Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006274.1 Hibiscus syriacus cultivar Beakdansim tig00014964_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62078
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:144 original size:81 final size:81
Alignment explanation
Indices: 1--295 Score: 497
Period size: 81 Copynumber: 3.6 Consensus size: 81
*
1 CAGATCAGATAACTCAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAAT
1 CAGATCAGATAACTCAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCCAATTCAAT
66 GATTGGTTTACCAAAC
66 GATTGGTTTACCAAAC
82 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTC-TCTTTCCAATTCA
1 CAGATCAGATAACTC-AAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTTCCAATTCA
*
145 ATGATTGGTTTACCAAGC
64 ATGATTGGTTTACCAAAC
163 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTT-CAATTTCA
1 CAGATCAGATAACTC-AAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCCAA-TTCA
*
227 ATGATTGGTTTTCCAAAC
64 ATGATTGGTTTACCAAAC
*
245 CAAATCAGATAACTCAAGAACACTTCCAGAAGATGCTATGAGCACATTCAT
1 CAGATCAGATAACTCAAGAACACTTCCAGAAGATGCTATGAGCACATTCAT
296 TTGTTCCAGT
Statistics
Matches: 204, Mismatches: 5, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
80 2 0.01
81 130 0.64
82 70 0.34
83 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (81 bp):
CAGATCAGATAACTCAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCCAATTCAAT
GATTGGTTTACCAAAC
Found at i:1066 original size:16 final size:17
Alignment explanation
Indices: 1028--1070 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1018 TCAATAAAAG
* *
1028 AATAAATTGAATTTTCG
1 AATAAATTGAATTCTCA
1045 AA-AAATTGAA-TCTCA
1 AATAAATTGAATTCTCA
1060 AATAAATTGAA
1 AATAAATTGAA
1071 CTTGAAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 5 0.22
16 16 0.70
17 2 0.09
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (17 bp):
AATAAATTGAATTCTCA
Found at i:1401 original size:1 final size:1
Alignment explanation
Indices: 1397--1462 Score: 69
Period size: 1 Copynumber: 66.0 Consensus size: 1
1387 TGACCCCCCC
* * * * * * *
1397 TTTTTTCTTTTTTCTCTTTTTTTTTTTCTCTTTTTTTTTCTCTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1462 T
1 T
1463 CTTCAAGCAT
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:1421 original size:12 final size:12
Alignment explanation
Indices: 1404--1457 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
1394 CCCTTTTTTC
* *
1404 TTTTTTCTCTTT
1 TTTTTTTTCTCT
1416 TTTTTTTTCTCT
1 TTTTTTTTCTCT
1428 TTTTTTTTCTCT
1 TTTTTTTTCTCT
1440 TTTTTTTT-T-T
1 TTTTTTTTCTCT
1450 TTTTTTTT
1 TTTTTTTT
1458 TTTTTCTTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
10 9 0.22
11 1 0.03
12 30 0.75
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTTTTTCTCT
Found at i:1421 original size:14 final size:14
Alignment explanation
Indices: 1398--1464 Score: 95
Period size: 14 Copynumber: 4.9 Consensus size: 14
1388 GACCCCCCCT
1398 TTTTTCTTTTTTCTC
1 TTTTT-TTTTTTCTC
1413 TTTTTTTTTTTCTC
1 TTTTTTTTTTTCTC
1427 --TTTTTTTTTCTC
1 TTTTTTTTTTTCTC
*
1439 TTTTTTTTTTT-TT
1 TTTTTTTTTTTCTC
1452 TTTTTTTTTTTCT
1 TTTTTTTTTTTCT
1465 TCAAGCATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
12 12 0.25
13 12 0.25
14 19 0.40
15 5 0.10
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTTCTC
Found at i:12778 original size:16 final size:16
Alignment explanation
Indices: 12736--12781 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
12726 TTCGATATTG
12736 AAAAATAAA-TATTAA
1 AAAAATAAATTATTAA
* **
12751 AATAATTTATTATTAA
1 AAAAATAAATTATTAA
12767 AAAAATAAATTATTA
1 AAAAATAAATTATTA
12782 TTTAATATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAAATAAATTATTAA
Found at i:13689 original size:15 final size:14
Alignment explanation
Indices: 13665--13706 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
13655 CCTCGGTAAG
*
13665 TTTCTCTTCTTTCTT
1 TTTCTTTTCTTTC-T
13680 TTTCTTTTCTTTCT
1 TTTCTTTTCTTTCT
13694 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
13707 GCTGCGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:13697 original size:20 final size:20
Alignment explanation
Indices: 13665--13706 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
13655 CCTCGGTAAG
*
13665 TTTCTCTTCTTTCTTTTTCT
1 TTTCTCTTCTTTCTGTTTCT
13685 TTTCT-TTCTTTTCTGTTTCT
1 TTTCTCTTC-TTTCTGTTTCT
13705 TT
1 TT
13707 GCTGCGTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTCTCTTCTTTCTGTTTCT
Found at i:14161 original size:12 final size:11
Alignment explanation
Indices: 14143--14224 Score: 69
Period size: 12 Copynumber: 7.2 Consensus size: 11
14133 TTATATATAT
14143 ATTTAAT-AT-
1 ATTTAATAATA
14152 ATTTAATAATA
1 ATTTAATAATA
*
14163 ATAATAATAATA
1 AT-TTAATAATA
*
14175 ATATTTATAATA
1 AT-TTAATAATA
14187 ATTATAATAATA
1 ATT-TAATAATA
*
14199 ATAATAATAATA
1 AT-TTAATAATA
*
14211 ATAATAATAATA
1 AT-TTAATAATA
14223 AT
1 AT
14225 AAATAAATCA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
9 7 0.11
10 2 0.03
11 3 0.05
12 51 0.81
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:14163 original size:3 final size:3
Alignment explanation
Indices: 14155--14226 Score: 117
Period size: 3 Copynumber: 24.0 Consensus size: 3
14145 TTAATATATT
* * *
14155 TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14203 TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
14227 ATAAATCAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:14619 original size:34 final size:36
Alignment explanation
Indices: 14575--14676 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
14565 TTTCGTCCTA
14575 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
14610 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
14645 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
14677 GTTCTACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 30 0.48
35 3 0.05
37 29 0.47
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:15127 original size:2 final size:2
Alignment explanation
Indices: 15122--15165 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
15112 TTAGTGTTAT
*
15122 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15163 TA T
1 TA T
15166 TTCCTATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:15289 original size:16 final size:18
Alignment explanation
Indices: 15270--15304 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
15260 TTTACTCATT
15270 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
15286 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
15304 T
1 T
15305 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:18546 original size:16 final size:14
Alignment explanation
Indices: 18495--18584 Score: 74
Period size: 16 Copynumber: 5.9 Consensus size: 14
18485 AATCAAGAAC
18495 AAAAAAGAAAAGAAG
1 AAAAAAGAAAA-AAG
18510 CAAAAAAGCAATAAAA-
1 -AAAAAAG-AA-AAAAG
*
18526 AACAAAGAAAAAGAG
1 AAAAAAGAAAAA-AG
*
18541 AAACAAGAACAAAAGG
1 AAAAAAGAA-AAAA-G
18557 AAAAAAGAGCAAAAAG
1 AAAAAAGA--AAAAAG
18573 AAAAAAGAAAAA
1 AAAAAAGAAAAA
18585 GGGACAAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
13 3 0.05
14 7 0.11
15 14 0.23
16 27 0.44
17 8 0.13
18 3 0.05
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.01
Consensus pattern (14 bp):
AAAAAAGAAAAAAG
Found at i:18565 original size:25 final size:23
Alignment explanation
Indices: 18496--18584 Score: 87
Period size: 23 Copynumber: 3.8 Consensus size: 23
18486 ATCAAGAACA
*
18496 AAAAAGAAAAGAAGCAAAAA-AGC
1 AAAAAGAAAA-AAGAAAAAAGAGC
18519 AATAAA-AAACAAAG-AAAAAGAG-
1 AA-AAAGAAA-AAAGAAAAAAGAGC
18541 AAACAAGAACAAAAGGAAAAAAGAGC
1 AAA-AAGAA-AAAA-GAAAAAAGAGC
18567 AAAAAGAAAAAAGAAAAA
1 AAAAAGAAAAAAGAAAAA
18585 GGGACAAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
21 1 0.02
22 9 0.16
23 21 0.37
24 10 0.18
25 13 0.23
26 3 0.05
ACGTcount: A:0.76, C:0.07, G:0.16, T:0.01
Consensus pattern (23 bp):
AAAAAGAAAAAAGAAAAAAGAGC
Found at i:18585 original size:6 final size:7
Alignment explanation
Indices: 18495--18584 Score: 74
Period size: 7 Copynumber: 11.7 Consensus size: 7
18485 AATCAAGAAC
18495 AAAAAAG
1 AAAAAAG
18502 AAAAGAAG
1 AAAA-AAG
18510 CAAAAAAG
1 -AAAAAAG
18518 CAATAAAA-
1 -AA-AAAAG
*
18526 AACAAAG
1 AAAAAAG
18533 AAAAAGAG
1 AAAAA-AG
*
18541 AAACAAG
1 AAAAAAG
18548 AACAAAAGG
1 AA-AAAA-G
18557 AAAAAAG
1 AAAAAAG
18564 AGCAAAAAG
1 A--AAAAAG
18573 AAAAAAG
1 AAAAAAG
18580 AAAAA
1 AAAAA
18585 GGGACAAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
6 3 0.04
7 27 0.39
8 22 0.31
9 18 0.26
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:19246 original size:22 final size:22
Alignment explanation
Indices: 19221--19269 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
19211 CCATCAATCT
* *
19221 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
19243 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
19265 TTTGA
1 TTTGA
19270 CCAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:19707 original size:18 final size:18
Alignment explanation
Indices: 19684--19719 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19674 TCAACATCAA
* *
19684 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
19702 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
19720 GGATTCAACA
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:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:20186 original size:36 final size:36
Alignment explanation
Indices: 20062--20479 Score: 156
Period size: 36 Copynumber: 11.8 Consensus size: 36
20052 CAGATGATTA
* * * *
20062 TCTCACTTGAGATTGCTTTT-TTAAAAC-AGACTTTG
1 TCTCTCTTGAGACTGTTTTTCTTGAAACAAGA-TTTG
* * * * * *
20097 TCTCACTTGGGACTGTTTTACTCGAAAGAAGATTTA
1 TCTCTCTTGAGACTGTTTTTCTTGAAACAAGATTTG
* * * * *
20133 TTTCAC-TCATGATTGTTTTTCTTAAAACAAGATTTG
1 TCTCTCTTGA-GACTGTTTTTCTTGAAACAAGATTTG
* * * * *
20169 TCTCGCTTGAGACTGTTTTCACTAG-AA-GAGTTTTG
1 TCTCTCTTGAGACTGTTTT-TCTTGAAACAAGATTTG
* **
20204 TCTCTCTTGAGACAGTTTCCCTTGAAACAA-ATTTTG
1 TCTCTCTTGAGACTGTTTTTCTTGAAACAAGA-TTTG
* *
20240 TCTCTCTTGAGACAGTTTCTCTTGAAACAA-ATTTCG
1 TCTCTCTTGAGACTGTTTTTCTTGAAACAAGATTT-G
* * ** *
20276 TCTATCTTGAGACAGTTTCCCTTGAAATAA-ATTTTG
1 TCTCTCTTGAGACTGTTTTTCTTGAAACAAGA-TTTG
** *
20312 TCTCTCTTGAGACAATTTTCCTTGAAACAA-A----
1 TCTCTCTTGAGACTGTTTTTCTTGAAACAAGATTTG
* * *
20343 -ATAT-TTGA-A-TATGTTTTCTTTGAAACAA-ATTTCG
1 TCTCTCTTGAGACTGT-TTTTC-TTGAAACAAGATTT-G
* ** * *
20377 TCTCCCTTGAGACAATTTCTT-TTGGAACTAAGTTTTG
1 TCTCTCTTGAGACTGTTT-TTCTTGAAAC-AAGATTTG
* * *
20414 TCTCTCTTGAGACAGTTTCTCTTGAAACAA-TTTTCG
1 TCTCTCTTGAGACTGTTTTTCTTGAAACAAGATTT-G
* * **
20450 TCTATCTTGAGACAGTTTCCCTTGAAACAA
1 TCTCTCTTGAGACTGTTTTTCTTGAAACAA
20480 AATCTTTGAA
Statistics
Matches: 300, Mismatches: 57, Indels: 51
0.74 0.14 0.12
Matches are distributed among these distances:
27 2 0.01
28 5 0.02
29 14 0.05
30 2 0.01
34 3 0.01
35 49 0.16
36 180 0.60
37 38 0.13
38 7 0.02
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (36 bp):
TCTCTCTTGAGACTGTTTTTCTTGAAACAAGATTTG
Found at i:20249 original size:71 final size:72
Alignment explanation
Indices: 20157--20480 Score: 242
Period size: 72 Copynumber: 4.6 Consensus size: 72
20147 GTTTTTCTTA
* * * * * *
20157 AAACAAGA-TTTGTCTCGCTTGAGACTGTTTTCACTAG-AA-GAGTTTTGTCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACAG-TTTCACTAGAAACAAATTTCGTCTATCTTGAGACAG
20219 TTTCCCTTG
64 TTTCCCTTG
* *
20228 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGTT
20293 TCCCTTG
66 TCCCTTG
* * * * *
20300 AAATAAATTTTGTCTCTCTTGAGACAATTTTC-CTTGAAACAAA------ATAT-TTGA-ATATG
1 AAACAAATTTTGTCTCTCTTGAGAC-AGTTTCACTAGAAACAAATTTCGTCTATCTTGAGACA-G
* *
20356 TTTTCTTTG
64 TTTCCCTTG
* * * ** * * * * *
20365 AAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCACTAGAAAC-AAATTTCGTCTATCTTGAGACAGT
*
20430 TTCTCTTG
65 TTCCCTTG
* * *
20438 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTCACTAGAAACAAA
20481 ATCTTTGAAT
Statistics
Matches: 202, Mismatches: 35, Indels: 31
0.75 0.13 0.12
Matches are distributed among these distances:
64 7 0.03
65 40 0.20
66 5 0.02
70 8 0.04
71 25 0.12
72 72 0.36
73 43 0.21
74 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (72 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGTT
TCCCTTG
Found at i:20301 original size:72 final size:71
Alignment explanation
Indices: 20200--20480 Score: 292
Period size: 72 Copynumber: 4.0 Consensus size: 71
20190 CTAGAAGAGT
* *
20200 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGA
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGA
20265 AACAAA
66 AACAAA
*
20271 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAATTT-TCCTT
1 TTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCT-CTT
20335 GAAACAAA
64 GAAACAAA
* * * * * * *
20343 -----ATAT-TTGA-ATATGTTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTG
1 TTTGTCTATCTTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTG
* *
20401 GAACTAAGT
65 AAAC-AA-A
* * * * *
20410 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAATTTCTCTTG
20474 AAACAAA
65 AAACAAA
20481 ATCTTTGAAT
Statistics
Matches: 169, Mismatches: 27, Indels: 28
0.75 0.12 0.12
Matches are distributed among these distances:
64 2 0.01
65 45 0.27
66 6 0.04
71 4 0.02
72 72 0.43
73 38 0.22
74 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (71 bp):
TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGA
AACAAA
Found at i:20438 original size:102 final size:102
Alignment explanation
Indices: 20255--20443 Score: 274
Period size: 102 Copynumber: 1.9 Consensus size: 102
20245 CTTGAGACAG
* *
20255 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAATTTCCCTTGAAATAAATTTTGTCTCTCTT
20320 GAGACAATTTTCCTTGAAACAAAATATTTGAATATGT
66 GAGACAATTTTCCTTGAAACAAAATATTTGAATATGT
* ** * *
20357 TTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAATTTCCCTT-GAAATAAATTTTGTCTCTCT
*
20421 TGAGAC-AGTTTCTCTTGAAACAA
65 TGAGACAATTTTC-CTTGAAACAA
20444 TTTTCGTCTA
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
101 38 0.49
102 39 0.51
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAATTTCCCTTGAAATAAATTTTGTCTCTCTT
GAGACAATTTTCCTTGAAACAAAATATTTGAATATGT
Found at i:20479 original size:138 final size:137
Alignment explanation
Indices: 20219--20543 Score: 427
Period size: 138 Copynumber: 2.4 Consensus size: 137
20209 CTTGAGACAG
* *
20219 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAATTTCGTCTATCTT
* *
20284 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAATTTTCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAATTTCCCTTGAAACAAAATATTT
*
20349 GAATATG
131 GAATATA
* * * * * * * *
20356 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAAC-AAATTTCGTCTATCT
* * * *
20421 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCT
65 TGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAATTTCCCTTGAAACAAAATAT
*
20485 TTGAATTTA
129 TTGAATATA
* * * *
20494 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACA
20544 CAAAATCTTC
Statistics
Matches: 159, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
137 49 0.31
138 110 0.69
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAATTTCCCTTGAAACAAAATATTT
GAATATA
Found at i:20542 original size:65 final size:65
Alignment explanation
Indices: 20438--20612 Score: 217
Period size: 67 Copynumber: 2.6 Consensus size: 65
20428 GTTTCTCTTG
** * **
20438 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCT
1 AAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCT
20502 A
65 A
* *
20503 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
20568 TA
64 TA
* * *
20570 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
20613 CAGATATCTT
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
65 25 0.26
66 12 0.13
67 31 0.33
68 27 0.28
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.37
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:20572 original size:67 final size:67
Alignment explanation
Indices: 20429--20611 Score: 219
Period size: 68 Copynumber: 2.7 Consensus size: 67
20419 CTTGAGACAG
* * ** * **
20429 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAAT
1 TTTCCCTTAAAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAAT
20491 TTA
65 TTA
* *
20494 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
20559 TA
66 TA
* * *
20561 TTTCCCTTAAAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACA
1 TTTCCCTTAAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
20612 ACAGATATCT
Statistics
Matches: 100, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
65 31 0.31
66 8 0.08
67 29 0.29
68 32 0.32
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
TA
Found at i:21440 original size:105 final size:105
Alignment explanation
Indices: 21255--22298 Score: 1693
Period size: 105 Copynumber: 10.0 Consensus size: 105
21245 GCACTCGAGG
* * * *
21255 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
*
21320 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
21361 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTACCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
21426 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
21466 CAACGCAAGTTCAACTTCATGACAAAGGGACACCGCTGCTTGTCAACAACAACTTCTCAATTTCA
1 CAACGCAAGTTCAACTTCACGACGAAGGG--ACCGCTGCTTGTCAACAACAACTTCTCAATTTCA
21531 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
64 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
21573 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
21638 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
21678 CAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
21743 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
21783 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
21848 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
21888 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
21953 GCCAATTTCAATTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
21993 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTAAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
22058 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
22098 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** *
22158 TTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * ** *
22198 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
* *
22263 AGCCAATTTCAACTTCACGACGGAGGATATTGGACT
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
22299 TGGAACAATG
Statistics
Matches: 881, Mismatches: 49, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
100 82 0.09
101 3 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 612 0.69
106 75 0.09
107 99 0.11
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:22898 original size:34 final size:36
Alignment explanation
Indices: 22846--22947 Score: 145
Period size: 34 Copynumber: 2.9 Consensus size: 36
22836 TTTCGTCCTA
*
22846 CTAGGATTTAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
* *
22881 -TATGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
22916 GCTAGGATTCAAACTCCTAAAAATATGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
22948 GTTCTACTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
34 28 0.48
35 3 0.05
37 27 0.47
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:22971 original size:37 final size:35
Alignment explanation
Indices: 22850--22981 Score: 140
Period size: 37 Copynumber: 3.7 Consensus size: 35
22840 GTCCTACTAG
*
22850 GATTTAAACTCCTAAAAATAGGATAGAATTT-TAT
1 GATTCAAACTCCTAAAAATAGGATAGAATTTCTAT
* *
22884 GATTCAAACTCCTAAAAATAGGATAAAATTTTGCTAG
1 GATTCAAACTCCTAAAAATAGGATAGAA-TTT-CTAT
* *
22921 GATTCAAACTCCTAAAAATATGATAGAGTTCTACTAT
1 GATTCAAACTCCTAAAAATAGGATAGAATT-T-CTAT
* * * *
22958 TATTTAAATTCCTAAAGATAGGAT
1 GATTCAAACTCCTAAAAATAGGAT
22982 CCACAAGCAC
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
34 26 0.32
35 3 0.04
36 2 0.02
37 50 0.62
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (35 bp):
GATTCAAACTCCTAAAAATAGGATAGAATTTCTAT
Found at i:23549 original size:16 final size:18
Alignment explanation
Indices: 23528--23562 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
23518 TTTACTCATT
23528 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
23544 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
23562 T
1 T
23563 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:25133 original size:3 final size:3
Alignment explanation
Indices: 25125--25189 Score: 103
Period size: 3 Copynumber: 21.0 Consensus size: 3
25115 GTCGAAAAAA
*
25125 TAT TAT TAT TAT TAT TAT TAT TAT TAGT TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
25171 TAT TAT TAT TATT TAT TAT
1 TAT TAT TAT TA-T TAT TAT
25190 CACTGCCCAT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
3 52 0.90
4 6 0.10
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:25215 original size:22 final size:22
Alignment explanation
Indices: 25190--25250 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
25180 TATTTATTAT
*
25190 CACTGCCCATTAAATAAAAACC
1 CACTACCCATTAAATAAAAACC
25212 CACTACCCATTAAATAAAAACC
1 CACTACCCATTAAATAAAAACC
* *
25234 AACTACCTATTAAATAA
1 CACTACCCATTAAATAA
25251 TCATCCCATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.49, C:0.28, G:0.02, T:0.21
Consensus pattern (22 bp):
CACTACCCATTAAATAAAAACC
Found at i:25299 original size:33 final size:33
Alignment explanation
Indices: 25256--25340 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
25246 AATAATCATC
* * *
25256 CCATGCTTCATGCTTCCACTAGCCTCCACCATT
1 CCATGTTTCATTCTTCCACTAACCTCCACCATT
25289 CCATGTTTCATTCTTCCACTAACCTCCACCATT
1 CCATGTTTCATTCTTCCACTAACCTCCACCATT
* *
25322 CCATATTTTATTCTTCCAC
1 CCATGTTTCATTCTTCCAC
25341 CCACAATAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.20, C:0.39, G:0.05, T:0.36
Consensus pattern (33 bp):
CCATGTTTCATTCTTCCACTAACCTCCACCATT
Found at i:25370 original size:2 final size:2
Alignment explanation
Indices: 25363--25498 Score: 272
Period size: 2 Copynumber: 68.0 Consensus size: 2
25353 TTTTCTTATG
25363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25405 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25447 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25489 AT AT AT AT AT
1 AT AT AT AT AT
25499 GTAATATGCT
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 134 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31436 original size:22 final size:22
Alignment explanation
Indices: 31411--31452 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
31401 ACACAAACAT
*
31411 TAAACGAACATGTTCATGAAGC
1 TAAACAAACATGTTCATGAAGC
* *
31433 TAAATAAACATGTTCGTGAA
1 TAAACAAACATGTTCATGAA
31453 CATATAAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (22 bp):
TAAACAAACATGTTCATGAAGC
Found at i:31526 original size:30 final size:30
Alignment explanation
Indices: 31490--31605 Score: 119
Period size: 30 Copynumber: 3.9 Consensus size: 30
31480 GTTTTTGAAT
* *
31490 AATAAATAAATGAACACGAACACGTTCAAA
1 AATAAATAAACGAACACGAACACATTCAAA
* *
31520 AATAAATAAACGAACACAAACACAATACTAAA
1 AATAAATAAACGAACACGAACAC-ATTC-AAA
* * *
31552 AAT--TTAAACGAACATGAACACCTTCAAA
1 AATAAATAAACGAACACGAACACATTCAAA
* *
31580 AATAAACAAACGAACATGAACACATT
1 AATAAATAAACGAACACGAACACATT
31606 TCGTTCAAGC
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
28 6 0.09
29 2 0.03
30 54 0.77
31 2 0.03
32 6 0.09
ACGTcount: A:0.58, C:0.19, G:0.07, T:0.16
Consensus pattern (30 bp):
AATAAATAAACGAACACGAACACATTCAAA
Found at i:37853 original size:64 final size:63
Alignment explanation
Indices: 37771--37928 Score: 183
Period size: 63 Copynumber: 2.5 Consensus size: 63
37761 TTCAAGGTGT
* * **
37771 ATCGATGCACATGAAGTGCATCGATGCACTCTGATAAAATAAAAACATCGAATGCCATT-AGTGC
1 ATCGATGCATAAGAAGTGCATCGATGCAC-CCCATAAAATAAAAACATCGAATGCCATTCA-TGC
* ** * **
37835 ATCGATGCATAAGGAGTGCATCGATGCACCCCATTGAATACAAACATCGAATGTGATTCATGC
1 ATCGATGCATAAGAAGTGCATCGATGCACCCCATAAAATAAAAACATCGAATGCCATTCATGC
* *
37898 ACCGATGCATAAGTAGTGCATCGATGCACCC
1 ATCGATGCATAAGAAGTGCATCGATGCACCC
37929 GTTAAGGAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
63 54 0.67
64 27 0.33
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (63 bp):
ATCGATGCATAAGAAGTGCATCGATGCACCCCATAAAATAAAAACATCGAATGCCATTCATGC
Found at i:38515 original size:18 final size:18
Alignment explanation
Indices: 38492--38600 Score: 155
Period size: 18 Copynumber: 5.9 Consensus size: 18
38482 AGGGATATAC
38492 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
38510 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
38528 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
*
38547 CAGTGGTCCTTTGGGACAT
1 -AGTGGTCCTTCGGGACAT
38566 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
38584 AATGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
38601 AATACTGAAC
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
18 64 0.79
19 4 0.05
20 13 0.16
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:38563 original size:38 final size:36
Alignment explanation
Indices: 38492--38600 Score: 146
Period size: 38 Copynumber: 3.0 Consensus size: 36
38482 AGGGATATAC
*
38492 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGAACATAGTGGTCCTTCGGGACAT
* *
38528 AGTGGTTCTTCGGAACAATCAGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGAAC-AT-AGTGGTCCTTCGGGACAT
* * *
38566 AGTGGTCCTTCGGGACATAATGGTCATTCGGGACA
1 AGTGGTCCTTCGGAACATAGTGGTCCTTCGGGACA
38601 AATACTGAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
36 28 0.44
37 4 0.06
38 31 0.49
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.28
Consensus pattern (36 bp):
AGTGGTCCTTCGGAACATAGTGGTCCTTCGGGACAT
Found at i:44100 original size:2 final size:2
Alignment explanation
Indices: 44087--44122 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
44077 TCACATATGA
*
44087 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44123 GTATTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:44441 original size:2 final size:2
Alignment explanation
Indices: 44436--44463 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44426 TGTATTTTCA
44436 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44464 TAAGGTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45195 original size:100 final size:100
Alignment explanation
Indices: 45017--45217 Score: 375
Period size: 100 Copynumber: 2.0 Consensus size: 100
45007 CAACCAGATC
45017 ACCAAAGTCTTCTCTAATTTTCAATTCTTAGTAATTTCCCTAAAACATAATTATAAATTTAAATT
1 ACCAAAGTCTTCTCTAATTTTCAATTCTTAGTAATTTCCCTAAAACATAATTATAAATTTAAATT
*
45082 TATTAACGGTATCAAAATCCGTAATTGTAACTTTA
66 TATTAACGGTATCAAAATCCGTAATTATAACTTTA
*
45117 ACCAAAGTCTTCTCTAATTTTTAATTCTTAGTAATTTCCCTAAAACATAATTATAAATTTAAATT
1 ACCAAAGTCTTCTCTAATTTTCAATTCTTAGTAATTTCCCTAAAACATAATTATAAATTTAAATT
*
45182 TATTAACGTTATCAAAATCCGTAATTATAACTTTA
66 TATTAACGGTATCAAAATCCGTAATTATAACTTTA
45217 A
1 A
45218 TGGTTAATCA
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (100 bp):
ACCAAAGTCTTCTCTAATTTTCAATTCTTAGTAATTTCCCTAAAACATAATTATAAATTTAAATT
TATTAACGGTATCAAAATCCGTAATTATAACTTTA
Found at i:47715 original size:70 final size:70
Alignment explanation
Indices: 47602--47737 Score: 238
Period size: 70 Copynumber: 1.9 Consensus size: 70
47592 CCCCAATGCC
*
47602 CACACTGCCTAAATATTTACAAACACTCACTCAATAATAAGCTCTTAATCATCAGTACTAGTTAA
1 CACACTGCCTAAATATTTACAAACACTAACTCAATAATAAGCTCTTAATCATCAGTACTAGTTAA
47667 AACAA
66 AACAA
*
47672 CACACTGCCTAAATATTTACAAACACTAACTCAATACA-AAGCTCTTATTCATCAGTACTAGTTA
1 CACACTGCCTAAATATTTACAAACACTAACTCAATA-ATAAGCTCTTAATCATCAGTACTAGTTA
47736 AA
65 AA
47738 TATCAATATT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
70 62 0.98
71 1 0.02
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.28
Consensus pattern (70 bp):
CACACTGCCTAAATATTTACAAACACTAACTCAATAATAAGCTCTTAATCATCAGTACTAGTTAA
AACAA
Found at i:49353 original size:59 final size:59
Alignment explanation
Indices: 49247--49358 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 59
49237 TTGAGTGATA
* *
49247 ATTTTGTAACTTTAATAGTTGAAGGACTCAACAAAGCAATACTCTATAGTCAGAGGATT
1 ATTTTGTAACTTTAATAGATGAAGGACTCAACAAAGCAACACTCTATAGTCAGAGGATT
* *
49306 ATTTTGTAACTTTTAATAGAT-AAGAGACT-AATAAAGTAACA-TCCTATAGTCAG
1 ATTTTGTAAC-TTTAATAGATGAAG-GACTCAACAAAGCAACACT-CTATAGTCAG
49359 GGGACCATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
58 1 0.02
59 32 0.70
60 13 0.28
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (59 bp):
ATTTTGTAACTTTAATAGATGAAGGACTCAACAAAGCAACACTCTATAGTCAGAGGATT
Found at i:50278 original size:30 final size:29
Alignment explanation
Indices: 50195--50294 Score: 139
Period size: 29 Copynumber: 3.4 Consensus size: 29
50185 AAATTTTTTG
50195 AATATTTTAGGTACCTATTTTGACCAAAA
1 AATATTTTAGGTACCTATTTTGACCAAAA
*
50224 AATACTTTAGGTACCTATTTTGACCAAAA
1 AATATTTTAGGTACCTATTTTGACCAAAA
* *
50253 ATATAATTTTGGGTACTTA-TTTGACCAAAA
1 A-AT-ATTTTAGGTACCTATTTTGACCAAAA
*
50283 AATACTTTAGGT
1 AATATTTTAGGT
50295 TCTTAAAATA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
28 7 0.11
29 31 0.49
30 14 0.22
31 11 0.17
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (29 bp):
AATATTTTAGGTACCTATTTTGACCAAAA
Found at i:58026 original size:3 final size:3
Alignment explanation
Indices: 58020--58063 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
58010 TTAATAGAAT
* *
58020 TAA TAA TAA TTAA TAA TAA TAA TAA TAAA TAA TTA TTA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
58064 CATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 31 0.84
4 6 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:58032 original size:19 final size:17
Alignment explanation
Indices: 58008--58051 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
57998 CTGAAAAAAA
58008 AATTAATAGAATTAATAAT
1 AATTAATA-AA-TAATAAT
58027 AATTAAT-AATAATAAT
1 AATTAATAAATAATAAT
*
58043 AATAAATAA
1 AATTAATAA
58052 TTATTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 13 0.57
17 3 0.13
19 7 0.30
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AATTAATAAATAATAAT
Found at i:58041 original size:16 final size:16
Alignment explanation
Indices: 58020--58063 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
58010 TTAATAGAAT
*
58020 TAATAATAATTAATAA
1 TAATAATAATAAATAA
58036 TAATAATAATAAATAA
1 TAATAATAATAAATAA
* *
58052 TTATTATAATAA
1 TAATAATAATAA
58064 CATATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAATAATAAATAA
Found at i:58052 original size:19 final size:19
Alignment explanation
Indices: 58020--58063 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
58010 TTAATAGAAT
*
58020 TAATAATAATTAATAATAA
1 TAATAATAAATAATAATAA
* *
58039 TAATAATAAATAATTATTA
1 TAATAATAAATAATAATAA
58058 TAATAA
1 TAATAA
58064 CATATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATAATAAATAATAATAA
Found at i:58604 original size:36 final size:36
Alignment explanation
Indices: 58547--58662 Score: 151
Period size: 36 Copynumber: 3.2 Consensus size: 36
58537 ATTTAAAGGT
*
58547 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
58583 TTTGTTTCAAGAGTAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
58619 TGTGTTACATGAGAAACTATCTCAAGAGAGACAGAAC
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA-AAA
58656 TTTGTTT
1 TTTGTTT
58663 GAGCAAATTA
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
36 60 0.90
37 7 0.10
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:58678 original size:36 final size:34
Alignment explanation
Indices: 58565--58679 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 34
58555 AAGGGAAACT
*
58565 GTCTCAAGAGAGACAAAATTTGTTTCAAGAGTAATT-
1 GTCTCAAGAGAGACAAAATTTGTTT---GAGAAATTA
* *
58601 GTCTCAAGAGAGACAAAATGTGTTACATGAGAAACTA
1 GTCTCAAGAGAGACAAAATTTGTT---TGAGAAATTA
*
58638 -TCTCAAGAGAGACAGAACTTTGTTTGAGCAAATTA
1 GTCTCAAGAGAGACA-AAATTTGTTTGAG-AAATTA
58673 GTCTCAA
1 GTCTCAA
58680 ACGAGACGAC
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
34 4 0.06
35 5 0.08
36 49 0.74
37 7 0.11
39 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (34 bp):
GTCTCAAGAGAGACAAAATTTGTTTGAGAAATTA
Found at i:59121 original size:106 final size:106
Alignment explanation
Indices: 58929--59690 Score: 1301
Period size: 106 Copynumber: 7.2 Consensus size: 106
58919 TGGATGGCCA
* *
58929 CTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* * *
58994 GCTCCGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCC
66 GCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
* * * *
59035 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGTTGTGCAGTTAAAATTG
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
*
59100 GCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
66 GCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
59141 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* *
59206 GCTTTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
66 GCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
59247 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
*
59312 GCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCC
66 GCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
* *
59353 CTTCGTCGTGAAGTTGAACTTGCGTTGTCAT-GAGTCCAATATCATTCGCTGTGAAGTTAAAATT
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
*
59417 GGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCC
65 GGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
*
59459 CTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
*
59524 GCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCC
66 GCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
* * *
59565 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCTAATATCCTTCGTTGTGAAGTTGAAGTTG
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* *
59630 GCTTTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
66 GCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
59671 CTTCGTCGTGAAGTTGAACT
1 CTTCGTCGTGAAGTTGAACT
59691 CTACTCTCGA
Statistics
Matches: 623, Mismatches: 31, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
105 1 0.00
106 621 1.00
107 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
GCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
Found at i:61049 original size:9 final size:8
Alignment explanation
Indices: 61035--61106 Score: 50
Period size: 7 Copynumber: 9.6 Consensus size: 8
61025 TTTGCATGTA
61035 CTTTTTGT
1 CTTTTTGT
61043 CCTTTTT-T
1 -CTTTTTGT
61051 CTTTTTGT
1 CTTTTTGT
*
61059 TTTTTTG-
1 CTTTTTGT
*
61066 CTCTTT-T
1 CTTTTTGT
61073 C-TTTTGT
1 CTTTTTGT
*
61080 TTTTTTG-
1 CTTTTTGT
61087 CTTCTTT-T
1 CTT-TTTGT
61095 CTTTTT-T
1 CTTTTTGT
61102 CTTTT
1 CTTTT
61107 GTTTTTGTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
6 3 0.06
7 23 0.45
8 19 0.37
9 6 0.12
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (8 bp):
CTTTTTGT
Found at i:61061 original size:22 final size:22
Alignment explanation
Indices: 61036--61108 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
61026 TTGCATGTAC
*
61036 TTTTTGTCCTTTTTTCTTTTTG
1 TTTTTGTGCTTTTTTCTTTTTG
* *
61058 TTTTTTTGCTCTTTTC-TTTTG
1 TTTTTGTGCTTTTTTCTTTTTG
*
61079 TTTTTTTGCTTCTTTTCTTTTT-
1 TTTTTGTGCTT-TTTTCTTTTTG
61101 TCTTTTGT
1 T-TTTTGT
61109 TTTTGTTATG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
21 15 0.35
22 19 0.44
23 9 0.21
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (22 bp):
TTTTTGTGCTTTTTTCTTTTTG
Found at i:61076 original size:29 final size:29
Alignment explanation
Indices: 61044--61112 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
61034 ACTTTTTGTC
*
61044 CTTTT-TTCTTTTTG-TTTTTTTGCTCTTTT
1 CTTTTGTT-TTTTTGCTTCTTTT-CTCTTTT
*
61073 CTTTTGTTTTTTTGCTTCTTTTCTTTTTT
1 CTTTTGTTTTTTTGCTTCTTTTCTCTTTT
61102 CTTTTGTTTTT
1 CTTTTGTTTTT
61113 GTTATGATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 28 0.78
30 8 0.22
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (29 bp):
CTTTTGTTTTTTTGCTTCTTTTCTCTTTT
Found at i:61077 original size:21 final size:22
Alignment explanation
Indices: 61047--61107 Score: 90
Period size: 21 Copynumber: 2.8 Consensus size: 22
61037 TTTTGTCCTT
61047 TTTTCTTTTTGTTTTTTTGC-TC
1 TTTTC-TTTTGTTTTTTTGCTTC
61069 TTTTCTTTTGTTTTTTTGCTTC
1 TTTTCTTTTGTTTTTTTGCTTC
*
61091 TTTTCTTTT-TTCTTTTG
1 TTTTCTTTTGTTTTTTTG
61108 TTTTTGTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
21 21 0.57
22 16 0.43
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (22 bp):
TTTTCTTTTGTTTTTTTGCTTC
Done.