Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000530.1 Hibiscus syriacus cultivar Beakdansim tig00001019_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: 75391
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:11084 original size:29 final size:31
Alignment explanation
Indices: 11019--11102 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 31
11009 AGATTTAAAC
11019 CTAAATTTTT-A-ATTTATAATATTATTATG
1 CTAAATTTTTAATATTTATAATATTATTATG
* * *
11048 CTATATTTTTTATGTTTATAATATTATT-T-
1 CTAAATTTTTAATATTTATAATATTATTATG
* *
11077 TTAAATTTTTAATATTTATAAAATTA
1 CTAAATTTTTAATATTTATAATATTA
11103 AAGATGTAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 30 0.65
30 2 0.04
31 14 0.30
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (31 bp):
CTAAATTTTTAATATTTATAATATTATTATG
Found at i:18657 original size:30 final size:30
Alignment explanation
Indices: 18621--18685 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
18611 CTATTGCATA
18621 GTTTCTATTTTAGTCAGTTAATTATTATTT
1 GTTTCTATTTTAGTCAGTTAATTATTATTT
18651 GTTTCTATTTTAGTCAGTTAATTATTATTT
1 GTTTCTATTTTAGTCAGTTAATTATTATTT
18681 GTTTC
1 GTTTC
18686 AAAGGTATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.22, C:0.08, G:0.11, T:0.60
Consensus pattern (30 bp):
GTTTCTATTTTAGTCAGTTAATTATTATTT
Found at i:20049 original size:31 final size:32
Alignment explanation
Indices: 19978--20056 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 32
19968 AGTTTCAAAA
* *
19978 GTTACAAATCGGTCACTAATGTTATCAATCTT
1 GTTACAAATTGATCACTAATGTTATCAATCTT
* * **
20010 -TTATAAATTGATCATTAATGTTATTGAT-TT
1 GTTACAAATTGATCACTAATGTTATCAATCTT
20040 GTTACAAATTGATCACT
1 GTTACAAATTGATCACT
20057 CGAAGTTAAC
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
30 2 0.05
31 36 0.95
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (32 bp):
GTTACAAATTGATCACTAATGTTATCAATCTT
Found at i:25368 original size:134 final size:135
Alignment explanation
Indices: 25202--25537 Score: 448
Period size: 134 Copynumber: 2.5 Consensus size: 135
25192 GATTACACAA
*
25202 CTCATACGTGATGAAGAGTTTTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGCGATGA
1 CTCATACGTGATGAAGAGTTATGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGCGATGA
* *
25267 GGACGCCTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTTTGGTC-AGTAGATGA
66 GGACGACTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGAG-AGATGA
*
25331 CATGG-
130 CACGGT
* * *
25336 CTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCAATAACACGGTTCCTATGCGATGA
1 CTCATACGTGATGAAGAGTTATGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGCGATGA
* * * *
25401 GGACGACTGGTTATCTAGGGGTGACACGGCTCCTGCGTGATGATGAGGTCTGGTCGAGGGATGAC
66 GGACGACTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGAGAGATGAC
25466 ACGGT
131 ACGGT
* * * * * * *
25471 TTC-TACATGATGATGACGGTAT-ACCATCTTTAAGG-AGGGTGATAACACGGTTCCTACGTGAT
1 CTCATACGTGATGAAGA-GTTATGGCCATCTTT-AGGAAGGGCGATAACACGGTTCCTACGCGAT
25533 GAGGA
64 GAGGA
25538 TGGCATGCCA
Statistics
Matches: 178, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
134 168 0.94
135 10 0.06
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (135 bp):
CTCATACGTGATGAAGAGTTATGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGCGATGA
GGACGACTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGAGAGATGAC
ACGGT
Found at i:25627 original size:30 final size:30
Alignment explanation
Indices: 25591--25752 Score: 159
Period size: 30 Copynumber: 5.3 Consensus size: 30
25581 TCAAAGATGA
*
25591 TGTTTCAAAAGAAACAAACTAAAAG-TCTTT
1 TGTTTCAAAAGAAACAAACTCAAAGAT-TTT
*
25621 TGTTTCAAGAGAAACAAACTCAAAGATTTT
1 TGTTTCAAAAGAAACAAACTCAAAGATTTT
* **
25651 TGTTTCAAAAGAAACAGACTCAAAGATGATGG
1 TGTTTCAAAAGAAACAAACTCAAAGAT--TTT
*
25683 TGTTTCAAAAGAAAC-GACTCAAAGATTTTTTTT
1 TGTTTCAAAAGAAACAAACTCAAAGA----TTTT
* *
25716 TGTTTAAAAAGAAAC-GACTCAAAGATTTT
1 TGTTTCAAAAGAAACAAACTCAAAGATTTT
*
25745 TTTTTCAA
1 TGTTTCAA
25753 GAAAAACTAT
Statistics
Matches: 114, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.09
30 51 0.45
31 11 0.10
32 16 0.14
33 25 0.22
35 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (30 bp):
TGTTTCAAAAGAAACAAACTCAAAGATTTT
Found at i:25726 original size:33 final size:33
Alignment explanation
Indices: 25618--25749 Score: 141
Period size: 33 Copynumber: 4.1 Consensus size: 33
25608 ACTAAAAGTC
* *
25618 TTTTGTTTCAAGAGAAACAAACTCAAAGA----T
1 TTTTGTTTCAAAAGAAAC-GACTCAAAGATTTTT
**
25648 TTTTGTTTCAAAAGAAACAGACTCAAAGA--TGA
1 TTTTGTTTCAAAAGAAAC-GACTCAAAGATTTTT
**
25680 TGGTGTTTCAAAAGAAACGACTCAAAGATTTTT
1 TTTTGTTTCAAAAGAAACGACTCAAAGATTTTT
*
25713 TTTTGTTTAAAAAGAAACGACTCAAAGATTTTT
1 TTTTGTTTCAAAAGAAACGACTCAAAGATTTTT
25746 TTTT
1 TTTT
25750 CAAGAAAAAC
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
30 27 0.31
31 10 0.11
32 16 0.18
33 35 0.40
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (33 bp):
TTTTGTTTCAAAAGAAACGACTCAAAGATTTTT
Found at i:25758 original size:33 final size:33
Alignment explanation
Indices: 25689--25758 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
25679 ATGGTGTTTC
****
25689 AAAAGAAACGACTCAAAGATTTTTTTTTGTTTA
1 AAAAGAAACGACTCAAAGATTTTTTTTTCAAGA
25722 AAAAGAAACGACTCAAAGATTTTTTTTTCAAGA
1 AAAAGAAACGACTCAAAGATTTTTTTTTCAAGA
25755 AAAA
1 AAAA
25759 CTATCTCTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (33 bp):
AAAAGAAACGACTCAAAGATTTTTTTTTCAAGA
Found at i:25810 original size:67 final size:66
Alignment explanation
Indices: 25714--25871 Score: 180
Period size: 66 Copynumber: 2.4 Consensus size: 66
25704 AAGATTTTTT
* * * * * *
25714 TTTGTTTAAAAAGAAAC-GACTCAAAGATTTTTTTTTCAAGAAAAACTATCTCTA-GAGAGACAA
1 TTTGTTTCAAAGGAAACAGACTCAAAGA-TTTTTTCTCAAAAAAAACTATCTCAATG-GAGAAAA
*
25777 GAA
64 AAA
*
25780 TTTGTTTCAAAGGAAACAGACTCAATGATTTTTTCTCAAAAAAAACTATCTCAATGGAGAAAAAA
1 TTTGTTTCAAAGGAAACAGACTCAAAGATTTTTTCTCAAAAAAAACTATCTCAATGGAGAAAAAA
25845 A
66 A
*
25846 ATTGTTTC-AAGAGAAACA-ACTCAAAG
1 TTTGTTTCAAAG-GAAACAGACTCAAAG
25872 GATAATGATA
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
65 10 0.13
66 59 0.75
67 10 0.13
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.28
Consensus pattern (66 bp):
TTTGTTTCAAAGGAAACAGACTCAAAGATTTTTTCTCAAAAAAAACTATCTCAATGGAGAAAAAA
A
Found at i:26881 original size:17 final size:17
Alignment explanation
Indices: 26859--26901 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
26849 CTGATCTTTT
26859 AATCTTTGATAGCTGTA
1 AATCTTTGATAGCTGTA
26876 AATCTTTGATAGCTGTA
1 AATCTTTGATAGCTGTA
26893 AATCTTTGA
1 AATCTTTGA
26902 CAAATATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (17 bp):
AATCTTTGATAGCTGTA
Found at i:29589 original size:21 final size:21
Alignment explanation
Indices: 29560--29599 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29550 CAAATTATGG
29560 TCAAGGTGTATCGATGCACAT
1 TCAAGGTGTATCGATGCACAT
*
29581 TCAATGTGTATCGATGCAC
1 TCAAGGTGTATCGATGCAC
29600 TCTTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (21 bp):
TCAAGGTGTATCGATGCACAT
Found at i:29680 original size:64 final size:64
Alignment explanation
Indices: 29590--29726 Score: 154
Period size: 64 Copynumber: 2.2 Consensus size: 64
29580 TTCAATGTGT
* *
29590 ATCGATGCA-CTCTTTAAATAAGAAACATCAAATGCAATTAGTGCATCGATGCATAAGG-AGTGC
1 ATCGATGCACCCCTTTAAATAAGAAACATCAAAGGCAATTAGTGCATCGATGCAT-AGGTAGTGC
* * ** * * *
29653 ATCGATGCACCCCTTTAAA-ATGAAAACATCGAAGGTGATTGGTGTATCGATGCATGGGTAGTGC
1 ATCGATGCACCCCTTTAAATAAG-AAACATCAAAGGCAATTAGTGCATCGATGCATAGGTAGTGC
29717 ATCGATGCAC
1 ATCGATGCAC
29727 ATGTTAAAGA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
63 13 0.21
64 49 0.79
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Consensus pattern (64 bp):
ATCGATGCACCCCTTTAAATAAGAAACATCAAAGGCAATTAGTGCATCGATGCATAGGTAGTGC
Found at i:29759 original size:20 final size:22
Alignment explanation
Indices: 29714--29771 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
29704 GCATGGGTAG
29714 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
29738 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
29758 TGTATCGATGCACT
1 TGCATCGATGCACT
29772 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:34243 original size:32 final size:31
Alignment explanation
Indices: 34207--34283 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
34197 CGGGGCCGTG
*
34207 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
34239 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
34270 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
34284 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:34266 original size:63 final size:63
Alignment explanation
Indices: 34160--34283 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
34150 CCCTAAGGGA
* * ** *
34160 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
34223 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
34284 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:35226 original size:17 final size:17
Alignment explanation
Indices: 35172--35229 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
35162 AAACGGTCAC
35172 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
35189 GGTAAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
35206 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
35223 GGTCAAC
1 GGTCAAC
35230 CCGGTTCAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.17, C:0.22, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:35247 original size:19 final size:19
Alignment explanation
Indices: 35223--35294 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
35213 AGTCGGGTCG
*
35223 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
35242 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
35261 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
35280 GGTCAAACCGGTTCA
1 GGTCAAACCGGTTCA
35295 AAACTGGTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
18 1 0.02
19 49 0.98
ACGTcount: A:0.25, C:0.32, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:35253 original size:9 final size:9
Alignment explanation
Indices: 35223--35311 Score: 79
Period size: 9 Copynumber: 9.3 Consensus size: 9
35213 AGTCGGGTCG
*
35223 GGTCAACCC
1 GGTCAAACC
*
35232 GGTTCAGACC
1 GG-TCAAACC
35242 GGTCAAACC
1 GGTCAAACC
*
35251 GGTTCAGACC
1 GG-TCAAACC
35261 GGTCAAACC
1 GGTCAAACC
*
35270 GGTTCGAACC
1 GG-TCAAACC
35280 GGTCAAACC
1 GGTCAAACC
*
35289 GGTTCAAAACT
1 GG-TC-AAACC
*
35300 GGTTAAACC
1 GGTCAAACC
35309 GGT
1 GGT
35312 TTTCCAGCAG
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
9 33 0.51
10 26 0.40
11 6 0.09
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:41599 original size:32 final size:31
Alignment explanation
Indices: 41563--41639 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
41553 CGGGGCCGTG
*
41563 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
41595 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
41626 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
41640 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:41622 original size:63 final size:63
Alignment explanation
Indices: 41516--41639 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
41506 CCCTAAGGGA
* * ** *
41516 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
41579 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
41640 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:42568 original size:34 final size:35
Alignment explanation
Indices: 42519--42586 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
42509 GTCAACAGTC
*
42519 AACGGTCACGGTCGGGTAAACGGTCGGGTCGGGTA
1 AACGGTCACGGTCGGGTAAACAGTCGGGTCGGGTA
* *
42554 AACGGTC-GGGTCGGGTCAACAGTCGGGTCGGGT
1 AACGGTCACGGTCGGGTAAACAGTCGGGTCGGGT
42587 CAACCTGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 23 0.77
35 7 0.23
ACGTcount: A:0.18, C:0.21, G:0.44, T:0.18
Consensus pattern (35 bp):
AACGGTCACGGTCGGGTAAACAGTCGGGTCGGGTA
Found at i:42590 original size:17 final size:17
Alignment explanation
Indices: 42528--42586 Score: 100
Period size: 17 Copynumber: 3.5 Consensus size: 17
42518 CAACGGTCAC
42528 GGTCGGGTAAACGGTCG
1 GGTCGGGTAAACGGTCG
42545 GGTCGGGTAAACGGTCG
1 GGTCGGGTAAACGGTCG
* *
42562 GGTCGGGTCAACAGTCG
1 GGTCGGGTAAACGGTCG
42579 GGTCGGGT
1 GGTCGGGT
42587 CAACCTGGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.15, C:0.19, G:0.47, T:0.19
Consensus pattern (17 bp):
GGTCGGGTAAACGGTCG
Found at i:42608 original size:19 final size:19
Alignment explanation
Indices: 42584--42655 Score: 112
Period size: 19 Copynumber: 3.8 Consensus size: 19
42574 AGTCGGGTCG
42584 GGTC-AACCTGGTTCAGACC
1 GGTCAAACC-GGTTCAGACC
42603 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
42622 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
42641 GGTCAAACCGGTTCA
1 GGTCAAACCGGTTCA
42656 AAACTGGTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
18 1 0.02
19 45 0.90
20 4 0.08
ACGTcount: A:0.25, C:0.31, G:0.26, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:42614 original size:9 final size:9
Alignment explanation
Indices: 42600--42672 Score: 74
Period size: 9 Copynumber: 7.7 Consensus size: 9
42590 CCTGGTTCAG
42600 ACCGGTCAA
1 ACCGGTCAA
*
42609 ACCGGTTCAG
1 ACCGG-TCAA
42619 ACCGGTCAA
1 ACCGGTCAA
*
42628 ACCGGTTCGA
1 ACCGG-TCAA
42638 ACCGGTCAA
1 ACCGGTCAA
42647 ACCGGTTCAAA
1 ACCGG-TC-AA
* *
42658 ACTGGTTAA
1 ACCGGTCAA
42667 ACCGGT
1 ACCGGT
42673 TTTCCAGCAG
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
9 28 0.53
10 19 0.36
11 6 0.11
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.18
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:44138 original size:45 final size:44
Alignment explanation
Indices: 44041--44142 Score: 107
Period size: 45 Copynumber: 2.3 Consensus size: 44
44031 CACATTCAAT
* *
44041 GTGTATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAAGTA
1 GTGTATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAAGTA
* * ** * *
44085 GTGCATCGATGCACCCCTTTAAA-ATGAAAACATCGAAGGTGATTG
1 GTGTATCGATGCA-CCCTTTAAAGAAG-AAACATCGAAGGCAAGTA
44130 GTGTATCGATGCA
1 GTGTATCGATGCA
44143 TGGGTAGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
44 14 0.30
45 33 0.70
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (44 bp):
GTGTATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAAGTA
Found at i:44195 original size:20 final size:20
Alignment explanation
Indices: 44170--44207 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
44160 AACATGTTAA
44170 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
44190 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
44208 TCAAGGGGAA
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:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:48286 original size:15 final size:17
Alignment explanation
Indices: 48261--48297 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
48251 AACGTCTTTT
48261 CAAAATAA-TTTTAAGA
1 CAAAATAATTTTTAAGA
*
48277 -AAAATCATTTTTAAGA
1 CAAAATAATTTTTAAGA
48293 CAAAA
1 CAAAA
48298 AACTGGTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 6 0.33
16 8 0.44
17 4 0.22
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (17 bp):
CAAAATAATTTTTAAGA
Found at i:50500 original size:91 final size:91
Alignment explanation
Indices: 50355--50567 Score: 275
Period size: 91 Copynumber: 2.3 Consensus size: 91
50345 TCTAAGGGTG
* * * * * ** *
50355 ACACGGCTCCTACGTGATGATGAGATTTGGTCGGTAGATGACACGGCTCATACGTGATGAAGAGT
1 ACACGGTTCCTACGCGATGAGGAGATCTGGTCGGTAGATAACACAACTCATACGTGATAAAGAGT
* *
50420 TCTAGCCATCTTTAGGAAGGGCGATA
66 TCTAGCAATCTTTAAGAAGGGCGATA
* * *
50446 ACACTGTTCCTACGCGATGAGGAGGTCTGGTCGGTGGATAACACAACTCATACGTGATAAAGAGT
1 ACACGGTTCCTACGCGATGAGGAGATCTGGTCGGTAGATAACACAACTCATACGTGATAAAGAGT
*
50511 TCTGGCAATCTTTAAGAAGGGCGATA
66 TCTAGCAATCTTTAAGAAGGGCGATA
*
50537 ACACGGTTCCTATGCGATGAGGATGA-CTGGT
1 ACACGGTTCCTACGCGATGAGGA-GATCTGGT
50568 TATCTATGGG
Statistics
Matches: 104, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
91 103 0.99
92 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (91 bp):
ACACGGTTCCTACGCGATGAGGAGATCTGGTCGGTAGATAACACAACTCATACGTGATAAAGAGT
TCTAGCAATCTTTAAGAAGGGCGATA
Found at i:50864 original size:30 final size:29
Alignment explanation
Indices: 50815--50979 Score: 120
Period size: 30 Copynumber: 5.4 Consensus size: 29
50805 AAGGGTAATC
**
50815 AACTCAAAGATGATGTTTCAAAAGAAACA
1 AACTCAAAGATTTTGTTTCAAAAGAAACA
* **
50844 AACTCGAAGACTTTTGTTTCAAGAA-AATTA
1 AACTCAAAGA-TTTTGTTTCAA-AAGAAACA
50874 AACTCAAAGATTTTTGTTTCAAAAGAAACA
1 AACTCAAAGA-TTTTGTTTCAAAAGAAACA
* *
50904 GAGTCAAAGATGATTGTGTTTCAAAAGAAAC-
1 AACTCAAAGAT--TT-TGTTTCAAAAGAAACA
* *
50935 GATTCAAAGATTTTTTTTTGTTTCAAAAGAAAC-
1 AACTCAAAGA-----TTTTGTTTCAAAAGAAACA
*
50968 GACTCAAAGATT
1 AACTCAAAGATT
50980 CTTTTCACGA
Statistics
Matches: 112, Mismatches: 13, Indels: 23
0.76 0.09 0.16
Matches are distributed among these distances:
28 2 0.02
29 12 0.11
30 43 0.38
31 13 0.12
32 15 0.13
33 24 0.21
34 2 0.02
36 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (29 bp):
AACTCAAAGATTTTGTTTCAAAAGAAACA
Found at i:50962 original size:33 final size:33
Alignment explanation
Indices: 50884--50984 Score: 125
Period size: 33 Copynumber: 3.1 Consensus size: 33
50874 AACTCAAAGA
* *
50884 TTTTTGTTTCAAAAGAAACAGAGTCAAAGA--TG
1 TTTTTGTTTCAAAAGAAAC-GACTCAAAGATTTT
* * *
50916 ATTGTGTTTCAAAAGAAACGATTCAAAGATTTT
1 TTTTTGTTTCAAAAGAAACGACTCAAAGATTTT
*
50949 TTTTTGTTTCAAAAGAAACGACTCAAAGATTCT
1 TTTTTGTTTCAAAAGAAACGACTCAAAGATTTT
50982 TTT
1 TTT
50985 CACGAAAAAC
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
31 9 0.15
32 17 0.29
33 33 0.56
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (33 bp):
TTTTTGTTTCAAAAGAAACGACTCAAAGATTTT
Found at i:53843 original size:20 final size:21
Alignment explanation
Indices: 53818--53856 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
53808 AGATAAATGC
53818 AATGTTTCAAGGTC-GAAAAG
1 AATGTTTCAAGGTCTGAAAAG
53838 AATGTTTCAAGGTCTGAAA
1 AATGTTTCAAGGTCTGAAA
53857 GAAAGGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.28
Consensus pattern (21 bp):
AATGTTTCAAGGTCTGAAAAG
Found at i:54092 original size:24 final size:24
Alignment explanation
Indices: 54061--54116 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
54051 TCGTTCAATT
54061 ATTTAATCTTAGAATGTAGCATAA
1 ATTTAATCTTAGAATGTAGCATAA
54085 ATTTAATCTTAGAATGTAGCATAA
1 ATTTAATCTTAGAATGTAGCATAA
*
54109 ATTCAATC
1 ATTTAATC
54117 ATTAAAGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (24 bp):
ATTTAATCTTAGAATGTAGCATAA
Found at i:58690 original size:13 final size:12
Alignment explanation
Indices: 58672--58713 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 12
58662 ATGTAAACAA
58672 AATAAATAATAAT
1 AATAAAT-ATAAT
*
58685 AATAAATATAAGA
1 AATAAATATAA-T
58698 AATAAATATAAT
1 AATAAATATAAT
58710 AATA
1 AATA
58714 TTTTTGGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (12 bp):
AATAAATATAAT
Found at i:63112 original size:32 final size:33
Alignment explanation
Indices: 63076--63140 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
63066 TTTCGGTTGA
63076 ACGCAA-TCTAAAATGTT-AGTTTTTTAACATTT
1 ACGCAACTCTAAAATGTTGA-TTTTTTAACATTT
*
63108 ACGCAACTTTAAAATGTTGATTTTTTAACATTT
1 ACGCAACTCTAAAATGTTGATTTTTTAACATTT
63141 CTGATTGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 6 0.20
33 23 0.77
34 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (33 bp):
ACGCAACTCTAAAATGTTGATTTTTTAACATTT
Done.