Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005628.1 Hibiscus syriacus cultivar Beakdansim tig00013111_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: 55807
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:219 original size:20 final size:20
Alignment explanation
Indices: 194--231 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
184 CCCCATTTTT
*
194 GCATCTTTGCATTTACATAA
1 GCATCTTTGCATTAACATAA
214 GCATCTTTGCATTAACAT
1 GCATCTTTGCATTAACAT
232 CCATACATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (20 bp):
GCATCTTTGCATTAACATAA
Found at i:1524 original size:8 final size:7
Alignment explanation
Indices: 1502--1579 Score: 59
Period size: 8 Copynumber: 10.1 Consensus size: 7
1492 ACACAAAAGG
1502 AAAGTAAA
1 AAAG-AAA
1510 AACAGAAA
1 AA-AGAAA
1518 AATAGAAA
1 AA-AGAAA
1526 AATAGAAA
1 AA-AGAAA
1534 AAAGGAAA
1 AAA-GAAA
1542 AAAGAAAGA
1 AAAG-AA-A
*
1551 GAAAGAGA
1 -AAAGAAA
1559 AAA-AAA
1 AAAGAAA
1565 AAAGAAA
1 AAAGAAA
*
1572 GAAGAAA
1 AAAGAAA
1579 A
1 A
1580 TAGACAGATC
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
6 5 0.08
7 14 0.24
8 32 0.54
9 4 0.07
10 4 0.07
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (7 bp):
AAAGAAA
Found at i:1561 original size:17 final size:18
Alignment explanation
Indices: 1523--1579 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
1513 AGAAAAATAG
* *
1523 AAAAATAGAAAAAAGGAAA
1 AAAAAAAGAAAGAA-GAAA
1542 AAAGAAAGAGAAAG-AGAAA
1 AAA-AAA-AGAAAGAAGAAA
1561 AAAAAAAGAAAGAAGAAA
1 AAAAAAAGAAAGAAGAAA
1579 A
1 A
1580 TAGACAGATC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
17 6 0.18
18 9 0.27
19 10 0.30
20 3 0.09
21 5 0.15
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (18 bp):
AAAAAAAGAAAGAAGAAA
Found at i:3681 original size:54 final size:54
Alignment explanation
Indices: 3544--3914 Score: 318
Period size: 54 Copynumber: 6.8 Consensus size: 54
3534 ATTTTTTATT
* * * * * *
3544 AGTTTTTAAAGAAACTAAGTGTGATTTTCAAAAGTTTCATGATGATTTTCAAGTG
1 AGTTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA-TTTCAAATA
* * *
3599 AGTTTTTAAAGAAACTAAGCCTGGTTTTCAGAAGTTTCTTGATGATTTCAAATA
1 AGTTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTCAAATA
* * *
3653 AGTTTTCAACGAAACTAAGTCTGATTTTCAGAAGTTTCATGATGATTTCAAATG
1 AGTTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTCAAATA
* * * * * * *
3707 TGTTTTTTTAAAGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGCTTTTGAAATG
1 AG--TTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG-ATTTCAAATA
* ** **
3764 TGTTTT-AAAGAAACTAAGTCTGATTTTTGGAAGTTTCTTGATTTTTCTCAAATTA
1 AGTTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATT-TCAAA-TA
* * * * ** *
3819 ACG--TTCAAAGAAATTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGA
1 A-GTTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTCAAAT-A
* * * **
3873 A-TTTTCAAAGAAATTAAGCCTGGTTTTCAGGGGTTTCTTGAT
1 AGTTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGAT
3915 TTTTTTTTGA
Statistics
Matches: 269, Mismatches: 37, Indels: 21
0.82 0.11 0.06
Matches are distributed among these distances:
53 4 0.01
54 139 0.52
55 78 0.29
56 38 0.14
57 10 0.04
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (54 bp):
AGTTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTCAAATA
Found at i:3714 original size:109 final size:108
Alignment explanation
Indices: 3544--3902 Score: 364
Period size: 109 Copynumber: 3.3 Consensus size: 108
3534 ATTTTTTATT
* * * * *
3544 AGTTTTTAAAGAAACTAAGTGTGATTTTCAAAAGTTTCATGATGATTTTCAAGTGAGTTTTTAAA
1 AGTTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCATGATGA-TTTCAAATGTGTTTTTAAA
* * *
3609 GAAACTAAGCCTGGTTTTCAGAAGTTTCTTGATGATTTCAAATA
65 GAAACTAAGCCTGATTTTTAGAAGTTTCTTGATGTTTTCAAATA
*
3653 AGTTTTCAACGAAACTAAGTCTGATTTTCAGAAGTTTCATGATGATTTCAAATGTGTTTTTTTAA
1 AGTTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCATGATGATTTCAAATGTG--TTTTTAA
* * * *
3718 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGCTTTTGAAATG
64 AGAAACTAAGCCTGATTTTTAGAAGTTTCTTGATG-TTTTCAAATA
* ** * ** *** *
3764 TGTTTT-AAAGAAACTAAGTCTGATTTTTGGAAGTTTCTTGATTTTTCTCAAAT-TAACGTTCAA
1 AGTTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCATGATGATT-TCAAATGT-GTTTTTAA
* * **
3827 AGAAATTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGA
64 AGAAACTAAGCCTGATTTTTAGAAGTTTCTTGATGTTTTCAAAT-A
* * *
3873 A-TTTTCAAAGAAATTAAGCCTGGTTTTCAG
1 AGTTTTCAAAGAAACTAAGTCTGATTTTCAG
3903 GGGTTTCTTG
Statistics
Matches: 205, Mismatches: 38, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
108 21 0.10
109 93 0.45
110 73 0.36
111 18 0.09
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (108 bp):
AGTTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCATGATGATTTCAAATGTGTTTTTAAAG
AAACTAAGCCTGATTTTTAGAAGTTTCTTGATGTTTTCAAATA
Found at i:3869 original size:165 final size:164
Alignment explanation
Indices: 3546--3871 Score: 386
Period size: 165 Copynumber: 2.0 Consensus size: 164
3536 TTTTTATTAG
* * *
3546 TTTTTAAAGAAACTAAGTGTGATTTTCAAAAGTTTCATGATGATTTTCAAGTGAGTTTTTAAAGA
1 TTTTTAAAGAAACTAAGTCTGATTTTCAAAAGTTTCATGACGATTTTCAAATGAGTTTTTAAAGA
* * * *
3611 AACTAAGCCTGGTTTTCAGAAGTTTCTTGATGATTTCAAATAAGTTTTCAACGAAACTAAGTCTG
66 AACTAAGCCTGATTTTCAGAAGTTTCTTGATGATTTCAAATAAG-TTTCAAAGAAACTAAGCCTA
3676 ATTTTCAGAAGTTTCATGATGATTTCAAATGTGTT
130 ATTTTCAGAAGTTTCATGATGATTTCAAATGTGTT
* * * * * *
3711 TTTTTAAAGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGCTTTTGAAATGTG-TTTTAAAGA
1 TTTTTAAAGAAACTAAGTCTGATTTTCAAAAGTTTCATGACGATTTTCAAATGAGTTTTTAAAGA
* ** ** *
3775 AACTAAGTCTGATTTTTGGAAGTTTCTTGATTTTTCTCAAATTAACG-TTCAAAGAAATTAAGCC
66 AACTAAGCCTGATTTTCAGAAGTTTCTTGATGATT-TCAAA-TAA-GTTTCAAAGAAACTAAGCC
* ** * *
3839 TAATTTTTAGGGGTTTCTTGATGTTTTCAAATG
128 TAATTTTCAGAAGTTTCATGATGATTTCAAATG
3872 AATTTTCAAA
Statistics
Matches: 134, Mismatches: 24, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
164 38 0.28
165 92 0.69
166 3 0.02
167 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (164 bp):
TTTTTAAAGAAACTAAGTCTGATTTTCAAAAGTTTCATGACGATTTTCAAATGAGTTTTTAAAGA
AACTAAGCCTGATTTTCAGAAGTTTCTTGATGATTTCAAATAAGTTTCAAAGAAACTAAGCCTAA
TTTTCAGAAGTTTCATGATGATTTCAAATGTGTT
Found at i:3909 original size:109 final size:109
Alignment explanation
Indices: 3606--3918 Score: 260
Period size: 110 Copynumber: 2.9 Consensus size: 109
3596 GTGAGTTTTT
** * * * *
3606 AAAGAAACTAAGCCTGGTTTTCAGAAGTTTCTTGATG-ATTTCAAAT-AAGTTTTCAACGAAACT
1 AAAGAAACTAAGCCTAATTTTTAGAAGTTTCTTGACGCTTTTCAAATGAA-TTTT-AAAGAAACT
* * ** **** *
3669 AAGTCTGATTTTCA-GAAGTTTCATGATGATT-TCAAATGTGTTTTTTT
64 AAGCCTGATTTT-AGGAAGTTTCTTGATTTTTCTCAAAT-T-AACGTTC
* * * **
3716 AAAGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGCTTTTGAAATGTGTTTTAAAGAAACTAA
1 AAAGAAACTAAGCCTAATTTTTAGAAGTTTCTTGACGCTTTTCAAATGAATTTTAAAGAAACTAA
* *
3781 GTCTGATTTTTGGAAGTTTCTTGATTTTTCTCAAATTAACGTTC
66 GCCTGATTTTAGGAAGTTTCTTGATTTTTCTCAAATTAACGTTC
* ** * *
3825 AAAGAAATTAAGCCTAATTTTTAGGGGTTTCTTGATG-TTTTCAAATGAATTTTCAAAGAAATTA
1 AAAGAAACTAAGCCTAATTTTTAGAAGTTTCTTGACGCTTTTCAAATGAATTTT-AAAGAAACTA
* *
3889 AGCCTGGTTTTCAGG-GGTTTCTTGATTTTT
65 AGCCTGATTTT-AGGAAGTTTCTTGATTTTT
3919 TTTTGAATTT
Statistics
Matches: 165, Mismatches: 32, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
108 13 0.08
109 65 0.39
110 70 0.42
111 17 0.10
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (109 bp):
AAAGAAACTAAGCCTAATTTTTAGAAGTTTCTTGACGCTTTTCAAATGAATTTTAAAGAAACTAA
GCCTGATTTTAGGAAGTTTCTTGATTTTTCTCAAATTAACGTTC
Found at i:5136 original size:139 final size:139
Alignment explanation
Indices: 4701--5209 Score: 726
Period size: 139 Copynumber: 3.7 Consensus size: 139
4691 AAGATGAACC
* * **
4701 GATCAACATTTCAAATGGAGAGCTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTC
1 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGA-TGAGGGAGAAGAAGTTC
*
4766 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGTAACACC
65 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACACATGGAGTTGAATCAGTAACACC
4831 TCACTCGAGG
130 TCACTCGAGG
* * *
4841 GATCAACATTTCCAGTGGATAGTTCATAATGAGAAGAACTCATCTGATAGAGGGAGAAGAAGTTC
1 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAT-GAGGGAGAAGAAGTTC
* * * * *
4906 ATAATGAGAAGAACTTGTTCGACC-TACCACTCGATTCAT--GACAT----TTCGAATCAGTGAT
65 ATAATGAGAAGAACTTGTTCAACCTTA--GCTCGATTCATCACACATGGAGTT-GAATCAGTAAC
* *
4964 GCTTCACTCGAGG
127 ACCTCACTCGAGG
4977 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
1 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
* * * *
5042 TAATGATAAGAACTTGTTCAATCTTAGCTCGATTCGTCACACATGGAGTTGAATCGGTAACACCT
66 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACACATGGAGTTGAATCAGTAACACCT
5107 CACTCGAGG
131 CACTCGAGG
* * *
5116 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCACCCGATGAGGGAGAAAAAGTTCA
1 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
5181 TAATGAGAAGAACTTGTTCAACCTTAGCT
66 TAATGAGAAGAACTTGTTCAACCTTAGCT
5210 TGTTTCCACC
Statistics
Matches: 324, Mismatches: 34, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
134 9 0.03
135 39 0.12
136 71 0.22
139 113 0.35
140 82 0.25
141 10 0.03
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (139 bp):
GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACACATGGAGTTGAATCAGTAACACCT
CACTCGAGG
Found at i:9267 original size:17 final size:18
Alignment explanation
Indices: 9245--9285 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
9235 AATAACTTAA
*
9245 TATAATATTCTAT-TATT
1 TATAATATTATATATATT
9262 TATAAT-TTATATATATT
1 TATAATATTATATATATT
*
9279 TTTAATA
1 TATAATA
9286 AAATTTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TATAATATTATATATATT
Found at i:9540 original size:49 final size:50
Alignment explanation
Indices: 9406--9597 Score: 235
Period size: 51 Copynumber: 3.8 Consensus size: 50
9396 ATATGTACAT
*
9406 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACAATGTTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTAC-ATTTTTTATTTTATTC
* ** * * *
9457 ATTTACACTAGTGTAAGTATCTATTAAGTACTACACTTTTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACA-TTTTTTATTTTATTC
* *
9508 ACTTACA-C-GTGTAAATATGTGTTAAGTGCTACATTTTTTAATTTTAATC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATTTTTT-ATTTTATTC
* **
9557 ACTTGCACCGGTGTAAGTATGTGTTAAGTTATACATTTTTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATTTTTT
9598 GTAGTATGAA
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
48 6 0.05
49 35 0.29
50 2 0.02
51 76 0.64
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (50 bp):
ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATTTTTTATTTTATTC
Found at i:9552 original size:100 final size:101
Alignment explanation
Indices: 9406--9597 Score: 248
Period size: 100 Copynumber: 1.9 Consensus size: 101
9396 ATATGTACAT
* * * *
9406 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACAATGTTTTATTTTATTCATTTACACTAGTGT
1 ACTTACACCGGTGTAAATATGTGTTAAGTGCTACAATGTTTTATTTTAATCACTTACACCAGTGT
9471 AAGTATCTATTAAG-TACTACACTTTTTTATTTTATTC
66 AAGTATCTATTAAGTTA-TACA-TTTTTTATTTTATTC
* * *
9508 ACTTACA-C-GTGTAAATATGTGTTAAGTGCTAC-ATTTTTTAATTTTAATCACTTGCACCGGTG
1 ACTTACACCGGTGTAAATATGTGTTAAGTGCTACAATGTTTT-ATTTTAATCACTTACACCAGTG
* *
9570 TAAGTATGTGTTAAGTTATACATTTTTT
65 TAAGTATCTATTAAGTTATACATTTTTT
9598 GTAGTATGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
99 12 0.15
100 57 0.72
101 3 0.04
102 7 0.09
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (101 bp):
ACTTACACCGGTGTAAATATGTGTTAAGTGCTACAATGTTTTATTTTAATCACTTACACCAGTGT
AAGTATCTATTAAGTTATACATTTTTTATTTTATTC
Found at i:20042 original size:40 final size:39
Alignment explanation
Indices: 19965--20069 Score: 122
Period size: 39 Copynumber: 2.7 Consensus size: 39
19955 TACAACTTAG
* * *
19965 AATGTTGGGGCATTTT-AAGGCTCATATCAACAAGAAAT
1 AATGTTGGAGCATTTTGAAGGCCCATACCAACAAGAAAT
** *
20003 AAATGTTGGAGCATTTTGAAGGCCCATACCAGTATGAAAT
1 -AATGTTGGAGCATTTTGAAGGCCCATACCAACAAGAAAT
* *
20043 AATGTTGGTGCATTGTGAAGGCCCATA
1 AATGTTGGAGCATTTTGAAGGCCCATA
20070 TCATCCAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
39 40 0.70
40 17 0.30
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (39 bp):
AATGTTGGAGCATTTTGAAGGCCCATACCAACAAGAAAT
Found at i:21252 original size:62 final size:62
Alignment explanation
Indices: 21085--21241 Score: 208
Period size: 62 Copynumber: 2.5 Consensus size: 62
21075 TCTAATAAAC
* * * *
21085 TCAATCTTTGACTTCCTCGTGAAGAGAAGTTAACCTTTTTTATTCAGGACTCCCCTATAGAG
1 TCAATCCTTGACTTCCTCGTAAAGAGAAGTCAACCTTTTTTATTCAGGACTCCCATATAGAG
* * ** *
21147 TCAATCCTTGACTTCTTTGTAAAGAGAAGTCAACCTTTTTTATTCCTGA-TTCCATAGTAGAG
1 TCAATCCTTGACTTCCTCGTAAAGAGAAGTCAACCTTTTTTATTCAGGACTCCCATA-TAGAG
*
21209 TCAATCCTTGAATTCCTCGTAAAGAGAAGTCAA
1 TCAATCCTTGACTTCCTCGTAAAGAGAAGTCAA
21242 TTTTTCTTAT
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
61 5 0.06
62 77 0.94
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (62 bp):
TCAATCCTTGACTTCCTCGTAAAGAGAAGTCAACCTTTTTTATTCAGGACTCCCATATAGAG
Found at i:21540 original size:137 final size:136
Alignment explanation
Indices: 21294--21669 Score: 522
Period size: 137 Copynumber: 2.8 Consensus size: 136
21284 AAAAAAAGGT
* ** * *
21294 TAGATGTCCTCAACACGAAGGAACAATGTCATCCACTAACCAGATCTCCTTATCACGTAGGAGTC
1 TAGATGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGATCTTCTCATCACGTAGGAGT-
** * * *
21359 GCATCATCCTTATATAGCCAGAATTCCTCATTGCATAGGAACTGTGTTATCTCCATTATCCCTAA
65 GTTTCATCCTTAGATAGCCAGAATTCCTCATCGCGTAGGAACTGTGTTATCTCCATTATCCCTAA
21424 AGATGGC
130 AGATGGC
*
21431 TAGATGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGATCTTCTCATCACGTAAGAGCT
1 TAGATGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGATCTTCTCATCACGTAGGAG-T
*
21496 GTTTCATCCTTAGATAGGCAGAATTCCTCATCGCGTAGGAACTGTGTTATCTCCATTATCCCTAA
65 GTTTCATCCTTAGATAGCCAGAATTCCTCATCGCGTAGGAACTGTGTTATCTCCATTATCCCTAA
21561 AGATGGC
130 AGATGGC
* * ** * * *
21568 AAAATGTCCTCATCACGAAGGAATGATGTCATCTATCGACCAGATC-TCTTCATCACGTAGGATT
1 TAGATGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGATCTTC-TCATCACGTAGGA-G
*
21632 TGTTTCATCTTTAGATAGCCA-AATTCCTCATCGCGTAG
64 TGTTTCATCCTTAGATAGCCAGAATTCCTCATCGCGTAG
21670 AATCGTGTAA
Statistics
Matches: 214, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
136 19 0.09
137 194 0.91
138 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (136 bp):
TAGATGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGATCTTCTCATCACGTAGGAGTG
TTTCATCCTTAGATAGCCAGAATTCCTCATCGCGTAGGAACTGTGTTATCTCCATTATCCCTAAA
GATGGC
Found at i:22433 original size:13 final size:13
Alignment explanation
Indices: 22415--22439 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22405 TTACGACCCG
22415 ACCCGACCCGTTA
1 ACCCGACCCGTTA
22428 ACCCGACCCGTT
1 ACCCGACCCGTT
22440 GACCGGGTGA
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:0.20, C:0.48, G:0.16, T:0.16
Consensus pattern (13 bp):
ACCCGACCCGTTA
Found at i:22542 original size:24 final size:24
Alignment explanation
Indices: 22507--22552 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
22497 GGAAATAGTG
* *
22507 CTATTTTTGTAATTTTTTAAAATT
1 CTATTTTCGTAATTTTTGAAAATT
22531 CTATTTTCGTAATTTTTGAAAA
1 CTATTTTCGTAATTTTTGAAAA
22553 AAATGACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (24 bp):
CTATTTTCGTAATTTTTGAAAATT
Found at i:22615 original size:29 final size:30
Alignment explanation
Indices: 22572--22629 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
22562 TTTAATAAAT
22572 ATTTTGAAAATGGTGCTATATTGGTAATTA
1 ATTTTGAAAATGGTGCTATATTGGTAATTA
* *
22602 ATTTT-AAAATGGTGCTATTTTTGTAATT
1 ATTTTGAAAATGGTGCTATATTGGTAATT
22630 TTGTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.48
Consensus pattern (30 bp):
ATTTTGAAAATGGTGCTATATTGGTAATTA
Found at i:28199 original size:29 final size:29
Alignment explanation
Indices: 28144--28199 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
28134 CCGTTGACCG
* * * *
28144 GGTGACATTTTAGTAATTATTTTGAAACT
1 GGTGACATATTAGGAATTAATTCGAAACT
*
28173 GGTGACATATTGGGAATTAATTCGAAA
1 GGTGACATATTAGGAATTAATTCGAAA
28200 AGGGTACTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (29 bp):
GGTGACATATTAGGAATTAATTCGAAACT
Found at i:28329 original size:29 final size:30
Alignment explanation
Indices: 28273--28330 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
28263 TTTAATAAAT
* *
28273 ATTTTGAAAATGGTTCTATATTGGTAATTA
1 ATTTTGAAAATGGTGCTATATTCGTAATTA
* *
28303 ATTTT-AAAATGGTGCTATTTTCTTAATT
1 ATTTTGAAAATGGTGCTATATTCGTAATT
28331 TTGTAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.50
Consensus pattern (30 bp):
ATTTTGAAAATGGTGCTATATTCGTAATTA
Found at i:33757 original size:92 final size:90
Alignment explanation
Indices: 33567--33737 Score: 213
Period size: 89 Copynumber: 1.9 Consensus size: 90
33557 ATATTAATTT
* * * *
33567 TAAAAATGATATTATAAAAGAAATTATATATCAAACATATTTTTTTAAATTAATATAAAAGTACC
1 TAAAAATGATATTATAAAAAAAATTATATATCAAACATA-TATTGTAAA-TAATATAAAAATACC
* * *
33632 TTAGTTTAAAAAAATAAATATAAATTT
64 TTAATTTAAAAAAATAAATATAAAATG
33659 TAAAAATGATATTATTAAAATAAAATTATATATCAAACATA-ATTGTAAA-AA-ATAAAAATACC
1 TAAAAATGATATTA-TAAAA-AAAATTATATATCAAACATATATTGTAAATAATATAAAAATACC
*
33721 TTAATTTATAAAAATAA
64 TTAATTTAAAAAAATAA
33738 TTTTTAAAAG
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
89 25 0.35
90 2 0.03
92 20 0.28
93 5 0.07
94 19 0.27
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.36
Consensus pattern (90 bp):
TAAAAATGATATTATAAAAAAAATTATATATCAAACATATATTGTAAATAATATAAAAATACCTT
AATTTAAAAAAATAAATATAAAATG
Found at i:35522 original size:17 final size:18
Alignment explanation
Indices: 35500--35540 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
35490 TTTTCACCCC
*
35500 ATTTTTTATAT-ATTATT
1 ATTTTTTATATAAATATT
35517 ATTTTTTATATAAATATT
1 ATTTTTTATATAAATATT
35535 ATTTTT
1 ATTTTT
35541 ATTTCTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTTTATATAAATATT
Found at i:39069 original size:46 final size:46
Alignment explanation
Indices: 39017--39116 Score: 191
Period size: 46 Copynumber: 2.2 Consensus size: 46
39007 GGCATGAGGT
*
39017 TAGGATTTTCTATAAACAAAGCATATGGGTAGAAATCTTGTTTGGG
1 TAGGATTTTCTATAAACAAAGCATATGGGTAGAAATCCTGTTTGGG
39063 TAGGATTTTCTATAAACAAAGCATATGGGTAGAAATCCTGTTTGGG
1 TAGGATTTTCTATAAACAAAGCATATGGGTAGAAATCCTGTTTGGG
39109 TAGGATTT
1 TAGGATTT
39117 ACTAAAGCAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (46 bp):
TAGGATTTTCTATAAACAAAGCATATGGGTAGAAATCCTGTTTGGG
Found at i:48447 original size:134 final size:134
Alignment explanation
Indices: 48264--48722 Score: 559
Period size: 134 Copynumber: 3.4 Consensus size: 134
48254 CTTGAAGACA
* * ** * * * *
48264 AGTGGAACAAGTATGCCTAAATTCAATCTTCCCTAAGTG-ACAGTGGAATGAATCAACTTCCCCA
1 AGTGAAACAAGTCTGCCTTGATTCAATCTTCCCTGAG-GAACAATGGAATGAATCAACATCCCTA
*
48328 GATCTGATTTTCCCTCAAAAAGAAGCGGAACAAATCCCTCTCTTTCAAAATTTGATATTCCCCGA
65 GATCTGATTTTCCCTCAAAAAGAAGCGGAACAAATCCCTCTCTTTCAAAATTTGATATTCCCTGA
48393 GTAAC
130 GTAAC
* *
48398 AGTGAAACAAGTCTGCCTTGATTCCATCTTCCCTGAGGAACAATGGAATGAATAAACATCCCTAG
1 AGTGAAACAAGTCTGCCTTGATTCAATCTTCCCTGAGGAACAATGGAATGAATCAACATCCCTAG
* * *
48463 ATCTGATTTTCCCTCAAGAAGAAGCGGAACATACCCCTCTCTTT-AAAGATTTGATATTCCCTGA
66 ATCTGATTTTCCCTCAAAAAGAAGCGGAACAAATCCCTCTCTTTCAAA-ATTTGATATTCCCTGA
48527 GTAAC
130 GTAAC
* * * * *
48532 AATGGAACAAGTCTGCCATGATTCAAT-TATCCCTGAGGAACAGTGGAATGAATCAACATCCATA
1 AGTGAAACAAGTCTGCCTTGATTCAATCT-TCCCTGAGGAACAATGGAATGAATCAACATCCCTA
* * * * *
48596 GAT-TCGCTTTTCCCTC-AAGAGAAAGCGGAACAGATCACTCTCTTTCAAGATTTGATATTCCCT
65 GATCT-GATTTTCCCTCAAAAAG-AAGCGGAACAAATCCCTCTCTTTCAAAATTTGATATTCCCT
* *
48659 TATTAAC
128 GAGTAAC
* * * * *
48666 AGTAAAACAAGGCTGCCTTGATTCAATCTTCCCTGAAGAACAACGAAATGAATCAAC
1 AGTGAAACAAGTCTGCCTTGATTCAATCTTCCCTGAGGAACAATGGAATGAATCAAC
48723 GTTTCTCGAT
Statistics
Matches: 279, Mismatches: 39, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
133 9 0.03
134 267 0.96
135 3 0.01
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (134 bp):
AGTGAAACAAGTCTGCCTTGATTCAATCTTCCCTGAGGAACAATGGAATGAATCAACATCCCTAG
ATCTGATTTTCCCTCAAAAAGAAGCGGAACAAATCCCTCTCTTTCAAAATTTGATATTCCCTGAG
TAAC
Found at i:49370 original size:6 final size:7
Alignment explanation
Indices: 49355--49379 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
49345 TTTTTTAAGT
49355 AAAATAA
1 AAAATAA
49362 AAAATAA
1 AAAATAA
49369 AAAATAA
1 AAAATAA
49376 AAAA
1 AAAA
49380 AATTCCTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:53661 original size:20 final size:20
Alignment explanation
Indices: 53614--53665 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
53604 TATTTGTTCA
*
53614 AAATTATA-AATTTAAAAAT
1 AAATTATATAATTTTAAAAT
* *
53633 -ATTTTTATAATTTTAAAAT
1 AAATTATATAATTTTAAAAT
53652 AAATTATAT-ATTTT
1 AAATTATATAATTTT
53666 CATATATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 5 0.19
19 15 0.58
20 6 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATTATATAATTTTAAAAT
Done.