Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2169
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: 170354
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
File 2 of 2
Found at i:106363 original size:33 final size:34
Alignment explanation
Indices: 106309--106397 Score: 121
Period size: 32 Copynumber: 2.7 Consensus size: 34
106299 TATTTTATAA
* *
106309 TTATAT-TTAAAATATTATATATTTATATAATTTT
1 TTATATATTAATATATT-TATATTTATATAAATTT
106343 TTATATATTAATA-ATTTATA-TTATATAAATTT
1 TTATATATTAATATATTTATATTTATATAAATTT
*
106375 TTATATATTTATATATTTATATT
1 TTATATATTAATATATTTATATT
106398 ATTTTTTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
32 23 0.47
33 11 0.22
34 10 0.20
35 5 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TTATATATTAATATATTTATATTTATATAAATTT
Found at i:106415 original size:21 final size:19
Alignment explanation
Indices: 106271--106427 Score: 64
Period size: 18 Copynumber: 8.3 Consensus size: 19
106261 TAAGTTGATC
*
106271 TATTA-ATTTAT-ATATTTA
1 TATTATATTTATAAT-TTTT
*
106289 TATTAT-TTT-TTATTTTAT
1 TATTATATTTATAATTTT-T
* * * *
106307 AATTATATTTAAAATATTA
1 TATTATATTTATAATTTTT
106326 TA-TAT-TTATATAATTTTT
1 TATTATATT-TATAATTTTT
*
106344 TA-TATATTAATAATTTATAT
1 TATTATATTTATAATTT-T-T
* * *
106364 TATATAAATTT-TTATATATT
1 TAT-TATATTTATAAT-TTTT
106384 TA-TATATTTATATTATTTTTT
1 TATTATATTTATA--A-TTTTT
106405 TATTATA-TTATAATTTTT
1 TATTATATTTATAATTTTT
106423 TATTA
1 TATTA
106428 CTTTTCGTAT
Statistics
Matches: 104, Mismatches: 18, Indels: 34
0.67 0.12 0.22
Matches are distributed among these distances:
17 6 0.06
18 53 0.51
19 9 0.09
20 10 0.10
21 15 0.14
22 11 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTATATTTATAATTTTT
Found at i:106426 original size:18 final size:17
Alignment explanation
Indices: 106334--106427 Score: 69
Period size: 18 Copynumber: 5.8 Consensus size: 17
106324 TATATATTTA
106334 TATAATTTTT-TATATAT
1 TATAATTTTTAT-TATAT
*
106351 TAATAATTTATATTATA-
1 T-ATAATTTTTATTATAT
106368 TA-AATTTTTA-TATAT
1 TATAATTTTTATTATAT
* *
106383 T-T-ATATAT-TTATAT
1 TATAATTTTTATTATAT
*
106397 TAT-TTTTTTATTATAT
1 TATAATTTTTATTATAT
106413 TATAATTTTTTATTA
1 TATAA-TTTTTATTA
106428 CTTTTCGTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
14 14 0.23
15 12 0.20
16 10 0.17
17 2 0.03
18 21 0.35
19 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATAATTTTTATTATAT
Found at i:107514 original size:20 final size:20
Alignment explanation
Indices: 107473--107514 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
107463 ATAAAGATTA
*
107473 ATCTTTCTTAAAAATTAATG
1 ATCTTTCTTAAAAAATAATG
* *
107493 ATCTTTTTTAAAAAATATTG
1 ATCTTTCTTAAAAAATAATG
107513 AT
1 AT
107515 TTGCTCTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (20 bp):
ATCTTTCTTAAAAAATAATG
Found at i:107637 original size:19 final size:18
Alignment explanation
Indices: 107604--107640 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
107594 TTCTCAAATA
*
107604 TTAAACCAAAATTTCAAT
1 TTAAACAAAAATTTCAAT
107622 TTAAACAAATAATTTCAAT
1 TTAAACAAA-AATTTCAAT
107641 ATTCATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAAACAAAAATTTCAAT
Found at i:108495 original size:15 final size:15
Alignment explanation
Indices: 108475--108512 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
108465 TAAAAAATCG
108475 TTTTAAAAACTTATT
1 TTTTAAAAACTTATT
*
108490 TTTT-AAAATTTATT
1 TTTTAAAAACTTATT
*
108504 TTATAAAAA
1 TTTTAAAAA
108513 AACTTATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTAAAAACTTATT
Found at i:109779 original size:27 final size:26
Alignment explanation
Indices: 109693--109781 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 26
109683 TTTTAATTAA
109693 ATAAAATTATAATTAAT-AAAATTTAT
1 ATAAAATT-TAATTAATAAAAATTTAT
* * * *
109719 TTAAAA-ATATTTAATAAATAAATTTAA
1 ATAAAATTTAATTAAT-AA-AAATTTAT
109746 AGTTAAAATTTAATTATATAAAAATTTAT
1 A--TAAAATTTAATTA-ATAAAAATTTAT
109775 ATAAAAT
1 ATAAAAT
109782 ATAAGATAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
24 7 0.15
26 6 0.12
27 13 0.27
29 13 0.27
30 7 0.15
31 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (26 bp):
ATAAAATTTAATTAATAAAAATTTAT
Found at i:110128 original size:23 final size:24
Alignment explanation
Indices: 110100--110148 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
110090 AACACGACAT
110100 AAACACAACATAAAAAATAAT-TA
1 AAACACAACATAAAAAATAATATA
*
110123 AAACACAGCATAAAAAATAATATA
1 AAACACAACATAAAAAATAATATA
110147 AA
1 AA
110149 TATGATACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.69, C:0.12, G:0.02, T:0.16
Consensus pattern (24 bp):
AAACACAACATAAAAAATAATATA
Found at i:110767 original size:8 final size:8
Alignment explanation
Indices: 110756--110811 Score: 71
Period size: 8 Copynumber: 7.2 Consensus size: 8
110746 GAATATATAA
110756 TTTTTTTC
1 TTTTTTTC
110764 -TTTTTTC
1 TTTTTTTC
110771 TTTTTTTC
1 TTTTTTTC
**
110779 -TCCTTTC
1 TTTTTTTC
110786 TTTTTTTC
1 TTTTTTTC
110794 TTTTTTTC
1 TTTTTTTC
*
110802 TTTCTTTC
1 TTTTTTTC
110810 TT
1 TT
110812 GGCAAAAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
7 12 0.29
8 29 0.71
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Found at i:110776 original size:15 final size:15
Alignment explanation
Indices: 110756--110811 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
110746 GAATATATAA
110756 TTTTTTTCTTTTTTC
1 TTTTTTTCTTTTTTC
**
110771 TTTTTTTCTCCTTTC
1 TTTTTTTCTTTTTTC
110786 TTTTTTTCTTTTTTTC
1 TTTTTTTC-TTTTTTC
*
110802 TTTCTTTCTT
1 TTTTTTTCTT
110812 GGCAAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
15 23 0.66
16 12 0.34
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTTCTTTTTTC
Found at i:110794 original size:23 final size:24
Alignment explanation
Indices: 110760--110811 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
110750 ATATAATTTT
110760 TTTC-TTTTTTCTTTTTTTC-TCC
1 TTTCTTTTTTTCTTTTTTTCTTCC
*
110782 TTTCTTTTTTTCTTTTTTTCTTTC
1 TTTCTTTTTTTCTTTTTTTCTTCC
110806 TTTCTT
1 TTTCTT
110812 GGCAAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 4 0.15
23 15 0.56
24 8 0.30
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTCTTTTTTTCTTTTTTTCTTCC
Found at i:111661 original size:17 final size:18
Alignment explanation
Indices: 111639--111681 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
111629 ACTTGAAAAT
*
111639 AATATACACACA-ATACA
1 AATATACACACATATAAA
* *
111656 AATATATATACATATAAA
1 AATATACACACATATAAA
111674 AATATACA
1 AATATACA
111682 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (18 bp):
AATATACACACATATAAA
Found at i:111691 original size:17 final size:17
Alignment explanation
Indices: 111639--111691 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
111629 ACTTGAAAAT
* * *
111639 AATATACACACAATACA
1 AATATACATAAAATAAA
* *
111656 AATATATATACATATAAA
1 AATATACATA-AAATAAA
111674 AATATACATAAAATAAA
1 AATATACATAAAATAAA
111691 A
1 A
111692 CAAATTATTC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.25
Consensus pattern (17 bp):
AATATACATAAAATAAA
Found at i:112762 original size:2 final size:2
Alignment explanation
Indices: 112755--112780 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
112745 TTATTCTATC
112755 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
112781 TCATACAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116791 original size:2 final size:2
Alignment explanation
Indices: 116780--116815 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
116770 TGATAGTATC
116780 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
116816 GAACATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:117295 original size:3 final size:3
Alignment explanation
Indices: 117281--117315 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
117271 ACAATTATCA
* *
117281 AAT AAT AGT AAT AAT AAT AAT AAT AAT AGT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
117316 AAAATTCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:118627 original size:44 final size:44
Alignment explanation
Indices: 118577--118666 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
118567 TGATTACATC
118577 AGTCTATGCCCTATTATGTGGATTTAGTCATTTGTTGGTTTTGA
1 AGTCTATGCCCTATTATGTGGATTTAGTCATTTGTTGGTTTTGA
118621 AGTCTATGCCCTATTATGTGGATTTAGTCATTTGTTGGTTTTGA
1 AGTCTATGCCCTATTATGTGGATTTAGTCATTTGTTGGTTTTGA
118665 AG
1 AG
118667 AGAGAGTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.19, C:0.11, G:0.23, T:0.47
Consensus pattern (44 bp):
AGTCTATGCCCTATTATGTGGATTTAGTCATTTGTTGGTTTTGA
Found at i:124859 original size:10 final size:10
Alignment explanation
Indices: 124825--124859 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
124815 TTGTATAGTA
124825 TTTATGTTATT
1 TTTA-GTTATT
*
124836 TTTTGTTATT
1 TTTAGTTATT
124846 TTTAGTTATT
1 TTTAGTTATT
124856 TTTA
1 TTTA
124860 TCTTATTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 19 0.86
11 3 0.14
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (10 bp):
TTTAGTTATT
Found at i:126549 original size:12 final size:13
Alignment explanation
Indices: 126522--126561 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
126512 TTAAAATATT
126522 ATTTTAATAATTAA
1 ATTTTAATAA-TAA
126536 ATTTTAATAA-AA
1 ATTTTAATAATAA
*
126548 ATTTTATTAATAA
1 ATTTTAATAATAA
126561 A
1 A
126562 CAATAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 11 0.46
13 3 0.12
14 10 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTTAATAATAA
Found at i:126931 original size:26 final size:26
Alignment explanation
Indices: 126900--126951 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
126890 ATCTTACCCA
* *
126900 ACTTTCAAAAGTTGGCATGGGAAGAT
1 ACTTTCAAAAGTTGGCAAGAGAAGAT
*
126926 ACTTTCAAAGGTTGGCAAGAGAAGAT
1 ACTTTCAAAAGTTGGCAAGAGAAGAT
126952 GGAGCCGCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.25
Consensus pattern (26 bp):
ACTTTCAAAAGTTGGCAAGAGAAGAT
Found at i:127175 original size:15 final size:15
Alignment explanation
Indices: 127129--127176 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
127119 TAAAAAAATT
*
127129 AAAAATTTAAATTTA
1 AAAAATTTAAATTCA
*
127144 AAATAAATTAAATTCA
1 AAA-AATTTAAATTCA
*
127160 AAAAATTTAAACTCA
1 AAAAATTTAAATTCA
127175 AA
1 AA
127177 CATAATGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAAATTTAAATTCA
Found at i:127360 original size:21 final size:20
Alignment explanation
Indices: 127335--127403 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
127325 AAAAATGAGT
127335 AATTTTTAAGAATAAATTGA
1 AATTTTTAAGAATAAATTGA
* *
127355 AGATTTTTTA-AATATAATTGGTT
1 A-ATTTTTAAGAATA-AATT-G-A
*
127378 AACTTTTAAGAATAAA-TGA
1 AATTTTTAAGAATAAATTGA
127397 AATTTTT
1 AATTTTT
127404 TTAAATAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
19 6 0.16
20 6 0.16
21 12 0.32
22 9 0.24
23 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.45
Consensus pattern (20 bp):
AATTTTTAAGAATAAATTGA
Found at i:129525 original size:21 final size:21
Alignment explanation
Indices: 129501--129543 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
129491 GACTCTGTTT
*
129501 CCTCATCATCTGAGCCGGTAA
1 CCTCATCATCTGAGCCCGTAA
*
129522 CCTCTTCATCTGAGCCCGTAA
1 CCTCATCATCTGAGCCCGTAA
129543 C
1 C
129544 TTCCTTTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.37, G:0.16, T:0.26
Consensus pattern (21 bp):
CCTCATCATCTGAGCCCGTAA
Found at i:134447 original size:27 final size:28
Alignment explanation
Indices: 134414--134491 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 28
134404 AATTATTATT
134414 TATTAATAAAAAATAATATTATTTA-AA
1 TATTAATAAAAAATAATATTATTTATAA
* *
134441 TATTAATATAAAATAATATTTTTTATAA
1 TATTAATAAAAAATAATATTATTTATAA
* * *
134469 TA-TAACAAATAATAATATAATTT
1 TATTAATAAAAAATAATATTATTT
134492 TTTTAGTTGA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 39 0.91
28 4 0.09
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (28 bp):
TATTAATAAAAAATAATATTATTTATAA
Found at i:135087 original size:21 final size:20
Alignment explanation
Indices: 135051--135099 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
135041 TACAATACTT
135051 ATATAATAAAAATAATTAAA
1 ATATAATAAAAATAATTAAA
* *
135071 ATTTAATAAAAATTAATTTAA
1 ATATAATAAAAA-TAATTAAA
135092 ATATAATA
1 ATATAATA
135100 TGATAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATAATAAAAATAATTAAA
Found at i:135445 original size:2 final size:2
Alignment explanation
Indices: 135440--135473 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
135430 AAAAATAAAT
135440 TA TA TA TA -A TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
135474 CATGTTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:136795 original size:302 final size:302
Alignment explanation
Indices: 136243--136803 Score: 806
Period size: 302 Copynumber: 1.9 Consensus size: 302
136233 GCTTTGTAGT
*
136243 TTTTAGTTATACAAATAAAACTTTTTTATAGTTTAATTTTTGTTGATTTTAAATGAAAAATTATA
1 TTTTAGTTATACAAATAAAACTTTTTTATAGTTCAATTTTTGTTGATTTTAAATGAAAAATTATA
* * *
136308 AACTGTGTTGATATCTTCTTTAGATGACTTATGAAAAATTATTCTGTCGGACCTAAAAAAAGACA
66 AACTATGTTGATATCTTCTTTAGATGACGTATGAAAAATTATTCTGTCAGACCTAAAAAAAGACA
* * * *
136373 AAAATTAAAAGGTGTCGAAGTTTGAAACTCCAAGCGCACTTTGATGCAAACTCTAAATGTACTTC
131 AAAATTAAAAGGTATCGAAGTTTGAAACTCCAAGCGCACTTTGATGCAAACTATAAACGTACTTA
* * *
136438 GATACTTAAGTCAGATAAAATCTAAGAAAATGATATTGAAACTAATGAAAAATATGATAAATATA
196 GACACTTAAATCAGATAAAATCTAAGAAAATGATATTGAAACTAATGAAAAATATGAGAAATATA
136503 AGTGGTGACAAAAGGAGGCTTTTTTTCCTTATGCTTTTATAG
261 AGTGGTGACAAAAGGAGGCTTTTTTTCCTTATGCTTTTATAG
*
136545 TTTTAGTTATACAAATAAAACTTTTTTATCA-TTCAATTTTTGTTGTTTTTAAATGAAAAATTAT
1 TTTTAGTTATACAAATAAAACTTTTTTAT-AGTTCAATTTTTGTTGATTTTAAATGAAAAATTAT
* * * *
136609 AAATTATGTTGATATCTTCTTTAGATGGCAGT-TGAAAAATTATTCTGTCAGACCTGAAAACAGA
65 AAACTATGTTGATATCTTCTTTAGATGAC-GTATGAAAAATTATTCTGTCAGACCTAAAAAAAGA
* * * * * * * * * *
136673 TAGAAGTTGAAAGGTATCGAAGTTTGAGACTCTAAGCGCATTTTGATGTC-GATTATGAACGTAC
129 CAAAAATTAAAAGGTATCGAAGTTTGAAACTCCAAGCGCACTTTGATG-CAAACTATAAACGTAC
* *
136737 TTAGACACTTAAATCAGATAAGATCTAAGAAAATGATATT-AGAACTAATGAGAAATATGAGAAA
193 TTAGACACTTAAATCAGATAAAATCTAAGAAAATGATATTGA-AACTAATGAAAAATATGAGAAA
136801 TAT
257 TAT
136804 GAAAAAGAAC
Statistics
Matches: 227, Mismatches: 28, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
301 1 0.00
302 223 0.98
303 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (302 bp):
TTTTAGTTATACAAATAAAACTTTTTTATAGTTCAATTTTTGTTGATTTTAAATGAAAAATTATA
AACTATGTTGATATCTTCTTTAGATGACGTATGAAAAATTATTCTGTCAGACCTAAAAAAAGACA
AAAATTAAAAGGTATCGAAGTTTGAAACTCCAAGCGCACTTTGATGCAAACTATAAACGTACTTA
GACACTTAAATCAGATAAAATCTAAGAAAATGATATTGAAACTAATGAAAAATATGAGAAATATA
AGTGGTGACAAAAGGAGGCTTTTTTTCCTTATGCTTTTATAG
Found at i:137053 original size:20 final size:20
Alignment explanation
Indices: 137028--137071 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
137018 AAGTCACAGA
137028 GATTTCTATTAGTTGACTAT
1 GATTTCTATTAGTTGACTAT
137048 GATTTCTATTAGTTGACTAT
1 GATTTCTATTAGTTGACTAT
137068 GATT
1 GATT
137072 CAATGTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.50
Consensus pattern (20 bp):
GATTTCTATTAGTTGACTAT
Found at i:138580 original size:19 final size:21
Alignment explanation
Indices: 138550--138591 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
138540 TTAATTCAAT
138550 TAAAAATATATAAAATT-AAA
1 TAAAAATATATAAAATTGAAA
*
138570 TAAAAAT-TATAATATTGAAA
1 TAAAAATATATAAAATTGAAA
138590 TA
1 TA
138592 CAATTATAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
TAAAAATATATAAAATTGAAA
Found at i:143383 original size:40 final size:39
Alignment explanation
Indices: 143335--143412 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
143325 GGTAAAAAGA
* *
143335 CATAATGTATCGATACATTGTAGAATATAACGATACATT
1 CATAATGTATCGATACATTGAAAAATATAACGATACATT
* * *
143374 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATAACGATACAT
143413 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATAACGATACATT
Found at i:143388 original size:20 final size:20
Alignment explanation
Indices: 143338--143412 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
143328 AAAAAGACAT
*
143338 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
* *
143357 GAATATAACGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
143378 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
143398 AATGTATCGATACAT
1 AATGTATCGATACAT
143413 CAGGGTATGA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:145882 original size:29 final size:29
Alignment explanation
Indices: 145825--145882 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
145815 TTATATTATT
* *
145825 ATTTAATAATAAAAATATTTTTAATTTAA
1 ATTTAATAATAAAAATATTATAAATTTAA
*
145854 ATTTAATTATAAAAATA-TATAAATATTAA
1 ATTTAATAATAAAAATATTATAAAT-TTAA
145883 TAATATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTTAATAATAAAAATATTATAAATTTAA
Found at i:147052 original size:78 final size:78
Alignment explanation
Indices: 146919--147245 Score: 193
Period size: 78 Copynumber: 4.2 Consensus size: 78
146909 CTAAATGCTT
* * * * * * *
146919 TTAATGGACATGCATCGACATGAAAGTACTCATGTGACCTTAGAGACTTGCTTTTGCTATAGC-A
1 TTAATGGATATGTATCGACATGAAAGTACTCATATAACCCTAAAGACTTGCTTTTGATATA-CTA
* * *
146983 TTATCTGACTAAAC
65 TTACCTAAATAAAC
* * *
146997 TTAATGGATATGTATGGACATGAAAGTATTCATATAACCCTAAAGATTTAG-TTTTGATATACTA
1 TTAATGGATATGTATCGACATGAAAGTACTCATATAACCCTAAAGACTT-GCTTTTGATATACTA
*
147061 TTACCTAAATAATC
65 TTACCTAAATAAAC
* * * * * * * *
147075 TTAATAGATATGTATCGACATAAAAGTAATTATCTGACTCTAAAAACTTAG-TTTCACTG-TA-A
1 TTAATGGATATGTATCGACATGAAAGTACTCATATAACCCTAAAGACTT-GCTTT---TGATATA
* *
147137 C-ATTACCTTAATGAAC
62 CTATTACCTAAATAAAC
* * * * * * * * * * ** *
147153 TTAATGAACATGTATGGATATGAAAGCACACACATGA-TCTGAAAAACTTAATTTTAATATACTA
1 TTAATGGATATGTATCGACATGAAAGTACTCATATAACCCT-AAAGACTTGCTTTTGATATACTA
*
147217 TTACCTAAAT-GAC
65 TTACCTAAATAAAC
147230 TTAATGGATATGTATC
1 TTAATGGATATGTATC
147246 AAAATAAGAA
Statistics
Matches: 193, Mismatches: 46, Indels: 21
0.74 0.18 0.08
Matches are distributed among these distances:
75 1 0.01
76 2 0.01
77 21 0.11
78 162 0.84
79 3 0.02
80 2 0.01
81 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (78 bp):
TTAATGGATATGTATCGACATGAAAGTACTCATATAACCCTAAAGACTTGCTTTTGATATACTAT
TACCTAAATAAAC
Found at i:148031 original size:14 final size:14
Alignment explanation
Indices: 148012--148039 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
148002 TCCCAAATGT
148012 TTTAAAAATTTTAA
1 TTTAAAAATTTTAA
148026 TTTAAAAATTTTAA
1 TTTAAAAATTTTAA
148040 ATAATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAAAAATTTTAA
Found at i:150077 original size:32 final size:32
Alignment explanation
Indices: 150014--150077 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
150004 TAATTCAATT
* *
150014 TCAAAATAACTCAAACTTAAAATATTTTAAAA
1 TCAAAATAACTCAAACTTAAAATAATATAAAA
*
150046 TCAAAATAA-TCTTAACTTAAAATAATATAAAA
1 TCAAAATAACTC-AAACTTAAAATAATATAAAA
150078 CTAAAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 2 0.07
32 26 0.93
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (32 bp):
TCAAAATAACTCAAACTTAAAATAATATAAAA
Found at i:150079 original size:17 final size:17
Alignment explanation
Indices: 150026--150089 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 17
150016 AAAATAACTC
* *
150026 AAACTTAAAATATTTTA
1 AAACTTAAAATAATATA
* *
150043 AAA-TCAAAATAATCT-
1 AAACTTAAAATAATATA
*
150058 TAACTTAAAATAATATA
1 AAACTTAAAATAATATA
150075 AAAC-TAAAATTAATA
1 AAACTTAAAA-TAATA
150090 ATACTACTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
15 2 0.05
16 24 0.65
17 11 0.30
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (17 bp):
AAACTTAAAATAATATA
Found at i:153006 original size:3 final size:3
Alignment explanation
Indices: 152998--153062 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
152988 AATTCTTTTG
* *
152998 TTC TTC TTC CTC TTC TTC TTC TTC TTC TTA TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
153046 TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TT
153063 TGTACCTTCT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:156060 original size:2 final size:2
Alignment explanation
Indices: 156053--156081 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
156043 ATCACCTTCG
156053 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
156082 TGCTACTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:157522 original size:15 final size:15
Alignment explanation
Indices: 157466--157522 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
157456 AATAAAAATT
157466 TATATAAATATAAAA
1 TATATAAATATAAAA
* *
157481 TATTTTAA-ATAAAA
1 TATATAAATATAAAA
*
157495 T-TATGACATATAAAA
1 TATAT-AAATATAAAA
*
157510 TATATAAACATAA
1 TATATAAATATAA
157523 TGTAAATTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
13 2 0.06
14 8 0.25
15 19 0.59
16 3 0.09
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (15 bp):
TATATAAATATAAAA
Found at i:157735 original size:21 final size:22
Alignment explanation
Indices: 157711--157756 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
157701 TTCAATATTT
157711 ATTTAT-ATATTTA-TTTTTAAA
1 ATTTATAAT-TTTATTTTTTAAA
*
157732 ATTTTTAATTTTATTTTTTAAA
1 ATTTATAATTTTATTTTTTAAA
157754 ATT
1 ATT
157757 AATTTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTATAATTTTATTTTTTAAA
Found at i:157970 original size:22 final size:22
Alignment explanation
Indices: 157932--158023 Score: 59
Period size: 22 Copynumber: 4.2 Consensus size: 22
157922 AAGAATTTAA
*
157932 TATTAAATTTTAA-ATTTAAATT
1 TATTAAA-TATAATATTTAAATT
*
157954 TATTAAATATAATATTTTAA-T
1 TATTAAATATAATATTTAAATT
* *
157975 TA-TAATTAT-ATGAATT-AATT
1 TATTAAATATAAT-ATTTAAATT
* *
157995 AAATTAAATATCATATTTAAATAT
1 -TATTAAATATAATATTTAAAT-T
158019 TATTA
1 TATTA
158024 TTTTAATTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
19 4 0.07
20 10 0.19
21 8 0.15
22 22 0.41
23 9 0.17
24 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (22 bp):
TATTAAATATAATATTTAAATT
Found at i:158032 original size:41 final size:42
Alignment explanation
Indices: 157955--158033 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 42
157945 ATTTAAATTT
*
157955 ATTAAATATAATATTTTAATTATAATTATATGAATTAATTAA
1 ATTAAATATAATATTTTAAATATAATTATATGAATTAATTAA
* * * *
157997 ATTAAATATCATA-TTTAAATATTATTATTTTAATTAA
1 ATTAAATATAATATTTTAAATATAATTATATGAATTAA
158034 GAAGAAACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
41 20 0.62
42 12 0.38
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (42 bp):
ATTAAATATAATATTTTAAATATAATTATATGAATTAATTAA
Found at i:158378 original size:13 final size:12
Alignment explanation
Indices: 158340--158379 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
158330 ATTTGATAAT
158340 TAATA-TATTTA
1 TAATATTATTTA
158351 TAAT-TTATTTA
1 TAATATTATTTA
158362 -AATATTATATTA
1 TAATATTAT-TTA
158374 TAATAT
1 TAATAT
158380 AATTACATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 3 0.12
11 14 0.56
12 3 0.12
13 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TAATATTATTTA
Found at i:158948 original size:19 final size:19
Alignment explanation
Indices: 158905--158952 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
158895 ATTTATATGA
* *
158905 AATAAGTTATTAATATTTT
1 AATAATTTATTAATATTAT
158924 AA-AATTTATATAATA-TAT
1 AATAATTTAT-TAATATTAT
158942 AATAATTTATT
1 AATAATTTATT
158953 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
AATAATTTATTAATATTAT
Found at i:162348 original size:26 final size:26
Alignment explanation
Indices: 162296--162350 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
162286 ATTTTGGTTT
* * *
162296 TATATATATATTAATTTTTTAATATA
1 TATATATATATTAATTTATCAAAATA
162322 TATATATATATCT-ATTTATCAAAATA
1 TATATATATAT-TAATTTATCAAAATA
162348 TAT
1 TAT
162351 GCAAGTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (26 bp):
TATATATATATTAATTTATCAAAATA
Found at i:163428 original size:26 final size:25
Alignment explanation
Indices: 163393--163444 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
163383 TAACTTAATG
163393 TTAAATCTTGAATTTCAAACCAAAC
1 TTAAATCTTGAATTTCAAACCAAAC
* *
163418 TTAAAGTCTTGAATTTTAAACCGAAC
1 TTAAA-TCTTGAATTTCAAACCAAAC
163444 T
1 T
163445 CAAGCTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (25 bp):
TTAAATCTTGAATTTCAAACCAAAC
Found at i:163566 original size:2 final size:2
Alignment explanation
Indices: 163555--163599 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
163545 TATGGTATTA
* *
163555 AT AT AG AT AT AT AT AT AT AT AT AT AT CT 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
163597 AT A
1 AT A
163600 CACACACACG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:165625 original size:14 final size:14
Alignment explanation
Indices: 165602--165634 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
165592 GTAATATTTA
*
165602 AATATATTAAAATT
1 AATATTTTAAAATT
165616 AATATTTTAAAATT
1 AATATTTTAAAATT
165630 -ATATT
1 AATATT
165635 CATATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTTTAAAATT
Found at i:167782 original size:23 final size:23
Alignment explanation
Indices: 167756--167813 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 23
167746 CCTAAATTCT
*
167756 ATTACAAATTATTTTTAAAATTA
1 ATTACAAATTATTATTAAAATTA
* *
167779 ATTA-ATATAAATTATTAAAATTA
1 ATTACAAAT-TATTATTAAAATTA
* *
167802 ATTTCAATTTAT
1 ATTACAAATTAT
167814 ATAATTTTTA
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
22 3 0.12
23 21 0.81
24 2 0.08
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTACAAATTATTATTAAAATTA
Done.