Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001848.1 Hibiscus syriacus cultivar Beakdansim tig00003743_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: 78181
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:7521 original size:25 final size:25
Alignment explanation
Indices: 7492--7545 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
7482 GGGGCTGTTT
7492 GTGCGAGAGGTGGCTGCTGGTGGCG
1 GTGCGAGAGGTGGCTGCTGGTGGCG
7517 GTGCGAGAGGTGGCTGCTGGTGGCG
1 GTGCGAGAGGTGGCTGCTGGTGGCG
7542 GTGC
1 GTGC
7546 AAGAAGGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.07, C:0.17, G:0.56, T:0.20
Consensus pattern (25 bp):
GTGCGAGAGGTGGCTGCTGGTGGCG
Found at i:27470 original size:20 final size:20
Alignment explanation
Indices: 27445--27537 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
27435 TTTTCCCAAT
27445 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
27465 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
27485 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
27506 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
27527 TCGCAATGCGA
1 TCGCAATGCGA
27538 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:27487 original size:41 final size:41
Alignment explanation
Indices: 27442--27537 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
27432 CGATTTTCCC
27442 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
27483 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
27524 AAATCGCAATGCGA
1 AATTCGCAATGCGA
27538 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:27491 original size:21 final size:20
Alignment explanation
Indices: 27445--27537 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
27435 TTTTCCCAAT
*
27445 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
27465 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
27485 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
27506 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
27527 TCGCAATGCGA
1 TCGCAATGCGA
27538 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:27551 original size:20 final size:20
Alignment explanation
Indices: 27526--27619 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
27516 AATTGGGAAA
*
27526 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
27546 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
27567 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
27587 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
27607 TTCGCAACGCGAT
1 ATCGCAACGCGAT
27620 TTACTTAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:27600 original size:41 final size:41
Alignment explanation
Indices: 27523--27600 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
27513 GCGAATTGGG
* * **
27523 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
27564 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
27601 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:28243 original size:20 final size:19
Alignment explanation
Indices: 28195--28360 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
28185 GAAACCAAAA
*
28195 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
28214 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
28233 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
28253 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
28269 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
28286 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
28300 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
28319 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
28339 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
28359 TC
1 TC
28361 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.34
20 49 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:28285 original size:33 final size:33
Alignment explanation
Indices: 28248--28335 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
28238 GTTGCGATTT
* *
28248 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
28281 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
28314 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
28336 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:30151 original size:29 final size:29
Alignment explanation
Indices: 30118--30176 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
30108 GTGAAGTTAG
* ** *
30118 TATTTGTCTTTGTTTTGTCTGTTTGAATA
1 TATTTATCTTTGTTTTCACTGTTTAAATA
30147 TATTTATCTTTGTTTTCACTGTTTAAATA
1 TATTTATCTTTGTTTTCACTGTTTAAATA
30176 T
1 T
30177 CATGTCTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.19, C:0.08, G:0.12, T:0.61
Consensus pattern (29 bp):
TATTTATCTTTGTTTTCACTGTTTAAATA
Found at i:30411 original size:42 final size:42
Alignment explanation
Indices: 30351--30473 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
30341 GCCCGACTCG
* * *
30351 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
30393 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
30435 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
30474 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:30431 original size:21 final size:21
Alignment explanation
Indices: 30407--30473 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
30397 TCATTCCTCG
30407 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
30428 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
30449 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
30470 AGAG
1 AGAG
30474 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:31851 original size:14 final size:14
Alignment explanation
Indices: 31832--31867 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
31822 ATTGTTTAAT
31832 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
31846 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
31860 TGATTTGT
1 TGATTTGT
31868 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:32068 original size:19 final size:19
Alignment explanation
Indices: 32046--32163 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
32036 CGAAATTAAA
32046 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
32065 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
32080 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
32098 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
32113 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
32131 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
32150 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
32164 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:32092 original size:33 final size:33
Alignment explanation
Indices: 32050--32143 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
32040 ATTAAATTCG
32050 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
32083 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
32116 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
32144 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:34444 original size:12 final size:12
Alignment explanation
Indices: 34427--34451 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34417 TCTTCGGGGA
34427 CTTTTTCTTCTT
1 CTTTTTCTTCTT
34439 CTTTTTCTTCTT
1 CTTTTTCTTCTT
34451 C
1 C
34452 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:35945 original size:14 final size:14
Alignment explanation
Indices: 35928--35964 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
35918 CATCAATTAA
35928 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
35942 ACAAATCATCTTTT
1 ACAAATCAACATTT
35956 ACAAATCAA
1 ACAAATCAA
35965 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:36354 original size:20 final size:20
Alignment explanation
Indices: 36329--36379 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
36319 ATTCATTTGA
*
36329 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
36349 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
36369 TTATCGCAACG
1 CTATCGCAACG
36380 AGAATATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:36446 original size:19 final size:19
Alignment explanation
Indices: 36405--36470 Score: 81
Period size: 18 Copynumber: 3.8 Consensus size: 19
36395 GAAATGAAAA
36405 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
36421 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
36438 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
36456 TTGCATTGCGATTTT
1 TCGCATTGCGATTTT
36471 ATCGTTGCGA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
14 11 0.26
16 3 0.07
17 3 0.07
18 17 0.40
19 9 0.21
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:38469 original size:20 final size:19
Alignment explanation
Indices: 38434--38500 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
38424 GAAACTTAAA
38434 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
38453 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
38473 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
38492 ATCGCAACG
1 ATCGCAACG
38501 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:38508 original size:14 final size:14
Alignment explanation
Indices: 38489--38546 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
38479 ATGCGAAATG
38489 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
38503 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
38519 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
38535 AAAATCGCAACG
1 AAAATCGCAACG
38547 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:38531 original size:32 final size:33
Alignment explanation
Indices: 38473--38551 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
38463 GGAAATGGCT
*
38473 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
38506 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
38538 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
38552 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:38580 original size:19 final size:17
Alignment explanation
Indices: 38558--38653 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
38548 GAAACACAAA
38558 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
38577 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
38593 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
38609 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
38625 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
38642 TCGCATTGCGAT
1 TCGC-TTGCGAT
38654 AGCCATTTCG
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:38599 original size:14 final size:14
Alignment explanation
Indices: 38580--38637 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
38570 TTTCATTTCG
38580 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
38594 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
38610 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
38626 CGTTGCGATTTT
1 CGTTGCGATTTT
38638 CATTTCGCAT
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:38644 original size:33 final size:33
Alignment explanation
Indices: 38563--38653 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
38553 ACAAATCGCA
38563 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
38596 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
38628 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
38654 AGCCATTTCG
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:39169 original size:18 final size:18
Alignment explanation
Indices: 39143--39187 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
39133 GTCGATCAGA
*
39143 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
39161 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
39179 TGATGGCTC
1 TGATGGCTC
39188 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:40532 original size:20 final size:20
Alignment explanation
Indices: 40507--40544 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40497 AATAGTTTCT
40507 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
40527 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
40545 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:40833 original size:22 final size:22
Alignment explanation
Indices: 40808--40851 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
40798 GATTTAGATA
40808 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
40830 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
40852 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:41064 original size:20 final size:20
Alignment explanation
Indices: 41039--41091 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
41029 GATTATGTAT
*
41039 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
41059 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
41079 TATCTCGTTGCGA
1 TATCGCGTTGCGA
41092 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:41104 original size:41 final size:41
Alignment explanation
Indices: 41059--41136 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
41049 CGAAAGTCAG
* * *
41059 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* **
41100 TATCGCATTGCGATAGTCGGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
41137 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:41152 original size:41 final size:41
Alignment explanation
Indices: 41122--41217 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
41112 ATAGTCGGTA
* * *
41122 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATGTACGTAT
* *
41163 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATGTACGTAT
41204 TCGCATTGCGAATT
1 TCGCATTGCGAATT
41218 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATGTACGTAT
Found at i:41166 original size:20 final size:20
Alignment explanation
Indices: 41122--41214 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
41112 ATAGTCGGTA
* **
41122 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
41143 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
41163 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
41184 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
41204 TCGCATTGCGA
1 TCGCATTGCGA
41215 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:42573 original size:23 final size:23
Alignment explanation
Indices: 42532--42575 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
42522 TTGGAAACCT
* **
42532 GTTGCAATTAAACTGCTATAATA
1 GTTGCAATCAAACAACTATAATA
42555 GTTGCAATCAAACAACTATAA
1 GTTGCAATCAAACAACTATAA
42576 CGACTGCAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (23 bp):
GTTGCAATCAAACAACTATAATA
Found at i:48811 original size:21 final size:21
Alignment explanation
Indices: 48787--48831 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
48777 ACGGATATAT
48787 TAAAAA-AATTAATATTTTAAA
1 TAAAAATAA-TAATATTTTAAA
*
48808 TAAAAATAATAATTTTTTAAA
1 TAAAAATAATAATATTTTAAA
48829 TAA
1 TAA
48832 TTTGTTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAA
Found at i:48817 original size:18 final size:17
Alignment explanation
Indices: 48781--48823 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
48771 ATTTTAACGG
* *
48781 ATATATTAAAAAAATTA
1 ATATTTTAAAAAAAATA
48798 ATATTTTAAATAAAAATA
1 ATATTTTAAA-AAAAATA
48816 ATAATTTT
1 AT-ATTTT
48824 TTAAATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 9 0.41
18 8 0.36
19 5 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTTTAAAAAAAATA
Found at i:64851 original size:25 final size:22
Alignment explanation
Indices: 64823--64872 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
64813 TTATGCATAA
*
64823 ATTATAATTATATTTTTTTATATTC
1 ATTAT-ATT-TATTTTCTTAT-TTC
*
64848 ATTATGTTTATTTTCTTATTTC
1 ATTATATTTATTTTCTTATTTC
64870 ATT
1 ATT
64873 CTTATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 6 0.26
23 10 0.43
24 2 0.09
25 5 0.22
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTATATTTATTTTCTTATTTC
Found at i:65033 original size:21 final size:20
Alignment explanation
Indices: 65003--65213 Score: 145
Period size: 21 Copynumber: 10.6 Consensus size: 20
64993 AATATGTAAA
*
65003 TCGCAATGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAA-T
* *
65024 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGTCCA-AT
65044 TCGCATTGCGATAGTCCAACT
1 TCGCATTGCGATAGTCCAA-T
*
65065 TCGCATTGCG--A---CTA-
1 TCGCATTGCGATAGTCCAAT
* *
65079 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGTCCA-AT
*
65099 TCGCATTGCGATAG-CCGACT
1 TCGCATTGCGATAGTCC-AAT
* *
65119 ATCGCATTGCGAT-TTACATAT
1 -TCGCATTGCGATAGTCCA-AT
65140 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAA-T
*
65161 TCGCATTGCGATAATCCAAAT
1 TCGCATTGCGATAGTCC-AAT
* *
65182 TCGCATTACGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAA-T
*
65203 TCGCGTTGCGA
1 TCGCATTGCGA
65214 ATCTGAAAAC
Statistics
Matches: 150, Mismatches: 21, Indels: 38
0.72 0.10 0.18
Matches are distributed among these distances:
14 10 0.07
16 2 0.01
18 1 0.01
19 2 0.01
20 47 0.31
21 86 0.57
22 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (20 bp):
TCGCATTGCGATAGTCCAAT
Found at i:65048 original size:20 final size:20
Alignment explanation
Indices: 65023--65151 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
65013 ATAGTCCAAG
65023 TTCGCATTGCGATTTACATA
1 TTCGCATTGCGATTTACATA
* *
65043 TTCGCATTGCGATAGTCCA-A
1 TTCGCATTGCGAT-TTACATA
65063 CTTCGCATTGCG----AC-TA
1 -TTCGCATTGCGATTTACATA
65079 -TCGCATTGCGATTTACATA
1 TTCGCATTGCGATTTACATA
***
65098 TTCGCATTGCGATAGCCGACTA
1 TTCGCATTGCGATTTAC-A-TA
65120 -TCGCATTGCGATTTACATA
1 TTCGCATTGCGATTTACATA
65139 TTCGCATTGCGAT
1 TTCGCATTGCGAT
65152 AGTCCAAGTT
Statistics
Matches: 88, Mismatches: 9, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
14 10 0.11
16 2 0.02
18 2 0.02
19 4 0.05
20 40 0.45
21 28 0.32
22 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (20 bp):
TTCGCATTGCGATTTACATA
Found at i:65108 original size:55 final size:58
Alignment explanation
Indices: 65023--65188 Score: 198
Period size: 55 Copynumber: 2.8 Consensus size: 58
65013 ATAGTCCAAG
65023 TTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAACTTCGCATTGCG-AC-TA
1 TTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAACTTCGCATTGCGTACATA
*
65079 -TCGCATTGCGATTTACATATTCGCATTGCGATAG-CCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAACT-TCGCATTGCG---TACATA
* * * *
65139 TTCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAATCCAAATTCGCATT
1 TTCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTCCAACTTCGCATT
65189 ACGATAGTCG
Statistics
Matches: 94, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
54 5 0.05
55 44 0.47
59 2 0.02
60 2 0.02
61 13 0.14
62 24 0.26
63 4 0.04
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (58 bp):
TTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAACTTCGCATTGCGTACATA
Found at i:65194 original size:42 final size:41
Alignment explanation
Indices: 65079--65213 Score: 173
Period size: 41 Copynumber: 3.3 Consensus size: 41
65069 ATTGCGACTA
* *
65079 TCGCATTGCGATTTACATATTCGCATTGCGATAG-CCGACT
1 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
65119 ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1 -TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
* * * * *
65161 TCGCATTGCGATAATCCAAATTCGCATTACGATAGTCGAAGT
1 TCGCATTGCGAT-TTACATATTCGCATTGCGATAGTCCAAGT
*
65203 TCGCGTTGCGA
1 TCGCATTGCGA
65214 ATCTGAAAAC
Statistics
Matches: 84, Mismatches: 8, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
41 46 0.55
42 38 0.45
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (41 bp):
TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
Found at i:66291 original size:3 final size:3
Alignment explanation
Indices: 66283--66333 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
66273 CGACTGCCCC
66283 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
66331 TAA
1 TAA
66334 GGGTAAACTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:68566 original size:39 final size:38
Alignment explanation
Indices: 68504--68746 Score: 147
Period size: 37 Copynumber: 6.8 Consensus size: 38
68494 AATATGATAT
68504 AAACTATA-A-ATATATA--TTTCAAAAATACGTTTTAGA
1 AAACTATATATATATATAGTTTTCAAAAATACGTTTT--A
*
68540 AAACTATATAT-TACATAGTTTTC--AAA-ACGTTTTA
1 AAACTATATATATATATAGTTTTCAAAAATACGTTTTA
*
68574 AAAATAT-TATATATATAAGTTTTCAAAAAT--GTTTTTA
1 AAACTATATATATATAT-AGTTTTCAAAAATACG-TTTTA
* * * *
68611 AAACTATAT-TATAGATA-ATTTCACAAAAAATGTTTTA
1 AAACTATATATATATATAGTTTTCA-AAAATACGTTTTA
*
68648 AAACTATATACTATATAT-GTTTTC-AAAGT--GTTTTA
1 AAACTATATA-TATATATAGTTTTCAAAAATACGTTTTA
* *
68683 AAAAT-TATATAATATAAAACGTTTTC-AAAAT--GTTTTCA
1 AAACTATATAT-ATAT-ATA-GTTTTCAAAAATACGTTTT-A
68721 AAACTATATATATA-AT-GTTTT-AAAAA
1 AAACTATATATATATATAGTTTTCAAAAA
68747 CTATATAATA
Statistics
Matches: 167, Mismatches: 16, Indels: 50
0.72 0.07 0.21
Matches are distributed among these distances:
33 4 0.02
34 28 0.17
35 23 0.14
36 22 0.13
37 61 0.37
38 10 0.06
39 19 0.11
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (38 bp):
AAACTATATATATATATAGTTTTCAAAAATACGTTTTA
Found at i:68610 original size:37 final size:34
Alignment explanation
Indices: 68539--68734 Score: 180
Period size: 37 Copynumber: 5.4 Consensus size: 34
68529 TACGTTTTAG
* *
68539 AAAACTATATAT-TACATAGTTTTCAAAACGTTTT
1 AAAACTATATATATATA-AGTTTTCAAAATGTTTT
*
68573 AAAAATATTATATATATAAGTTTTCAAAAATGTTTTT
1 AAAACTA-TATATATATAAGTTTTC-AAAATG-TTTT
* *
68610 AAAACTATATTATAGATAA-TTTCACAAAAAATGTTTT
1 AAAACTATA-TATATATAAGTTT-TC--AAAATGTTTT
* *
68647 AAAACTATATACTATATATGTTTTCAAAGTGTTTT
1 AAAACTATATA-TATATAAGTTTTCAAAATGTTTT
* *
68682 AAAAATTATATAATATAAAACGTTTTCAAAATGTTTT
1 -AAAACTATAT-ATATATAA-GTTTTCAAAATGTTTT
68719 CAAAACTATATATATA
1 -AAAACTATATATATA
68735 ATGTTTTAAA
Statistics
Matches: 134, Mismatches: 16, Indels: 22
0.78 0.09 0.13
Matches are distributed among these distances:
34 6 0.04
35 21 0.16
36 34 0.25
37 63 0.47
38 10 0.07
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (34 bp):
AAAACTATATATATATAAGTTTTCAAAATGTTTT
Found at i:68738 original size:23 final size:24
Alignment explanation
Indices: 68711--68759 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
68701 ACGTTTTCAA
*
68711 AATGTTTTCAAAACTATAT-ATAT
1 AATGTTTTAAAAACTATATAATAT
68734 AATGTTTTAAAAACTATATAATAT
1 AATGTTTTAAAAACTATATAATAT
68758 AA
1 AA
68760 ACGTTTCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (24 bp):
AATGTTTTAAAAACTATATAATAT
Found at i:68744 original size:60 final size:60
Alignment explanation
Indices: 68676--68806 Score: 196
Period size: 59 Copynumber: 2.2 Consensus size: 60
68666 GTTTTCAAAG
*
68676 TGTTTTAAAAATTATATAATATAAAACGTTTTCAAAATGTTTTCAAAACTATATA-TATA-A
1 TGTTTTAAAAATTATATAATAT-AAACGTTTCCAAAATGTTTTC-AAACTATATATTATATA
*
68736 TGTTTTAAAAACTATATAATATAAACGTTTCCAAAATGTTTTCAAACTATATATTATATA
1 TGTTTTAAAAATTATATAATATAAACGTTTCCAAAATGTTTTCAAACTATATATTATATA
*
68796 T-ATTTAAAAAT
1 TGTTTTAAAAAT
68807 ATTTTCAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
58 10 0.15
59 32 0.49
60 23 0.35
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.42
Consensus pattern (60 bp):
TGTTTTAAAAATTATATAATATAAACGTTTCCAAAATGTTTTCAAACTATATATTATATA
Found at i:68820 original size:37 final size:40
Alignment explanation
Indices: 68779--68870 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 40
68769 AAATGTTTTC
*
68779 AAACTATATATTATATATA-TTT-AAAAAT-ATTTTCAAA
1 AAACTATATATTATATAAATTTTCAAAAATCATTTTCAAA
* **
68816 AAACTATATA-TATATAAATTTTCGAAAATCATTTTCTGA
1 AAACTATATATTATATAAATTTTCAAAAATCATTTTCAAA
*
68855 AAATTATATATTATAT
1 AAACTATATATTATAT
68871 TTTGTCAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
36 7 0.15
37 13 0.28
38 5 0.11
39 16 0.35
40 5 0.11
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (40 bp):
AAACTATATATTATATAAATTTTCAAAAATCATTTTCAAA
Found at i:68826 original size:39 final size:38
Alignment explanation
Indices: 68783--68885 Score: 106
Period size: 38 Copynumber: 2.7 Consensus size: 38
68773 GTTTTCAAAC
*
68783 TATATATTATATATATTT-AAAAAT-ATTTTCAAAAAAC
1 TATATATTATATAT-TTTCAAAAATCATTTTCAAAAAAT
* * **
68820 TATATATATATAAATTTTCGAAAATCATTTTCTGAAAAT
1 TATATAT-TATATATTTTCAAAAATCATTTTCAAAAAAT
68859 TATATATTATAT-TTTGTCAAAAA-CATT
1 TATATATTATATATTT-TCAAAAATCATT
68886 ACAAACTGTA
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
37 17 0.31
38 21 0.38
39 17 0.31
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (38 bp):
TATATATTATATATTTTCAAAAATCATTTTCAAAAAAT
Found at i:69638 original size:81 final size:81
Alignment explanation
Indices: 69544--69804 Score: 294
Period size: 81 Copynumber: 3.2 Consensus size: 81
69534 CTTTTGGTCA
69544 CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAGCTTGATTTGCCTCTAAGTTGAATATATCAA
1 CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAGCTTGATTTGCCTCTAAGTTGAATATATCAA
69609 ACTCAAAGGTCTTTAG
66 ACTCAAAGGTCTTTAG
* * * * * * * * * ****
69625 CAGATAACCCTTCTTGACTTAAGCTATGCTGCAA--ATGATGTGCCT-TGGAGCTGAGCGGAGTC
1 CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAGCTTGATTTGCCTCT-AAGTTGAATATA-TC
* * *
69687 GAACTCGAAGGTCTTTTGG
64 AAACTCAAAGGTC-TTTAG
69706 TCACAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAGCTTGATTTGCCTCTAAGTTGAATATAA
1 ---CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAGCTTGATTTGCCTCTAAGTTGAATAT-A
69771 TCAAACTCAAAGGTCTTTAG
62 TCAAACTCAAAGGTCTTTAG
69791 CAGATAACCCTTCT
1 CAGATAACCCTTCT
69805 TGACTTAAGC
Statistics
Matches: 138, Mismatches: 32, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
78 1 0.01
79 15 0.11
80 13 0.09
81 33 0.24
82 14 0.10
84 29 0.21
85 4 0.03
86 27 0.20
87 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (81 bp):
CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAGCTTGATTTGCCTCTAAGTTGAATATATCAA
ACTCAAAGGTCTTTAG
Found at i:69722 original size:84 final size:82
Alignment explanation
Indices: 69479--70320 Score: 749
Period size: 84 Copynumber: 10.2 Consensus size: 82
69469 GATTTGCCTC
69479 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCAG-AGTCGAACTCGAAGGTCTTTTGGTC
1 TAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGC-GTAGTCGAACTCGAAGGTC-TTTGGTC
*
69543 ACAGATAACCCTTCTAGCCT
63 ACAGATAACCCTTCTAGACT
* * * * * * * *** * * *
69563 TGAGCTATTCTGTAAGCTTGATTTGCCTCTAAGTTGAATATA-TCAAACTCAAAGGTCTTTAG--
1 TAAGCTATGCTGCAA--ATGATGTGCCT-TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTC
*
69625 -CAGATAACCCTTCTTGACT
63 ACAGATAACCCTTCTAGACT
*
69644 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCA
1 TAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTCA
*
69709 CAGATAACCCTTCTAGCCT
64 CAGATAACCCTTCTAGACT
* * * * * * * *** * * * *
69728 TGAGCTATTCTGTAAGCTTGATTTGCCTCTAAGTTGAATATAATCAAACTCAAAGGTCTTTAG--
1 TAAGCTATGCTGCAA--ATGATGTGCCT-TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTC
*
69791 -CAGATAACCCTTCTTGACT
63 ACAGATAACCCTTCTAGACT
*
69810 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCA
1 TAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTCA
*
69875 CAGATAACCCTTCTAGCCT
64 CAGATAACCCTTCTAGACT
* * * * * **
69894 TGAGCTATTCTG-TAATGATGTG---TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGGCA
1 TAAGCTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCACA
*
69955 GACAACCCTTCTAGACT
66 GATAACCCTTCTAGACT
* * ** * **
69972 TAAGTTGTATTGCAAATGATGTGCCTTGGAGCTGAGCGAAGTCGAACTCGAAGGTCTTTGGTTGG
1 TAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TCA
* *
70037 CAGATAGCCCTTCTCGACT
64 CAGATAACCCTTCTAGACT
* * * * * **
70056 TAAGCTATGCCGCAAATGATGTGCCGTTGAGCTGATCGTAGTCAAACTCAAAGGTCTTTTGTTGG
1 TAAGCTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTCA
*
70121 CAGACAACCCTTCTAGACT
64 CAGATAACCCTTCTAGACT
* * * *
70140 TAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTCAC
1 TAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCAC
*
70205 AGATAACCCTTCTAGCCT
65 AGATAACCCTTCTAGACT
* * **
70223 TGAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTC-AAGGTC-TTGGTGGC
1 TAAGCTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCAC
* * * *
70286 AGGTAGCCCTTCTGGCCT
65 AGATAACCCTTCTAGACT
* *
70304 TGAGCTAAGCTGCAAAT
1 TAAGCTATGCTGCAAAT
70321 AGTTTGTTCA
Statistics
Matches: 606, Mismatches: 124, Indels: 59
0.77 0.16 0.07
Matches are distributed among these distances:
78 30 0.05
79 51 0.08
80 42 0.07
81 73 0.12
82 36 0.06
83 105 0.17
84 201 0.33
85 23 0.04
86 43 0.07
87 2 0.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (82 bp):
TAAGCTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCACA
GATAACCCTTCTAGACT
Found at i:69751 original size:165 final size:166
Alignment explanation
Indices: 69479--70226 Score: 957
Period size: 166 Copynumber: 4.5 Consensus size: 166
69469 GATTTGCCTC
*
69479 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCAGAGTCGAACTCGAAGGTCTTTTGGTCA
1 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCA
*
69544 CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAGCTTGATTTGCCTCTAAGTTGAATATA-TCA
66 CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAA--TTGATTTGCCTCTAAGCTGAATATAGTCA
* *
69608 AACTCAAAGGTC-T-TTAGCAGATAACCCTTCTTGACT
129 AACTCAAAGGTCTTGTTAGCAGACAACCCTTCTAGACT
69644 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCA
1 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCA
* *
69709 CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAGCTTGATTTGCCTCTAAGTTGAATATAATCA
66 CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAA--TTGATTTGCCTCTAAGCTGAATATAGTCA
* *
69774 AACTCAAAGGTC-T-TTAGCAGATAACCCTTCTTGACT
129 AACTCAAAGGTCTTGTTAGCAGACAACCCTTCTAGACT
69810 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCA
1 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCA
* * *** *
69875 CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAA-TGA--TG--TGTGAGCTGAGCGTAGTCGAA
66 CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAATTGATTTGCCTCTAAGCTGAATATAGTCAAA
*
69935 CTCAAAGGTCTTTGTTGGCAGACAACCCTTCTAGACT
131 CTCAAAGGTC-TTGTTAGCAGACAACCCTTCTAGACT
* * ** * *
69972 TAAGTTGTATTGCAAATGATGTGCCTTGGAGCTGAGCGAAGTCGAACTCGAAGGTC-TTTGGTTG
1 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGG-TC
* * * * * * * * * * * *
70036 GCAGATAGCCCTTCTCGACTTAAGCTATGCCGCAAATGATGTGCCGT-TGAGCTG-ATCGTAGTC
65 ACAGATAACCCTTCTAGCCTTGAGCTATTCTGTAATTGATTTGCC-TCTAAGCTGAAT-ATAGTC
*
70099 AAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACT
128 AAACTCAAAGGTC--TTGTTAGCAGACAACCCTTCTAGACT
* * * **
70140 TAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTC-TTTGGTCA
1 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCA
70204 CAGATAACCCTTCTAGCCTTGAG
66 CAGATAACCCTTCTAGCCTTGAG
70227 TTATGCTGCA
Statistics
Matches: 530, Mismatches: 40, Indels: 24
0.89 0.07 0.04
Matches are distributed among these distances:
159 23 0.04
161 8 0.02
162 99 0.19
163 6 0.01
165 127 0.24
166 138 0.26
167 45 0.08
168 84 0.16
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (166 bp):
TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCA
CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAATTGATTTGCCTCTAAGCTGAATATAGTCAAA
CTCAAAGGTCTTGTTAGCAGACAACCCTTCTAGACT
Found at i:70058 original size:246 final size:246
Alignment explanation
Indices: 69605--70320 Score: 693
Period size: 246 Copynumber: 2.9 Consensus size: 246
69595 GTTGAATATA
* * * *
69605 TCAAACTCAAAGGTC-TTTAG---CAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGT
1 TCAAACTCAAAGGTCTTTTGGTCACAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATAT
** * * * *
69666 GCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGA
66 G-C-TGGAGCTGAGCATAGTCGAACTCAAAGGTC-TTTGGTCACAGACAACCCTTCTAGACTTAA
* * * * * * * ** * * *
69731 GCTATTCTGTAAGCTTGATTTGCC-TCTAAGTTGA-ATATAATCAAACTCAAAGGTCTT--TAGC
128 GTTATACTGCAA--ATGATGTGCCGT-TGAGCTGAGCGA-AGTCGAACTC-AAGGTCTTGGTGGC
* *
69792 AGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGGAG
188 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGGAG
* * * * * * * *
69851 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGCTATTCTG-TAATGATGT
1 TCAAACTCAAAGGTCTTTTGGTCACAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATAT
* * **
69915 G-T-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGGCAGACAACCCTTCTAGACTTAAGTT
66 GCTGGAGCTGAGCATAGTCGAACTCAAAGGTCTTTGGTCACAGACAACCCTTCTAGACTTAAGTT
* *
69978 GTATTGCAAATGATGTGCC-TTGGAGCTGAGCGAAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
131 ATACTGCAAATGATGTGCCGTT-GAGCTGAGCGAAGTCGAACTC-AAGGTC-TTGG-TGGCAGAT
* * *
70042 AGCCCTTCTCGACTTAAGCTATGCCGCAAATGATGTGCCGTTGAGCTGATCGTAG
192 AGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGGAG
* ** * *
70097 TCAAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
1 TCAAACTCAAAGGTCTTTTGGTCACAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATAT
* * * *
70162 GCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 G-C-TGGAGCTGAGCATAGTCGAACTCAAAGGTCTTTGGTCACAGACAACCCTTCTAGACTTAAG
* * *
70227 TTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAGGTCTTGGTGGCAGGTAG
129 TTATACTGCAAATGATGTGCCGTTGAGCTGAGCGAAGTCGAACTCAAGGTCTTGGTGGCAGATAG
* * * *
70292 CCCTTCTGGCCTTGAGCTAAGCTGCAAAT
194 CCCTTCTCGACTTAAGCTATGCTGCAAAT
70321 AGTTTGTTCA
Statistics
Matches: 386, Mismatches: 67, Indels: 32
0.80 0.14 0.07
Matches are distributed among these distances:
241 1 0.00
242 28 0.07
243 3 0.01
244 31 0.08
245 26 0.07
246 112 0.29
247 14 0.04
248 33 0.09
249 13 0.03
250 34 0.09
251 89 0.23
252 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.29
Consensus pattern (246 bp):
TCAAACTCAAAGGTCTTTTGGTCACAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATAT
GCTGGAGCTGAGCATAGTCGAACTCAAAGGTCTTTGGTCACAGACAACCCTTCTAGACTTAAGTT
ATACTGCAAATGATGTGCCGTTGAGCTGAGCGAAGTCGAACTCAAGGTCTTGGTGGCAGATAGCC
CTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGGAG
Found at i:73639 original size:18 final size:18
Alignment explanation
Indices: 73616--73659 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
73606 AGTTAATGTG
73616 AATGCAAAGAAAATAACA
1 AATGCAAAGAAAATAACA
*
73634 AATGCAAAGAAAATAAGA
1 AATGCAAAGAAAATAACA
73652 AATGCAAA
1 AATGCAAA
73660 TGTCTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.66, C:0.09, G:0.14, T:0.11
Consensus pattern (18 bp):
AATGCAAAGAAAATAACA
Found at i:77074 original size:38 final size:35
Alignment explanation
Indices: 76984--77304 Score: 214
Period size: 38 Copynumber: 8.9 Consensus size: 35
76974 ATATACATAG
*
76984 TTTTCAAAACG-TTTTAAAA-TATATATTATATAA
1 TTTTCAAAATGTTTTTAAAACTATATATTATATAA
77017 GTTTTCAAAAATGTTTTTAAAACTATATATTATATAA
1 -TTTTC-AAAATGTTTTTAAAACTATATATTATATAA
* * *
77054 TTTCACAAAAAATGTTTTTAAAACTATATACTATATATG
1 TTT-TC--AAAATGTTTTTAAAACTATATATTATATA-A
* * * *
77093 TTTTCAAAGTGTTTTAAAAATTATATAATATATAAA
1 TTTTCAAAATGTTTTTAAAACTATATATTATAT-AA
*
77129 CGTTTTCAAAATGTTTTCAAAACTATATA-T-TAT-A
1 --TTTTCAAAATGTTTTTAAAACTATATATTATATAA
* *
77163 ---T---AATGTTTTAAAAACTATATAATATATAAA
1 TTTTCAAAATGTTTTTAAAACTATATATTATAT-AA
* *
77193 CGTTTCCAAAATGTTTTCAAAACTATATATTATATATA
1 --TTTTCAAAATGTTTTTAAAACTATATATTATATA-A
** * * *
77231 TTTAAAAAATATTTTCAAAAACTATATAATATATAAA
1 TTTTCAAAATGTTTT-TAAAACTATATATTATAT-AA
* *
77268 TTTTCGAAAATCATTTTCTGAAAATTATATATTATAT
1 TTTTC-AAAAT-GTTTT-T-AAAACTATATATTATAT
77305 TTTGTCAAAA
Statistics
Matches: 233, Mismatches: 27, Indels: 48
0.76 0.09 0.16
Matches are distributed among these distances:
26 19 0.08
27 1 0.00
28 3 0.01
29 1 0.00
30 1 0.00
34 6 0.03
35 5 0.02
36 50 0.21
37 38 0.16
38 85 0.36
39 9 0.04
40 15 0.06
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (35 bp):
TTTTCAAAATGTTTTTAAAACTATATATTATATAA
Found at i:77118 original size:74 final size:74
Alignment explanation
Indices: 76995--77304 Score: 267
Period size: 74 Copynumber: 4.3 Consensus size: 74
76985 TTTCAAAACG
* * *
76995 TTTTAAAA-TATATATTATATAAGTTTTCAAAAATGTTTTTAAAACTATATATTATAT-AA-TTT
1 TTTTAAAACTATATATTATATATGTTTTCAAAAATGTTTTAAAAACTATATAATATATAAACTTT
77057 CACAAAAAATGT
66 -AC--AAAATGT
* * *
77069 TTTTAAAACTATATACTATATATGTTTTC-AAAGTGTTTTAAAAATTATATAATATATAAACGTT
1 TTTTAAAACTATATATTATATATGTTTTCAAAAATGTTTTAAAAACTATATAATATATAAAC-TT
*
77133 TTCAAAATGT
65 TACAAAATGT
*
77143 TTTCAAAACTATATA-T-TATA-----T----AATGTTTTAAAAACTATATAATATATAAACGTT
1 TTTTAAAACTATATATTATATATGTTTTCAAAAATGTTTTAAAAACTATATAATATATAAAC-TT
*
77197 TCCAAAATGT
65 TACAAAATGT
* * * *
77207 TTTCAAAACTATATATTATATAT-ATTTAAAAAATATTTTCAAAAACTATATAATATATAAA-TT
1 TTTTAAAACTATATATTATATATGTTTTCAAAAATGTTTT-AAAAACTATATAATATATAAACTT
* *
77270 TTCGAAAATCAT
65 TAC-AAAAT-GT
*
77282 TTTCTGAAAATTATATATTATAT
1 TTT-T-AAAACTATATATTATAT
77305 TTTGTCAAAA
Statistics
Matches: 201, Mismatches: 16, Indels: 35
0.80 0.06 0.14
Matches are distributed among these distances:
64 55 0.27
65 1 0.00
66 4 0.02
67 1 0.00
70 1 0.00
72 4 0.02
73 5 0.02
74 65 0.32
75 45 0.22
76 1 0.00
77 19 0.09
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (74 bp):
TTTTAAAACTATATATTATATATGTTTTCAAAAATGTTTTAAAAACTATATAATATATAAACTTT
ACAAAATGT
Found at i:77167 original size:26 final size:26
Alignment explanation
Indices: 77138--77191 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
77128 ACGTTTTCAA
* *
77138 AATGTTTTCAAAACTATATATTATAT
1 AATGTTTTAAAAACTATATAATATAT
77164 AATGTTTTAAAAACTATATAATATAT
1 AATGTTTTAAAAACTATATAATATAT
77190 AA
1 AA
77192 ACGTTTCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (26 bp):
AATGTTTTAAAAACTATATAATATAT
Found at i:77185 original size:64 final size:64
Alignment explanation
Indices: 77102--77228 Score: 236
Period size: 64 Copynumber: 2.0 Consensus size: 64
77092 GTTTTCAAAG
* *
77102 TGTTTTAAAAATTATATAATATATAAACGTTTTCAAAATGTTTTCAAAACTATATATTATATAA
1 TGTTTTAAAAACTATATAATATATAAACGTTTCCAAAATGTTTTCAAAACTATATATTATATAA
77166 TGTTTTAAAAACTATATAATATATAAACGTTTCCAAAATGTTTTCAAAACTATATATTATATA
1 TGTTTTAAAAACTATATAATATATAAACGTTTCCAAAATGTTTTCAAAACTATATATTATATA
77229 TATTTAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.43
Consensus pattern (64 bp):
TGTTTTAAAAACTATATAATATATAAACGTTTCCAAAATGTTTTCAAAACTATATATTATATAA
Found at i:77203 original size:28 final size:26
Alignment explanation
Indices: 77143--77203 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
77133 TTCAAAATGT
* *
77143 TTTC-AAAACTATATATTATATAATG
1 TTTCAAAAACTATATAATATATAACG
*
77168 TTTTAAAAACTATATAATATATAAACG
1 TTTCAAAAACTATATAATATAT-AACG
*
77195 TTTCCAAAA
1 TTTCAAAAA
77204 TGTTTTCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 3 0.10
26 16 0.55
27 10 0.34
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (26 bp):
TTTCAAAAACTATATAATATATAACG
Done.