT
1 CAAAT-TTTATCTCTCTAA-GTTGTAGTGGAGCAAAATGAAGCTACAACAC
31500674 CAAAT
1 CAAAT
31500679 CATATACCCT
Statistics
Matches: 80, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
49 1 0.01
50 38 0.47
51 40 0.50
52 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.28
Consensus pattern (49 bp):
CAAATTTTATCTCTCTAAGTTGTAGTGGAGCAAAATGAAGCTACAACAC
Found at i:31500717 original size:50 final size:50
Alignment explanation
Indices: 31500558--31500802 Score: 162
Period size: 50 Copynumber: 4.9 Consensus size: 50
31500548 GTAGAGCAAG
* * *
31500558 ATGAAGCTACAACACCAAATCCTATACCTTTGAAGTTGTAGTGGGTCAGA
1 ATGAAGCTACAACACCAAATCATATACCCTTGAAGTTGTAGTGGGACAGA
* * * * * * *
31500608 TTGAAGCTATAGA-AGCAAAT-ATTTATCTCTCT-AAGGTTGCAGT-GGAGCAAA
1 ATGAAGCTACA-ACACCAAATCATATA-CCCT-TGAA-GTTGTAGTGGGA-CAGA
*
31500659 ATGAAGCTACAACATCAAATCATATACCCTTGAAGTTGTAGTGGGACAGA
1 ATGAAGCTACAACACCAAATCATATACCCTTGAAGTTGTAGTGGGACAGA
* * ** * * *
31500709 TTGAAGCTATAGA-AGTAAATCTTAT-CTCCTTGAAGATGAAGTGAGG-CAGA
1 ATGAAGCTACA-ACACCAAATCATATAC-CCTTGAAGTTGTAGTG-GGACAGA
* * * * *
31500759 ATGAAGTTACAACACCAAATCCTATATCCTTGAATTTATAGTGG
1 ATGAAGCTACAACACCAAATCATATACCCTTGAAGTTGTAGTGG
31500803 ATCGAATTAA
Statistics
Matches: 146, Mismatches: 35, Indels: 29
0.70 0.17 0.14
Matches are distributed among these distances:
49 6 0.04
50 98 0.67
51 38 0.26
52 4 0.03
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (50 bp):
ATGAAGCTACAACACCAAATCATATACCCTTGAAGTTGTAGTGGGACAGA
Found at i:31501812 original size:42 final size:42
Alignment explanation
Indices: 31501741--31502031 Score: 393
Period size: 42 Copynumber: 6.9 Consensus size: 42
31501731 TTACGAAATA
* * *
31501741 TCATGCTCATCCCGAGTCACGAGTCTTCCTTTAAATATAATC
1 TCATGCTCATCCCGAGACATGAGTCTTCCTTTAAACATAATC
* * *
31501783 TCATGCTCATCCTGAGACATGAGTTTTCCTTTAAACCTAATC
1 TCATGCTCATCCCGAGACATGAGTCTTCCTTTAAACATAATC
* *
31501825 TCATGCTCATCCCAAGACATGAGTCTTCCTTTAAACGTAATC
1 TCATGCTCATCCCGAGACATGAGTCTTCCTTTAAACATAATC
** * * * *
31501867 TCATGCTGTTCTCGAGATATGACTCTTCCTTTAAACATAATA
1 TCATGCTCATCCCGAGACATGAGTCTTCCTTTAAACATAATC
* *
31501909 TCATGCTCATCCCGAGACACGAGTCTTCCTTTTAACATAATC
1 TCATGCTCATCCCGAGACATGAGTCTTCCTTTAAACATAATC
*
31501951 TCATGCTCATCTCGAGACATGAGTCTTCCTTTAAACATAATC
1 TCATGCTCATCCCGAGACATGAGTCTTCCTTTAAACATAATC
* * *
31501993 TTATGCTCATCCCGAGGCATGAGTCTTCCATTTATACAT
1 TCATGCTCATCCCGAGACATGAGTCTTCC-TTTAAACAT
31502032 CAAGTGATTC
Statistics
Matches: 215, Mismatches: 33, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
42 207 0.96
43 8 0.04
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (42 bp):
TCATGCTCATCCCGAGACATGAGTCTTCCTTTAAACATAATC
Found at i:31503156 original size:42 final size:42
Alignment explanation
Indices: 31503100--31503372 Score: 356
Period size: 42 Copynumber: 6.5 Consensus size: 42
31503090 TATGCTCTAA
* * * * *
31503100 CGAGTCATAAGTCTTCCTTTAATCGA-ATTCTTATTCTCATCC
1 CGAGACATGAGTCTTCCTTTAATC-ATAATCTCATTCTCATCT
31503142 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
* *
31503184 CGAGACATGAATCTTCCTTTAATCATAATCTCATTCTTATCT
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
*
31503226 AGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
*
31503268 CGAGACATGAGTCTTCCTTTAATCATAATCTCCTTCTCATCT
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
* * *
31503310 CAAGACATGAGTCTTCCATTT-ATACA-AATCCTCATGCTCAAC-
1 CGAGACATGAGTCTTCC-TTTAAT-CATAAT-CTCATTCTCATCT
*
31503352 CTGAGACACGAGTCTTCCTTT
1 C-GAGACATGAGTCTTCCTTT
31503373 TTATACATCA
Statistics
Matches: 208, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
41 1 0.00
42 179 0.86
43 28 0.13
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (42 bp):
CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
Found at i:31507790 original size:13 final size:12
Alignment explanation
Indices: 31507774--31507807 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
31507764 TATGCACCCC
31507774 TTTTATTTTATAT
1 TTTTATTTTAT-T
31507787 TTTTATTTTATT
1 TTTTATTTTATT
31507799 TATTTATTT
1 T-TTTATTT
31507808 CATGCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 18 0.90
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:31513546 original size:42 final size:42
Alignment explanation
Indices: 31513498--31513585 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
31513488 CACACAATCG
* * * *
31513498 TGTGTTCCAAGTTCGTGTGTCACACGGGCTGGGACACGGTCA
1 TGTGTTCAAAGTTAGTATGTCACACGGGCTGGCACACGGTCA
* * *
31513540 TGTGTTCAAAGTTAGTATGTTACACGGTCTGGCACACGGTCG
1 TGTGTTCAAAGTTAGTATGTCACACGGGCTGGCACACGGTCA
31513582 TGTG
1 TGTG
31513586 ACTCAACTCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.18, C:0.20, G:0.32, T:0.30
Consensus pattern (42 bp):
TGTGTTCAAAGTTAGTATGTCACACGGGCTGGCACACGGTCA
Found at i:31519209 original size:41 final size:41
Alignment explanation
Indices: 31519130--31519316 Score: 205
Period size: 41 Copynumber: 4.5 Consensus size: 41
31519120 TTATGCTCTT
* * * * *
31519130 TCGAGTCATAAGTCTTCCTTTAACCATATTCTCATTCTCATC
1 TCGAGACATGAGTCTTCC-TTAATCAAAATCTCATTCTCATC
*
31519172 TCAAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATC
*
31519213 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATT
1 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATC
* * * ** * *
31519254 TCGAGTCATGAGTCTTTCATTTATACAATTTCTCATGCTCAAC
1 TCGAGACATGAGTC-TTCCTTAAT-CAAAATCTCATTCTCATC
31519297 -CTGAGACATGAGTCTTCCTT
1 TC-GAGACATGAGTCTTCCTT
31519317 TTTATACACC
Statistics
Matches: 124, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
41 72 0.58
42 28 0.23
43 24 0.19
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (41 bp):
TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATC
Found at i:31523083 original size:21 final size:21
Alignment explanation
Indices: 31523057--31523096 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31523047 TAGGTTGTTA
*
31523057 CATTAATTTTATATAATTTAG
1 CATTAATTTTACATAATTTAG
31523078 CATTAATTTTACATAATTT
1 CATTAATTTTACATAATTT
31523097 TACTATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (21 bp):
CATTAATTTTACATAATTTAG
Found at i:31524565 original size:15 final size:16
Alignment explanation
Indices: 31524533--31524566 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
31524523 TTTTCATCTC
31524533 ATTTGCATTTACGTTA
1 ATTTGCATTTACGTTA
31524549 ATTTGCATTTA-GTTA
1 ATTTGCATTTACGTTA
31524564 ATT
1 ATT
31524567 ACTTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.53
Consensus pattern (16 bp):
ATTTGCATTTACGTTA
Found at i:31540313 original size:123 final size:124
Alignment explanation
Indices: 31540186--31540416 Score: 340
Period size: 123 Copynumber: 1.9 Consensus size: 124
31540176 ATGGAAGGTT
** *
31540186 TATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTTAATAT
1 TATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATAATTTAATAAACCTTCAATAT
* * *
31540251 ATTTCTTTAAAGG-A-ATATTTCCATTTTAATATGAGATATTATATATAAGGAAATTGAA
66 ATTCCTCT-AAGGAATATATTTCCATTGTAATATGAGATATTATATATAAGGAAATTGAA
* *
31540309 TATTAAAAACATGGAAGTTAATATCCTTTTGGAAATGATATAATAATTTAATAAACCTTCCATAT
1 TATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATAATTTAATAAACCTTCAATAT
**
31540374 ATTCCTCTAAGGATATATATTTTTATTGTAATATGAGATATTA
66 ATTCCTCTAAGGA-ATATATTTCCATTGTAATATGAGATATTA
31540417 AAAATAAAAG
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
122 4 0.04
123 66 0.69
124 1 0.01
125 24 0.25
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (124 bp):
TATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATAATTTAATAAACCTTCAATAT
ATTCCTCTAAGGAATATATTTCCATTGTAATATGAGATATTATATATAAGGAAATTGAA
Found at i:31544987 original size:24 final size:24
Alignment explanation
Indices: 31544941--31544987 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31544931 ATTGTCTATA
* *
31544941 ATTTGCTCTGACATTTTATATTCC
1 ATTTGCGCTGACAATTTATATTCC
31544965 ATTTGCGCTGACAGATTTA-ATTC
1 ATTTGCGCTGACA-ATTTATATTC
31544988 TTAACTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (24 bp):
ATTTGCGCTGACAATTTATATTCC
Found at i:31552900 original size:24 final size:24
Alignment explanation
Indices: 31552854--31552900 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31552844 ATTTTCCATA
* *
31552854 ATTTGCTCTGACATTTTATATTCC
1 ATTTGCGCTGACAATTTATATTCC
31552878 ATTTGCGCTGACAGATTTA-ATTC
1 ATTTGCGCTGACA-ATTTATATTC
31552901 TTAACTTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (24 bp):
ATTTGCGCTGACAATTTATATTCC
Found at i:31562080 original size:21 final size:22
Alignment explanation
Indices: 31562054--31562095 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
31562044 AGAAAAAAGA
31562054 AAAAGAAAAATGAGT-AGAAAC
1 AAAAGAAAAATGAGTAAGAAAC
**
31562075 AAAAGAAGCATGAGTAAGAAA
1 AAAAGAAAAATGAGTAAGAAA
31562096 ACATGTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.64, C:0.05, G:0.21, T:0.10
Consensus pattern (22 bp):
AAAAGAAAAATGAGTAAGAAAC
Found at i:31564715 original size:108 final size:106
Alignment explanation
Indices: 31564586--31564914 Score: 478
Period size: 108 Copynumber: 3.1 Consensus size: 106
31564576 TTTACTGAAT
* * * *
31564586 ATAATTTAACGTAATTATAATTATTAATTTTAATGATTTTGTTAAATACTAAAACATGGAAGTTA
1 ATAATTTAACGTAATTATAATTATTAATTATAATAATTTCGTTAAATATTAAAACATGGAAGTTA
* *
31564651 ATATCCTTTTGGAAAGGATATATAATGTTTTAATAAATGTTCC
66 ATATCATTTTGGAAAGG--ATATAATGTTTTAATAAATATTCC
* *
31564694 ATAATTTAATGTAATTATAATTATTAATTATAATTATTTCGTTAAATATTAAAACATGGAAGTTA
1 ATAATTTAACGTAATTATAATTATTAATTATAATAATTTCGTTAAATATTAAAACATGGAAGTTA
* * *
31564759 ATATTATTTTGGAAAGGATATAATGTTTTAATAAACATTCA
66 ATATCATTTTGGAAAGGATATAATGTTTTAATAAATATTCC
* *
31564800 ATAATTTAACATAATTATAATTATTAATTATAATAATTTCGTTAAATATTAAAAACATGAAAGTT
1 ATAATTTAACGTAATTATAATTATTAATTATAATAATTTCGTTAAATATT-AAAACATGGAAGTT
* * *
31564865 AATATCTTTTTGGAAAGGATATAATGATTTAATAAATTTTCC
65 AATATCATTTTGGAAAGGATATAATGTTTTAATAAATATTCC
31564907 ATATATTT
1 ATA-ATTT
31564915 CTTTAAAGGA
Statistics
Matches: 199, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
106 68 0.34
107 52 0.26
108 79 0.40
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (106 bp):
ATAATTTAACGTAATTATAATTATTAATTATAATAATTTCGTTAAATATTAAAACATGGAAGTTA
ATATCATTTTGGAAAGGATATAATGTTTTAATAAATATTCC
Found at i:31564723 original size:13 final size:13
Alignment explanation
Indices: 31564705--31564731 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31564695 TAATTTAATG
31564705 TAATTATAATTAT
1 TAATTATAATTAT
31564718 TAATTATAATTAT
1 TAATTATAATTAT
31564731 T
1 T
31564732 TCGTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATTATAATTAT
Found at i:31564941 original size:107 final size:105
Alignment explanation
Indices: 31564601--31564914 Score: 416
Period size: 106 Copynumber: 2.9 Consensus size: 105
31564591 TTAACGTAAT
* * * * *
31564601 TATAATTATTAATTTTAATGATTTTGTTAAATACTAAAACATGGAAGTTAATATCCTTTTGGAAA
1 TATAATTATTAATTATAATAATTTCGTTAAATATTAAAACATGGAAGTTAATATCTTTTTGGAAA
* * *
31564666 GGATATATAATGTTTTAATAAATGTTCCATAATTTAATGTAA
66 GG--ATATAATGTTTTAATAAATATTCCATAATTTACTATAA
*
31564708 TTATAATTATTAATTATAATTATTTCGTTAAATATTAAAACATGGAAGTTAATAT-TATTTTGGA
1 -TATAATTATTAATTATAATAATTTCGTTAAATATTAAAACATGGAAGTTAATATCT-TTTTGGA
* *
31564772 AAGGATATAATGTTTTAATAAACATTCAATAATTTAAC-ATAA
64 AAGGATATAATGTTTTAATAAATATTCCATAATTT-ACTATAA
*
31564814 TTATAATTATTAATTATAATAATTTCGTTAAATATTAAAAACATGAAAGTTAATATCTTTTTGGA
1 -TATAATTATTAATTATAATAATTTCGTTAAATATT-AAAACATGGAAGTTAATATCTTTTTGGA
* *
31564879 AAGGATATAATGATTTAATAAATTTTCCATATATTT
64 AAGGATATAATGTTTTAATAAATATTCCATA-ATTT
31564915 CTTTAAAGGA
Statistics
Matches: 185, Mismatches: 16, Indels: 10
0.88 0.08 0.05
Matches are distributed among these distances:
106 66 0.36
107 53 0.29
108 66 0.36
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.43
Consensus pattern (105 bp):
TATAATTATTAATTATAATAATTTCGTTAAATATTAAAACATGGAAGTTAATATCTTTTTGGAAA
GGATATAATGTTTTAATAAATATTCCATAATTTACTATAA
Found at i:31564987 original size:123 final size:122
Alignment explanation
Indices: 31564844--31565198 Score: 530
Period size: 123 Copynumber: 2.9 Consensus size: 122
31564834 AATTTCGTTA
* * *
31564844 AATATTAAAAACATGAAAGTTAATATCTTTTTGGAAAGGATATAATGATTTAATAAATTTTCCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAATTTT-CAT
* *
31564909 ATATTTCTTTAAAGGAATATTTCTATTTTAATATGAGATATTATATAAAAAGAAATTG
65 ATATTTCTTTAAAGAAATATTTCCATTTTAATATGAGATATTATATAAAAAGAAATTG
* * ** *
31564967 AATATTAAAAAGATGGAAGTTAATATCCTTTTGAAAATAATATAATGTTTTAATAAACCTTTCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAA-TTTTCAT
* * *
31565032 ATATTTCTTTAAAGAAATATTTCCATTTTAATATGAGATATTATATATAAGGAAGTTG
65 ATATTTCTTTAAAGAAATATTTCCATTTTAATATGAGATATTATATAAAAAGAAATTG
*
31565090 AATATTAAAAACATGGAAGTTAATATCCTTTTGGGAAGGATATAATGTTTTAATAAATTTTCATA
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAATTTTCATA
* *
31565155 TATTTCTCTAAAGATATATATTTCCAGTTTAATATGAGATATTA
66 TATTTCTTTAAAGA-A-ATATTTCCATTTTAATATGAGATATTA
31565199 AAAATAAAAG
Statistics
Matches: 208, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
122 20 0.10
123 159 0.76
124 29 0.14
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (122 bp):
AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAATTTTCATA
TATTTCTTTAAAGAAATATTTCCATTTTAATATGAGATATTATATAAAAAGAAATTG
Found at i:31578090 original size:3 final size:3
Alignment explanation
Indices: 31578082--31578111 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
31578072 GAGAAAGGAC
31578082 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
31578112 CACCATGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:31578242 original size:17 final size:18
Alignment explanation
Indices: 31578220--31578259 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
31578210 ATAGTTTTCA
*
31578220 TGCATTTT-TATTGTCAT
1 TGCATTTTATATTGTCAC
*
31578237 TGCATTTTATTTTGTCAC
1 TGCATTTTATATTGTCAC
31578255 TGCAT
1 TGCAT
31578260 CCCTTTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.55
Consensus pattern (18 bp):
TGCATTTTATATTGTCAC
Found at i:31579018 original size:16 final size:16
Alignment explanation
Indices: 31578985--31579018 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31578975 TTCATGCCTA
*
31578985 TAAATTGTCGGCGCAT
1 TAAATTGTCAGCGCAT
*
31579001 TAAATTGTCAGCGTAT
1 TAAATTGTCAGCGCAT
31579017 TA
1 TA
31579019 TTCTATCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (16 bp):
TAAATTGTCAGCGCAT
Found at i:31581619 original size:81 final size:81
Alignment explanation
Indices: 31581525--31581684 Score: 284
Period size: 81 Copynumber: 2.0 Consensus size: 81
31581515 GCCTTAACAC
*
31581525 CACTTAAACTATAATAATTATTCACCTCTTAGACATATTTATTCGATATCAAAAACTATTTTTAA
1 CACTTAAACTATAATAATTAATCACCTCTTAGACATATTTATTCGATATCAAAAACTATTTTTAA
*
31581590 CCGTCATTATTTACAT
66 CAGTCATTATTTACAT
*
31581606 CACTTAAATTATAATAATTAATCACCTCTTAGACATATTTATTCGATATCAAAAACTATTTTTAA
1 CACTTAAACTATAATAATTAATCACCTCTTAGACATATTTATTCGATATCAAAAACTATTTTTAA
*
31581671 CAGTTATTATTTAC
66 CAGTCATTATTTAC
31581685 CATTTGAACA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.41
Consensus pattern (81 bp):
CACTTAAACTATAATAATTAATCACCTCTTAGACATATTTATTCGATATCAAAAACTATTTTTAA
CAGTCATTATTTACAT
Found at i:31582780 original size:18 final size:19
Alignment explanation
Indices: 31582759--31582796 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
31582749 TTTGTTTTCA
* *
31582759 TTTTGT-TTTTTTTTGTTT
1 TTTTGTCTTTATTTTATTT
31582777 TTTTGTCTTTATTTTATTT
1 TTTTGTCTTTATTTTATTT
31582796 T
1 T
31582797 GTTCTAACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.05, C:0.03, G:0.08, T:0.84
Consensus pattern (19 bp):
TTTTGTCTTTATTTTATTT
Found at i:31596302 original size:76 final size:76
Alignment explanation
Indices: 31596176--31596334 Score: 309
Period size: 76 Copynumber: 2.1 Consensus size: 76
31596166 TTTTTTTCTT
*
31596176 ACAATGTAAACATTCTTACAATGCCACTTATCTTCAGTTTGAACTTAGATAATCAATGAGCTAAT
1 ACAATTTAAACATTCTTACAATGCCACTTATCTTCAGTTTGAACTTAGATAATCAATGAGCTAAT
31596241 ATTTGCTTGTC
66 ATTTGCTTGTC
31596252 ACAATTTAAACATTCTTACAATGCCACTTATCTTCAGTTTGAACTTAGATAATCAATGAGCTAAT
1 ACAATTTAAACATTCTTACAATGCCACTTATCTTCAGTTTGAACTTAGATAATCAATGAGCTAAT
31596317 ATTTGCTTGTC
66 ATTTGCTTGTC
31596328 ACAATTT
1 ACAATTT
31596335 CGCTATGCAT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 82 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (76 bp):
ACAATTTAAACATTCTTACAATGCCACTTATCTTCAGTTTGAACTTAGATAATCAATGAGCTAAT
ATTTGCTTGTC
Found at i:31597801 original size:165 final size:165
Alignment explanation
Indices: 31597529--31597854 Score: 589
Period size: 165 Copynumber: 2.0 Consensus size: 165
31597519 ACAGATTAAC
*
31597529 AAAATAGCAGTTGAGAAATCAACTTTAAATACTTGTGTAAACAACAGATGAAAGGAATAAATGAA
1 AAAATAGCAGTTGAGAAATCAAATTTAAATACTTGTGTAAACAACAGATGAAAGGAATAAATGAA
*
31597594 TTTCTGGAACAATAAAAATATATAGATTTTTTCATACTCTTTTTGATCTAATTTCATGCAAATTC
66 TTTCTGGAACAATAAAAATATATAGATTTTTTCATACTCTTTTTGACCTAATTTCATGCAAATTC
31597659 TGAGTAATTAATGTCGAAAAATATAATTTATTTTA
131 TGAGTAATTAATGTCGAAAAATATAATTTATTTTA
*
31597694 AAAATAGCAGTTGAGAAATCAAATTTAAATACTTGTGTAAACAACAGATGAAAGGAATGAATGAA
1 AAAATAGCAGTTGAGAAATCAAATTTAAATACTTGTGTAAACAACAGATGAAAGGAATAAATGAA
* * *
31597759 TTTCTGGATCAATGAAAATATATAGATTTTTTCGTACTCTTTTTGACCTAATTTCATGCAAATTC
66 TTTCTGGAACAATAAAAATATATAGATTTTTTCATACTCTTTTTGACCTAATTTCATGCAAATTC
*
31597824 TGAGTAATTAATGTTGAAAAATATAATTTAT
131 TGAGTAATTAATGTCGAAAAATATAATTTAT
31597855 GTATAAAATA
Statistics
Matches: 154, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
165 154 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (165 bp):
AAAATAGCAGTTGAGAAATCAAATTTAAATACTTGTGTAAACAACAGATGAAAGGAATAAATGAA
TTTCTGGAACAATAAAAATATATAGATTTTTTCATACTCTTTTTGACCTAATTTCATGCAAATTC
TGAGTAATTAATGTCGAAAAATATAATTTATTTTA
Found at i:31600210 original size:23 final size:23
Alignment explanation
Indices: 31600184--31600324 Score: 178
Period size: 23 Copynumber: 6.1 Consensus size: 23
31600174 ACACTAGCAC
*
31600184 GCTCTCCGATTAGCACTGTGTGT
1 GCTCTCCGTTTAGCACTGTGTGT
31600207 GCTCTCCGTTTAGCACTGTGTGT
1 GCTCTCCGTTTAGCACTGTGTGT
*
31600230 GCTCTCCGTTTAGCACTTTGTGT
1 GCTCTCCGTTTAGCACTGTGTGT
**
31600253 GCTCTCCGTTTAGCAC-GCCTCGT
1 GCTCTCCGTTTAGCACTGTGT-GT
31600276 GCTCTCCGTTTAGCACT-TCGTGT
1 GCTCTCCGTTTAGCACTGT-GTGT
*** *
31600299 GCTCTCTAATTAGCACTTTGTGT
1 GCTCTCCGTTTAGCACTGTGTGT
31600322 GCT
1 GCT
31600325 TAGTACTTTG
Statistics
Matches: 104, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
22 1 0.01
23 101 0.97
24 2 0.02
ACGTcount: A:0.11, C:0.28, G:0.23, T:0.38
Consensus pattern (23 bp):
GCTCTCCGTTTAGCACTGTGTGT
Found at i:31600354 original size:39 final size:39
Alignment explanation
Indices: 31600285--31600363 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
31600275 TGCTCTCCGT
* *
31600285 TTAGCACTTCGTGTGCTCTCTAATTAGCACTTTGTGTGC
1 TTAGCACTTCGTGTACTCTCTAATTAGCACTATGTGTGC
* * **
31600324 TTAGTACTTTGTGTACTCTCTGTTTAGCACTATGTGTGC
1 TTAGCACTTCGTGTACTCTCTAATTAGCACTATGTGTGC
31600363 T
1 T
31600364 CTCTGTTGCC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.44
Consensus pattern (39 bp):
TTAGCACTTCGTGTACTCTCTAATTAGCACTATGTGTGC
Found at i:31600359 original size:23 final size:23
Alignment explanation
Indices: 31600324--31600370 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
31600314 CTTTGTGTGC
* *
31600324 TTAGTACTTTGTGTACTCTCTGT
1 TTAGCACTATGTGTACTCTCTGT
*
31600347 TTAGCACTATGTGTGCTCTCTGT
1 TTAGCACTATGTGTACTCTCTGT
31600370 T
1 T
31600371 GCCCAGCACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.49
Consensus pattern (23 bp):
TTAGCACTATGTGTACTCTCTGT
Found at i:31615255 original size:97 final size:96
Alignment explanation
Indices: 31615117--31615307 Score: 303
Period size: 97 Copynumber: 2.0 Consensus size: 96
31615107 TTTCATTTGA
* * *
31615117 ATTTAATGTTATTTTTATTTTTCGAATTTTGATAATTTTTAATATTAATTATAAATTAAATTTTA
1 ATTTAATGTTATTCTTATTTTTCAAATTTTGATAATCTTTAATATTAATTATAAATTAAATTTTA
*
31615182 TAAATTATATTAATTATTATCAAAAGTTTTC
66 TAAATTACATTAATTATTATCAAAAGTTTTC
31615213 ATTTAAATGTT-TTCTTATTTTTCAAAGTTTTGATAATCTTTAATATTAATTATAAATTAAATTT
1 ATTT-AATGTTATTCTTATTTTTCAAA-TTTTGATAATCTTTAATATTAATTATAAATTAAATTT
* *
31615277 TATAATTTACATTAATTATTATCCAAAGTTT
64 TATAAATTACATTAATTATTATCAAAAGTTT
31615308 GAATTAGGAT
Statistics
Matches: 87, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
96 17 0.20
97 70 0.80
ACGTcount: A:0.37, C:0.05, G:0.04, T:0.54
Consensus pattern (96 bp):
ATTTAATGTTATTCTTATTTTTCAAATTTTGATAATCTTTAATATTAATTATAAATTAAATTTTA
TAAATTACATTAATTATTATCAAAAGTTTTC
Found at i:31616243 original size:22 final size:22
Alignment explanation
Indices: 31616209--31616255 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
31616199 TTGTGAACGA
* *
31616209 ATTAATTATATTGATGGTATAG
1 ATTAATTACATTGATGATATAG
* *
31616231 ATTAGTTACATTGATGATGTAG
1 ATTAATTACATTGATGATATAG
31616253 ATT
1 ATT
31616256 GAACAAAATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (22 bp):
ATTAATTACATTGATGATATAG
Found at i:31616442 original size:23 final size:23
Alignment explanation
Indices: 31616385--31616435 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
31616375 CCTAAATTCA
*
31616385 ACGGTATAGATTGAGTTACATTT
1 ACGGTATAGATTGAGTTACATTG
*
31616408 ATGGTATAGATTGAGTTACATTG
1 ACGGTATAGATTGAGTTACATTG
31616431 ACGGT
1 ACGGT
31616436 TAAGATTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.08, G:0.25, T:0.37
Consensus pattern (23 bp):
ACGGTATAGATTGAGTTACATTG
Found at i:31625587 original size:33 final size:33
Alignment explanation
Indices: 31625523--31625587 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
31625513 TGGCAATGAT
* * *
31625523 CTGATGTCGACCATTGATGACCCATTGTCAGGC
1 CTGATGTCGACCATTGAAGACCCACTATCAGGC
*
31625556 CTGATGTCGGCCATTGAAG-CCCAACTATCAGG
1 CTGATGTCGACCATTGAAGACCC-ACTATCAGG
31625588 TGCTTTTGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (33 bp):
CTGATGTCGACCATTGAAGACCCACTATCAGGC
Found at i:31632493 original size:31 final size:31
Alignment explanation
Indices: 31632458--31632563 Score: 123
Period size: 31 Copynumber: 3.5 Consensus size: 31
31632448 TTGATACTTG
*
31632458 AACTTGATACTTTTTTCTAATTTGGTACCTA
1 AACTTGACACTTTTTTCTAATTTGGTACCTA
* *
31632489 AACTT----TTTTTTATCCAATTTGGTACAC-A
1 AACTTGACACTTTTT-TCTAATTTGGTAC-CTA
*
31632517 AACTTGACACTTTTTTCTAATTTGGTACTTA
1 AACTTGACACTTTTTTCTAATTTGGTACCTA
31632548 AACTTGACACTTTTTT
1 AACTTGACACTTTTTT
31632564 TTTAAGTTGC
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
27 5 0.08
28 18 0.29
29 1 0.02
31 34 0.54
32 5 0.08
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.48
Consensus pattern (31 bp):
AACTTGACACTTTTTTCTAATTTGGTACCTA
Found at i:31632508 original size:28 final size:27
Alignment explanation
Indices: 31632468--31632521 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
31632458 AACTTGATAC
*
31632468 TTTTTTCTAATTTGGTAC-CTAAACTTT
1 TTTTTTCCAATTTGGTACAC-AAACTTT
31632495 TTTTTATCCAATTTGGTACACAAACTT
1 TTTTT-TCCAATTTGGTACACAAACTT
31632522 GACACTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.21
28 18 0.75
29 1 0.04
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (27 bp):
TTTTTTCCAATTTGGTACACAAACTTT
Found at i:31632578 original size:32 final size:31
Alignment explanation
Indices: 31632516--31632582 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 31
31632506 TTTGGTACAC
* *
31632516 AAACTTGACACTTTTTTCTAATTTGGTACTT
1 AAACTTGACACTTTTTTCTAAGTTGCTACTT
*
31632547 AAACTTGACACTTTTTTTTTAAGTTGCTACTT
1 AAACTTGACAC-TTTTTTCTAAGTTGCTACTT
31632579 AAAC
1 AAAC
31632583 CTTTTGGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 11 0.34
32 21 0.66
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.46
Consensus pattern (31 bp):
AAACTTGACACTTTTTTCTAAGTTGCTACTT
Found at i:31632878 original size:24 final size:26
Alignment explanation
Indices: 31632824--31632880 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 26
31632814 GGAAAAAATG
31632824 AAAAGTTTAGGTATTAAATTGAGTTTAAA
1 AAAAGTTTAGGTATTAAATTGAG--T-AA
31632853 AAAAGTTTAGGTATTAAATTG-G-AA
1 AAAAGTTTAGGTATTAAATTGAGTAA
31632877 AAAA
1 AAAA
31632881 CTATCAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.21
28 1 0.04
29 21 0.75
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (26 bp):
AAAAGTTTAGGTATTAAATTGAGTAA
Found at i:31633538 original size:19 final size:19
Alignment explanation
Indices: 31633514--31633551 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
31633504 TAATGAAAAG
31633514 TTAGGATTAGACTTTTGAA
1 TTAGGATTAGACTTTTGAA
31633533 TTAGGATTAGACTTTTGAA
1 TTAGGATTAGACTTTTGAA
31633552 GACTTCAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (19 bp):
TTAGGATTAGACTTTTGAA
Found at i:31637484 original size:42 final size:42
Alignment explanation
Indices: 31637430--31637569 Score: 177
Period size: 42 Copynumber: 3.4 Consensus size: 42
31637420 CAAATATGAT
31637430 TTAAAAGAGTTTTAAATAAA-AGATAATTAAATAGAATTTTAA
1 TTAAAAGAGTTTTAAATAAATA-ATAATTAAATAGAATTTTAA
* *
31637472 TTAAAAGAGTTTTAGATAAATAATAATT--AT---ATTGTTAT
1 TTAAAAGAGTTTTAAATAAATAATAATTAAATAGAATT-TTAA
*
31637510 TTAAAAGAGTTTTAGATAAATAATAATTAAAATAGAA-TTTAA
1 TTAAAAGAGTTTTAAATAAATAATAATT-AAATAGAATTTTAA
31637552 TTAAAAGAGTTTTAAATA
1 TTAAAAGAGTTTTAAATA
31637570 TAATTTAACA
Statistics
Matches: 86, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
37 3 0.03
38 31 0.36
40 2 0.02
41 2 0.02
42 45 0.52
43 2 0.02
44 1 0.01
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (42 bp):
TTAAAAGAGTTTTAAATAAATAATAATTAAATAGAATTTTAA
Found at i:31639809 original size:15 final size:16
Alignment explanation
Indices: 31639777--31639814 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
31639767 TTAAGATGGA
*
31639777 ATTTTGAATTCATTTG
1 ATTTTGAATTCATATG
31639793 ATTTTGAA-TCATATG
1 ATTTTGAATTCATATG
31639808 ATATTTG
1 AT-TTTG
31639815 TGAATCTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (16 bp):
ATTTTGAATTCATATG
Found at i:31643568 original size:22 final size:22
Alignment explanation
Indices: 31643540--31643595 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
31643530 TACAAAGTCT
31643540 AAAAATAAAAAACCATAAACTA
1 AAAAATAAAAAACCATAAACTA
*
31643562 AAAAATAAAAAACCCTAAACTA
1 AAAAATAAAAAACCATAAACTA
31643584 AAAAATAAAAAA
1 AAAAATAAAAAA
31643596 AAACTTAGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.75, C:0.12, G:0.00, T:0.12
Consensus pattern (22 bp):
AAAAATAAAAAACCATAAACTA
Found at i:31644267 original size:29 final size:29
Alignment explanation
Indices: 31644203--31644267 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
31644193 AATTTTAATT
* *
31644203 TTTATTTATCTTGTTATTATTTATTTTCA
1 TTTATTTATCATGTTATTATTTATTTACA
*
31644232 TGCTATTTATCAT-TTATTATTTAATTTACA
1 T-TTATTTATCATGTTATTATTT-ATTTACA
31644262 TTTATT
1 TTTATT
31644268 GTTATTATCC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.65
Consensus pattern (29 bp):
TTTATTTATCATGTTATTATTTATTTACA
Found at i:31652072 original size:11 final size:12
Alignment explanation
Indices: 31652048--31652096 Score: 68
Period size: 11 Copynumber: 4.3 Consensus size: 12
31652038 CCAAACTAGT
31652048 AAAA-AAAAGAA
1 AAAAGAAAAGAA
31652059 AAAAGAAAAG-A
1 AAAAGAAAAGAA
*
31652070 AAAAG-AGAGAA
1 AAAAGAAAAGAA
31652081 AAAAGAAAAGAA
1 AAAAGAAAAGAA
31652093 AAAA
1 AAAA
31652097 AGGGAGGGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
10 3 0.09
11 16 0.48
12 14 0.42
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:31653493 original size:81 final size:81
Alignment explanation
Indices: 31653342--31654010 Score: 853
Period size: 81 Copynumber: 8.2 Consensus size: 81
31653332 TACATCATCT
* * * * *
31653342 CATCCAATCTCTTACCCTAACCATGGGGTAGATTAAAGAACATCCAATCTTTTACCCTAACCAAA
1 CATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAG-CCATCCAATCTTTTACCCTAACCAGA
*
31653407 GGGCAGATTAAAGACAC
65 GGGCAGATTGAAGACAC
* * * *
31653424 CATCCAATCTCTTACCCCGACCATGAGGCAGATTGAAGTCATCCAATCTTTTACCCTAACCAGAT
1 CATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGAG
31653489 GGCAGATTGAAGACAC
66 GGCAGATTGAAGACAC
* * * * *
31653505 CAT-CATATCTCTTA-CCTAGGCCATGGAGCAGATTAAAGGCATCCAATCTTTTACCCTAACCAA
1 CATCCA-ATCTCTTACCCT-GACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAG
*
31653568 AGGGTAGATTGAAGACAC
64 AGGGCAGATTGAAGACAC
* *
31653586 CATCCAAACTCTTACCCTGACCATGGGGCAGATTCAAGCCATCCAATCTTTTACCCTAACCAGAG
1 CATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGAG
*
31653651 GGAAGATTGAAGACAC
66 GGCAGATTGAAGACAC
* * *
31653667 CATCCAATCTATTA-CCTCGACCACGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAAA
1 CATCCAATCTCTTACCCT-GACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGA
*
31653731 GGGCAAATTGAAGACAC
65 GGGCAGATTGAAGACAC
* * * * *
31653748 CATCTAATCTCTTATACC-GACCATGGGGCAGATTGAAGTCATCCAATCTTTTACCATAACTAGA
1 CATCCAATCTCTTA-CCCTGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGA
31653812 GGGCAGATTGAAGACAC
65 GGGCAGATTGAAGACAC
* * *
31653829 CATCCAATCTCTTACCTTGACCATGGGACAGATTGAAACCATCCAATCTTTTACCCTAACCAGAG
1 CATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGAG
31653894 GGCAGATTGAAGACAC
66 GGCAGATTGAAGACAC
* ** * * **
31653910 CATCCAATCTCTTACTCTGACCATAAGGCAGATTGAAACCATCCAGTCTTTTACCTCTAACTTGG
1 CATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACC-CTAAC-CAG
*
31653975 AGGGGCATATTGAAG-CAAC
64 A-GGGCAGATTGAAGAC-AC
* *
31653994 CATCTAATCTTTTACCC
1 CATCCAATCTCTTACCC
31654011 CTAATCTAGA
Statistics
Matches: 515, Mismatches: 60, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
80 8 0.02
81 431 0.84
82 43 0.08
83 5 0.01
84 28 0.05
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (81 bp):
CATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGAG
GGCAGATTGAAGACAC
Found at i:31654005 original size:45 final size:45
Alignment explanation
Indices: 31653935--31654262 Score: 319
Period size: 45 Copynumber: 7.3 Consensus size: 45
31653925 TCTGACCATA
* * *
31653935 AGGCAGATTG-A--AACCATCCAGTCTTTTACCTCTAA-CTTGGAG
1 AGGCAGATTGAAGCAACCATCTAGTCTTTTACCCCTAATC-TAGAG
* * *
31653977 GGGCATATTGAAGCAACCATCTAATCTTTTACCCCTAATCTAGAG
1 AGGCAGATTGAAGCAACCATCTAGTCTTTTACCCCTAATCTAGAG
* * * * *
31654022 AGGTAGATTGAAGCCACCAGCCAGTCTTTTACCCTTAATCTAGAG
1 AGGCAGATTGAAGCAACCATCTAGTCTTTTACCCCTAATCTAGAG
* * * * * *
31654067 GGGCAAATTGAAGCAACCATCCAGTCTTTTACCCCTAATCCAAAA
1 AGGCAGATTGAAGCAACCATCTAGTCTTTTACCCCTAATCTAGAG
* *
31654112 AGGCAGATTGAAGCCACCATCTAGTCTTTTACCCTTAATCTAGAG
1 AGGCAGATTGAAGCAACCATCTAGTCTTTTACCCCTAATCTAGAG
* *
31654157 -GGACGGATTGAAGCAACCAT-TCAATCTTTTACCCCTAATCTAGAG
1 AGG-CAGATTGAAGCAACCATCT-AGTCTTTTACCCCTAATCTAGAG
* * *
31654202 AGGCAGATTGAAGTC-ACCAAATCTAATCTTTTATCCCTAAATCTAGGG
1 AGGCAGATTGAAG-CAACC--ATCTAGTCTTTTACCCCT-AATCTAGAG
*
31654250 TGGCAGATTGAAG
1 AGGCAGATTGAAG
31654263 TTACAACACC
Statistics
Matches: 235, Mismatches: 39, Indels: 18
0.80 0.13 0.06
Matches are distributed among these distances:
42 8 0.03
43 1 0.00
44 3 0.01
45 183 0.78
46 4 0.02
47 15 0.06
48 21 0.09
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (45 bp):
AGGCAGATTGAAGCAACCATCTAGTCTTTTACCCCTAATCTAGAG
Found at i:31654068 original size:90 final size:90
Alignment explanation
Indices: 31653935--31654262 Score: 382
Period size: 90 Copynumber: 3.6 Consensus size: 90
31653925 TCTGACCATA
* *
31653935 AGGCAGATTGAA---ACCATCCAGTCTTTTA-CCTCTAA-CTTGGAGGGGCATATTGAAGCAACC
1 AGGCAGATTGAAGCCACCATCCAGTCTTTTACCCT-TAATC-TAGAGGGGCAAATTGAAGCAACC
31653995 ATCTAATCTTTTACCCCTAATCTAGAG
64 ATCTAATCTTTTACCCCTAATCTAGAG
* *
31654022 AGGTAGATTGAAGCCACCAGCCAGTCTTTTACCCTTAATCTAGAGGGGCAAATTGAAGCAACCAT
1 AGGCAGATTGAAGCCACCATCCAGTCTTTTACCCTTAATCTAGAGGGGCAAATTGAAGCAACCAT
* * * * *
31654087 CCAGTCTTTTACCCCTAATCCAAAA
66 CTAATCTTTTACCCCTAATCTAGAG
* * **
31654112 AGGCAGATTGAAGCCACCATCTAGTCTTTTACCCTTAATCTAGAGGGACGGATTGAAGCAACCAT
1 AGGCAGATTGAAGCCACCATCCAGTCTTTTACCCTTAATCTAGAGGGGCAAATTGAAGCAACCAT
31654177 -TCAATCTTTTACCCCTAATCTAGAG
66 CT-AATCTTTTACCCCTAATCTAGAG
* * * * *
31654202 AGGCAGATTGAAGTCACCAAATCTAATCTTTTATCCCTAAATCTAG-GGTGGCAGATTGAAG
1 AGGCAGATTGAAGCCACC--ATCCAGTCTTTTA-CCCTTAATCTAGAGG-GGCAAATTGAAG
31654263 TTACAACACC
Statistics
Matches: 206, Mismatches: 25, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
87 11 0.05
90 156 0.76
91 4 0.02
92 14 0.07
93 21 0.10
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (90 bp):
AGGCAGATTGAAGCCACCATCCAGTCTTTTACCCTTAATCTAGAGGGGCAAATTGAAGCAACCAT
CTAATCTTTTACCCCTAATCTAGAG
Found at i:31654258 original size:48 final size:44
Alignment explanation
Indices: 31653630--31654263 Score: 207
Period size: 45 Copynumber: 14.8 Consensus size: 44
31653620 CAAGCCATCC
* * * * *
31653630 AATCTTTTACCCTAA-CCAGAGGGAAGATTGAAGACACC-ATCC
1 AATCTTTTACCCTAATCTAGGGGGCAGATTGAAGTCACCAATCT
* * * * *
31653672 AATCTATTA-CCTCGA-CCACGGGGCAGATTGAAG---CC-ATCC
1 AATCTTTTACCCT-AATCTAGGGGGCAGATTGAAGTCACCAATCT
* ** * *
31653711 AATCTTTTACCCTAA-CCAAAGGGCAAATTGAAGACACC-ATCT
1 AATCTTTTACCCTAATCTAGGGGGCAGATTGAAGTCACCAATCT
* * * *
31653753 AATCTCTTATA-CC-GA-CCATGGGGCAGATTGAAGT---C-ATCC
1 AATCT-TT-TACCCTAATCTAGGGGGCAGATTGAAGTCACCAATCT
* * * *
31653792 AATCTTTTACCATAA-CTAGAGGGCAGATTGAAGACACC-ATCC
1 AATCTTTTACCCTAATCTAGGGGGCAGATTGAAGTCACCAATCT
* * * * * * *
31653834 AATCTCTTACCTTGA-CCATGGGACAGATTGAA---ACC-ATCC
1 AATCTTTTACCCTAATCTAGGGGGCAGATTGAAGTCACCAATCT
* * * *
31653873 AATCTTTTACCCTAA-CCAGAGGGCAGATTGAAGACACC-ATCC
1 AATCTTTTACCCTAATCTAGGGGGCAGATTGAAGTCACCAATCT
* * * * * *
31653915 AATCTCTTACTCTGACCATA--AGGCAGATTGAA---ACC-ATCC
1 AATCTTTTACCCTAATC-TAGGGGGCAGATTGAAGTCACCAATCT
* * *
31653954 AGTCTTTTACCTCTAA-CTTGGAGGGGCATATTGAAG-CAACC-ATCT
1 AATCTTTTACC-CTAATC-TAG-GGGGCAGATTGAAGTC-ACCAATCT
* * * * *
31653999 AATCTTTTACCCCTAATCTAGAGAGGTAGATTGAAGCCACC-AGCC
1 AATCTTTTA-CCCTAATCTAG-GGGGCAGATTGAAGTCACCAATCT
* * *
31654044 AGTCTTTTACCCTTAATCTAGAGGGGCAAATTGAAG-CAACC-ATCC
1 AATCTTTTACCC-TAATCTAG-GGGGCAGATTGAAGTC-ACCAATCT
* * *** *
31654089 AGTCTTTTACCCCTAATCCAAAAAGGCAGATTGAAGCCACC-ATCT
1 AATCTTTTA-CCCTAAT-CTAGGGGGCAGATTGAAGTCACCAATCT
* * * *
31654134 AGTCTTTTACCCTTAATCTAGAGGGACGGATTGAAG-CAACCATTC-
1 AATCTTTTACCC-TAATCTAG-GGGGCAGATTGAAGTC-ACCAATCT
*
31654179 AATCTTTTACCCCTAATCTAGAGAGGCAGATTGAAGTCACCAAATCT
1 AATCTTTTA-CCCTAATCTAG-GGGGCAGATTGAAGTCACC-AATCT
31654226 AATCTTTTATCCCTAAATCTAGGGTGGCAGATTGAAGT
1 AATCTTTTA-CCCT-AATCTAGGG-GGCAGATTGAAGT
31654264 TACAACACCA
Statistics
Matches: 468, Mismatches: 82, Indels: 78
0.75 0.13 0.12
Matches are distributed among these distances:
37 2 0.00
38 3 0.01
39 105 0.22
40 6 0.01
41 3 0.01
42 120 0.26
43 5 0.01
44 13 0.03
45 158 0.34
46 19 0.04
47 14 0.03
48 20 0.04
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (44 bp):
AATCTTTTACCCTAATCTAGGGGGCAGATTGAAGTCACCAATCT
Found at i:31655109 original size:25 final size:25
Alignment explanation
Indices: 31655081--31655154 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 25
31655071 TTATTTTAGC
*
31655081 ATTTAATTTTTATTT-TTATTTATTT
1 ATTTAATTTATATTTATTA-TTATTT
* **
31655106 ATTTTCA-TGCTATTTATTATTATTT
1 A-TTTAATTTATATTTATTATTATTT
* *
31655131 ATTTAATTTATATTCATTGTTATT
1 ATTTAATTTATATTTATTATTATT
31655155 ATCTTGTTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
24 4 0.11
25 27 0.71
26 7 0.18
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.68
Consensus pattern (25 bp):
ATTTAATTTATATTTATTATTATTT
Found at i:31655495 original size:22 final size:24
Alignment explanation
Indices: 31655457--31655509 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
31655447 ACTATAACTA
** *
31655457 TAATTATATTTTTTTGTGTT-A-T
1 TAATTATATTTGATTGTCTTCATT
31655479 TAATTATATTTGATTGTCTTCATT
1 TAATTATATTTGATTGTCTTCATT
31655503 TAATTAT
1 TAATTAT
31655510 TTATATTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 17 0.65
23 1 0.04
24 8 0.31
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.62
Consensus pattern (24 bp):
TAATTATATTTGATTGTCTTCATT
Found at i:31656256 original size:28 final size:28
Alignment explanation
Indices: 31656213--31656492 Score: 159
Period size: 28 Copynumber: 10.6 Consensus size: 28
31656203 AAACGTGTGC
*
31656213 AAGCTGA-AGAGCGTAAATGCATATGTAT
1 AAGCTGACA-AGCGTAAACGCATATGTAT
* **
31656241 AAGCTGACAAGTGTAAA--C-T-TGTGC
1 AAGCTGACAAGCGTAAACGCATATGTAT
*
31656265 AAGCTGGCAAGCGTAAACGCATATGTAT
1 AAGCTGACAAGCGTAAACGCATATGTAT
**
31656293 AAGCTGATGAGCGTAAACGCATATGTAT
1 AAGCTGACAAGCGTAAACGCATATGTAT
* * * *
31656321 AAGCTAACGAGCATAAACG----TGTGT
1 AAGCTGACAAGCGTAAACGCATATGTAT
* * *
31656345 AAGCTGACGAGTGTAAACGTATATGTAT
1 AAGCTGACAAGCGTAAACGCATATGTAT
* * **
31656373 AAGCTGACAAGCATAAA---A-GTGTGC
1 AAGCTGACAAGCGTAAACGCATATGTAT
* * *
31656397 AAGCTGGCGAGTGTAAACGCATATGTAT
1 AAGCTGACAAGCGTAAACGCATATGTAT
* * **
31656425 AAGTTGACGAGCGTAAA--C--ATGTGC
1 AAGCTGACAAGCGTAAACGCATATGTAT
*
31656449 AAGCT-AGCGAGC-T-AACGCATATGTAT
1 AAGCTGA-CAAGCGTAAACGCATATGTAT
*
31656475 AAGCTGACGAGCGTAAAC
1 AAGCTGACAAGCGTAAAC
31656493 ATGTGCAAGC
Statistics
Matches: 192, Mismatches: 39, Indels: 42
0.70 0.14 0.15
Matches are distributed among these distances:
22 2 0.01
23 2 0.01
24 68 0.35
25 2 0.01
26 17 0.09
27 4 0.02
28 96 0.50
29 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.23
Consensus pattern (28 bp):
AAGCTGACAAGCGTAAACGCATATGTAT
Found at i:31656309 original size:52 final size:52
Alignment explanation
Indices: 31656189--31656311 Score: 176
Period size: 52 Copynumber: 2.4 Consensus size: 52
31656179 GAAAGTGTGC
*
31656189 AAGCTGATGAGCGTAAACGTGTGCAAGCTGAAGAGCGTAAATGCATATGTAT
1 AAGCTGATGAGCGTAAACGTGTGCAAGCTGAAGAGCGTAAACGCATATGTAT
** * * *
31656241 AAGCTGACAAGTGTAAACTTGTGCAAGCTGGCA-AGCGTAAACGCATATGTAT
1 AAGCTGATGAGCGTAAACGTGTGCAAGCT-GAAGAGCGTAAACGCATATGTAT
31656293 AAGCTGATGAGCGTAAACG
1 AAGCTGATGAGCGTAAACG
31656312 CATATGTATA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
52 58 0.97
53 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (52 bp):
AAGCTGATGAGCGTAAACGTGTGCAAGCTGAAGAGCGTAAACGCATATGTAT
Found at i:31656315 original size:80 final size:80
Alignment explanation
Indices: 31656213--31656379 Score: 226
Period size: 80 Copynumber: 2.1 Consensus size: 80
31656203 AAACGTGTGC
* * ** * *
31656213 AAGCTGAAGAGCGTAAATGCATATGTATAAGCTGACAAGTGTAAACTTGTGCAAGCTGGCAAGCG
1 AAGCTGAAGAGCGTAAACGCATATGTATAAGCTAACAAGCATAAACGTGTGCAAGCTGACAAGCG
31656278 TAAACGCATATGTAT
66 TAAACGCATATGTAT
* * * * *
31656293 AAGCTGATGAGCGTAAACGCATATGTATAAGCTAACGAGCATAAACGTGTGTAAGCTGACGAGTG
1 AAGCTGAAGAGCGTAAACGCATATGTATAAGCTAACAAGCATAAACGTGTGCAAGCTGACAAGCG
*
31656358 TAAACGTATATGTAT
66 TAAACGCATATGTAT
31656373 AAGCTGA
1 AAGCTGA
31656380 CAAGCATAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (80 bp):
AAGCTGAAGAGCGTAAACGCATATGTATAAGCTAACAAGCATAAACGTGTGCAAGCTGACAAGCG
TAAACGCATATGTAT
Found at i:31656348 original size:52 final size:52
Alignment explanation
Indices: 31656293--31656521 Score: 295
Period size: 52 Copynumber: 4.4 Consensus size: 52
31656283 GCATATGTAT
* * * *
31656293 AAGCTGATGAGCGTAAACGCATATGTATAAGCTAACGAGCATAAACGTGTGT
1 AAGCTGACGAGCGTAAACGCATATGTATAAGCTGACGAGCATAAACATGTGC
* * *
31656345 AAGCTGACGAGTGTAAACGTATATGTATAAGCTGACAAGCATAAA-AGTGTGC
1 AAGCTGACGAGCGTAAACGCATATGTATAAGCTGACGAGCATAAACA-TGTGC
* * * *
31656397 AAGCTGGCGAGTGTAAACGCATATGTATAAGTTGACGAGCGTAAACATGTGC
1 AAGCTGACGAGCGTAAACGCATATGTATAAGCTGACGAGCATAAACATGTGC
*
31656449 AAGCT-AGCGAGC-T-AACGCATATGTATAAGCTGACGAGCGTAAACATGTGC
1 AAGCTGA-CGAGCGTAAACGCATATGTATAAGCTGACGAGCATAAACATGTGC
*
31656499 AAGCTGGCGAGCGTAAACGCATA
1 AAGCTGACGAGCGTAAACGCATA
31656522 AATATCTTGC
Statistics
Matches: 155, Mismatches: 16, Indels: 12
0.85 0.09 0.07
Matches are distributed among these distances:
50 46 0.30
51 2 0.01
52 106 0.68
53 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (52 bp):
AAGCTGACGAGCGTAAACGCATATGTATAAGCTGACGAGCATAAACATGTGC
Found at i:31656354 original size:24 final size:24
Alignment explanation
Indices: 31656183--31656517 Score: 127
Period size: 24 Copynumber: 13.0 Consensus size: 24
31656173 GGTTTCGAAA
* *
31656183 GTGTGCAAGCTGATGAGCGTAAAC
1 GTGTGTAAGCTGACGAGCGTAAAC
* *
31656207 GTGTGCAAGCTGAAGAGCGTAAATGC
1 GTGTGTAAGCTGACGAGCGTAAA--C
* * * *
31656233 ATATGTATAAGCTGACAAGTGTAAAC
1 --GTGTGTAAGCTGACGAGCGTAAAC
* * * *
31656259 TTGTGCAAGCTGGCAAGCGTAAAC
1 GTGTGTAAGCTGACGAGCGTAAAC
* *
31656283 GCATATGTATAAGCTGATGAGCGTAAAC
1 G----TGTGTAAGCTGACGAGCGTAAAC
* * *
31656311 GCATATGTATAAGCTAACGAGCATAAAC
1 G----TGTGTAAGCTGACGAGCGTAAAC
*
31656339 GTGTGTAAGCTGACGAGTGTAAAC
1 GTGTGTAAGCTGACGAGCGTAAAC
* * * *
31656363 GTATATGTATAAGCTGACAAGCATAAAA
1 G----TGTGTAAGCTGACGAGCGTAAAC
* * *
31656391 GTGTGCAAGCTGGCGAGTGTAAAC
1 GTGTGTAAGCTGACGAGCGTAAAC
* *
31656415 GCATATGTATAAGTTGACGAGCGTAAAC
1 G----TGTGTAAGCTGACGAGCGTAAAC
* *
31656443 ATGTGCAAGCT-AGCGAGC-T-AAC
1 GTGTGTAAGCTGA-CGAGCGTAAAC
*
31656465 GCATATGTATAAGCTGACGAGCGTAAAC
1 G----TGTGTAAGCTGACGAGCGTAAAC
* * *
31656493 ATGTGCAAGCTGGCGAGCGTAAAC
1 GTGTGTAAGCTGACGAGCGTAAAC
31656517 G
1 G
31656518 CATAAATATC
Statistics
Matches: 233, Mismatches: 54, Indels: 48
0.70 0.16 0.14
Matches are distributed among these distances:
22 3 0.01
23 2 0.01
24 110 0.47
26 15 0.06
27 2 0.01
28 101 0.43
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.22
Consensus pattern (24 bp):
GTGTGTAAGCTGACGAGCGTAAAC
Found at i:31656426 original size:132 final size:132
Alignment explanation
Indices: 31656197--31656442 Score: 366
Period size: 132 Copynumber: 1.9 Consensus size: 132
31656187 GCAAGCTGAT
* * ** **
31656197 GAGCGTAAACGTGTGCAAGCTGAAGAGCGTAAATGCATATGTATAAGCTGACAAGTGTAAACTTG
1 GAGCATAAACGTGTGCAAGCTGAAGAGCGTAAACGCATATGTATAAGCTGACAAGCATAAAAGTG
*
31656262 TGCAAGCTGGCAAGCGTAAACGCATATGTATAAGCTGATGAGCGTAAACGCATATGTATAAGCTA
66 TGCAAGCTGGCAAGCGTAAACGCATATGTATAAGCTGACGAGCGTAAACGCATATGTATAAGCTA
31656327 AC
131 AC
* * * *
31656329 GAGCATAAACGTGTGTAAGCTGACGAGTGTAAACGTATATGTATAAGCTGACAAGCATAAAAGTG
1 GAGCATAAACGTGTGCAAGCTGAAGAGCGTAAACGCATATGTATAAGCTGACAAGCATAAAAGTG
* * *
31656394 TGCAAGCTGGCGAGTGTAAACGCATATGTATAAGTTGACGAGCGTAAAC
66 TGCAAGCTGGCAAGCGTAAACGCATATGTATAAGCTGACGAGCGTAAAC
31656443 ATGTGCAAGC
Statistics
Matches: 100, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
132 100 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (132 bp):
GAGCATAAACGTGTGCAAGCTGAAGAGCGTAAACGCATATGTATAAGCTGACAAGCATAAAAGTG
TGCAAGCTGGCAAGCGTAAACGCATATGTATAAGCTGACGAGCGTAAACGCATATGTATAAGCTA
AC
Found at i:31656485 original size:26 final size:27
Alignment explanation
Indices: 31656397--31656490 Score: 81
Period size: 26 Copynumber: 3.6 Consensus size: 27
31656387 AAAAGTGTGC
* *
31656397 AAGCTGGCGAGTGTAAACGCATATGTAT
1 AAGCTGACGAGCGT-AACGCATATGTAT
* * **
31656425 AAGTTGACGAGCGTAA---ACATGTGC
1 AAGCTGACGAGCGTAACGCATATGTAT
31656449 AAGCT-AGCGAGC-TAACGCATATGTAT
1 AAGCTGA-CGAGCGTAACGCATATGTAT
31656475 AAGCTGACGAGCGTAA
1 AAGCTGACGAGCGTAA
31656491 ACATGTGCAA
Statistics
Matches: 50, Mismatches: 10, Indels: 13
0.68 0.14 0.18
Matches are distributed among these distances:
23 4 0.08
24 14 0.28
26 15 0.30
27 6 0.12
28 11 0.22
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (27 bp):
AAGCTGACGAGCGTAACGCATATGTAT
Found at i:31656515 original size:102 final size:104
Alignment explanation
Indices: 31656301--31656521 Score: 306
Period size: 102 Copynumber: 2.1 Consensus size: 104
31656291 ATAAGCTGAT
* * * *
31656301 GAGCGTAAACGCATATGTATAAGCTAACGAGCATAAACGTGTGTAAGCTGACGAGTGTAAACGTA
1 GAGCGTAAACGCATATGTATAAGCTAACGAGCATAAACATGTGCAAGCTGACGAGTCTAAACGCA
31656366 TATGTATAAGCTGACAAGCATAAAAGTGTGCAAGCTGGC
66 TATGTATAAGCTGACAAGCATAAAAGTGTGCAAGCTGGC
* * * *
31656405 GAGTGTAAACGCATATGTATAAGTTGACGAGCGTAAACATGTGCAAGCT-AGCGAG-CT-AACGC
1 GAGCGTAAACGCATATGTATAAGCTAACGAGCATAAACATGTGCAAGCTGA-CGAGTCTAAACGC
* *
31656467 ATATGTATAAGCTGACGAGCGTAAACA-TGTGCAAGCTGGC
65 ATATGTATAAGCTGACAAGCATAAA-AGTGTGCAAGCTGGC
31656507 GAGCGTAAACGCATA
1 GAGCGTAAACGCATA
31656522 AATATCTTGC
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
102 54 0.52
103 3 0.03
104 47 0.45
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (104 bp):
GAGCGTAAACGCATATGTATAAGCTAACGAGCATAAACATGTGCAAGCTGACGAGTCTAAACGCA
TATGTATAAGCTGACAAGCATAAAAGTGTGCAAGCTGGC
Found at i:31656569 original size:24 final size:24
Alignment explanation
Indices: 31656537--31656597 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
31656527 CTTGCACACG
*
31656537 TTTAAGCTCGTTAGCTTATATACC
1 TTTAAGCTCGTCAGCTTATATACC
* * * *
31656561 TTTACGCTCATCCGCTTATATACG
1 TTTAAGCTCGTCAGCTTATATACC
*
31656585 TTTATGCTCGTCA
1 TTTAAGCTCGTCA
31656598 ACTTGCACAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.41
Consensus pattern (24 bp):
TTTAAGCTCGTCAGCTTATATACC
Found at i:31661989 original size:24 final size:24
Alignment explanation
Indices: 31661956--31662147 Score: 107
Period size: 24 Copynumber: 8.0 Consensus size: 24
31661946 ACACATATAT
* *
31661956 GTTTATGCTCGTCAGCTTGCACAC
1 GTTTACGCTCGTCAGCTTACACAC
* * *
31661980 GTTTACGCTCATCAACTTGCACA-
1 GTTTACGCTCGTCAGCTTACACAC
* * * * *
31662003 GATTTGCGCTCATCAGCTTATATAT
1 G-TTTACGCTCGTCAGCTTACACAC
* * *
31662028 GTTTATGCTTGTCAGCTTGCACAC
1 GTTTACGCTCGTCAGCTTACACAC
* * * *
31662052 ATTTACGCTCGTCAACTTATATAC
1 GTTTACGCTCGTCAGCTTACACAC
* ** * ***
31662076 ATTTGTGCTCGTCAACTTATGTAC
1 GTTTACGCTCGTCAGCTTACACAC
*** *
31662100 GTTTACGCTCGTCAGCTTATGTAT
1 GTTTACGCTCGTCAGCTTACACAC
*
31662124 GTTTACGCTCGTCAGCTTGCACAC
1 GTTTACGCTCGTCAGCTTACACAC
31662148 ACACATATAT
Statistics
Matches: 130, Mismatches: 36, Indels: 4
0.76 0.21 0.02
Matches are distributed among these distances:
23 1 0.01
24 128 0.98
25 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (24 bp):
GTTTACGCTCGTCAGCTTACACAC
Found at i:31662047 original size:48 final size:48
Alignment explanation
Indices: 31661957--31662146 Score: 168
Period size: 48 Copynumber: 4.0 Consensus size: 48
31661947 CACATATATG
* ** * * * * *
31661957 TTTATGCTCGTCAGCTTGCACACGTTTACGCTCATCAACTTGCACAGA
1 TTTACGCTCGTCAGCTTATATATGTTTATGCTCGTCAGCTTGCACAGA
* * * *
31662005 TTTGCGCTCATCAGCTTATATATGTTTATGCTTGTCAGCTTGCACACA
1 TTTACGCTCGTCAGCTTATATATGTTTATGCTCGTCAGCTTGCACAGA
* ** * * *
31662053 TTTACGCTCGTCAACTTATATACATTTGTGCTCGTCAACTTATGTAC-G-
1 TTTACGCTCGTCAGCTTATATATGTTTATGCTCGTCAGC-T-TGCACAGA
* *
31662101 TTTACGCTCGTCAGCTTATGTATGTTTACGCTCGTCAGCTTGCACA
1 TTTACGCTCGTCAGCTTATATATGTTTATGCTCGTCAGCTTGCACA
31662147 CACACATATA
Statistics
Matches: 109, Mismatches: 30, Indels: 7
0.75 0.21 0.05
Matches are distributed among these distances:
46 4 0.04
47 1 0.01
48 99 0.91
49 1 0.01
50 4 0.04
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (48 bp):
TTTACGCTCGTCAGCTTATATATGTTTATGCTCGTCAGCTTGCACAGA
Found at i:31662080 original size:72 final size:72
Alignment explanation
Indices: 31661950--31662117 Score: 219
Period size: 72 Copynumber: 2.3 Consensus size: 72
31661940 AAAACAACAC
* * *
31661950 ATATATGTTTATGCTCGTCAGCTTGCACACGTTTACGCTCATCAACTTGCACAGATTTGCGCTCA
1 ATATATGTTTATGCTCGTCAGCTTGCACACATTTACGCTCATCAACTTACACACATTTGCGCTCA
*
31662015 TCAGCTT
66 TCAACTT
* * * * * *
31662022 ATATATGTTTATGCTTGTCAGCTTGCACACATTTACGCTCGTCAACTTATATACATTTGTGCTCG
1 ATATATGTTTATGCTCGTCAGCTTGCACACATTTACGCTCATCAACTTACACACATTTGCGCTCA
31662087 TCAACTT
66 TCAACTT
* * *
31662094 ATGTACGTTTACGCTCGTCAGCTT
1 ATATATGTTTATGCTCGTCAGCTT
31662118 ATGTATGTTT
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
72 82 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (72 bp):
ATATATGTTTATGCTCGTCAGCTTGCACACATTTACGCTCATCAACTTACACACATTTGCGCTCA
TCAACTT
Found at i:31665322 original size:15 final size:16
Alignment explanation
Indices: 31665290--31665322 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
31665280 TCAAGATGGA
*
31665290 ATTTTGAATTCATTTG
1 ATTTTGAATTCATATG
31665306 ATTTTGAA-TCATATG
1 ATTTTGAATTCATATG
31665321 AT
1 AT
31665323 ACTTGTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (16 bp):
ATTTTGAATTCATATG
Found at i:31666362 original size:26 final size:26
Alignment explanation
Indices: 31666325--31666377 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
31666315 CATCCAGAAC
*
31666325 TATCGCTACATGAACATGTCTAAAAT
1 TATCGCTACATGAACATGTCCAAAAT
* *
31666351 TATCGCTGCATGAACGTGTCCAAAAT
1 TATCGCTACATGAACATGTCCAAAAT
31666377 T
1 T
31666378 GCGCCCAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (26 bp):
TATCGCTACATGAACATGTCCAAAAT
Found at i:31670620 original size:23 final size:23
Alignment explanation
Indices: 31670594--31670667 Score: 96
Period size: 23 Copynumber: 3.3 Consensus size: 23
31670584 GAACTGAACT
31670594 GTTGACTTTGATCGAACCAAACC
1 GTTGACTTTGATCGAACCAAACC
* *
31670617 GTTGACTTTGATCAAACCAAACT
1 GTTGACTTTGATCGAACCAAACC
* *
31670640 GTTGA-TTTGACCGAACCGAACC
1 GTTGACTTTGATCGAACCAAACC
*
31670662 ATTGAC
1 GTTGAC
31670668 CATTGACTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 17 0.40
23 26 0.60
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (23 bp):
GTTGACTTTGATCGAACCAAACC
Found at i:31671754 original size:2 final size:2
Alignment explanation
Indices: 31671747--31671771 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31671737 GTTTTCTTTT
31671747 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
31671772 TATTTCAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31673310 original size:196 final size:195
Alignment explanation
Indices: 31672977--31673365 Score: 724
Period size: 196 Copynumber: 2.0 Consensus size: 195
31672967 ATTAGTTTAG
31672977 GAAGGGACTTCGACTCTCGTTATAGGATAAGTCTCTATACATCATGATAGGGTATTTAGTGACTT
1 GAAGGGACTTCGACTCTCGTTATAGGATAAGTCTCTATACATCATGATAGGGTATTTAGTGACTT
* *
31673042 GGTTTATCGAGCTAGGACTGTTAAAAGTTTGGAGGCTCGTAAGAGGGCTCAAGATGGAGAGCGTG
66 GGTTTATCGAGCTAGGACTGTTAAAAGTTGGGAGGCTCGTAAGAGGGCTCAAGATAGAGAGCGTG
*
31673107 GTAAAAAGCAAACAAGCACAACAGTTTAGATTGTTTCTGTTAGTCATTCTAGTAAGAGGCCTAAA
131 GTAAAAAGCAAACAAGCACAACAGTTCAGATTGTTTCTGTTAGTCATTCTAGTAAGAGGCCTAAA
31673172 GAAGGGACTTCGACTCTCGTTATAGGATGAAGTCTCTATACATCATGATAGGGTATTTAGTGACT
1 GAAGGGACTTCGACTCTCGTTATAGGAT-AAGTCTCTATACATCATGATAGGGTATTTAGTGACT
* *
31673237 TGGTTTATCGAGCTAGGATTGTTAAGAGTTGGGAGGCTCGTAAGAGGGCTCAAGATAGAGAGCGT
65 TGGTTTATCGAGCTAGGACTGTTAAAAGTTGGGAGGCTCGTAAGAGGGCTCAAGATAGAGAGCGT
31673302 GGTAAAAAGCAAACAAGCACAACAGTTCAGATTGTTTCTGTTAGTCATTCTAGTAAGAGGCCTA
130 GGTAAAAAGCAAACAAGCACAACAGTTCAGATTGTTTCTGTTAGTCATTCTAGTAAGAGGCCTA
31673366 GAGCAGAGGC
Statistics
Matches: 188, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
195 28 0.15
196 160 0.85
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (195 bp):
GAAGGGACTTCGACTCTCGTTATAGGATAAGTCTCTATACATCATGATAGGGTATTTAGTGACTT
GGTTTATCGAGCTAGGACTGTTAAAAGTTGGGAGGCTCGTAAGAGGGCTCAAGATAGAGAGCGTG
GTAAAAAGCAAACAAGCACAACAGTTCAGATTGTTTCTGTTAGTCATTCTAGTAAGAGGCCTAAA
Found at i:31683237 original size:33 final size:33
Alignment explanation
Indices: 31683195--31683260 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
31683185 ATCATCCGGG
31683195 TAAGGCTAATGTTGTAGCTGATGCCCTTAGTCA
1 TAAGGCTAATGTTGTAGCTGATGCCCTTAGTCA
31683228 TAAGGCTAATGTTGTAGCTGATGCCCTTAGTCA
1 TAAGGCTAATGTTGTAGCTGATGCCCTTAGTCA
31683261 GAAATCGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (33 bp):
TAAGGCTAATGTTGTAGCTGATGCCCTTAGTCA
Found at i:31685868 original size:26 final size:26
Alignment explanation
Indices: 31685839--31685891 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
31685829 CAATCCAATA
*
31685839 TGGTAAGTTCGTAGTGTAAATCTTAC
1 TGGTAAGTTCATAGTGTAAATCTTAC
31685865 TGGTAAGTTCATAGTGTAAATCTTAC
1 TGGTAAGTTCATAGTGTAAATCTTAC
31685891 T
1 T
31685892 TAATATTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (26 bp):
TGGTAAGTTCATAGTGTAAATCTTAC
Found at i:31687430 original size:12 final size:12
Alignment explanation
Indices: 31687413--31687456 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
31687403 TAGGTTCTTT
31687413 TTCTTCTTTCTC
1 TTCTTCTTTCTC
31687425 TTCTTCCTTTC-C
1 TTCTT-CTTTCTC
* *
31687437 TTCTTTTTTTTC
1 TTCTTCTTTCTC
31687449 TTCTTCTT
1 TTCTTCTT
31687457 GATCTTTCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 3 0.11
12 19 0.70
13 5 0.19
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
TTCTTCTTTCTC
Found at i:31696951 original size:25 final size:25
Alignment explanation
Indices: 31696909--31697275 Score: 457
Period size: 25 Copynumber: 14.6 Consensus size: 25
31696899 GACTCTTAAC
* *
31696909 TCTGGCTCATAAGTGCGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
* *
31696934 TCTGGCTTGTAAAAGCGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
***
31696959 TCCAACTCGTAAGAGCGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
*
31696984 TCTGGCTCATAAGAGCGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
* *
31697009 TCTGACTCGTAAGAGCAATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
***
31697034 TCCAACTCGTAAGAGCGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
*
31697059 TCTGGCTCATAAGAGCGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
* *
31697084 TCTGACTCGTAAGAGTGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
*
31697109 TCTAGCTCGTAAGAGCGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
*
31697134 TCTGGCTCATAAGAGCGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
* *
31697159 TCTGACTCGTAAGAGTGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
*
31697184 TCTAGCTCGTAAGAGCGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
* *
31697209 TTTGGCTCATAAGAGCGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
* * *
31697234 TCTAGCTCATAAGAGC-ATTATTTTG
1 TCTGGCTCGTAAGAGCGA-TATTCTG
* *
31697259 TCTAGACTCGTATGAGC
1 TCT-GGCTCGTAAGAGC
31697276 TAAATATTCT
Statistics
Matches: 293, Mismatches: 47, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
24 1 0.00
25 283 0.97
26 9 0.03
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (25 bp):
TCTGGCTCGTAAGAGCGATATTCTG
Found at i:31697002 original size:75 final size:75
Alignment explanation
Indices: 31696909--31697275 Score: 549
Period size: 75 Copynumber: 4.9 Consensus size: 75
31696899 GACTCTTAAC
* * * *
31696909 TCTGGCTCATAAGTGCGATATTCTGTCTGGCTTGTAAAAGCGATATTCTGTCCAACTCGTAAGAG
1 TCTGGCTCATAAGAGCGATATTCTGTCTGACTCGTAAGAGCGATATTCTGTCCAACTCGTAAGAG
31696974 CGATATTCTG
66 CGATATTCTG
*
31696984 TCTGGCTCATAAGAGCGATATTCTGTCTGACTCGTAAGAGCAATATTCTGTCCAACTCGTAAGAG
1 TCTGGCTCATAAGAGCGATATTCTGTCTGACTCGTAAGAGCGATATTCTGTCCAACTCGTAAGAG
31697049 CGATATTCTG
66 CGATATTCTG
* * *
31697059 TCTGGCTCATAAGAGCGATATTCTGTCTGACTCGTAAGAGTGATATTCTGTCTAGCTCGTAAGAG
1 TCTGGCTCATAAGAGCGATATTCTGTCTGACTCGTAAGAGCGATATTCTGTCCAACTCGTAAGAG
31697124 CGATATTCTG
66 CGATATTCTG
* * *
31697134 TCTGGCTCATAAGAGCGATATTCTGTCTGACTCGTAAGAGTGATATTCTGTCTAGCTCGTAAGAG
1 TCTGGCTCATAAGAGCGATATTCTGTCTGACTCGTAAGAGCGATATTCTGTCCAACTCGTAAGAG
31697199 CGATATTCTG
66 CGATATTCTG
* * * * *
31697209 TTTGGCTCATAAGAGCGATATTCTGTCT-AGCTCATAAGAGC-ATTATTTTGTCTAGACTCGTAT
1 TCTGGCTCATAAGAGCGATATTCTGTCTGA-CTCGTAAGAGCGA-TATTCTGTCCA-ACTCGTAA
31697272 GAGC
63 GAGC
31697276 TAAATATTCT
Statistics
Matches: 274, Mismatches: 15, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
74 2 0.01
75 262 0.96
76 10 0.04
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (75 bp):
TCTGGCTCATAAGAGCGATATTCTGTCTGACTCGTAAGAGCGATATTCTGTCCAACTCGTAAGAG
CGATATTCTG
Found at i:31700600 original size:16 final size:17
Alignment explanation
Indices: 31700563--31700602 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
31700553 ACCCACGGAA
31700563 TATTTTT-TATTTTTCT
1 TATTTTTGTATTTTTCT
31700579 TATTTTTGTATTTTT-T
1 TATTTTTGTATTTTTCT
*
31700595 TGTTTTTG
1 TATTTTTG
31700603 CAATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.10, C:0.03, G:0.07, T:0.80
Consensus pattern (17 bp):
TATTTTTGTATTTTTCT
Found at i:31701944 original size:21 final size:21
Alignment explanation
Indices: 31701905--31701944 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31701895 CATCTCTCAA
*
31701905 TCATTTCTCTCTTTTATTCTC
1 TCATTTCTCTCTTTCATTCTC
31701926 TCATTTC-CTCTCTTCATTC
1 TCATTTCTCTCT-TTCATTC
31701945 CCATGCATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.10, C:0.33, G:0.00, T:0.57
Consensus pattern (21 bp):
TCATTTCTCTCTTTCATTCTC
Found at i:31708414 original size:28 final size:28
Alignment explanation
Indices: 31708329--31708414 Score: 127
Period size: 28 Copynumber: 3.1 Consensus size: 28
31708319 GATATTCGAT
* *
31708329 TTACTCCCTATTGACCCAAAGGTTATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
*
31708357 TAACTCCCTGTTGACCCAAAGGTCATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
* *
31708385 TTACTCCTTGTTGAGCCAAAGGTCATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
31708413 TT
1 TT
31708415 GTTAACAGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.31
Consensus pattern (28 bp):
TTACTCCCTGTTGACCCAAAGGTCATGC
Found at i:31711895 original size:27 final size:25
Alignment explanation
Indices: 31711861--31711918 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 25
31711851 TAAACTAATC
31711861 TATTAATTTAAT-TTATAAATATAATTT
1 TATTAATTT-ATCTTA-AAATAT-ATTT
*
31711888 TATTAATTTTTCTTAAAATATATTT
1 TATTAATTTATCTTAAAATATATTT
31711913 TATTAA
1 TATTAA
31711919 ATTCAAATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 10 0.34
26 7 0.24
27 12 0.41
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTAATTTATCTTAAAATATATTT
Found at i:31712696 original size:45 final size:45
Alignment explanation
Indices: 31712644--31712874 Score: 298
Period size: 45 Copynumber: 5.3 Consensus size: 45
31712634 CACAATTGGC
* *
31712644 GAGGGTGGTGGTTTTATAGCAGGTGGTGGT-GT-AC-CAGTAGGA
1 GAGGGAGGTGGTTTTATAGCAGGTGATGGTGGTGACACAGTAGGA
*
31712686 GAGGGAGGTGG-TTTAGTAGCAGGTGATGGTGGTGCCACAGTAGGA
1 GAGGGAGGTGGTTTTA-TAGCAGGTGATGGTGGTGACACAGTAGGA
* *
31712731 GAGGGTGGTGGTTTTATAGCAGGTGGTGGT-GT-AC-CAGTAGGA
1 GAGGGAGGTGGTTTTATAGCAGGTGATGGTGGTGACACAGTAGGA
* *
31712773 GTGGGAGGTGGTTTAATAGCAGGTGATGGTGGTGACACAGTAGGA
1 GAGGGAGGTGGTTTTATAGCAGGTGATGGTGGTGACACAGTAGGA
* *
31712818 GTGGGAGGTGG-TTTAGTAGCAGGTGATGGTGGTGCCACAGTAGGA
1 GAGGGAGGTGGTTTTA-TAGCAGGTGATGGTGGTGACACAGTAGGA
*
31712863 GAGGGTGGTGGT
1 GAGGGAGGTGGT
31712875 GTACCAGTAG
Statistics
Matches: 165, Mismatches: 14, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
41 4 0.02
42 57 0.35
43 5 0.03
44 8 0.05
45 87 0.53
46 4 0.02
ACGTcount: A:0.20, C:0.07, G:0.47, T:0.26
Consensus pattern (45 bp):
GAGGGAGGTGGTTTTATAGCAGGTGATGGTGGTGACACAGTAGGA
Found at i:31712737 original size:87 final size:87
Alignment explanation
Indices: 31712644--31712874 Score: 347
Period size: 87 Copynumber: 2.6 Consensus size: 87
31712634 CACAATTGGC
*
31712644 GAGGGTGGTGGTTTTATAGCAGGTGGTGGTGTACCAGTAGGAGAGGGAGGTGGTTTAGTAGCAGG
1 GAGGGTGGTGGTTTTATAGCAGGTGGTGGTGTACCAGTAGGAGAGGGAGGTGGTTTAATAGCAGG
*
31712709 TGATGGTGGTGCCACAGTAGGA
66 TGATGGTGGTGACACAGTAGGA
*
31712731 GAGGGTGGTGGTTTTATAGCAGGTGGTGGTGTACCAGTAGGAGTGGGAGGTGGTTTAATAGCAGG
1 GAGGGTGGTGGTTTTATAGCAGGTGGTGGTGTACCAGTAGGAGAGGGAGGTGGTTTAATAGCAGG
31712796 TGATGGTGGTGACACAGTAGGA
66 TGATGGTGGTGACACAGTAGGA
* * * * *
31712818 GTGGGAGGTGG-TTTAGTAGCAGGTGATGGTGGTGCCACAGTAGGAGAGGGTGGTGGT
1 GAGGGTGGTGGTTTTA-TAGCAGGTGGTGGT-GT-AC-CAGTAGGAGAGGGAGGTGGT
31712875 GTACCAGTAG
Statistics
Matches: 131, Mismatches: 9, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
86 4 0.03
87 106 0.81
88 2 0.02
89 1 0.01
90 18 0.14
ACGTcount: A:0.20, C:0.07, G:0.47, T:0.26
Consensus pattern (87 bp):
GAGGGTGGTGGTTTTATAGCAGGTGGTGGTGTACCAGTAGGAGAGGGAGGTGGTTTAATAGCAGG
TGATGGTGGTGACACAGTAGGA
Found at i:31712782 original size:24 final size:23
Alignment explanation
Indices: 31712755--31712898 Score: 88
Period size: 24 Copynumber: 6.3 Consensus size: 23
31712745 TATAGCAGGT
31712755 GGTGGTGTACCAGTAGGAGTGGGA
1 GGTGGTGTACCAGTAGGAG-GGGA
* * *
31712779 GGTGGTTTA--A-TAGCAGGTGA
1 GGTGGTGTACCAGTAGGAGGGGA
31712799 TGGTGGTG-ACACAGTAGGAGTGGGA
1 -GGTGGTGTAC-CAGTAGGAG-GGGA
* * *
31712824 GGTGGT-T--TAGTAGCAGGTGA
1 GGTGGTGTACCAGTAGGAGGGGA
* *
31712844 TGGTGGTG-CCACAGTAGGAGAGGGT
1 -GGTGGTGTAC-CAGTAGGAG-GGGA
31712869 GGTGGTGTACCAGTAGGAGAGGGA
1 GGTGGTGTACCAGTAGGAG-GGGA
31712893 GGTGGT
1 GGTGGT
31712899 TTCGTTGCGG
Statistics
Matches: 91, Mismatches: 15, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
20 7 0.08
21 24 0.26
22 1 0.01
23 1 0.01
24 52 0.57
25 6 0.07
ACGTcount: A:0.22, C:0.08, G:0.48, T:0.23
Consensus pattern (23 bp):
GGTGGTGTACCAGTAGGAGGGGA
Found at i:31722805 original size:25 final size:23
Alignment explanation
Indices: 31722777--31722822 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
31722767 GTTGGATCCA
31722777 AATTAAATTCTAAAAAGATAATTAT
1 AATTAAA-TCTAAAAA-ATAATTAT
*
31722802 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
31722823 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAT
Found at i:31722865 original size:21 final size:20
Alignment explanation
Indices: 31722837--31722875 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
31722827 AATTGGATCC
* *
31722837 AAATTAAACTCTAAATTATA
1 AAATTAAAATATAAATTATA
31722857 AAATCTAAAATATAAATTA
1 AAAT-TAAAATATAAATTA
31722876 AATATAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATTAAAATATAAATTATA
Found at i:31726821 original size:19 final size:19
Alignment explanation
Indices: 31726799--31726844 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
31726789 AAACTCAATT
31726799 GGTCAATGA-AAA-AGTCAA
1 GGTCAATGATAAATAGTC-A
31726817 CGGTCAATGATAAATAGTCA
1 -GGTCAATGATAAATAGTCA
31726837 GGTCAATG
1 GGTCAATG
31726845 GTCAATGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 17 0.68
20 4 0.16
21 4 0.16
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (19 bp):
GGTCAATGATAAATAGTCA
Found at i:31727922 original size:29 final size:29
Alignment explanation
Indices: 31727879--31728050 Score: 166
Period size: 29 Copynumber: 5.9 Consensus size: 29
31727869 TCGTAAAGTG
* * *
31727879 AGCCTTTGTGATTGATCTTTGTTATTAAA
1 AGCCTTTATGGTTGATCTTTGTTATTGAA
*
31727908 AGCCTTTATGGTTGATCTTTGTTATTGGA
1 AGCCTTTATGGTTGATCTTTGTTATTGAA
* * *
31727937 AGCCTTTGTGGTTGATCTATGTTATTGGA
1 AGCCTTTATGGTTGATCTTTGTTATTGAA
* * * * *
31727966 AGCCTTCATGGCT-ATCTCTATTAAATGAA
1 AGCCTTTATGGTTGATCTTTGTT-ATTGAA
* * * *
31727995 TGCCTCTATGGCTGGTCTTTGTTATTGAA
1 AGCCTTTATGGTTGATCTTTGTTATTGAA
**
31728024 AGCCTTCGTGGTTGATCTTTGTTATTG
1 AGCCTTTATGGTTGATCTTTGTTATTG
31728051 GAAATCTTCG
Statistics
Matches: 115, Mismatches: 26, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
28 7 0.06
29 102 0.89
30 6 0.05
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.45
Consensus pattern (29 bp):
AGCCTTTATGGTTGATCTTTGTTATTGAA
Found at i:31727969 original size:58 final size:58
Alignment explanation
Indices: 31727879--31728070 Score: 199
Period size: 58 Copynumber: 3.3 Consensus size: 58
31727869 TCGTAAAGTG
* * *
31727879 AGCCTTTGTGATTGATCTTTGTTATTAAAAGCCTTTATGGTTGATCTTTGTTATTGGA
1 AGCCTTTGTGGTTGATCTTTGTTATTGAAAGCCTTCATGGTTGATCTTTGTTATTGGA
* * * * * *
31727937 AGCCTTTGTGGTTGATCTATGTTATTGGAAGCCTTCATGGCT-ATCTCTATTAAAT-GA
1 AGCCTTTGTGGTTGATCTTTGTTATTGAAAGCCTTCATGGTTGATCTTTGTT-ATTGGA
* * * * *
31727994 ATGCCTCTATGGCTGGTCTTTGTTATTGAAAGCCTTCGTGGTTGATCTTTGTTATTGGA
1 A-GCCTTTGTGGTTGATCTTTGTTATTGAAAGCCTTCATGGTTGATCTTTGTTATTGGA
** *
31728053 AATCTTCGTGGTTGATCT
1 AGCCTTTGTGGTTGATCT
31728071 CTATTATAGG
Statistics
Matches: 103, Mismatches: 27, Indels: 8
0.75 0.20 0.06
Matches are distributed among these distances:
57 10 0.10
58 83 0.81
59 10 0.10
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.44
Consensus pattern (58 bp):
AGCCTTTGTGGTTGATCTTTGTTATTGAAAGCCTTCATGGTTGATCTTTGTTATTGGA
Done.