Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003280.1 Hibiscus syriacus cultivar Beakdansim tig00006900_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: 88157
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3266 original size:62 final size:64
Alignment explanation
Indices: 3189--3405 Score: 223
Period size: 62 Copynumber: 3.5 Consensus size: 64
3179 TTGAAGGTGT
* **
3189 ATCGATGCATTAGTAGTGCATCGATGC-TCTTTTAA-AATTCAAACATCGAATGCAATT-CATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCATTAATAA-TCAAACATCGAATGCAATTGCATGC
* ** *
3251 ATCGATGCATAAGTAGTGCATCGATGCATCCATTAATAATGAAACATCGAATGCAATTGGGTGT
1 ATCGATGCATAAGTAGTGCATCGATGCATCCATTAATAATCAAACATCGAATGCAATTGCATGC
* ** * * **
3315 ATCGATGCATTAAG-AGTGCATCGATGTATCCCAGCAATAAT--AACATCGAATAC-CTTTTATG
1 ATCGATGCA-TAAGTAGTGCATCGATGCAT-CCATTAATAATCAAACATCGAATGCAATTGCATG
3376 C
64 C
*
3377 ATCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
3406 ACCTTCATTA
Statistics
Matches: 131, Mismatches: 18, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
61 3 0.02
62 53 0.40
63 35 0.27
64 27 0.21
65 13 0.10
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCATTAATAATCAAACATCGAATGCAATTGCATGC
Found at i:3335 original size:64 final size:64
Alignment explanation
Indices: 3184--3345 Score: 208
Period size: 64 Copynumber: 2.6 Consensus size: 64
3174 ATTGTTTGAA
**
3184 GGTGTATCGATGCATT-AGTAGTGCATCGATGC-TCTTTTAAAATTCAAACATCGAATGCAATT
1 GGTGTATCGATGCATTAAGTAGTGCATCGATGCATCCATTAAAATTCAAACATCGAATGCAATT
** * *
3246 CATGCATCGATGCA-TAAGTAGTGCATCGATGCATCCATTAATAA-TGAAACATCGAATGCAATT
1 GGTGTATCGATGCATTAAGTAGTGCATCGATGCATCCATTAA-AATTCAAACATCGAATGCAATT
*
3309 GGGTGTATCGATGCATTAAG-AGTGCATCGATGTATCC
1 -GGTGTATCGATGCATTAAGTAGTGCATCGATGCATCC
3346 CAGCAATAAT
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
61 1 0.01
62 27 0.32
63 24 0.28
64 29 0.34
65 4 0.05
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (64 bp):
GGTGTATCGATGCATTAAGTAGTGCATCGATGCATCCATTAAAATTCAAACATCGAATGCAATT
Found at i:3721 original size:12 final size:12
Alignment explanation
Indices: 3703--3738 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3693 TATATATGTT
3703 CATGTGATATGA
1 CATGTGATATGA
*
3715 TATGTGATATGA
1 CATGTGATATGA
*
3727 CCTGTGATATGA
1 CATGTGATATGA
3739 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:3901 original size:15 final size:15
Alignment explanation
Indices: 3883--3960 Score: 147
Period size: 15 Copynumber: 5.2 Consensus size: 15
3873 GAGGGTATAA
*
3883 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGATG
3898 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
3913 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
3928 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
3943 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
3958 TAG
1 TAG
3961 GAGTCCTACG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 62 1.00
ACGTcount: A:0.14, C:0.21, G:0.33, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:9862 original size:64 final size:64
Alignment explanation
Indices: 9794--10014 Score: 268
Period size: 64 Copynumber: 3.5 Consensus size: 64
9784 TTGAAGGTGT
* **
9794 ATCGATGCATTAGTAGTGCATCGATGCA-CTCTTTTAA-AATTTAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAA-TTAAACATCGAATGCAATTCATG
9857 C
64 C
* **
9858 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATTAAACATCGAATGCAATTCATGC
* * * * ** *
9922 ATCGATGCATAAGGAGTGTATCGATGCATCCCAGTAATAA-TAATACATCGAATACCTTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATTAA-ACATCGAATGCAATTCATGC
*
9986 ATCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
10015 ACCTTCATTA
Statistics
Matches: 136, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
63 2 0.01
64 131 0.96
65 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATTAAACATCGAATGCAATTCATGC
Found at i:10341 original size:12 final size:12
Alignment explanation
Indices: 10324--10357 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
10314 TATATGTTCA
10324 TGTGATATGA-T
1 TGTGATATGACT
10335 CTGTGATATGACT
1 -TGTGATATGACT
10348 TGTGATATGA
1 TGTGATATGA
10358 GAACATGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 20 0.95
13 1 0.05
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.41
Consensus pattern (12 bp):
TGTGATATGACT
Found at i:10519 original size:15 final size:15
Alignment explanation
Indices: 10501--10578 Score: 147
Period size: 15 Copynumber: 5.2 Consensus size: 15
10491 GAGGGTATAA
*
10501 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGATG
10516 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
10531 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
10546 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
10561 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
10576 TAG
1 TAG
10579 GAGTCCTACG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 62 1.00
ACGTcount: A:0.14, C:0.21, G:0.33, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:17332 original size:39 final size:39
Alignment explanation
Indices: 17269--17356 Score: 140
Period size: 39 Copynumber: 2.2 Consensus size: 39
17259 TTTAGTATAT
* *
17269 ATATAATATATAATATATAGTTTTTGAAAACATTTTGAAA
1 ATAT-ATATATAATAAATAATTTTTGAAAACATTTTGAAA
17309 ATATATATATAATAAATAATTTTTGAAAACATTTTGAAA
1 ATATATATATAATAAATAATTTTTGAAAACATTTTGAAA
*
17348 AAATATATA
1 ATATATATA
17357 ATTTTTAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 41 0.91
40 4 0.09
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (39 bp):
ATATATATATAATAAATAATTTTTGAAAACATTTTGAAA
Found at i:17381 original size:30 final size:30
Alignment explanation
Indices: 17300--17383 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 30
17290 TTTTGAAAAC
* *
17300 ATTTTGAAAATATA-TATAT--AATAAATA
1 ATTTTTAAAATATATTATATAAAATATATA
* *
17327 ATTTTTGAAAACAT-TT-TGAAAAAATATATA
1 ATTTTT-AAAATATATTAT-ATAAAATATATA
17357 ATTTTTAAAATATATTATATAAAATAT
1 ATTTTTAAAATATATTATATAAAATAT
17384 TTATGTATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
27 6 0.14
28 8 0.18
29 6 0.14
30 23 0.52
31 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (30 bp):
ATTTTTAAAATATATTATATAAAATATATA
Found at i:17402 original size:5 final size:5
Alignment explanation
Indices: 17389--17465 Score: 61
Period size: 5 Copynumber: 15.2 Consensus size: 5
17379 AATATTTATG
* * *
17389 TATTA TATTT TATTATT TATTA TATTT TCTTT TCATTT TA-TT TATTT
1 TATTT TATTT TA-T-TT TATTT TATTT TATTT T-ATTT TATTT TATTT
*
17436 TA-TT TATTT TCTTT T-TTT TATATT TATTT T
1 TATTT TATTT TATTT TATTT TAT-TT TATTT T
17466 GGTCCAAAAG
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
4 12 0.20
5 32 0.54
6 11 0.19
7 4 0.07
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (5 bp):
TATTT
Found at i:17409 original size:17 final size:17
Alignment explanation
Indices: 17384--17443 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
17374 TATAAAATAT
*
17384 TTATGTATTATATTTTA
1 TTATTTATTATATTTTA
*
17401 TTATTTATTATATTTTC
1 TTATTTATTATATTTTA
* * *
17418 TT-TTCATTTTATTTATT
1 TTATTTATTATATTT-TA
17435 TTATTTATT
1 TTATTTATT
17444 TTCTTTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
16 10 0.29
17 20 0.57
18 5 0.14
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (17 bp):
TTATTTATTATATTTTA
Found at i:17429 original size:25 final size:24
Alignment explanation
Indices: 17401--17465 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 24
17391 TTATATTTTA
* *
17401 TTATTTATTATATTTTCTTTTCATT
1 TTATTTATTTTATTTTATTTTC-TT
17426 TTATTTATTTTA-TTTATTTTCTT
1 TTATTTATTTTATTTTATTTTCTT
*
17449 TTTTTTATATTTATTTT
1 TTATTTAT-TTTATTTT
17466 GGTCCAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.26
24 12 0.34
25 14 0.40
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (24 bp):
TTATTTATTTTATTTTATTTTCTT
Found at i:17437 original size:9 final size:9
Alignment explanation
Indices: 17389--17456 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
17379 AATATTTATG
17389 TATTATATTT
1 TATT-TATTT
17399 TA-TTA-TT
1 TATTTATTT
17406 TATTATATTT
1 TATT-TATTT
*
17416 TCTTTTCATTT
1 T-ATTT-ATTT
17427 TATTTATTT
1 TATTTATTT
17436 TATTTATTT
1 TATTTATTT
* *
17445 TCTTTTTTT
1 TATTTATTT
17454 TAT
1 TAT
17457 ATTTATTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
7 4 0.08
8 3 0.06
9 25 0.52
10 9 0.19
11 7 0.15
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (9 bp):
TATTTATTT
Found at i:17443 original size:29 final size:29
Alignment explanation
Indices: 17394--17465 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
17384 TTATGTATTA
17394 TATTTTA-TTA-TTTATTATATTTTCTTT
1 TATTTTATTTATTTTATTATATTTTCTTT
17421 TCATTTTATTTATTTTATT-TATTTTCTTT
1 T-ATTTTATTTATTTTATTATATTTTCTTT
*
17450 TTTTTATATTTATTTT
1 TATTT-TATTTATTTT
17466 GGTCCAAAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
27 1 0.03
28 9 0.22
29 24 0.60
30 6 0.15
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.76
Consensus pattern (29 bp):
TATTTTATTTATTTTATTATATTTTCTTT
Found at i:18473 original size:15 final size:15
Alignment explanation
Indices: 18453--18487 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18443 CCTTTTTATT
*
18453 TTTTTATTTATTGAC
1 TTTTTATTTATTAAC
*
18468 TTTTTATTTTTTAAC
1 TTTTTATTTATTAAC
18483 TTTTT
1 TTTTT
18488 TTAAATTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTTATTTATTAAC
Found at i:21326 original size:24 final size:24
Alignment explanation
Indices: 21299--21398 Score: 103
Period size: 24 Copynumber: 4.2 Consensus size: 24
21289 TATATCAAAA
* *
21299 ATCAAAACATAATTCAGGTCAAGT
1 ATCAAATCAGAATTCAGGTCAAGT
* * *
21323 ATCATATCA-AAATCTATGTCAAGT
1 ATCAAATCAGAATTC-AGGTCAAGT
* *
21347 ATCAGATCAGAATCCAGGTCAAGT
1 ATCAAATCAGAATTCAGGTCAAGT
* *
21371 ATCAAATCAGAATCCAAGTCAAGT
1 ATCAAATCAGAATTCAGGTCAAGT
21395 ATCA
1 ATCA
21399 TAACAAAATT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
23 4 0.06
24 57 0.89
25 3 0.05
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (24 bp):
ATCAAATCAGAATTCAGGTCAAGT
Found at i:26265 original size:24 final size:24
Alignment explanation
Indices: 26238--26346 Score: 121
Period size: 24 Copynumber: 4.5 Consensus size: 24
26228 TATATCAAAA
* * *
26238 ATCAAAACATAATTCAGGTCAAGT
1 ATCAAATCAAAATCCAGGTCAAGT
* *
26262 ATCATATCAAAATCCATGTCAAGT
1 ATCAAATCAAAATCCAGGTCAAGT
* *
26286 ATCAGATCAGAATCCAGGTCAAGT
1 ATCAAATCAAAATCCAGGTCAAGT
* *
26310 ATCAAATCAGAATCCATGTCAAGT
1 ATCAAATCAAAATCCAGGTCAAGT
26334 ATCATAA-CAAAAT
1 ATCA-AATCAAAAT
26347 TAAAATCGAA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
24 71 0.97
25 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (24 bp):
ATCAAATCAAAATCCAGGTCAAGT
Found at i:32060 original size:17 final size:17
Alignment explanation
Indices: 32040--32081 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
32030 TGTATCGCCG
32040 ACAAAATTTTACTATTC
1 ACAAAATTTTACTATTC
*
32057 ACAAAAATTTACTATTC
1 ACAAAATTTTACTATTC
32074 ACATAAAT
1 ACA-AAAT
32082 AGTAACCCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.36
Consensus pattern (17 bp):
ACAAAATTTTACTATTC
Found at i:35113 original size:32 final size:32
Alignment explanation
Indices: 35067--35502 Score: 252
Period size: 32 Copynumber: 14.7 Consensus size: 32
35057 TATTGTAGTT
*
35067 GTATAGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
35099 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
35122 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
35153 GTATGGATTGATTTATTTT--A-AA---A-TA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
35178 -TA--GATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
35207 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
35230 -TATGGATTGATTTATTTTAAATAAATTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
35261 GTATGAATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
35293 GTATGGGTTGATTTATTTTAAAATATGGATTGATTTA
1 GTATGGATTGATTTATTTT-AAATA---ATTTA-TTA
* * * *
35330 TTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTA
1 GTA-TGGA-TTG-AT--TTA------TTTTAAATAATTTATTA
35373 GTATGGATTGATTTATTTT-AA-AA--TA-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
35399 G-A---ATTGATTTATTTTAAAA---------
1 GTATGGATTGATTTATTTTAAATAATTTATTA
35418 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
35449 GTATAGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
35481 GTATAGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
35503 ATATAGATTG
Statistics
Matches: 321, Mismatches: 21, Indels: 124
0.69 0.05 0.27
Matches are distributed among these distances:
19 1 0.00
22 71 0.22
23 10 0.03
24 3 0.01
25 7 0.02
26 8 0.02
27 1 0.00
28 9 0.03
29 6 0.02
30 5 0.02
31 10 0.03
32 142 0.44
33 5 0.02
36 4 0.01
37 4 0.01
38 3 0.01
39 3 0.01
40 4 0.01
41 3 0.01
42 4 0.01
43 5 0.02
44 4 0.01
47 5 0.02
48 4 0.01
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:35125 original size:22 final size:22
Alignment explanation
Indices: 35100--35142 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
35090 AATTTATTAG
35100 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
35122 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
35143 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:35141 original size:54 final size:54
Alignment explanation
Indices: 35072--35694 Score: 555
Period size: 54 Copynumber: 11.5 Consensus size: 54
35062 TAGTTGTATA
35072 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
*
35126 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATA
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
35180 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
* *
35234 GATTGATTTATTTTAAATAAATTATTAGTATGAATTGATTTATTTT-AAATA--
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
* * * * * * * ***
35285 -ATTTATTTGTATGGGTTGATTTATTT-TAAAATATGGATTGATTTATTATTGTAGTTGTATG
1 GATTGA-TT-TAT--TTTAAATAATTTAT-TAGTATGGATTGATTTA-T-TT-TA-AAATATG
35346 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
* ** ** * ** * * * *
35400 AATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAGTATA
1 GATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATATG
* * *
35454 GATTGATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATA
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
* * * * * *
35508 GATTGATTTATTATT--GTAGTTGTA-T-GTATTGATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTATT-TTAAATAATT-TATTAGTATGGATTGA-TTT--AT--TTTA-AAATATG
* * * * ***
35566 GATTGATTTATTTT-AA-AA--TA-T-GGATTGATTTA-TTATTGTAGTTGTATG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAATATG
35614 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
35668 GATTGATTTATTTTAAATAATTTATTA
1 GATTGATTTATTTTAAATAATTTATTA
35695 TTGTAGTTGT
Statistics
Matches: 464, Mismatches: 69, Indels: 72
0.77 0.11 0.12
Matches are distributed among these distances:
48 23 0.05
49 2 0.00
50 8 0.02
51 2 0.00
52 19 0.04
53 26 0.06
54 292 0.63
55 25 0.05
56 7 0.02
57 9 0.02
58 39 0.08
59 3 0.01
60 3 0.01
61 2 0.00
62 4 0.01
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
Found at i:35183 original size:22 final size:22
Alignment explanation
Indices: 35158--35250 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
35148 TATTAGTATG
35158 GATTGATTTATTTTAAAATATA
1 GATTGATTTATTTTAAAATATA
35180 GATTGATTTATTTTAAATAATTTATTA
1 GATTGATTTATTTT-AA-AA--TA-TA
* *
35207 GTATGGATTGATTTATTTTAAAATATG
1 G-ATTGA-T---TTATTTTAAAATATA
35234 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
35251 TAAATTATTA
Statistics
Matches: 58, Mismatches: 3, Indels: 20
0.72 0.04 0.25
Matches are distributed among these distances:
22 24 0.41
23 2 0.03
24 2 0.03
25 1 0.02
26 6 0.10
27 5 0.09
28 6 0.10
29 1 0.02
30 2 0.03
31 2 0.03
32 7 0.12
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.52
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATA
Found at i:35399 original size:22 final size:22
Alignment explanation
Indices: 35374--35438 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
35364 AATTTATTAG
35374 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
35396 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
35418 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
35439 TAATTTATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:35415 original size:188 final size:188
Alignment explanation
Indices: 35073--35662 Score: 818
Period size: 188 Copynumber: 3.1 Consensus size: 188
35063 AGTTGTATAG
*
35073 ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
1 ATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--
* * *
35138 TTAAATAATTTA-TTAGTATGGATTGATTTATTTT-AA-AA--TA-TAG-ATTGATTTATTTTAA
64 TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA-TTT--
* * *
35196 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAAATTATTA
121 AT--TTTA-AAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
35261 GTATGA
183 GTATGA
*
35267 ATTGATTTATTTTAAATAATTTATTTGTATGGGTTGATTTATTTTAAAATATGGATTGATTTATT
1 ATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
35332 ATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT
66 ATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT
*
35397 ATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTAT-A
131 ATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGA
* *
35454 GATTGATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATAGATTGATTTAT
1 -ATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
*
35519 TATTGTAGTTGTATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
65 TATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*** *
35584 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGG
130 TATGGATTGATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGA
35647 ATTGATTTATTTTAAA
1 ATTGATTTATTTTAAA
35663 ATATGGATTG
Statistics
Matches: 365, Mismatches: 18, Indels: 28
0.89 0.04 0.07
Matches are distributed among these distances:
187 1 0.00
188 216 0.59
189 9 0.02
190 6 0.02
191 4 0.01
192 55 0.15
193 6 0.02
194 68 0.19
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (188 bp):
ATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
ATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT
ATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGA
Found at i:35446 original size:14 final size:14
Alignment explanation
Indices: 35427--35480 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
35417 ATATGGATTG
35427 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
35441 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
35459 ATTTATTTTAAATA
1 ATTTATTTTAAATA
35473 ATTTATTT
1 ATTTATTT
35481 GTATAGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:35464 original size:18 final size:18
Alignment explanation
Indices: 35441--35520 Score: 60
Period size: 18 Copynumber: 4.4 Consensus size: 18
35431 ATTTTAAATA
35441 ATTTATTAGTATAGATTG
1 ATTTATTAGTATAGATTG
* *
35459 ATTTATT--T-TA-AATA
1 ATTTATTAGTATAGATTG
*
35473 ATTTATTTGTATAGATTG
1 ATTTATTAGTATAGATTG
*
35491 ATTTATTTTAAAATATAGATTG
1 ATTTA--TT--AGTATAGATTG
35513 ATTTATTA
1 ATTTATTA
35521 TTGTAGTTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
14 9 0.19
15 2 0.04
16 2 0.04
17 2 0.04
18 15 0.31
20 4 0.08
22 14 0.29
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATAGATTG
Found at i:35578 original size:22 final size:23
Alignment explanation
Indices: 35553--35626 Score: 71
Period size: 22 Copynumber: 3.2 Consensus size: 23
35543 ATTTTAAATA
35553 ATTTAT-TAGTATGGATTGATTT
1 ATTTATATAGTATGGATTGATTT
* *
35575 ATTT-TAAAATATGGATTGATTT
1 ATTTATATAGTATGGATTGATTT
* *
35597 ATTATTGTAGTTGTATGGATTGATTT
1 A-T-TTATA-TAGTATGGATTGATTT
35623 ATTT
1 ATTT
35627 TAAATAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
21 1 0.02
22 19 0.45
23 1 0.02
24 4 0.10
25 3 0.07
26 14 0.33
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (23 bp):
ATTTATATAGTATGGATTGATTT
Found at i:35592 original size:80 final size:79
Alignment explanation
Indices: 35396--35679 Score: 426
Period size: 80 Copynumber: 3.5 Consensus size: 79
35386 TATTTTAAAA
* *
35396 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAGTATAGATTGA
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT-GTAT-GATTGA
*
35460 TTTATTTTAAATAATTTATTTG
58 TTTATTTTAAATAATTTATTAG
* *
35482 TATAGATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTGTATGTATTGATTTATTT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATG-ATTGATTTATTT
35547 TAAATAATTTATTAG
65 TAAATAATTTATTAG
35562 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTAT-GATTGATTTATTT
35627 TAAATAATTTATTAG
65 TAAATAATTTATTAG
35642 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT
35680 TTAAATAATT
Statistics
Matches: 188, Mismatches: 7, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
79 1 0.01
80 147 0.78
81 3 0.02
82 2 0.01
84 2 0.01
86 33 0.18
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (79 bp):
TATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGATTGATTTATTTT
AAATAATTTATTAG
Found at i:35667 original size:22 final size:22
Alignment explanation
Indices: 35642--35684 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
35632 AATTTATTAG
35642 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
35664 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
35685 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:35744 original size:31 final size:31
Alignment explanation
Indices: 35709--35767 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
35699 AGTTGTATGG
* * *
35709 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAATATTGCAAAACTAAA
35740 ATTATTTAAATCTCAATATTGCAAAACT
1 ATTATTTAAATCTCAATATTGCAAAACT
35768 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAATATTGCAAAACTAAA
Found at i:38469 original size:3 final size:3
Alignment explanation
Indices: 38463--38593 Score: 167
Period size: 3 Copynumber: 43.7 Consensus size: 3
38453 TTTTTACCCA
* *
38463 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT CCA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * *
38511 TAT TAT AAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT CCA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* *
38556 TAT TAT AAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
38594 AAAATATTAA
Statistics
Matches: 110, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.02
3 106 0.96
4 2 0.02
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:38522 original size:45 final size:45
Alignment explanation
Indices: 38466--38593 Score: 247
Period size: 45 Copynumber: 2.8 Consensus size: 45
38456 TTACCCATAT
*
38466 TATTATTATTATTATTATTATCATTATTATTATTATTATTATCCA
1 TATTATAATTATTATTATTATCATTATTATTATTATTATTATCCA
38511 TATTATAATTATTATTATTATCATTATTATTATTATTATTATCCA
1 TATTATAATTATTATTATTATCATTATTATTATTATTATTATCCA
38556 TATTATAATTATTATTATTATCATTATTATTATTATTA
1 TATTATAATTATTATTATTATCATTATTATTATTATTA
38594 AAAATATTAA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (45 bp):
TATTATAATTATTATTATTATCATTATTATTATTATTATTATCCA
Found at i:40044 original size:13 final size:13
Alignment explanation
Indices: 40028--40067 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
40018 ATATAATAAA
40028 TAAATATTTATTT
1 TAAATATTTATTT
*
40041 TAAATAAATTATTT
1 TAAAT-ATTTATTT
40055 T-AATATTTATTT
1 TAAATATTTATTT
40067 T
1 T
40068 TTAATATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:51428 original size:14 final size:14
Alignment explanation
Indices: 51410--51444 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
51400 TATTATGCTT
51410 GAAAAAAAGAAAGAA
1 GAAAAAAAGAAA-AA
51425 -AAAAAAAGAAAAA
1 GAAAAAAAGAAAAA
51438 GAAAAAA
1 GAAAAAA
51445 TGGGGGGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 17 0.89
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
GAAAAAAAGAAAAA
Found at i:51794 original size:16 final size:18
Alignment explanation
Indices: 51775--51821 Score: 71
Period size: 16 Copynumber: 2.7 Consensus size: 18
51765 CTATTTCAAG
51775 TTCAATTTATTTG-AG-A
1 TTCAATTTATTTGTAGAA
51791 TTCAATTTATTTGTAGAAA
1 TTCAATTTATTTGTAG-AA
51810 TTCAATTTATTT
1 TTCAATTTATTT
51822 TTATATATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.46
17 2 0.07
19 13 0.46
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (18 bp):
TTCAATTTATTTGTAGAA
Found at i:52948 original size:83 final size:82
Alignment explanation
Indices: 52592--53213 Score: 1163
Period size: 82 Copynumber: 7.5 Consensus size: 82
52582 GAAAGAGACT
*
52592 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTGGACAGAACAATCATTGAAT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
52657 TTAGAAGATGAATTTGC
66 TTAGAAGATGAATTTGC
52674 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
*
52739 TTAGAAGATAAATTTGC
66 TTAGAAGATGAATTTGC
52756 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
*
52821 TTAGAAGATAAATTTGC
66 TTAGAAGATGAATTTGC
52838 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-CAATCATTGAA
52903 TTTAGAAGATGAATTTGC
65 TTTAGAAGATGAATTTGC
52921 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
52986 TTAGAAGATGAATTTGC
66 TTAGAAGATGAATTTGC
*
53003 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-CAATCATTGAA
53068 TTTAGAAGATGAATTTGC
65 TTTAGAAGATGAATTTGC
*
53086 CAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-CAATCATTGAA
53151 TTTAGAAGATGAATTTGC
65 TTTAGAAGATGAATTTGC
*
53169 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
53214 TGGTAAGAAC
Statistics
Matches: 530, Mismatches: 8, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
82 296 0.56
83 234 0.44
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (82 bp):
CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
TTAGAAGATGAATTTGC
Found at i:52987 original size:165 final size:165
Alignment explanation
Indices: 52592--53213 Score: 1174
Period size: 165 Copynumber: 3.8 Consensus size: 165
52582 GAAAGAGACT
*
52592 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTGGACAGAACAATCATTGAAT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
52657 TTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
66 TTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
*
52722 CAGAA-CAATCATTGAATTTAGAAGATAAATTTGC
131 CAGAACCAATCATTGAATTTAGAAGATGAATTTGC
52756 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
*
52821 TTAGAAGATAAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
66 TTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
52886 CAGAACCAATCATTGAATTTAGAAGATGAATTTGC
131 CAGAACCAATCATTGAATTTAGAAGATGAATTTGC
52921 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
*
52986 TTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAA
66 TTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
53051 CAGAACCAATCATTGAATTTAGAAGATGAATTTGC
131 CAGAACCAATCATTGAATTTAGAAGATGAATTTGC
*
53086 CAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-CAATCATTGAA
*
53151 TTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTT
65 TTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
53214 TGGTAAGAAC
Statistics
Matches: 449, Mismatches: 7, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
164 133 0.30
165 243 0.54
166 73 0.16
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (165 bp):
CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
TTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
CAGAACCAATCATTGAATTTAGAAGATGAATTTGC
Found at i:54154 original size:113 final size:113
Alignment explanation
Indices: 53946--54617 Score: 1215
Period size: 113 Copynumber: 6.0 Consensus size: 113
53936 CAAAGATTCA
* *
53946 AATCTATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
54011 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
54059 AATCCATCACTTGATGGATTAT-TTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATTATCTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
54123 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
54172 AATCCATCACTTGATGGATTAT-TTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATTATCTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
54236 AAGGAATAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
54285 AATCCATCATTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
54350 AGGAATAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
54398 AATCCATCATTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
54463 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
54511 AATCCATCATTTGATGGATTATCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
54575 AGAAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACTTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
54618 GCATAATTCT
Statistics
Matches: 546, Mismatches: 11, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
112 76 0.14
113 466 0.85
114 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (113 bp):
AATCCATCATTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:54953 original size:3 final size:3
Alignment explanation
Indices: 54938--55110 Score: 224
Period size: 3 Copynumber: 57.7 Consensus size: 3
54928 TTTTTACCCA
* *
54938 TAT TAT AAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
54986 TAT CCA- TAT TAT AAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT
1 TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
55031 TAT TAT CCA- TAT TAT AAT TAT TAT TAT TAT CAT TAT CAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
55076 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
55111 AAAATATTAA
Statistics
Matches: 146, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.01
3 142 0.97
4 2 0.01
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:55592 original size:20 final size:20
Alignment explanation
Indices: 55537--55595 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
55527 TGAAAAAAAA
55537 GAAAAAGAAAAAACAGAGACC
1 GAAAAA-AAAAAACAGAGACC
* *
55558 -AAAAGAAGAACACAGAG-CC
1 GAAAA-AAAAAAACAGAGACC
55577 GGAAAAAAAAAAACAGAGA
1 -GAAAAAAAAAAACAGAGA
55596 AATAATATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
19 2 0.07
20 23 0.77
21 5 0.17
ACGTcount: A:0.66, C:0.14, G:0.20, T:0.00
Consensus pattern (20 bp):
GAAAAAAAAAAACAGAGACC
Found at i:56563 original size:13 final size:13
Alignment explanation
Indices: 56547--56586 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
56537 ATATAATAAA
56547 TAAATATTTATTT
1 TAAATATTTATTT
*
56560 TAAATAAATTATTT
1 TAAAT-ATTTATTT
56574 T-AATATTTATTT
1 TAAATATTTATTT
56586 T
1 T
56587 TTAATATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:58555 original size:24 final size:24
Alignment explanation
Indices: 58530--58605 Score: 89
Period size: 24 Copynumber: 3.2 Consensus size: 24
58520 AAACGAAGAT
*
58530 ATCAGAAATCAAAACAGAATTCAT
1 ATCAGAAATCAAAACAGAATTCAG
* * *
58554 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
58578 ATAAGAAATCAGAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
58602 ATCA
1 ATCA
58606 TAAACCAGAT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:58623 original size:36 final size:36
Alignment explanation
Indices: 58574--58655 Score: 112
Period size: 36 Copynumber: 2.3 Consensus size: 36
58564 ATAACAGAAT
* * *
58574 CCAGATAAGAAATCAGAACATAATTCAGATC-ATAAA
1 CCAGATAAAAAATCAGAACAGAATTCAAATCGA-AAA
58610 CCAGATAAAAAATCAGAACAGAATTCAAATCGAAAA
1 CCAGATAAAAAATCAGAACAGAATTCAAATCGAAAA
*
58646 TCAGATAAAA
1 CCAGATAAAA
58656 CATTCATGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 40 0.98
37 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.11, T:0.17
Consensus pattern (36 bp):
CCAGATAAAAAATCAGAACAGAATTCAAATCGAAAA
Found at i:68886 original size:3 final size:3
Alignment explanation
Indices: 68873--68925 Score: 88
Period size: 3 Copynumber: 17.0 Consensus size: 3
68863 CTTTAAAAAC
68873 TTA TTA TTTA TTA TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
68920 TTA TTA
1 TTA TTA
68926 CATTTGTGCA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 42 0.88
4 6 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:71833 original size:30 final size:31
Alignment explanation
Indices: 71793--71852 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
71783 ACATGCTGCC
**
71793 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
71824 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
71853 TAAAAGCTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:74267 original size:5 final size:5
Alignment explanation
Indices: 74257--74283 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
74247 GAACTTCTCT
74257 TTTTC TTTTC TTTTC TTTTC TTTTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT
74284 CTTTTATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:76026 original size:20 final size:20
Alignment explanation
Indices: 75985--76026 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
75975 AATGAAATGC
*
75985 AAACATAATAAATGAATCTA
1 AAACATAATAAATGAATATA
*
76005 AAACATAGTAACAT-AATATA
1 AAACATAATAA-ATGAATATA
76025 AA
1 AA
76027 GCTAGTAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.24
Consensus pattern (20 bp):
AAACATAATAAATGAATATA
Found at i:76473 original size:23 final size:25
Alignment explanation
Indices: 76428--76479 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
76418 AATAAAGGGG
*
76428 ATAATAATATAAGTAATGAAAATAA
1 ATAATAATATAAGAAATGAAAATAA
*
76453 ATAATAATA-ATGAAATG-AAATAA
1 ATAATAATATAAGAAATGAAAATAA
76476 ATAA
1 ATAA
76480 AGGATAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
24 6 0.24
25 9 0.36
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (25 bp):
ATAATAATATAAGAAATGAAAATAA
Found at i:81713 original size:14 final size:13
Alignment explanation
Indices: 81694--81744 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
81684 TTTGAAATCT
81694 TTTTCTTTTTCTTC
1 TTTT-TTTTTCTTC
*
81708 TTTTCTTCTTCTTC
1 TTTT-TTTTTCTTC
*
81722 TTCTTTTTGTCTT-
1 TT-TTTTTTTCTTC
81735 TTTTTTTTTC
1 TTTTTTTTTC
81745 ATTTTTTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 7 0.22
13 2 0.06
14 21 0.66
15 2 0.06
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTTTTTTCTTC
Found at i:81716 original size:17 final size:16
Alignment explanation
Indices: 81693--81737 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
81683 TTTTGAAATC
81693 TTTTTCTTTTTCTTCT
1 TTTTTCTTTTTCTTCT
*
81709 TTTCTTCTTCTTCTTCT
1 TTT-TTCTTTTTCTTCT
81726 TTTTGTCTTTTT
1 TTTT-TCTTTTT
81738 TTTTTTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTTTCTTTTTCTTCT
Found at i:82061 original size:23 final size:25
Alignment explanation
Indices: 82016--82067 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
82006 AATAAAGGGG
*
82016 ATAATAATATAAGTAATGAAAATAA
1 ATAATAATATAAGAAATGAAAATAA
*
82041 ATAATAATA-ATGAAATG-AAATAA
1 ATAATAATATAAGAAATGAAAATAA
82064 ATAA
1 ATAA
82068 AGGATAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
24 6 0.24
25 9 0.36
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (25 bp):
ATAATAATATAAGAAATGAAAATAA
Done.