Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001930.1 Hibiscus syriacus cultivar Beakdansim tig00003902_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: 80489
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:12892 original size:17 final size:18
Alignment explanation
Indices: 12862--12906 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
12852 AGGAATTGGT
*
12862 ATAA-TGAAATTATATGA
1 ATAAGTGAAAATATATGA
12879 ATAAGT-AAAATATATGA
1 ATAAGTGAAAATATATGA
12896 ATAAGTGAAAA
1 ATAAGTGAAAA
12907 AGTAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (18 bp):
ATAAGTGAAAATATATGA
Found at i:18110 original size:17 final size:18
Alignment explanation
Indices: 18080--18123 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
18070 AGGAATTGGT
18080 ATAA-TGAAATTATATGA
1 ATAAGTGAAATTATATGA
18097 ATAAGTGAAA-TATATGA
1 ATAAGTGAAATTATATGA
*
18114 ACAAGTGAAA
1 ATAAGTGAAA
18124 AAGTAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.55, C:0.02, G:0.16, T:0.27
Consensus pattern (18 bp):
ATAAGTGAAATTATATGA
Found at i:18514 original size:23 final size:23
Alignment explanation
Indices: 18484--18576 Score: 118
Period size: 23 Copynumber: 4.0 Consensus size: 23
18474 ATGGTTCTAC
*
18484 GTGGTCCTTAGGGACATTTATAT
1 GTGGTCCTTCGGGACATTTATAT
*
18507 GTGGTCCTTCGGG--ATATATAT
1 GTGGTCCTTCGGGACATTTATAT
*
18528 GTGGTCCTTCGGGACATTTCTAT
1 GTGGTCCTTCGGGACATTTATAT
*
18551 GTGGTCCTTCGAGACAAATTTATAT
1 GTGGTCCTTCGGGAC--ATTTATAT
18576 G
1 G
18577 CCCCTAGTGG
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
21 20 0.33
23 32 0.53
25 8 0.13
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38
Consensus pattern (23 bp):
GTGGTCCTTCGGGACATTTATAT
Found at i:19476 original size:23 final size:22
Alignment explanation
Indices: 19450--19493 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
19440 TCTAACGAAC
* *
19450 TAAAAATTCTAATTAATAAATTT
1 TAAAAATCCTAAATAA-AAATTT
19473 TAAAAATCCTAAATAAAAATT
1 TAAAAATCCTAAATAAAAATT
19494 ATATGCAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAAAATCCTAAATAAAAATTT
Found at i:22523 original size:30 final size:30
Alignment explanation
Indices: 22452--22563 Score: 127
Period size: 30 Copynumber: 3.6 Consensus size: 30
22442 TCGGATTAGC
22452 ACTATAGTGTGCT-AGGACACTTAGTACATATAGT
1 ACTATAGTGTG-TAAGGACACTTAGTAC----AGT
22486 ACTATAGTGTGTAAGGACACTTAGTACAGT
1 ACTATAGTGTGTAAGGACACTTAGTACAGT
* * * *
22516 GCTATAGTGTGTAAGGAAACTTAGTATAGC
1 ACTATAGTGTGTAAGGACACTTAGTACAGT
*
22546 ACTGTAGTGTGTAAGGAC
1 ACTATAGTGTGTAAGGAC
22564 GCTCAGTGCA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
30 44 0.63
33 1 0.01
34 25 0.36
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.30
Consensus pattern (30 bp):
ACTATAGTGTGTAAGGACACTTAGTACAGT
Found at i:22579 original size:30 final size:30
Alignment explanation
Indices: 22545--22601 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
22535 CTTAGTATAG
* *
22545 CACTGTAGTGTGTAAGGACGCTCAGTGCAT
1 CACTGTAGTATGTAAGGACACTCAGTGCAT
*
22575 CACTGTGGTATGTAAGGACACTCAGTG
1 CACTGTAGTATGTAAGGACACTCAGTG
22602 TATATAGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (30 bp):
CACTGTAGTATGTAAGGACACTCAGTGCAT
Found at i:26208 original size:3 final size:3
Alignment explanation
Indices: 26195--26224 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
26185 TAATGAGTAA
*
26195 AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
26225 TAAATAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:31192 original size:23 final size:22
Alignment explanation
Indices: 31166--31208 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
31156 TCTAACGAAC
* *
31166 TAAAACTCCTAATTAATAAATAT
1 TAAAAATCCTAAATAA-AAATAT
31189 TAAAAATCCTAAATAAAAAT
1 TAAAAATCCTAAATAAAAAT
31209 TATATGCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAATCCTAAATAAAAATAT
Found at i:38334 original size:31 final size:30
Alignment explanation
Indices: 38280--38404 Score: 128
Period size: 31 Copynumber: 4.0 Consensus size: 30
38270 GATCCTCGGC
* *
38280 AACTGTCCATAGGTTCCGAAGAACCTAGGT
1 AACTGTCCATATGTTCCGAAGAACATAGGT
**
38310 GAACTGTCCATATGTTCCTTAGAACATAGGT
1 -AACTGTCCATATGTTCCGAAGAACATAGGT
*
38341 ATACTGTTCATATG-TCTCGAA-AGACATAGGT
1 A-ACTGTCCATATGTTC-CGAAGA-ACATAGGT
*
38372 AATTCTGTCCATATGTTCCGTAGAACATAGGT
1 AA--CTGTCCATATGTTCCGAAGAACATAGGT
38404 A
1 A
38405 CCCTCGACTC
Statistics
Matches: 78, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
30 5 0.06
31 48 0.62
32 22 0.28
33 3 0.04
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (30 bp):
AACTGTCCATATGTTCCGAAGAACATAGGT
Found at i:43442 original size:20 final size:20
Alignment explanation
Indices: 43397--43442 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
43387 GACCAACAAA
*
43397 ATCGCAATGCGATCGCTAAT
1 ATCGCAACGCGATCGCTAAT
* *
43417 -TCGCAACGCGATCTCTATT
1 ATCGCAACGCGATCGCTAAT
43436 ATCGCAA
1 ATCGCAA
43443 ATCAGTTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCGCTAAT
Found at i:43614 original size:21 final size:21
Alignment explanation
Indices: 43580--43652 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
43570 ATACTGACTA
* *
43580 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
43601 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
** *
43621 TCGCGTTGTGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
43642 TCGCAATGCGA
1 TCGCAATGCGA
43653 ATACGTAAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:43667 original size:20 final size:20
Alignment explanation
Indices: 43642--43755 Score: 158
Period size: 20 Copynumber: 5.7 Consensus size: 20
43632 TTTTCATAAT
43642 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
43662 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
43682 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
*
43702 TCGCAATGCGAATTA-ATAAAA
1 TCGCAATGCGAA-TACGT-AAA
43723 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
43743 TCGCAATGCGAAT
1 TCGCAATGCGAAT
43756 CTTACTATCA
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
20 66 0.79
21 18 0.21
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:44329 original size:19 final size:19
Alignment explanation
Indices: 44276--44337 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
44266 AGAATAGTTT
44276 CGAG-AATGAAAATCGCAA
1 CGAGAAATGAAAATCGCAA
* *
44294 CGCGGAAAT-AACTATCGCAA
1 CG-AGAAATGAA-AATCGCAA
44314 CGAGAAATGAAAATCGCAA
1 CGAGAAATGAAAATCGCAA
44333 CGAGA
1 CGAGA
44338 TAATCGCAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 2 0.06
19 20 0.56
20 14 0.39
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (19 bp):
CGAGAAATGAAAATCGCAA
Found at i:48040 original size:14 final size:14
Alignment explanation
Indices: 48020--48056 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
48010 GATTGTTTAA
48020 TTGATTTGTAAAA-
1 TTGATTTGTAAAAG
48033 TGTGATTTGTAAAAG
1 T-TGATTTGTAAAAG
48048 TTGATTTGT
1 TTGATTTGT
48057 TTAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:48190 original size:19 final size:19
Alignment explanation
Indices: 48168--48259 Score: 69
Period size: 19 Copynumber: 5.4 Consensus size: 19
48158 AAAAATTACT
48168 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
48187 ATCGCAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
48201 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* * *
48220 ATCACAA--C--TA-GAGA
1 ATCGCAATGCGAAATGAAA
*
48234 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
48253 ATCGCAA
1 ATCGCAA
48260 CGACAAAATC
Statistics
Matches: 54, Mismatches: 9, Indels: 20
0.65 0.11 0.24
Matches are distributed among these distances:
14 19 0.35
15 2 0.04
16 3 0.06
17 3 0.06
18 2 0.04
19 25 0.46
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:48210 original size:33 final size:33
Alignment explanation
Indices: 48168--48280 Score: 163
Period size: 33 Copynumber: 3.4 Consensus size: 33
48158 AAAAATTACT
*
48168 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
* * *
48201 ATCGCAATGCGAAATGAAAATCACAACTAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
* *
48234 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
48267 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
48281 CTAAATTCGC
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 71 1.00
ACGTcount: A:0.48, C:0.20, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:48367 original size:52 final size:52
Alignment explanation
Indices: 48286--48403 Score: 200
Period size: 52 Copynumber: 2.3 Consensus size: 52
48276 CGAAACTAAA
* *
48286 TTCGCGTTGCGATTTTCATTTCGCTTTGCGATTCCCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
* *
48338 TTCGCATTGCGATTTTCATTTTGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
48390 TTCGCATTGCGATT
1 TTCGCATTGCGATT
48404 ATCTCATTGC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.47
Consensus pattern (52 bp):
TTCGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
Found at i:48381 original size:33 final size:33
Alignment explanation
Indices: 48342--48435 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
48332 TTTCATTTCG
* *
48342 CATTGCGATTTTCATTTTGCATTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCATTGCGATTATCT
*
48375 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CATTGCGATTTTCATTTCGCATTGCGATTATCT
48408 CATTGCGATTTTCATTTCGCATTGCGAT
1 CATTGCGATTTTCATTTCGCATTGCGAT
48436 AGTAATTTCC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.46
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCATTGCGATTATCT
Found at i:48501 original size:20 final size:20
Alignment explanation
Indices: 48429--48501 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
48419 TCATTTCGCA
* *
48429 TTGCGATAGTAATTTCCGCG
1 TTGCGATAGTCATTTCCGTG
* **
48449 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCCG-TG
48469 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCCGTG
48490 TTGCGATAGTCA
1 TTGCGATAGTCA
48502 AATGATTGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.08
20 22 0.55
21 12 0.30
22 3 0.08
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:50652 original size:12 final size:12
Alignment explanation
Indices: 50635--50671 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
50625 TCTTCGGGGA
50635 CTTTTTCTTCTT
1 CTTTTTCTTCTT
50647 CTTTTTCTTCTT
1 CTTTTTCTTCTT
50659 CTTTTTCTTCTT
1 CTTTTTCTTCTT
50671 C
1 C
50672 AGGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:51761 original size:41 final size:41
Alignment explanation
Indices: 51716--51828 Score: 122
Period size: 41 Copynumber: 2.8 Consensus size: 41
51706 GCGAATTTGG
*
51716 AAAATCGCAATGCGATACTGACTATCACAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCACAACGAGATAATAC
* * * *
51757 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTATCACAACGAGATAAT-AC
** * *
51799 --TTTCGCAACGCGATACTGACTTTCGCAACG
1 AAAATCGCAACGCGATACTGACTATCACAACG
51829 CGATTCTGAC
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
40 28 0.44
41 34 0.53
42 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.21
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCACAACGAGATAATAC
Found at i:51877 original size:20 final size:20
Alignment explanation
Indices: 51761--51868 Score: 189
Period size: 20 Copynumber: 5.4 Consensus size: 20
51751 TAATACAAAA
51761 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
51781 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
51801 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
51821 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
* *
51841 TCGCAACGAGATTCTGACTT
1 TCGCAACGCGATACTGACTT
51861 TCGCAACG
1 TCGCAACG
51869 AGATTCTGAA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 86 1.00
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:51885 original size:40 final size:40
Alignment explanation
Indices: 51715--51886 Score: 182
Period size: 40 Copynumber: 4.3 Consensus size: 40
51705 TGCGAATTTG
* * * *
51715 GAAAATCGCAATGCGATACTGACTATCACAACGAGATAAT
1 GAAAATCGCAACGCGATACTGACTTTCGCAACGAGATACT
* *
51755 ACAAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT
1 -GAAAATCGCAACGCGATACTGACTTTCGCAACGAGATACT
*** * *
51796 GACTTTCGCAACGCGATACTGACTTTCGCAACGCGATTCT
1 GAAAATCGCAACGCGATACTGACTTTCGCAACGAGATACT
*** * * *
51836 GACTTTCGCAACGAGATTCTGACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGCGATACTGACTTTCGCAACGAGATACT
51876 GAAAATCGCAA
1 GAAAATCGCAA
51887 TCATCTTCAA
Statistics
Matches: 114, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
40 80 0.70
41 34 0.30
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (40 bp):
GAAAATCGCAACGCGATACTGACTTTCGCAACGAGATACT
Found at i:51885 original size:60 final size:60
Alignment explanation
Indices: 51720--51886 Score: 199
Period size: 60 Copynumber: 2.8 Consensus size: 60
51710 ATTTGGAAAA
* * * * * *
51720 TCGCAATGCGATACTGACTATCACAACGAGATAATACAAAATCGCAACGCGATACTGACTT
1 TCGCAACGAGATACTGACTTTCGCAACGAGATACT-GAAAATCGCAACGCGATACTGACTT
* * *** *
51781 TCGCAACGCGATACTGACTTTCGCAACGCGATACTGACTTTCGCAACGCGATTCTGACTT
1 TCGCAACGAGATACTGACTTTCGCAACGAGATACTGAAAATCGCAACGCGATACTGACTT
* *
51841 TCGCAACGAGATTCTGACTTTCGCAACGAGATTCTGAAAATCGCAA
1 TCGCAACGAGATACTGACTTTCGCAACGAGATACTGAAAATCGCAA
51887 TCATCTTCAA
Statistics
Matches: 89, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 59 0.66
61 30 0.34
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (60 bp):
TCGCAACGAGATACTGACTTTCGCAACGAGATACTGAAAATCGCAACGCGATACTGACTT
Found at i:52125 original size:20 final size:20
Alignment explanation
Indices: 52100--52178 Score: 140
Period size: 20 Copynumber: 4.0 Consensus size: 20
52090 CAACGGGGAA
52100 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
52120 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* *
52140 ATTGCAACGCGAAAATGGTT
1 ATCGCAACGCGAAAATGGCT
52160 ATCGCAACGCGAAAATGGC
1 ATCGCAACGCGAAAATGGC
52179 AATGCGAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:52127 original size:34 final size:34
Alignment explanation
Indices: 52084--52187 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 34
52074 ATTCATTTGA
* *
52084 CTATCGCAACGGGGAAATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATCGCAACGCGAAAATGG
52118 CTATCGCAACGCGAAAATGGCTATTGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAAT--C----GCAACGCGAAAATGG
* * *
52158 TTATCGCAACGCGAAAATGGCAATGCGAAA
1 CTATCGCAACGCGAAAATCGCAACGCGAAA
52188 TGAAAATCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
34 26 0.44
36 1 0.02
40 32 0.54
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (34 bp):
CTATCGCAACGCGAAAATCGCAACGCGAAAATGG
Found at i:52240 original size:19 final size:19
Alignment explanation
Indices: 52218--52257 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
52208 TCTCGTTGCA
52218 ATTTTCATTTCGCATTACG
1 ATTTTCATTTCGCATTACG
*
52237 ATTTTCATTTCGCATTGCG
1 ATTTTCATTTCGCATTACG
52256 AT
1 AT
52258 ATTCTCGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.47
Consensus pattern (19 bp):
ATTTTCATTTCGCATTACG
Found at i:53887 original size:41 final size:42
Alignment explanation
Indices: 53842--53933 Score: 132
Period size: 41 Copynumber: 2.2 Consensus size: 42
53832 CCTCTTCAAC
* * *
53842 GATGACAGTGGCCTCTTGAACGGTAG-GGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATAGAAGGGGACTCTTGAGG
* *
53883 GATGATAGGGGCCTCTTGAACGATTGAAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATAGAAGGGGACTCTTGAGG
53925 GATGACAGG
1 GATGACAGG
53934 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 22 0.50
42 22 0.50
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATAGAAGGGGACTCTTGAGG
Found at i:53898 original size:21 final size:20
Alignment explanation
Indices: 53869--53929 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
53859 GAACGGTAGG
53869 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGA-A
* **
53890 GGGGCCTCTTGAACGATTGAA
1 GGGGACTCTTGAGGGA-TGAA
53911 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
53930 CAGGTGAGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 3 0.09
21 27 0.82
22 3 0.09
ACGTcount: A:0.23, C:0.13, G:0.41, T:0.23
Consensus pattern (20 bp):
GGGGACTCTTGAGGGATGAA
Found at i:54296 original size:20 final size:20
Alignment explanation
Indices: 54271--54343 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
54261 GAAGAATAGT
*
54271 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
54291 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* * * *
54311 TGACTATCGCAACGCGGAAA
1 TTACTTTCGCAACACGAAAA
* *
54331 TGACTATCGCAAC
1 TTACTTTCGCAAC
54344 GCGGAAATGG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:54321 original size:40 final size:39
Alignment explanation
Indices: 54277--54383 Score: 133
Period size: 40 Copynumber: 2.7 Consensus size: 39
54267 TAGTTTACTT
* * *
54277 TCGCAACACGAAACTTACTTTCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAA-TGACTATCGCAACGCGAAAATGACTA
* *
54317 TCGCAACGCGGAAATGACTATCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGACTATCGCAACGCGAAAATGACTA
**
54357 TCGCAACGCGAAATGAAAATCGCAACG
1 TCGCAACGCGAAATGACTATCGCAACG
54384 ACAAAATCGC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
39 16 0.27
40 39 0.66
41 4 0.07
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.16
Consensus pattern (39 bp):
TCGCAACGCGAAATGACTATCGCAACGCGAAAATGACTA
Found at i:54344 original size:20 final size:20
Alignment explanation
Indices: 54297--54383 Score: 131
Period size: 20 Copynumber: 4.4 Consensus size: 20
54287 AAACTTACTT
*
54297 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
54317 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
54337 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
**
54357 TCGCAACGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
54376 TCGCAACG
1 TCGCAACG
54384 ACAAAATCGC
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
19 15 0.24
20 47 0.76
ACGTcount: A:0.37, C:0.25, G:0.24, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:54391 original size:14 final size:14
Alignment explanation
Indices: 54372--54428 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
54362 ACGCGAAATG
54372 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
54386 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
*
54405 AAAATCTCAACGAC
1 AAAATCGCAACGAC
54419 AAAATCGCAA
1 AAAATCGCAA
54429 TGCGAAACAC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.51, C:0.23, G:0.14, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:54443 original size:33 final size:33
Alignment explanation
Indices: 54356--54435 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
54346 GGAAATGGCT
*
54356 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
54389 ATCGCAATGCGAAATGAAAATCTCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
54422 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
54436 CACAAATCGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:54464 original size:19 final size:19
Alignment explanation
Indices: 54442--54538 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
54432 GAAACACAAA
54442 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
54461 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
54477 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
54494 TCGCATTGTGA-TTT--TG
1 TCGCATTGCGATTTTCATT
54510 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
54527 TCGCATTGCGAT
1 TCGCATTGCGAT
54539 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 11 0.18
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 22 0.36
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:54483 original size:14 final size:14
Alignment explanation
Indices: 54464--54522 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
54454 TTTCATTTCG
54464 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
54478 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
*
54495 CGCATTGTGATTTTGT
1 CG--TTGCGATTTTGT
54511 CGTTGCGATTTT
1 CGTTGCGATTTT
54523 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 17 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 5 0.14
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:54489 original size:33 final size:33
Alignment explanation
Indices: 54447--54538 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
54437 ACAAATCGCA
*
54447 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
54480 TTGCGATTTTCATTTCGCATTGTGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
54513 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
54539 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:54557 original size:20 final size:19
Alignment explanation
Indices: 54523--54577 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
54513 TTGCGATTTT
*
54523 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
54542 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
54562 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
54578 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:55141 original size:18 final size:18
Alignment explanation
Indices: 55118--55165 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
55108 CGGGTCGATC
*
55118 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTAGGTG
*
55136 AGGTGATAGCTCTAGGTG
1 AGGTGATGGCTCTAGGTG
55154 AGGTGATGGCTC
1 AGGTGATGGCTC
55166 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.12, G:0.44, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTAGGTG
Found at i:56510 original size:20 final size:20
Alignment explanation
Indices: 56485--56522 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56475 AATAGTTTCT
*
56485 GAAAATGAAAATTGCAACAC
1 GAAAATGAAAATCGCAACAC
*
56505 GAAAATGACAATCGCAAC
1 GAAAATGAAAATCGCAAC
56523 GCAAATTTGA
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:0.53, C:0.18, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:56834 original size:22 final size:22
Alignment explanation
Indices: 56807--56849 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
56797 ATGGAGATAC
*
56807 ACGGATTTTATCGGAGATGGGG
1 ACGGATTTCATCGGAGATGGGG
*
56829 ACGGATTTCGTCGGAGATGGG
1 ACGGATTTCATCGGAGATGGG
56850 TGAGAGAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.42, T:0.26
Consensus pattern (22 bp):
ACGGATTTCATCGGAGATGGGG
Found at i:57066 original size:20 final size:20
Alignment explanation
Indices: 57036--57191 Score: 154
Period size: 20 Copynumber: 7.7 Consensus size: 20
57026 GATTATGTAT
* *
57036 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * * *
57056 TATTGCGTTGCGAAATTAAG
1 TATCGCGTTGCGATAGTCAG
* *
57076 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
57096 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
* *
57117 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
57138 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
57158 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
57178 TATCGCGTTGCGAT
1 TATCGCGTTGCGAT
57192 TTTCCAAATT
Statistics
Matches: 119, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
19 3 0.03
20 79 0.66
21 35 0.29
22 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:57122 original size:21 final size:22
Alignment explanation
Indices: 57091--57194 Score: 130
Period size: 21 Copynumber: 5.0 Consensus size: 22
57081 AGTTGCGAAA
57091 GTCAGTATCGCGTTGCGATTTT
1 GTCAGTATCGCGTTGCGATTTT
*
57113 GT-ATTATCGCGTTGCGATTTT
1 GTCAGTATCGCGTTGCGATTTT
* *
57134 GT-ATTATCGCGTTGCGA--TA
1 GTCAGTATCGCGTTGCGATTTT
*
57153 GTCAGTATCGCGTTGCGA--TA
1 GTCAGTATCGCGTTGCGATTTT
57173 GTCAGTATCGCGTTGCGATTTT
1 GTCAGTATCGCGTTGCGATTTT
57195 CCAAATTCGC
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
19 3 0.04
20 34 0.45
21 35 0.47
22 3 0.04
ACGTcount: A:0.16, C:0.17, G:0.27, T:0.39
Consensus pattern (22 bp):
GTCAGTATCGCGTTGCGATTTT
Found at i:57149 original size:62 final size:61
Alignment explanation
Indices: 57036--57194 Score: 187
Period size: 62 Copynumber: 2.6 Consensus size: 61
57026 GATTATGTAT
* * * ** * *
57036 TATCTCGTTGCGAAAGTCAGTATTGCGTTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTGTATTATCGAGTTGCGAAAGTCAG
* * * *
57096 TATCGCGTTGCGATTTTGT-ATTATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGA--TAGTCAGTATCGCGTTGCGATTTTGTATTATCGAGTTGCGAAAGTCAG
57158 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTT
1 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTT
57195 CCAAATTCGC
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
60 15 0.18
61 33 0.40
62 34 0.41
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.36
Consensus pattern (61 bp):
TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTGTATTATCGAGTTGCGAAAGTCAG
Found at i:57178 original size:82 final size:81
Alignment explanation
Indices: 57016--57194 Score: 225
Period size: 82 Copynumber: 2.2 Consensus size: 81
57006 CGCTTTGAAA
* * * * *
57016 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGTATTGCGTTGCGAAATTAAGTATCG
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTAAGTATCG
57081 AGTTGCGAAAGTCAGT
66 AGTTGCGAAAGTCAGT
** * * *
57097 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATTTTGT-ATTATCGCGTTGCGATAGTCAGTAT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGTAT
* *
57161 CGCGTTGCGATAGTCAGT
64 CGAGTTGCGAAAGTCAGT
57179 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
57195 CCAAATTCGC
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
81 30 0.36
82 52 0.62
83 2 0.02
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (81 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTAAGTATCG
AGTTGCGAAAGTCAGT
Found at i:57210 original size:82 final size:82
Alignment explanation
Indices: 57060--57215 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 82
57050 AGTCAGTATT
* ** * *
57060 GCGTTGCGAAATTAAGTATCGAGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCGT
1 GCGTTGCGAAAGTAAGTATCGAGTTGCGAAAGTCAGTATCGCGTTGCGATTTTCAAATATCGCAT
57125 TGCGATTTTGTATTATC
66 TGCGATTTTGTATTATC
* * * *
57142 GCGTTGCGATAGTCAGTATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT-TCGCA
1 GCGTTGCGAAAGTAAGTATCGAGTTGCGAAAGTCAGTATCGCGTTGCGATTTT-CAAATATCGCA
57206 TTGCGATTTT
65 TTGCGATTTT
57216 CCAAATTCGC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
82 62 0.97
83 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.37
Consensus pattern (82 bp):
GCGTTGCGAAAGTAAGTATCGAGTTGCGAAAGTCAGTATCGCGTTGCGATTTTCAAATATCGCAT
TGCGATTTTGTATTATC
Found at i:57231 original size:82 final size:82
Alignment explanation
Indices: 57074--57233 Score: 198
Period size: 82 Copynumber: 2.0 Consensus size: 82
57064 TGCGAAATTA
** * * ** *
57074 AGTATCGAGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCGTTGCGATTTTGTATT
1 AGTATCGAGTTGCGAAAGTCAGTATCGCGTTGCGATTTTCAAATATCGCATTGCGATTTTCAAAT
*
57139 ATCGCGTTGCGATAGTC
66 ATCGCATTGCGATAGTC
* *
57156 AGTATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT-TCGCATTGCGATTTTCCAA
1 AGTATCGAGTTGCGAAAGTCAGTATCGCGTTGCGATTTT-CAAATATCGCATTGCGATTTT-CAA
57220 AT-TCGCATTGCGAT
64 ATATCGCATTGCGAT
57234 TTTCCAAATT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
82 62 0.94
83 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (82 bp):
AGTATCGAGTTGCGAAAGTCAGTATCGCGTTGCGATTTTCAAATATCGCATTGCGATTTTCAAAT
ATCGCATTGCGATAGTC
Found at i:57266 original size:20 final size:21
Alignment explanation
Indices: 57180--57273 Score: 154
Period size: 21 Copynumber: 4.5 Consensus size: 21
57170 ATAGTCAGTA
*
57180 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
57201 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
57222 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
57243 TCGCATTGCGATTTACC-TAT
1 TCGCATTGCGATTTTCCAAAT
57263 TCGCATTGCGA
1 TCGCATTGCGA
57274 ATTGGGAAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
20 13 0.19
21 57 0.81
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:57288 original size:41 final size:42
Alignment explanation
Indices: 57180--57288 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
57170 ATAGTCAGTA
* * * * *
57180 TCGCGTTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGAATTGCCAAAATCGCATTGCGATTTACCAAAT
* * * *
57222 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACC-TAT
1 TCGCATTGCGAATTGCCAAAATCGCATTGCGATTTACCAAAT
**
57263 TCGCATTGCGAATTGGGAAAATCGCA
1 TCGCATTGCGAATTGCCAAAATCGCA
57289 ACGCGATATT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 23 0.39
42 36 0.61
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (42 bp):
TCGCATTGCGAATTGCCAAAATCGCATTGCGATTTACCAAAT
Found at i:57288 original size:62 final size:63
Alignment explanation
Indices: 57179--57316 Score: 143
Period size: 62 Copynumber: 2.2 Consensus size: 63
57169 GATAGTCAGT
* * * * * ** *
57179 ATCGCGTTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTACCAAATTCGCATTGCGAATTGCCAAAATCGCAACGCGATATTCCAAA
* * ** **
57242 TTCGCATTGCGATTTACC-TATTCGCATTGCGAATTGGGAAAATCGCAACGCGATATTGGAAA
1 ATCGCATTGCGATTTACCAAATTCGCATTGCGAATTGCCAAAATCGCAACGCGATATTCCAAA
57304 ATCGCATTGCGAT
1 ATCGCATTGCGAT
57317 AGTCATAATC
Statistics
Matches: 60, Mismatches: 15, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
62 45 0.75
63 15 0.25
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (63 bp):
ATCGCATTGCGATTTACCAAATTCGCATTGCGAATTGCCAAAATCGCAACGCGATATTCCAAA
Found at i:57294 original size:21 final size:21
Alignment explanation
Indices: 57270--57309 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
57260 TATTCGCATT
57270 GCGA-ATTGGGAAAATCGCAAC
1 GCGATATT-GGAAAATCGCAAC
57291 GCGATATTGGAAAATCGCA
1 GCGATATTGGAAAATCGCA
57310 TTGCGATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGATATTGGAAAATCGCAAC
Found at i:57694 original size:30 final size:30
Alignment explanation
Indices: 57658--57729 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
57648 CCCGCAGAAC
*
57658 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
57688 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
57718 CTGTCCATAGGT
1 CTATCCAGAGGT
57730 TTCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:57770 original size:31 final size:30
Alignment explanation
Indices: 57716--57840 Score: 92
Period size: 31 Copynumber: 4.0 Consensus size: 30
57706 GATCCTCGGC
* * *
57716 AACTGTCCATAGGTTTCGAAGAACCTAGGT
1 AACTGTCCATATGTTCCGAAGAACATAGGT
**
57746 GAACTGTCCATATGTTCCTTAGAACATAGGT
1 -AACTGTCCATATGTTCCGAAGAACATAGGT
* *
57777 ATATTGTCCATATG-TCTCGAA-AGATATAGGT
1 A-ACTGTCCATATGTTC-CGAAGA-ACATAGGT
* * *
57808 AATTATGTCCATATCTTCCGTAGAACATAGGT
1 AA--CTGTCCATATGTTCCGAAGAACATAGGT
57840 A
1 A
57841 CCCTCGACTC
Statistics
Matches: 74, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
30 5 0.07
31 46 0.62
32 20 0.27
33 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (30 bp):
AACTGTCCATATGTTCCGAAGAACATAGGT
Found at i:57838 original size:32 final size:31
Alignment explanation
Indices: 57750--57840 Score: 80
Period size: 32 Copynumber: 2.9 Consensus size: 31
57740 CTAGGTGAAC
*
57750 TGTCCATATGTTCCTTAGAACATAGGT-ATAT
1 TGTCCATAT-TTCCGTAGAACATAGGTAATAT
* * *
57781 TGTCCATATGTCTCG-AAAGATATAGGTAAT-T
1 TGTCCATATTTC-CGTAGA-ACATAGGTAATAT
57812 ATGTCCATATCTTCCGTAGAACATAGGTA
1 -TGTCCATAT-TTCCGTAGAACATAGGTA
57841 CCCTCGACTC
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
30 4 0.09
31 18 0.38
32 21 0.45
33 4 0.09
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (31 bp):
TGTCCATATTTCCGTAGAACATAGGTAATAT
Found at i:62475 original size:13 final size:13
Alignment explanation
Indices: 62457--62481 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62447 TAAAAATATA
62457 TTTTATTTTGATT
1 TTTTATTTTGATT
62470 TTTTATTTTGAT
1 TTTTATTTTGAT
62482 ATGATTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
TTTTATTTTGATT
Found at i:62591 original size:51 final size:52
Alignment explanation
Indices: 62499--62598 Score: 123
Period size: 51 Copynumber: 1.9 Consensus size: 52
62489 ATTTTAACAA
* * **
62499 AAAAATATTATATTTTATTAAAATTTATCACTTCAAAATAATAAATTTAAAT
1 AAAAATATTATATTTTATTAAAACTCATCAAATCAAAATAATAAATTTAAAT
* *
62551 AAAAATA-TATTTTTTATTAAAACTCATCAAAT-AAAGATAATAATTTTA
1 AAAAATATTATATTTTATTAAAACTCATCAAATCAAA-ATAATAAATTTA
62599 TTCTATAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 3 0.07
51 31 0.76
52 7 0.17
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (52 bp):
AAAAATATTATATTTTATTAAAACTCATCAAATCAAAATAATAAATTTAAAT
Found at i:64032 original size:13 final size:13
Alignment explanation
Indices: 64014--64038 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64004 GCTTTTTCTA
64014 TAAATTTAAAAAT
1 TAAATTTAAAAAT
64027 TAAATTTAAAAA
1 TAAATTTAAAAA
64039 AACATGTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAATTTAAAAAT
Found at i:69897 original size:50 final size:50
Alignment explanation
Indices: 69835--69932 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 50
69825 GAAAGCGTGT
* * * *
69835 CCCCTGCACCGCGCTATATGCTGATTTGGCATCACGTGGGTATAGCGCAC
1 CCCCTGCACCGCGATATACGCTGATCTGGCACCACGTGGGTATAGCGCAC
* * *
69885 CCCCTGCCCCGCGATATACGGTGATCTGGCGCCACGTGGGTATAGCGC
1 CCCCTGCACCGCGATATACGCTGATCTGGCACCACGTGGGTATAGCGC
69933 GGTCCATGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.16, C:0.34, G:0.29, T:0.21
Consensus pattern (50 bp):
CCCCTGCACCGCGATATACGCTGATCTGGCACCACGTGGGTATAGCGCAC
Found at i:73802 original size:15 final size:15
Alignment explanation
Indices: 73784--73814 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
73774 TCGTCGTCAC
73784 CATCGTCATAGTCGT
1 CATCGTCATAGTCGT
*
73799 CATCGTCATTGTCGT
1 CATCGTCATAGTCGT
73814 C
1 C
73815 GTCCTGAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.29, G:0.19, T:0.35
Consensus pattern (15 bp):
CATCGTCATAGTCGT
Found at i:74171 original size:18 final size:18
Alignment explanation
Indices: 74148--74183 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
74138 GCGATGGCGA
74148 CATCATATATGGATGCGG
1 CATCATATATGGATGCGG
*
74166 CATCATATATGGTTGCGG
1 CATCATATATGGATGCGG
74184 TGGCTGCTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (18 bp):
CATCATATATGGATGCGG
Found at i:75828 original size:111 final size:110
Alignment explanation
Indices: 75691--75903 Score: 381
Period size: 111 Copynumber: 1.9 Consensus size: 110
75681 ATTACAAAAA
* *
75691 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
75756 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
66 AATT-AAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
75802 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
75867 AATTAAACGTTAAAATGTTACCGTATTAGCAAAGTGT
66 AATTAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
75904 AGACATATAT
Statistics
Matches: 98, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
110 31 0.32
111 67 0.68
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (110 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:76048 original size:12 final size:10
Alignment explanation
Indices: 76034--76074 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
76024 ACCTTAAAAA
*
76034 GAGAGTATTT
1 GAGAGAATTT
76044 GAGAGAAATTT
1 GAGAG-AATTT
76055 -AGAGAATTT
1 GAGAGAATTT
76064 GAGAGAATTT
1 GAGAGAATTT
76074 G
1 G
76075 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:76250 original size:50 final size:50
Alignment explanation
Indices: 76196--76315 Score: 125
Period size: 50 Copynumber: 2.4 Consensus size: 50
76186 AGATATCCAG
* * * *
76196 GTATAGCGCGGATCAGGGGGCGCACTATACCCACATGGCGCCAGATCACC
1 GTATAGCGCGGAGCAGAGAGCGCACTATACCCACATGGCGCCAAATCACC
* * ** * *
76246 GTATATCGCGGGGCAGAGAGCGTGCTATACCCACGTGGCGCCAAATCAGC
1 GTATAGCGCGGAGCAGAGAGCGCACTATACCCACATGGCGCCAAATCACC
* *
76296 ATATAGCGCGGTGCAG-GAGC
1 GTATAGCGCGGAGCAGAGAGC
76316 CGCGTTTTCC
Statistics
Matches: 57, Mismatches: 13, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
49 4 0.07
50 53 0.93
ACGTcount: A:0.24, C:0.28, G:0.33, T:0.15
Consensus pattern (50 bp):
GTATAGCGCGGAGCAGAGAGCGCACTATACCCACATGGCGCCAAATCACC
Found at i:77110 original size:14 final size:14
Alignment explanation
Indices: 77091--77140 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
77081 AAGTAGTTTT
*
77091 AAATATGTAATTTA
1 AAATATATAATTTA
* *
77105 AAATATTTAAATATTT
1 AAATATAT-AAT-TTA
77121 AAATATATAATTTA
1 AAATATATAATTTA
77135 AAATAT
1 AAATAT
77141 TTAAAATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 15 0.50
15 6 0.20
16 9 0.30
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
AAATATATAATTTA
Found at i:77114 original size:9 final size:9
Alignment explanation
Indices: 77100--77148 Score: 55
Period size: 9 Copynumber: 5.1 Consensus size: 9
77090 TAAATATGTA
77100 ATTTAAAAT
1 ATTTAAAAT
77109 ATTT-AAAT
1 ATTTAAAAT
77117 ATTTAAATATAT
1 ATTT-AA-A-AT
77129 AATTTAAAAT
1 -ATTTAAAAT
77139 ATTTAAAAT
1 ATTTAAAAT
77148 A
1 A
77149 ATCATAATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
8 8 0.23
9 14 0.40
10 3 0.09
11 2 0.06
12 4 0.11
13 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATTTAAAAT
Found at i:77118 original size:8 final size:8
Alignment explanation
Indices: 77088--77145 Score: 52
Period size: 8 Copynumber: 7.8 Consensus size: 8
77078 ATCAAGTAGT
77088 TTTAAATA
1 TTTAAATA
*
77096 TGT-AAT-
1 TTTAAATA
*
77102 TTAAAATA
1 TTTAAATA
77110 TTTAAATA
1 TTTAAATA
77118 TTTAAATA
1 TTTAAATA
*
77126 TAT-AAT-
1 TTTAAATA
*
77132 TTAAAATA
1 TTTAAATA
77140 TTTAAA
1 TTTAAA
77146 ATAATCATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
6 2 0.05
7 12 0.32
8 24 0.63
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (8 bp):
TTTAAATA
Found at i:77124 original size:30 final size:30
Alignment explanation
Indices: 77088--77145 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
77078 ATCAAGTAGT
*
77088 TTTAAATATGTAATTTAAAATATTTAAATA
1 TTTAAATATATAATTTAAAATATTTAAATA
77118 TTTAAATATATAATTTAAAATATTTAAA
1 TTTAAATATATAATTTAAAATATTTAAA
77146 ATAATCATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
TTTAAATATATAATTTAAAATATTTAAATA
Found at i:78172 original size:27 final size:28
Alignment explanation
Indices: 78142--78195 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
78132 TTAGTAATAA
*
78142 TTTATTTATTTAATTTTT-T-ATTATTAG
1 TTTATATA-TTAATTTTTGTAATTATTAG
78169 TTTATATATTAATTTTTGTAATTATTA
1 TTTATATATTAATTTTTGTAATTATTA
78196 ATAATTTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 8 0.33
28 7 0.29
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (28 bp):
TTTATATATTAATTTTTGTAATTATTAG
Done.