Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001493.1 Hibiscus syriacus cultivar Beakdansim tig00002908_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: 70144
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6823 original size:14 final size:15
Alignment explanation
Indices: 6804--6834 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
6794 TTTCCTTGGA
6804 TTTATTGGTG-AGAT
1 TTTATTGGTGAAGAT
6818 TTTATTGGTGAAGAT
1 TTTATTGGTGAAGAT
6833 TT
1 TT
6835 AAATATTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.52
Consensus pattern (15 bp):
TTTATTGGTGAAGAT
Found at i:8802 original size:11 final size:11
Alignment explanation
Indices: 8786--8835 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
8776 TTTTTTCAAA
8786 AAAAAAAAATC
1 AAAAAAAAATC
8797 ---AAAAAATC
1 AAAAAAAAATC
8805 AAAAAAAAATC
1 AAAAAAAAATC
* *
8816 AAAAAAACACC
1 AAAAAAAAATC
8827 AAAAAAAAA
1 AAAAAAAAA
8836 ATTGCAAACG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 8 0.24
11 25 0.76
ACGTcount: A:0.82, C:0.12, G:0.00, T:0.06
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:8830 original size:19 final size:19
Alignment explanation
Indices: 8786--8834 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
8776 TTTTTTCAAA
*
8786 AAAAAAAAATCAAAAAATC
1 AAAAAAAAATCAAAAAAAC
8805 AAAAAAAAATCAAAAAAAC
1 AAAAAAAAATCAAAAAAAC
8824 ACCAAAAAAAA
1 A--AAAAAAAA
8835 AATTGCAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 19 0.70
21 8 0.30
ACGTcount: A:0.82, C:0.12, G:0.00, T:0.06
Consensus pattern (19 bp):
AAAAAAAAATCAAAAAAAC
Found at i:22291 original size:1 final size:1
Alignment explanation
Indices: 22287--22357 Score: 52
Period size: 1 Copynumber: 71.0 Consensus size: 1
22277 AAATTTTGGC
* *** * * ** * *
22287 TTTTTTTTTGTTTTTTTTGCCTTTTTGTTTTGTTTTTTTTTTTGCTTTTTTTTGTTTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
22352 TTTTTT
1 TTTTTT
22358 CGAAAAAAAT
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (1 bp):
T
Found at i:22301 original size:11 final size:11
Alignment explanation
Indices: 22287--22357 Score: 81
Period size: 11 Copynumber: 6.5 Consensus size: 11
22277 AAATTTTGGC
22287 TTTTTTTTTGT
1 TTTTTTTTTGT
***
22298 TTTTTTTGCCT
1 TTTTTTTTTGT
*
22309 TTTTGTTTTGT
1 TTTTTTTTTGT
22320 TTTTTTTTT-T
1 TTTTTTTTTGT
*
22330 GCTTTTTTTTGT
1 -TTTTTTTTTGT
22342 TTTTTTTTTGT
1 TTTTTTTTTGT
22353 TTTTT
1 TTTTT
22358 CGAAAAAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
10 1 0.02
11 46 0.96
12 1 0.02
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:22337 original size:13 final size:13
Alignment explanation
Indices: 22297--22339 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
22287 TTTTTTTTTG
*
22297 TTTTTTTTGCCTT
1 TTTTTTTTGCTTT
*
22310 TTTGTTTTG-TTT
1 TTTTTTTTGCTTT
22322 TTTTTTTTGCTTT
1 TTTTTTTTGCTTT
22335 TTTTT
1 TTTTT
22340 GTTTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (13 bp):
TTTTTTTTGCTTT
Found at i:22344 original size:17 final size:16
Alignment explanation
Indices: 22290--22355 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 16
22280 TTTTGGCTTT
22290 TTTTTTGTTTTTTTTG
1 TTTTTTGTTTTTTTTG
* *
22306 CCTTTTTGTTTTGTTTTT
1 -TTTTTTGTTTT-TTTTG
22324 TTTTTTGCTTTTTTTTG
1 TTTTTTG-TTTTTTTTG
22341 TTTTTT-TTTTGTTTT
1 TTTTTTGTTTT-TTTT
22356 TTCGAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
15 4 0.10
16 4 0.10
17 26 0.62
18 8 0.19
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.85
Consensus pattern (16 bp):
TTTTTTGTTTTTTTTG
Found at i:23233 original size:15 final size:16
Alignment explanation
Indices: 23213--23250 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
23203 GATTAGAATA
23213 AAATAAGCAAAAGAT-
1 AAATAAGCAAAAGATG
* *
23228 AAATAAACGAAAGATG
1 AAATAAGCAAAAGATG
23244 AAATAAG
1 AAATAAG
23251 ATAATAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.66, C:0.05, G:0.16, T:0.13
Consensus pattern (16 bp):
AAATAAGCAAAAGATG
Found at i:24154 original size:10 final size:10
Alignment explanation
Indices: 24139--24176 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
24129 ATTTTTTTTC
24139 CAAAAAAAAA
1 CAAAAAAAAA
24149 C--AAAAAAA
1 CAAAAAAAAA
24157 CAAAAAAAAA
1 CAAAAAAAAA
24167 CAAAAAAAAA
1 CAAAAAAAAA
24177 AGCCAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 8 0.31
10 18 0.69
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:24184 original size:18 final size:18
Alignment explanation
Indices: 24139--24174 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
24129 ATTTTTTTTC
24139 CAAAAAAAAACAAAAAAA
1 CAAAAAAAAACAAAAAAA
24157 CAAAAAAAAACAAAAAAA
1 CAAAAAAAAACAAAAAAA
24175 AAAGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (18 bp):
CAAAAAAAAACAAAAAAA
Found at i:26785 original size:9 final size:9
Alignment explanation
Indices: 26771--26797 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
26761 TAATAACTCG
26771 GATATTTCT
1 GATATTTCT
26780 GATATTTCT
1 GATATTTCT
26789 GATATTTCT
1 GATATTTCT
26798 ACCCATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (9 bp):
GATATTTCT
Found at i:29788 original size:18 final size:18
Alignment explanation
Indices: 29765--29832 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 18
29755 ATATCATTTA
29765 TTGCATGAGTTTTATTAG
1 TTGCATGAGTTTTATTAG
* * *
29783 TTGCATGCCATTCATTTCATGAAT
1 TTGCATG--AGT--TTT-AT-TAG
29807 TTGCATGAGTTTTATTAG
1 TTGCATGAGTTTTATTAG
29825 TTGCATGA
1 TTGCATGA
29833 CATTCATTGC
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
18 16 0.42
19 2 0.05
20 5 0.13
22 5 0.13
23 2 0.05
24 8 0.21
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.46
Consensus pattern (18 bp):
TTGCATGAGTTTTATTAG
Found at i:29932 original size:17 final size:16
Alignment explanation
Indices: 29892--29961 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 16
29882 TTAAAGCATA
*
29892 TAGTTCATTGAATAAAGT
1 TAGTTCATT-AATAAA-C
29910 TAGTTCATTAATTAAAC
1 TAGTTCATTAA-TAAAC
*
29927 TAGTTCATTCATCAAAC
1 TAGTTCATTAAT-AAAC
*
29944 TAGTTCATTTATAAAC
1 TAGTTCATTAATAAAC
29960 TA
1 TA
29962 ACTCTTAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
16 7 0.15
17 27 0.57
18 13 0.28
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (16 bp):
TAGTTCATTAATAAAC
Found at i:32013 original size:35 final size:35
Alignment explanation
Indices: 31975--32088 Score: 201
Period size: 35 Copynumber: 3.3 Consensus size: 35
31965 GATTTATATT
* *
31975 TTATCATATGTTTGTATTTACCTCTCGTGATATGT
1 TTATCATATGTTTGTATTTACCTCTTGTGATATGC
*
32010 TTATCATATGTTTGTATTTACCTCTTATGATATGC
1 TTATCATATGTTTGTATTTACCTCTTGTGATATGC
32045 TTATCATATGTTTGTATTTACCTCTTGTGATATGC
1 TTATCATATGTTTGTATTTACCTCTTGTGATATGC
32080 TTATCATAT
1 TTATCATAT
32089 TATATCATTC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 75 1.00
ACGTcount: A:0.22, C:0.14, G:0.12, T:0.52
Consensus pattern (35 bp):
TTATCATATGTTTGTATTTACCTCTTGTGATATGC
Found at i:32257 original size:21 final size:17
Alignment explanation
Indices: 32194--32268 Score: 98
Period size: 17 Copynumber: 4.4 Consensus size: 17
32184 TTTAAAGCAT
32194 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
32211 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
32229 CTAGTTCATTAATTAAA
1 CTAGTTCATTAATTAAA
* *
32246 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
32263 CTAGTT
1 CTAGTT
32269 AAACTAACTC
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
17 39 0.75
18 13 0.25
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:34440 original size:17 final size:17
Alignment explanation
Indices: 34400--34470 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
34390 TTCATACATT
*
34400 TAGTTCATTGAA-TAAAGT
1 TAGTTCATT-AATTAAA-C
*
34418 TAGTTCCTTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
34435 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
* *
34452 TAATTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
34469 TA
1 TA
34471 ACTCTTAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
17 32 0.73
18 12 0.27
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:40060 original size:96 final size:96
Alignment explanation
Indices: 39926--40105 Score: 254
Period size: 96 Copynumber: 1.9 Consensus size: 96
39916 CAATAGATTT
39926 TGATCCATAAATTAGGAACAATCATATTTTCCAATGAAAACAGAAAACCAGATAACACATTTCAG
1 TGATCCATAAATTAGGAACAATCATATTTTCCAATGAAAACAGAAAACCAGATAACACATTTCAG
*
39991 GTAACCATAGTTCATAAACCGTTAGATTCCA
66 GAAACCATAGTTCATAAACCGTTAGATTCCA
* * * * ** * * *
40022 TGATCCATAAATCTA-GAACTATTATATTTTCTATTGAAAATGGGAAACCATATAATACATTTCA
1 TGATCCATAAAT-TAGGAACAATCATATTTTCCAATGAAAACAGAAAACCAGATAACACATTTCA
40086 GGAAACCATAGTTCATAAAC
65 GGAAACCATAGTTCATAAAC
40106 AGTAAATTAG
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
96 71 0.97
97 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (96 bp):
TGATCCATAAATTAGGAACAATCATATTTTCCAATGAAAACAGAAAACCAGATAACACATTTCAG
GAAACCATAGTTCATAAACCGTTAGATTCCA
Found at i:41077 original size:147 final size:147
Alignment explanation
Indices: 40810--41106 Score: 585
Period size: 147 Copynumber: 2.0 Consensus size: 147
40800 TCACTTAATC
40810 CAAGTCATAAAGATATTTAGGTAATATTGACATTTAGGGTTATTTTAGTCATTTTTTGGTCCAGA
1 CAAGTCATAAAGATATTTAGGTAATATTGACATTTAGGGTTATTTTAGTCATTTTTTGGTCCAGA
*
40875 CACATTAGTTATTTCAAAACTTGAGAATAATTCATCATTTAAATATTTTTGTGACGTGACACACT
66 CACATTAGTTATTTCAAAACTTGAGAATAATTCATCATTTAAATACTTTTGTGACGTGACACACT
40940 TCCAGTAATCTAATCCT
131 TCCAGTAATCTAATCCT
40957 CAAGTCATAAAGATATTTAGGTAATATTGACATTTAGGGTTATTTTAGTCATTTTTTGGTCCAGA
1 CAAGTCATAAAGATATTTAGGTAATATTGACATTTAGGGTTATTTTAGTCATTTTTTGGTCCAGA
41022 CACATTAGTTATTTCAAAACTTGAGAATAATTCATCATTTAAATACTTTTGTGACGTGACACACT
66 CACATTAGTTATTTCAAAACTTGAGAATAATTCATCATTTAAATACTTTTGTGACGTGACACACT
41087 TCCAGTAATCTAATCCT
131 TCCAGTAATCTAATCCT
41104 CAA
1 CAA
41107 TTAATCATTC
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 149 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (147 bp):
CAAGTCATAAAGATATTTAGGTAATATTGACATTTAGGGTTATTTTAGTCATTTTTTGGTCCAGA
CACATTAGTTATTTCAAAACTTGAGAATAATTCATCATTTAAATACTTTTGTGACGTGACACACT
TCCAGTAATCTAATCCT
Found at i:45471 original size:12 final size:12
Alignment explanation
Indices: 45454--45502 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
45444 CTGAAATTTT
45454 AAAACATGTTAG
1 AAAACATGTTAG
45466 AAAACATGTTAG
1 AAAACATGTTAG
**
45478 --AATGTGTTA-
1 AAAACATGTTAG
45487 AAAACATGTTAG
1 AAAACATGTTAG
45499 AAAA
1 AAAA
45503 AGTGGTATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
10 7 0.23
11 7 0.23
12 16 0.53
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (12 bp):
AAAACATGTTAG
Found at i:45492 original size:21 final size:22
Alignment explanation
Indices: 45460--45500 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
45450 TTTTAAAACA
45460 TGTTAGAAAACATGTTAGAATG
1 TGTTAGAAAACATGTTAGAATG
45482 TGTTA-AAAACATGTTAGAA
1 TGTTAGAAAACATGTTAGAA
45501 AAAGTGGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.32
Consensus pattern (22 bp):
TGTTAGAAAACATGTTAGAATG
Found at i:46217 original size:81 final size:81
Alignment explanation
Indices: 46076--46487 Score: 524
Period size: 81 Copynumber: 5.1 Consensus size: 81
46066 CTATTTTAAA
* * * *
46076 TAAAAGATTAATT-TCCTAGCTATACGTTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAA
1 TAAAAGATTAATTGT-CTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
46140 GGTTTAATACCTTTGAG
65 GGTTTAATACCTTTGAG
* *
46157 AAAAATATTAATTGTCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGTCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
46222 GTTTAATACCTTTGAG
66 GTTTAATACCTTTGAG
** * *
46238 TAAAAGATTAATTACCTAG-TCGTGCATTTAACAGAAAGGTATCAATTATGCCAGTTAGATGAAA
1 TAAAAGATTAATTGTCTAGCT-GTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
46302 GGTTTAATACCTTTGAG
65 GGTTTAATACCTTTGAG
* *
46319 TAAAAGATTAATT-TCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTATATGAAA
1 TAAAAGATTAATTGT-CTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
* * ** *
46383 GGCTAAATGGCTTTGAT
65 GGTTTAATACCTTTGAG
* * * * * * *
46400 TTAAAGACTAAATGTCTAGCTGTGCATTTGGCAGAAATGTGTCAATCATGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGTCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* * * *
46465 GCTAAATTCCTTTGGG
66 GTTTAATACCTTTGAG
46481 TAAAAGA
1 TAAAAGA
46488 CTAAATGTTG
Statistics
Matches: 290, Mismatches: 36, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
80 1 0.00
81 286 0.99
82 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (81 bp):
TAAAAGATTAATTGTCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTTAATACCTTTGAG
Found at i:49366 original size:18 final size:18
Alignment explanation
Indices: 49343--49384 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
49333 GCTTTTAAAA
49343 GATTATGATTTGATTATT
1 GATTATGATTTGATTATT
49361 GATTATGATTTGATTATT
1 GATTATGATTTGATTATT
49379 GATTAT
1 GATTAT
49385 CATCCCGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.55
Consensus pattern (18 bp):
GATTATGATTTGATTATT
Found at i:51821 original size:96 final size:95
Alignment explanation
Indices: 51650--51831 Score: 237
Period size: 96 Copynumber: 1.9 Consensus size: 95
51640 CGATACCAAA
* * *
51650 AAGGAAAGTATCAATACCATGGATTCCAGAATGCCAAAATGGTATCGATACTGAAAGGGAGTATC
1 AAGGAAAGTATCAATACCATAGATACCAGAATGCCAAAATGGTATCGATACCGAAAGGGAGTATC
*
51715 GATACCATAGTATAGAAGTATCAGTACTAT
66 GATACCATAGTATAAAAGTATCAGTACTAT
*
51745 AAGGAAAGTATCGATACCATAGA-ACCAGAATG-CATAAATGGTGAGT-GCATACCGAAAGGGAG
1 AAGGAAAGTATCAATACCATAGATACCAGAATGCCA-AAATGGT-A-TCG-ATACCGAAAGGGAG
*
51807 TATC-AGTACTATAGTATAAAAGTAT
62 TATCGA-TACCATAGTATAAAAGTAT
51832 TGATACCATG
Statistics
Matches: 76, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
93 2 0.03
94 15 0.20
95 24 0.32
96 35 0.46
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (95 bp):
AAGGAAAGTATCAATACCATAGATACCAGAATGCCAAAATGGTATCGATACCGAAAGGGAGTATC
GATACCATAGTATAAAAGTATCAGTACTAT
Found at i:53685 original size:24 final size:24
Alignment explanation
Indices: 53626--53691 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
53616 GGTTCTACGC
* *
53626 GGTCCTTCGGGA-AAAATCTATGT
1 GGTCATTCGGGACAAATTCTATGT
* **
53649 GGTCCTTTTGGACAAATTCTATGT
1 GGTCATTCGGGACAAATTCTATGT
*
53673 TGTCATTCGGGACAAATTC
1 GGTCATTCGGGACAAATTC
53692 GACGTGGCAC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
23 10 0.29
24 25 0.71
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (24 bp):
GGTCATTCGGGACAAATTCTATGT
Found at i:55452 original size:8 final size:8
Alignment explanation
Indices: 55439--55499 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 8
55429 CTATTTTTTT
55439 CAAAAAAA
1 CAAAAAAA
55447 CAAAAAAAA
1 C-AAAAAAA
55456 CAAAAAAAAA
1 C--AAAAAAA
55466 GGCAAAAAAA
1 --CAAAAAAA
**
55476 CAAAAAGG
1 CAAAAAAA
55484 CAAAAAAA
1 CAAAAAAA
*
55492 TAAAAAAA
1 CAAAAAAA
55500 AAGCCAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 20 0.45
9 8 0.18
10 15 0.34
12 1 0.02
ACGTcount: A:0.82, C:0.10, G:0.07, T:0.02
Consensus pattern (8 bp):
CAAAAAAA
Found at i:55454 original size:9 final size:9
Alignment explanation
Indices: 55440--55464 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
55430 TATTTTTTTC
55440 AAAAAAACA
1 AAAAAAACA
55449 AAAAAAACA
1 AAAAAAACA
55458 AAAAAAA
1 AAAAAAA
55465 AGGCAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:55465 original size:20 final size:20
Alignment explanation
Indices: 55440--55481 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
55430 TATTTTTTTC
55440 AAAAAA-ACAAAAAAAACAAA
1 AAAAAAGAC-AAAAAAACAAA
*
55460 AAAAAAGGCAAAAAAACAAA
1 AAAAAAGACAAAAAAACAAA
55480 AA
1 AA
55482 GGCAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.86, C:0.10, G:0.05, T:0.00
Consensus pattern (20 bp):
AAAAAAGACAAAAAAACAAA
Found at i:55480 original size:16 final size:16
Alignment explanation
Indices: 55439--55497 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
55429 CTATTTTTTT
55439 CAAAAAAACAAAAA--
1 CAAAAAAACAAAAAGG
55453 -AAACAAAA-AAAAAGG
1 CAAA-AAAACAAAAAGG
55468 CAAAAAAACAAAAAGG
1 CAAAAAAACAAAAAGG
*
55484 CAAAAAAATAAAAA
1 CAAAAAAACAAAAA
55498 AAAAGCCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
13 8 0.21
14 4 0.10
15 4 0.10
16 23 0.59
ACGTcount: A:0.81, C:0.10, G:0.07, T:0.02
Consensus pattern (16 bp):
CAAAAAAACAAAAAGG
Found at i:55500 original size:20 final size:19
Alignment explanation
Indices: 55449--55508 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
55439 CAAAAAAACA
55449 AAAAAAACAAAAAAAAAGGC
1 AAAAAAA-AAAAAAAAAGGC
*
55469 ---AAAAAAACAAAAAGGC
1 AAAAAAAAAAAAAAAAGGC
*
55485 AAAAAAATAAAAAAAAAGCC
1 AAAAAAA-AAAAAAAAAGGC
55505 AAAA
1 AAAA
55509 TTTCAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
16 11 0.33
17 4 0.12
19 4 0.12
20 14 0.42
ACGTcount: A:0.80, C:0.10, G:0.08, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAAGGC
Found at i:64524 original size:20 final size:21
Alignment explanation
Indices: 64499--64546 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
64489 ATCAGATTGT
*
64499 CCAGGGGTAA-AGATTCCCCC
1 CCAGGGGGAACAGATTCCCCC
*
64519 CCAGGGGGAACAGATT-CCCA
1 CCAGGGGGAACAGATTCCCCC
64539 CCAGGGGG
1 CCAGGGGG
64547 TATCGATTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.25, C:0.31, G:0.33, T:0.10
Consensus pattern (21 bp):
CCAGGGGGAACAGATTCCCCC
Found at i:64586 original size:34 final size:35
Alignment explanation
Indices: 64524--64607 Score: 125
Period size: 34 Copynumber: 2.4 Consensus size: 35
64514 CCCCCCCAGG
*
64524 GGGAACAGATTCCCACCAGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
*
64559 GGGAACATATTCCCCCCA-GGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
* *
64593 AGGTACAGATTCCCC
1 GGGAACAGATTCCCC
64608 TGCATGGTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 28 0.64
35 16 0.36
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.19
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
Found at i:64591 original size:19 final size:19
Alignment explanation
Indices: 64499--64592 Score: 63
Period size: 20 Copynumber: 5.0 Consensus size: 19
64489 ATCAGATTGT
*
64499 CCAGGGGTAAAGATTCCCCC
1 CCAGGGGTAACGATT-CCCC
* *
64519 CCAGGGGGAACAGATTCCCA
1 CCAGGGGTAAC-GATTCCCC
*
64539 CCAGGGGGTATCGATT--CC
1 CCA-GGGGTAACGATTCCCC
*
64557 CC--GGG-AACATATTCCCC
1 CCAGGGGTAAC-GATTCCCC
*
64574 CCAGGGGTATCGATTCCCC
1 CCAGGGGTAACGATTCCCC
64593 AGGTACAGAT
Statistics
Matches: 56, Mismatches: 10, Indels: 17
0.67 0.12 0.20
Matches are distributed among these distances:
14 2 0.04
15 6 0.11
17 4 0.07
18 3 0.05
19 10 0.18
20 21 0.38
21 10 0.18
ACGTcount: A:0.22, C:0.34, G:0.27, T:0.17
Consensus pattern (19 bp):
CCAGGGGTAACGATTCCCC
Found at i:64744 original size:21 final size:21
Alignment explanation
Indices: 64720--64761 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
64710 ATTCGAATAT
*
64720 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
64741 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
64762 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:65068 original size:34 final size:32
Alignment explanation
Indices: 65029--65098 Score: 77
Period size: 34 Copynumber: 2.1 Consensus size: 32
65019 TTTTGTAAAG
* * *
65029 GGGAAAGGTTCTAGCTTAGCTCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCG-G-AAAAACTA
* *
65063 GGGAAATGTTATAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
65095 GGGA
1 GGGA
65099 GTTTGTAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 11 0.35
33 1 0.03
34 19 0.61
ACGTcount: A:0.33, C:0.13, G:0.30, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:68061 original size:18 final size:18
Alignment explanation
Indices: 68046--68118 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
68036 ATCAGATTGT
*
68046 CCAGGGGGTACAGATTCC
1 CCAGGGGGAACAGATTCC
68064 CCAGGGGGAACAGATTCCCC
1 CCAGGGGGAACAGATT--CC
*
68084 CCAGGGGGTATC-GATTCC
1 CCAGGGGG-AACAGATTCC
68102 CC---GGGAACAGATTCC
1 CCAGGGGGAACAGATTCC
68117 CC
1 CC
68119 CCAGGGGTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
14 2 0.04
15 11 0.23
18 19 0.40
20 14 0.29
21 2 0.04
ACGTcount: A:0.22, C:0.33, G:0.30, T:0.15
Consensus pattern (18 bp):
CCAGGGGGAACAGATTCC
Found at i:68126 original size:34 final size:35
Alignment explanation
Indices: 68046--68153 Score: 148
Period size: 34 Copynumber: 3.0 Consensus size: 35
68036 ATCAGATTGT
68046 CCAGGGGGTA-CAGATTCCCCAGGGGGAACAGATTCCCC
1 CCAGGGGGTATC-GATTCCCC---GGGAACAGATTCCCC
68084 CCAGGGGGTATCGATTCCCCGGGAACAGATTCCCC
1 CCAGGGGGTATCGATTCCCCGGGAACAGATTCCCC
* *
68119 CCA-GGGGTATCGATTCCCCGGGTACATATTCCCC
1 CCAGGGGGTATCGATTCCCCGGGAACAGATTCCCC
68153 C
1 C
68154 TGCTTGGTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
34 30 0.45
35 18 0.27
38 18 0.27
39 1 0.01
ACGTcount: A:0.20, C:0.34, G:0.28, T:0.18
Consensus pattern (35 bp):
CCAGGGGGTATCGATTCCCCGGGAACAGATTCCCC
Found at i:68220 original size:21 final size:22
Alignment explanation
Indices: 68190--68231 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
68180 ATATTACTCG
68190 GAGGGAACCGATTCCC-CACTT
1 GAGGGAACCGATTCCCTCACTT
*
68211 GAGGGTACCGATTCCCTCACT
1 GAGGGAACCGATTCCCTCACT
68232 GTTCATCAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.21, C:0.33, G:0.24, T:0.21
Consensus pattern (22 bp):
GAGGGAACCGATTCCCTCACTT
Found at i:68292 original size:21 final size:21
Alignment explanation
Indices: 68266--68307 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
68256 ATTTGAATAT
*
68266 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
68287 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
68308 CCATTCTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Done.