Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000730.1 Hibiscus syriacus cultivar Beakdansim tig00001417_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: 139936
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1334 original size:2 final size:2
Alignment explanation
Indices: 1327--1352 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1317 CATATTACAC
1327 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
1353 TACATATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2096 original size:17 final size:17
Alignment explanation
Indices: 2074--2114 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
2064 ATGTCGCTTA
*
2074 ACTTATTTTGTTCTTTC
1 ACTTATTTTGCTCTTTC
2091 ACTTATTTTGCTCTTTC
1 ACTTATTTTGCTCTTTC
2108 ACTTATT
1 ACTTATT
2115 CATATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.15, C:0.20, G:0.05, T:0.61
Consensus pattern (17 bp):
ACTTATTTTGCTCTTTC
Found at i:3216 original size:63 final size:63
Alignment explanation
Indices: 3086--3217 Score: 140
Period size: 63 Copynumber: 2.1 Consensus size: 63
3076 CCCTTAACGT
* * * * * *
3086 GTGCATCGATGCACTATTTATGTATTGGTACACAAATCCCATTCGATGTTTGTATTTTAGTGG
1 GTGCATCGATGCACTATTTATGCATCGATACACAAATCCCATTCGATGTTTATATTTTAGAGA
* * * ** *
3149 GTGCATCGATGCACTCTTTATGCATCGATGCACTAATTGCATTCGATGTTTAT-TTATTTGAGA
1 GTGCATCGATGCACTATTTATGCATCGATACACAAATCCCATTCGATGTTTATATT-TTAGAGA
3212 GTGCAT
1 GTGCAT
3218 TGGTACACAT
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
62 2 0.04
63 54 0.96
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.39
Consensus pattern (63 bp):
GTGCATCGATGCACTATTTATGCATCGATACACAAATCCCATTCGATGTTTATATTTTAGAGA
Found at i:4294 original size:24 final size:23
Alignment explanation
Indices: 4254--4305 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 23
4244 GCTACTTTTG
4254 GGTGCCCCTTTTTTAATTCATTC
1 GGTGCCCCTTTTTTAATTCATTC
*
4277 GGTGACCCTTTTTTTAATTCATTC
1 GGTG-CCCCTTTTTTAATTCATTC
4301 GGTGC
1 GGTGC
4306 ATTAACTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.46
Consensus pattern (23 bp):
GGTGCCCCTTTTTTAATTCATTC
Found at i:8401 original size:16 final size:16
Alignment explanation
Indices: 8382--8416 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
8372 TTATCAATAG
8382 AAAATATAAAAAAATT
1 AAAATATAAAAAAATT
* *
8398 AAAATATATAATAATT
1 AAAATATAAAAAAATT
8414 AAA
1 AAA
8417 TTTTTTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATAAAAAAATT
Found at i:8830 original size:6 final size:6
Alignment explanation
Indices: 8819--8844 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
8809 GGTAATAATT
8819 TTTTAA TTTTAA TTTTAA TTTTAA TT
1 TTTTAA TTTTAA TTTTAA TTTTAA TT
8845 ATTATATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:9900 original size:91 final size:91
Alignment explanation
Indices: 9617--9901 Score: 264
Period size: 91 Copynumber: 3.1 Consensus size: 91
9607 AATAAGCACG
* *
9617 TGTCTAAAATATTATATTTAAACATATAAAAATGTATATAAATAAATTTGAGATTTGAGAATATA
1 TGTCAAAAATATTATATTTAAACATATAAAAATTTATATAAATAAATTTGAGATTTGAGAATATA
9682 ATAATAAAAATTTGTTGATATTGAGA
66 ATAATAAAAATTTGTTGATATTGAGA
** * ** * *
9708 TGTCAAAAATA--AT-TTTAAAC-T-TAATAGGTTTATATACACAAAAATTAAAAATAATTTTA-
1 TGTCAAAAATATTATATTTAAACATATAA-AAATTTATATA-A-ATAAATT--TGA-GATTTGAG
** * * * * *
9767 AATACT-A-AATCTACATATT-TTAAAATAAGCACA
60 AATA-TAATAATAAAAAT-TTGTTGATAT-TG-AGA
*
9800 TGTCTAAAATATTATATTTAAACATATAAAAATTTATATAAATAAATTTGAGATTTGAGAATATA
1 TGTCAAAAATATTATATTTAAACATATAAAAATTTATATAAATAAATTTGAGATTTGAGAATATA
9865 ATAATAAAAATTTGTTGATATTGAGA
66 ATAATAAAAATTTGTTGATATTGAGA
9891 TGTCAAAAATA
1 TGTCAAAAATA
9902 AATTTTAAAC
Statistics
Matches: 143, Mismatches: 32, Indels: 38
0.67 0.15 0.18
Matches are distributed among these distances:
86 3 0.02
87 9 0.06
88 8 0.06
89 8 0.06
90 11 0.08
91 37 0.26
92 27 0.19
93 11 0.08
94 8 0.06
95 8 0.06
96 10 0.07
97 3 0.02
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.37
Consensus pattern (91 bp):
TGTCAAAAATATTATATTTAAACATATAAAAATTTATATAAATAAATTTGAGATTTGAGAATATA
ATAATAAAAATTTGTTGATATTGAGA
Found at i:10171 original size:3 final size:3
Alignment explanation
Indices: 10163--10226 Score: 112
Period size: 3 Copynumber: 21.3 Consensus size: 3
10153 TACACTTTCA
10163 AAG AAG AAG -AG AAAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
10208 AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG A
10227 TAATCTATCC
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.93
4 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:10264 original size:3 final size:3
Alignment explanation
Indices: 10256--10763 Score: 808
Period size: 3 Copynumber: 169.7 Consensus size: 3
10246 ACACTTTCAA
10256 AAG AAG AAG AAG AAG AAG AAG AAG AAAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG
10302 AAG AAG AAG AAG AAG -AG AAG AAG AAG AAG AAG AAG AAG AA- AA- AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
10347 AAG AAG AAG AAG AAG AAG AA- AAG AAG AA- AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
10393 AAG AAG AAAG AAG AAG -AG AAG AAG AAG AAG AAG AAG AA- AAG AAG
1 AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
10437 AAAG AAG AAG AAAG AAG AAG AAG AA- AA- AAA AAG AAG AA- AAG AAG
1 -AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
10481 AAG AAG AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
10528 AAAG AAG AAG AAAG AAG AAG AAG AAG AAG AAG AAAG AAG AAG AAG AAAG
1 -AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG -AAG
10577 AAG AAG AAAG AAAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAAG
1 AAG AAG -AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG
10625 AAG AAG AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
10672 AAG AAG AAAG AAG AAG AAG -AG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
10717 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
10764 ATACAAAATT
Statistics
Matches: 482, Mismatches: 1, Indels: 44
0.91 0.00 0.08
Matches are distributed among these distances:
2 26 0.05
3 419 0.87
4 37 0.08
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:10855 original size:45 final size:45
Alignment explanation
Indices: 10791--10880 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
10781 AAATTACAGT
10791 TTGTGAACTTTAGGCTAAGGTGGGGTTCTCGTTCCAGTGGGCGGA
1 TTGTGAACTTTAGGCTAAGGTGGGGTTCTCGTTCCAGTGGGCGGA
10836 TTGTGAACTTTAGGCTAAGGTGGGGTTCTCGTTCCAGTGGGCGGA
1 TTGTGAACTTTAGGCTAAGGTGGGGTTCTCGTTCCAGTGGGCGGA
10881 GTATGACCGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.16, C:0.16, G:0.38, T:0.31
Consensus pattern (45 bp):
TTGTGAACTTTAGGCTAAGGTGGGGTTCTCGTTCCAGTGGGCGGA
Found at i:11045 original size:104 final size:104
Alignment explanation
Indices: 10836--11035 Score: 373
Period size: 104 Copynumber: 1.9 Consensus size: 104
10826 AGTGGGCGGA
10836 TTGTGAACTTTAGGCTAAGGTGGGGTTCTCGTTCCAGTGGGCGGAGTATGACCGTCCGATCCTTT
1 TTGTGAACTTTAGGCTAAGGTGGGGTTCTCGTTCCAGTGGGCGGAGTATGACCGTCCGATCCTTT
* *
10901 TGAATGATCATTGGACGATTGTATCAATCCAAGCACAGT
66 GGAAGGATCATTGGACGATTGTATCAATCCAAGCACAGT
10940 TTGTGAACTTTAGGCTAAGGTGGGGTTCTCGTTCCAGTGGGCGGAGTATGACCGTCCGATCCTTT
1 TTGTGAACTTTAGGCTAAGGTGGGGTTCTCGTTCCAGTGGGCGGAGTATGACCGTCCGATCCTTT
*
11005 GGAAGGGTCATTGGACGATTGTATCAATCCA
66 GGAAGGATCATTGGACGATTGTATCAATCCA
11036 TCATCAGTTT
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 93 1.00
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (104 bp):
TTGTGAACTTTAGGCTAAGGTGGGGTTCTCGTTCCAGTGGGCGGAGTATGACCGTCCGATCCTTT
GGAAGGATCATTGGACGATTGTATCAATCCAAGCACAGT
Found at i:27739 original size:21 final size:21
Alignment explanation
Indices: 27693--27740 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
27683 CCTAATATTG
* *
27693 CAATGTCAAAATTAGGTGTAA
1 CAATGTCAAAATTAAGTGCAA
27714 CAATGTCAAAATTAAGTGCAA
1 CAATGTCAAAATTAAGTGCAA
*
27735 TAATGT
1 CAATGT
27741 TTGAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (21 bp):
CAATGTCAAAATTAAGTGCAA
Found at i:32377 original size:21 final size:21
Alignment explanation
Indices: 32352--32399 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
32342 CCTAATATTG
32352 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
32373 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
32394 TAATGT
1 CAATGT
32400 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:35467 original size:30 final size:31
Alignment explanation
Indices: 35420--35479 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
35410 AAAAAAAATA
35420 AGAATGAGTGAAAGCTTAGAAAAGC-TAGAG
1 AGAATGAGTGAAAGCTTAGAAAAGCATAGAG
* *
35450 AGAATCGAG-GAATGCTTAGCAAAGCATAGA
1 AGAAT-GAGTGAAAGCTTAGAAAAGCATAGA
35480 ATAGCGAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.45, C:0.10, G:0.28, T:0.17
Consensus pattern (31 bp):
AGAATGAGTGAAAGCTTAGAAAAGCATAGAG
Found at i:39705 original size:15 final size:15
Alignment explanation
Indices: 39672--39706 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39662 CCAATGCATG
* *
39672 CCCTTTTCCAGTAGG
1 CCCTTTTCCAGCAGA
39687 CCCTTTTCCAGCAGA
1 CCCTTTTCCAGCAGA
39702 CCCTT
1 CCCTT
39707 CACCATTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.40, G:0.14, T:0.31
Consensus pattern (15 bp):
CCCTTTTCCAGCAGA
Found at i:41481 original size:5 final size:5
Alignment explanation
Indices: 41471--41497 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
41461 TGTCCCCGAT
41471 TTTTC TTTTC TTTTC TTTTC TTTTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT
41498 GCTTTGATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:47395 original size:80 final size:80
Alignment explanation
Indices: 47303--47464 Score: 315
Period size: 80 Copynumber: 2.0 Consensus size: 80
47293 TTAATATCAT
*
47303 ATGTATATTTTATTTTTTCTAATATTTTTTTTACAGAAGGACAAAATAACTAATTTCAGTCTTGA
1 ATGTATATTTTATTTTTTCTAATATTTTTTTTACAAAAGGACAAAATAACTAATTTCAGTCTTGA
47368 CATACAGATAAAATA
66 CATACAGATAAAATA
47383 ATGTATATTTTATTTTTTCTAATATTTTTTTTACAAAAGGACAAAATAACTAATTTCAGTCTTGA
1 ATGTATATTTTATTTTTTCTAATATTTTTTTTACAAAAGGACAAAATAACTAATTTCAGTCTTGA
47448 CATACAGATAAAATA
66 CATACAGATAAAATA
47463 AT
1 AT
47465 TGGTATCGAC
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.43
Consensus pattern (80 bp):
ATGTATATTTTATTTTTTCTAATATTTTTTTTACAAAAGGACAAAATAACTAATTTCAGTCTTGA
CATACAGATAAAATA
Found at i:56812 original size:50 final size:51
Alignment explanation
Indices: 56708--56817 Score: 150
Period size: 50 Copynumber: 2.2 Consensus size: 51
56698 CCCATGTACT
* ** *
56708 GCGCTATACGATGATTTGGCGCCACGTGGGGTATAGTGTGCCCCCTGCACC
1 GCGCTATACGATGAGTTGGCGCCACGTGGGGTATAACGCGCCCCCTGCACC
* * *
56759 GCGCTATACGGTGAGTTGGCGCCACGT-GGGTATAACGCGGCCCCTGCAGC
1 GCGCTATACGATGAGTTGGCGCCACGTGGGGTATAACGCGCCCCCTGCACC
56809 GCGCTATAC
1 GCGCTATAC
56818 CTGTATATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
50 27 0.52
51 25 0.48
ACGTcount: A:0.16, C:0.30, G:0.33, T:0.21
Consensus pattern (51 bp):
GCGCTATACGATGAGTTGGCGCCACGTGGGGTATAACGCGCCCCCTGCACC
Found at i:57217 original size:110 final size:111
Alignment explanation
Indices: 57089--57301 Score: 365
Period size: 110 Copynumber: 1.9 Consensus size: 111
57079 ATATATATCT
* *
57089 ACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATATTTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
* * *
57154 T-ATTTATTTAATGCATGATTATTATATTAATAATTAAATATCTCG
66 TGATTCATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
*
57199 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTATTAATAATTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
57264 TGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
57302 TTTTTGTAAT
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
110 63 0.66
111 33 0.34
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (111 bp):
ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
TGATTCATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
Found at i:59143 original size:16 final size:16
Alignment explanation
Indices: 59124--59176 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
59114 CCATAACCCC
59124 TATCACACATATATCA
1 TATCACACATATATCA
** * *
59140 TATCATGCACACATCA
1 TATCACACATATATCA
59156 TATCACACATCATATACA
1 TATCACACAT-ATAT-CA
59174 TAT
1 TAT
59177 ATCACATACA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (16 bp):
TATCACACATATATCA
Found at i:59530 original size:23 final size:23
Alignment explanation
Indices: 59504--59572 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
59494 CACCACAGCT
*
59504 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
59527 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
59550 CGTAGAATTGCATCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
59573 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:59759 original size:103 final size:103
Alignment explanation
Indices: 59588--59805 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
59578 TAATGTCCAT
* *
59588 AAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCACTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
59653 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
59691 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCACTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
59756 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
59794 AAGGACCACATA
1 AAGGACCACATA
59806 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCACTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:60601 original size:21 final size:22
Alignment explanation
Indices: 60563--60603 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
60553 TTCACATAGT
60563 CTTATATTTCATTATCATATTA
1 CTTATATTTCATTATCATATTA
*
60585 CTTATATTT-ATTCTCATAT
1 CTTATATTTCATTATCATAT
60604 GACTCTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (22 bp):
CTTATATTTCATTATCATATTA
Found at i:62092 original size:18 final size:18
Alignment explanation
Indices: 62064--62104 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
62054 CCCAGCAGCC
*
62064 ACCGTAGCCATATATGAT
1 ACCGCAGCCATATATGAT
*
62082 GCCGCAGCCATATATGAT
1 ACCGCAGCCATATATGAT
62100 ACCGC
1 ACCGC
62105 CATCGCCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (18 bp):
ACCGCAGCCATATATGAT
Found at i:62766 original size:38 final size:38
Alignment explanation
Indices: 62688--62766 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 38
62678 CGTTTTTTTA
**
62688 TTACCATTTAATATCAGTTATTATAATTTGGTTATCAT
1 TTACCATTTAATATCAGTTATTATAATTTGGTTAAAAT
* *
62726 TTACCATTTAATACTTA-TTGTTATTAATTT-GTTAAAAT
1 TTACCATTTAATA-TCAGTTATTA-TAATTTGGTTAAAAT
62764 TTA
1 TTA
62767 ATGATTGTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
38 27 0.77
39 8 0.23
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.52
Consensus pattern (38 bp):
TTACCATTTAATATCAGTTATTATAATTTGGTTAAAAT
Found at i:66180 original size:50 final size:51
Alignment explanation
Indices: 66117--66232 Score: 171
Period size: 51 Copynumber: 2.3 Consensus size: 51
66107 TATAGCGTGC
* ** *
66117 TGCAGGGGCCGCGCTATA-CCCACGTGGCGCCAGCTCACCGTATAGCGCAG
1 TGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCACCGTATAGCACAG
* *
66167 TGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCATCGTATAGCACGG
1 TGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCACCGTATAGCACAG
66218 TGCAGGGGGCGCGCT
1 TGCAGGGGGCGCGCT
66233 TTACTGCTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 17 0.29
51 42 0.71
ACGTcount: A:0.18, C:0.33, G:0.34, T:0.15
Consensus pattern (51 bp):
TGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCACCGTATAGCACAG
Found at i:66792 original size:18 final size:19
Alignment explanation
Indices: 66771--66810 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
66761 ATATAACAAC
*
66771 TTAATTAA-ATTATTAGAT
1 TTAATTAATATTATTAAAT
*
66789 TTAATTAATATTTTTAAAT
1 TTAATTAATATTATTAAAT
66808 TTA
1 TTA
66811 TATTTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TTAATTAATATTATTAAAT
Found at i:67185 original size:27 final size:27
Alignment explanation
Indices: 67133--67186 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
67123 TAAAAATTTG
*
67133 ATAAATTTAAGAGTTAATTTTCTTTTA
1 ATAAATTTAAGAGTTAATTTTATTTTA
67160 ATAAATTTAA-A-TCTAATCTTTATTTTA
1 ATAAATTTAAGAGT-TAAT-TTTATTTTA
67187 TCTAAAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 1 0.04
26 5 0.21
27 18 0.75
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.52
Consensus pattern (27 bp):
ATAAATTTAAGAGTTAATTTTATTTTA
Found at i:68798 original size:44 final size:42
Alignment explanation
Indices: 68746--69014 Score: 193
Period size: 43 Copynumber: 6.2 Consensus size: 42
68736 TTTTTTTTTA
*
68746 AAAAAAATTATAGTCCTCAATTATAAAAGTAAAAGGTGGGATT
1 AAAAAAATTATAG-CCTCAATTATAAAAGTAAAAAGTGGGATT
* * *
68789 AAAAAAAATTAAAAGCCTCAATTATAAAAGTAAAAAATGAGATT
1 -AAAAAAATT-ATAGCCTCAATTATAAAAGTAAAAAGTGGGATT
* * * * * *
68833 AAATAAATTATGAGCCTTAGTCATAAAGGTAAAAAGTTGGATT
1 AAAAAAATTAT-AGCCTCAATTATAAAAGTAAAAAGTGGGATT
* * * *
68876 AAAAAAATTATAGGCTTCAATTATAAATA-TAGATAGTGAGATT
1 AAAAAAATTATA-GCCTCAATTATAAA-AGTAAAAAGTGGGATT
* * * ** * *
68919 GAAAAAGTAAGGGACCTCAATTATAAAAGTAAAAAATGTGATT
1 AAAAAAATTATAG-CCTCAATTATAAAAGTAAAAAGTGGGATT
* * * * *
68962 -AAAAAATAAATA-CCTCAATTGTAAAGGTAAAAAAATGAGATT
1 AAAAAAAT-TATAGCCTCAATTATAAAAGT-AAAAAGTGGGATT
69004 GAAAAAAATTA
1 -AAAAAAATTA
69015 AAAGTATTAA
Statistics
Matches: 175, Mismatches: 40, Indels: 21
0.74 0.17 0.09
Matches are distributed among these distances:
41 14 0.08
42 22 0.13
43 94 0.54
44 42 0.24
45 3 0.02
ACGTcount: A:0.53, C:0.06, G:0.14, T:0.26
Consensus pattern (42 bp):
AAAAAAATTATAGCCTCAATTATAAAAGTAAAAAGTGGGATT
Found at i:68945 original size:86 final size:86
Alignment explanation
Indices: 68760--69039 Score: 221
Period size: 86 Copynumber: 3.2 Consensus size: 86
68750 AAATTATAGT
* *
68760 CCTCAATTATAAAAGTAAAAGGTGGGATTAAAAAAAATTAAAAGCCTCAATTATAAAAGTAAAAA
1 CCTCAATTATAAAAGTAAAAAGTTGGATT-AAAAAAATTAAAAGCCTCAATTATAAAAGTAAAAA
* *
68825 ATGAGATTAAATAAATTATGAG
65 ATGAGATTAAATAAAGTAAGAG
* * * * * * * * *
68847 CCTTAGTCATAAAGGTAAAAAGTTGGATTAAAAAAATTATAGGCTTCAATTATAAATA-TAGATA
1 CCTCAATTATAAAAGTAAAAAGTTGGATTAAAAAAATTAAAAGCCTCAATTATAAA-AGTAAAAA
* * *
68911 GTGAGATTGAA-AAAGTAAGGG
65 ATGAGATTAAATAAAGTAAGAG
* * *
68932 ACCTCAATTATAAAAGTAAAAA-ATGTGATT-AAAAAA-TAAATA-CCTCAATTGTAAAGGTAAA
1 -CCTCAATTATAAAAGTAAAAAGTTG-GATTAAAAAAATTAAA-AGCCTCAATTATAAAAGT-AA
* * *
68993 AAAATGAGATTGAAAAAAATTAAAAG
62 AAAATGAGATT-AAATAAAGTAAGAG
** * *
69019 TATTAATTATAAAAATAAAAA
1 CCTCAATTATAAAAGTAAAAA
69040 ACTAAAATCT
Statistics
Matches: 148, Mismatches: 37, Indels: 17
0.73 0.18 0.08
Matches are distributed among these distances:
84 15 0.10
85 25 0.17
86 77 0.52
87 31 0.21
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (86 bp):
CCTCAATTATAAAAGTAAAAAGTTGGATTAAAAAAATTAAAAGCCTCAATTATAAAAGTAAAAAA
TGAGATTAAATAAAGTAAGAG
Found at i:70915 original size:25 final size:25
Alignment explanation
Indices: 70887--70965 Score: 104
Period size: 25 Copynumber: 3.0 Consensus size: 25
70877 AATTCGATGC
*
70887 CCCCCTTAGCCTCACTAATTGACTT
1 CCCCCTTAGCCACACTAATTGACTT
*
70912 CCCCCTTAGCTAGTCGCACTAATTGACTT
1 CCCCCTTAGC----CACACTAATTGACTT
70941 CCCCCTTAGCCACACTAATTGACTT
1 CCCCCTTAGCCACACTAATTGACTT
70966 TACAATCTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
25 24 0.50
29 24 0.50
ACGTcount: A:0.22, C:0.38, G:0.10, T:0.30
Consensus pattern (25 bp):
CCCCCTTAGCCACACTAATTGACTT
Found at i:77698 original size:28 final size:28
Alignment explanation
Indices: 77658--77713 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
77648 ACACATAGTT
77658 CCGGTTCTTGTGGAACTGCTGAAGAGGG
1 CCGGTTCTTGTGGAACTGCTGAAGAGGG
77686 CCGGTTCTTGTGGAACTGCTGAAGAGGG
1 CCGGTTCTTGTGGAACTGCTGAAGAGGG
77714 AGATGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.39, T:0.25
Consensus pattern (28 bp):
CCGGTTCTTGTGGAACTGCTGAAGAGGG
Found at i:83017 original size:6 final size:6
Alignment explanation
Indices: 82994--83063 Score: 68
Period size: 6 Copynumber: 11.7 Consensus size: 6
82984 GAGGAACGTG
* * * * * *
82994 GAGGTA GAGGAA GGGGGA GAGGGA GAGGGA GAGGTA GAGGAA GGGGGA
1 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA
* *
83042 GAGGGA GAGAGA GTGGGA GAGG
1 GAGGGA GAGGGA GAGGGA GAGG
83064 AGGAAGAGAG
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.63, T:0.04
Consensus pattern (6 bp):
GAGGGA
Found at i:83030 original size:30 final size:30
Alignment explanation
Indices: 82994--83064 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
82984 GAGGAACGTG
*
82994 GAGGTAGAGGAAGGGGGAGAGGGAGAGGGA
1 GAGGTAGAGGAAGGGGGAGAGGGAGAGAGA
83024 GAGGTAGAGGAAGGGGGAGAGGGAGAGAGA
1 GAGGTAGAGGAAGGGGGAGAGGGAGAGAGA
* *
83054 GTGGGAGAGGA
1 GAGGTAGAGGA
83065 GGAAGAGAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.62, T:0.04
Consensus pattern (30 bp):
GAGGTAGAGGAAGGGGGAGAGGGAGAGAGA
Found at i:83071 original size:21 final size:21
Alignment explanation
Indices: 83035--83081 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
83025 AGGTAGAGGA
83035 AGGGGGAGA-G-GG-AGAGAG
1 AGGGGGAGAGGAGGAAGAGAG
*
83053 AGTGGGAGAGGAGGAAGAGAG
1 AGGGGGAGAGGAGGAAGAGAG
83074 AGGGGGAG
1 AGGGGGAG
83082 GGTTGGCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.33
19 1 0.04
20 2 0.08
21 13 0.54
ACGTcount: A:0.34, C:0.00, G:0.64, T:0.02
Consensus pattern (21 bp):
AGGGGGAGAGGAGGAAGAGAG
Found at i:84941 original size:12 final size:12
Alignment explanation
Indices: 84924--84948 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
84914 CCACCGTCAC
84924 CCTCATTATCTT
1 CCTCATTATCTT
84936 CCTCATTATCTT
1 CCTCATTATCTT
84948 C
1 C
84949 TCTTAAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (12 bp):
CCTCATTATCTT
Found at i:85984 original size:12 final size:12
Alignment explanation
Indices: 85967--85991 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
85957 ATTCTTAAGA
85967 GAAGATAATGAG
1 GAAGATAATGAG
85979 GAAGATAATGAG
1 GAAGATAATGAG
85991 G
1 G
85992 GTGACGGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (12 bp):
GAAGATAATGAG
Found at i:89059 original size:18 final size:17
Alignment explanation
Indices: 89038--89095 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
89028 ACATATTTTA
89038 AAATAAATCAATCTATAT
1 AAATAAATCAATCTA-AT
* * *
89056 AAATAAATTATTTTAAAT
1 AAATAAATCAATCT-AAT
*
89074 AAATAAATCTATACTAAT
1 AAATAAATCAAT-CTAAT
89092 AAAT
1 AAAT
89096 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
18 29 0.94
19 2 0.06
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATAAATCAATCTAAT
Found at i:89083 original size:32 final size:32
Alignment explanation
Indices: 89031--89119 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
89021 AATCAATACA
89031 TATTTTAAAATAAATCAATCTATA-TAAATAAAT
1 TATTTT-AAATAAATCAATCTATACT-AATAAAT
*
89064 TATTTTAAATAAATAAATCTATACTAATAAAT
1 TATTTTAAATAAATCAATCTATACTAATAAAT
* *
89096 TATTTAAAATAAATCAATCCATAC
1 TATTTTAAATAAATCAATCTATAC
89120 AACTACAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
32 44 0.86
33 7 0.14
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (32 bp):
TATTTTAAATAAATCAATCTATACTAATAAAT
Found at i:89109 original size:112 final size:112
Alignment explanation
Indices: 88944--89198 Score: 440
Period size: 112 Copynumber: 2.3 Consensus size: 112
88934 ACAACTACAA
*
88944 TAATAAATTATTTAAAATAAATCAATCCATACTAAGAAATTATTTAAAATAAATCAATCCATACA
1 TAATAAATTATTTAAAATAAATCAATCTATACTAAGAAATTATTTAAAATAAATCAATCCATACA
*
89009 ACTACAATAATAAATCAATACATATTTTAAAATAAATCAATCTATA-
66 ACTACAATAATAAATCAATACATATTTTAAAATAAATCAATCCATAC
* * *
89055 TAAATAAATTATTTTAAATAAATAAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAC
1 T-AATAAATTATTTAAAATAAATCAATCTATACTAAGAAATTATTTAAAATAAATCAATCCATAC
*
89120 AACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
65 AACTACAATAATAAATCAATACATATTTTAAAATAAATCAATCCATAC
89168 TAATAAATTATTTAAAATAAATCAATCTATA
1 TAATAAATTATTTAAAATAAATCAATCTATA
89199 TTTTAAAATA
Statistics
Matches: 134, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
111 1 0.01
112 132 0.99
113 1 0.01
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (112 bp):
TAATAAATTATTTAAAATAAATCAATCTATACTAAGAAATTATTTAAAATAAATCAATCCATACA
ACTACAATAATAAATCAATACATATTTTAAAATAAATCAATCCATAC
Found at i:89175 original size:22 final size:23
Alignment explanation
Indices: 89100--89174 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
89090 ATAAATTATT
89100 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
89122 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
89148 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
89171 TAAA
1 TAAA
89175 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:89185 original size:32 final size:31
Alignment explanation
Indices: 89146--89387 Score: 181
Period size: 32 Copynumber: 8.7 Consensus size: 31
89136 CAATCCATAT
89146 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
89178 TTTAAAATAAATC-A---AT-CT-AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
89200 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
* *
89232 TTTAAAATAAATCAATTCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
89262 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
89280 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
89312 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
89334 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
89366 TTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATCCATAC
89388 AACTACAATA
Statistics
Matches: 169, Mismatches: 5, Indels: 72
0.69 0.02 0.29
Matches are distributed among these distances:
20 1 0.01
22 43 0.25
23 4 0.02
24 4 0.02
25 1 0.01
26 21 0.12
27 4 0.02
28 8 0.05
30 3 0.02
31 6 0.04
32 74 0.44
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACTAATAAATA
Found at i:89187 original size:54 final size:54
Alignment explanation
Indices: 89017--89252 Score: 245
Period size: 54 Copynumber: 4.3 Consensus size: 54
89007 CAACTACAAT
* *
89017 AATAAATCAATACATATTTTAAAATAAATCAATCTATA-TAAATAAATTATTTTAAATA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACT-AATAAATTA-TTT--A-A
* * *
89075 AATAAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTACA--A--T--
1 AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAA
89129 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
89183 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
89237 AATAAATCAATTCATA
1 AATAAATCAATCCATA
89253 CAACTACAAT
Statistics
Matches: 152, Mismatches: 11, Indels: 34
0.77 0.06 0.17
Matches are distributed among these distances:
48 25 0.16
49 3 0.02
50 2 0.01
52 3 0.02
53 1 0.01
54 77 0.51
58 10 0.07
59 1 0.01
60 2 0.01
62 2 0.01
63 3 0.02
64 23 0.15
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:89229 original size:22 final size:22
Alignment explanation
Indices: 89180--89228 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
89170 ATAAATTATT
* **
89180 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
89202 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
89225 TAAA
1 TAAA
89229 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:89235 original size:134 final size:134
Alignment explanation
Indices: 89064--89457 Score: 736
Period size: 134 Copynumber: 2.9 Consensus size: 134
89054 ATAAATAAAT
*
89064 TATTTT-AAATAAATAAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAA
1 TATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAA
89128 TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
66 TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
*
89193 TCTA
131 TCCA
* *
89197 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAA
1 TATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAA
89262 TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
66 TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
89327 TCCA
131 TCCA
89331 TATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAA
1 TATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAA
*
89396 TAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAAT
66 TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
89458 TATTTTAAAA
Statistics
Matches: 253, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
133 6 0.02
134 247 0.98
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (134 bp):
TATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAA
TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
TCCA
Found at i:89267 original size:80 final size:80
Alignment explanation
Indices: 88954--89332 Score: 384
Period size: 80 Copynumber: 4.7 Consensus size: 80
88944 TAATAAATTA
*
88954 TTTAAAATAAATCAATCCATACTAAGAAATTATTTAAAATAAATCAATCCATAC-AACTACAA-T
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAA-TACAATT
89017 AATAAATCAATACATAT
65 AATAAATCAAT-CATAT
* * * *
89034 TTTAAAATAAATCAATCTATA-TAAATAAATTATTTTAAATAAATAAATCTATACTAATA-AATT
1 TTTAAAATAAATCAATCCATACT-AATAAATTATTTAAAATAAATCAATCCATACTAATACAATT
* *
89097 ATTTAAAATAAATCA-AT
65 A-AT-AAATCAATCATAT
** * ** ** *
89114 CCATACAACTACAAT-AATAAAT-C-AATCCA-TATTTTAAAATAAATCAATCCATACTAATAAA
1 -TTTA-AAATA-AATCAATCCATACTAATAAATTA-TTTAAAATAAATCAATCCATACTAATACA
89175 TTATTTAAAATAAATCAATCTATAT
62 --A-TT--AATAAATCAATC-ATAT
*
89200 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATAC-AACTACAA-T
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAA-TACAATT
89263 AATAAATCAATCCATAT
65 AATAAATCAAT-CATAT
89280 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
89333 TTTTAAAATA
Statistics
Matches: 246, Mismatches: 29, Indels: 48
0.76 0.09 0.15
Matches are distributed among these distances:
79 5 0.02
80 148 0.60
81 9 0.04
82 17 0.07
83 7 0.03
84 20 0.08
85 7 0.03
86 31 0.13
87 2 0.01
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (80 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATACAATTA
ATAAATCAATCATAT
Found at i:89309 original size:22 final size:22
Alignment explanation
Indices: 89234--89308 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
89224 ATAAATTATT
* *
89234 TAAAATAAATCAATTCATACAA
1 TAAAATAAATCAATCCATATAA
**
89256 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
89282 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
89305 TAAA
1 TAAA
89309 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:89316 original size:112 final size:106
Alignment explanation
Indices: 88954--89332 Score: 307
Period size: 112 Copynumber: 3.5 Consensus size: 106
88944 TAATAAATTA
* *
88954 TTTAAAATAAATCAATCCATACTAAGAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1 TTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTA-AAT-A
* * * * **
89019 TAAATCAATACATATT-TTAAAATAAATCAATCTATATAAATAAATTAT
64 TAAATAAAT-CA-ATTCATAAAATAAAT-AA--TAAATCAATCCA-TAT
* *
89067 TTT-AAATAAATAAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACA-AT-
1 TTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTAAATATA
* ** *
89129 AATAAATCAATCCAT-ATTTTAA-AATAAATCAATCCATACT
66 AATAAATCAATTCATAAAATAAATAATAAATCAATCCATA-T
** *
89169 AATAAATTATTTAAAATAAATCAAT-CT-AT--A-T-TTTAAAATAAATCAATCCATACTAA-TA
1 TTTAAA--A--T-AAATAAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTA
*
89227 AATTATTTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCCATAT
60 AA-TA--T-AAATAAATCAATTCATA-AAATA-AATAATAAATCAATCCATAT
*
89280 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1 TTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
89333 TTTTAAAATA
Statistics
Matches: 215, Mismatches: 26, Indels: 51
0.74 0.09 0.17
Matches are distributed among these distances:
101 2 0.01
102 35 0.16
103 5 0.02
104 4 0.02
105 1 0.00
106 19 0.09
107 9 0.04
108 33 0.15
109 3 0.01
110 3 0.01
111 9 0.04
112 89 0.41
113 3 0.01
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (106 bp):
TTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTAAATATA
AATAAATCAATTCATAAAATAAATAATAAATCAATCCATAT
Found at i:89332 original size:54 final size:54
Alignment explanation
Indices: 89263--89386 Score: 239
Period size: 54 Copynumber: 2.3 Consensus size: 54
89253 CAACTACAAT
89263 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
89317 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
89371 AATAAATCAATCCATA
1 AATAAATCAATCCATA
89387 CAACTACAAT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:89363 original size:22 final size:22
Alignment explanation
Indices: 89314--89362 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
89304 ATAAATTATT
**
89314 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
89336 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
89359 TAAA
1 TAAA
89363 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:89422 original size:22 final size:22
Alignment explanation
Indices: 89397--89492 Score: 75
Period size: 22 Copynumber: 4.2 Consensus size: 22
89387 CAACTACAAT
89397 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
* **
89419 AATAAATCAATTCATACTAATAA
1 AATAAATCAATCCATA-TTTTAA
* ** * **
89442 ATTATTTAAAATAAATTATTTTAA
1 AATAAAT-CAATCCA-TATTTTAA
*
89466 AATAAATCAATCCATATTTTAT
1 AATAAATCAATCCATATTTTAA
89488 AATAA
1 AATAA
89493 TTTATTTTAA
Statistics
Matches: 53, Mismatches: 18, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
22 27 0.51
23 12 0.23
24 12 0.23
25 2 0.04
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:89465 original size:47 final size:48
Alignment explanation
Indices: 89303--89554 Score: 157
Period size: 54 Copynumber: 5.1 Consensus size: 48
89293 AATCCATACT
* * * *
89303 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACT
1 AATAAATTATTTTAAAATAAATCAATCCATA--CT--AATAAAT-TAT-TTTA-A
*
89357 AATAAATTA-TTTAAAATAAATCAATCCATAC-AACTACAA-TA--AT-A
1 AATAAATTATTTTAAAATAAATCAATCCATACTAA-TA-AATTATTTTAA
* *
89401 AATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTA-TTTAA
1 AATAAAT---TATTTTAAAATAAATCAATCCATACTAATAAATTATTTTAA
* *
89451 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATA----CTAATAAATTATTTTAA
* * ** *
89503 AATAAATTATTTTATAATAAAT-TAT-TTTA-TAATAAAATATTTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATACTAATAAATTATTTTAA
89548 AATAAAT
1 AATAAAT
89555 AACCTTATTA
Statistics
Matches: 167, Mismatches: 16, Indels: 39
0.75 0.07 0.18
Matches are distributed among these distances:
44 6 0.04
45 21 0.13
46 2 0.01
47 27 0.16
48 25 0.15
49 6 0.04
50 11 0.07
51 13 0.08
52 26 0.16
54 30 0.18
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (48 bp):
AATAAATTATTTTAAAATAAATCAATCCATACTAATAAATTATTTTAA
Found at i:89466 original size:15 final size:15
Alignment explanation
Indices: 89437--89554 Score: 121
Period size: 15 Copynumber: 7.5 Consensus size: 15
89427 AATTCATACT
89437 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
89451 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
89466 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
89488 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
89503 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
89518 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
89533 AATAAAATATTTTAA
1 AATAAATTATTTTAA
89548 AATAAAT
1 AATAAAT
89555 AACCTTATTA
Statistics
Matches: 88, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.10
15 62 0.70
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.11
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:89479 original size:69 final size:67
Alignment explanation
Indices: 89397--89538 Score: 187
Period size: 67 Copynumber: 2.1 Consensus size: 67
89387 CAACTACAAT
*
89397 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTA-TTTAAAATAAATTAT
1 AATAAATCAATCCATATTTTAAAAT-AATCAATT-ATA-AAATAAATTATTTTAAAATAAATTAT
89461 TTTAA
63 TTTAA
* ** * *
89466 AATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAATTATTTTATAATAAATTATTTT
1 AATAAATCAATCCATATTTTAAAATAATCAATTATAAAATAAATTATTTTAAAATAAATTATTTT
*
89531 AT
66 AA
89533 AATAAA
1 AATAAA
89539 ATATTTTAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
66 9 0.14
67 26 0.40
68 6 0.09
69 24 0.37
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (67 bp):
AATAAATCAATCCATATTTTAAAATAATCAATTATAAAATAAATTATTTTAAAATAAATTATTTT
AA
Found at i:91443 original size:16 final size:16
Alignment explanation
Indices: 91410--91443 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
91400 TTAATATTCA
* *
91410 CGTGAATAGTGAATTT
1 CGTGAATAGTAAAATT
91426 CGTGAATAGTAAAATT
1 CGTGAATAGTAAAATT
91442 CG
1 CG
91444 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTAAAATT
Found at i:99945 original size:30 final size:30
Alignment explanation
Indices: 99925--99980 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 30
99915 TTTTTGTTTG
99925 AACTTATTAAATAT-TTTTATTTTTATCTT
1 AACTTATTAAATATATTTTATTTTTATCTT
* *
99954 AATTTATTAAATATATTTTGTTTTTAT
1 AACTTATTAAATATATTTTATTTTTAT
99981 TTTCAGCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (30 bp):
AACTTATTAAATATATTTTATTTTTATCTT
Found at i:100237 original size:29 final size:29
Alignment explanation
Indices: 100199--100271 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
100189 TTCAAGCTGA
* *
100199 AAAATAAAAACAAAATATATTTAATAAATT
1 AAAACAAAAATAAAA-ATATTTAATAAATT
* *
100229 AAGACAAAAATAAAAATATTTAATAAGTT
1 AAAACAAAAATAAAAATATTTAATAAATT
100258 AAAACAAAAATAAA
1 AAAACAAAAATAAA
100272 GATAATTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
29 26 0.68
30 12 0.32
ACGTcount: A:0.68, C:0.04, G:0.03, T:0.25
Consensus pattern (29 bp):
AAAACAAAAATAAAAATATTTAATAAATT
Found at i:101525 original size:128 final size:129
Alignment explanation
Indices: 101297--101548 Score: 375
Period size: 128 Copynumber: 2.0 Consensus size: 129
101287 TATATGGTCA
* * * *
101297 TTGTATAATCTTAAGGGCTAGTTTTTTTAAGTTAATGATTATAGAAAAATATCTTAATTATATGT
1 TTGTATAATCTTAAGGACTAGTCTTTTTAACTTAATGATTATAGAAAAATATCTTAATTATATAT
* *
101362 TTAGTTTACGATTATGATTATAAATATTTATTATAATTATGATTAT-TTTTAAATAAAATTACC
66 ATAATTTACGATTATGATTATAAATATTTATTATAATTATGATTATATTTTAAATAAAATTACC
*
101425 TTGTATAATCTTAAGTGACTAG-CTTTTTATCTTAATGATTATA-AGAAAATATCTTAATTATAT
1 TTGTATAATCTTAAG-GACTAGTCTTTTTAACTTAATGATTATAGA-AAAATATCTTAATTATAT
* * *
101488 ATATAATTTATGATTATGATTATAAATATTTATTATAATTATTATTATATTTTTAATAAAA
64 ATATAATTTACGATTATGATTATAAATATTTATTATAATTATGATTATATTTTAAATAAAA
101549 CTAACAATTT
Statistics
Matches: 111, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
127 1 0.01
128 94 0.85
129 16 0.14
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.48
Consensus pattern (129 bp):
TTGTATAATCTTAAGGACTAGTCTTTTTAACTTAATGATTATAGAAAAATATCTTAATTATATAT
ATAATTTACGATTATGATTATAAATATTTATTATAATTATGATTATATTTTAAATAAAATTACC
Found at i:105288 original size:70 final size:69
Alignment explanation
Indices: 105158--105339 Score: 179
Period size: 70 Copynumber: 2.6 Consensus size: 69
105148 TCATAAAAAC
* * * *
105158 CATAACAAAATTTTTTACGTTC-TTCTTACTATAGAATTGGGTATGTTTTAATCCATACATTCAA
1 CATAACAAGATCTTTTACTTTCTTTC-TATTATAGAATTGGGTATGTTTTAATCCA-ACATTCAA
105222 AAAGAT
64 AAAGAT
* * *
105228 CATAACAAGATCTTTTACTTTCTTTCTATTATAGAATTGGGTATGTTTTTACTCGC-ACATTTAT
1 CATAACAAGATCTTTTACTTTCTTTCTATTATAGAATTGGGTATG-TTTTAATC-CAACATTCAA
*
105292 ATAGAT
64 AAAGAT
* * *
105298 CATAACATGATTTTTCTTTTACTTTCTTTTTATGATAGAATT
1 CATAACAAGA----TCTTTTACTTTCTTTCTATTATAGAATT
105340 TGATACATTT
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
70 57 0.61
71 10 0.11
72 1 0.01
74 26 0.28
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.46
Consensus pattern (69 bp):
CATAACAAGATCTTTTACTTTCTTTCTATTATAGAATTGGGTATGTTTTAATCCAACATTCAAAA
AGAT
Found at i:128718 original size:2 final size:2
Alignment explanation
Indices: 128711--128739 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
128701 AAATAATAAT
128711 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 T
128740 TTGTGTCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:135421 original size:21 final size:21
Alignment explanation
Indices: 135395--135434 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
135385 GATTTTCCAT
135395 AAAATTCATGCAAAATCAATA
1 AAAATTCATGCAAAATCAATA
135416 AAAATTCATGCAAAATCAA
1 AAAATTCATGCAAAATCAA
135435 AAGAATGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.05, T:0.23
Consensus pattern (21 bp):
AAAATTCATGCAAAATCAATA
Found at i:136484 original size:19 final size:19
Alignment explanation
Indices: 136460--136496 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
136450 ATGACCAATA
*
136460 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
136479 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
136497 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:136558 original size:20 final size:19
Alignment explanation
Indices: 136533--136573 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
136523 CGCAACGCGA
136533 ATTTGAAAAATCGCAATACG
1 ATTTG-AAAATCGCAATACG
**
136553 ATTTGACTATCGCAATACG
1 ATTTGAAAATCGCAATACG
136572 AT
1 AT
136574 AATCCGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (19 bp):
ATTTGAAAATCGCAATACG
Found at i:136617 original size:21 final size:21
Alignment explanation
Indices: 136570--136617 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
136560 TATCGCAATA
*
136570 CGATAATCCGAATTCGCGTTG
1 CGATAGTCCGAATTCGCGTTG
136591 CGATAGTCCGAATTCGCGTTG
1 CGATAGTCCGAATTCGCGTTG
136612 CGATAG
1 CGATAG
136618 ACTGTTCACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (21 bp):
CGATAGTCCGAATTCGCGTTG
Found at i:136644 original size:21 final size:21
Alignment explanation
Indices: 136607--136667 Score: 90
Period size: 20 Copynumber: 3.0 Consensus size: 21
136597 TCCGAATTCG
136607 CGTTGCGATAG-ACTGTTCAC
1 CGTTGCGATAGCACTGTTCAC
136627 CGTTGCGATAGCACTGTTCA-
1 CGTTGCGATAGCACTGTTCAC
* *
136647 CATTGCGATAACACTGTTCAC
1 CGTTGCGATAGCACTGTTCAC
136668 ATTGCGAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 29 0.78
21 8 0.22
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (21 bp):
CGTTGCGATAGCACTGTTCAC
Found at i:136668 original size:20 final size:20
Alignment explanation
Indices: 136609--136674 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
136599 CGAATTCGCG
* *
136609 TTGCGAT-AGACTGTTCACCG
1 TTGCGATAACACTGTTCA-CA
*
136629 TTGCGATAGCACTGTTCACA
1 TTGCGATAACACTGTTCACA
136649 TTGCGATAACACTGTTCACA
1 TTGCGATAACACTGTTCACA
136669 TTGCGA
1 TTGCGA
136675 ATTTACGATA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 33 0.80
21 8 0.20
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (20 bp):
TTGCGATAACACTGTTCACA
Found at i:136924 original size:21 final size:22
Alignment explanation
Indices: 136900--136947 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
136890 ACTGAAAGGA
136900 AAAAATTTACA-AAAACAAGAT
1 AAAAATTTACACAAAACAAGAT
*
136921 AAAAATTTACACAAAATAAGAT
1 AAAAATTTACACAAAACAAGAT
136943 AAAAA
1 AAAAA
136948 CTTGAACAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.69, C:0.08, G:0.04, T:0.19
Consensus pattern (22 bp):
AAAAATTTACACAAAACAAGAT
Found at i:136956 original size:22 final size:22
Alignment explanation
Indices: 136900--136956 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
136890 ACTGAAAGGA
*
136900 AAAAATTTACA-AAAACAAGAT
1 AAAAATTGACACAAAACAAGAT
* *
136921 AAAAATTTACACAAAATAAGAT
1 AAAAATTGACACAAAACAAGAT
136943 AAAAACTTGA-ACAA
1 AAAAA-TTGACACAA
136957 TTTTTGTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 11 0.34
22 18 0.56
23 3 0.09
ACGTcount: A:0.65, C:0.11, G:0.05, T:0.19
Consensus pattern (22 bp):
AAAAATTGACACAAAACAAGAT
Found at i:137247 original size:16 final size:17
Alignment explanation
Indices: 137218--137269 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
137208 ATCATAAATA
*
137218 ATTTAGAATTTATATTT
1 ATTTAAAATTTATATTT
*
137235 ATTT-AATTTTATA-TT
1 ATTTAAAATTTATATTT
137250 ATTTAAAATTTATAATTT
1 ATTTAAAATTTAT-ATTT
137268 AT
1 AT
137270 AATAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 14 0.48
17 5 0.17
18 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTTAAAATTTATATTT
Found at i:137454 original size:21 final size:21
Alignment explanation
Indices: 137428--137485 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
137418 TCGTAATGTG
137428 AACAGTGTTATCGCAACGGTA
1 AACAGTGTTATCGCAACGGTA
*
137449 AACAGTGTTATCGCAACGGTG
1 AACAGTGTTATCGCAACGGTA
*
137470 AACAGTGTTATTGCAA
1 AACAGTGTTATCGCAA
137486 TGATTTTGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (21 bp):
AACAGTGTTATCGCAACGGTA
Found at i:137514 original size:21 final size:21
Alignment explanation
Indices: 137490--137530 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
137480 TTGCAATGAT
*
137490 TTTGTACTATCGCAACGCGAA
1 TTTGGACTATCGCAACGCGAA
*
137511 TTTGGACTATCGCAATGCGA
1 TTTGGACTATCGCAACGCGA
137531 TAGTTAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (21 bp):
TTTGGACTATCGCAACGCGAA
Done.