Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001507.1 Hibiscus syriacus cultivar Beakdansim tig00002951_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: 70571
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:964 original size:20 final size:20
Alignment explanation
Indices: 939--978 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
929 AGCAACAGAA
*
939 TAAAAATGATTTTATCTAAT
1 TAAAAATGATCTTATCTAAT
959 TAAAAATGATCTTATCTAAT
1 TAAAAATGATCTTATCTAAT
979 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (20 bp):
TAAAAATGATCTTATCTAAT
Found at i:1021 original size:20 final size:21
Alignment explanation
Indices: 992--1031 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
982 TAATAGAATA
*
992 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
1013 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
1032 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:1070 original size:20 final size:20
Alignment explanation
Indices: 1045--1083 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1035 TAATAGAATA
*
1045 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
1065 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
1084 ATTTAATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:1074 original size:52 final size:52
Alignment explanation
Indices: 935--1084 Score: 257
Period size: 52 Copynumber: 2.9 Consensus size: 52
925 AATTAGCAAC
* *
935 AGAATAAAAA-TGATTTTATCTAATTAAAAATGATCTTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
986 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
*
1039 AGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
1085 TTTAATTAGA
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 5 0.05
52 45 0.48
53 44 0.47
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:5650 original size:20 final size:20
Alignment explanation
Indices: 5625--5664 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5615 AGCAACAGAA
**
5625 TAAAAATGATTTTATCTAAT
1 TAAAAATGATCATATCTAAT
5645 TAAAAATGATCATATCTAAT
1 TAAAAATGATCATATCTAAT
5665 AACTAATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (20 bp):
TAAAAATGATCATATCTAAT
Found at i:5707 original size:20 final size:21
Alignment explanation
Indices: 5678--5717 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
5668 TAATAGAATA
*
5678 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
5699 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
5718 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:5756 original size:20 final size:20
Alignment explanation
Indices: 5731--5769 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5721 TAATAGAATA
*
5731 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
5751 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
5770 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:5760 original size:52 final size:52
Alignment explanation
Indices: 5621--5770 Score: 257
Period size: 52 Copynumber: 2.9 Consensus size: 52
5611 AATTAGCAAC
* *
5621 AGAATAAAAA-TGATTTTATCTAATTAAAAATGATCATATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
5672 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
*
5725 AGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
5771 TTTAATTTAG
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 5 0.05
52 45 0.48
53 44 0.47
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:9109 original size:26 final size:26
Alignment explanation
Indices: 9079--9167 Score: 178
Period size: 26 Copynumber: 3.4 Consensus size: 26
9069 AGGTTAGGTA
9079 TTGCAGTTGAACTGTTGAACCCTGGT
1 TTGCAGTTGAACTGTTGAACCCTGGT
9105 TTGCAGTTGAACTGTTGAACCCTGGT
1 TTGCAGTTGAACTGTTGAACCCTGGT
9131 TTGCAGTTGAACTGTTGAACCCTGGT
1 TTGCAGTTGAACTGTTGAACCCTGGT
9157 TTGCAGTTGAA
1 TTGCAGTTGAA
9168 ATGGTCCCGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 63 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (26 bp):
TTGCAGTTGAACTGTTGAACCCTGGT
Found at i:17197 original size:122 final size:123
Alignment explanation
Indices: 16989--17285 Score: 354
Period size: 123 Copynumber: 2.4 Consensus size: 123
16979 ATTTAGTATG
* * * * * * *
16989 TAAACTATCAATTTTGATCCATTTTAGTACAC-AAACTTTC-ATTT-ATTCAAAATCATACCTAA
1 TAAACTATCAGTTTTGGTACTTTTTAGTAC-CTAAACCTTCAATTTGTTTCAAAATCATACATAA
* * *
17051 TGTTTAGTTTTTGTTTCATTTTAGTGCTCC-CCATTAAAAACTT-AACACGTTTAGTACC
65 TGTTTAGTTTTCGTTTCATCTTAGTGC-CCGCCATTAAAAACTTAAACACGTTTAATACC
* * * *
17109 TCAACTATCAGTTTTGG-CCTATTTTAGTACCTAAGCCTTCAATTTTTTTCAAAATCATACATAA
1 TAAACTATCAGTTTTGGTACT-TTTTAGTACCTAAACCTTCAATTTGTTTCAAAATCATACATAA
* * *
17173 TGTTTAGTTTTCGTTTCATCTTAGTGCCCGTCGTTAAAAACTTAAACGCGTTTAATACC
65 TGTTTAGTTTTCGTTTCATCTTAGTGCCCGCCATTAAAAACTTAAACACGTTTAATACC
* *
17232 TAAACTATGAGTTTTGGTACTTTTTAGTACCTAAACTTTCAATTTGTTTCAAAA
1 TAAACTATCAGTTTTGGTACTTTTTAGTACCTAAACCTTCAATTTGTTTCAAAA
17286 CTTAATGTTG
Statistics
Matches: 150, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
119 3 0.02
120 29 0.19
121 6 0.04
122 52 0.35
123 58 0.39
124 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.42
Consensus pattern (123 bp):
TAAACTATCAGTTTTGGTACTTTTTAGTACCTAAACCTTCAATTTGTTTCAAAATCATACATAAT
GTTTAGTTTTCGTTTCATCTTAGTGCCCGCCATTAAAAACTTAAACACGTTTAATACC
Found at i:17284 original size:123 final size:121
Alignment explanation
Indices: 16989--17285 Score: 361
Period size: 122 Copynumber: 2.4 Consensus size: 121
16979 ATTTAGTATG
* * * *
16989 TAAACTATCAATTTT-GATCCATTTTAGTACAC-AAACTTTC-ATTTATTCAAAATCATACCTAA
1 TAAACTATCAGTTTTGGA-CTATTTTAGTAC-CTAAACTTTCAATTTTTTCAAAATCATACATAA
* * *
17051 TGTTTAGTTTTTGTTTCATTTTAGTGCTCCCCATTAAAAACTTAACACGTTTAGTACC
64 TGTTTAGTTTTCGTTTCATCTTAGTGCTCCCCATTAAAAACTTAACACGTTTAATACC
* * * *
17109 TCAACTATCAGTTTTGGCCTATTTTAGTACCTAAGCCTTCAATTTTTTTCAAAATCATACATAAT
1 TAAACTATCAGTTTTGGACTATTTTAGTACCTAAACTTTCAA-TTTTTTCAAAATCATACATAAT
* * *
17174 GTTTAGTTTTCGTTTCATCTTAGTGC-CCGTCGTTAAAAACTTAAACGCGTTTAATACC
65 GTTTAGTTTTCGTTTCATCTTAGTGCTCC-CCATTAAAAACTT-AACACGTTTAATACC
*
17232 TAAACTATGAGTTTTGGTACT-TTTTAGTACCTAAACTTTCAATTTGTTTCAAAA
1 TAAACTATCAGTTTTGG-ACTATTTTAGTACCTAAACTTTCAATTT-TTTCAAAA
17286 CTTAATGTTG
Statistics
Matches: 150, Mismatches: 19, Indels: 13
0.82 0.10 0.07
Matches are distributed among these distances:
119 1 0.01
120 30 0.20
121 4 0.03
122 58 0.39
123 55 0.37
124 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.42
Consensus pattern (121 bp):
TAAACTATCAGTTTTGGACTATTTTAGTACCTAAACTTTCAATTTTTTCAAAATCATACATAATG
TTTAGTTTTCGTTTCATCTTAGTGCTCCCCATTAAAAACTTAACACGTTTAATACC
Found at i:17640 original size:20 final size:21
Alignment explanation
Indices: 17615--17654 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
17605 CTTTACATAG
*
17615 TAGTATTAATACCA-CAGGCA
1 TAGTATCAATACCATCAGGCA
*
17635 TAGTATCGATACCATCAGGC
1 TAGTATCAATACCATCAGGC
17655 CCCAACGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (21 bp):
TAGTATCAATACCATCAGGCA
Found at i:20934 original size:117 final size:116
Alignment explanation
Indices: 20628--20934 Score: 315
Period size: 117 Copynumber: 2.7 Consensus size: 116
20618 GCCACAATCG
* *
20628 AACCCT-AAACCCTAATCATTCAGACCATGCATG-AAGTA-AGAAAA-TT-GGGTTTAGGGTTTA
1 AACCCTAAAACCCTAATCATTCAAACCAAG-ATGAAAGTAGAGAAAATTTAGGGTTTAGGGTTTA
* *
20688 TTGTCTTTCACTCCATACTAACTCCATTCCTAGATGTATACAATAAGACAGGT
65 TTGTC-TTCACTCCATACTAACTCCATTCCCAGAGGTATACAATAAGACAGGT
* * ** * * *
20741 AACCCTAAAACCCTAATTACTCAAATTAATAATGAAA-TTGATAAAATTTAGGGTTTAGGGTTTA
1 AACCCTAAAACCCTAATCATTCAAACCAA-GATGAAAGTAGAGAAAATTTAGGGTTTAGGGTTTA
* * * * * * *
20805 ATATCCTTCACTCCATCCTAACTCCATTCCCAGGGGTGT-CATTGAGACAGGT
65 TTGT-CTTCACTCCATACTAACTCCATTCCCAGAGGTATACAATAAGACAGGT
*
20857 AACCCCTAAAACCCTAATCATTCAAACCAAGAGTGAAAGTAGA-AAAATTTAGGGTTTGGGGTTT
1 AA-CCCTAAAACCCTAATCATTCAAACCAAGA-TGAAAGTAGAGAAAATTTAGGGTTTAGGGTTT
*
20921 CTTGTCTTCCACTC
64 ATTGTCTT-CACTC
20935 AAGAAGTAGT
Statistics
Matches: 155, Mismatches: 28, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
113 6 0.04
114 20 0.13
115 7 0.05
116 19 0.12
117 99 0.64
118 4 0.03
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (116 bp):
AACCCTAAAACCCTAATCATTCAAACCAAGATGAAAGTAGAGAAAATTTAGGGTTTAGGGTTTAT
TGTCTTCACTCCATACTAACTCCATTCCCAGAGGTATACAATAAGACAGGT
Found at i:22157 original size:17 final size:17
Alignment explanation
Indices: 22123--22157 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22113 TTTTTTTCAT
* *
22123 ATATTTAAAAATTAAAA
1 ATATATAAAAATAAAAA
22140 ATATATAAAAATAAAAA
1 ATATATAAAAATAAAAA
22157 A
1 A
22158 AGAATAAGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATATATAAAAATAAAAA
Found at i:23988 original size:30 final size:29
Alignment explanation
Indices: 23930--23988 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
23920 ATTATAGAAT
* *
23930 GACTTGATTAAGACTTGAACGATGTTGAA
1 GACTTGATTAAGAATTGAACGATCTTGAA
23959 GACTTGATTATAGAATTGAA-GAATCTTGAA
1 GACTTGATTA-AGAATTGAACG-ATCTTGAA
23989 CGGCCGATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.32
Consensus pattern (29 bp):
GACTTGATTAAGAATTGAACGATCTTGAA
Found at i:24066 original size:77 final size:76
Alignment explanation
Indices: 23935--24089 Score: 265
Period size: 77 Copynumber: 2.0 Consensus size: 76
23925 AGAATGACTT
*
23935 GATTAAGACTTGAACGATGTTGAAGACTTGATTATAGAATTGAAGAATCTTGAACGGCCGATTGG
1 GATTAAGACTTGAACGATGTTGAAGACTTGATTATAGAATTGAAGAATCTTGAACGACCGATTGG
24000 TGAATAATGGA
66 TGAATAATGGA
* * *
24011 GATTTAGACTTGAACGATGTTGAAGACTTTGATTGTAGAATTGACGAATCTTGAACGACCGATTG
1 GATTAAGACTTGAACGATGTTGAAGAC-TTGATTATAGAATTGAAGAATCTTGAACGACCGATTG
24076 GTGAATAATGGA
65 GTGAATAATGGA
24088 GA
1 GA
24090 GAGTCGTTCA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
76 26 0.35
77 48 0.65
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (76 bp):
GATTAAGACTTGAACGATGTTGAAGACTTGATTATAGAATTGAAGAATCTTGAACGACCGATTGG
TGAATAATGGA
Found at i:36838 original size:163 final size:160
Alignment explanation
Indices: 36535--36982 Score: 533
Period size: 163 Copynumber: 2.8 Consensus size: 160
36525 TCCACCCCTG
* * * *
36535 TTTGCTATTGAACGCTCATACTCCTTACATTCATGGTGCTCAAGGAATAACAACAATTCCTTTAT
1 TTTGCCATTGAACGCTCATACTCCTAACATTCATGATGCTCAAGGAATAAC-ACAATTCCTTTAC
* * * * * *
36600 CAC-GGATGTTGTTTGGTTTGTGCTATTGATATGATTTTTTTAGATTAATCTGGGATAAGTACAA
65 CACTGG-TGTCGCTTGGTTCGTGCTAATGGTTTGATTTTTTTAGATTAATCTGGGATAAGTACAA
* *
36664 GGTAATATTTGTTCAATGATAACTCTCAATCA
129 GGTAATATTTGTTCAATGACAACTCTCAATAA
* * ** * * *
36696 TTTGTCATTGAACGCTAATACTCCTGGCCTTCATGCTGCTCAAGAAATAACGACAATTCCTTTAC
1 TTTGCCATTGAACGCTCATACTCCTAACATTCATGATGCTCAAGGAATAAC-ACAATTCCTTTAC
* *
36761 CACTGGGGTCGCTTGGTTCGTGCTAATGGTTTGATTCTTTTTTAGATTAATCTGTGATAAGTACA
65 CACTGGTGTCGCTTGGTTCGTGCTAATGGTTTGA-T-TTTTTTAGATTAATCTGGGATAAGTACA
*
36826 AGGTAGTATTTGTTCAATGACAACTCTCAATAA
128 AGGTAATATTTGTTCAATGACAACTCTCAATAA
* * **
36859 TTTGCCATTCAACGCTCATACTCTTAACATTCATGATGCTCAAGGAGGAACATCAATTCCTTTAC
1 TTTGCCATTGAACGCTCATACTCCTAACATTCATGATGCTCAAGGAATAACA-CAATTCCTTTAC
* * * * *
36924 TA-TCGATGTCGCTTGGTTCATGCTAATGGTTCGA-TTTTTTAGATTAATCTGGGGTAAGT
65 CACT-GGTGTCGCTTGGTTCGTGCTAATGGTTTGATTTTTTTAGATTAATCTGGGATAAGT
36983 CCATCAAACA
Statistics
Matches: 243, Mismatches: 39, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
160 23 0.09
161 79 0.33
162 5 0.02
163 136 0.56
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (160 bp):
TTTGCCATTGAACGCTCATACTCCTAACATTCATGATGCTCAAGGAATAACACAATTCCTTTACC
ACTGGTGTCGCTTGGTTCGTGCTAATGGTTTGATTTTTTTAGATTAATCTGGGATAAGTACAAGG
TAATATTTGTTCAATGACAACTCTCAATAA
Found at i:42367 original size:13 final size:13
Alignment explanation
Indices: 42366--42441 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 13
42356 CCGTTTACCC
42366 GACCCGACCCGTT
1 GACCCGACCCGTT
*
42379 TACCCGACCCGTT
1 GACCCGACCCGTT
42392 GACCCGACTCGACCCGTT
1 GA--C--C-CGACCCGTT
42410 GACCCGACCCGTT
1 GACCCGACCCGTT
*
42423 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
42438 GACC
1 GACC
42442 GTTGATTGGC
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 26 0.49
14 1 0.02
15 13 0.25
16 1 0.02
17 1 0.02
18 11 0.21
ACGTcount: A:0.16, C:0.43, G:0.22, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:42385 original size:31 final size:31
Alignment explanation
Indices: 42348--42426 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
42338 GTCATAACCC
*
42348 GACCCGACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
42379 TACCCGACCCGTTGACCCGACTCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
42410 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
42427 GTTGACCCGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.16, C:0.47, G:0.20, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:42395 original size:8 final size:8
Alignment explanation
Indices: 42384--42446 Score: 64
Period size: 8 Copynumber: 8.2 Consensus size: 8
42374 CCGTTTACCC
42384 GACCCGTT
1 GACCCGTT
*
42392 GACCCGACTC
1 GACCCG--TT
42402 GACCCGTT
1 GACCCGTT
42410 GACCC---
1 GACCCGTT
42415 GACCCGTT
1 GACCCGTT
42423 GA-CCGTT
1 GACCCGTT
42430 GACCCGTT
1 GACCCGTT
42438 GA-CCGTT
1 GACCCGTT
42445 GA
1 GA
42447 TTGGCGTTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
5 5 0.11
7 14 0.30
8 21 0.45
10 7 0.15
ACGTcount: A:0.16, C:0.38, G:0.25, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:42404 original size:18 final size:18
Alignment explanation
Indices: 42344--42420 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 18
42334 ACCGGTCATA
*
42344 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
42362 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
42379 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
42393 ACCCGACTCGACCCGTTG
1 ACCCGACCCGACCCGTTG
42411 ACCCGACCCG
1 ACCCGACCCG
42421 TTGACCGTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
13 12 0.24
18 38 0.76
ACGTcount: A:0.17, C:0.49, G:0.19, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:42435 original size:15 final size:15
Alignment explanation
Indices: 42402--42446 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
42392 GACCCGACTC
*
42402 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
42415 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
42430 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
42445 GA
1 GA
42447 TTGGCGTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.41
15 17 0.59
ACGTcount: A:0.16, C:0.36, G:0.27, T:0.22
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:43785 original size:18 final size:18
Alignment explanation
Indices: 43759--43793 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43749 TCGAAAGGAC
*
43759 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
43777 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
43794 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:44983 original size:12 final size:12
Alignment explanation
Indices: 44968--45037 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
44958 GATAAATGAC
44968 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
44980 CTGATTTCTGAT
1 CTGAATTCTGTT
* *
44992 ATGGATTCTGTT
1 CTGAATTCTGTT
45004 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
45016 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
45028 TTGATTTCTG
1 CTGAATTCTG
45038 ATATCTTCGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:44987 original size:48 final size:48
Alignment explanation
Indices: 44931--45041 Score: 152
Period size: 48 Copynumber: 2.3 Consensus size: 48
44921 AAATATTTTA
44931 TCTGATTTCTGACT-TGAATTCTGTTCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGA-TATGAATTCTGTTCTGATAAATGACCTGAATTCTGT
* ** **
44979 TCTGATTTCTGATATGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGTTCTGATAAATGACCTGAATTCTGT
*
45027 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
45042 CTTCGTTTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
47 1 0.02
48 55 0.98
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (48 bp):
TCTGATTTCTGATATGAATTCTGTTCTGATAAATGACCTGAATTCTGT
Found at i:44999 original size:24 final size:24
Alignment explanation
Indices: 44931--45041 Score: 116
Period size: 24 Copynumber: 4.6 Consensus size: 24
44921 AAATATTTTA
44931 TCTGATTTCTGACT-TGAATTCTGT
1 TCTGATTTCTGA-TATGAATTCTGT
*** **
44955 TCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
44979 TCTGATTTCTGATATGGATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* * *
45003 TCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
45027 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
45042 CTTCGTTTAA
Statistics
Matches: 68, Mismatches: 18, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTCTGT
Found at i:45017 original size:17 final size:18
Alignment explanation
Indices: 44974--45025 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 18
44964 TGACCTGAAT
44974 TCTGTTCTGATTTCTGATA
1 TCTGTTCTGA-TTCTGATA
*
44993 T-GGATTCTG-TTCTGATA
1 TCTG-TTCTGATTCTGATA
45010 TCTGTTCTGAATTCTG
1 TCTGTTCTG-ATTCTG
45026 TTTTGATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
17 14 0.52
18 2 0.07
19 11 0.41
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.50
Consensus pattern (18 bp):
TCTGTTCTGATTCTGATA
Found at i:47175 original size:13 final size:13
Alignment explanation
Indices: 47174--47249 Score: 62
Period size: 13 Copynumber: 5.3 Consensus size: 13
47164 CCGTTTACCC
47174 GACCCGACCCGTT
1 GACCCGACCCGTT
*
47187 TACCCGACCCGTT
1 GACCCGACCCGTT
*
47200 GACCCGAATCGACCCATT
1 GA-CC----CGACCCGTT
47218 GACCCGACCCGTT
1 GACCCGACCCGTT
*
47231 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
47246 GACC
1 GACC
47250 GTTGACCGGC
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
13 25 0.49
14 2 0.04
15 12 0.24
17 2 0.04
18 10 0.20
ACGTcount: A:0.18, C:0.42, G:0.21, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:47175 original size:18 final size:18
Alignment explanation
Indices: 47152--47197 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
47142 ACCGGTCATA
47152 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
47170 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
47188 ACCCGACCCG
1 ACCCGACCCG
47198 TTGACCCGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.52, G:0.17, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:47192 original size:31 final size:31
Alignment explanation
Indices: 47156--47234 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
47146 GTCATAACCC
* * *
47156 GACCCGACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGAACCGACCCATT
* *
47187 TACCCGACCCGTTGACCCGAATCGACCCATT
1 GACCCGACCCGTTGACCCGAACCGACCCATT
47218 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
47235 GTTGACCCGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.19, C:0.46, G:0.19, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGAACCGACCCATT
Found at i:47203 original size:8 final size:8
Alignment explanation
Indices: 47192--47276 Score: 63
Period size: 8 Copynumber: 10.5 Consensus size: 8
47182 CCGTTTACCC
47192 GACCCGTT
1 GACCCGTT
*
47200 GACCCGAATC
1 GACCCG--TT
*
47210 GACCCATT
1 GACCCGTT
47218 GACCC---
1 GACCCGTT
47223 GACCCGTT
1 GACCCGTT
47231 GA-CCGTT
1 GACCCGTT
47238 GACCCGTT
1 GACCCGTT
47246 GA-CCGTT
1 GACCCGTT
47253 GACCGGCGTT
1 GACC--CGTT
47263 GACCACTGTT
1 GACC-C-GTT
47273 GACC
1 GACC
47277 AAAACTTTGA
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
5 5 0.08
7 14 0.22
8 22 0.35
9 1 0.02
10 21 0.33
ACGTcount: A:0.18, C:0.36, G:0.25, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:47238 original size:7 final size:7
Alignment explanation
Indices: 47226--47257 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
47216 TTGACCCGAC
47226 CCGTTGA
1 CCGTTGA
47233 CCGTTGA
1 CCGTTGA
47240 CCCGTTGA
1 -CCGTTGA
47248 CCGTTGA
1 CCGTTGA
47255 CCG
1 CCG
47258 GCGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:47243 original size:15 final size:15
Alignment explanation
Indices: 47223--47266 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 15
47213 CCATTGACCC
47223 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
47238 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
47253 GACCGGCGTTGACC
1 GACC--CGTTGACC
47267 ACTGTTGACC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 19 0.70
17 8 0.30
ACGTcount: A:0.14, C:0.34, G:0.30, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:48593 original size:18 final size:18
Alignment explanation
Indices: 48567--48601 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48557 TCGAAAGGAC
*
48567 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
48585 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
48602 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:49795 original size:12 final size:12
Alignment explanation
Indices: 49780--49849 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
49770 GATAAATGAC
49780 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
49792 CTGATTTCTGAT
1 CTGAATTCTGTT
* *
49804 ATGGATTCTGTT
1 CTGAATTCTGTT
49816 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
49828 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
49840 TTGATTTCTG
1 CTGAATTCTG
49850 ATATCTTCGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:49799 original size:48 final size:48
Alignment explanation
Indices: 49743--49853 Score: 152
Period size: 48 Copynumber: 2.3 Consensus size: 48
49733 AAATATTTTA
49743 TCTGATTTCTGACT-TGAATTCTGTTCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGA-TATGAATTCTGTTCTGATAAATGACCTGAATTCTGT
* ** **
49791 TCTGATTTCTGATATGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGTTCTGATAAATGACCTGAATTCTGT
*
49839 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
49854 CTTCGTTTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
47 1 0.02
48 55 0.98
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (48 bp):
TCTGATTTCTGATATGAATTCTGTTCTGATAAATGACCTGAATTCTGT
Found at i:49811 original size:24 final size:24
Alignment explanation
Indices: 49743--49853 Score: 116
Period size: 24 Copynumber: 4.6 Consensus size: 24
49733 AAATATTTTA
49743 TCTGATTTCTGACT-TGAATTCTGT
1 TCTGATTTCTGA-TATGAATTCTGT
*** **
49767 TCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
49791 TCTGATTTCTGATATGGATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* * *
49815 TCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
49839 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
49854 CTTCGTTTAA
Statistics
Matches: 68, Mismatches: 18, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTCTGT
Found at i:49829 original size:17 final size:18
Alignment explanation
Indices: 49786--49837 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 18
49776 TGACCTGAAT
49786 TCTGTTCTGATTTCTGATA
1 TCTGTTCTGA-TTCTGATA
*
49805 T-GGATTCTG-TTCTGATA
1 TCTG-TTCTGATTCTGATA
49822 TCTGTTCTGAATTCTG
1 TCTGTTCTG-ATTCTG
49838 TTTTGATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
17 14 0.52
18 2 0.07
19 11 0.41
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.50
Consensus pattern (18 bp):
TCTGTTCTGATTCTGATA
Found at i:50751 original size:3 final size:3
Alignment explanation
Indices: 50743--50781 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
50733 TTGTCTGGGG
*
50743 TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA ATA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
50782 TTACATTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:52631 original size:5 final size:5
Alignment explanation
Indices: 52621--52680 Score: 59
Period size: 5 Copynumber: 12.0 Consensus size: 5
52611 ATAGTAATAT
** * *
52621 TTTTA TTTTA TTTT- TTTTA TGATA TTTTA TTTTA TTTTTA TATTG TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA
*
52671 TTTAA TTTTA
1 TTTTA TTTTA
52681 AGTATTGATA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
4 4 0.09
5 34 0.79
6 5 0.12
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:52660 original size:21 final size:21
Alignment explanation
Indices: 52623--52679 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
52613 AGTAATATTT
52623 TTATTTTA-TTT-TTTTTATGA
1 TTATTTTATTTTATTTTTAT-A
52643 -TATTTTATTTTATTTTTATA
1 TTATTTTATTTTATTTTTATA
* *
52663 TTGTTTTATTTAATTTT
1 TTATTTTATTTTATTTT
52680 AAGTATTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 7 0.22
20 4 0.12
21 21 0.66
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (21 bp):
TTATTTTATTTTATTTTTATA
Found at i:55294 original size:45 final size:44
Alignment explanation
Indices: 55243--55423 Score: 258
Period size: 45 Copynumber: 4.0 Consensus size: 44
55233 TACAACTTTC
* *
55243 TTACCAATATACATATCATTTATCCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTAT-CCATAAGCTCGTAAGCTTATT
55288 TTACCAATATACTTACCATTTAATCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTT-ATCCATAAGCTCGTAAGCTTATT
*
55333 TTACCAATATACTTACCATTTAGTCTATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTA-TCCATAAGCTCGTAAGCTTATT
* *
55378 TTATCC-ATATATTTGCCA-TTATTCCATAAGCTCGTAAGCTTATT
1 TTA-CCAATATACTTACCATTTA-TCCATAAGCTCGTAAGCTTATT
55422 TT
1 TT
55424 CCTAGTTACC
Statistics
Matches: 126, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
44 27 0.21
45 95 0.75
46 4 0.03
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (44 bp):
TTACCAATATACTTACCATTTATCCATAAGCTCGTAAGCTTATT
Found at i:59509 original size:2 final size:2
Alignment explanation
Indices: 59502--59531 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
59492 CACAAGTGAA
59502 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
59532 TTAATCATCT
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:62451 original size:45 final size:44
Alignment explanation
Indices: 62400--62581 Score: 269
Period size: 45 Copynumber: 4.1 Consensus size: 44
62390 AATACAACTT
* * *
62400 TTTTACCAATATACATATCATTTATCCCATAAGCTCATAAGCTTA
1 TTTTACCAATATACTTACCATTTAT-CCATAAGCTCGTAAGCTTA
62445 TTTTACCAATATACTTACCATTTAATCCATAAGCTCGTAAGCTTA
1 TTTTACCAATATACTTACCATTT-ATCCATAAGCTCGTAAGCTTA
62490 TTTTACCAATATACTTACCATTTAGTCCATAAGCTCGTAAGCTTA
1 TTTTACCAATATACTTACCATTTA-TCCATAAGCTCGTAAGCTTA
*
62535 TTTTATCC-ATATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTA
1 TTTTA-CCAATATACTTACCATTTA-TCCATAAGCTCGTAAGCTTA
62579 TTT
1 TTT
62582 GCCTGGTTAC
Statistics
Matches: 129, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
44 27 0.21
45 98 0.76
46 4 0.03
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (44 bp):
TTTTACCAATATACTTACCATTTATCCATAAGCTCGTAAGCTTA
Done.