Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004022.1 Hibiscus syriacus cultivar Beakdansim tig00008783_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: 155348
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1238 original size:8 final size:8
Alignment explanation
Indices: 1211--1241 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1201 ACATACGCAT
1211 ATGTATGC
1 ATGTATGC
*
1219 ATGCATGC
1 ATGTATGC
1227 ATGTATGC
1 ATGTATGC
1235 ATGTATG
1 ATGTATG
1242 TTATAATGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (8 bp):
ATGTATGC
Found at i:9114 original size:22 final size:22
Alignment explanation
Indices: 9074--9115 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
9064 TAATCTTGAC
*
9074 AAAAATAGAAAGGCCACAAATA
1 AAAAATAGAAAGGCAACAAATA
9096 AAAAATAGTAAA-GCAACAAA
1 AAAAATAG-AAAGGCAACAAA
9116 GCAGAAGGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.67, C:0.12, G:0.12, T:0.10
Consensus pattern (22 bp):
AAAAATAGAAAGGCAACAAATA
Found at i:10068 original size:99 final size:99
Alignment explanation
Indices: 9897--10099 Score: 397
Period size: 99 Copynumber: 2.1 Consensus size: 99
9887 CCAAATCTTA
9897 CAAAAACAGGTCACAAGAAGCTAGTTGCAGTTGACATAAAAACACTCTAGTATGAGTGGTTTTGG
1 CAAAAACAGGTCACAAGAAGCTAGTTGCAGTTGACATAAAAACACTCTAGTATGAGTGGTTTTGG
9962 TCAATATATTTGGCACATGATTTTTCTTCAAGCT
66 TCAATATATTTGGCACATGATTTTTCTTCAAGCT
9996 CAAAAACAGGTCACAAGAAGCTAGTTGCAGTTGACATAAAAACACTCTAGTATGAGTGGTTTTGG
1 CAAAAACAGGTCACAAGAAGCTAGTTGCAGTTGACATAAAAACACTCTAGTATGAGTGGTTTTGG
*
10061 TCAATATATTTGGTACATGATTTTTCTTCAAGCT
66 TCAATATATTTGGCACATGATTTTTCTTCAAGCT
10095 CAAAA
1 CAAAA
10100 CTCCAATTAA
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 103 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (99 bp):
CAAAAACAGGTCACAAGAAGCTAGTTGCAGTTGACATAAAAACACTCTAGTATGAGTGGTTTTGG
TCAATATATTTGGCACATGATTTTTCTTCAAGCT
Found at i:12434 original size:22 final size:22
Alignment explanation
Indices: 12408--12451 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12398 TTCGTGAACG
*
12408 CTAAACGAATATTAAATAAACA
1 CTAAACGAACATTAAATAAACA
* *
12430 CTAAACGAGCATTAAATGAACA
1 CTAAACGAACATTAAATAAACA
12452 TGTTCATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.16, G:0.09, T:0.20
Consensus pattern (22 bp):
CTAAACGAACATTAAATAAACA
Found at i:12518 original size:23 final size:23
Alignment explanation
Indices: 12492--12538 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
12482 GATCATATAC
*
12492 ACGAACACATTCGCGAACATTAA
1 ACGAACACATTCGCGAACAATAA
***
12515 ACGAACGTGTTCGCGAACAATAA
1 ACGAACACATTCGCGAACAATAA
12538 A
1 A
12539 TAAACGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (23 bp):
ACGAACACATTCGCGAACAATAA
Found at i:12544 original size:23 final size:23
Alignment explanation
Indices: 12501--12544 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12491 CACGAACACA
* *
12501 TTCGCGAACATTAAACGAACGTG
1 TTCGCGAACAATAAACAAACGTG
*
12524 TTCGCGAACAATAAATAAACG
1 TTCGCGAACAATAAACAAACG
12545 AAAACGAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.20
Consensus pattern (23 bp):
TTCGCGAACAATAAACAAACGTG
Found at i:21848 original size:20 final size:19
Alignment explanation
Indices: 21808--21869 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
21798 CTGGAAAACT
* *
21808 GGTTTAACCGGTTTTGAACC
1 GGTTTGACCGG-TTAGAACC
*
21828 GATTTTGACCGGTTAGAACC
1 G-GTTTGACCGGTTAGAACC
21848 GGTTTGACCGGTCT-GAACC
1 GGTTTGACCGGT-TAGAACC
21867 GGT
1 GGT
21870 CCGACCCGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 18 0.50
20 10 0.28
21 8 0.22
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (19 bp):
GGTTTGACCGGTTAGAACC
Found at i:21859 original size:9 final size:10
Alignment explanation
Indices: 21808--21869 Score: 58
Period size: 10 Copynumber: 6.3 Consensus size: 10
21798 CTGGAAAACT
21808 GGTTT-AACC
1 GGTTTGAACC
21817 GGTTTTGAACC
1 GG-TTTGAACC
*
21828 GATTTTG-ACC
1 G-GTTTGAACC
*
21838 GGTTAGAACC
1 GGTTTGAACC
21848 GGTTTG-ACC
1 GGTTTGAACC
*
21857 GGTCTGAACC
1 GGTTTGAACC
21867 GGT
1 GGT
21870 CCGACCCGAC
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
9 13 0.30
10 21 0.49
11 9 0.21
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (10 bp):
GGTTTGAACC
Found at i:21875 original size:19 final size:19
Alignment explanation
Indices: 21834--21875 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
21824 AACCGATTTT
**
21834 GACCGGTTAGAACCGGTTT
1 GACCGGTTAGAACCGGTCC
21853 GACCGGTCT-GAACCGGTCC
1 GACCGGT-TAGAACCGGTCC
21872 GACC
1 GACC
21876 CGACCCGACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.19, C:0.31, G:0.31, T:0.19
Consensus pattern (19 bp):
GACCGGTTAGAACCGGTCC
Found at i:21880 original size:5 final size:5
Alignment explanation
Indices: 21870--21912 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
21860 CTGAACCGGT
* *
21870 CCGAC CCGAC CCGAC CCGAC CGTTGAC CTGAC CCGAC CCGAC C
1 CCGAC CCGAC CCGAC CCGAC C--CGAC CCGAC CCGAC CCGAC C
21913 GTTGACCTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 30 0.88
7 4 0.12
ACGTcount: A:0.19, C:0.53, G:0.21, T:0.07
Consensus pattern (5 bp):
CCGAC
Found at i:21902 original size:22 final size:22
Alignment explanation
Indices: 21872--21920 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
21862 GAACCGGTCC
*
21872 GACCCGACCCGACCCGACCGTT
1 GACCTGACCCGACCCGACCGTT
21894 GACCTGACCCGACCCGACCGTT
1 GACCTGACCCGACCCGACCGTT
21916 GACCT
1 GACCT
21921 CCTTTGACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.12
Consensus pattern (22 bp):
GACCTGACCCGACCCGACCGTT
Found at i:28398 original size:20 final size:20
Alignment explanation
Indices: 28354--28395 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
28344 AAAAGCATCC
* *
28354 CCAACGGCTCCAAATAATTT
1 CCAACGGCTACAAACAATTT
28374 CCAACGGCTACAAACACATTT
1 CCAACGGCTACAAACA-ATTT
28395 C
1 C
28396 AACTTATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.21
Consensus pattern (20 bp):
CCAACGGCTACAAACAATTT
Found at i:28813 original size:36 final size:36
Alignment explanation
Indices: 28742--28814 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
28732 GTTAGAAAAT
*
28742 ATTTATATATTTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
*
28778 ATTTATATAATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATT-AAAATCATAAA
28814 A
1 A
28815 AAGGTTTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 24 0.73
37 9 0.27
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
Found at i:30364 original size:32 final size:32
Alignment explanation
Indices: 30323--30386 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
30313 TTCATCATGG
* *
30323 ATAACCTTTAAGACTTCTTCATCTACTTTATT
1 ATAACCTTTAAGACTTCTTCATCAACTCTATT
30355 ATAACCTTTAAGACTTCTTCATCAACTCTATT
1 ATAACCTTTAAGACTTCTTCATCAACTCTATT
30387 GCAGAAGTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.44
Consensus pattern (32 bp):
ATAACCTTTAAGACTTCTTCATCAACTCTATT
Found at i:44418 original size:7 final size:7
Alignment explanation
Indices: 44406--44461 Score: 112
Period size: 7 Copynumber: 8.0 Consensus size: 7
44396 ACCAGAGGGC
44406 ATGAAGA
1 ATGAAGA
44413 ATGAAGA
1 ATGAAGA
44420 ATGAAGA
1 ATGAAGA
44427 ATGAAGA
1 ATGAAGA
44434 ATGAAGA
1 ATGAAGA
44441 ATGAAGA
1 ATGAAGA
44448 ATGAAGA
1 ATGAAGA
44455 ATGAAGA
1 ATGAAGA
44462 CTGGGCTCTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (7 bp):
ATGAAGA
Found at i:47833 original size:23 final size:23
Alignment explanation
Indices: 47806--47879 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
47796 CATCTCGTAT
*
47806 AAATGCACCGAAGTGCCGCATAA
1 AAATGCACCGAAGTGCCACATAA
* * *
47829 AAATGCACCGTAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACATAA
* * *
47852 AATTGCATCGAAGTGCCATATAA
1 AAATGCACCGAAGTGCCACATAA
*
47875 TAATG
1 AAATG
47880 TCCATAAGGA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAA
Found at i:52938 original size:23 final size:23
Alignment explanation
Indices: 52912--52977 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
52902 CACCACAGCT
* *
52912 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
52935 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
52958 CGTAGAATTACACCGAAGTG
1 CGTAGAAATGCACCGAAGTG
52978 TCATATAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:57440 original size:21 final size:21
Alignment explanation
Indices: 57414--57460 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
57404 TAAATTGACA
57414 GTCGTTGTTTAAATCACATGT
1 GTCGTTGTTTAAATCACATGT
57435 GTCGTTGTTTAAATCACATGT
1 GTCGTTGTTTAAATCACATGT
57456 GTCGT
1 GTCGT
57461 CATTATCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.43
Consensus pattern (21 bp):
GTCGTTGTTTAAATCACATGT
Found at i:58005 original size:2 final size:2
Alignment explanation
Indices: 57998--58029 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
57988 AGTTACCCTA
57998 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
58030 GTATGTATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67132 original size:2 final size:2
Alignment explanation
Indices: 67127--67163 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
67117 TATTCGTGTG
67127 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
67164 GAAATAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:67602 original size:51 final size:51
Alignment explanation
Indices: 67526--67630 Score: 174
Period size: 51 Copynumber: 2.1 Consensus size: 51
67516 TTCAAGTCGG
* * * *
67526 ATAGAATTTCACTAAATCTAGATTGATTCTAGTGATGGGTAGAGAAATGCT
1 ATAGAATTTCACTAAATCTAGATTGAATCGAGTAATGGGTAAAGAAATGCT
67577 ATAGAATTTCACTAAATCTAGATTGAATCGAGTAATGGGTAAAGAAATGCT
1 ATAGAATTTCACTAAATCTAGATTGAATCGAGTAATGGGTAAAGAAATGCT
67628 ATA
1 ATA
67631 TTCAGCTCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (51 bp):
ATAGAATTTCACTAAATCTAGATTGAATCGAGTAATGGGTAAAGAAATGCT
Found at i:72174 original size:21 final size:22
Alignment explanation
Indices: 72147--72197 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
72137 TGAATTGTAA
*
72147 ATTATTTTTAC-ATTATCA-GC
1 ATTATTTTCACAATTATCAGGC
*
72167 ATATATTTTCACAATTATTAGGC
1 AT-TATTTTCACAATTATCAGGC
72190 ATTATTTT
1 ATTATTTT
72198 ATATTATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 2 0.08
21 8 0.31
22 12 0.46
23 4 0.15
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (22 bp):
ATTATTTTCACAATTATCAGGC
Found at i:72635 original size:21 final size:21
Alignment explanation
Indices: 72609--72654 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
72599 ATTATATTGG
72609 GTTTAGGGTTTAGAATTTAGA
1 GTTTAGGGTTTAGAATTTAGA
72630 GTTTAGGGTTTAGAATTTAGA
1 GTTTAGGGTTTAGAATTTAGA
72651 GTTT
1 GTTT
72655 GTTCAAGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (21 bp):
GTTTAGGGTTTAGAATTTAGA
Found at i:97495 original size:71 final size:70
Alignment explanation
Indices: 97413--97558 Score: 231
Period size: 71 Copynumber: 2.1 Consensus size: 70
97403 TGTTAATTTA
* * *
97413 TTTATATATAAATAAAATTGATTCTGTCAATCATATAATTAAA-TCTTAATTTTGTATTCAATTA
1 TTTATAAATAAATAAAATTGATTCTATCAATCATATAATTAAACT-TTAATTTTATATTCAATTA
97477 TGTCAT
65 TGTCAT
*
97483 TCTTATAAATAAATAAAATTGATTCTATCAATTATATAATTAAACTTTAATTTTATATTCAATTA
1 T-TTATAAATAAATAAAATTGATTCTATCAATCATATAATTAAACTTTAATTTTATATTCAATTA
97548 TGTCAT
65 TGTCAT
97554 TTTAT
1 TTTAT
97559 TGTTAAATCA
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
70 5 0.07
71 64 0.91
72 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (70 bp):
TTTATAAATAAATAAAATTGATTCTATCAATCATATAATTAAACTTTAATTTTATATTCAATTAT
GTCAT
Found at i:97863 original size:6 final size:6
Alignment explanation
Indices: 97843--97875 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
97833 TACGTGTGCG
97843 TTTT-A TTTTAA -TTTAA TTTTAA TTTTAA TTTTA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
97876 TAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 9 0.35
6 17 0.65
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:97936 original size:20 final size:20
Alignment explanation
Indices: 97911--97953 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
97901 CTCGTTTTTC
97911 ATTTTATAATCCGGCGGCTA
1 ATTTTATAATCCGGCGGCTA
**
97931 ATTTTATTTTCCGGCGGCTA
1 ATTTTATAATCCGGCGGCTA
97951 ATT
1 ATT
97954 GCATATACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (20 bp):
ATTTTATAATCCGGCGGCTA
Found at i:98334 original size:13 final size:13
Alignment explanation
Indices: 98316--98340 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
98306 TTTTTCAAAT
98316 AAATTATTTTTTC
1 AAATTATTTTTTC
98329 AAATTATTTTTT
1 AAATTATTTTTT
98341 AATTTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
AAATTATTTTTTC
Found at i:100999 original size:23 final size:23
Alignment explanation
Indices: 100944--100999 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
100934 CGTATAATTG
* *
100944 CACCGAAGTGCCACGTAGAATTA
1 CACCGAAGTGACACGTAGAAATA
* *
100967 TACC-ATAGTGACGCGTAGAAATA
1 CACCGA-AGTGACACGTAGAAATA
100990 CACCGAAGTG
1 CACCGAAGTG
101000 TCATATAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
22 1 0.04
23 24 0.92
24 1 0.04
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (23 bp):
CACCGAAGTGACACGTAGAAATA
Found at i:102656 original size:63 final size:62
Alignment explanation
Indices: 102541--102664 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 62
102531 ATCCTCAGTA
* * *
102541 ACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCGAAGAACATAGGTAAACTATCCATATGTTCCGTAGAACATAGGTAT
* *
102603 ACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTATCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTATCCATATGTTCCGTAGAACATAGGTA
102665 AACCCTCGAC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
61 1 0.02
62 24 0.44
63 30 0.55
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCGAAGAACATAGGTAAACTATCCATATGTTCCGTAGAACATAGGTAT
Found at i:102660 original size:32 final size:31
Alignment explanation
Indices: 102540--102667 Score: 143
Period size: 31 Copynumber: 4.1 Consensus size: 31
102530 GATCCTCAGT
* * * *
102540 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
102571 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
102602 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
*
102634 AACTATCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
102665 AAC
1 AAC
102668 CCTCGACTCT
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.63
32 22 0.27
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:104055 original size:21 final size:21
Alignment explanation
Indices: 104031--104075 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
104021 TTTTGTTCGT
* *
104031 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
104052 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
104073 TTG
1 TTG
104076 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:110677 original size:20 final size:21
Alignment explanation
Indices: 110640--110683 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
110630 ATTAAATTTG
110640 ATACAAATATATC-ATTTTAA
1 ATACAAATATATCTATTTTAA
*
110660 ATAC-AATATATACTTTTTTAA
1 ATACAAATATAT-CTATTTTAA
110681 ATA
1 ATA
110684 ATTTTAGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (21 bp):
ATACAAATATATCTATTTTAA
Found at i:120092 original size:5 final size:5
Alignment explanation
Indices: 120082--120150 Score: 57
Period size: 5 Copynumber: 12.0 Consensus size: 5
120072 ACCGGTCACA
120082 ACCCG ACCCG ACCCGTTG ACCCG ACCCG ACCCG TTTACCCG ACCCG ACCCGTTG
1 ACCCG ACCCG ACCC---G ACCCG ACCCG ACCCG ---ACCCG ACCCG ACCC---G
120136 ACCCG ACCCG ACCCG
1 ACCCG ACCCG ACCCG
120151 TTGACCGTTG
Statistics
Matches: 55, Mismatches: 0, Indels: 18
0.75 0.00 0.25
Matches are distributed among these distances:
5 40 0.73
8 15 0.27
ACGTcount: A:0.17, C:0.52, G:0.20, T:0.10
Consensus pattern (5 bp):
ACCCG
Found at i:120105 original size:18 final size:18
Alignment explanation
Indices: 120082--120156 Score: 141
Period size: 18 Copynumber: 4.2 Consensus size: 18
120072 ACCGGTCACA
120082 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
120100 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
120118 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
120136 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
120154 ACC
1 ACC
120157 GTTGACCGTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.17, C:0.51, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:122659 original size:48 final size:48
Alignment explanation
Indices: 122607--122738 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
122597 AATATTTTAC
*
122607 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
122655 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
122703 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
122739 CTGATTTATA
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:122745 original size:24 final size:24
Alignment explanation
Indices: 122624--122738 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
122614 TCGATTTGAT
122624 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
122648 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
122672 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
122696 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
122719 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
122739 CTGATTTATA
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:122755 original size:24 final size:24
Alignment explanation
Indices: 122675--122747 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
122665 ACATGGATTC
* * *
122675 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
122699 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
122723 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
122747 T
1 T
122748 ATTTTGATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:124919 original size:5 final size:5
Alignment explanation
Indices: 124909--124977 Score: 57
Period size: 5 Copynumber: 12.0 Consensus size: 5
124899 ACCGGTCACA
124909 ACCCG ACCCG ACCCGTTG ACCCG ACCCG ACCCG TTTACCCG ACCCG ACCCGTTG
1 ACCCG ACCCG ACCC---G ACCCG ACCCG ACCCG ---ACCCG ACCCG ACCC---G
124963 ACCCG ACCCG ACCCG
1 ACCCG ACCCG ACCCG
124978 TTGACCGTTG
Statistics
Matches: 55, Mismatches: 0, Indels: 18
0.75 0.00 0.25
Matches are distributed among these distances:
5 40 0.73
8 15 0.27
ACGTcount: A:0.17, C:0.52, G:0.20, T:0.10
Consensus pattern (5 bp):
ACCCG
Found at i:124932 original size:18 final size:18
Alignment explanation
Indices: 124909--124983 Score: 141
Period size: 18 Copynumber: 4.2 Consensus size: 18
124899 ACCGGTCACA
124909 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
124927 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
124945 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
124963 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
124981 ACC
1 ACC
124984 GTTGACCCGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.17, C:0.51, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:124987 original size:7 final size:7
Alignment explanation
Indices: 124975--125021 Score: 76
Period size: 7 Copynumber: 6.4 Consensus size: 7
124965 CCGACCCGAC
124975 CCGTTGA
1 CCGTTGA
124982 CCGTTGA
1 CCGTTGA
124989 CCCGTTGA
1 -CCGTTGA
124997 CCGTTGA
1 CCGTTGA
125004 CCCGTTGA
1 -CCGTTGA
125012 CCGTTGA
1 CCGTTGA
125019 CCG
1 CCG
125022 GAGTTGACCA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 24 0.63
8 14 0.37
ACGTcount: A:0.13, C:0.34, G:0.28, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:124992 original size:15 final size:15
Alignment explanation
Indices: 124972--125020 Score: 98
Period size: 15 Copynumber: 3.3 Consensus size: 15
124962 GACCCGACCC
124972 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
124987 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
125002 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
125017 GACC
1 GACC
125021 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:125003 original size:22 final size:22
Alignment explanation
Indices: 124976--125021 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
124966 CGACCCGACC
124976 CGTTGACCGTTGACCCGTTGAC
1 CGTTGACCGTTGACCCGTTGAC
124998 CGTTGACCCGTTGA-CCGTTGAC
1 CGTTGA-CCGTTGACCCGTTGAC
125020 CG
1 CG
125022 GAGTTGACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.13, C:0.33, G:0.28, T:0.26
Consensus pattern (22 bp):
CGTTGACCGTTGACCCGTTGAC
Found at i:127509 original size:48 final size:48
Alignment explanation
Indices: 127457--127588 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
127447 AATATTTTAC
*
127457 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
127505 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
127553 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
127589 CTGATTTATA
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:127595 original size:24 final size:24
Alignment explanation
Indices: 127474--127588 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
127464 TCGATTTGAT
127474 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
127498 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
127522 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
127546 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
127569 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
127589 CTGATTTATA
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:127605 original size:24 final size:24
Alignment explanation
Indices: 127525--127597 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
127515 ACATGGATTC
* * *
127525 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
127549 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
127573 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
127597 T
1 T
127598 ATTTTGATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:136374 original size:4 final size:4
Alignment explanation
Indices: 136367--136427 Score: 56
Period size: 4 Copynumber: 16.0 Consensus size: 4
136357 CCCATACATA
* * * * *
136367 ATGT ATGT ATGT ATAT ATGT ATGC GTGT GTGT ATGT AAGT A--T ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
136413 ATGT AT-T ATGT ATGT
1 ATGT ATGT ATGT ATGT
136428 GTTAGTTCAA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
2 2 0.04
3 3 0.06
4 42 0.89
ACGTcount: A:0.26, C:0.02, G:0.25, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:151374 original size:15 final size:15
Alignment explanation
Indices: 151354--151384 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
151344 TAGCTTGTTC
151354 ATGTTCGTTCAATTA
1 ATGTTCGTTCAATTA
151369 ATGTTCGTTCAATTA
1 ATGTTCGTTCAATTA
151384 A
1 A
151385 ATGATAAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (15 bp):
ATGTTCGTTCAATTA
Found at i:151403 original size:10 final size:10
Alignment explanation
Indices: 151388--151516 Score: 61
Period size: 10 Copynumber: 12.5 Consensus size: 10
151378 CAATTAAATG
151388 ATAAACGAAC
1 ATAAACGAAC
151398 ATAAACGAAC
1 ATAAACGAAC
151408 GGATGTAAACGAAC
1 --A--TAAACGAAC
151422 ATAAACGAAC
1 ATAAACGAAC
* *
151432 AAAATATACGAAT
1 ---ATAAACGAAC
*
151445 GTAAACGAAC
1 ATAAACGAAC
*
151455 ACAAACGAAC
1 ATAAACGAAC
*
151465 --GAACGTAA-
1 ATAAACG-AAC
*
151473 ATAGAC--AC
1 ATAAACGAAC
*
151481 AATAAATGAAC
1 -ATAAACGAAC
151492 ATAAACGAAC
1 ATAAACGAAC
* *
151502 GTAAACTAAC
1 ATAAACGAAC
151512 ATAAA
1 ATAAA
151517 TGAAAAAATA
Statistics
Matches: 89, Mismatches: 16, Indels: 28
0.67 0.12 0.21
Matches are distributed among these distances:
7 1 0.01
8 4 0.04
9 6 0.07
10 57 0.64
11 2 0.02
12 2 0.02
13 8 0.09
14 9 0.10
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:151452 original size:33 final size:34
Alignment explanation
Indices: 151388--151464 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 34
151378 CAATTAAATG
*
151388 ATAAACGAACATAAACGAACGGATGTAAACGAAC
1 ATAAACGAACATAAACGAACGAATGTAAACGAAC
*
151422 ATAAACGAACA-AAA-TATACGAATGTAAACGAAC
1 ATAAACGAACATAAACGA-ACGAATGTAAACGAAC
*
151455 ACAAACGAAC
1 ATAAACGAAC
151465 GAACGTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 27 0.69
34 11 0.28
ACGTcount: A:0.56, C:0.18, G:0.14, T:0.12
Consensus pattern (34 bp):
ATAAACGAACATAAACGAACGAATGTAAACGAAC
Found at i:152370 original size:2 final size:2
Alignment explanation
Indices: 152363--152405 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
152353 ATCCGACCTA
*
152363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
152405 A
1 A
152406 ATTACAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:153789 original size:168 final size:168
Alignment explanation
Indices: 153553--153891 Score: 494
Period size: 168 Copynumber: 2.0 Consensus size: 168
153543 AAATTAAATG
*
153553 TTTTTAATTAAAAAAAAGTTTATAATTAATTTAAAAATATAATTATAAAATAAAAATTTCAGATA
1 TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAAAATATAATTATAAAATAAAAATTTCAGATA
*
153618 ATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAATTATTATTGGGTT
66 ATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT--ATC-T-ATTATTATTGGATT
* *
153683 TT-AATGGTTTGGGTTTAGCCCATATGTTATATATATATATATA
127 TTAAATGGTTTGGGTTGAGCCC-TATGTTATATA-ATATATAAA
* * *
153726 TTTTTAATT-AAAAAAA-TTTACAATTAATTT-AATATA-ATATTAT-AAA-AAAAATTTTATAT
1 TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAAAATATA-ATTATAAAATAAAAATTTCAGAT
*
153785 AATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTATCTCTTATTATTGGATTTTA
65 AATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTATCTATTATTATTGGATTTTA
153850 AATGGTTTGGGTTGAGCCCTATGTTATATAATATATAAA
130 AATGGTTTGGGTTGAGCCCTATGTTATATAATATATAAA
153889 TTT
1 TTT
153892 AAATTTAATT
Statistics
Matches: 156, Mismatches: 8, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
163 11 0.07
164 25 0.16
165 19 0.12
166 3 0.02
168 55 0.35
169 4 0.03
170 10 0.06
171 13 0.08
172 7 0.04
173 9 0.06
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (168 bp):
TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAAAATATAATTATAAAATAAAAATTTCAGATA
ATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTATCTATTATTATTGGATTTTAA
ATGGTTTGGGTTGAGCCCTATGTTATATAATATATAAA
Done.