Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003618.1 Hibiscus syriacus cultivar Beakdansim tig00007651_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: 103197
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:960 original size:2 final size:2
Alignment explanation
Indices: 955--1004 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
945 CACCTATGTT
955 TA TA TA TA TA TA -A TA TA TA TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
995 T- TA TA TA TA T
1 TA TA TA TA TA T
1005 CATCAAGTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 42 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:973 original size:13 final size:13
Alignment explanation
Indices: 955--1003 Score: 84
Period size: 13 Copynumber: 3.9 Consensus size: 13
945 CACCTATGTT
955 TATATATATATAA
1 TATATATATATAA
968 TATATATATATAA
1 TATATATATATAA
981 TATATATATAT-A
1 TATATATATATAA
993 TAT-TATATATA
1 TATATATATATA
1004 TCATCAAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 7 0.20
12 4 0.11
13 24 0.69
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TATATATATATAA
Found at i:975 original size:15 final size:15
Alignment explanation
Indices: 955--1004 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
945 CACCTATGTT
955 TATATATATAT-A-A
1 TATATATATATAATA
968 TATATATATATAATA
1 TATATATATATAATA
*
983 TATATATATATATTA
1 TATATATATATAATA
998 TATATAT
1 TATATAT
1005 CATCAAGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
13 11 0.32
14 1 0.03
15 22 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATATATATAATA
Found at i:9980 original size:18 final size:19
Alignment explanation
Indices: 9957--9992 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
9947 TTAATATTTT
9957 CATTAAAAT-ATATTAAAC
1 CATTAAAATAATATTAAAC
*
9975 CATTAAATTAATATTAAA
1 CATTAAAATAATATTAAA
9993 TAAATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (19 bp):
CATTAAAATAATATTAAAC
Found at i:10124 original size:18 final size:18
Alignment explanation
Indices: 10097--10131 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10087 ATACAAAAGA
* *
10097 ATTAGGAAAATGAATTAT
1 ATTAGAAAAATCAATTAT
10115 ATTAGAAAAATCAATTA
1 ATTAGAAAAATCAATTA
10132 CATCTATCAA
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:0.54, C:0.03, G:0.11, T:0.31
Consensus pattern (18 bp):
ATTAGAAAAATCAATTAT
Found at i:18262 original size:3 final size:3
Alignment explanation
Indices: 18237--18301 Score: 62
Period size: 3 Copynumber: 21.7 Consensus size: 3
18227 TTTTGGTAAA
* * * *
18237 TAT TAC TAT TAGT TAT AAT TAT TAT TGAC TA- TAT T-T TAT TAT AAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
18282 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
18302 ATCCTGATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
2 4 0.08
3 42 0.82
4 5 0.10
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:21659 original size:30 final size:29
Alignment explanation
Indices: 21616--21696 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
21606 ATTAGCACCC
*
21616 TTTT-AAAATTAATTACGAAAATAGT-ATCAT
1 TTTTCAAAA-TAATTACCAAAATA-TCAT-AT
* *
21646 TTTTCGAAATAATTACCAAAATATCATTT
1 TTTTCAAAATAATTACCAAAATATCATAT
21675 TTTTCAAAATAATTACCAAAAT
1 TTTTCAAAATAATTACCAAAAT
21697 CACTTTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
29 23 0.51
30 19 0.42
31 3 0.07
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.40
Consensus pattern (29 bp):
TTTTCAAAATAATTACCAAAATATCATAT
Found at i:21687 original size:29 final size:28
Alignment explanation
Indices: 21645--21718 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 28
21635 AATAGTATCA
21645 TTTTTCGAAATAATTACCAAAAT-ATCATT
1 TTTTTCGAAATAATTACCAAAATCA-C-TT
*
21674 TTTTTCAAAATAATTACCAAAATCACTT
1 TTTTTCGAAATAATTACCAAAATCACTT
*
21702 TTTTTCGAAATATTTAC
1 TTTTTCGAAATAATTAC
21719 GCAACTAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
28 17 0.41
29 23 0.56
30 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.03, T:0.43
Consensus pattern (28 bp):
TTTTTCGAAATAATTACCAAAATCACTT
Found at i:21703 original size:28 final size:29
Alignment explanation
Indices: 21645--21718 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 29
21635 AATAGTATCA
21645 TTTTTCGAAATAATTACCAAAATATCATT
1 TTTTTCGAAATAATTACCAAAATATCATT
*
21674 TTTTTCAAAATAATTACC-AAA-ATCACTT
1 TTTTTCGAAATAATTACCAAAATATCA-TT
*
21702 TTTTTCGAAATATTTAC
1 TTTTTCGAAATAATTAC
21719 GCAACTAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 4 0.10
28 20 0.49
29 17 0.41
ACGTcount: A:0.39, C:0.15, G:0.03, T:0.43
Consensus pattern (29 bp):
TTTTTCGAAATAATTACCAAAATATCATT
Found at i:21767 original size:29 final size:29
Alignment explanation
Indices: 21711--21780 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
21701 TTTTTTCGAA
*
21711 ATATTTACGCAACTAACACCTTCATAAC-
1 ATATTTACGAAACTAACACCTTCATAACT
** **
21739 AGTATTTACGAAACTAACATTTTTTTAACT
1 A-TATTTACGAAACTAACACCTTCATAACT
21769 ATATTTACGAAA
1 ATATTTACGAAA
21781 ATACCACCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 1 0.03
29 33 0.94
30 1 0.03
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.36
Consensus pattern (29 bp):
ATATTTACGAAACTAACACCTTCATAACT
Found at i:22447 original size:21 final size:21
Alignment explanation
Indices: 22421--22462 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
22411 CTATATTTAA
* *
22421 TATTTATAGTGTTTATTATTT
1 TATTTATAATGCTTATTATTT
22442 TATTTATAATGCTTATTATTT
1 TATTTATAATGCTTATTATTT
22463 ATATATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.64
Consensus pattern (21 bp):
TATTTATAATGCTTATTATTT
Found at i:28590 original size:29 final size:31
Alignment explanation
Indices: 28542--28611 Score: 99
Period size: 29 Copynumber: 2.3 Consensus size: 31
28532 CAATTTTTAG
*
28542 AAATAATTACCAAAATATCATTTTTTTTTCA
1 AAATAATTACCAAAATATCACTTTTTTTTCA
*
28573 AAATAATTACC-AAA-ATCACTTTTTTTTCG
1 AAATAATTACCAAAATATCACTTTTTTTTCA
*
28602 AAATATTTAC
1 AAATAATTAC
28612 ACAACTAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 22 0.61
30 3 0.08
31 11 0.31
ACGTcount: A:0.41, C:0.14, G:0.01, T:0.43
Consensus pattern (31 bp):
AAATAATTACCAAAATATCACTTTTTTTTCA
Found at i:29497 original size:20 final size:21
Alignment explanation
Indices: 29472--29564 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
29462 TTTTCCCAAT
*
29472 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
29492 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
29513 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
29533 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
29554 TCGCAATGCGA
1 TCGCAATGCGA
29565 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:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:29517 original size:41 final size:41
Alignment explanation
Indices: 29472--29564 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
29462 TTTTCCCAAT
29472 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
29513 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
29554 TCGCAATGCGA
1 TCGCAATGCGA
29565 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:29577 original size:41 final size:41
Alignment explanation
Indices: 29491--29625 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
29481 GAATAAGTAA
* *
29491 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
29532 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
29573 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
29614 TTCGCAACGCGA
1 ATCGCAACGCGA
29626 TACTGTCTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:29578 original size:20 final size:20
Alignment explanation
Indices: 29553--29647 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
29543 AATTGGGAAA
*
29553 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
29573 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
29594 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
29614 TTCGCAACGCGATACTGTCT
1 ATCGCAACGCGATACTGACT
* *
29634 TTCGCAACACGATA
1 ATCGCAACGCGATA
29648 ATACATAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:29861 original size:22 final size:22
Alignment explanation
Indices: 29833--29876 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
29823 CTCTCTCTCA
29833 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
29855 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
29877 TATCTAAATC
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:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:30165 original size:20 final size:20
Alignment explanation
Indices: 30140--30177 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30130 CGATTCTCTC
30140 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
30160 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
30178 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:31517 original size:18 final size:18
Alignment explanation
Indices: 31496--31540 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
31486 TCCACTTCGG
*
31496 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
31514 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
31532 GAGCCATCA
1 GAGCCATCA
31541 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:32063 original size:19 final size:20
Alignment explanation
Indices: 32009--32075 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
31999 TAGTTTACTT
* *
32009 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
32029 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
32049 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
32068 TCGCAACG
1 TCGCAACG
32076 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:32083 original size:14 final size:14
Alignment explanation
Indices: 32064--32121 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
32054 ATGCGAAATG
32064 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
32078 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
32094 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
32110 AAAATCGCAACG
1 AAAATCGCAACG
32122 CGAAATGAAA
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:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:32106 original size:32 final size:33
Alignment explanation
Indices: 32048--32138 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
32038 GGAAATGGCT
32048 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
32081 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
32113 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
32139 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:32184 original size:19 final size:19
Alignment explanation
Indices: 32169--32256 Score: 97
Period size: 19 Copynumber: 4.6 Consensus size: 19
32159 GCGATTTTGT
32169 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
32187 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* *** *
32206 CATTGCGATAGCCATTTCCA
1 CGTTGCGATTTTCATTT-CG
**
32226 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
32245 CGTTGCGATTTT
1 CGTTGCGATTTT
32257 AAGTTTCGTA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
18 8 0.14
19 34 0.59
20 16 0.28
ACGTcount: A:0.15, C:0.23, G:0.22, T:0.41
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:34293 original size:19 final size:19
Alignment explanation
Indices: 34271--34390 Score: 161
Period size: 19 Copynumber: 6.8 Consensus size: 19
34261 ATCGCAACGA
*
34271 GAAAATCGCAATGCGAAGT
1 GAAAATCGCAATGCGAAAT
34290 GAAAATCGCAATGC-----
1 GAAAATCGCAATGCGAAAT
34304 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
34323 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
34342 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
34361 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
34375 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
34391 TTTTCATTTC
Statistics
Matches: 93, Mismatches: 0, Indels: 18
0.84 0.00 0.16
Matches are distributed among these distances:
14 25 0.27
15 1 0.01
16 2 0.02
17 2 0.02
19 63 0.68
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:34355 original size:38 final size:33
Alignment explanation
Indices: 34242--34390 Score: 190
Period size: 33 Copynumber: 4.4 Consensus size: 33
34232 AAAATAGACT
* ***
34242 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
* * *
34275 ATCGCAATGCGAAGTGAAAATCGCAATGCGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
34308 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
34346 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
34379 ATCGCAATGCGA
1 ATCGCAATGCGA
34391 TTTTCATTTC
Statistics
Matches: 101, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
33 67 0.66
34 1 0.01
35 1 0.01
36 2 0.02
38 30 0.30
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:34466 original size:20 final size:20
Alignment explanation
Indices: 34409--34466 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
34399 TCGCATTGCG
* *
34409 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
34429 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
34449 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
34467 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:35551 original size:24 final size:24
Alignment explanation
Indices: 35524--35577 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
35514 GTATTCGAAA
* *
35524 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
35548 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
35572 TTTGAT
1 TTTGAT
35578 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:38072 original size:19 final size:19
Alignment explanation
Indices: 38050--38180 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
38040 GGAAATTACT
38050 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
38069 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
38083 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
38102 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
38116 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
38135 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
38149 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
38168 ATCGCAACGCGAA
1 ATCGCAATGCGAA
38181 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 26 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.46
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:38183 original size:33 final size:33
Alignment explanation
Indices: 38051--38183 Score: 214
Period size: 33 Copynumber: 4.0 Consensus size: 33
38041 GAAATTACTA
* *
38051 TCGCAATGCGAAATGAAAATCGCAACGAGAGA-A
1 TCGCAATGCGAAATGAAAATCGCAACGCGA-ATT
*
38084 TCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
*
38117 TCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
38150 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
38183 T
1 T
38184 AATTTCGCGT
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
32 1 0.01
33 94 0.99
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:38198 original size:19 final size:20
Alignment explanation
Indices: 38176--38218 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
38166 AAATCGCAAC
38176 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
38195 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
38215 GCGA
1 GCGA
38219 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:38380 original size:14 final size:14
Alignment explanation
Indices: 38359--38409 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
38349 CATCAATTAA
38359 ACAAATCAACTTTT
1 ACAAATCAACTTTT
* *
38373 AAAAATCACCTTTT
1 ACAAATCAACTTTT
*
38387 ACAAATCACCTTTT
1 ACAAATCAACTTTT
38401 ACAAATCAA
1 ACAAATCAA
38410 TTAAACAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:41752 original size:20 final size:19
Alignment explanation
Indices: 41721--41899 Score: 126
Period size: 19 Copynumber: 9.8 Consensus size: 19
41711 TCTTTTGGTT
41721 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
41740 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
41761 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
41780 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
41794 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
41810 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
* * *
41827 GAAATAAAAATCACAACGC
1 GAAATGAAAATCGCAACGA
*
41846 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
41865 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
41884 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
41900 TGCGATTTTG
Statistics
Matches: 128, Mismatches: 20, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
14 17 0.13
15 1 0.01
16 4 0.03
17 4 0.03
18 1 0.01
19 70 0.55
20 29 0.23
21 2 0.02
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:41803 original size:33 final size:33
Alignment explanation
Indices: 41746--41831 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
41736 ACGAGATAAT
*
41746 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
41780 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
*
41813 GACAATCGCAACGCGAAAT
1 GAGAATCGCAACGCGAAAT
41832 AAAAATCACA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:41838 original size:19 final size:19
Alignment explanation
Indices: 41816--41904 Score: 151
Period size: 19 Copynumber: 4.7 Consensus size: 19
41806 GCGACCAGAC
*
41816 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
*
41835 AATCACAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
41854 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
41873 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
41892 AATCGCAATGCGA
1 AATCGCAACGCGA
41905 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 66 1.00
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:41933 original size:19 final size:19
Alignment explanation
Indices: 41900--41980 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
41890 AAAATCGCAA
**
41900 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
41919 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
41938 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
41952 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
41972 TGCGATTTT
1 TGCGATTTT
41981 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:42566 original size:21 final size:21
Alignment explanation
Indices: 42533--42633 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
42523 TGCGAAAGTA
* * *
42533 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
42554 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
42574 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
42596 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
42617 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
42634 CCCAATTCGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:42589 original size:20 final size:20
Alignment explanation
Indices: 42496--42589 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
42486 CGCTATGTAA
*
42496 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
42516 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
42536 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
42557 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
42577 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
42590 TTTCCCAATT
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):
ATCGCGTTGCGATAGTCAGT
Found at i:42608 original size:41 final size:41
Alignment explanation
Indices: 42517--42651 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
42507 AAAGTCAGTA
* * * ** *
42517 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
42557 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
42599 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
42640 TCGCGTTGCGAT
1 TCGCGTTGCGAT
42652 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:42643 original size:21 final size:20
Alignment explanation
Indices: 42578--42670 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
42568 ATAGTCAGTA
*
42578 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
42599 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
*
42619 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
42640 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
42660 TCGCATTGCGA
1 TCGCATTGCGA
42671 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:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:42652 original size:41 final size:41
Alignment explanation
Indices: 42578--42670 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
42568 ATAGTCAGTA
42578 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
42619 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
42660 TCGCATTGCGA
1 TCGCATTGCGA
42671 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:42966 original size:21 final size:22
Alignment explanation
Indices: 42933--42990 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
42923 TAGTGCTCTA
* *
42933 TATTTAATATTTATAGTGTTTAT
1 TATTT-ATATTTATAATGCTTAT
42956 TATTT-TATTTATAATGCTTAT
1 TATTTATATTTATAATGCTTAT
*
42977 TATTTATATATATA
1 TATTTATATTTATA
42991 TTTTTCTAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.61
22 7 0.23
23 5 0.16
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (22 bp):
TATTTATATTTATAATGCTTAT
Found at i:53244 original size:37 final size:36
Alignment explanation
Indices: 53126--53227 Score: 161
Period size: 35 Copynumber: 2.8 Consensus size: 36
53116 TGGCAACCAA
53126 CTTTGAAAAATTGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAA-TGGTTTTCAAAGTTTGGTAAATGTTT
*
53163 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
53198 CTTTGAAAAATAGTTTTTCAAAGTTTGGTA
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTA
53228 GACGTTTGTT
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
35 30 0.49
36 9 0.15
37 22 0.36
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:56518 original size:17 final size:17
Alignment explanation
Indices: 56496--56528 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
56486 AAAATCCTCA
56496 GTGCATCGATGCATGGT
1 GTGCATCGATGCATGGT
56513 GTGCATCGATGCATGG
1 GTGCATCGATGCATGG
56529 AATGCATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.36, T:0.27
Consensus pattern (17 bp):
GTGCATCGATGCATGGT
Found at i:56533 original size:63 final size:64
Alignment explanation
Indices: 56386--56544 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 64
56376 TGCACTAAGA
* *
56386 GTGCATCGATGCATCAAGTGCATTCGATGTT-TCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCAT-AAATGCATTCGATGTTCTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * *
56450 GTGCATCGATGCATCAAATGCATTCGATGTTCTTATAAA-ATCCTCAGTGCATCGATGCATGG-T
1 GTGCATCGATGCAT-AAATGCATTCGATGTTCTCA-AAATAGCCACAGTGCATCGATGCATGGCT
56513 -
64 G
*
56513 GTGCATCGATGCATGGAATGCATTCGATGTTC
1 GTGCATCGATGCAT-AAATGCATTCGATGTTC
56545 AATTTAATTC
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
63 30 0.35
64 31 0.36
65 22 0.26
66 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAAATGCATTCGATGTTCTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:56534 original size:17 final size:17
Alignment explanation
Indices: 56497--56541 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
56487 AAATCCTCAG
**
56497 TGCATCGATGCATGGTG
1 TGCATCGATGCATGGAA
56514 TGCATCGATGCATGGAA
1 TGCATCGATGCATGGAA
56531 TGCATTCGATG
1 TGCA-TCGATG
56542 TTCAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (17 bp):
TGCATCGATGCATGGAA
Found at i:62312 original size:22 final size:21
Alignment explanation
Indices: 62270--62309 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
62260 GAGTTTATTT
*
62270 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
62291 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
62310 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:64296 original size:18 final size:17
Alignment explanation
Indices: 64242--64290 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
64232 TTGGACCCTT
* *
64242 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
64260 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
64278 AGTGCATTCGATG
1 AGTGCA-TCGATG
64291 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:65559 original size:43 final size:43
Alignment explanation
Indices: 65366--65584 Score: 294
Period size: 43 Copynumber: 5.1 Consensus size: 43
65356 TGGTAACAAA
*** * * * ** *
65366 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTCTAAT
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
* * *
65409 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTCAAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
*
65452 AAACGCCGCAATAGGTGTTGAGATTTAGCGGAGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
*
65495 AAACGCCGCAATAGGTGTTGAGATTTAGCGTCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
* *
65538 AAACGCCGCAATAGGTCTTGAGATTTAGCGGCATTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
65581 AAAC
1 AAAC
65585 ATCGCAAAAG
Statistics
Matches: 159, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 159 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
Found at i:65591 original size:86 final size:86
Alignment explanation
Indices: 65409--65634 Score: 278
Period size: 86 Copynumber: 2.6 Consensus size: 86
65399 TTTGTCTAAT
* * * *
65409 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTCAACAAACGCCGCAATAGGTGTTGAG
1 AAACACCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTCTTGAG
65474 ATTTAGCGGAGTTTTTCCCAC
66 ATTTAGCGGAGTTTTTCCCAC
* * *
65495 AAACGCCGCAATAGGTGTTGAGATTTAGCGTCGTTTTTCCCACAAACGCCGCAATAGGTCTTGAG
1 AAACACCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTCTTGAG
65560 ATTTAGCGGCA-TTTTTCCCAC
66 ATTTAGCGG-AGTTTTTCCCAC
* * * * * **
65581 AAACATCGCAAAAGAT-CTG-GTATATAGCGGCGTTTTTTAGAACAAACGCCGCAA
1 AAACACCGCAATAGGTGTTGAG-ATTTAGCGGCG-TTTTTCCAACAAACGCCGCAA
65635 AAGATCATAT
Statistics
Matches: 122, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
84 1 0.01
85 11 0.09
86 109 0.89
87 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (86 bp):
AAACACCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTCTTGAG
ATTTAGCGGAGTTTTTCCCAC
Found at i:65618 original size:43 final size:43
Alignment explanation
Indices: 65388--65640 Score: 168
Period size: 43 Copynumber: 5.9 Consensus size: 43
65378 AGGTAACGAT
* ** * * * * * *
65388 ATATAGCGGCGTTTGTCTAATAAACGCCGCAATAGGTGTTGAT
1 ATATAGCGGCGTTTTTCCCACAAACACCGCAAAAGATCTTGAG
* * * * * * *
65431 ATTTAGCGGCGTTTTTTCAACAAACGCCGCAATAGGTGTTGAG
1 ATATAGCGGCGTTTTTCCCACAAACACCGCAAAAGATCTTGAG
* * * * * *
65474 ATTTAGCGGAGTTTTTCCCACAAACGCCGCAATAGGTGTTGAG
1 ATATAGCGGCGTTTTTCCCACAAACACCGCAAAAGATCTTGAG
* * * * *
65517 ATTTAGCGTCGTTTTTCCCACAAACGCCGCAATAGGTCTTGAG
1 ATATAGCGGCGTTTTTCCCACAAACACCGCAAAAGATCTTGAG
* * *
65560 ATTTAGCGGCATTTTTCCCACAAACATCGCAAAAGATC-TG-G
1 ATATAGCGGCGTTTTTCCCACAAACACCGCAAAAGATCTTGAG
*** *
65601 TATATAGCGGCGTTTTTTAGAACAAACGCCGCAAAAGATC
1 -ATATAGCGGCG-TTTTTCCCACAAACACCGCAAAAGATC
65641 ATATCTATAG
Statistics
Matches: 183, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
41 1 0.01
42 11 0.06
43 171 0.93
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (43 bp):
ATATAGCGGCGTTTTTCCCACAAACACCGCAAAAGATCTTGAG
Found at i:65813 original size:21 final size:21
Alignment explanation
Indices: 65787--65827 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
65777 ATTTTCCAAT
* *
65787 AAACTTGACATCCATAACAAC
1 AAACTTAAAATCCATAACAAC
65808 AAACTTAAAATCCATAACAA
1 AAACTTAAAATCCATAACAA
65828 GAAAAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.24, G:0.02, T:0.20
Consensus pattern (21 bp):
AAACTTAAAATCCATAACAAC
Found at i:66756 original size:36 final size:36
Alignment explanation
Indices: 66715--66830 Score: 205
Period size: 36 Copynumber: 3.2 Consensus size: 36
66705 GGAATGTATC
66715 TAAATTCCACTTGAACATCATCAGTAGAATGTTAAT
1 TAAATTCCACTTGAACATCATCAGTAGAATGTTAAT
66751 TAAATTCCACTTGAACATCATCAGTAGAATGTTAAT
1 TAAATTCCACTTGAACATCATCAGTAGAATGTTAAT
* * *
66787 TAAATTCCACTTGAACAGCAGCAGTAGAATGTTGAT
1 TAAATTCCACTTGAACATCATCAGTAGAATGTTAAT
66823 TAAATTCC
1 TAAATTCC
66831 CAACCGTTCA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 77 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (36 bp):
TAAATTCCACTTGAACATCATCAGTAGAATGTTAAT
Found at i:69909 original size:41 final size:41
Alignment explanation
Indices: 69842--70225 Score: 461
Period size: 41 Copynumber: 9.4 Consensus size: 41
69832 TTTAAAAAAC
* *
69842 AAACGCCACTAAAGTACAAGTC--TAGCGGCGTTTTTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
*
69881 AAACGCCACTAATGTACGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
69922 AAACACCACTAATGTACGAGTCTATAGCGGTGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * *
69963 AAACACCACTAAAGTACAAGCCTATAGCGGCGTTTGTAAACA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA-A
* *
70005 CAAACGCCACAAAATTA-GAGTCTATAGCGGCGTTTGTATAA
1 -AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
70046 AAACGCCACTAAAGTACTACTCTATCGCGGCGTTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCG-TTTGTATAA
* *
70088 AAACACCGCTAAAGT-CGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
** * * * * * *
70128 AAACGCTGCTAAAGTACTACTCTATTGTGGCATTTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGC-GTTTGTATAA
*
70170 AAACGCCACTAAAGTACGAGTCTATAACGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
*
70211 AAACGCCGCTAAAGT
1 AAACGCCACTAAAGT
70226 TACCATTTTG
Statistics
Matches: 293, Mismatches: 44, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
39 20 0.07
40 36 0.12
41 149 0.51
42 75 0.26
43 13 0.04
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:70109 original size:165 final size:165
Alignment explanation
Indices: 69825--70225 Score: 517
Period size: 165 Copynumber: 2.4 Consensus size: 165
69815 TTTTAAACTT
* *
69825 GCGGCGTTTTAAAAAACAAACGCCACTAAAGTACAAGTC--TAGCGGCGTTTTTATAAAAACGCC
1 GCGGCGTTTT-AAAAACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* * * *
69888 ACTAATGTACGAGTCTATAGCGGCGTTTGTATAAAAACACCACTAATGTACGAGTCTATAGCGGT
65 ACTAAAGTACGACTCTATAGCGGCGTTTGTATAAAAACACCACTAAAGTACGAGTCTATAGCGGC
69953 GTTTGTATAAAAACACCACTAAAGTACAAGC-CTATA
130 GTTTGTATAAAAACACCACTAAAGTACAA-CTCTATA
* * *
69989 GCGGCGTTTGTAAACACAAACGCCACAAAATTA-GAGTCTATAGCGGCGTTTGTATAAAAACGCC
1 GCGGCGTTT-TAAAAACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* * *
70053 ACTAAAGTACTACTCTATCGCGGCGTTTTGTATAAAAACACCGCTAAAGT-CGAGTCTATAGCGG
65 ACTAAAGTACGACTCTATAGCGGCG-TTTGTATAAAAACACCACTAAAGTACGAGTCTATAGCGG
* ** * *
70117 CGTTTGTATAAAAACGCTGCTAAAGTACTACTCTATT
129 CGTTTGTATAAAAACACCACTAAAGTACAACTCTATA
* * * *
70154 GTGGCATTTTATATAA-AAACGCCACTAAAGTACGAGTCTATAACGGCGTTTGTATAAAAACGCC
1 GCGGCGTTTTA-AAAACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
*
70218 GCTAAAGT
65 ACTAAAGT
70226 TACCATTTTG
Statistics
Matches: 205, Mismatches: 25, Indels: 13
0.84 0.10 0.05
Matches are distributed among these distances:
163 4 0.02
164 45 0.22
165 134 0.65
166 22 0.11
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (165 bp):
GCGGCGTTTTAAAAACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCA
CTAAAGTACGACTCTATAGCGGCGTTTGTATAAAAACACCACTAAAGTACGAGTCTATAGCGGCG
TTTGTATAAAAACACCACTAAAGTACAACTCTATA
Found at i:72214 original size:37 final size:36
Alignment explanation
Indices: 72096--72197 Score: 170
Period size: 35 Copynumber: 2.8 Consensus size: 36
72086 TGGCAACCAA
72096 CTTTGAAAAATTGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAA-TGGTTTTCAAAGTTTGGTAAATGTTT
72133 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
72168 CTTTGAAAAATAGTTTTTCAAAGTTTGGTA
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTA
72198 GACGTTTGTT
Statistics
Matches: 62, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
35 31 0.50
36 9 0.15
37 22 0.35
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:75496 original size:17 final size:17
Alignment explanation
Indices: 75474--75506 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
75464 AAAATCCTCA
*
75474 GTGCATCGGTGCATGGT
1 GTGCATCGATGCATGGT
75491 GTGCATCGATGCATGG
1 GTGCATCGATGCATGG
75507 AATGCATTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.18, G:0.39, T:0.27
Consensus pattern (17 bp):
GTGCATCGATGCATGGT
Found at i:75512 original size:17 final size:17
Alignment explanation
Indices: 75475--75519 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
75465 AAATCCTCAG
* **
75475 TGCATCGGTGCATGGTG
1 TGCATCGATGCATGGAA
75492 TGCATCGATGCATGGAA
1 TGCATCGATGCATGGAA
75509 TGCATTCGATG
1 TGCA-TCGATG
75520 TTCAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (17 bp):
TGCATCGATGCATGGAA
Found at i:75516 original size:63 final size:64
Alignment explanation
Indices: 75364--75522 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 64
75354 TGCACTAAGA
* *
75364 GTGCATCGATGCATCAAGTGCATTCGATGTT-TCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCAT-AAATGCATTCGATGTTCTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * * * *
75428 GTGCATCGATGCATCAAATGTATTCGATGTTCTTATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCAT-AAATGCATTCGATGTTCTCA-AAATAGCCACAGTGCATCGATGCATGGCT
75491 -
64 G
*
75491 GTGCATCGATGCATGGAATGCATTCGATGTTC
1 GTGCATCGATGCAT-AAATGCATTCGATGTTC
75523 AATTTAATTC
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
63 29 0.35
64 30 0.36
65 21 0.25
66 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAAATGCATTCGATGTTCTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:81290 original size:22 final size:21
Alignment explanation
Indices: 81248--81287 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
81238 GAGTTTATTT
*
81248 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
81269 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
81288 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:83274 original size:18 final size:17
Alignment explanation
Indices: 83220--83268 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
83210 TTGGACCCTT
* *
83220 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
83238 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
83256 AGTGCATTCGATG
1 AGTGCA-TCGATG
83269 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:87261 original size:6 final size:6
Alignment explanation
Indices: 87226--87260 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
87216 ATCCTCACTC
*
87226 TCCTCG TCCTCG TCCTCG TCCTCG TCCTCA TCCTC
1 TCCTCG TCCTCG TCCTCG TCCTCG TCCTCG TCCTC
87261 ACTCTCCACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.03, C:0.51, G:0.11, T:0.34
Consensus pattern (6 bp):
TCCTCG
Found at i:96810 original size:21 final size:21
Alignment explanation
Indices: 96784--96828 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
96774 GATTTCTGGG
* *
96784 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
96805 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
96826 CAA
1 CAA
96829 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:98292 original size:31 final size:31
Alignment explanation
Indices: 98248--98453 Score: 197
Period size: 30 Copynumber: 6.8 Consensus size: 31
98238 ACCTATATCT
* * * *
98248 TTCAAGACATATGGACAGTTTACCTAGGTTC
1 TTCAGGACCTATGGACAGTTTACCGAGGATC
*
98279 TTCGGGACCTATGGACAGTTTACCGAGGATC
1 TTCAGGACCTATGGACAGTTTACCGAGGATC
* * *
98310 TTTATGACCTCTGGACAG-TTACCGAGGATC
1 TTCAGGACCTATGGACAGTTTACCGAGGATC
* * *
98340 TTTATGACCTCTGGACAG-TTACCGAGGATC
1 TTCAGGACCTATGGACAGTTTACCGAGGATC
* * *
98370 TTTATGACCTCTGGACAG-TTACCGAGGATC
1 TTCAGGACCTATGGACAGTTTACCGAGGATC
* * *
98400 TTTATGACCTCTGGACAG-TTACCGAGGATC
1 TTCAGGACCTATGGACAGTTTACCGAGGATC
* * *
98430 TTTATGACCTCTGGACAG-TTACCG
1 TTCAGGACCTATGGACAGTTTACCG
98454 GGGTCTTTGT
Statistics
Matches: 166, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 126 0.76
31 40 0.24
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (31 bp):
TTCAGGACCTATGGACAGTTTACCGAGGATC
Found at i:98334 original size:30 final size:30
Alignment explanation
Indices: 98284--98473 Score: 337
Period size: 30 Copynumber: 6.3 Consensus size: 30
98274 GGTTCTTCGG
*
98284 GACCTATGGACAGTTTACCGAGGATCTTTAT
1 GACCTCTGGACAG-TTACCGAGGATCTTTAT
98315 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
98345 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
98375 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
98405 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* *
98435 GACCTCTGGACAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
98464 GACCTCTGGA
1 GACCTCTGGA
98474 TAGGTCCTTC
Statistics
Matches: 156, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
29 18 0.12
30 126 0.81
31 12 0.08
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:99649 original size:24 final size:24
Alignment explanation
Indices: 99620--99672 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
99610 TAAACCGGTT
99620 GAACCGCTACTAGTGAACCGGCCA
1 GAACCGCTACTAGTGAACCGGCCA
99644 GAACCGCTACTAGTGAACCGGCCA
1 GAACCGCTACTAGTGAACCGGCCA
99668 GAACC
1 GAACC
99673 ACTGAACCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.34, G:0.25, T:0.11
Consensus pattern (24 bp):
GAACCGCTACTAGTGAACCGGCCA
Found at i:103025 original size:23 final size:24
Alignment explanation
Indices: 102986--103036 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
102976 AATTATAAAT
* *
102986 ATTTTTTATTCATAGATAGTTTAG
1 ATTTTTTATTCATAGATAATTTAA
103010 ATTTTTTA-T-ATAAGATAATTTAA
1 ATTTTTTATTCAT-AGATAATTTAA
103033 ATTT
1 ATTT
103037 AGTTTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.08
23 14 0.58
24 8 0.33
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (24 bp):
ATTTTTTATTCATAGATAATTTAA
Done.