Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001221.1 Hibiscus syriacus cultivar Beakdansim tig00002410_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: 59697
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Found at i:263 original size:2 final size:2
Alignment explanation
Indices: 256--321 Score: 74
Period size: 2 Copynumber: 36.0 Consensus size: 2
246 GGGTTTAGGA
256 AT AT AT AT AT A- AT AT AT AT AT A- AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
295 AT AT AT -T AT A- AT AGT AT -T AT AT A- AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
322 GTAACGACGA
Statistics
Matches: 56, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
1 7 0.12
2 47 0.84
3 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:271 original size:11 final size:11
Alignment explanation
Indices: 255--321 Score: 97
Period size: 11 Copynumber: 6.5 Consensus size: 11
245 CGGGTTTAGG
255 AATATATATAT
1 AATATATATAT
266 AATATATATAT
1 AATATATATAT
277 AATATATATAT
1 AATATATATAT
288 AATATATATAT
1 AATATATATAT
299 -AT-TATA-AT
1 AATATATATAT
*
307 AGTAT-TATAT
1 AATATATATAT
317 AATAT
1 AATAT
322 GTAACGACGA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
8 2 0.04
9 7 0.14
10 9 0.18
11 33 0.65
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (11 bp):
AATATATATAT
Found at i:274 original size:13 final size:13
Alignment explanation
Indices: 256--321 Score: 77
Period size: 13 Copynumber: 5.2 Consensus size: 13
246 GGGTTTAGGA
256 ATATATATAT-A-
1 ATATATATATAAT
267 ATATATATATAAT
1 ATATATATATAAT
280 ATATATATA-ATAT
1 ATATATATATA-AT
293 ATATATATTATAAT
1 ATATATA-TATAAT
307 AGTAT-TATATAAT
1 A-TATATATATAAT
320 AT
1 AT
322 GTAACGACGA
Statistics
Matches: 49, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
11 10 0.20
12 3 0.06
13 25 0.51
14 7 0.14
15 4 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
ATATATATATAAT
Found at i:1401 original size:31 final size:31
Alignment explanation
Indices: 1331--1439 Score: 105
Period size: 31 Copynumber: 3.5 Consensus size: 31
1321 TAAATTATCG
* *
1331 TTAAATATATCAA-TTATTATAAAATAATTA
1 TTAAATTTATCAACTTATTATAAAATAATAA
* ** *
1361 TCATTTTTATCAACTTATTATAAAATGATAA
1 TTAAATTTATCAACTTATTATAAAATAATAA
* *
1392 TTAAATTTATCAAATTATT-TAAAAATAATCA
1 TTAAATTTATCAACTTATTAT-AAAATAATAA
*
1423 TTAAAATTATCGAACTT
1 TTAAATTTATC-AACTT
1440 TATGATCATA
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
30 10 0.16
31 48 0.77
32 4 0.06
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (31 bp):
TTAAATTTATCAACTTATTATAAAATAATAA
Found at i:2967 original size:22 final size:22
Alignment explanation
Indices: 2941--2983 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2931 GTATGAACGG
*
2941 TGAACAATACCGTGAACAGTAA
1 TGAACAATACCATGAACAGTAA
*
2963 TGAACATTACCATGAACAGTA
1 TGAACAATACCATGAACAGTA
2984 CCCGAATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (22 bp):
TGAACAATACCATGAACAGTAA
Found at i:3674 original size:13 final size:14
Alignment explanation
Indices: 3650--3679 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3640 TAATTTATTC
3650 CATATAACATATCA
1 CATATAACATATCA
3664 CATAT-ACATATCA
1 CATATAACATATCA
3677 CAT
1 CAT
3680 TCAATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (14 bp):
CATATAACATATCA
Found at i:4669 original size:2 final size:2
Alignment explanation
Indices: 4662--4703 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4652 TTATGTAAAC
4662 AT AT AT AT AT AT 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 AT AT AT AT AT AT
4704 CACACAACAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5066 original size:20 final size:20
Alignment explanation
Indices: 5041--5078 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5031 TTTTCTTTAG
5041 GGGGGAATC-GATACCCCCCA
1 GGGGGAATCTG-TACCCCCCA
5061 GGGGGAATCTGTACCCCC
1 GGGGGAATCTGTACCCCC
5079 TGCACAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.21, C:0.34, G:0.32, T:0.13
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCCA
Found at i:5129 original size:21 final size:21
Alignment explanation
Indices: 5099--5140 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5089 GGAATTTTTC
5099 GTTCAAGCCCAGAAAA-TCACT
1 GTTCAAGCCCA-AAAATTCACT
*
5120 GTTCATGCCCAAAAATTCACT
1 GTTCAAGCCCAAAAATTCACT
5141 ATATCACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.24
Consensus pattern (21 bp):
GTTCAAGCCCAAAAATTCACT
Found at i:7551 original size:16 final size:18
Alignment explanation
Indices: 7516--7552 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
7506 TTTACATTCC
7516 TTTCATATCATTTATACT
1 TTTCATATCATTTATACT
*
7534 TTTCAT-TC-TTTATCCT
1 TTTCATATCATTTATACT
7550 TTT
1 TTT
7553 AACTTTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 2 0.11
18 6 0.33
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTCATATCATTTATACT
Found at i:11491 original size:20 final size:20
Alignment explanation
Indices: 11466--11504 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
11456 TTTTTTCTTT
11466 AGGGGGAATC-GATACCCCCC
1 AGGGGGAATCTG-TACCCCCC
11486 AGGGGGAATCTGTACCCCC
1 AGGGGGAATCTGTACCCCC
11505 TGCACAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.13
Consensus pattern (20 bp):
AGGGGGAATCTGTACCCCCC
Found at i:11561 original size:20 final size:22
Alignment explanation
Indices: 11525--11566 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
11515 GGAATTTTTC
11525 GTTCAAGCCCAGAAAA-TCACT
1 GTTCAAGCCCAGAAAATTCACT
*
11546 GTTCATGCCC-GAAAATTCACT
1 GTTCAAGCCCAGAAAATTCACT
11567 ATATCAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (22 bp):
GTTCAAGCCCAGAAAATTCACT
Found at i:12511 original size:2 final size:2
Alignment explanation
Indices: 12504--12546 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
12494 AAGTATATGC
12504 AT AT AT AT AT AT 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 AT AT AT AT AT AT
12546 A
1 A
12547 ATAATTTAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15208 original size:2 final size:2
Alignment explanation
Indices: 15201--15273 Score: 85
Period size: 2 Copynumber: 35.5 Consensus size: 2
15191 AAATTTGATG
15201 AT AT AT AT AT AT 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 AT AT AT AT AT AT
* * *
15243 TT AT CAA AT GAT AT AT ACT AT A- AA AT AT AT A
1 AT AT -AT AT -AT AT AT A-T AT AT AT AT AT AT A
15274 GTGTTGATGT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
1 1 0.02
2 56 0.90
3 5 0.08
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:28507 original size:18 final size:19
Alignment explanation
Indices: 28465--28504 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
28455 TTTGGTTCAC
*
28465 GGAATGGAAGATTATCAGTG
1 GGAATGGAAGATTACCAG-G
*
28485 GGAATGTAAGATTACCAGG
1 GGAATGGAAGATTACCAGG
28504 G
1 G
28505 AATATGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.23
Consensus pattern (19 bp):
GGAATGGAAGATTACCAGG
Found at i:30704 original size:20 final size:19
Alignment explanation
Indices: 30658--30705 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
30648 ATGACCAACA
* * *
30658 AATTCGCAACGCGATCTCG
1 AATTCGCAAAGCGAACTCC
30677 AATTCGCAAAGCGAACTCC
1 AATTCGCAAAGCGAACTCC
30696 AATTTCGCAA
1 AA-TTCGCAA
30706 CACAGTTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (19 bp):
AATTCGCAAAGCGAACTCC
Found at i:30946 original size:22 final size:22
Alignment explanation
Indices: 30920--30967 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
30910 CTACGGTGAC
30920 ATCCGTCCCCATCTCTGACGAA
1 ATCCGTCCCCATCTCTGACGAA
*
30942 ATCCGTCCCCATCTCTGGCGAA
1 ATCCGTCCCCATCTCTGACGAA
30964 ATCC
1 ATCC
30968 ATCTATCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.42, G:0.15, T:0.23
Consensus pattern (22 bp):
ATCCGTCCCCATCTCTGACGAA
Found at i:31375 original size:20 final size:19
Alignment explanation
Indices: 31340--31393 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
31330 AATTCGCAAC
31340 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
31359 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
*
31379 GCGAATTTAAGTTTC
1 GCG-ATTTTAGTTTC
31394 AGAAACTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.27
20 18 0.60
21 4 0.13
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:33207 original size:4 final size:4
Alignment explanation
Indices: 33198--33243 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
33188 TTTTTCGGCA
* * * *
33198 TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
33244 TTAGCGGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:33423 original size:21 final size:21
Alignment explanation
Indices: 33393--33505 Score: 97
Period size: 21 Copynumber: 5.4 Consensus size: 21
33383 CCTGTCATCA
* *
33393 TTCAAGAGGCATTTTCTATCG
1 TTCAAGAGGCACTTCCTATCG
* *
33414 TTCAATAGGCCCTTCCTATCG
1 TTCAAGAGGCACTTCCTATCG
* * *
33435 TTCAAGAGGCCCCTCCTACCG
1 TTCAAGAGGCACTTCCTATCG
* *
33456 TTCAAGAGGC-CTCTCCCACCG
1 TTCAAGAGGCACT-TCCTATCG
*
33477 TTCAAGAGGCCCTGT-C-ATCG
1 TTCAAGAGGCACT-TCCTATCG
33497 TTCAAGAGG
1 TTCAAGAGG
33506 TCCCTCCCAC
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
20 13 0.16
21 63 0.80
22 3 0.04
ACGTcount: A:0.21, C:0.32, G:0.20, T:0.27
Consensus pattern (21 bp):
TTCAAGAGGCACTTCCTATCG
Found at i:33513 original size:41 final size:41
Alignment explanation
Indices: 33408--33525 Score: 141
Period size: 41 Copynumber: 2.8 Consensus size: 41
33398 GAGGCATTTT
* * *
33408 CTATCGTTCAATAGGCCCTTCCTATCGTTCAAGAGGCCCCTC
1 CTATCGTTCAAGAGGCCC-TCCCACCGTTCAAGAGGCCCCTC
*
33450 CTACCGTTCAAGAGGCCTCTCCCACCGTTCAAGAGG-CCCT-
1 CTATCGTTCAAGAGGCC-CTCCCACCGTTCAAGAGGCCCCTC
*
33490 GTCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAG
1 CT-ATCGTTCAAGAGG-CCCTCCCACCGTTCAAGAG
33526 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
40 1 0.01
41 33 0.49
42 32 0.48
43 1 0.01
ACGTcount: A:0.20, C:0.36, G:0.19, T:0.24
Consensus pattern (41 bp):
CTATCGTTCAAGAGGCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:33519 original size:21 final size:20
Alignment explanation
Indices: 33412--33525 Score: 129
Period size: 21 Copynumber: 5.5 Consensus size: 20
33402 CATTTTCTAT
* * *
33412 CGTTCAATAGGCCCTTCCTAT
1 CGTTCAAGAGGCCC-TCCCAC
*
33433 CGTTCAAGAGGCCCCTCCTAC
1 CGTTCAAGAGG-CCCTCCCAC
33454 CGTTCAAGAGGCCTCTCCCAC
1 CGTTCAAGAGGCC-CTCCCAC
** *
33475 CGTTCAAGAGGCCCTGTCAT
1 CGTTCAAGAGGCCCTCCCAC
33495 CGTTCAAGAGGTCCCTCCCAC
1 CGTTCAAGAGG-CCCTCCCAC
33516 CGTTCAAGAG
1 CGTTCAAGAG
33526 CCCGATTCAC
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
20 17 0.21
21 61 0.75
22 3 0.04
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.23
Consensus pattern (20 bp):
CGTTCAAGAGGCCCTCCCAC
Found at i:38458 original size:14 final size:15
Alignment explanation
Indices: 38422--38459 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
38412 GAAATCATTG
38422 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
38437 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
38452 AAAAATTA
1 AAAAATTA
38460 GAGATAGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:38646 original size:20 final size:20
Alignment explanation
Indices: 38618--38672 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
38608 TAAAATTCGT
*
38618 GTTGCGAATTCGAAAATCGA
1 GTTGTGAATTCGAAAATCGA
*
38638 GTTGTGAATTC-AGAAATTGA
1 GTTGTGAATTCGA-AAATCGA
*
38658 GTTGTGAATTTGAAA
1 GTTGTGAATTCGAAA
38673 TTCAGTATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (20 bp):
GTTGTGAATTCGAAAATCGA
Found at i:43930 original size:19 final size:19
Alignment explanation
Indices: 43906--43975 Score: 131
Period size: 19 Copynumber: 3.7 Consensus size: 19
43896 ACCAACTAAA
*
43906 TCGCAAAGCGATCGATAAT
1 TCGCAACGCGATCGATAAT
43925 TCGCAACGCGATCGATAAT
1 TCGCAACGCGATCGATAAT
43944 TCGCAACGCGATCGATAAT
1 TCGCAACGCGATCGATAAT
43963 TCGCAACGCGATC
1 TCGCAACGCGATC
43976 TCCGGTATCG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (19 bp):
TCGCAACGCGATCGATAAT
Found at i:44073 original size:21 final size:22
Alignment explanation
Indices: 44043--44225 Score: 163
Period size: 21 Copynumber: 8.6 Consensus size: 22
44033 GATTTACATA
* *
44043 TTCGCATTGCGA-TAGTCCAAG
1 TTCGCGTTGCGATTATTCCAAG
44064 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAG
* *
44087 TT--CGTTGCGA-TAGTCGAAG
1 TTCGCGTTGCGATTATTCCAAG
*
44106 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA-TTATTCCAAG
44129 TT--CGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAG
*
44150 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA-TTATTCCAAG
* *
44173 TT--CGTTGCGA-TAGTCGAAG
1 TTCGCGTTGCGATTATTCCAAG
*
44192 TTCGTGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAG
44215 TT--CGTTGCGAT
1 TTCGCGTTGCGAT
44226 AGTCCAAAAT
Statistics
Matches: 134, Mismatches: 16, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
19 17 0.13
20 1 0.01
21 69 0.51
23 47 0.35
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (22 bp):
TTCGCGTTGCGATTATTCCAAG
Found at i:44100 original size:42 final size:42
Alignment explanation
Indices: 44049--44232 Score: 296
Period size: 42 Copynumber: 4.3 Consensus size: 42
44039 CATATTCGCA
*
44049 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
44091 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
44133 TTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * *
44177 TTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
44219 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
44233 AATCGCAACG
Statistics
Matches: 131, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
42 91 0.69
44 40 0.31
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:44148 original size:86 final size:86
Alignment explanation
Indices: 44058--44225 Score: 309
Period size: 86 Copynumber: 2.0 Consensus size: 86
44048 ATTGCGATAG
*
44058 TCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
44123 TCCAAATTCGTTGCGATTTAT
66 TCCAAATTCGTTGCGATTTAT
*
44144 TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGTGTTGCGATTTAT
1 TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
44209 TCCAAGTTCGTTGCGAT
66 TCCAAATTCGTTGCGAT
44226 AGTCCAAAAT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (86 bp):
TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
TCCAAATTCGTTGCGATTTAT
Found at i:44868 original size:6 final size:6
Alignment explanation
Indices: 44847--44883 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
44837 TCTCGTCTCG
44847 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
44884 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:45005 original size:21 final size:21
Alignment explanation
Indices: 44981--45178 Score: 187
Period size: 21 Copynumber: 9.5 Consensus size: 21
44971 TTTTGGACTA
*
44981 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
45002 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
45023 TCGCATTACGATAGTCG-ACT
1 TCGCATTGCGATAGTCGAAGT
*
45043 ATCGCATTGCGAT-TTAC-ATA-T
1 -TCGCATTGCGATAGT-CGA-AGT
* *
45064 TCGCATTGCGATAGCCG-ACT
1 TCGCATTGCGATAGTCGAAGT
*
45084 ATCGCATTGCGAT-TTAC-ATA-T
1 -TCGCATTGCGATAGT-CGA-AGT
*
45105 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
*
45126 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
45147 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
45168 TCGCGTTGCGA
1 TCGCATTGCGA
45179 ATCTGGAAAT
Statistics
Matches: 149, Mismatches: 14, Indels: 28
0.78 0.07 0.15
Matches are distributed among these distances:
19 1 0.01
20 31 0.21
21 115 0.77
22 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:45069 original size:20 final size:20
Alignment explanation
Indices: 45044--45116 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
45034 TAGTCGACTA
45044 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
***
45064 TCGCATTGCGATAGCCGACTA-
1 TCGCATTGCGATTTAC-A-TAT
45085 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
45105 TCGCATTGCGAT
1 TCGCATTGCGAT
45117 AGTCCAAGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.05
20 26 0.59
21 14 0.32
22 2 0.05
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:45083 original size:41 final size:41
Alignment explanation
Indices: 45022--45160 Score: 183
Period size: 41 Copynumber: 3.4 Consensus size: 41
45012 ATAGTCCAAG
* *
45022 TTCGCATTACGATAGTCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGCCGACTATCGCATTGCGATTTACATA
45063 TTCGCATTGCGATAGCCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGCCGACTATCGCATTGCGATTTACATA
* * * *
45104 TTCGCATTGCGATAGTCCAAGT-TCGCATTGCGATAGTCCA-A
1 TTCGCATTGCGATAG-CCGACTATCGCATTGCGAT-TTACATA
45145 GTTCGCATTGCGATAG
1 -TTCGCATTGCGATAG
45161 TCGAAGTTCG
Statistics
Matches: 89, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
41 67 0.75
42 22 0.25
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (41 bp):
TTCGCATTGCGATAGCCGACTATCGCATTGCGATTTACATA
Found at i:45393 original size:21 final size:20
Alignment explanation
Indices: 45368--45425 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
45358 TTATTTTTAA
*
45368 AAAAATAAATAAATATGCAAT
1 AAAAATAAATAAAAATG-AAT
*
45389 AAAAATGAATTAAAAATGAAT
1 AAAAAT-AAATAAAAATGAAT
* *
45410 AAAATTCAATAAAAAT
1 AAAAATAAATAAAAAT
45426 ATAATGTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 8 0.26
21 14 0.45
22 9 0.29
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.24
Consensus pattern (20 bp):
AAAAATAAATAAAAATGAAT
Found at i:45412 original size:10 final size:10
Alignment explanation
Indices: 45368--45425 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
45358 TTATTTTTAA
*
45368 AAAAATAAAT
1 AAAAATGAAT
*
45378 AAATATGCAAT
1 AAAAATG-AAT
45389 AAAAATGAATT
1 AAAAATGAA-T
45400 AAAAATGAAT
1 AAAAATGAAT
* *
45410 AAAATTCAAT
1 AAAAATGAAT
45420 AAAAAT
1 AAAAAT
45426 ATAATGTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 21 0.52
11 19 0.47
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.24
Consensus pattern (10 bp):
AAAAATGAAT
Found at i:46610 original size:7 final size:7
Alignment explanation
Indices: 46598--46631 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
46588 CATTTTTAAT
46598 AAAATTA
1 AAAATTA
46605 AAAATTA
1 AAAATTA
*
46612 AAAATTT
1 AAAATTA
46619 AAAATTA
1 AAAATTA
46626 AAAATT
1 AAAATT
46632 TATATTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AAAATTA
Found at i:46751 original size:11 final size:11
Alignment explanation
Indices: 46712--46749 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
46702 CTTTACATTA
46712 TATTTTTATTG
1 TATTTTTATTG
*
46723 -AATTTTATTG
1 TATTTTTATTG
46733 TATTTTTATT-
1 TATTTTTATTG
46743 TATTTTT
1 TATTTTT
46750 TAAATAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (11 bp):
TATTTTTATTG
Found at i:48233 original size:15 final size:15
Alignment explanation
Indices: 48209--48242 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
48199 CTGTAGGACC
*
48209 ACTACATCCCGAAGG
1 ACTACATCCCAAAGG
*
48224 ACTACGTCCCAAAGG
1 ACTACATCCCAAAGG
48239 ACTA
1 ACTA
48243 TTATACCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (15 bp):
ACTACATCCCAAAGG
Found at i:48369 original size:29 final size:29
Alignment explanation
Indices: 48327--48407 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
48317 TTTTATATGT
48327 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
48355 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
48384 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
48408 ATATCACATA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 7 0.14
29 39 0.76
30 5 0.10
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:55134 original size:22 final size:22
Alignment explanation
Indices: 55108--55163 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
55098 TTCAGTATTC
*
55108 GTCCCGAATGACTGTCATATAT
1 GTCCCGAAGGACTGTCATATAT
*
55130 GTCCCGTAGGACTGTCATATAT
1 GTCCCGAAGGACTGTCATATAT
*
55152 GTCCCGTAGGAC
1 GTCCCGAAGGAC
55164 CACTACGTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (22 bp):
GTCCCGAAGGACTGTCATATAT
Found at i:55767 original size:64 final size:63
Alignment explanation
Indices: 55698--55854 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 63
55688 TAATGAAGGT
* **
55698 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAA-AA
55761 G
63 G
* * * *
55762 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
*
55825 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
55855 ACGCCTTCAA
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
63 3 0.04
64 66 0.85
65 9 0.12
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:57803 original size:18 final size:18
Alignment explanation
Indices: 57782--57820 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
57772 ACATTTGATA
*
57782 CTCTGGACGAGGTTGTTC
1 CTCTGGACGAGCTTGTTC
* *
57800 CTCTGGAGGTGCTTGTTC
1 CTCTGGACGAGCTTGTTC
57818 CTC
1 CTC
57821 GTACTGATCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.26, G:0.31, T:0.36
Consensus pattern (18 bp):
CTCTGGACGAGCTTGTTC
Done.