Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004528.1 Hibiscus syriacus cultivar Beakdansim tig00009991_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: 64305
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:5748 original size:140 final size:137
Alignment explanation
Indices: 5499--5775 Score: 527
Period size: 140 Copynumber: 2.0 Consensus size: 137
5489 GGTTTCTAGT
5499 TATCTTTAATCTTTTTTATACTATTTAGTATTGTATGGATTTACTTAACTTTGCAAATGTTGAAA
1 TATCTTTAATCTTTTTTATACTATTTAGTATTGTATGGATTTACTTAACTTTGCAAATGTTGAAA
5564 GGGGATATGAACCATTGTTTAAAATTCAACTTAACTTCCTTGATTAAAAAAAACCTTGACTTTGA
66 GGGGATATGAACCATTGTTTAAAATTCAACTTAACTTCCTTGATTAAAAAAAACCTTGACTTTGA
5629 ATTTCCA
131 ATTTCCA
5636 TATCTTTAATCTTTTTTATATACTATTTAGTATTTGTATGGATTTACTTAACTTTGCAAATGTTG
1 TATCTTTAATC-TTTTT-TATACTATTTAGTA-TTGTATGGATTTACTTAACTTTGCAAATGTTG
5701 AAAGGGGATATGAACCATTGTTTAAAATTCAACTTAACTTCCTTGATTAAAAAAAACCTTGACTT
63 AAAGGGGATATGAACCATTGTTTAAAATTCAACTTAACTTCCTTGATTAAAAAAAACCTTGACTT
5766 TGAATTTCCA
128 TGAATTTCCA
5776 GAGAGAGATT
Statistics
Matches: 137, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
137 11 0.08
138 5 0.04
139 14 0.10
140 107 0.78
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.43
Consensus pattern (137 bp):
TATCTTTAATCTTTTTTATACTATTTAGTATTGTATGGATTTACTTAACTTTGCAAATGTTGAAA
GGGGATATGAACCATTGTTTAAAATTCAACTTAACTTCCTTGATTAAAAAAAACCTTGACTTTGA
ATTTCCA
Found at i:8448 original size:2 final size:2
Alignment explanation
Indices: 8441--8470 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8431 AGTGCATAAC
8441 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
8471 GTGTGTGTGT
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:24881 original size:21 final size:20
Alignment explanation
Indices: 24852--24902 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
24842 GTTGAGTTGA
*
24852 TATCGATACTAGATGAACTAG
1 TATCCATACT-GATGAACTAG
24873 TATCCATACCTGATGAACTAG
1 TATCCATA-CTGATGAACTAG
24894 TATCCATAC
1 TATCCATAC
24903 CGGACGAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 1 0.04
21 25 0.89
22 2 0.07
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (20 bp):
TATCCATACTGATGAACTAG
Found at i:24903 original size:21 final size:21
Alignment explanation
Indices: 24863--24903 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
24853 ATCGATACTA
24863 GATGAACTAGTATCCATACCT
1 GATGAACTAGTATCCATACCT
24884 GATGAACTAGTATCCATACC
1 GATGAACTAGTATCCATACC
24904 GGACGAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (21 bp):
GATGAACTAGTATCCATACCT
Found at i:24917 original size:21 final size:21
Alignment explanation
Indices: 24866--24910 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
24856 GATACTAGAT
* *
24866 GAACTAGTATCCATACCTGAT
1 GAACTAGTATCCATACCGGAC
24887 GAACTAGTATCCATACCGGAC
1 GAACTAGTATCCATACCGGAC
24908 GAA
1 GAA
24911 TTGGTATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (21 bp):
GAACTAGTATCCATACCGGAC
Found at i:24944 original size:21 final size:21
Alignment explanation
Indices: 24918--24965 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
24908 GAATTGGTAT
*
24918 TTGGTATCTATACCAAATGAG
1 TTGGTATCTATACCAAATAAG
* * *
24939 TTGGTATTTATATCAGATAAG
1 TTGGTATCTATACCAAATAAG
24960 TTGGTA
1 TTGGTA
24966 CCCATACCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (21 bp):
TTGGTATCTATACCAAATAAG
Found at i:25049 original size:14 final size:14
Alignment explanation
Indices: 25030--25057 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25020 TTTGGTATTA
25030 ATACACAAAGTGGT
1 ATACACAAAGTGGT
25044 ATACACAAAGTGGT
1 ATACACAAAGTGGT
25058 TGAGAGTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
ATACACAAAGTGGT
Found at i:25929 original size:24 final size:24
Alignment explanation
Indices: 25902--25949 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
25892 CAATTATTTG
25902 ATACTCAGGAAACAATGAGGACAC
1 ATACTCAGGAAACAATGAGGACAC
*
25926 ATACTCGGGAAACAATGAGGACAC
1 ATACTCAGGAAACAATGAGGACAC
25950 CTGAGCTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (24 bp):
ATACTCAGGAAACAATGAGGACAC
Found at i:26067 original size:22 final size:22
Alignment explanation
Indices: 26037--26078 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
26027 GCACTTTAGT
*
26037 ATATCAGTGCTAGTGCACTTCC
1 ATATCAGTGATAGTGCACTTCC
*
26059 ATATTAGTGATAGTGCACTT
1 ATATCAGTGATAGTGCACTT
26079 ATGTATCCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (22 bp):
ATATCAGTGATAGTGCACTTCC
Found at i:34472 original size:76 final size:76
Alignment explanation
Indices: 34375--34524 Score: 237
Period size: 76 Copynumber: 2.0 Consensus size: 76
34365 CAGATTGCCC
* * *
34375 AGAGGTTACCGATACCCCCATGTAAGATTTGGCTCCAAGAAATAATAGATTGCTCGGAGGGTACC
1 AGAGGGTACCGATACCCCCATGTAAGATTTGGCTCCAAGAAATAACAGATTGCTCAGAGGGTACC
34440 GATACCCCCCA
66 GATACCCCCCA
* * * *
34451 AGAGGGTACTGATACCCCCATGTAAGATTTGGCTCCGAGAAATAACATATTTCTCAGAGGGTACC
1 AGAGGGTACCGATACCCCCATGTAAGATTTGGCTCCAAGAAATAACAGATTGCTCAGAGGGTACC
34516 GATACCCCC
66 GATACCCCC
34525 ATCTCATAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 67 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (76 bp):
AGAGGGTACCGATACCCCCATGTAAGATTTGGCTCCAAGAAATAACAGATTGCTCAGAGGGTACC
GATACCCCCCA
Found at i:41330 original size:20 final size:20
Alignment explanation
Indices: 41302--41340 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41292 TTTCCCACAA
* *
41302 ATTTTTAAAACCTCCGGGTC
1 ATTTGTAAAACCTCAGGGTC
41322 ATTTGTAAAACCTCAGGGT
1 ATTTGTAAAACCTCAGGGT
41341 AGGATGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (20 bp):
ATTTGTAAAACCTCAGGGTC
Found at i:41455 original size:119 final size:119
Alignment explanation
Indices: 41302--41826 Score: 818
Period size: 119 Copynumber: 4.4 Consensus size: 119
41292 TTTCCCACAA
* *
41302 ATTTTTAAAACCTCCGGGTCATTTGTAAAACCTCAGGGTAGGATGTTTTTGCATGAAAATGAGAA
1 ATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTTGCATGAAAATGAGAA
* * *
41367 AGCGATTTTCAAAGTTTCTTATTTAATGTTCTAAAAAATTAAATCCTCCGGGTG
66 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGAGTG
**
41421 ATTTGTAAAACCTTAGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTTGCATGAAAATGA-AA
1 ATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTTGCATGAAAATGAGAA
* *
41485 AGCGATTTTCAAATTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGCGTG
66 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGAGTG
* * * * *
41539 ATTTGTAAAACCTCTGTGTCATATGTAAAACTTCAGGGTAGGATGTTTTCGCATGAAAATGAGAA
1 ATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTTGCATGAAAATGAGAA
* * * *
41604 AGCGATTTTCAAAGTTCCTCATTTAATGTTCTATAAAATCAAATCCTCCGTGTG
66 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGAGTG
* * * * *
41658 ATTTATAAAACGTCCGGGTCATCTGTAAAGCCTCAGGGTAGGATATTTTTGCATTAAAATGAGAA
1 ATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTTGCATGAAAATGAGAA
*
41723 AGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGAGTG
66 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGAGTG
*
41777 ATTTGTAAAACCTCCGGGTCATCTGTAAAGCCTCAGGGTAGGATGTTTTT
1 ATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTT
41827 ATTTACTAAT
Statistics
Matches: 368, Mismatches: 37, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
118 108 0.29
119 260 0.71
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (119 bp):
ATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTTGCATGAAAATGAGAA
AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGAGTG
Found at i:42063 original size:17 final size:17
Alignment explanation
Indices: 41972--42064 Score: 68
Period size: 17 Copynumber: 5.4 Consensus size: 17
41962 AATTATATTT
* *
41972 ATTATTACTATTATATA
1 ATTATTATTATTATAAA
41989 ATTATTATTATTACT---
1 ATTATTATTATTA-TAAA
* *
42004 ATTATTATATATAATATA
1 ATTATTAT-TATTATAAA
*
42022 ATATATTA-TATTATTAAGT
1 AT-TATTATTATTA-TAA-A
42041 ATTATTATTATTATAAA
1 ATTATTATTATTATAAA
42058 ATTATTA
1 ATTATTA
42065 CAAGACCAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
15 9 0.15
16 4 0.07
17 23 0.38
18 13 0.21
19 12 0.20
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (17 bp):
ATTATTATTATTATAAA
Found at i:42064 original size:3 final size:3
Alignment explanation
Indices: 41970--42054 Score: 68
Period size: 3 Copynumber: 28.3 Consensus size: 3
41960 ATAATTATAT
* * *
41970 TTA TTA TTA CTA TTA -TA TAA TTA TTA TTA TTA CTA TTA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * *
42017 ATA TAA TATA TTA -TA TTA TTAA GTA TTA TTA TTA TTA T
1 TTA TTA T-TA TTA TTA TTA TT-A TTA TTA TTA TTA TTA T
42055 AAAATTATTA
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
2 6 0.09
3 52 0.81
4 6 0.09
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:43388 original size:29 final size:27
Alignment explanation
Indices: 43333--43389 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 27
43323 ATTTAATCCT
*
43333 TTATTTTTAATACTTTAATTTTAAATA
1 TTATTTTTAATACTTTAATGTTAAATA
43360 TTATTTTATAATA-TTTCAGATGTTAAATA
1 TTATTTT-TAATACTTT-A-ATGTTAAATA
43389 T
1 T
43390 GTTGCAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 10 0.38
28 6 0.23
29 10 0.38
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (27 bp):
TTATTTTTAATACTTTAATGTTAAATA
Found at i:45750 original size:8 final size:8
Alignment explanation
Indices: 45737--45761 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
45727 GATTTAGTTC
45737 TATTATTT
1 TATTATTT
45745 TATTATTT
1 TATTATTT
45753 TATTATTT
1 TATTATTT
45761 T
1 T
45762 TCTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTATTT
Found at i:45777 original size:10 final size:9
Alignment explanation
Indices: 45758--45799 Score: 66
Period size: 9 Copynumber: 4.4 Consensus size: 9
45748 TATTTTATTA
45758 TTTTTCTTT
1 TTTTTCTTT
45767 TTTTTCTTT
1 TTTTTCTTT
45776 TTTTTCTTTT
1 TTTTTC-TTT
45786 TTTTTCTATT
1 TTTTTCT-TT
45796 TTTT
1 TTTT
45800 GATTCTTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 16 0.52
10 15 0.48
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:45786 original size:19 final size:19
Alignment explanation
Indices: 45753--45799 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 19
45743 TTTATTATTT
45753 TATTATTTTTCTTTTTTTTC
1 TATT-TTTTTCTTTTTTTTC
45773 T-TTTTTTTCTTTTTTTTTC
1 TATTTTTTTC-TTTTTTTTC
45792 TATTTTTT
1 TATTTTTT
45800 GATTCTTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.24
19 12 0.48
20 7 0.28
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (19 bp):
TATTTTTTTCTTTTTTTTC
Found at i:46372 original size:263 final size:256
Alignment explanation
Indices: 45827--46618 Score: 859
Period size: 263 Copynumber: 3.0 Consensus size: 256
45817 TTTGTCAAAT
* * * *
45827 ATTAAATAAGAAACTTTGAAAATCGCTTTC-TCTTTTTATTTACAAA-GTCATATGAAAACATCA
1 ATTAAATAAGAAACTTTGAAAATCACTTTCTTATTTTTTTTTACAAATATCATATGAAAACATCA
* * * * *
45890 TACCTGAAGATCTTATAAATGACCCGAAAGACTTATCATCTTGCTCAAAAGACTTATAGATGACC
66 T-GCTGAAGGTCTTATAAATGACCAG-AAGACTTATCATCTTGCT-TAAAGACTTAAAGATGACC
* * * * *** *
45955 CGGGGATTTAATCA-CTAGGTTCAGAAGATTTACAAATGGCCTAGAGGACTTACTAATTTTAGAA
128 AGAGGATTTAATCATC-AGGCTCAGAAGACTTATTGATGGCCCAGAGGACTTACTAATTTTAGAA
* *
46019 ATAGTCTACTAGGT-AACA-TTGGAAATCATTTTCTTACTTTTCAAAAACTTCATTTTTAGAAAA
192 ATAGTCTACTAGGTAAAAATTTGGAAATCATTTT-TTACTTTTCAAAAATTTCATTTTTAGAAAA
46082 G
256 G
*
46083 ATTAAATAAGAAACTTTGATAATCACTTTCTTATTTTTTTTTCACAAATATCATATGAAAACATC
1 ATTAAATAAGAAACTTTGAAAATCACTTTCTTATTTTTTTTT-ACAAATATCATATGAAAACATC
* * *
46148 ATGCT-AGAGGTGTTATAAATTGTCCAGAAGACTTATCATCTTGCTTGAAAGACTTAAATATGAC
65 ATGCTGA-AGGTCTTATAAA-TGACCAGAAGACTTATCATCTTGCTT-AAAGACTTAAAGATGAC
* * * * *
46212 CTAGAGGATTTAATCATCAAGCTCGGGAGACTTATTGATGGCCCAGTGGACTTATTAATTTT-GC
127 C-AGAGGATTTAATCATCAGGCTCAGAAGACTTATTGATGGCCCAGAGGACTTACTAATTTTAG-
* **
46276 AAATAGTCTACTAGGTAAAATATTTTGGAAATTGATTTTTTACTTTTCAAAAATTTCATTTTCGG
190 AAATAGTCTACTAGGTAAAA-A-TTTGGAAA-TCATTTTTTACTTTTCAAAAATTTCATTTTTAG
46341 AAAAG
252 AAAAG
*
46346 ATTAAATAAGACACTTTGAAAATCACTTTCTTATTTTTTTTTACAAATATCATATGAAAACATCA
1 ATTAAATAAGAAACTTTGAAAATCACTTTCTTATTTTTTTTTACAAATATCATATGAAAACATCA
* * * * * *
46411 TGCCCGTAGGTCTTATAAATGACCCATAGGACTTATCATCTTACTCTAAAGA-TATACAGATGAC
66 TG-CTGAAGGTCTTATAAATGA-CCAGAAGACTTATCATCTTGCT-TAAAGACT-TAAAGATGAC
* * * *
46475 CAAGATGAATTAATCATTAGGCTCAGAAGACTT-TGTGATGGCCC-GAAGGACTTACTAGTTTTA
127 C-AGAGGATTTAATCATCAGGCTCAGAAGACTTAT-TGATGGCCCAG-AGGACTTACTAATTTTA
* * * * *
46538 GAAATAGTTTACTAGGTAACAAATTTAGAAATCACTTTCTTACTTTTC-AAATTTTCATTTTTTG
189 GAAATAGTCTACTAGGTAA-AAATTTGGAAATCA-TTTTTTACTTTTCAAAAATTTCATTTTTAG
*
46602 AAAAC
252 AAAAG
*
46607 ATTAAATGAGAA
1 ATTAAATAAGAA
46619 TTTAAAAAAT
Statistics
Matches: 450, Mismatches: 62, Indels: 43
0.81 0.11 0.08
Matches are distributed among these distances:
256 28 0.06
257 10 0.02
258 52 0.12
259 83 0.18
260 3 0.01
261 30 0.07
262 49 0.11
263 185 0.41
264 10 0.02
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (256 bp):
ATTAAATAAGAAACTTTGAAAATCACTTTCTTATTTTTTTTTACAAATATCATATGAAAACATCA
TGCTGAAGGTCTTATAAATGACCAGAAGACTTATCATCTTGCTTAAAGACTTAAAGATGACCAGA
GGATTTAATCATCAGGCTCAGAAGACTTATTGATGGCCCAGAGGACTTACTAATTTTAGAAATAG
TCTACTAGGTAAAAATTTGGAAATCATTTTTTACTTTTCAAAAATTTCATTTTTAGAAAAG
Found at i:58675 original size:89 final size:89
Alignment explanation
Indices: 58528--58944 Score: 356
Period size: 89 Copynumber: 4.7 Consensus size: 89
58518 AGTGATGTCA
* * * * * ** ** * * *
58528 TTCTTGACTTTCTCATGAGGAGAAATCAACCTTTTAGTGGCGTTGTTATTGAATTTCTCGTGGAG
1 TTCTTGACTTTTTCGTGAAGAGAAGTCAATCTTTTAGTGATGTCATTCTTGACTTTCTCGTGAAG
* * *
58593 AGAAGCCAATCTTTCAGCGTTATC
66 AGAAGTCAATCTTTTAGTGTTATC
58617 TTCCTTGACTTTTTCGTGAAGAGAAGTCAATC-TTTAGTGATGTCATTCTTGACTTTCTCGTGAA
1 TT-CTTGACTTTTTCGTGAAGAGAAGTCAATCTTTTAGTGATGTCATTCTTGACTTTCTCGTGAA
* *
58681 GAGAAGTCAACCTTTTAGTGGTGT-TA
65 GAGAAGTCAATCTTTTAGT-GT-TATC
* * * *
58707 TTCTTGACTTTTTCGTGGAA-AGTAGTCAACCTTTTAATGATGTCACTCTTGACTTTCTCGTGAA
1 TTCTTGACTTTTTCGT-GAAGAGAAGTCAATCTTTTAGTGATGTCATTCTTGACTTTCTCGTGAA
* * *
58771 GAGAAGTCAATATTTAAGTATTATC
65 GAGAAGTCAATCTTTTAGTGTTATC
** ** * * * * *
58796 AACTTGACTTTTTATTGAAAAGAAGTCAATCTTTTAGTGTTGTC-TTCCTTAACTTTCTCATAAA
1 TTCTTGACTTTTTCGTGAAGAGAAGTCAATCTTTTAGTGATGTCATT-CTTGACTTTCTCGTGAA
* *
58860 GAGGAGTCAATCTTTTAGTGTTTTC
65 GAGAAGTCAATCTTTTAGTGTTATC
* *** * * * * *
58885 ATTCTTGACTTTCTCAAAAAGAGAAATCAATCTTTCAGTGTTATGATTCTTGACTTTCTC
1 -TTCTTGACTTTTTCGTGAAGAGAAGTCAATCTTTTAGTGATGTCATTCTTGACTTTCTC
58945 AAAAAGTGGA
Statistics
Matches: 262, Mismatches: 56, Indels: 19
0.78 0.17 0.06
Matches are distributed among these distances:
88 5 0.02
89 133 0.51
90 121 0.46
91 3 0.01
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.41
Consensus pattern (89 bp):
TTCTTGACTTTTTCGTGAAGAGAAGTCAATCTTTTAGTGATGTCATTCTTGACTTTCTCGTGAAG
AGAAGTCAATCTTTTAGTGTTATC
Found at i:58758 original size:134 final size:134
Alignment explanation
Indices: 58512--58834 Score: 357
Period size: 134 Copynumber: 2.4 Consensus size: 134
58502 GGAAGAGTTC
* * *
58512 ATCTTTAGTGATGTCATTCTTGACTTTCTCATGAGGAGAAATCAACCTTTTAGTGGCGTTGTTAT
1 ATCTTTAGTGATGTCATTCTTGACTTTCTCATGAAGAGAAGTCAACCTTTTAGTGGCGTTATTAT
* * * * * *
58577 TGAATTTCTCGTGGAGAGAAGCCAATCTTTCAGCGTTATCTTCCTTGACTTTTTCGTGAAGAGAA
66 TGAATTTCTCGTGGAAAGAAGCCAACCTTTCAACGATATCCTCCTTGACTTTCTCGTGAAGAGAA
58642 GTCA
131 GTCA
* * *
58646 ATCTTTAGTGATGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAACCTTTTAGTGGTGTTATTCT
1 ATCTTTAGTGATGTCATTCTTGACTTTCTCATGAAGAGAAGTCAACCTTTTAGTGGCGTTATTAT
* * * * * * *
58711 TGACTTTTTCGTGGAAAGTAGTCAACCTTTTAATGATGTCACT-CTTGACTTTCTCGTGAAGAGA
66 TGAATTTCTCGTGGAAAGAAGCCAACCTTTCAACGATATC-CTCCTTGACTTTCTCGTGAAGAGA
58775 AGTCA
130 AGTCA
* * * * * *
58780 ATATTTAAGT-ATTATCA-ACTTGACTTT-TTATTGAAAAGAAGTCAATCTTTTAGTG
1 ATCTTT-AGTGA-TGTCATTCTTGACTTTCTCA-TGAAGAGAAGTCAACCTTTTAGTG
58835 TTGTCTTCCT
Statistics
Matches: 159, Mismatches: 26, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
133 1 0.01
134 150 0.94
135 8 0.05
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (134 bp):
ATCTTTAGTGATGTCATTCTTGACTTTCTCATGAAGAGAAGTCAACCTTTTAGTGGCGTTATTAT
TGAATTTCTCGTGGAAAGAAGCCAACCTTTCAACGATATCCTCCTTGACTTTCTCGTGAAGAGAA
GTCA
Found at i:58868 original size:134 final size:134
Alignment explanation
Indices: 58620--58943 Score: 314
Period size: 134 Copynumber: 2.4 Consensus size: 134
58610 CGTTATCTTC
* * * * * *
58620 CTTGACTTTTTCGTGAAGAGAAGTCAATCTTTAGTGATGTCATTCTTGACTTTCTCGTGAAGAGA
1 CTTGACTTTCTCGTGAAGAGAAGTCAATATTTAGTGATATCATACTTGACTTTCTAGTGAAAAGA
* * * * * *
58685 AGTCAACCTTTTAGTGGTGTTATTCTTGACTTTTTCGTGGAAAGTAGTCAACCTTTTAATGATGT
66 AGTCAACCTTTTAGTGGTGTTATCCTTAACTTTCTCATGAAAAGGAGTCAACCTTTTAATGATGT
58750 CACT
131 CACT
* *
58754 CTTGACTTTCTCGTGAAGAGAAGTCAATATTTAAGT-ATTATCA-ACTTGACTTTTTATTGAAAA
1 CTTGACTTTCTCGTGAAGAGAAGTCAATATTT-AGTGA-TATCATACTTGACTTTCTAGTGAAAA
* * * *
58817 GAAGTCAATCTTTTAGTGTTGTCT-TCCTTAACTTTCTCAT-AAAGAGGAGTCAATCTTTTAGTG
64 GAAGTCAACCTTTTAGTGGTGT-TATCCTTAACTTTCTCATGAAA-AGGAGTCAACCTTTTAATG
* * *
58880 TTTTCATT
127 ATGTCACT
*** * * * * *
58888 CTTGACTTTCTCAAAAAGAGAAATCAATCTTTCAGTGTTATGATTCTTGACTTTCT
1 CTTGACTTTCTCGTGAAGAGAAGTCAATATTT-AGTGATATCATACTTGACTTTCT
58944 CAAAAAGTGG
Statistics
Matches: 153, Mismatches: 31, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
133 2 0.01
134 133 0.87
135 18 0.12
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (134 bp):
CTTGACTTTCTCGTGAAGAGAAGTCAATATTTAGTGATATCATACTTGACTTTCTAGTGAAAAGA
AGTCAACCTTTTAGTGGTGTTATCCTTAACTTTCTCATGAAAAGGAGTCAACCTTTTAATGATGT
CACT
Found at i:58938 original size:179 final size:178
Alignment explanation
Indices: 58515--58944 Score: 420
Period size: 179 Copynumber: 2.4 Consensus size: 178
58505 AGAGTTCATC
* * * * * *
58515 TTTAGTGATGTCATTCTTGACTTTCTCATGAGGAGAAATCAACCTTTTAGTGGCGTTG-TTATTG
1 TTTAGTGTTTTCATTCTTGACTTTCTCAAGAAGAGAAATCAACCTTTTAGT-G-ATTGATTCTTG
* * * * * ** * *
58579 AATTTCTCGTGGAGAGAAGCCAATCTTTCAGCGTTATCTTCCTTGACTTTTTCGTGAAGAGAAGT
64 ACTTTCTCGTGAAGAGAAGCCAATATTTAAGCATTATCTAACTTGACTTTTTAGTGAAAAGAAGT
* * *
58644 CAATCTTTAGTGATGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAACCT
129 CAATCTTTAGTGATGTCATTCTTAACTTTCTCATAAAGAGAAGTCAACCT
* * ** * * * * *
58694 TTTAGTGGTGTT-ATTCTTGACTTTTTCGTGGAA-AGTAGTCAACCTTTTAATGATGTCACTCTT
1 TTTAGT-GTTTTCATTCTTGACTTTCTC-AAGAAGAGAAATCAACCTTTTAGTGAT-TGATTCTT
* * *
58757 GACTTTCTCGTGAAGAGAAGTCAATATTTAAGTATTATC-AACTTGACTTTTTATTGAAAAGAAG
63 GACTTTCTCGTGAAGAGAAGCCAATATTTAAGCATTATCTAACTTGACTTTTTAGTGAAAAGAAG
* * *
58821 TCAATCTTTTAGTGTTGTC-TTCCTTAACTTTCTCATAAAGAGGAGTCAATCT
128 TCAATC-TTTAGTGATGTCATT-CTTAACTTTCTCATAAAGAGAAGTCAACCT
* * * *
58873 TTTAGTGTTTTCATTCTTGACTTTCTCAAAAAGAGAAATCAATCTTTCAGTGTTATGATTCTTGA
1 TTTAGTGTTTTCATTCTTGACTTTCTCAAGAAGAGAAATCAACCTTTTAGTGAT-TGATTCTTGA
58938 CTTTCTC
65 CTTTCTC
58945 AAAAAGTGGA
Statistics
Matches: 197, Mismatches: 46, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
177 1 0.01
178 36 0.18
179 156 0.79
180 4 0.02
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.41
Consensus pattern (178 bp):
TTTAGTGTTTTCATTCTTGACTTTCTCAAGAAGAGAAATCAACCTTTTAGTGATTGATTCTTGAC
TTTCTCGTGAAGAGAAGCCAATATTTAAGCATTATCTAACTTGACTTTTTAGTGAAAAGAAGTCA
ATCTTTAGTGATGTCATTCTTAACTTTCTCATAAAGAGAAGTCAACCT
Found at i:58945 original size:45 final size:44
Alignment explanation
Indices: 58591--58969 Score: 205
Period size: 45 Copynumber: 8.5 Consensus size: 44
58581 TTTCTCGTGG
* * * * * ***
58591 AGAGAAGCCAATCTTTCAGCGTTATCTTCCTTGACTTTTTCGTGA
1 AGAGAAGTCAATCTTTTAGTGTTATATT-CTTGACTTTCTCAAAA
* * ***
58636 AGAGAAGTCAATC-TTTAGTGATGTCATTCTTGACTTTCTCGTGA
1 AGAGAAGTCAATCTTTTAGTGTTAT-ATTCTTGACTTTCTCAAAA
* * ***
58680 AGAGAAGTCAACCTTTTAGTGGTGT-TATTCTTGACTTTTTCGTGGA
1 AGAGAAGTCAATCTTTTAGT-GT-TATATTCTTGACTTTCTC-AAAA
* * * * * * ***
58726 A-AGTAGTCAACCTTTTAATGATGTCACTCTTGACTTTCTCGTGA
1 AGAGAAGTCAATCTTTTAGTGTTAT-ATTCTTGACTTTCTCAAAA
* * * * * *
58770 AGAGAAGTCAATATTTAAGTATTATCA-ACTTGACTTT-TTATTGAA
1 AGAGAAGTCAATCTTTTAGTGTTAT-ATTCTTGACTTTCTCA--AAA
* * * *
58815 A-AGAAGTCAATCTTTTAGTGTTGTCTTCCTTAACTTTCTCATAA
1 AGAGAAGTCAATCTTTTAGTGTTATATT-CTTGACTTTCTCAAAA
* *
58859 AGAGGAGTCAATCTTTTAGTGTTTTCATTCTTGACTTTCTCAAAA
1 AGAGAAGTCAATCTTTTAGTGTTAT-ATTCTTGACTTTCTCAAAA
* *
58904 AGAGAAATCAATCTTTCAGTGTTATGATTCTTGACTTTCTCAAAA
1 AGAGAAGTCAATCTTTTAGTGTTAT-ATTCTTGACTTTCTCAAAA
* *
58949 AGTGGAGTCAA-CATTTTAGTG
1 AGAGAAGTCAATC-TTTTAGTG
58970 ATGTCATTAT
Statistics
Matches: 263, Mismatches: 55, Indels: 32
0.75 0.16 0.09
Matches are distributed among these distances:
43 2 0.01
44 71 0.27
45 180 0.68
46 9 0.03
47 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (44 bp):
AGAGAAGTCAATCTTTTAGTGTTATATTCTTGACTTTCTCAAAA
Found at i:59009 original size:50 final size:50
Alignment explanation
Indices: 58952--59065 Score: 128
Period size: 49 Copynumber: 2.3 Consensus size: 50
58942 CTCAAAAAGT
* * * * *
58952 GGAGTCAACATTTT-AGT-GATGTCATTATCAATTTGACTTTCTCGTGGAGA
1 GGAGTCAACATTTTCAATAGATGCCATTATCAACTTGACTTGCAC--GGAGA
*
59002 GGAGTCAAC-TTTTCAATAGATGCCATTCTCAACTTGACTTGCACGGAGA
1 GGAGTCAACATTTTCAATAGATGCCATTATCAACTTGACTTGCACGGAGA
59051 GGAGTCAA-ATTTTCA
1 GGAGTCAACATTTTCA
59066 GTAGTATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
49 23 0.42
50 11 0.20
51 21 0.38
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (50 bp):
GGAGTCAACATTTTCAATAGATGCCATTATCAACTTGACTTGCACGGAGA
Found at i:59788 original size:55 final size:55
Alignment explanation
Indices: 59695--60301 Score: 720
Period size: 55 Copynumber: 11.1 Consensus size: 55
59685 AAATGGATCA
* * * **
59695 AAAGATTTTTTGAGTCTTATATCCCTGAAAGAATAGTGGAGCAGATTCGTCTTCC
1 AAAGATTTTTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCC
* * *
59750 AAATATTTTTCAAGTCTTATCGCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCC
1 AAAGATTTTTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCC
** * * * *
59805 AAAGATTTTTTTAGTCTTATCTCCCAGAAAGAATAGTGGAGCAGACTCATCTTCC
1 AAAGATTTTTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCC
* *
59860 AAATATTTTT-GAGTCTTATC-CCTCCGAAAGAAGAGTGGAGCAGACCCGTCTTCC
1 AAAGATTTTTCGAGTCTTATCTCC-CTGAAAGAAGAGTGGAGCAGACCCGTCTTCC
* * *
59914 AAAGATTTTTCGAGTCTTATCTCCCTGAAAGAATAGTGGAGAAGACCTGTCTTCC
1 AAAGATTTTTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCC
* *
59969 AAAGATTTTTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTATTCC
1 AAAGATTTTTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCC
* * * *
60024 AGAGATTTTTCAATTCTTATCTCCCTGAAAGAAGAGTGGAGCATACCCGTCTTCC
1 AAAGATTTTTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCC
* * * * * **
60079 AAAGATATTTT-GGGTCTTATCTTCCTAAAAGAAGTGTGGAGCAGGCCCAACTTCC
1 AAAGAT-TTTTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCC
* * * * * **
60134 AAATATTTTTTGAGTATAATCTCCCTGAAAGAAGAGT-GAGCATACCCGTCTTTT
1 AAAGATTTTTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCC
* * * ** *
60188 AAAGATTTTTCGAGTCTTATCTCCCTGGAAGAATAGTGAAGCAGACCTATTTTCC
1 AAAGATTTTTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCC
* *
60243 AAAGATTTCTT-GAGTCTTATCTCCCCTGAAAAAAGAGTGGAGTAGACCCGTCTTCC
1 AAAGATTT-TTCGAGTCTTATCT-CCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCC
60299 AAA
1 AAA
60302 ATTGATCTGA
Statistics
Matches: 461, Mismatches: 83, Indels: 15
0.82 0.15 0.03
Matches are distributed among these distances:
53 2 0.00
54 91 0.20
55 332 0.72
56 36 0.08
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (55 bp):
AAAGATTTTTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCC
Found at i:60184 original size:274 final size:274
Alignment explanation
Indices: 59695--60301 Score: 862
Period size: 274 Copynumber: 2.2 Consensus size: 274
59685 AAATGGATCA
* * ** *
59695 AAAGATTTTTTGAGTCTTATATCCCTGAAAGAATAGTGGAGCAGATTCGTCTTCCAAATATTTTT
1 AAAGATTTTTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTT
* *
59760 CAAGTCTTATCGCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTTTAGTCTTAT
66 CAAGTCTTATCGCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATATTTTGAGTCTTAT
* * * *
59825 CTCCCAGAAAGAATAGTGGAGCAGACTCATCTTCCAAATATTTTTGAGTCTTATCCCTCCGAAAG
131 CTCCCAGAAAGAATAGTGGAGCAGACCCAACTTCCAAATATTTTTGAGTATAATCCCTCCGAAAG
*
59890 AAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCGAGTCTTATCTCCCTGAAAGAATAGTGGAG
196 AAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCGAGTCTTATCTCCCTGAAAGAATAGTGAAG
*
59955 AAGACCTGTCTTCC
261 AAGACCTATCTTCC
* *
59969 AAAGATTTTTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTATTCCAGAGATTTTT
1 AAAGATTTTTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTT
* * * *
60034 CAATTCTTATCTCCCTGAAAGAAGAGTGGAGCATACCCGTCTTCCAAAGATATTTTGGGTCTTAT
66 CAAGTCTTATCGCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATATTTTGAGTCTTAT
* * *
60099 CTTCCTA-AAAGAAGT-GTGGAGCAGGCCCAACTTCCAAATATTTTTTGAGTATAATCTCC-CTG
131 C-TCCCAGAAAGAA-TAGTGGAGCAGACCCAACTTCCAAATA-TTTTTGAGTATAATC-CCTCCG
* ** *
60161 AAAGAAGAGT-GAGCATACCCGTCTTTTAAAGATTTTTCGAGTCTTATCTCCCTGGAAGAATAGT
192 AAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCGAGTCTTATCTCCCTGAAAGAATAGT
* *
60225 GAAGCAGACCTATTTTCC
257 GAAGAAGACCTATCTTCC
* * *
60243 AAAGATTTCTTGAGTCTTATCTCCCCTGAAAAAAGAGTGGAGTAGACCCGTCTTCCAAA
1 AAAGATTTTTTGAGTCTTATCT-CCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAA
60302 ATTGATCTGA
Statistics
Matches: 295, Mismatches: 33, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
274 231 0.78
275 62 0.21
276 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (274 bp):
AAAGATTTTTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTT
CAAGTCTTATCGCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATATTTTGAGTCTTAT
CTCCCAGAAAGAATAGTGGAGCAGACCCAACTTCCAAATATTTTTGAGTATAATCCCTCCGAAAG
AAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTCGAGTCTTATCTCCCTGAAAGAATAGTGAAG
AAGACCTATCTTCC
Found at i:63480 original size:10 final size:10
Alignment explanation
Indices: 63465--63502 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
63455 AGCTTTAACC
63465 ACCGCCTTGA
1 ACCGCCTTGA
63475 ACCGCCTTGA
1 ACCGCCTTGA
*
63485 ATCGCCTTGA
1 ACCGCCTTGA
*
63495 ATCGCCTT
1 ACCGCCTT
63503 TGCAAGCTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.18, C:0.37, G:0.18, T:0.26
Consensus pattern (10 bp):
ACCGCCTTGA
Done.