Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007722.1 Hibiscus syriacus cultivar Beakdansim tig00109958_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: 237237
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:517 original size:19 final size:19
Alignment explanation
Indices: 479--533 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
469 TTCGAGAATG
*
479 AAAATCGCAATGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
499 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
518 AAAATCGCAACGCGAA
1 AAAATCGCAACGCGAA
534 CCAAATCGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 20 0.67
20 10 0.33
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:568 original size:19 final size:19
Alignment explanation
Indices: 539--721 Score: 147
Period size: 19 Copynumber: 10.1 Consensus size: 19
529 GCGAACCAAA
*
539 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
558 TCACGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
577 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
596 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
616 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
632 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
649 TCGCGTTGCG---TTC---
1 TCGCGTTGCGATTTTCATT
* **
662 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
681 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
701 ATCTCGTTGCGA-TTTCATT
1 -TCGCGTTGCGATTTTCATT
720 TC
1 TC
722 AACCAAAAGA
Statistics
Matches: 133, Mismatches: 17, Indels: 29
0.74 0.09 0.16
Matches are distributed among these distances:
13 9 0.07
14 10 0.08
15 1 0.01
16 5 0.04
17 1 0.01
18 3 0.02
19 61 0.46
20 42 0.32
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:615 original size:39 final size:38
Alignment explanation
Indices: 539--628 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
529 GCGAACCAAA
*
539 TCGCATTGCGATTTTCATTTCACGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCACGTTGCGATTTTCATT
* *
577 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCAC-GTTGCGATTTTCATT
616 TCGCGTTGCGATT
1 TCGCGTTGCGATT
629 GTCTGGTCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 20 0.42
39 28 0.58
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCACGTTGCGATTTTCATT
Found at i:639 original size:39 final size:39
Alignment explanation
Indices: 562--639 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
552 TTCATTTCAC
* **
562 GTTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCG
1 GTTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCG
601 GTTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 GTTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
640 ATAGTCATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 33 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.27, T:0.45
Consensus pattern (39 bp):
GTTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCG
Found at i:678 original size:32 final size:33
Alignment explanation
Indices: 601--697 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 33
591 TTATTTCGCG
** * *
601 GTTGCGATTTTCATTTCGCGTTGCGATTGTCTG
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
*
634 GTCGCGATAGTCATTTCGCGTTGCG-TTCTCTC
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
666 GTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 GTTGCGATAGTCATTT-CGCGTTGCGATTCTC
698 ATTATCTCGT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
32 20 0.36
33 31 0.55
34 5 0.09
ACGTcount: A:0.10, C:0.24, G:0.26, T:0.40
Consensus pattern (33 bp):
GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
Found at i:699 original size:20 final size:19
Alignment explanation
Indices: 665--721 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
655 TGCGTTCTCT
*
665 CGTTGCGATAGTCATTTCCG
1 CGTTGCGAT-TTCATTTCCG
*
685 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATT-TCATT-TCCG
705 CGTTGCGATTTCATTTC
1 CGTTGCGATTTCATTTC
722 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 1 0.03
19 5 0.16
20 25 0.78
21 1 0.03
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTCATTTCCG
Found at i:4167 original size:13 final size:14
Alignment explanation
Indices: 4151--4185 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4141 ATTGTTTAAT
4151 TGATTTGT-AAAGG
1 TGATTTGTAAAAGG
*
4164 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
4178 TGATTTGT
1 TGATTTGT
4186 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:4193 original size:13 final size:14
Alignment explanation
Indices: 4138--4186 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
4128 TGCTTATTTT
*
4138 TTGA-TTGTTTAA-
1 TTGATTTGTTAAAG
4150 TTGATTTG-TAAAG
1 TTGATTTGTTAAAG
* *
4163 GTGATTTGTAAAAG
1 TTGATTTGTTAAAG
4177 TTGATTTGTT
1 TTGATTTGTT
4187 TAATTGATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 7 0.24
13 10 0.34
14 12 0.41
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (14 bp):
TTGATTTGTTAAAG
Found at i:4447 original size:33 final size:31
Alignment explanation
Indices: 4359--4518 Score: 184
Period size: 33 Copynumber: 5.1 Consensus size: 31
4349 GCGAAATTAA
4359 ATTCGCGTTGCGA-TTTCATTTCGCATTGCG
1 ATTCGCGTTGCGATTTTCATTTCGCATTGCG
4389 AATTCGCG-TGCGA-TTTCA-TTCGCATTGCG
1 -ATTCGCGTTGCGATTTTCATTTCGCATTGCG
*
4418 ATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
1 ATT--CGCGTTGCGATTTTCATTTCGCATTGCG
* **
4451 AAATTAGCGTTGCGATTTTCATTTCGCATTGTA
1 --ATTCGCGTTGCGATTTTCATTTCGCATTGCG
*
4484 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCG
1 A-T-TCGCGTTGCGATTTTCATTTCGCATTGCG
4517 AT
1 AT
4519 AGAAATTTCC
Statistics
Matches: 111, Mismatches: 9, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
28 3 0.03
29 11 0.10
30 13 0.12
31 13 0.12
32 7 0.06
33 61 0.55
35 3 0.03
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (31 bp):
ATTCGCGTTGCGATTTTCATTTCGCATTGCG
Found at i:4451 original size:19 final size:19
Alignment explanation
Indices: 4427--4518 Score: 60
Period size: 19 Copynumber: 5.4 Consensus size: 19
4417 GATTCCCTCG
4427 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
4446 TTGCGA-----AATTAGCG
1 TTGCGATTTTCATTTCGCA
4460 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
4479 TTG-TA-ATTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4493 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4512 TTGCGAT
1 TTGCGAT
4519 AGAAATTTCC
Statistics
Matches: 51, Mismatches: 12, Indels: 20
0.61 0.14 0.24
Matches are distributed among these distances:
14 14 0.27
15 1 0.02
16 7 0.14
17 7 0.14
18 1 0.02
19 21 0.41
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:4498 original size:66 final size:63
Alignment explanation
Indices: 4364--4517 Score: 231
Period size: 66 Copynumber: 2.4 Consensus size: 63
4354 ATTAAATTCG
* *
4364 CGTTGCGA-TTTCATTTCGCATTGCG-AATTCGCGTGCGATTTCATTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGAAATTAGCGTGCGATTTCATTCGCATTGCAATTCCCT
* *
4425 CGTTGCGATTTTCATTTCGCATTGCGAAATTAGCGTTGCGATTTTCATTTCGCATTGTAATTCTC
1 CGTTGCGATTTTCATTTCGCATTGCGAAATTAGCG-TGCGA-TTTCA-TTCGCATTGCAATTCCC
4490 T
63 T
4491 CGTTGCGATTTTCATTTCGCATTGCGA
1 CGTTGCGATTTTCATTTCGCATTGCGA
4518 TAGAAATTTC
Statistics
Matches: 84, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
61 8 0.10
62 17 0.20
63 7 0.08
64 5 0.06
65 5 0.06
66 42 0.50
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (63 bp):
CGTTGCGATTTTCATTTCGCATTGCGAAATTAGCGTGCGATTTCATTCGCATTGCAATTCCCT
Found at i:6821 original size:12 final size:12
Alignment explanation
Indices: 6804--6828 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6794 TCTTCGGGGA
6804 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6816 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6828 C
1 C
6829 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:7041 original size:23 final size:23
Alignment explanation
Indices: 7010--7054 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
7000 ATCATCAAAA
* *
7010 TCCGTGTATTGACCAATATCAAG
1 TCCGGGTATTGACCAAGATCAAG
7033 TCCGGGTATTGACCAAGATCAA
1 TCCGGGTATTGACCAAGATCAA
7055 ATTTCGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (23 bp):
TCCGGGTATTGACCAAGATCAAG
Found at i:8135 original size:20 final size:20
Alignment explanation
Indices: 8110--8187 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
8100 ATTCATTTGA
8110 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
8130 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
8150 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
8170 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
8188 CGCAATGCGA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:8229 original size:14 final size:14
Alignment explanation
Indices: 8210--8263 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
8200 TGAAATCGCA
8210 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
8224 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
8241 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
8257 TTGCGAT
1 TTGCGAT
8264 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:8242 original size:33 final size:33
Alignment explanation
Indices: 8205--8282 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
8195 CGAAATGAAA
***
8205 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
8238 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
8271 TCGCGTTGCGAT
1 TCGCATTGCGAT
8283 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:10305 original size:20 final size:19
Alignment explanation
Indices: 10270--10336 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
10260 GAAACTTAAA
10270 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
10289 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
10309 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
10328 ATCGCAACG
1 ATCGCAACG
10337 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:10344 original size:14 final size:14
Alignment explanation
Indices: 10325--10382 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
10315 ATGCGAAATG
10325 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
10339 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
10355 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
10371 AAAATCGCAACG
1 AAAATCGCAACG
10383 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:10367 original size:32 final size:33
Alignment explanation
Indices: 10309--10387 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
10299 GGAAATGGCT
*
10309 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
10342 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
10374 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
10388 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:10416 original size:19 final size:16
Alignment explanation
Indices: 10394--10489 Score: 65
Period size: 19 Copynumber: 5.7 Consensus size: 16
10384 GAAACACAAA
10394 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTT-ATT
*
10413 TCGCGTTGCGATTT-TG
1 TCGC-TTGCGATTTATT
10429 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTT-ATT
*
10445 TCGCGTTGCGATTT-TG
1 TCGC-TTGCGATTTATT
10461 TCG-TTGCGATTTTTATT
1 TCGCTTGCGA--TTTATT
10478 TCGCATTGCGAT
1 TCGC-TTGCGAT
10490 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 15 0.24
16 15 0.24
17 5 0.08
18 12 0.19
19 16 0.25
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (16 bp):
TCGCTTGCGATTTATT
Found at i:10435 original size:14 final size:14
Alignment explanation
Indices: 10416--10473 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
10406 TTTCATTTCG
10416 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
10430 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
10446 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
10462 CGTTGCGATTTT
1 CGTTGCGATTTT
10474 TATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:10446 original size:32 final size:33
Alignment explanation
Indices: 10399--10489 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
10389 ACAAATCGCA
10399 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
10432 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
10464 TTGCGATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
10490 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 32 0.58
33 23 0.42
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:10511 original size:20 final size:20
Alignment explanation
Indices: 10483--10526 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
10473 TTATTTCGCA
*
10483 TTGCGATAGCCATTTCCGTG
1 TTGCAATAGCCATTTCCGTG
* *
10503 TTGCAATAGTCATTTTCGTG
1 TTGCAATAGCCATTTCCGTG
10523 TTGC
1 TTGC
10527 GAAAGTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (20 bp):
TTGCAATAGCCATTTCCGTG
Found at i:11027 original size:18 final size:18
Alignment explanation
Indices: 11001--11045 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
10991 GTCGATCAGA
*
11001 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
11019 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
11037 TGATGGCTC
1 TGATGGCTC
11046 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:12385 original size:20 final size:20
Alignment explanation
Indices: 12360--12397 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12350 AATAGTTTCT
12360 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
12380 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
12398 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:12686 original size:22 final size:22
Alignment explanation
Indices: 12661--12704 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
12651 GATTTAGATA
12661 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
12683 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
12705 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:12914 original size:20 final size:20
Alignment explanation
Indices: 12889--12982 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
12879 GATTATGTAT
12889 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
12909 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
12929 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
12950 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
12970 TATCGCATTGCGA
1 TATCGCGTTGCGA
12983 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:12983 original size:20 final size:20
Alignment explanation
Indices: 12869--12983 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
12859 CGCTTTGAAA
*
12869 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
12890 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
12910 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
12930 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
12951 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
12971 ATCGCATTGCGAT
1 ATCGCATTGCGAT
12984 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:13002 original size:41 final size:41
Alignment explanation
Indices: 12911--13041 Score: 122
Period size: 41 Copynumber: 3.2 Consensus size: 41
12901 AAAGTCAGTA
* * * ** *
12911 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
12951 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
12993 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
13034 TCGCGTTG
1 TCGCGTTG
13042 TGATTTACTT
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 69 0.93
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:13016 original size:20 final size:20
Alignment explanation
Indices: 12972--13064 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
12962 ATAGTCAGTA
* **
12972 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
12993 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
13013 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
* *
13034 TCGCGTTGTGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
13054 TCGCATTGCGA
1 TCGCATTGCGA
13065 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:13047 original size:41 final size:41
Alignment explanation
Indices: 12972--13067 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
12962 ATAGTCAGTA
*
12972 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
*
13013 TCGCATTGCGAATTTCCCAATTCGCGTTGTGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
13054 TCGCATTGCGAATT
1 TCGCATTGCGAATT
13068 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:13427 original size:14 final size:13
Alignment explanation
Indices: 13408--13438 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
13398 AGTTTAGGGG
13408 TTTAGGGTTTATAA
1 TTTAGGGTTTAT-A
13422 TTTAGGGTTTATA
1 TTTAGGGTTTATA
13435 TTTA
1 TTTA
13439 TTATTTAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (13 bp):
TTTAGGGTTTATA
Found at i:14455 original size:2 final size:2
Alignment explanation
Indices: 14448--14495 Score: 66
Period size: 2 Copynumber: 25.0 Consensus size: 2
14438 CCATGCCCCA
14448 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14487 ACT AT AT AT
1 A-T AT AT AT
14496 TTTTTAGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.07
2 38 0.90
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18737 original size:19 final size:18
Alignment explanation
Indices: 18715--18760 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
18705 TTTATCTTAC
* *
18715 TTTTTGTTTTGTTTATAGG
1 TTTTTATTTTG-TTATACG
18734 TTTTTATTTTGTTATACG
1 TTTTTATTTTGTTATACG
18752 -TTTTATTTT
1 TTTTTATTTT
18761 AAATTTAGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.36
18 6 0.24
19 10 0.40
ACGTcount: A:0.13, C:0.02, G:0.13, T:0.72
Consensus pattern (18 bp):
TTTTTATTTTGTTATACG
Found at i:20851 original size:2 final size:2
Alignment explanation
Indices: 20844--20874 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20834 TACAGCAATC
20844 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 A
20875 CACACACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21288 original size:35 final size:35
Alignment explanation
Indices: 21242--21313 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
21232 ATAGTTGGGA
21242 AATGAGATTAGTTAGTAGTGCCTATTATTTGAACT
1 AATGAGATTAGTTAGTAGTGCCTATTATTTGAACT
*
21277 AATGAGATTAGTTAGTAGTGTCTATTATTTGAACT
1 AATGAGATTAGTTAGTAGTGCCTATTATTTGAACT
21312 AA
1 AA
21314 CTTATCACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.40
Consensus pattern (35 bp):
AATGAGATTAGTTAGTAGTGCCTATTATTTGAACT
Found at i:26027 original size:20 final size:20
Alignment explanation
Indices: 26002--26046 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
25992 TTTTTTAGGG
26002 TAAATTAT-GTATTTAGTATC
1 TAAATTATAGT-TTTAGTATC
26022 TAAATTATCAGTTTTAGTATC
1 TAAATTAT-AGTTTTAGTATC
26043 TAAA
1 TAAA
26047 CTTTCAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.35
21 13 0.57
22 2 0.09
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (20 bp):
TAAATTATAGTTTTAGTATC
Found at i:26039 original size:21 final size:21
Alignment explanation
Indices: 26013--26057 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
26003 AAATTATGTA
26013 TTTAGTATCTAAA-TTATCAGT
1 TTTAGTATCTAAACTT-TCAGT
26034 TTTAGTATCTAAACTTTCAGT
1 TTTAGTATCTAAACTTTCAGT
26055 TTT
1 TTT
26058 TTCAAAACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (21 bp):
TTTAGTATCTAAACTTTCAGT
Found at i:33142 original size:34 final size:36
Alignment explanation
Indices: 33083--33151 Score: 115
Period size: 34 Copynumber: 2.0 Consensus size: 36
33073 GCCATATGTA
*
33083 ATTATATCAACAAACTTAATTAATGACCATTTTGTG
1 ATTATATCAACAAACGTAATTAATGACCATTTTGTG
33119 ATTATATCAAC-AA-GTAATTAATGACCATTTTGT
1 ATTATATCAACAAACGTAATTAATGACCATTTTGT
33152 AACATTGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 19 0.59
35 2 0.06
36 11 0.34
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (36 bp):
ATTATATCAACAAACGTAATTAATGACCATTTTGTG
Found at i:54460 original size:39 final size:39
Alignment explanation
Indices: 54406--54482 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
54396 CATTGGATGA
* * *
54406 CTGGCTCAAGGACATGTCAGCAGTGGTATAGGGCATTTT
1 CTGGCTCAAGGACATGGCAGCAGTGGCATAGAGCATTTT
54445 CTGGCTCAAGGACATGGCAGCAGTGGCATAGAGCATTT
1 CTGGCTCAAGGACATGGCAGCAGTGGCATAGAGCATTT
54483 GATTTGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (39 bp):
CTGGCTCAAGGACATGGCAGCAGTGGCATAGAGCATTTT
Found at i:61992 original size:67 final size:68
Alignment explanation
Indices: 61836--62049 Score: 324
Period size: 68 Copynumber: 3.1 Consensus size: 68
61826 AATTACACTA
* *
61836 TATACACGTAAATGTTTGAAC-CTATAGAGGAGAGGAATAAATGGGAGTGCTCGTAATTGATCTA
1 TATA-ACGTAAATGTTTGAACTC-AAAGAGGAGAGGAAGAAATGGGAGTGCTCGTAATTGATCTA
*
61900 AAATC
64 GAATC
* *
61905 TATATCGTAAATGTTTGAACTCAAAGAGGAGAGAAAGAAATGGGAGTGCTCGTAA-TGATCTAGA
1 TATAACGTAAATGTTTGAACTCAAAGAGGAGAGGAAGAAATGGGAGTGCTCGTAATTGATCTAGA
61969 ATC
66 ATC
* *
61972 TATAACGTAAATGTTTGAACTCAAAGAGGAGAGGAAGAAATGAGAGTGCACGTAATTGATCTAGA
1 TATAACGTAAATGTTTGAACTCAAAGAGGAGAGGAAGAAATGGGAGTGCTCGTAATTGATCTAGA
62037 ATC
66 ATC
*
62040 TATGACGTAA
1 TATAACGTAA
62050 GAGAATTATT
Statistics
Matches: 133, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
67 62 0.47
68 66 0.50
69 5 0.04
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (68 bp):
TATAACGTAAATGTTTGAACTCAAAGAGGAGAGGAAGAAATGGGAGTGCTCGTAATTGATCTAGA
ATC
Found at i:63589 original size:20 final size:23
Alignment explanation
Indices: 63566--63611 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 23
63556 CTTTTTACAT
63566 AATTATGTT-AAATC-AGATT-A
1 AATTATGTTAAAATCAAGATTCA
63586 AATTATGTTAAAATCAAGATTCA
1 AATTATGTTAAAATCAAGATTCA
63609 AAT
1 AAT
63612 ATACACACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.39
21 5 0.22
22 5 0.22
23 4 0.17
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.37
Consensus pattern (23 bp):
AATTATGTTAAAATCAAGATTCA
Found at i:66144 original size:19 final size:19
Alignment explanation
Indices: 66108--66146 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
66098 CCGAAGTTTT
* *
66108 CAAAAAATTTGATAAGACC
1 CAAAAAAATAGATAAGACC
*
66127 CAAAAAAATAGATTAGACC
1 CAAAAAAATAGATAAGACC
66146 C
1 C
66147 TTACAAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.18, G:0.10, T:0.18
Consensus pattern (19 bp):
CAAAAAAATAGATAAGACC
Found at i:66919 original size:47 final size:47
Alignment explanation
Indices: 66850--66986 Score: 229
Period size: 47 Copynumber: 2.9 Consensus size: 47
66840 ATGATGTGTA
66850 TTGCTGCGAGGGAACAAGCAAATTACAAAGATGACCGTGACCTAACC
1 TTGCTGCGAGGGAACAAGCAAATTACAAAGATGACCGTGACCTAACC
66897 TTGCTGCGAGGGAACAAGCAAATTACAAAGATGACCGTGACCTAACC
1 TTGCTGCGAGGGAACAAGCAAATTACAAAGATGACCGTGACCTAACC
* * * * *
66944 TTGCTGCGAGGGAACAAGTATATCACAAAGATAACTGTGACCT
1 TTGCTGCGAGGGAACAAGCAAATTACAAAGATGACCGTGACCT
66987 TATCTACCAT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 85 1.00
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (47 bp):
TTGCTGCGAGGGAACAAGCAAATTACAAAGATGACCGTGACCTAACC
Found at i:75217 original size:111 final size:111
Alignment explanation
Indices: 75023--75355 Score: 578
Period size: 111 Copynumber: 3.0 Consensus size: 111
75013 ATTACAAAAA
**
75023 TTAATTCTTTCTCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * *
75088 AATTAAAATGTTAAAATGTTATCGTATCAGCAAAGTGTCTAGATAT
66 AATTAAAAAGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
75134 TTAATT-TGTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATT
1 TTAATTCT-TAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATT
75198 AAATTAAAAAGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
65 AAATTAAAAAGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
75245 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
75310 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAAAGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
75356 ATGATTTCCA
Statistics
Matches: 212, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
110 1 0.00
111 210 0.99
112 1 0.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAAAGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:78827 original size:16 final size:17
Alignment explanation
Indices: 78794--78831 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
78784 TTTTTTAACT
78794 TAAAACTTAATATCAAA
1 TAAAACTTAATATCAAA
78811 TAAAACTTAAT-TCAAA
1 TAAAACTTAATATCAAA
78827 TAAAA
1 TAAAA
78832 TCAACTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAACTTAATATCAAA
Found at i:81765 original size:24 final size:24
Alignment explanation
Indices: 81716--81782 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
81706 AATAATCTCG
*
81716 TGAACATATAAATGAATACGTACA
1 TGAACATATAAATGAACACGTACA
* * *
81740 TGAACATATAAATGAGCATGTTCA
1 TGAACATATAAATGAACACGTACA
*
81764 TGAACAT-TAAACGAACACG
1 TGAACATATAAATGAACACG
81783 AACACCTTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 9 0.25
24 27 0.75
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (24 bp):
TGAACATATAAATGAACACGTACA
Found at i:81810 original size:41 final size:41
Alignment explanation
Indices: 81765--81848 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
81755 GCATGTTCAT
* * *
81765 GAACATTAAACGAACACGAACACCTTCAAAAATAAATAAAC
1 GAACATGAAACAAACACGAACACCTTCAAAAATAAACAAAC
* * * *
81806 GAACATGAACCAAACATGAACATCTTCGAAAATAAACAAAC
1 GAACATGAAACAAACACGAACACCTTCAAAAATAAACAAAC
81847 GA
1 GA
81849 TACGAATATA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.55, C:0.21, G:0.10, T:0.14
Consensus pattern (41 bp):
GAACATGAAACAAACACGAACACCTTCAAAAATAAACAAAC
Found at i:94221 original size:42 final size:42
Alignment explanation
Indices: 94174--94265 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
94164 AAAAAAGCCG
*
94174 CAATAGGTTCATA-TATTTAGC-GCGTTTTTCTTACAAATGCCA
1 CAATAGGTTCA-AGCATTTAGCGGCG-TTTTCTTACAAATGCCA
* *
94216 CAATAGGTTCAAGCATTTAGCGGCGTTTTCTTATAAATGCCG
1 CAATAGGTTCAAGCATTTAGCGGCGTTTTCTTACAAATGCCA
94258 CAATAGGT
1 CAATAGGT
94266 AGGTAATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 1 0.02
42 41 0.91
43 3 0.07
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (42 bp):
CAATAGGTTCAAGCATTTAGCGGCGTTTTCTTACAAATGCCA
Found at i:98092 original size:12 final size:12
Alignment explanation
Indices: 98075--98099 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
98065 ACAAAGCACC
98075 ATTTGGTGCCTA
1 ATTTGGTGCCTA
98087 ATTTGGTGCCTA
1 ATTTGGTGCCTA
98099 A
1 A
98100 ATTATTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:102664 original size:12 final size:12
Alignment explanation
Indices: 102647--102671 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
102637 TGACAACACC
102647 ATTTGGTGCCTA
1 ATTTGGTGCCTA
102659 ATTTGGTGCCTA
1 ATTTGGTGCCTA
102671 A
1 A
102672 ATTATTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:108313 original size:21 final size:21
Alignment explanation
Indices: 108283--108327 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
108273 TAGTTTTAAA
* *
108283 AAAATTAAAAGTTT-AGATATT
1 AAAATAAAAAATTTAAG-TATT
108304 AAAATAAAAAATTTAAGTATT
1 AAAATAAAAAATTTAAGTATT
108325 AAA
1 AAA
108328 CGCTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (21 bp):
AAAATAAAAAATTTAAGTATT
Found at i:111144 original size:18 final size:18
Alignment explanation
Indices: 111121--111165 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
111111 GTTATCATTC
111121 AAACAAGACGTGGCATAG
1 AAACAAGACGTGGCATAG
111139 AAACAAGACGTGGCATAG
1 AAACAAGACGTGGCATAG
*
111157 AAACCAGAC
1 AAACAAGAC
111166 TAATACCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.47, C:0.20, G:0.24, T:0.09
Consensus pattern (18 bp):
AAACAAGACGTGGCATAG
Found at i:124149 original size:28 final size:29
Alignment explanation
Indices: 124108--124171 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 29
124098 TATACATATA
* *
124108 ATATATATCACATCATCACTTATGTACAC
1 ATATATATCACATCATAACTTATGCACAC
* *
124137 ATAT-TATCACATCTTAATTTATGCACAC
1 ATATATATCACATCATAACTTATGCACAC
124165 ATA-ATAT
1 ATATATAT
124172 GTATTATGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.38
Consensus pattern (29 bp):
ATATATATCACATCATAACTTATGCACAC
Found at i:133781 original size:23 final size:22
Alignment explanation
Indices: 133753--133802 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
133743 TAGACACAAT
133753 TAAAATTTTAAGATAAATATAAA
1 TAAAATTTTAAGATAAA-ATAAA
*
133776 TAAAATTTTAAGATGAAATAAA
1 TAAAATTTTAAGATAAAATAAA
133798 -AAAAT
1 TAAAAT
133803 AGCTGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 5 0.19
22 5 0.19
23 16 0.62
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (22 bp):
TAAAATTTTAAGATAAAATAAA
Found at i:133925 original size:17 final size:18
Alignment explanation
Indices: 133886--133932 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
133876 TGTTTCTGAG
133886 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
133904 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
133921 GGAATTGGAATC
1 GGAATTGGAATC
133933 CAATTCCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:134626 original size:257 final size:248
Alignment explanation
Indices: 134312--134820 Score: 713
Period size: 257 Copynumber: 2.0 Consensus size: 248
134302 ATTTTTATTC
*
134312 AATATATGAATTAGAAACCCGACCCGACACGACACGAAATAATAAAAAAATATTTTTATTCAATA
1 AATATATGAAATAGAAACCCGACCCGACACGACACGAAATAATAAAAAAATATTTTTATTCAATA
* *
134377 AAAACATTGACTTAATTGAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATAT
66 AAAACAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTATTACTGTAATTATTCCTAAATAT
* * * * *
134442 ATAAGGTAAAATAATATATTTTTTTTCGGGTCGGGTCCGATTTTTTTCACCCTAAACCCG-A-C-
131 ATAAGGTAAAAT--TATATATATTTTCAGGTC---T-AG-TATTTTTCACCCTAAACCCGAACCA
134504 CGACCCGAATATCACACTT-AAAAAACCAGACCCGACCCGAACAAAATAAAGTTTCACCCGACCC
189 CGACCCGAATATCACACTTAAAAAAACCA-ACCCGA--C---CAAAATAAAGTTTCACCCGACCC
134568 G
248 G
* * *
134569 AATATATGAAATAGAAATCCGACCCGACCCGACCCGAAATAA-AAAAAAATTATTTTTATTCAAT
1 AATATATGAAATAGAAACCCGACCCGACACGACACGAAATAATAAAAAAA-TATTTTTATTCAAT
* *
134633 AAAAACAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTATTACTGTAATTATTCTTAATTA
65 AAAAACAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTATTACTGTAATTATTCCTAAATA
134698 TATAAGGTAAAATTATATATATTTTCAGGTCTAGTATTTTTCACCCTAAACCCGAACTCGATCGA
130 TATAAGGTAAAATTATATATATTTTCAGGTCTAGTATTTTTCACCCTAAACCCGAAC-C-A-CGA
134763 CCCGAATATCACACTTAAAAAAACCAACCCGACCAAAATAAAGTTTCACCCGACCCG
192 CCCGAATATCACACTTAAAAAAACCAACCCGACCAAAATAAAGTTTCACCCGACCCG
134820 A
1 A
134821 CCCGACCCGA
Statistics
Matches: 231, Mismatches: 13, Indels: 22
0.87 0.05 0.08
Matches are distributed among these distances:
250 19 0.08
251 27 0.12
252 1 0.00
253 1 0.00
254 1 0.00
255 15 0.06
256 32 0.14
257 135 0.58
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (248 bp):
AATATATGAAATAGAAACCCGACCCGACACGACACGAAATAATAAAAAAATATTTTTATTCAATA
AAAACAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTATTACTGTAATTATTCCTAAATAT
ATAAGGTAAAATTATATATATTTTCAGGTCTAGTATTTTTCACCCTAAACCCGAACCACGACCCG
AATATCACACTTAAAAAAACCAACCCGACCAAAATAAAGTTTCACCCGACCCG
Found at i:134874 original size:257 final size:255
Alignment explanation
Indices: 134312--134880 Score: 696
Period size: 257 Copynumber: 2.2 Consensus size: 255
134302 ATTTTTATTC
134312 AATATATGAATTAGAAACCCGACCCGACACGACACGAAATAATAAAAAAA-TATTTTTATTCAAT
1 AATATATGAATTAGAAACCCGACCCG--AC--C-CGAAATAATAAAAAAATTATTTTTATTCAAT
* *
134376 AAAAACATTGACTTAATTGAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATA
61 AAAAACAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTATTACTGTAATTATTCCTAAATA
* * * * *
134441 TATAAGGTAAAATAATATATTTTTTTTCGGGTCGGGTCCGATTTTTTTCACCCTAAACCCGACCG
126 TATAAGGTAAAAT-ATATATATATTTTCAGGTC--GTCAGATATTTTTCACCCTAAACCCGACCG
134506 ACCCGAATATCACACTTAAAAAACCAGACCCGACCCGAACAAAATAAAGTTTCACCCGACCCGAA
188 ACCCGAATATCACACTTAAAAAACCAGACCCGA-CC--ACAAAATAAAGTTTCACCCGACCCGAA
* * *
134571 TATATG
250 GACACG
**
134577 AA-ATA-GAAATCCG--ACCCGACCCGACCCGAAATAA-AAAAAAATTATTTTTATTCAATAAAA
1 AATATATG-AATTAGAAACCCGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAA
* *
134637 ACAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTATTACTGTAATTATTCTTAATTATATA
65 ACAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTATTACTGTAATTATTCCTAAATATATA
134702 AGGTAAAAT-TATATATATTTTCAGGTC-T-AG-TATTTTTCACCCTAAACCCGAACTCGATCGA
130 AGGTAAAATATATATATATTTTCAGGTCGTCAGATATTTTTCACCCTAAACCCG-A--C---CGA
*
134763 CCCGAATATCACACTTAAAAAAACCA-ACCCGA-C-CAAAATAAAGTTTCACCCGACCCGACCCG
189 CCCGAATATCACACTT-AAAAAACCAGACCCGACCACAAAATAAAGTTTCACCCGACCCGA--AG
*
134825 ACCCG
251 ACACG
*
134830 AATATATGAATTAGAAACCTGACCCGACCCGAAATAATAAAAAAAATTATT
1 AATATATGAATTAGAAACCCGACCCGACCCGAAATAAT-AAAAAAATTATT
134881 CAATATATGA
Statistics
Matches: 268, Mismatches: 19, Indels: 41
0.82 0.06 0.12
Matches are distributed among these distances:
250 19 0.07
251 27 0.10
252 1 0.00
253 5 0.02
254 8 0.03
255 16 0.06
256 52 0.19
257 105 0.39
258 13 0.05
260 2 0.01
262 10 0.04
263 1 0.00
264 7 0.03
265 2 0.01
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.27
Consensus pattern (255 bp):
AATATATGAATTAGAAACCCGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAA
CAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTATTACTGTAATTATTCCTAAATATATAA
GGTAAAATATATATATATTTTCAGGTCGTCAGATATTTTTCACCCTAAACCCGACCGACCCGAAT
ATCACACTTAAAAAACCAGACCCGACCACAAAATAAAGTTTCACCCGACCCGAAGACACG
Found at i:137300 original size:29 final size:30
Alignment explanation
Indices: 137268--137324 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
137258 TCATTTTCGG
*
137268 TCATTTAAATTTTAAA-AATTATAAAATAA
1 TCATTCAAATTTTAAACAATTATAAAATAA
** *
137297 TCATTCATTTTTTAAACGATTATAAAAT
1 TCATTCAAATTTTAAACAATTATAAAAT
137325 TATGATTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 13 0.57
30 10 0.43
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (30 bp):
TCATTCAAATTTTAAACAATTATAAAATAA
Found at i:140968 original size:18 final size:17
Alignment explanation
Indices: 140945--140979 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
140935 TTAAGGAGTA
140945 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACA-AGTG
*
140963 GTCCTTTGGGACAAGTG
1 GTCCTTCGGGACAAGTG
140980 TTCAGTGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (17 bp):
GTCCTTCGGGACAAGTG
Found at i:143448 original size:19 final size:19
Alignment explanation
Indices: 143413--143451 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
143403 TAAGGAACCT
*
143413 AAAATCTAAGGCTTAATTA
1 AAAATCTAAGACTTAATTA
143432 AAAATCTAAAGAC-TAATTA
1 AAAATCT-AAGACTTAATTA
143451 A
1 A
143452 TATTTAGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (19 bp):
AAAATCTAAGACTTAATTA
Found at i:145153 original size:17 final size:17
Alignment explanation
Indices: 145131--145164 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
145121 ATTATTTAAT
145131 ATGCAATGCAACATGAA
1 ATGCAATGCAACATGAA
**
145148 ATGCAATTTAACATGAA
1 ATGCAATGCAACATGAA
145165 TTAATATGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (17 bp):
ATGCAATGCAACATGAA
Found at i:150955 original size:18 final size:19
Alignment explanation
Indices: 150932--150970 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
150922 TTAATGTTTT
* *
150932 ATTTTTTACA-AATTTTAA
1 ATTTTTGACATAAATTTAA
150950 ATTTTTGACATAAATTTAA
1 ATTTTTGACATAAATTTAA
150969 AT
1 AT
150971 GTTTATGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (19 bp):
ATTTTTGACATAAATTTAA
Found at i:151958 original size:20 final size:20
Alignment explanation
Indices: 151930--151973 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
151920 TTTTGCAGAA
* *
151930 AAATTATCCCTAACGGCTAC
1 AAATCATCCCCAACGGCTAC
*
151950 AAATCATCCCCAACGGCTAG
1 AAATCATCCCCAACGGCTAC
151970 AAAT
1 AAAT
151974 GGCCACAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.30, G:0.11, T:0.20
Consensus pattern (20 bp):
AAATCATCCCCAACGGCTAC
Found at i:152549 original size:14 final size:13
Alignment explanation
Indices: 152522--152554 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
152512 TATTAGATAA
152522 ATATAT-ACATAT
1 ATATATAACATAT
152534 ATATATAACATGAT
1 ATATATAACAT-AT
152548 ATATATA
1 ATATATA
152555 CGTACATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 4 0.21
14 9 0.47
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (13 bp):
ATATATAACATAT
Found at i:153970 original size:32 final size:31
Alignment explanation
Indices: 153917--154011 Score: 147
Period size: 31 Copynumber: 3.0 Consensus size: 31
153907 CCCGAAGGAC
* *
153917 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
153948 CAGTCCATATGTCCCCGAAGAACATAGGTAAA
1 CAGTCCATATGT-CCCGAAGAACATAGGTAAA
153980 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
154011 C
1 C
154012 CCTCGACCCT
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
31 30 0.50
32 30 0.50
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:154859 original size:64 final size:63
Alignment explanation
Indices: 154663--154885 Score: 191
Period size: 64 Copynumber: 3.5 Consensus size: 63
154653 AATAAAGGTA
* * ** * * *
154663 TGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGTATTATTGCT-GAGA
1 TGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTA-T-TTATT-TTAAAGA
154727 -
63 G
* * * ** * * * *
154727 CGCATCGATGCACTCCTTATACATCGATGCACCAATTGCATTCGATGT-TTCACTATTAATGGG
1 TGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTATTTA-TTTTAAAGAG
*
154790 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTATTTTAAAAGAG
1 -TGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTATTTATTTT-AAAGAG
** *
154855 TGCATCGATGCACTACCAATGCATCGGTGCA
1 TGCATCGATGCACTACTTATGCATCGATGCA
154886 CATTCAAACA
Statistics
Matches: 125, Mismatches: 28, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
61 3 0.02
62 3 0.02
64 112 0.90
65 7 0.06
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (63 bp):
TGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTATTTATTTTAAAGAG
Found at i:156873 original size:36 final size:36
Alignment explanation
Indices: 156808--156977 Score: 108
Period size: 36 Copynumber: 4.9 Consensus size: 36
156798 CGTTTCAAGG
* * *
156808 GAAAACTATCTCAAGCGAGA-CAAAATTTGTTTTTAC
1 GAAAACAATCTCAAGCGAGATC-AATTTTGTTTTTAA
*
156844 GAAAACAATCTCAAGCGAGATCAATTTTG-TTTCAA
1 GAAAACAATCTCAAGCGAGATCAATTTTGTTTTTAA
* * * ** *
156879 GTGAAACAATTTCAA---A-AT---TTGTGTTTCGAGT
1 G-AAAACAATCTCAAGCGAGATCAATTTTGTTTTTA-A
* * *
156910 GAAAACTATCTCAAGCGAGA-CAAAATTTGTTTTTAG
1 GAAAACAATCTCAAGCGAGATC-AATTTTGTTTTTAA
*
156946 GAAAACAATCTCAAGAGAGATCAATTTTGTTT
1 GAAAACAATCTCAAGCGAGATCAATTTTGTTT
156978 CAAGTGAAAA
Statistics
Matches: 100, Mismatches: 21, Indels: 26
0.68 0.14 0.18
Matches are distributed among these distances:
29 4 0.04
30 13 0.13
31 1 0.01
32 2 0.02
33 2 0.02
34 1 0.01
35 5 0.05
36 63 0.63
37 9 0.09
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (36 bp):
GAAAACAATCTCAAGCGAGATCAATTTTGTTTTTAA
Found at i:156905 original size:102 final size:102
Alignment explanation
Indices: 156764--157139 Score: 457
Period size: 102 Copynumber: 3.7 Consensus size: 102
156754 TATGAGATAA
* *
156764 AATTTTGTTTCGAGTGAAACAATTTCAAAATTTGCGTTTCAAGGGAAAACTATCTCAAGCGAGAC
1 AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTATCTCAAGCGAGAC
*
156829 AAAATTTGTTTTTACGAAAACAATCTCAAGCGAGATC
66 AAAATTTGTTTTTACGAAAACAATCTCAAGAGAGATC
* *
156866 AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCGAGTGAAAACTATCTCAAGCGAGAC
1 AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTATCTCAAGCGAGAC
*
156931 AAAATTTGTTTTTAGGAAAACAATCTCAAGAGAGATC
66 AAAATTTGTTTTTACGAAAACAATCTCAAGAGAGATC
* * *
156968 AATTTTGTTTCAAGTGAAAAAATTTCAAAATTTATGTTTCAAGGG-AAACTGTCTCAAGCGAGAC
1 AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTATCTCAAGCGAGAC
* ** * *
157032 GAAACTTTGTTTCGA-GAGAATCAATCTCAA-A-TG-T-
66 -AAAATTTGTTTTTACGA-AAACAATCTCAAGAGAGATC
* * * * * *
157066 --TTATGTTTCAAGAGAAACAATCT-AAAAGGTTTATGTTTCAAGAG-AAACTGTCTCAAGCGAG
1 AATTTTGTTTCAAGTGAAACAATTTCAAAA--TTTGTGTTTCAAGGGAAAACTATCTCAAGCGAG
*
157127 ATAAAATTTGTTT
64 ACAAAATTTGTTT
157140 CAAGAGAAAC
Statistics
Matches: 247, Mismatches: 23, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
95 4 0.02
96 29 0.12
97 32 0.13
99 1 0.00
100 1 0.00
101 21 0.09
102 159 0.64
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (102 bp):
AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTATCTCAAGCGAGAC
AAAATTTGTTTTTACGAAAACAATCTCAAGAGAGATC
Found at i:157080 original size:30 final size:30
Alignment explanation
Indices: 157039--157179 Score: 122
Period size: 30 Copynumber: 4.5 Consensus size: 30
157029 GACGAAACTT
* * * *
157039 TGTTTCGAGAGAATCAATCTCAAATGTTTA
1 TGTTTCAAGAGAAACAATCTAAAAGGTTTA
157069 TGTTTCAAGAGAAACAATCTAAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTAAAAGGTTTA
** * *
157099 TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAATT-
1 TGTTTCAAGAGAAACAATCT-AA--AAGGT----TTA
* *
157135 TGTTTCAAGAGAAACAATGTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTAAAAGGTTTA
157165 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
157180 TGTCTCAAGT
Statistics
Matches: 89, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
29 2 0.02
30 59 0.66
31 2 0.02
33 6 0.07
35 1 0.01
36 17 0.19
37 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAATCTAAAAGGTTTA
Found at i:157139 original size:36 final size:35
Alignment explanation
Indices: 157099--157225 Score: 122
Period size: 36 Copynumber: 3.7 Consensus size: 35
157089 AAAAGGTTTA
157099 TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAG-GAGATAAAATT
** * *
157135 TGTTTCAAGAGAAACAATGTCAA--AGGT----TT
1 TGTTTCAAGAGAAACTGTCTCAAGGAGATAAAATT
*
157164 ATGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATT
1 -TGTTTCAAGAGAAACTGTCTCAAG-GAGATAAAATT
* *
157201 TGTTTCAAGAAAAATTGTCTCAAGG
1 TGTTTCAAGAGAAACTGTCTCAAGG
157226 GAGACAGACA
Statistics
Matches: 72, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
29 2 0.03
30 20 0.28
33 5 0.07
35 1 0.01
36 42 0.58
37 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.29
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTGTCTCAAGGAGATAAAATT
Found at i:157175 original size:66 final size:66
Alignment explanation
Indices: 157069--157210 Score: 248
Period size: 66 Copynumber: 2.2 Consensus size: 66
157059 CAAATGTTTA
*
157069 TGTTTCAAGAGAAACAATCTAAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAAT
1 TGTTTCAAGAGAAACAATCTAAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAAT
157134 T
66 T
* * *
157135 TGTTTCAAGAGAAACAATGTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAAT
1 TGTTTCAAGAGAAACAATCTAAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAAT
157200 T
66 T
157201 TGTTTCAAGA
1 TGTTTCAAGA
157211 AAAATTGTCT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 72 1.00
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (66 bp):
TGTTTCAAGAGAAACAATCTAAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAAT
T
Found at i:159352 original size:7 final size:7
Alignment explanation
Indices: 159342--159455 Score: 56
Period size: 7 Copynumber: 15.9 Consensus size: 7
159332 TCAGTTTTAT
159342 TTTTTTC
1 TTTTTTC
159349 -TTTTTC
1 TTTTTTC
159355 -TTTTTC
1 TTTTTTC
159361 TTTTTT-
1 TTTTTTC
*
159367 TTATTT-
1 TTTTTTC
*
159373 TTTTCTC
1 TTTTTTC
* * *
159380 TATATTG
1 TTTTTTC
*
159387 TTTCTCTATA
1 TTT-T-T-TC
*
159397 TTTTTCC
1 TTTTTTC
159404 TTTTTTTC
1 T-TTTTTC
159412 TTTTTTTC
1 -TTTTTTC
159420 TTTTTTCCC
1 TTTTTT--C
*
159429 TTTTTCC
1 TTTTTTC
*
159436 CTTTTTC
1 TTTTTTC
159443 TTTTTTC
1 TTTTTTC
159450 TTTTTT
1 TTTTTT
159456 TATTCTTTTC
Statistics
Matches: 81, Mismatches: 17, Indels: 18
0.70 0.15 0.16
Matches are distributed among these distances:
6 21 0.26
7 35 0.43
8 12 0.15
9 9 0.11
10 4 0.05
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.78
Consensus pattern (7 bp):
TTTTTTC
Found at i:159352 original size:8 final size:8
Alignment explanation
Indices: 159336--159467 Score: 69
Period size: 8 Copynumber: 16.9 Consensus size: 8
159326 CTCCTTTCAG
*
159336 TTTTATTT
1 TTTTCTTT
159344 TTTTC--T
1 TTTTCTTT
159350 TTTTCTTT
1 TTTTCTTT
*
159358 TTCT-TTT
1 TTTTCTTT
*
159365 TTTTATTT
1 TTTTCTTT
*
159373 TTTTCTCT
1 TTTTCTTT
* * *
159381 ATAT-TGT
1 TTTTCTTT
*
159388 TTCTCTATAT
1 TTTTCT-T-T
159398 TTTTCCTTT
1 TTTT-CTTT
159407 TTTTCTTT
1 TTTTCTTT
159415 TTTTC-TT
1 TTTTCTTT
**
159422 TTTTCCCT
1 TTTTCTTT
**
159430 TTTTCCCT
1 TTTTCTTT
159438 TTTTC-TT
1 TTTTCTTT
159445 TTTTCTTT
1 TTTTCTTT
* *
159453 TTTTATTC
1 TTTTCTTT
159461 TTTTCTT
1 TTTTCTT
159468 CAAGTGTAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 18
0.74 0.13 0.14
Matches are distributed among these distances:
6 6 0.06
7 23 0.23
8 57 0.58
9 5 0.05
10 5 0.05
11 2 0.02
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.78
Consensus pattern (8 bp):
TTTTCTTT
Found at i:159456 original size:23 final size:23
Alignment explanation
Indices: 159397--159456 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
159387 TTTCTCTATA
* **
159397 TTTTTCCTTTTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTCCCTTTTTC
**
159420 TTTTTTCCCTTTTTCCCTTTTTC
1 TTTTTTCTTTTTTTCCCTTTTTC
159443 TTTTTTCTTTTTTT
1 TTTTTTCTTTTTTT
159457 ATTCTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTCTTTTTTTCCCTTTTTC
Found at i:159464 original size:23 final size:22
Alignment explanation
Indices: 159341--159467 Score: 64
Period size: 23 Copynumber: 5.7 Consensus size: 22
159331 TTCAGTTTTA
159341 TTTTTTTCTTTT-TCTTTTTC-T
1 TTTTTTTCTTTTCT-TTTTTCTT
* *
159362 TTTTTTT-ATTT-TTTTCTCTAT
1 TTTTTTTCTTTTCTTTTTTCT-T
* * * * *
159383 ATTGTTTCTCTATATTTTTCCTT
1 TTTTTTTCT-TTTCTTTTTTCTT
* **
159406 TTTTTCTTTTTTTCTTTTTTCCC
1 TTTTT-TTCTTTTCTTTTTTCTT
**
159429 TTTTTCCCTTTTTCTTTTTTCTT
1 TTTTTTTC-TTTTCTTTTTTCTT
159452 TTTTTATTCTTTTCTT
1 TTTTT-TTCTTTTCTT
159468 CAAGTGTAAT
Statistics
Matches: 75, Mismatches: 23, Indels: 14
0.67 0.21 0.12
Matches are distributed among these distances:
19 5 0.07
20 4 0.05
21 13 0.17
23 43 0.57
24 10 0.13
ACGTcount: A:0.05, C:0.17, G:0.01, T:0.78
Consensus pattern (22 bp):
TTTTTTTCTTTTCTTTTTTCTT
Found at i:164798 original size:14 final size:14
Alignment explanation
Indices: 164775--164815 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
164765 ATAGGGACTG
*
164775 AAATAAAATAAATA
1 AAATACAATAAATA
*
164789 AAATACAATAAATC
1 AAATACAATAAATA
164803 AAAT-CAA-AAATA
1 AAATACAATAAATA
164815 A
1 A
164816 TAAGAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 5 0.21
13 3 0.12
14 16 0.67
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATACAATAAATA
Found at i:176110 original size:3 final size:3
Alignment explanation
Indices: 176104--176136 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
176094 AATCATCATC
176104 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
176137 TAAATTACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:176174 original size:3 final size:3
Alignment explanation
Indices: 176166--176199 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
176156 CATAATGATT
176166 TTA TTA TTA TTA TTA TTGA TTAA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT-A TT-A TTA TTA TTA TT
176200 TAAGTAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:176212 original size:63 final size:61
Alignment explanation
Indices: 176105--176230 Score: 198
Period size: 63 Copynumber: 2.0 Consensus size: 61
176095 ATCATCATCA
*
176105 TTATTATTATTATTATTATTATTATTATTATTTAAATTACAATCAATGATACATAATGATT
1 TTATTATTATTATTATTATTATTATTATTATTTAAATAACAATCAATGATACATAATGATT
* * *
176166 TTATTATTATTATTATTGATTAATTATTATTATTTAAGTAATAATCAATGATATATAATGATT
1 TTATTATTATTATTATT-ATT-ATTATTATTATTTAAATAACAATCAATGATACATAATGATT
176229 TT
1 TT
176231 TTTAATTAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
61 17 0.29
62 3 0.05
63 39 0.66
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (61 bp):
TTATTATTATTATTATTATTATTATTATTATTTAAATAACAATCAATGATACATAATGATT
Found at i:176454 original size:31 final size:31
Alignment explanation
Indices: 176408--176468 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
176398 GAAACGGTCT
* *
176408 CTAACGTTATCGATTCGTTCGATTTTAATCC
1 CTAACATTATCGATTCGTTAGATTTTAATCC
*
176439 CTAACATTATTGATTCGTTAGATTTTAATC
1 CTAACATTATCGATTCGTTAGATTTTAATC
176469 TCTCAATCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.44
Consensus pattern (31 bp):
CTAACATTATCGATTCGTTAGATTTTAATCC
Found at i:178257 original size:104 final size:103
Alignment explanation
Indices: 178077--178282 Score: 261
Period size: 104 Copynumber: 2.0 Consensus size: 103
178067 TTCCGGGAAA
* *
178077 GCTATTTAAGAGCCATTGGCTAACCAGAGCATGTAGAAAAATTGCCTTTAGGAACAATTCAGGGT
1 GCTATTTAAGAGCAATTGGCTAACCAGAGCATGTACAAAAATTGCCTTTA-GAACAATTCAGGGT
* * * *
178142 CAGAACTTGAATCAGCCAATGATTTAAATCAATAAGGTC
65 CAAAACTTGAATCAACCAATGACTAAAATCAATAAGGTC
* * * * *
178181 GCTATTTAAGAGTAATTGGCTAATCAGAGCATGTTCAAAGATTGTTCTTTCA-AACAATTCAGGG
1 GCTATTTAAGAGCAATTGGCTAACCAGAGCATGTACAAAAATTG-CCTTT-AGAACAATTCAGGG
* *
178245 TCAAAACTTGAATCAACCAGTGACTAAAATTAATAAGG
64 TCAAAACTTGAATCAACCAATGACTAAAATCAATAAGG
178283 CCTCAGTGTT
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
104 82 0.94
105 4 0.05
106 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (103 bp):
GCTATTTAAGAGCAATTGGCTAACCAGAGCATGTACAAAAATTGCCTTTAGAACAATTCAGGGTC
AAAACTTGAATCAACCAATGACTAAAATCAATAAGGTC
Found at i:193811 original size:21 final size:21
Alignment explanation
Indices: 193787--193848 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
193777 AACTTTGAAA
193787 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
**
193808 AAAT-G-TTTC----TTTGAA
1 AAATGGTTTTCAAAGTTTGGT
*
193823 AAATAGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
193844 AAATG
1 AAATG
193849 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 12
0.64 0.11 0.26
Matches are distributed among these distances:
15 8 0.27
16 1 0.03
17 4 0.13
19 4 0.13
20 1 0.03
21 12 0.40
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.42
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:193879 original size:37 final size:36
Alignment explanation
Indices: 193779--193898 Score: 188
Period size: 36 Copynumber: 3.3 Consensus size: 36
193769 TGGTAACCAA
*
193779 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
193816 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
193852 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
193889 -GTTGAAAAAT
1 CTTTGAAAAAT
193899 GATAATGGGA
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
36 52 0.66
37 27 0.34
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:203572 original size:90 final size:90
Alignment explanation
Indices: 203419--203585 Score: 316
Period size: 90 Copynumber: 1.9 Consensus size: 90
203409 CCTAACACAC
*
203419 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
203484 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGGAATTTAATAAT
*
203509 CCTTTTATATCCAAGTTACCCTAATCGTATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
203574 ATTTAATTAATT
66 ATTTAATTAATT
203586 AAAATTAAAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 75 1.00
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (90 bp):
CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGGAATTTAATAAT
Found at i:203583 original size:20 final size:20
Alignment explanation
Indices: 203558--203627 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 20
203548 TATTATTTCA
203558 AATTAATT-AAATCTATATTT
1 AATTAATTAAAAT-TATATTT
203578 AATTAATTAAAATTAAATATTT
1 AATTAATTAAAATT--ATATTT
203600 GATATT-ATTAAAATATATATTT
1 -A-ATTAATTAAAAT-TATATTT
203622 AATTAA
1 AATTAA
203628 CTCTAGATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
20 12 0.28
21 6 0.14
22 12 0.28
23 9 0.21
24 4 0.09
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (20 bp):
AATTAATTAAAATTATATTT
Found at i:203597 original size:22 final size:21
Alignment explanation
Indices: 203558--203627 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
203548 TATTATTTCA
**
203558 AATTAATT-AAATCTATATTT
1 AATTAATTAAAATAAATATTT
203578 AATTAATTAAAATTAAATATTT
1 AATTAATTAAAA-TAAATATTT
*
203600 GATATT-ATTAAAATATATATTT
1 -A-ATTAATTAAAATAAATATTT
203622 AATTAA
1 AATTAA
203628 CTCTAGATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
20 11 0.26
21 5 0.12
22 15 0.36
23 8 0.19
24 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (21 bp):
AATTAATTAAAATAAATATTT
Found at i:205675 original size:18 final size:18
Alignment explanation
Indices: 205644--205678 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
205634 TATCAAAGTA
* *
205644 ACTCAGTGACTAAAGAAC
1 ACTCAATGAATAAAGAAC
205662 ACTCAATGAATAAAGAA
1 ACTCAATGAATAAAGAA
205679 AACCATGTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (18 bp):
ACTCAATGAATAAAGAAC
Found at i:215104 original size:23 final size:23
Alignment explanation
Indices: 215074--215124 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
215064 GAACTTTCCG
215074 TTGAACGATCCATAAACAATTCA
1 TTGAACGATCCATAAACAATTCA
*
215097 TTGAACGATCCATAAATAATTCA
1 TTGAACGATCCATAAACAATTCA
215120 TTGAA
1 TTGAA
215125 TGTTCGGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (23 bp):
TTGAACGATCCATAAACAATTCA
Found at i:218361 original size:37 final size:36
Alignment explanation
Indices: 218286--218361 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
218276 TTTTTATATT
*
218286 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
218322 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
218359 TTT
1 TTT
218362 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:218730 original size:4 final size:4
Alignment explanation
Indices: 218721--218749 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
218711 CTAATCAGAC
218721 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
218750 AACCTGATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:227447 original size:24 final size:24
Alignment explanation
Indices: 227396--227447 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
227386 GACTATTGAT
* *
227396 AAATCTAAGAAAACTGTTCATGAC
1 AAATCTAAGAAAACTGTTCAAGAA
227420 AAATCTAAGAAAACTGTTCAAGAA
1 AAATCTAAGAAAACTGTTCAAGAA
227444 AAAT
1 AAAT
227448 TTACTGATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.13, G:0.12, T:0.23
Consensus pattern (24 bp):
AAATCTAAGAAAACTGTTCAAGAA
Found at i:229131 original size:10 final size:10
Alignment explanation
Indices: 229116--229145 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
229106 CACCTTCTGT
*
229116 TTTTATTTTA
1 TTTTATATTA
229126 TTTTATATTA
1 TTTTATATTA
229136 TTTTATATTA
1 TTTTATATTA
229146 AAATAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTATATTA
Found at i:231023 original size:43 final size:43
Alignment explanation
Indices: 230975--231059 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
230965 TCCCTCTGCG
230975 GCTCTGCCTTCAGTGAAATTATTTTTGAAGCACGAACTAAGCT
1 GCTCTGCCTTCAGTGAAATTATTTTTGAAGCACGAACTAAGCT
**
231018 GCTCTGCCTTTGGTGAAATTATTTTTGAAGCACGAACTAAGC
1 GCTCTGCCTTCAGTGAAATTATTTTTGAAGCACGAACTAAGC
231060 GACCTCAGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (43 bp):
GCTCTGCCTTCAGTGAAATTATTTTTGAAGCACGAACTAAGCT
Found at i:231082 original size:11 final size:11
Alignment explanation
Indices: 231066--231093 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
231056 AAGCGACCTC
231066 AGTTGTAAAAG
1 AGTTGTAAAAG
231077 AGTTGTAAAAG
1 AGTTGTAAAAG
231088 AGTTGT
1 AGTTGT
231094 TATTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (11 bp):
AGTTGTAAAAG
Done.