Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009148.1 Hibiscus syriacus cultivar Beakdansim tig00112663_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: 70675
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2213 original size:2 final size:2
Alignment explanation
Indices: 2206--2235 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2196 AAATGCATGG
2206 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2236 GATTGGTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3689 original size:21 final size:18
Alignment explanation
Indices: 3647--3720 Score: 112
Period size: 18 Copynumber: 3.9 Consensus size: 18
3637 ACTAAATATT
3647 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
3665 TGTCTCGAAGGACCACTGATA
1 TGTCCCGAAGGACCAC---TA
3686 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3704 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
3721 GATAATCCTC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
18 34 0.67
21 17 0.33
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3701 original size:39 final size:39
Alignment explanation
Indices: 3647--3724 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
3637 ACTAAATATT
*
3647 TGTCCCGAAGGACCACTATGTCTCGAAGGACCACTGATA
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGATA
3686 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGATA
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGATA
3725 ATCCTCGACT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.19
Consensus pattern (39 bp):
TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGATA
Found at i:6955 original size:2 final size:2
Alignment explanation
Indices: 6950--7003 Score: 99
Period size: 2 Copynumber: 26.5 Consensus size: 2
6940 TGTGTGTGTG
6950 TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
6992 TA TA TA TCA TA T
1 TA TA TA T-A TA T
7004 GATTTGGTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 49 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7417 original size:23 final size:23
Alignment explanation
Indices: 7353--7417 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
7343 ATTATATTGT
7353 ACTTCGGTGCATTTCTACGCGGC
1 ACTTCGGTGCATTTCTACGCGGC
* * *
7376 ACTACGGTGCAATTCTACGTGGC
1 ACTTCGGTGCATTTCTACGCGGC
*
7399 ACTTCGGTGCATTTATACG
1 ACTTCGGTGCATTTCTACG
7418 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (23 bp):
ACTTCGGTGCATTTCTACGCGGC
Found at i:11999 original size:6 final size:6
Alignment explanation
Indices: 11985--12030 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
11975 TGATAATGAA
*
11985 AGTGGT AGTGAT AGTGGT AGTGGT AGTGGT AGTGGT AGTGGT AGTG
1 AGTGGT AGTGGT AGTGGT AGTGGT AGTGGT AGTGGT AGTGGT AGTG
12031 CAGCATGTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.20, C:0.00, G:0.48, T:0.33
Consensus pattern (6 bp):
AGTGGT
Found at i:12017 original size:18 final size:18
Alignment explanation
Indices: 11968--12030 Score: 90
Period size: 18 Copynumber: 3.5 Consensus size: 18
11958 GTAGAAACAC
* **
11968 GTGGTAGTGATAATGAAA
1 GTGGTAGTGATAGTGGTA
11986 GTGGTAGTGATAGTGGTA
1 GTGGTAGTGATAGTGGTA
*
12004 GTGGTAGTGGTAGTGGTA
1 GTGGTAGTGATAGTGGTA
12022 GTGGTAGTG
1 GTGGTAGTG
12031 CAGCATGTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (18 bp):
GTGGTAGTGATAGTGGTA
Found at i:18186 original size:28 final size:28
Alignment explanation
Indices: 18094--18186 Score: 64
Period size: 28 Copynumber: 3.1 Consensus size: 28
18084 CTTGCTTAAG
18094 TGTTTAGCATGTGGTGATGATATCAAAT
1 TGTTTAGCATGTGGTGATGATATCAAAT
* * **
18122 TGTCTTTTATGGTCAAT-TGATGCTGATAT-ATTGT
1 TG---TTTA--G-C-ATGTGGTGATGATATCA-AAT
18156 TGTTTAGCATGTGGTGATGATATCAAAT
1 TGTTTAGCATGTGGTGATGATATCAAAT
18184 TGT
1 TGT
18187 CTTTTTAGGC
Statistics
Matches: 47, Mismatches: 8, Indels: 20
0.63 0.11 0.27
Matches are distributed among these distances:
27 2 0.04
28 17 0.36
29 2 0.04
31 8 0.17
33 2 0.04
34 14 0.30
35 2 0.04
ACGTcount: A:0.25, C:0.08, G:0.24, T:0.44
Consensus pattern (28 bp):
TGTTTAGCATGTGGTGATGATATCAAAT
Found at i:18186 original size:31 final size:32
Alignment explanation
Indices: 18094--18194 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 32
18084 CTTGCTTAAG
18094 TGTTTAGCATGTGGTGATGATATCAAATTGTC
1 TGTTTAGCATGTGGTGATGATATCAAATTGTC
* *
18126 T-TTTATGGTCAAT-TGATGCTGATAT---ATTGT-
1 TGTTTA--G-C-ATGTGGTGATGATATCAAATTGTC
18156 TGTTTAGCATGTGGTGATGATATCAAATTGTC
1 TGTTTAGCATGTGGTGATGATATCAAATTGTC
*
18188 TTTTTAG
1 TGTTTAG
18195 GCAGCTGGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 20
0.68 0.06 0.25
Matches are distributed among these distances:
27 2 0.04
28 11 0.20
29 1 0.02
30 1 0.02
31 18 0.33
32 7 0.13
33 1 0.02
34 11 0.20
35 2 0.04
ACGTcount: A:0.24, C:0.08, G:0.23, T:0.46
Consensus pattern (32 bp):
TGTTTAGCATGTGGTGATGATATCAAATTGTC
Found at i:28888 original size:20 final size:21
Alignment explanation
Indices: 28863--28914 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
28853 TTTTCCCAAT
*
28863 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
28883 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
28904 TCGCAATGCGA
1 TCGCAATGCGA
28915 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:28927 original size:41 final size:41
Alignment explanation
Indices: 28900--28977 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
28890 GCGAATTGGG
* * *
28900 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
28941 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
28978 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:28928 original size:20 final size:20
Alignment explanation
Indices: 28903--28996 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
28893 AATTGGGAAA
*
28903 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
28923 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
28944 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
28964 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
28984 TTCGCAACGCGAT
1 ATCGCAACGCGAT
28997 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:29558 original size:19 final size:19
Alignment explanation
Indices: 29513--29560 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
29503 TTCGAGAATG
*
29513 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGCGGAAAC
*
29532 AACTATCGCAACGC-GAAACC
1 AA-AATCGCAACGCGGAAA-C
29552 AAAATCGCA
1 AAAATCGCA
29561 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.46, C:0.27, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGGAAAC
Found at i:29578 original size:19 final size:19
Alignment explanation
Indices: 29556--29626 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
29546 GAAACCAAAA
29556 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
29575 TCGCGTTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
*
29594 TCGCGGTTGCGATTTTCATT
1 TCGC-ATTGCGATTTTCATT
29614 TCGCATTGCGATT
1 TCGCATTGCGATT
29627 GTCTGGTCGC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
19 29 0.62
20 18 0.38
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:29602 original size:20 final size:19
Alignment explanation
Indices: 29556--29721 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
29546 GAAACCAAAA
*
29556 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
29575 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
29594 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
29614 TCGCATTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
29630 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
29647 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
29661 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
29680 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
29700 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
29720 TC
1 TC
29722 AACCAAAAGA
Statistics
Matches: 117, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
14 19 0.16
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 40 0.34
20 49 0.42
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:29637 original size:39 final size:39
Alignment explanation
Indices: 29561--29637 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
29551 CAAAATCGCA
* * **
29561 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCATTGCGATTTCTAGGTCGCGG
29600 TTGCGATTTTCATTTCGCATTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCATTGCGATT-TCTAGGTCGCG
29638 ATAGTCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCTAGGTCGCGG
Found at i:29646 original size:33 final size:33
Alignment explanation
Indices: 29609--29696 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
29599 GTTGCGATTT
* * *
29609 TCATTTCGCATTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
29642 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
29675 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
29697 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:31783 original size:42 final size:42
Alignment explanation
Indices: 31723--31815 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
31713 GCCCGACTCG
* * *
31723 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
31765 CCTATCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
31807 ACTGTCATC
1 CCTATCATC
31816 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.23, C:0.38, G:0.16, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:31808 original size:21 final size:21
Alignment explanation
Indices: 31779--31845 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
31769 TCATTCCTCG
*
31779 AGAGTCCACTCCCACCGTTCA
1 AGAGGCCACTCCCACCGTTCA
** * *
31800 AGAGGCCACTGTCATCGTTGA
1 AGAGGCCACTCCCACCGTTCA
* * *
31821 AGAGGTCTCTCCCACCATTCA
1 AGAGGCCACTCCCACCGTTCA
31842 AGAG
1 AGAG
31846 CCCGATTCAC
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.21
Consensus pattern (21 bp):
AGAGGCCACTCCCACCGTTCA
Found at i:33224 original size:14 final size:14
Alignment explanation
Indices: 33205--33240 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
33195 ATTGTTTAAT
33205 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
33219 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
33233 TGATTTGT
1 TGATTTGT
33241 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:33450 original size:19 final size:19
Alignment explanation
Indices: 33419--33549 Score: 112
Period size: 19 Copynumber: 7.7 Consensus size: 19
33409 CGAAATTAAA
33419 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
33438 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
33454 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
33471 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
33485 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
33504 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
33520 TTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
33537 TTCGCATTGCGAT
1 TTCGCATTGCGAT
33550 AGTAATTTCC
Statistics
Matches: 87, Mismatches: 10, Indels: 30
0.69 0.08 0.24
Matches are distributed among these distances:
14 23 0.26
16 14 0.16
17 14 0.16
19 36 0.41
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:33467 original size:33 final size:32
Alignment explanation
Indices: 33425--33549 Score: 180
Period size: 33 Copynumber: 3.8 Consensus size: 32
33415 TAAATTCGCA
*
33425 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATT-CATCG
*
33458 TTGCGATTTTCATTTCGCATTGCGAAATT-AGCG
1 TTGCGATTTTCATTTCGCATTGCG--ATTCATCG
*
33491 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTC-ATCG
33524 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
33550 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (32 bp):
TTGCGATTTTCATTTCGCATTGCGATTCATCG
Found at i:33512 original size:66 final size:66
Alignment explanation
Indices: 33416--33548 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
33406 ACGCGAAATT
*
33416 AAATTCGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
33481 G
66 G
* **
33482 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
33547 G
66 G
33548 A
1 A
33549 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:36063 original size:24 final size:24
Alignment explanation
Indices: 36029--36082 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
36019 CTGAAACATC
* *
36029 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
36053 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
36077 ATCAAA
1 ATCAAA
36083 TTTCAAATAC
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:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:37170 original size:20 final size:20
Alignment explanation
Indices: 37142--37199 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
37132 ATTCATTTGA
37142 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
37162 CTATTGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
37182 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
37200 CACAATGCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:37242 original size:14 final size:16
Alignment explanation
Indices: 37222--37295 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
37212 TGAAAATCGC
37222 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
37237 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
37254 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
37273 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
37289 -TTGCGAT
1 ATTGCGAT
37296 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:37259 original size:19 final size:19
Alignment explanation
Indices: 37218--37285 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
37208 GAAATGAAAA
37218 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
37234 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
37251 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
37270 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
37286 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:39340 original size:20 final size:19
Alignment explanation
Indices: 39305--39371 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
39295 GAAACTTAAA
* *
39305 ATCGCAATGTGAAATGACT
1 ATCGCAACGCGAAATGACT
*
39324 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
39344 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
39363 ATCGCAACG
1 ATCGCAACG
39372 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:39366 original size:19 final size:19
Alignment explanation
Indices: 39286--39403 Score: 77
Period size: 20 Copynumber: 6.4 Consensus size: 19
39276 TAGTTTACTT
* *
39286 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* * **
39306 TCGCAATGTGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
39325 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
39345 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
39364 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
39378 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
39396 TCGCAACG
1 TCGCAACG
39404 ACAAAATCGC
Statistics
Matches: 77, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 12 0.16
19 23 0.30
20 27 0.35
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:39379 original size:14 final size:14
Alignment explanation
Indices: 39360--39417 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
39350 ATGCGAAATG
39360 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
39374 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
39390 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
39406 AAAATCGCAACG
1 AAAATCGCAACG
39418 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:39402 original size:32 final size:33
Alignment explanation
Indices: 39344--39422 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
39334 GGAAATGGCT
*
39344 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
39377 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
39409 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
39423 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:39470 original size:14 final size:14
Alignment explanation
Indices: 39451--39508 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
39441 TTTCATTTCG
39451 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
39465 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
39481 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
39497 CGTTGTGATTTT
1 CGTTGCGATTTT
39509 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:39515 original size:33 final size:33
Alignment explanation
Indices: 39434--39524 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
39424 ACAAATCGCA
39434 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
39467 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
39499 TTGTGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
39525 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:39543 original size:20 final size:19
Alignment explanation
Indices: 39509--39563 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
39499 TTGTGATTTT
*
39509 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
39528 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
39548 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
39564 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:40062 original size:18 final size:18
Alignment explanation
Indices: 40036--40080 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
40026 GTCGATCAGA
*
40036 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
40054 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
40072 TGATGGCTC
1 TGATGGCTC
40081 CCGAAGTGGA
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:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:41424 original size:20 final size:20
Alignment explanation
Indices: 41399--41452 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
41389 AATAGTTTCT
41399 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
41419 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
41439 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
41453 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:41702 original size:22 final size:22
Alignment explanation
Indices: 41677--41720 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41667 GATTTAGATA
41677 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
41699 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
41721 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:41933 original size:20 final size:20
Alignment explanation
Indices: 41908--42001 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
41898 GATTATGTAT
41908 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
41928 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
41948 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
41969 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
41989 TATCGCATTGCGA
1 TATCGCGTTGCGA
42002 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:42002 original size:20 final size:20
Alignment explanation
Indices: 41888--42002 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
41878 CGCTTTGAAA
*
41888 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
41909 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
41929 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
41949 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
41970 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
41990 ATCGCATTGCGAT
1 ATCGCATTGCGAT
42003 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:42020 original size:21 final size:21
Alignment explanation
Indices: 41991--42087 Score: 133
Period size: 21 Copynumber: 4.7 Consensus size: 21
41981 ATAGTCAGTA
*
41991 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* **
42012 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
*
42032 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
42053 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
*
42074 TCGTGTTGCGATTT
1 TCGCGTTGCGATTT
42088 ACTTATTCGC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 16 0.25
21 49 0.75
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.41
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:42021 original size:41 final size:41
Alignment explanation
Indices: 41930--42064 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
41920 AAAGTCAGTA
* * * ** *
41930 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
41970 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
42012 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
42053 TCGCGTTGCGAT
1 TCGCGTTGCGAT
42065 TTTCCCAATT
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:43475 original size:20 final size:20
Alignment explanation
Indices: 43450--43501 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
43440 TTGTTTGATC
43450 ATGAAACTTTCTGTCCATTT
1 ATGAAACTTTCTGTCCATTT
* *
43470 ATGAAAATGTTTTGTCCATTT
1 ATGAAACT-TTCTGTCCATTT
43491 ATGAAAACTTT
1 ATG-AAACTTT
43502 TCAATTTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.26
21 16 0.59
22 4 0.15
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGAAACTTTCTGTCCATTT
Found at i:48029 original size:21 final size:22
Alignment explanation
Indices: 47999--48039 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
47989 TTAGGATCAA
*
47999 TGGGATTAGGAATAGGATTTTG
1 TGGGATTAGGAAGAGGATTTTG
*
48021 TGGGA-TAGGAGGAGGATTT
1 TGGGATTAGGAAGAGGATTT
48040 ACAGGAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.27, C:0.00, G:0.41, T:0.32
Consensus pattern (22 bp):
TGGGATTAGGAAGAGGATTTTG
Found at i:48806 original size:22 final size:22
Alignment explanation
Indices: 48724--48807 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
48714 CAGAAACCCC
* *
48724 AGGGGGTATCGATTCCCCTAC-
1 AGGGGGAATCGATTCCCCTTCA
*
48745 AGGGGAGAATCGGTTCCCCTTCAA
1 AGGGG-GAATCGATTCCCCTTC-A
* *
48769 AGGAGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
* *
48791 AGGGGGTATTGATTCCC
1 AGGGGGAATCGATTCCC
48808 TCTGCCCTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 5 0.10
22 27 0.52
23 16 0.31
24 4 0.08
ACGTcount: A:0.21, C:0.25, G:0.30, T:0.24
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:55648 original size:75 final size:75
Alignment explanation
Indices: 55521--55699 Score: 241
Period size: 75 Copynumber: 2.4 Consensus size: 75
55511 ACCGGTTAAC
** * * * ** * *
55521 ATAAAATAGATGCTACCTATTATGTTAAACTACCTACTGATTTATTTGAAGGTTACTAATATTGT
1 ATAAAATAGGCGCTACCTATTACGTTAAAATACATACCAATTTATTTAAAGGTTACTAATAATGT
**
55586 AAACGGTAAA
66 AAACAATAAA
*
55596 ATAAAATAGGCGCTACCTATTACGTTAAAATACATACCAATTTGTTTAAAGGTTACTAATAATGT
1 ATAAAATAGGCGCTACCTATTACGTTAAAATACATACCAATTTATTTAAAGGTTACTAATAATGT
55661 AAACAATAAA
66 AAACAATAAA
*
55671 AGAAAATAGGCGCTACCTATTACGTTAAA
1 ATAAAATAGGCGCTACCTATTACGTTAAA
55700 TAGGCACTAC
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 91 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (75 bp):
ATAAAATAGGCGCTACCTATTACGTTAAAATACATACCAATTTATTTAAAGGTTACTAATAATGT
AAACAATAAA
Found at i:55704 original size:23 final size:23
Alignment explanation
Indices: 55674--55724 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
55664 CAATAAAAGA
*
55674 AAATAGGCGCTACCTATTACGTT
1 AAATAGGCACTACCTATTACGTT
*
55697 AAATAGGCACTACTTATTACGTT
1 AAATAGGCACTACCTATTACGTT
55720 AAATA
1 AAATA
55725 AGCGTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (23 bp):
AAATAGGCACTACCTATTACGTT
Found at i:55735 original size:23 final size:23
Alignment explanation
Indices: 55674--55745 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
55664 CAATAAAAGA
* * *
55674 AAATAGGCGCTACCTATTACGTT
1 AAATAAGCACTACTTATTACGTT
*
55697 AAATAGGCACTACTTATTACGTT
1 AAATAAGCACTACTTATTACGTT
** * *
55720 AAATAAGCGTTTCTTATTGCGTT
1 AAATAAGCACTACTTATTACGTT
55743 AAA
1 AAA
55746 CTAGCTACCG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (23 bp):
AAATAAGCACTACTTATTACGTT
Found at i:59720 original size:61 final size:62
Alignment explanation
Indices: 59625--59748 Score: 241
Period size: 61 Copynumber: 2.0 Consensus size: 62
59615 CTGTTTTTAA
59625 ACTAAGTTTCAGGTGAAGTTTAAAATTTGGTCAGTGTGCAATCT-TGATTTCATTGCATTAC
1 ACTAAGTTTCAGGTGAAGTTTAAAATTTGGTCAGTGTGCAATCTCTGATTTCATTGCATTAC
59686 ACTAAGTTTCAGGTGAAGTTTAAAATTTGGTCAGTGTGCAATCTCTGATTTCATTGCATTAC
1 ACTAAGTTTCAGGTGAAGTTTAAAATTTGGTCAGTGTGCAATCTCTGATTTCATTGCATTAC
59748 A
1 A
59749 ACAGGCTGGA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
61 44 0.71
62 18 0.29
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (62 bp):
ACTAAGTTTCAGGTGAAGTTTAAAATTTGGTCAGTGTGCAATCTCTGATTTCATTGCATTAC
Found at i:68144 original size:23 final size:22
Alignment explanation
Indices: 68118--68180 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 22
68108 GTAGAATTTG
68118 TCCCGAAGGACCACGTAGAAAT
1 TCCCGAAGGACCACGTAGAAAT
* * *
68140 ATCCCGAATGATCACATAG--AT
1 -TCCCGAAGGACCACGTAGAAAT
* *
68161 TCCCAAAGGACCGCGTAGAA
1 TCCCGAAGGACCACGTAGAA
68181 CCCTGACTCT
Statistics
Matches: 30, Mismatches: 8, Indels: 5
0.70 0.19 0.12
Matches are distributed among these distances:
20 13 0.43
21 2 0.07
23 15 0.50
ACGTcount: A:0.37, C:0.27, G:0.21, T:0.16
Consensus pattern (22 bp):
TCCCGAAGGACCACGTAGAAAT
Done.