Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024848.1 Corchorus olitorius cultivar O-4 contig24881, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 17306
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Found at i:982 original size:131 final size:131
Alignment explanation
Indices: 729--1028 Score: 512
Period size: 131 Copynumber: 2.3 Consensus size: 131
719 TAAAGCCCAA
*
729 ACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATTGAACTTAGATGCGAAAAAATGAAACT
1 ACCCTTCGACCGGAAGGGTATTTTTGGAAATAGAAAATTGAACTTAGATGCGAAAAAATGAAACT
*
794 GACCTTTCGACCGGAAGGGTATTTTTGGAAAACAAAATTGAACTTAGATGCGAAAATATGAAACT
66 GACCCTTCGACCGGAAGGGTATTTTTGGAAAACAAAATTGAACTTAGATGCGAAAATATGAAACT
859 G
131 G
* *
860 ACCCTTCGACCGGAAGGGTATTTTTGGAAA-ATAAAATTGAACTTAGATGCGAAAATATGAAACT
1 ACCCTTCGACCGGAAGGGTATTTTTGGAAATAGAAAATTGAACTTAGATGCGAAAAAATGAAACT
* * *
924 GACCCTTCGATCGGAAGGGTATTTTTGGACATAGAAAATTGAACTTAGATGCGAAAATATGAAAC
66 GACCCTTCGACCGGAAGGGTATTTTTGGA-AAACAAAATTGAACTTAGATGCGAAAATATGAAAC
989 TG
130 TG
*
991 ACCCTTCGACCGGAAGGGTATTTTTGGACATAGAAAAT
1 ACCCTTCGACCGGAAGGGTATTTTTGGAAATAGAAAAT
1029 AGAGCTTTAC
Statistics
Matches: 158, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
130 59 0.37
131 93 0.59
132 6 0.04
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (131 bp):
ACCCTTCGACCGGAAGGGTATTTTTGGAAATAGAAAATTGAACTTAGATGCGAAAAAATGAAACT
GACCCTTCGACCGGAAGGGTATTTTTGGAAAACAAAATTGAACTTAGATGCGAAAATATGAAACT
G
Found at i:998 original size:66 final size:65
Alignment explanation
Indices: 729--1028 Score: 501
Period size: 65 Copynumber: 4.6 Consensus size: 65
719 TAAAGCCCAA
* *
729 ACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATTGAACTTAGATGCGAAAAAATGAAACT
1 ACCCTTCGACCGGAAGGGTATTTTTGG-AATAGAAAATTGAACTTAGATGCGAAAATATGAAACT
794 G
65 G
* * *
795 ACCTTTCGACCGGAAGGGTATTTTTGGAAAACAAAATTGAACTTAGATGCGAAAATATGAAACTG
1 ACCCTTCGACCGGAAGGGTATTTTTGGAATAGAAAATTGAACTTAGATGCGAAAATATGAAACTG
* *
860 ACCCTTCGACCGGAAGGGTATTTTTGGAAAATAAAATTGAACTTAGATGCGAAAATATGAAACTG
1 ACCCTTCGACCGGAAGGGTATTTTTGGAATAGAAAATTGAACTTAGATGCGAAAATATGAAACTG
*
925 ACCCTTCGATCGGAAGGGTATTTTTGGACATAGAAAATTGAACTTAGATGCGAAAATATGAAACT
1 ACCCTTCGACCGGAAGGGTATTTTTGGA-ATAGAAAATTGAACTTAGATGCGAAAATATGAAACT
990 G
65 G
991 ACCCTTCGACCGGAAGGGTATTTTTGGACATAGAAAAT
1 ACCCTTCGACCGGAAGGGTATTTTTGGA-ATAGAAAAT
1029 AGAGCTTTAC
Statistics
Matches: 222, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
65 125 0.56
66 97 0.44
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (65 bp):
ACCCTTCGACCGGAAGGGTATTTTTGGAATAGAAAATTGAACTTAGATGCGAAAATATGAAACTG
Found at i:1722 original size:18 final size:18
Alignment explanation
Indices: 1699--1734 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1689 AGACATTAAA
1699 GCCCAAAACAAATCCAAG
1 GCCCAAAACAAATCCAAG
* *
1717 GCCCAAAGCAAATTCAAG
1 GCCCAAAACAAATCCAAG
1735 TTACTACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.31, G:0.14, T:0.08
Consensus pattern (18 bp):
GCCCAAAACAAATCCAAG
Found at i:3818 original size:26 final size:26
Alignment explanation
Indices: 3687--3924 Score: 102
Period size: 27 Copynumber: 8.3 Consensus size: 26
3677 CACCTTTTTC
3687 TTACTCTTTTTTACTGATTACCATTGTT
1 TTACTCTTTTTTACTGATTACCA-T-TT
* *
3715 TTCTCTCTTTTTTACTGATT-TCATGTT
1 TT-ACTCTTTTTTACTGATTACCAT-TT
* * * **
3742 CTACTCTTTTTAACTAAGTTATTGATTACT
1 TTACTCTTTTTTACTGA-TTA-CCATT--T
3772 CTTACTCTTTTTTACTGATTACCAATTT
1 -TTACTCTTTTTTACTGATTACC-ATTT
*
3800 TTACTC-TTTTTACTTATTACCATTTT
1 TTACTCTTTTTTACTGATTACCA-TTT
* * *
3826 CTTACCTAATTTTTTACTGGTTTCCATTT
1 -TTA-CT-CTTTTTTACTGATTACCATTT
* * *
3855 TTGACGTTTTTACTTTAATTATTGAATACCATTT
1 TT-AC-----T-CTTT-TTTACTGATTACCATTT
** *
3889 TTACTCTTTTTTCACTTTTTACCACTT
1 TTACTCTTTTTT-ACTGATTACCATTT
3916 TTACTCTTT
1 TTACTCTTT
3925 GAACTTTAAT
Statistics
Matches: 160, Mismatches: 29, Indels: 43
0.69 0.12 0.19
Matches are distributed among these distances:
25 1 0.01
26 31 0.19
27 38 0.24
28 12 0.08
29 23 0.14
30 20 0.12
31 14 0.09
33 7 0.04
34 14 0.09
ACGTcount: A:0.19, C:0.19, G:0.05, T:0.57
Consensus pattern (26 bp):
TTACTCTTTTTTACTGATTACCATTT
Found at i:3830 original size:27 final size:28
Alignment explanation
Indices: 3682--3855 Score: 133
Period size: 26 Copynumber: 6.1 Consensus size: 28
3672 CCGATCACCT
3682 TTTTCTTACTCTTTTTTACTGATTACCA
1 TTTTCTTACTCTTTTTTACTGATTACCA
* *
3710 TTGTT-TTCTCTCTTTTTTACTGATT-TCA
1 TT-TTCTT-ACTCTTTTTTACTGATTACCA
* * * **
3738 TGTTC-TACTCTTTTTAACTAAGTTATTGA
1 TTTTCTTACTCTTTTTTACTGA-TTA-CCA
*
3767 TTACTCTTACTCTTTTTTACTGATTACCA
1 TT-TTCTTACTCTTTTTTACTGATTACCA
* *
3796 ATTT-TTACTC-TTTTTACTTATTACCA
1 TTTTCTTACTCTTTTTTACTGATTACCA
* * *
3822 TTTTCTTACCTAATTTTTTACTGGTTTCCA
1 TTTTCTTA-CT-CTTTTTTACTGATTACCA
3852 TTTT
1 TTTT
3856 TGACGTTTTT
Statistics
Matches: 113, Mismatches: 21, Indels: 22
0.72 0.13 0.14
Matches are distributed among these distances:
26 30 0.27
27 14 0.12
28 10 0.09
29 23 0.20
30 22 0.19
31 14 0.12
ACGTcount: A:0.18, C:0.19, G:0.05, T:0.57
Consensus pattern (28 bp):
TTTTCTTACTCTTTTTTACTGATTACCA
Found at i:4011 original size:21 final size:21
Alignment explanation
Indices: 3938--4164 Score: 175
Period size: 21 Copynumber: 11.4 Consensus size: 21
3928 CTTTAATTAT
*
3938 TGATTACCATTTACTC-TTTAC
1 TGATTACTA-TTACTCTTTTAC
*
3959 TGATTACTATTA-TCATTTTAT
1 TGATTACTATTACTC-TTTTAC
3980 TG-TT-C----ACTCTTTTAC
1 TGATTACTATTACTCTTTTAC
* *
3995 TGATTACTATGACTC--TTCC
1 TGATTACTATTACTCTTTTAC
* *
4014 TTGATTACTCTTTACT-TTTTTC
1 -TGATTACT-ATTACTCTTTTAC
* *
4036 TGACTATTATTACTCTTTTAC
1 TGATTACTATTACTCTTTTAC
4057 ----T-CT-TTACTCTTTTAC
1 TGATTACTATTACTCTTTTAC
*
4072 TGATTACTCTTTACTC-TTTAC
1 TGATTACT-ATTACTCTTTTAC
4093 TGATTACTATTACTCTTTTAC
1 TGATTACTATTACTCTTTTAC
* *
4114 TGATTACTCTTTACTCTTTCAC
1 TGATTACT-ATTACTCTTTTAC
4136 TGATTACTATTACTCTTTTAC
1 TGATTACTATTACTCTTTTAC
4157 TGATTACT
1 TGATTACT
4165 CTTATCATTT
Statistics
Matches: 166, Mismatches: 17, Indels: 46
0.72 0.07 0.20
Matches are distributed among these distances:
15 20 0.12
16 5 0.03
17 2 0.01
19 7 0.04
20 26 0.16
21 78 0.47
22 28 0.17
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (21 bp):
TGATTACTATTACTCTTTTAC
Found at i:4029 original size:77 final size:78
Alignment explanation
Indices: 3933--4291 Score: 278
Period size: 77 Copynumber: 4.6 Consensus size: 78
3923 TTGAACTTTA
* *
3933 ATTA-TTGATTAC-CATTTACTCTTTACTGATTACTATTA-TCATTTTATTGTTCACTCTTTTAC
1 ATTACTTGATTACTC-TTTACTCTTTACTGATTACTATTACTC-TTTTATTCTTTACTCTTTTAC
*
3995 TGATTACTATGACTC
64 TGATTACTATTACTC
* * * * * *
4010 -TTCCTTGATTACTCTTTACTTTTTTCTGACTATTATTACTCTTTTACTCTTTACTCTTTTACTG
1 ATTACTTGATTACTCTTTACTCTTTACTGATTACTATTACTCTTTTATTCTTTACTCTTTTACTG
*
4074 ATTACTCTTTACTC
66 ATTACT-ATTACTC
* * *
4088 TTTAC-TGATTACT-ATTACTCTTTTACTGATTACTCTTTACTCTTTCACTGATTACTATTACTC
1 ATTACTTGATTACTCTTTACTC-TTTACTGATTACT-ATTACTCTTT---T-ATT-CT-TTACTC
*
4151 TTTTACTGATTACTCTTA-TC
58 TTTTACTGATTACTATTACTC
* * * * ** *
4171 ATTTCTTAATTACTCTTTACTCTTTACTGATCA-TTTTACT-GATTACTCTTTACTCTTTTACTG
1 ATTACTTGATTACTCTTTACTCTTTACTGATTACTATTACTCTTTTATTCTTTACTCTTTTACTG
*
4234 ATTATTATTAC-C
66 ATTACTATTACTC
4246 AATTTAC-TGATTACTC-TTAC-CATTT-CTTGATTACTCATTACTCTTT
1 -A-TTACTTGATTACTCTTTACTC-TTTAC-TGATTACT-ATTACTCTTT
4292 ACTGATTGAC
Statistics
Matches: 224, Mismatches: 35, Indels: 45
0.74 0.12 0.15
Matches are distributed among these distances:
74 2 0.01
75 35 0.16
76 14 0.06
77 69 0.31
78 28 0.12
79 12 0.05
81 1 0.00
82 7 0.03
83 8 0.04
84 22 0.10
85 26 0.12
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.53
Consensus pattern (78 bp):
ATTACTTGATTACTCTTTACTCTTTACTGATTACTATTACTCTTTTATTCTTTACTCTTTTACTG
ATTACTATTACTC
Found at i:4226 original size:96 final size:96
Alignment explanation
Indices: 4108--4297 Score: 310
Period size: 96 Copynumber: 2.0 Consensus size: 96
4098 ACTATTACTC
* *
4108 TTTTACTGATTACTCTTTACTCTTTCACTGATTACTATTACTC-TTTTACTGATTACTCTTATCA
1 TTTTACTGATTACTCTTTACTCTTTCACTGATTACTATTAC-CAATTTACTGATTACTCTTACCA
*
4172 TTTCTTAATTACTCTTTACTCTTTACTGATCA
65 TTTCTTAATTACTCATTACTCTTTACTGATCA
* *
4204 TTTTACTGATTACTCTTTACTCTTTTACTGATTATTATTACCAATTTACTGATTACTCTTACCAT
1 TTTTACTGATTACTCTTTACTCTTTCACTGATTACTATTACCAATTTACTGATTACTCTTACCAT
*
4269 TTCTTGATTACTCATTACTCTTTACTGAT
66 TTCTTAATTACTCATTACTCTTTACTGAT
4298 TGACCCCATT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
95 1 0.01
96 86 0.99
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.52
Consensus pattern (96 bp):
TTTTACTGATTACTCTTTACTCTTTCACTGATTACTATTACCAATTTACTGATTACTCTTACCAT
TTCTTAATTACTCATTACTCTTTACTGATCA
Found at i:4232 original size:8 final size:7
Alignment explanation
Indices: 4045--4228 Score: 87
Period size: 7 Copynumber: 26.3 Consensus size: 7
4035 CTGACTATTA
4045 TTACTCTT
1 TTACTC-T
4053 TTACTCT
1 TTACTCT
4060 TTACTCTT
1 TTACTC-T
**
4068 TTACTGA
1 TTACTCT
4075 TTACTCT
1 TTACTCT
4082 TTACTCT
1 TTACTCT
**
4089 TTACTGA
1 TTACTCT
*
4096 TTACT-A
1 TTACTCT
4102 TTACTCTT
1 TTACTC-T
**
4110 TTACTGA
1 TTACTCT
4117 TTACTCT
1 TTACTCT
4124 TTACTCT
1 TTACTCT
**
4131 TTCACTGA
1 TT-ACTCT
*
4139 TTACT-A
1 TTACTCT
4145 TTACTCTT
1 TTACTC-T
**
4153 TTACTGA
1 TTACTCT
4160 TTACTC-
1 TTACTCT
4166 TTA-TCAT
1 TTACTC-T
4173 TT-CT-T
1 TTACTCT
4178 AATTACTCT
1 --TTACTCT
4187 TTACTCT
1 TTACTCT
**
4194 TTACTGA
1 TTACTCT
*
4201 TCA-T-T
1 TTACTCT
**
4206 TTACTGA
1 TTACTCT
4213 TTACTCT
1 TTACTCT
4220 TTACTCT
1 TTACTCT
4227 TT
1 TT
4229 TACTGATTAT
Statistics
Matches: 136, Mismatches: 25, Indels: 31
0.71 0.13 0.16
Matches are distributed among these distances:
5 5 0.04
6 17 0.12
7 84 0.62
8 29 0.21
9 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.04, T:0.54
Consensus pattern (7 bp):
TTACTCT
Found at i:4287 original size:7 final size:7
Alignment explanation
Indices: 4053--4294 Score: 72
Period size: 7 Copynumber: 34.7 Consensus size: 7
4043 TATTACTCTT
*
4053 TTACTCT
1 TTACTCA
*
4060 TTACTCTT
1 TTACTC-A
*
4068 TTACTGA
1 TTACTCA
*
4075 TTACTCT
1 TTACTCA
*
4082 TTACTCT
1 TTACTCA
*
4089 TTACTGA
1 TTACTCA
4096 TTACT-A
1 TTACTCA
*
4102 TTACTCTT
1 TTACTC-A
*
4110 TTACTGA
1 TTACTCA
*
4117 TTACTCT
1 TTACTCA
*
4124 TTACTCT
1 TTACTCA
*
4131 TTCACTGA
1 TT-ACTCA
4139 TTACT-A
1 TTACTCA
*
4145 TTACTCTT
1 TTACTC-A
*
4153 TTACTGA
1 TTACTCA
4160 TTACTC-
1 TTACTCA
4166 TTA-TCA
1 TTACTCA
* *
4172 TTTCTTAA
1 TTAC-TCA
*
4180 TTACTCT
1 TTACTCA
*
4187 TTACTCT
1 TTACTCA
*
4194 TTACTGA
1 TTACTCA
* *
4201 TCA-T-T
1 TTACTCA
*
4206 TTACTGA
1 TTACTCA
*
4213 TTACTCT
1 TTACTCA
*
4220 TTACTCTT
1 TTACTC-A
*
4228 TTACTGA
1 TTACTCA
*
4235 TTA-TTA
1 TTACTCA
4241 TTAC-CAA
1 TTACTC-A
*
4248 TTTACTGA
1 -TTACTCA
4256 TTACTC-
1 TTACTCA
4262 TTAC-CA
1 TTACTCA
* *
4268 TTTCTTGA
1 TTAC-TCA
4276 TTACTCA
1 TTACTCA
*
4283 TTACTCT
1 TTACTCA
4290 TTACT
1 TTACT
4295 GATTGACCCC
Statistics
Matches: 175, Mismatches: 41, Indels: 38
0.69 0.16 0.15
Matches are distributed among these distances:
5 5 0.03
6 31 0.18
7 98 0.56
8 41 0.23
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.52
Consensus pattern (7 bp):
TTACTCA
Found at i:4386 original size:25 final size:25
Alignment explanation
Indices: 4338--4387 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
4328 AGATTTTTCT
* *
4338 TTTATGACTCTTAATTTATTGATGC
1 TTTATGACTCTTAATATATGGATGC
4363 TTTA-GACTCTTAAATATATGGATGC
1 TTTATGACTCTT-AATATATGGATGC
4388 ACATGATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (25 bp):
TTTATGACTCTTAATATATGGATGC
Found at i:4698 original size:19 final size:18
Alignment explanation
Indices: 4670--4708 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
4660 TTCTCTTTTT
*
4670 ACTAATCTATGACAATTAA
1 ACTAAACTATG-CAATTAA
*
4689 ACTAAACTATGGAATTAA
1 ACTAAACTATGCAATTAA
4707 AC
1 AC
4709 AAATGCTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (18 bp):
ACTAAACTATGCAATTAA
Found at i:6217 original size:24 final size:24
Alignment explanation
Indices: 6190--6250 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
6180 ATTAAAAAAA
*
6190 AGATAAATAGGTATAGAG-ATAAAT
1 AGATAAATAGGTACAGAGAAT-AAT
*
6214 AGATAAATAGATACAGAGAATAAT
1 AGATAAATAGGTACAGAGAATAAT
6238 AGATAAATAGGTA
1 AGATAAATAGGTA
6251 ACTAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.20, T:0.23
Consensus pattern (24 bp):
AGATAAATAGGTACAGAGAATAAT
Found at i:6275 original size:4 final size:4
Alignment explanation
Indices: 6266--6402 Score: 64
Period size: 4 Copynumber: 37.2 Consensus size: 4
6256 AAATAATAAT
** * *
6266 AATA AATA AATA AAT- AATA GCTA AATT AATA AA-A AA-A AGTA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
* * *
6311 AATA GAT- AAT- AATT AA-A AATA AA-A AA-A AATA AAT- AGTA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
* ** * * *
6353 AATA GAT- AATA GTTA AA-A AAAA AATA GATA AAT- AGTA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
*
6398 GATA A
1 AATA A
6403 TAGTTAAAAA
Statistics
Matches: 98, Mismatches: 26, Indels: 18
0.69 0.18 0.13
Matches are distributed among these distances:
3 30 0.31
4 68 0.69
ACGTcount: A:0.69, C:0.01, G:0.07, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:6320 original size:83 final size:83
Alignment explanation
Indices: 6254--6412 Score: 195
Period size: 79 Copynumber: 2.0 Consensus size: 83
6244 ATAGGTAACT
* ** *
6254 AAAAATAAT-AATAATAAATAAATAAATAATAGCTAAATTAATAA-A-A-AAA-AGTAAATAAAT
1 AAAAAAAATAAATAATAAATAAATAAATAATAGCTAAAAAAAAAATAGATAAATAGTAAATAAAT
6314 AGATAATA-ATTAAAAATA
66 AGATAATAGA-TAAAAATA
* * *
6332 AAAAAAAATAAATAGTAAATAAATAGATAATAGTTAAAAAAAAAATAGATAAATAGTAAATAAAT
1 AAAAAAAATAAATAATAAATAAATAAATAATAGCTAAAAAAAAAATAGATAAATAGTAAATAAAT
*
6397 AGATAATAGTTAAAAA
66 AGATAATAGATAAAAA
6413 AAATAGTAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
78 8 0.12
79 29 0.43
80 1 0.01
81 1 0.01
82 3 0.04
83 25 0.37
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.25
Consensus pattern (83 bp):
AAAAAAAATAAATAATAAATAAATAAATAATAGCTAAAAAAAAAATAGATAAATAGTAAATAAAT
AGATAATAGATAAAAATA
Found at i:6384 original size:72 final size:72
Alignment explanation
Indices: 6208--6467 Score: 216
Period size: 72 Copynumber: 3.6 Consensus size: 72
6198 AGGTATAGAG
* * * * * * * *
6208 ATAAATAGATAAATAGATACAGAGAATAATAGATAAATAGGTAACTAAA-A-ATAATAATAATAA
1 ATAAATAGAT-AATAGTTA-AAAAAAAAATAGATAAATAGATAA-TAAATAGAAAATAAAAAAAA
*
6271 ATAA-A-TAA
63 AAAATAGTAA
* * *
6279 AT-AATAGCTAA-A-TTAATAAAAAAAAGTAAATAAATAGATAATAATTA-AAAATAAAAAAAAA
1 ATAAATAGATAATAGTTAA-AAAAAAAA-TAGATAAATAGATAATAAATAGAAAATAAAAAAAAA
6340 TAAATAGTAA
64 -AAATAGTAA
* ***
6350 ATAAATAGATAATAGTTAAAAAAAAAATAGATAAATAG-TAAATAAATAGATAATAGTTAAAAAA
1 ATAAATAGATAATAGTTAAAAAAAAAATAGATAAATAGAT-AATAAATAGAAAATAAAAAAAAAA
6414 AATAGTAA
65 AATAGTAA
* *
6422 ATAAATAGATAATAGTTAAAAAAATAAATAG-TGAATAAATAATAAA
1 ATAAATAGATAATAGTTAAAAAAA-AAATAGATAAATAGATAATAAA
6468 AAAAATCTTT
Statistics
Matches: 155, Mismatches: 21, Indels: 25
0.77 0.10 0.12
Matches are distributed among these distances:
66 1 0.01
67 10 0.06
68 26 0.17
69 4 0.03
70 7 0.05
71 8 0.05
72 69 0.45
73 26 0.17
74 4 0.03
ACGTcount: A:0.66, C:0.01, G:0.08, T:0.25
Consensus pattern (72 bp):
ATAAATAGATAATAGTTAAAAAAAAAATAGATAAATAGATAATAAATAGAAAATAAAAAAAAAAA
ATAGTAA
Found at i:6388 original size:41 final size:40
Alignment explanation
Indices: 6254--6429 Score: 198
Period size: 41 Copynumber: 4.4 Consensus size: 40
6244 ATAGGTAACT
* * * **
6254 AAAAATAAT-AATAATAAATAAATAAATAATAGCTAAATT
1 AAAAATAATAAATAGTAAATAAATAGATAATAGTTAAAAA
* *
6293 AATAA-AA-AAA-AGTAAATAAATAGATAATAATTAAAAATA
1 AAAAATAATAAATAGTAAATAAATAGATAATAGTT-AAAA-A
*
6332 AAAAAAAATAAATAGTAAATAAATAGATAATAGTTAAAAA
1 AAAAATAATAAATAGTAAATAAATAGATAATAGTTAAAAA
6372 AAAAATAGATAAATAGTAAATAAATAGATAATAGTTAAAAA
1 AAAAATA-ATAAATAGTAAATAAATAGATAATAGTTAAAAA
*
6413 AAATAGTAAATAAATAG
1 AAA-AAT-AATAAATAG
6430 ATAATAGTTA
Statistics
Matches: 117, Mismatches: 11, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
37 18 0.15
38 7 0.06
39 8 0.07
40 9 0.08
41 43 0.37
42 31 0.26
43 1 0.01
ACGTcount: A:0.68, C:0.01, G:0.07, T:0.24
Consensus pattern (40 bp):
AAAAATAATAAATAGTAAATAAATAGATAATAGTTAAAAA
Found at i:6420 original size:31 final size:31
Alignment explanation
Indices: 6382--6445 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
6372 AAAAATAGAT
6382 AAATAGTAAATAAATAGATAATAGTTAAAAA
1 AAATAGTAAATAAATAGATAATAGTTAAAAA
6413 AAATAGTAAATAAATAGATAATAGTTAAAAA
1 AAATAGTAAATAAATAGATAATAGTTAAAAA
6444 AA
1 AA
6446 TAAATAGTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (31 bp):
AAATAGTAAATAAATAGATAATAGTTAAAAA
Found at i:6424 original size:7 final size:8
Alignment explanation
Indices: 6190--6281 Score: 61
Period size: 8 Copynumber: 12.1 Consensus size: 8
6180 ATTAAAAAAA
6190 AGATAAAT
1 AGATAAAT
* * *
6198 AGGTATAG
1 AGATAAAT
6206 AGATAAAT
1 AGATAAAT
6214 AGATAAAT
1 AGATAAAT
* *
6222 AGATACAG
1 AGATAAAT
6230 AGA-ATAAT
1 AGATA-AAT
6238 AGATAAAT
1 AGATAAAT
* *
6246 AGGTAACT
1 AGATAAAT
6254 A-A-AAAT
1 AGATAAAT
6260 A-AT-AAT
1 AGATAAAT
6266 A-ATAAAT
1 AGATAAAT
*
6273 AAATAAAT
1 AGATAAAT
6281 A
1 A
6282 ATAGCTAAAT
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
6 11 0.17
7 5 0.08
8 48 0.74
9 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.13, T:0.24
Consensus pattern (8 bp):
AGATAAAT
Found at i:6426 original size:42 final size:41
Alignment explanation
Indices: 6293--6429 Score: 204
Period size: 41 Copynumber: 3.3 Consensus size: 41
6283 TAGCTAAATT
* *
6293 AATAAA-AAAAAGTAAATAAATAGATAATAATTAAAAATAAA
1 AATAAATAAATAGTAAATAAATAGATAATAGTTAAAAA-AAA
*
6334 AAAAAATAAATAGTAAATAAATAGATAATAGTTAAAAAAAA
1 AATAAATAAATAGTAAATAAATAGATAATAGTTAAAAAAAA
*
6375 AATAGATAAATAGTAAATAAATAGATAATAGTTAAAAAAAA
1 AATAAATAAATAGTAAATAAATAGATAATAGTTAAAAAAAA
*
6416 TAGTAAATAAATAG
1 -AATAAATAAATAG
6430 ATAATAGTTA
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
41 47 0.54
42 40 0.46
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (41 bp):
AATAAATAAATAGTAAATAAATAGATAATAGTTAAAAAAAA
Found at i:6468 original size:23 final size:23
Alignment explanation
Indices: 6254--6473 Score: 70
Period size: 22 Copynumber: 9.4 Consensus size: 23
6244 ATAGGTAACT
6254 AAAAAT-AATA-ATAATAAATAA
1 AAAAATAAATAGATAATAAATAA
* * *
6275 ATAAATAATAGCTAAATTAATAAAAAA
1 AAAAATAA-A--TAGA-TAATAAATAA
*
6302 AAGTAAATAAATAGATAATAATTAA
1 AA--AAATAAATAGATAATAAATAA
6327 AAATAA-AAA-A-A-AATAAAT-A
1 AAA-AATAAATAGATAATAAATAA
** **
6346 GTAAATAAATAGATAATAGTTAA
1 AAAAATAAATAGATAATAAATAA
*
6369 AAAAA-AAATAGATAA-ATAGTAA
1 AAAAATAAATAGATAATA-AATAA
* * *
6391 ATAAATAGATA-ATAGTTAAA-AA
1 AAAAATAAATAGATA-ATAAATAA
* * *
6413 AAATAGTAAATAAATAGATAATAGTTA
1 AAA-AATAAATAGATA-ATAA-A-TAA
6440 AAAAAATAAATAG-TGAATAAATAA
1 AAA-AATAAATAGAT-AATAAATAA
6464 TAAAAA-AAAT
1 -AAAAATAAAT
6474 CTTTTTGGTC
Statistics
Matches: 146, Mismatches: 28, Indels: 48
0.66 0.13 0.22
Matches are distributed among these distances:
18 2 0.01
19 5 0.03
20 7 0.05
21 8 0.05
22 31 0.21
23 24 0.16
24 14 0.10
25 17 0.12
26 9 0.06
27 22 0.15
28 1 0.01
29 6 0.04
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (23 bp):
AAAAATAAATAGATAATAAATAA
Found at i:8078 original size:35 final size:35
Alignment explanation
Indices: 8037--8682 Score: 810
Period size: 35 Copynumber: 17.9 Consensus size: 35
8027 TTTGGGGATA
* ** *
8037 AACTCTGACCATTGAAAACTTCTTGGAATGAGATC
1 AACTCTGATCATAAAAAACTTCTTGAAATGAGATC
8072 AACTCTGATCATAAAAAAAAAACTTCTTGAAATGAGATC
1 AACTCTGATCAT----AAAAAACTTCTTGAAATGAGATC
*
8111 AACTCTGATCATCAAAAACTTCTTGAAATGAGATC
1 AACTCTGATCATAAAAAACTTCTTGAAATGAGATC
* *
8146 AACTCTGATCATCAAAAACTTCTTGAAACGA-ATC
1 AACTCTGATCATAAAAAACTTCTTGAAATGAGATC
* *
8180 AACTCTGATCATCAAAAACTTCTTGAAAGGAGATC
1 AACTCTGATCATAAAAAACTTCTTGAAATGAGATC
*
8215 AACTCTGATCATAAAAAACTTCTTGAAACGAGATC
1 AACTCTGATCATAAAAAACTTCTTGAAATGAGATC
** *
8250 AACTCTGATCATCGAAAACTTCTTAAAATGAGATC
1 AACTCTGATCATAAAAAACTTCTTGAAATGAGATC
**
8285 AACTCTGATCATCGAAAACTTCTTGAAATGAGATC
1 AACTCTGATCATAAAAAACTTCTTGAAATGAGATC
*
8320 AACTCTGATCATAAAAAACTTCTTGGAATGAGATC
1 AACTCTGATCATAAAAAACTTCTTGAAATGAGATC
* *
8355 AACTCTGATCATCAAAAACTTCTTGAAACGAGATC
1 AACTCTGATCATAAAAAACTTCTTGAAATGAGATC
*
8390 AACTCTGATCAATAAAAAAAAAAACTTCTTGAAACGAGATC
1 AACTCTGATC-AT-----AAAAAACTTCTTGAAATGAGATC
*
8431 AACTCTGATCATAAAAAAAACTTACTTGAAAGGAGATC
1 AACTCTGATCAT--AAAAAACTT-CTTGAAATGAGATC
*
8469 AACTCTGATCATAAAAAAAACTTTTTGAAATGAGATC
1 AACTCTGATCAT--AAAAAACTTCTTGAAATGAGATC
* * *
8506 AACTCTAATCA-ACGAAAACTTCTTGAAAGGAGATC
1 AACTCTGATCATA-AAAAACTTCTTGAAATGAGATC
*
8541 AACTCTGATCATAAAAAAACTTCTTGGAATGAGATC
1 AACTCTGATCAT-AAAAAACTTCTTGAAATGAGATC
*
8577 AACTCTGATCATCAAAAAACTTCTTGAAACGAGATC
1 AACTCTGATCAT-AAAAAACTTCTTGAAATGAGATC
* *
8613 AACTCTGATAAATAAAAAAACTTCTTGAAAGGAGATC
1 AACTCTGAT-CAT-AAAAAACTTCTTGAAATGAGATC
* *
8650 AACTCTGATCATAAAGAAAACTTCATGGAATGA
1 AACTCTGATCAT-AA-AAAACTTCTTGAAATGA
8683 CCGCATCGGT
Statistics
Matches: 552, Mismatches: 42, Indels: 32
0.88 0.07 0.05
Matches are distributed among these distances:
34 34 0.06
35 267 0.48
36 68 0.12
37 81 0.15
38 36 0.07
39 32 0.06
40 2 0.00
41 32 0.06
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (35 bp):
AACTCTGATCATAAAAAACTTCTTGAAATGAGATC
Found at i:8842 original size:161 final size:163
Alignment explanation
Indices: 8647--8984 Score: 445
Period size: 161 Copynumber: 2.1 Consensus size: 163
8637 TTGAAAGGAG
*
8647 ATCAACTCTGATCATAAAGAAAACTTCATGGAATGACCGCA-TCGGTTCATCTGGGGATCAACTC
1 ATCAACTCTGATCA-AAAGAAAACTTCATGGAATGACCGCACT-GGATCATCTGGGGATCAACTC
* *
8711 CGATCACTGAAAACTTCTTTTG-AATGATCGCACTGGATAATCTAGGGATCAACTCTGATC--TC
64 CGATCACTGAAAACTTC--TTGAAATGATCGCACTAGATAATCTAGGGATCAACTCTAATCATTC
*
8773 TAAAACTTATAGGAATGACCGCACTGGGCCATCT-GGA
127 -AAAACTTATAGGAATGACCGCACTGGACCATCTGGGA
* * *
8810 ATCAACTCTGATC-AACGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTG
1 ATCAACTCTGATCAAAAGAAAACTTCATGGAATGACCGCACTGGATCATCTGGGGATCAACTCCG
* * * *
8874 ATCACTGAAAACTTCTTGAAATGATCGCACTAGATCATTTGGGGATCAACTCTAATCATTCGAAA
66 ATCACTGAAAACTTCTTGAAATGATCGCACTAGATAATCTAGGGATCAACTCTAATCATTCAAAA
* * * * *
8939 CTTCTTGGAATGATCTCACTGGACCATCTGGGG
131 CTTATAGGAATGACCGCACTGGACCATCTGGGA
8972 ATCAACTCTGATC
1 ATCAACTCTGATC
8985 TCTAAAAACT
Statistics
Matches: 154, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
159 3 0.02
160 33 0.21
161 87 0.56
162 18 0.12
163 13 0.08
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (163 bp):
ATCAACTCTGATCAAAAGAAAACTTCATGGAATGACCGCACTGGATCATCTGGGGATCAACTCCG
ATCACTGAAAACTTCTTGAAATGATCGCACTAGATAATCTAGGGATCAACTCTAATCATTCAAAA
CTTATAGGAATGACCGCACTGGACCATCTGGGA
Found at i:9021 original size:54 final size:54
Alignment explanation
Indices: 8646--9169 Score: 389
Period size: 54 Copynumber: 9.7 Consensus size: 54
8636 CTTGAAAGGA
** * *
8646 GATCAACTCTGATCATAAAGAAAACTTC-ATGGAATGACCGCA-TCGGTTCATCTGGG
1 GATCAACTCTGATC-T-CTGAAAACTTCTAT-GAAAGACCGCACT-GGATCATCTGGG
* * * * * * *
8702 GATCAACTCCGATCACTGAAAACTTCTTTTGAATGATCGCACTGGATAATCTAGG
1 GATCAACTCTGATCTCTGAAAACTTC-TATGAAAGACCGCACTGGATCATCTGGG
* * * **
8757 GATCAACTCTGATCTCT-AAAACTTATAGGAATGACCGCACTGGGCCATCT-GG
1 GATCAACTCTGATCTCTGAAAACTTCTATGAAAGACCGCACTGGATCATCTGGG
* * *
8809 AATCAACTCTGATCAAC-GAAAACTTCT-TGGAATGACCGCACTGGATCATCTGGG
1 GATCAACTCTGATC-TCTGAAAACTTCTAT-GAAAGACCGCACTGGATCATCTGGG
* * * *
8863 GATCAACTCTGATCACTGAAAACTTCT-TGAAATGATCGCACTAGATCATTTGGG
1 GATCAACTCTGATCTCTGAAAACTTCTATGAAA-GACCGCACTGGATCATCTGGG
* * * * *
8917 GATCAACTCTAATCAT-TCG-AAACTTCT-TGGAATGATCTCACTGGACCATCTGGG
1 GATCAACTCTGATC-TCT-GAAAACTTCTAT-GAAAGACCGCACTGGATCATCTGGG
* ** * **
8971 GATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACAC-CGAGTCATCTGAA
1 GATCAACTCTGATCTCTGAAAACTTCTATGAAAGACCGCACTGGA-TCATCTGGG
* * **
9025 GATCAACT-T-ATCTCTGAAAGCTTCTATGAAAGACCGCACAAGG-TCATCCT-AA
1 GATCAACTCTGATCTCTGAAAACTTCTATGAAAGACCGCAC-TGGATCAT-CTGGG
* * **
9077 AATCAACT-TAGATCTCTGAAAACTTCTATGAAAGACCGCACTGGGTCATCTGAA
1 GATCAACTCT-GATCTCTGAAAACTTCTATGAAAGACCGCACTGGATCATCTGGG
* *
9131 AATCAACT-TAGATCTCTGAAAGCTTCTATGAAAGACCGC
1 GATCAACTCT-GATCTCTGAAAACTTCTATGAAAGACCGC
9170 CCAGGGCTTA
Statistics
Matches: 390, Mismatches: 55, Indels: 48
0.79 0.11 0.10
Matches are distributed among these distances:
52 55 0.14
53 63 0.16
54 218 0.56
55 39 0.10
56 15 0.04
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (54 bp):
GATCAACTCTGATCTCTGAAAACTTCTATGAAAGACCGCACTGGATCATCTGGG
Found at i:9099 original size:106 final size:107
Alignment explanation
Indices: 8972--9169 Score: 310
Period size: 106 Copynumber: 1.9 Consensus size: 107
8962 CCATCTGGGG
*
8972 ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACACCGAGTCATCTGAAGATCAACTT-AT
1 ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACACCGAGTCATCTGAAAATCAACTTAAT
9036 CTCTGAAAGCTTCTATGAAAGACCGCACAAGGTCATCCTAAA
66 CTCTGAAAGCTTCTATGAAAGACCGCACAAGGTCATCCTAAA
* ** * *
9078 ATCAACT-TAGATCTCTGAAAACTTCTATGAAAGACCGCACTGGGTCATCTGAAAATCAACTTAG
1 ATCAACTCT-GATCTCTAAAAACTTCTATGAAAGACAACACCGAGTCATCTGAAAATCAACTTA-
9142 ATCTCTGAAAGCTTCTATGAAAGACCGC
64 ATCTCTGAAAGCTTCTATGAAAGACCGC
9170 CCAGGGCTTA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
105 1 0.01
106 54 0.65
108 28 0.34
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (107 bp):
ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACACCGAGTCATCTGAAAATCAACTTAAT
CTCTGAAAGCTTCTATGAAAGACCGCACAAGGTCATCCTAAA
Found at i:9257 original size:92 final size:93
Alignment explanation
Indices: 9083--9267 Score: 275
Period size: 92 Copynumber: 2.0 Consensus size: 93
9073 CTAAAATCAA
* *
9083 CTTAGATCTCTGAAAACTTCTATGAAAGACCGCACTGGGTCATCTGAAAATCAACTTAGATCTCT
1 CTTAGATCTCTGAAAACTTCTATGAAAGACCGCAATGGGTCATCTGAAAATCAACTTAAATCTCT
* *
9148 GAAAGCTTCTATGAAAGACCGCCCAGGG
66 GAAAACTTCTATGAAAGACCGCACAGGG
* * * *
9176 CTTAGATCTCTGAAAGCTTCTATTAAAGACCGCAAAT-GGTC-TCTTAAGATCAACTTAAATCTC
1 CTTAGATCTCTGAAAACTTCTATGAAAGACCGC-AATGGGTCATCTGAAAATCAACTTAAATCTC
9239 TGAAAACTTCTATGAAAGACCGCACAGGG
65 TGAAAACTTCTATGAAAGACCGCACAGGG
9268 TGCTTGAAGG
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
92 46 0.55
93 35 0.42
94 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (93 bp):
CTTAGATCTCTGAAAACTTCTATGAAAGACCGCAATGGGTCATCTGAAAATCAACTTAAATCTCT
GAAAACTTCTATGAAAGACCGCACAGGG
Found at i:10451 original size:37 final size:38
Alignment explanation
Indices: 10382--10453 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 38
10372 AAAAACATTT
** * *
10382 TTTTTCTCTTTTGAAAAGATTGCACTTTGAGGAAAACA
1 TTTTTCTCTTTTGAAAAGATCACACCTAGAGGAAAACA
*
10420 TTTTT-TCTTTTGAAAATATCACACCTAGAGGAAA
1 TTTTTCTCTTTTGAAAAGATCACACCTAGAGGAAA
10454 GTTTCATTCC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 24 0.83
38 5 0.17
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (38 bp):
TTTTTCTCTTTTGAAAAGATCACACCTAGAGGAAAACA
Found at i:10658 original size:20 final size:18
Alignment explanation
Indices: 10633--10698 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 18
10623 TGTTCCTCCG
10633 TCTTTTGCTTTTCAACTTTT
1 TCTTTT-CTTTTCAA-TTTT
10653 TCTTTTCTTTTTCAATTCTTT
1 TCTTTTC-TTTTCAA-T-TTT
*
10674 TCTTCTTTTTTTC-ATTTT
1 TCTT-TTCTTTTCAATTTT
10692 TCTTTTC
1 TCTTTTC
10699 CTCTCCTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
17 2 0.05
18 7 0.17
19 2 0.05
20 15 0.38
21 12 0.30
22 2 0.05
ACGTcount: A:0.08, C:0.20, G:0.02, T:0.71
Consensus pattern (18 bp):
TCTTTTCTTTTCAATTTT
Found at i:13772 original size:24 final size:24
Alignment explanation
Indices: 13745--13805 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
13735 ATTAAAAAAA
*
13745 AGATAAATAGGTATAGAG-ATAAAT
1 AGATAAATAGGTACAGAGAAT-AAT
*
13769 AGATAAATAGATACAGAGAATAAT
1 AGATAAATAGGTACAGAGAATAAT
13793 AGATAAATAGGTA
1 AGATAAATAGGTA
13806 ACTAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.20, T:0.23
Consensus pattern (24 bp):
AGATAAATAGGTACAGAGAATAAT
Found at i:13839 original size:11 final size:11
Alignment explanation
Indices: 13787--13992 Score: 60
Period size: 11 Copynumber: 18.7 Consensus size: 11
13777 AGATACAGAG
*
13787 AATAATAGATA
1 AATAATAAATA
* *
13798 AATAGGTAACTA
1 AATA-ATAAATA
13810 AA-AAT-AAT-
1 AATAATAAATA
13818 AATAATAAATA
1 AATAATAAATA
13829 AATAA-ATAATA
1 AATAATA-AATA
** *
13840 GCTAATTAATA
1 AATAATAAATA
13851 AA-AAGTAAATA
1 AATAA-TAAATA
*
13862 AATAGAT-AGTA
1 AATA-ATAAATA
*
13873 ATTGAA-AAATA
1 AAT-AATAAATA
13884 AA-AA-AAATA
1 AATAATAAATA
*
13893 AATAGTAAATA
1 AATAATAAATA
*
13904 AATAGATAATAGTTC
1 AATA-ATAA-A--TA
13919 AA-AA-AAATA
1 AATAATAAATA
13928 AATAGATAAAT-
1 AATA-ATAAATA
*
13939 AGTAAATAAATA
1 AAT-AATAAATA
* **
13951 GATAATAGTTA
1 AATAATAAATA
*
13962 AA-AATGAAAAA
1 AATAAT-AAATA
*
13973 AATAGTAAATA
1 AATAATAAATA
13984 AATAGATAA
1 AATA-ATAA
13993 TAGTCTAAAA
Statistics
Matches: 139, Mismatches: 31, Indels: 49
0.63 0.14 0.22
Matches are distributed among these distances:
8 2 0.01
9 17 0.12
10 12 0.09
11 76 0.55
12 25 0.18
13 3 0.02
14 1 0.01
15 3 0.02
ACGTcount: A:0.65, C:0.01, G:0.09, T:0.25
Consensus pattern (11 bp):
AATAATAAATA
Found at i:13859 original size:29 final size:29
Alignment explanation
Indices: 13817--13897 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 29
13807 CTAAAAATAA
13817 TAATAATAAATAAATAAATA-ATAGCTAAT
1 TAATAATAAATAAATAAATAGATAG-TAAT
13846 TAATAA-AAAGTAAATAAATAGATAGTAAT
1 TAATAATAAA-TAAATAAATAGATAGTAAT
* *
13875 TGAAAAATAAAAAAAATAAATAG
1 T-AATAAT-AAATAAATAAATAG
13898 TAAATAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
28 3 0.07
29 21 0.47
30 8 0.18
31 10 0.22
32 3 0.07
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.26
Consensus pattern (29 bp):
TAATAATAAATAAATAAATAGATAGTAAT
Found at i:13955 original size:8 final size:8
Alignment explanation
Indices: 13745--13946 Score: 65
Period size: 8 Copynumber: 26.1 Consensus size: 8
13735 ATTAAAAAAA
13745 AGATAAAT
1 AGATAAAT
* * *
13753 AGGTATAG
1 AGATAAAT
13761 AGATAAAT
1 AGATAAAT
13769 AGATAAAT
1 AGATAAAT
* *
13777 AGATACAG
1 AGATAAAT
13785 AGA-ATAAT
1 AGATA-AAT
13793 AGATAAAT
1 AGATAAAT
* *
13801 AGGTAACT
1 AGATAAAT
13809 A-A-AAAT
1 AGATAAAT
13815 A-AT-AAT
1 AGATAAAT
13821 A-ATAAAT
1 AGATAAAT
*
13828 AAATAAAT
1 AGATAAAT
**
13836 A-ATAGCT
1 AGATAAAT
*
13843 A-ATTAAT
1 AGATAAAT
13850 A-A-AAAGT
1 AGATAAA-T
*
13857 AAATAAAT
1 AGATAAAT
13865 AGATAGTAAT
1 AGATA--AAT
* *
13875 TGAAAAAT
1 AGATAAAT
13883 A-A-AAA-
1 AGATAAAT
*
13888 AAATAAAT
1 AGATAAAT
13896 AGTAAATAAAT
1 AG---ATAAAT
13907 AGAT-AAT
1 AGATAAAT
* *
13914 AGTTCAAAA
1 AGAT-AAAT
*
13923 AAATAAAT
1 AGATAAAT
13931 AGATAAAT
1 AGATAAAT
13939 AG-TAAAT
1 AGATAAAT
13946 A
1 A
13947 AATAGATAAT
Statistics
Matches: 145, Mismatches: 31, Indels: 37
0.68 0.15 0.17
Matches are distributed among these distances:
5 1 0.01
6 17 0.12
7 33 0.23
8 72 0.50
9 8 0.06
10 6 0.04
11 8 0.06
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.25
Consensus pattern (8 bp):
AGATAAAT
Found at i:14003 original size:80 final size:83
Alignment explanation
Indices: 13848--14012 Score: 239
Period size: 80 Copynumber: 2.0 Consensus size: 83
13838 TAGCTAATTA
*
13848 ATAAAAAGTAAATAAATAGATAGTAATTGAAAAATAAAAAAAATAAATAGTAAATAAATAGATAA
1 ATAAAAAGTAAATAAATAGATAATAATTGAAAAAT--AAAAAATAAATAGTAAATAAATAGATAA
13913 TAGTTCAAAAAAATAAATAG
64 TAGTTCAAAAAAATAAATAG
* * *
13933 ATAAATAGTAAATAAATAGATAATAGTT-AAAAAT-GAAAA-AAATAGTAAATAAATAGATAATA
1 ATAAAAAGTAAATAAATAGATAATAATTGAAAAATAAAAAATAAATAGTAAATAAATAGATAATA
13995 G-TCTAAAAAAATAAATAG
66 GTTC-AAAAAAATAAATAG
14013 TGAATAAATA
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
79 2 0.03
80 38 0.51
81 4 0.05
84 6 0.08
85 25 0.33
ACGTcount: A:0.65, C:0.01, G:0.10, T:0.24
Consensus pattern (83 bp):
ATAAAAAGTAAATAAATAGATAATAATTGAAAAATAAAAAATAAATAGTAAATAAATAGATAATA
GTTCAAAAAAATAAATAG
Found at i:15279 original size:13 final size:13
Alignment explanation
Indices: 15261--15287 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15251 ACATGGACCC
15261 ATAAAAAAAAATA
1 ATAAAAAAAAATA
15274 ATAAAAAAAAATA
1 ATAAAAAAAAATA
15287 A
1 A
15288 AACATGAGTT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
ATAAAAAAAAATA
Done.