Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001980.1 Hibiscus syriacus cultivar Beakdansim tig00004027_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: 164856
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:11425 original size:2 final size:2
Alignment explanation
Indices: 11418--11460 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
11408 AAAAATTCAA
11418 AT AT AT AT AT 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 AT AT AT AT AT
11460 A
1 A
11461 AATAAATAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11492 original size:11 final size:12
Alignment explanation
Indices: 11416--11500 Score: 57
Period size: 12 Copynumber: 7.0 Consensus size: 12
11406 ATAAAAATTC
*
11416 AAATATATATAT
1 AAATATATATAA
* *
11428 ATATATATATAT
1 AAATATATATAA
* *
11440 ATATATATATAT
1 AAATATATATAA
*
11452 ATATATATA-AA
1 AAATATATATAA
* *
11463 TAAATAGTAAATACG
1 -AAATA-TATATA-A
11478 AAATATA-ATAA
1 AAATATATATAA
11489 AAATATATATAA
1 AAATATATATAA
11501 GTATAAAGGA
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
11 8 0.13
12 43 0.69
13 5 0.08
14 6 0.10
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (12 bp):
AAATATATATAA
Found at i:16359 original size:21 final size:20
Alignment explanation
Indices: 16329--16389 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
16319 ATGCAAAAAA
16329 AAAT-AATTAAGTAAAATATT
1 AAATAAATTAA-TAAAATATT
16349 AAATAAATTAAATACAAAATATT
1 AAATAAATT-AAT--AAAATATT
16372 -AA-AAATATAATAAAATAT
1 AAATAAAT-TAATAAAATAT
16390 ACCTTAGACA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
19 7 0.19
20 4 0.11
21 12 0.33
22 5 0.14
23 8 0.22
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
AAATAAATTAATAAAATATT
Found at i:23792 original size:24 final size:24
Alignment explanation
Indices: 23760--23810 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
23750 TACTAAATAA
*
23760 ATTATTTTAATATTTAAA-AATATT
1 ATTATTTTAATA-ATAAATAATATT
*
23784 ATTATTTTATTAATAAATAATATT
1 ATTATTTTAATAATAAATAATATT
23808 ATT
1 ATT
23811 TATTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTATTTTAATAATAAATAATATT
Found at i:23794 original size:21 final size:21
Alignment explanation
Indices: 23773--23815 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
23763 ATTTTAATAT
*
23773 TTAA-AAATATTATTATTTTA
1 TTAATAAATAATATTATTTTA
23793 TTAATAAATAATATTA-TTTA
1 TTAATAAATAATATTATTTTA
23813 TTA
1 TTA
23816 TATTTGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAATAAATAATATTATTTTA
Found at i:24023 original size:3 final size:3
Alignment explanation
Indices: 24015--24041 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
24005 AATTACTTTA
24015 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
24042 AAACATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:24202 original size:2 final size:2
Alignment explanation
Indices: 24195--24240 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
24185 CTTCCCTCTC
24195 AT AT AT AT AT 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 AT AT AT AT AT
24237 AT AT
1 AT AT
24241 CATCTGTCAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29814 original size:36 final size:35
Alignment explanation
Indices: 29774--29856 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 35
29764 AATCTACCAC
*
29774 GGAGAAAACAATGATAATTATCTCTTGATAAAAAAA
1 GGAGAAAACAACGATAATTATCTCTTGAT-AAAAAA
29810 GGAGAAAACAACGATAATTATCTCTTGATAAAAAA
1 GGAGAAAACAACGATAATTATCTCTTGATAAAAAA
*
29845 GAAGAAAACAAC
1 GGAGAAAACAAC
29857 TCACAAGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 17 0.38
36 28 0.62
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.20
Consensus pattern (35 bp):
GGAGAAAACAACGATAATTATCTCTTGATAAAAAA
Found at i:31555 original size:149 final size:149
Alignment explanation
Indices: 31316--31620 Score: 565
Period size: 149 Copynumber: 2.0 Consensus size: 149
31306 CGAAGTGCCA
*
31316 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
* *
31381 CATATACATATACTAGGGATCAAGTATGTGTCTTACAATACTTCACACATGTTCCACAGAATATA
66 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
31446 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
**
31465 CGTAGAATTGCACCGTAGTGTTATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
31530 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
31595 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
31614 CGTAGAA
1 CGTAGAA
31621 CCCTCGACTC
Statistics
Matches: 151, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:33523 original size:21 final size:21
Alignment explanation
Indices: 33497--33541 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
33487 GATTTCTGGG
* *
33497 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
33518 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
33539 CAA
1 CAA
33542 ACGAATAAAA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:35068 original size:31 final size:31
Alignment explanation
Indices: 34916--35074 Score: 196
Period size: 31 Copynumber: 5.1 Consensus size: 31
34906 AGAGTCGAGG
34916 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
34947 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
34979 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* *
35010 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
35041 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
35072 GTT
1 GTT
35075 ACCGAGGATC
Statistics
Matches: 113, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
31 85 0.75
32 28 0.25
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:35094 original size:30 final size:30
Alignment explanation
Indices: 35033--35129 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
35023 CTAAGGAACA
* * ***
35033 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
35064 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* *
35094 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
35124 TCTGGA
1 TATGGA
35130 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 50 0.85
31 9 0.15
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:35130 original size:30 final size:30
Alignment explanation
Indices: 35060--35132 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
35050 GGTTCTTCGG
* *
35060 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
35090 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
35120 GACCTCTGGATAG
1 GACCTCTGGATAG
35133 GTCCTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:36182 original size:45 final size:44
Alignment explanation
Indices: 36087--36190 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 44
36077 TGCACTACAC
* *
36087 CATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGG
1 CATGCATCGATGCATAAATCATATTCGATGTTTCTATTTAAT-GG
* * *
36132 GATGCATCGATGCATAAATCATATTCGATGTTTTCTTTTTAAAT-T
1 CATGCATCGATGCATAAATCATATTCGATG-TTTCTATTT-AATGG
36177 CATGCATCGATGCA
1 CATGCATCGATGCA
36191 CCTTAAACAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
45 41 0.80
46 7 0.14
47 3 0.06
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.38
Consensus pattern (44 bp):
CATGCATCGATGCATAAATCATATTCGATGTTTCTATTTAATGG
Found at i:37213 original size:24 final size:23
Alignment explanation
Indices: 37186--37270 Score: 58
Period size: 26 Copynumber: 3.7 Consensus size: 23
37176 TTATTTCAAT
37186 AATTTAATATAATTTACATATTTA
1 AATTTAATATAATTTA-ATATTTA
*
37210 AA-TT-A-A-AA-TTGATATATT-
1 AATTTAATATAATTTAATAT-TTA
37228 AATTTAATAT-ATTATAATATTAATA
1 AATTTAATATAATT-TAATATT--TA
37253 AATTTAAATATAATTTAA
1 AATTT-AATATAATTTAA
37271 ATTAATATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 22
0.66 0.03 0.31
Matches are distributed among these distances:
18 6 0.13
19 6 0.13
20 3 0.06
21 3 0.06
22 3 0.06
23 7 0.15
24 3 0.06
25 5 0.11
26 8 0.17
27 3 0.06
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (23 bp):
AATTTAATATAATTTAATATTTA
Found at i:37258 original size:25 final size:25
Alignment explanation
Indices: 37228--37296 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
37218 TTGATATATT
37228 AATTTAATATATTATAATATTAATA
1 AATTTAATATATTATAATATTAATA
37253 AATTTAAATATAATT-TAA-ATTAATA
1 AATTT-AATAT-ATTATAATATTAATA
** *
37278 TTTTTAA-ATTTTATAATAT
1 AATTTAATATATTATAATAT
37297 AAGGTATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
22 2 0.05
23 5 0.14
24 4 0.11
25 15 0.41
26 8 0.22
27 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AATTTAATATATTATAATATTAATA
Found at i:37277 original size:15 final size:14
Alignment explanation
Indices: 37215--37287 Score: 64
Period size: 13 Copynumber: 5.4 Consensus size: 14
37205 ATTTAAATTA
*
37215 AAATTGATATA-TT
1 AAATTAATATATTT
*
37228 AATTTAATATATTAT
1 AAATTAATATATT-T
*
37243 AATATTAATAAATTT
1 AA-ATTAATATATTT
37258 AAA-T-ATA-ATTT
1 AAATTAATATATTT
*
37269 AAATTAATATTTTT
1 AAATTAATATATTT
37283 AAATT
1 AAATT
37288 TTATAATATA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
11 7 0.14
12 4 0.08
13 13 0.27
14 10 0.20
15 6 0.12
16 9 0.18
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (14 bp):
AAATTAATATATTT
Found at i:46246 original size:23 final size:23
Alignment explanation
Indices: 46220--46287 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
46210 CAGCTCGTAT
*
46220 AATTGCACCGAAGTGCCATGTAG
1 AATTGCACCGAAGTGCCATATAG
* **
46243 AATTGCACCGGAGTGCCGCATAG
1 AATTGCACCGAAGTGCCATATAG
*
46266 AATTGCACCGTAGTGCCATATA
1 AATTGCACCGAAGTGCCATATA
46288 ATAATGTCCA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCATATAG
Found at i:46462 original size:103 final size:103
Alignment explanation
Indices: 46299--46511 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 103
46289 TAATGTCCAT
* * * *
46299 AAGGACTACATATCATTCCTTAAGAATCATATATATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
46364 GACTTCACACATGTTCCAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
46402 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
46467 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
46505 AAGGACC
1 AAGGACC
46512 GCGTAGACCC
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:48216 original size:21 final size:21
Alignment explanation
Indices: 48192--48236 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
48182 TTTTGTTCGT
* *
48192 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
48213 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
48234 TTG
1 TTG
48237 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:50656 original size:20 final size:20
Alignment explanation
Indices: 50609--50699 Score: 103
Period size: 20 Copynumber: 4.5 Consensus size: 20
50599 AAATGACCAA
* *
50609 CAAATTCGCAACGC-GAACT
1 CAAATTCGCAACACAGAAGT
* *
50628 CCAATTTCGCAACCCAGAAGT
1 -CAAATTCGCAACACAGAAGT
* *
50649 CAAATTCGCAACATATAAGT
1 CAAATTCGCAACACAGAAGT
*
50669 CAAATTCGCAACACATAAGT
1 CAAATTCGCAACACAGAAGT
50689 CAAATTCGCAA
1 CAAATTCGCAA
50700 AGCACGTTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 58 0.94
21 4 0.06
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACACAGAAGT
Found at i:51276 original size:20 final size:20
Alignment explanation
Indices: 51253--51292 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
51243 ACTTAAATTT
*
51253 GCAACACGAAAATGAAAATC
1 GCAACACGAAAATAAAAATC
*
51273 GCAACGCGAAAATAAAAATC
1 GCAACACGAAAATAAAAATC
51293 ACAATGCGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.20, G:0.15, T:0.10
Consensus pattern (20 bp):
GCAACACGAAAATAAAAATC
Found at i:51301 original size:20 final size:20
Alignment explanation
Indices: 51254--51301 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
51244 CTTAAATTTG
* * *
51254 CAACACGAAAATGAAAATCG
1 CAACGCGAAAATAAAAATCA
51274 CAACGCGAAAATAAAAATCA
1 CAACGCGAAAATAAAAATCA
*
51294 CAATGCGA
1 CAACGCGA
51302 TTTTAGTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.54, C:0.21, G:0.15, T:0.10
Consensus pattern (20 bp):
CAACGCGAAAATAAAAATCA
Found at i:51333 original size:20 final size:19
Alignment explanation
Indices: 51297--51351 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
51287 AAAATCACAA
*
51297 TGCGATTTTAGTTTCGCGT
1 TGCGATTTTATTTTCGCGT
51316 TGCGATTTTCATTTTCGCGT
1 TGCGATTTT-ATTTTCGCGT
*
51336 TGCGAATTTAATTTTC
1 TGCG-ATTTTATTTTC
51352 AGAAACTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 9 0.28
20 19 0.59
21 4 0.12
ACGTcount: A:0.15, C:0.16, G:0.20, T:0.49
Consensus pattern (19 bp):
TGCGATTTTATTTTCGCGT
Found at i:54023 original size:25 final size:25
Alignment explanation
Indices: 53989--54038 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
53979 TATTATTTTC
*
53989 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
54014 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
54039 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:54559 original size:25 final size:28
Alignment explanation
Indices: 54531--54593 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
54521 ATTTTATTAT
54531 TATTATTAAAT-TTA-T-TATTATTAAA
1 TATTATTAAATATTATTATATTATTAAA
*
54556 TATTATT-ATTATTATTATATTATTAAA
1 TATTATTAAATATTATTATATTATTAAA
54583 TAATTATTAAA
1 T-ATTATTAAA
54594 AGCCCAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
24 2 0.06
25 10 0.32
26 1 0.03
27 11 0.35
28 6 0.19
29 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TATTATTAAATATTATTATATTATTAAA
Found at i:54562 original size:34 final size:33
Alignment explanation
Indices: 54517--54580 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 33
54507 TTTTTTTCAT
*
54517 TTAAATTTTATTATTATTATTAAATTTATTATTA
1 TTAAATATTATTATTATTATTAAA-TTATTATTA
*
54551 TTAAATATTATTATTATTATTATATTATTA
1 TTAAATATTATTATTATTATTAAATTATTA
54581 AATAATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 6 0.21
34 22 0.79
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (33 bp):
TTAAATATTATTATTATTATTAAATTATTATTA
Found at i:54573 original size:28 final size:29
Alignment explanation
Indices: 54525--54591 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 29
54515 ATTTAAATTT
54525 TATTATTATTATTAAATTTATTATTATTAAA
1 TATTATTATTATT-AATTTA-TATTATTAAA
54556 TATTATTATTATT-A-TTATATTATTAAA
1 TATTATTATTATTAATTTATATTATTAAA
54583 TAATTATTA
1 T-ATTATTA
54592 AAAGCCCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
27 11 0.31
28 10 0.29
29 1 0.03
31 13 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TATTATTATTATTAATTTATATTATTAAA
Found at i:54588 original size:11 final size:10
Alignment explanation
Indices: 54546--54593 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
54536 TTAAATTTAT
54546 TATTATTAAA
1 TATTATTAAA
*
54556 TATTATT-AT
1 TATTATTAAA
54565 TATTATT--A
1 TATTATTAAA
54573 TATTATTAAA
1 TATTATTAAA
54583 TAATTATTAAA
1 T-ATTATTAAA
54594 AGCCCAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 7 0.21
9 8 0.24
10 9 0.27
11 9 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TATTATTAAA
Found at i:54591 original size:3 final size:3
Alignment explanation
Indices: 54524--54580 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
54514 CATTTAAATT
* *
54524 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT-A TTA TTA TTA TTA TTA
54570 TTA -TA TTA TTA
1 TTA TTA TTA TTA
54581 AATAATTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 3 0.07
3 40 0.87
4 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:56739 original size:18 final size:18
Alignment explanation
Indices: 56718--56785 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 18
56708 TTTTATATAC
56718 TTATTATTTTCATAGTAT
1 TTATTATTTTCATAGTAT
*
56736 TTATATATTTTCTTATTAATAT
1 TTAT-TATTTTC--A-TAGTAT
*
56758 TTCATTATTTGCA-AGTATT
1 TT-ATTATTTTCATAGTA-T
56777 TTATTATTT
1 TTATTATTT
56786 ACTTTTCTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
18 14 0.34
19 10 0.24
20 1 0.02
21 1 0.02
22 13 0.32
23 2 0.05
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (18 bp):
TTATTATTTTCATAGTAT
Found at i:61493 original size:20 final size:21
Alignment explanation
Indices: 61450--61494 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
61440 CAAGAAAGAA
*
61450 AAAAGAAAACGAAAAAAAATG
1 AAAAGAAAACGAAAAAAAAGG
* *
61471 AAAA-AAAATGAAAAAAAGGG
1 AAAAGAAAACGAAAAAAAAGG
61491 AAAA
1 AAAA
61495 TTGAATCAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (21 bp):
AAAAGAAAACGAAAAAAAAGG
Found at i:61494 original size:10 final size:10
Alignment explanation
Indices: 61450--61487 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
61440 CAAGAAAGAA
*
61450 AAAAGAAAACG
1 AAAA-AAAATG
61461 AAAAAAAATG
1 AAAAAAAATG
61471 AAAAAAAATG
1 AAAAAAAATG
61481 AAAAAAA
1 AAAAAAA
61488 GGGAAAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 22 0.85
11 4 0.15
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.05
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:63893 original size:114 final size:114
Alignment explanation
Indices: 63710--63935 Score: 380
Period size: 114 Copynumber: 2.0 Consensus size: 114
63700 AAGTGCCATG
* *
63710 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
63775 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATT
66 TGGTTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATT
* *
63824 TGCTCATAGTAAAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATT
1 TGCTCATAGTAAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
63889 TGGTTCGGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 TGGTTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
63936 CTACATGATC
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 104 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATT
Found at i:66244 original size:22 final size:22
Alignment explanation
Indices: 66215--66269 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
66205 ATCTACACTC
66215 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
66237 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
66259 TTCAAAAATGA
1 TTCAAAGATGA
66270 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:66981 original size:186 final size:186
Alignment explanation
Indices: 66641--67150 Score: 923
Period size: 186 Copynumber: 2.7 Consensus size: 186
66631 AGTGCATTCA
* *
66641 ATCTTTTCTAAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTTACTTAGT
1 ATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCATAG--TTTTTTACTTAGT
66706 AAACTATTTCCCACATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
63 AAACTATTTCCCACATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
66771 TTGATGTTGTTATTTTGAAAAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTTT
128 TTGATGTTGTTATTTTGAAAAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTTT
66830 ATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCATAGTTTTTTACTTAGTAAA
1 ATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCATAGTTTTTTACTTAGTAAA
* *
66895 CTATTTCCCACATCTGTAAGTCCTGCAGTGCATGATGTTTCAAAAAAAGCATTCGGGAGCTTTTT
66 CTATTTCCCACATCTGTAAGTCCTGCAGTGCATGATGTTTC-CAAAAAGCCTTCGGGAGCTTTTT
66960 GATGTTGTTATTTTG-AAAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTTT
130 GATGTTGTTATTTTGAAAAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTTT
*
67016 ATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCATAGTTTCTTACTTAGTAAA
1 ATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCATAGTTTTTTACTTAGTAAA
*
67081 CTATTTCCCACATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
66 CTATTTCCCACATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
67146 ATGTT
131 ATGTT
67151 TTCAAAGCCT
Statistics
Matches: 312, Mismatches: 8, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
185 27 0.09
186 202 0.65
187 36 0.12
188 38 0.12
189 9 0.03
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (186 bp):
ATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCATAGTTTTTTACTTAGTAAA
CTATTTCCCACATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
ATGTTGTTATTTTGAAAAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTTT
Found at i:67217 original size:76 final size:76
Alignment explanation
Indices: 67091--67505 Score: 758
Period size: 76 Copynumber: 5.5 Consensus size: 76
67081 CTATTTCCCA
*
67091 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
67156 AGCCTTAGGGT
66 AGCCTTAGGGT
*
67167 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
67232 AGCCTTAGGGT
66 AGCCTTAGGGT
67243 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
67308 AGCCTTAGGGT
66 AGCCTTAGGGT
67319 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
67384 AGCCTTCGGGT
66 AGCCTTAGGGT
*
67395 CATCTGTAAGTCATTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
67460 AGCCTTCGGGT
66 AGCCTTAGGGT
* * *
67471 CATCTGTAAGCCCTTCAGTCCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
67506 CATTTCCATC
Statistics
Matches: 332, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 332 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:67669 original size:25 final size:23
Alignment explanation
Indices: 67639--67704 Score: 52
Period size: 22 Copynumber: 2.9 Consensus size: 23
67629 AAATTTTATT
67639 ATTATTATTA-AAT-TTATTATT
1 ATTATTATTATAATATTATTATT
*
67660 ATTAAATATTAT--TATTATTATT
1 ATT-ATTATTATAATATTATTATT
67682 ATTATAATATTA-AATAATTATTA
1 ATTAT--TATTATAAT-ATTATTA
67705 CAAGCCCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
21 5 0.14
22 17 0.49
23 5 0.14
24 1 0.03
25 7 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTATTATTATAATATTATTATT
Found at i:67671 original size:31 final size:29
Alignment explanation
Indices: 67635--67704 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 29
67625 ATTTAAATTT
67635 TATTATTATTATTAAATTTATTAT-TATTAAA
1 TATTATTATTATT--A-TTATTATATATTAAA
67666 TATTATTATTATTATTATTATAATATTAAA
1 TATTATTATTATTATTATTAT-ATATTAAA
67696 TAATTATTA
1 T-ATTATTA
67705 CAAGCCCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
28 7 0.19
29 1 0.03
30 8 0.22
31 20 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TATTATTATTATTATTATTATATATTAAA
Found at i:67704 original size:3 final size:3
Alignment explanation
Indices: 67634--67686 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
67624 CATTTAAATT
* *
67634 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT-A TTA TTA TTA TTA TTA
67680 TTA TTA T
1 TTA TTA T
67687 AATATTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 1 0.02
3 39 0.91
4 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:71931 original size:24 final size:24
Alignment explanation
Indices: 71897--71950 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
71887 CTGAAACATC
*
71897 ATCAAAATCCGAGTATTGACTAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
71921 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
71945 ATCAAA
1 ATCAAA
71951 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:72949 original size:19 final size:20
Alignment explanation
Indices: 72889--72979 Score: 105
Period size: 19 Copynumber: 4.6 Consensus size: 20
72879 ATTAAAACCT
* *
72889 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTCGA
* * *
72908 GTTGTGAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTCGA
72928 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
*
72947 GTTGCGAATTTGAAATTCAA
1 GTTGCGAATTTGAAATTCGA
72967 TGTTGCGAATTTG
1 -GTTGCGAATTTG
72980 GAACTCGCCT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 27 0.44
20 22 0.36
21 12 0.20
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:72972 original size:40 final size:41
Alignment explanation
Indices: 72888--72979 Score: 109
Period size: 39 Copynumber: 2.3 Consensus size: 41
72878 AATTAAAACC
* * * *
72888 TGTTGCGAAATT-AAATTCGTGTTGTGAATTCGAAAATCGA
1 TGTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCAA
* *
72928 -GTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTCAA
1 TGTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCAA
72967 TGTTGCGAATTTG
1 TGTTGCGAATTTG
72980 GAACTCGCCT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
39 26 0.59
40 18 0.41
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (41 bp):
TGTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCAA
Found at i:76521 original size:31 final size:31
Alignment explanation
Indices: 76425--76525 Score: 116
Period size: 31 Copynumber: 3.3 Consensus size: 31
76415 TTCAAAAGTA
* *
76425 ACAAATTGGTC-TCTAACGTTATTGATTTGTA-
1 ACAAAATGGTCATC-AACGTTATCGATTTG-AG
* * *
76456 ACAAAATTGTCACCAACGTTATCGATTTGTG
1 ACAAAATGGTCATCAACGTTATCGATTTGAG
*
76487 ACAAAATGGTCATCAACGTCATCGATTTGAG
1 ACAAAATGGTCATCAACGTTATCGATTTGAG
76518 ACAAAATG
1 ACAAAATG
76526 ATCACTCGAC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (31 bp):
ACAAAATGGTCATCAACGTTATCGATTTGAG
Found at i:78620 original size:2 final size:2
Alignment explanation
Indices: 78613--78645 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
78603 ATGACAAATA
78613 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
78646 CCAAGTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:79460 original size:22 final size:22
Alignment explanation
Indices: 79432--79478 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
79422 AACATCTCGA
*
79432 GACAATAATGAACGATGTGAGT
1 GACAATAATAAACGATGTGAGT
* *
79454 GACAATAATAAATGATGTGGGT
1 GACAATAATAAACGATGTGAGT
79476 GAC
1 GAC
79479 GACAAAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.28, T:0.23
Consensus pattern (22 bp):
GACAATAATAAACGATGTGAGT
Found at i:79902 original size:26 final size:26
Alignment explanation
Indices: 79873--79954 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 26
79863 TTAATTTTTT
79873 TATAGTTTAAATTGATATAATTCATA
1 TATAGTTTAAATTGATATAATTCATA
* ** * *
79899 TATA--ATAATATTTTTTTAAATTTAT-
1 TATAGTTTAA-ATTGATAT-AATTCATA
79924 TATAGTTTAAATTGATATAATTCATA
1 TATAGTTTAAATTGATATAATTCATA
79950 TATAG
1 TATAG
79955 ATGCAAATAT
Statistics
Matches: 41, Mismatches: 10, Indels: 10
0.67 0.16 0.16
Matches are distributed among these distances:
24 3 0.07
25 15 0.37
26 20 0.49
27 3 0.07
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.50
Consensus pattern (26 bp):
TATAGTTTAAATTGATATAATTCATA
Found at i:79902 original size:51 final size:51
Alignment explanation
Indices: 79847--79953 Score: 151
Period size: 51 Copynumber: 2.1 Consensus size: 51
79837 ATTATATAAA
* * * *
79847 ATATATTATTATTAAATTAATTTTTTTATAGTTTAAATTGATATAATTCAT
1 ATATAATAATATTAAATTAAATTTATTATAGTTTAAATTGATATAATTCAT
***
79898 ATATAATAATATTTTTTTAAATTTATTATAGTTTAAATTGATATAATTCAT
1 ATATAATAATATTAAATTAAATTTATTATAGTTTAAATTGATATAATTCAT
79949 ATATA
1 ATATA
79954 GATGCAAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (51 bp):
ATATAATAATATTAAATTAAATTTATTATAGTTTAAATTGATATAATTCAT
Found at i:85050 original size:30 final size:28
Alignment explanation
Indices: 85027--85081 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
85017 CGGTGATCGG
*
85027 TATATTTATCGATCTAACACCGGTCAGAT
1 TATATTTACCGATCTAACACCGGT-AGAT
*
85056 TATATTTACCGATCTAACACCCGTAG
1 TATATTTACCGATCTAACACCGGTAG
85082 CAGTAAAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.33
Consensus pattern (28 bp):
TATATTTACCGATCTAACACCGGTAGAT
Found at i:85344 original size:10 final size:10
Alignment explanation
Indices: 85329--85378 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
85319 TTTATCACAC
85329 CAAATTCTCT
1 CAAATTCTCT
85339 CAAATTCTCT
1 CAAATTCTCT
*
85349 CAAATTATCT
1 CAAATTCTCT
85359 -AAATTTCTCT
1 CAAA-TTCTCT
*
85369 CAAATACTCT
1 CAAATTCTCT
85379 ATCTTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 3 0.09
10 29 0.83
11 3 0.09
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:85645 original size:111 final size:111
Alignment explanation
Indices: 85513--85811 Score: 571
Period size: 111 Copynumber: 2.7 Consensus size: 111
85503 ATATATCTTT
*
85513 ACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATATTTAGT
1 ACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
85578 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
85624 ACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
85689 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
* *
85735 ATACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
85800 TGATTTATTTAA
66 TGATTTATTTAA
85812 ATATCTATGT
Statistics
Matches: 185, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 185 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
Found at i:86057 original size:3 final size:3
Alignment explanation
Indices: 86049--86113 Score: 78
Period size: 3 Copynumber: 21.7 Consensus size: 3
86039 ACCTGCTCAG
* * * *
86049 GAC GAC GAC GAC GAC GAC GAC GAT GAC GAC GAC GAT GAC GA- TAGT
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA-C
86094 GAC GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GA
86114 TGATGACAGC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 1 0.02
3 51 0.96
4 1 0.02
ACGTcount: A:0.34, C:0.26, G:0.34, T:0.06
Consensus pattern (3 bp):
GAC
Found at i:86282 original size:22 final size:23
Alignment explanation
Indices: 86214--86282 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
86204 GCATCGATAG
* *
86214 ATTTTTT-TTA-TTATATTTGTA
1 ATTTTTTATTATTTTTAATTGTA
* *
86235 TTTATTTTATTTTTTTTAATTGTA
1 ATT-TTTTATTATTTTTAATTGTA
*
86259 ATTTTTTATTATTTTTCATT-TA
1 ATTTTTTATTATTTTTAATTGTA
86281 AT
1 AT
86283 ACTTACTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
21 2 0.05
22 8 0.21
23 17 0.45
24 11 0.29
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.72
Consensus pattern (23 bp):
ATTTTTTATTATTTTTAATTGTA
Found at i:86372 original size:35 final size:33
Alignment explanation
Indices: 86333--86417 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
86323 ATATTTCAGT
86333 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
86368 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
86403 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
86418 TAAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:91861 original size:21 final size:21
Alignment explanation
Indices: 91835--91879 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
91825 GATTTCTGGG
* *
91835 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
91856 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
91877 CAA
1 CAA
91880 ACGACAAAAT
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:92482 original size:18 final size:18
Alignment explanation
Indices: 92459--92493 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
92449 CTAGGAGATT
92459 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
92477 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
92494 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:92579 original size:21 final size:22
Alignment explanation
Indices: 92550--92593 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
92540 GTTGTATGAT
92550 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
92571 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
92593 A
1 A
92594 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:93660 original size:149 final size:149
Alignment explanation
Indices: 93479--93782 Score: 554
Period size: 149 Copynumber: 2.0 Consensus size: 149
93469 GAGTCGAGGG
93479 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
93544 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
93609 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
93628 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
*
93693 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTT
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
*
93758 TATGGCACTATGGTGCAAT
131 TATGGCACTACGGTGCAAT
93777 TCTACG
1 TCTACG
93783 GGGCACTTCG
Statistics
Matches: 149, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:93805 original size:23 final size:23
Alignment explanation
Indices: 93761--93805 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
93751 ATCATTTTAT
*
93761 GGCACTATGGTGCAATTCTACGG
1 GGCACTATGGTGCAATTATACGG
*
93784 GGCACT-TCGGTGCATTTATACG
1 GGCACTAT-GGTGCAATTATACG
93806 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (23 bp):
GGCACTATGGTGCAATTATACGG
Found at i:96947 original size:21 final size:21
Alignment explanation
Indices: 96921--96965 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
96911 GATTTCTAGG
* *
96921 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
96942 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
96963 CAA
1 CAA
96966 ACGACAAAAT
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:97568 original size:18 final size:18
Alignment explanation
Indices: 97545--97579 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
97535 CTAGGAGATT
97545 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
97563 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
97580 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:97665 original size:21 final size:22
Alignment explanation
Indices: 97636--97679 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
97626 GTTGTATGAT
97636 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
97657 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
97679 A
1 A
97680 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:98750 original size:149 final size:149
Alignment explanation
Indices: 98569--98870 Score: 550
Period size: 149 Copynumber: 2.0 Consensus size: 149
98559 GAGTCGAGGG
98569 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
98634 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATAGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATAGACATCATTA
*
98699 TATGGCACTACGGTGCAAT
131 TATGCCACTACGGTGCAAT
* *
98718 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
*
98783 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATAGACATCATTA
98848 TATGCCACTACGGTGCAAT
131 TATGCCACTACGGTGCAAT
98867 TCTA
1 TCTA
98871 ACGGGCACTT
Statistics
Matches: 147, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 147 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATAGACATCATTA
TATGCCACTACGGTGCAAT
Found at i:101655 original size:37 final size:37
Alignment explanation
Indices: 101607--101677 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
101597 GATCAAACTG
* *
101607 AGGGATCGATACACAGGTTAAGTTATTAAGCTGAGGT
1 AGGGATCGATACACAGGTCAAGATATTAAGCTGAGGT
* *
101644 AGGGATTGATACACTGGTCAAGATATTAAGCTGA
1 AGGGATCGATACACAGGTCAAGATATTAAGCTGA
101678 TGGAACAGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (37 bp):
AGGGATCGATACACAGGTCAAGATATTAAGCTGAGGT
Found at i:102429 original size:20 final size:20
Alignment explanation
Indices: 102392--102431 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
102382 TTCCCCTTCA
*
102392 TTTTCTTCTCTTTCTTCCTC
1 TTTTCTTCTCATTCTTCCTC
102412 TTTTCTTCTCCATT-TTCCTC
1 TTTTCTTCT-CATTCTTCCTC
102432 CCTTTTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTCTTCTCATTCTTCCTC
Found at i:102439 original size:22 final size:22
Alignment explanation
Indices: 102402--102447 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
102392 TTTTCTTCTC
*
102402 TTTCTTCCTCTTTTCTTCTCCAT
1 TTTCCTCCTCTTTTC-TCTCCAT
*
102425 TTTCCTCC-CTTTTCTCTTCAT
1 TTTCCTCCTCTTTTCTCTCCAT
102446 TT
1 TT
102448 CTTTCCTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 6 0.29
23 7 0.33
ACGTcount: A:0.04, C:0.35, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTCCTCCTCTTTTCTCTCCAT
Found at i:103999 original size:183 final size:182
Alignment explanation
Indices: 103692--104051 Score: 666
Period size: 183 Copynumber: 2.0 Consensus size: 182
103682 TATAATTAAA
*
103692 ATAAAAAATTAAATTTGAGAGTTAAGTGATTAAATTAGGAGTAATTTGAAAGTTAAATAATTAAA
1 ATAAAAAATTAAATTTGAGAGTTAAGTAATTAAATTAGGAGTAATTTGAAAGTTAAATAATTAAA
* *
103757 TCAAAATAATTAAAATTTTAGTGACCAAAACAAGAATGATAAGATAGTCGAGTGATTAATGATTG
66 TCAAAATAATTAAAACTTCAGTGACCAAAACAAGAATGATAAGATAGTCGAGTGATTAATGATTG
103822 AATTTACCCATAAAATATACCATGTTATAACAGTTGCTAAGTTTTTACCCCC
131 AATTTACCCATAAAATATACCATGTTATAACAGTTGCTAAGTTTTTACCCCC
* *
103874 ATAAAAAATTAAATTTGAGTGTTAGAGTAATTAAATTATGAGTAATTTGAAAGTTAAATAATTAA
1 ATAAAAAATTAAATTTGAGAGTTA-AGTAATTAAATTAGGAGTAATTTGAAAGTTAAATAATTAA
103939 ATCAAAATAATTAAAACTTCAGTGACCAAAACAAGAATGATAAGATAGTCGAGTGATTAATGATT
65 ATCAAAATAATTAAAACTTCAGTGACCAAAACAAGAATGATAAGATAGTCGAGTGATTAATGATT
104004 GAATTTACCCATAAAATATACCATGTTATAACAGTTGCTAAGTTTTTA
130 GAATTTACCCATAAAATATACCATGTTATAACAGTTGCTAAGTTTTTA
104052 AAGGGGAAGT
Statistics
Matches: 172, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
182 23 0.13
183 149 0.87
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.33
Consensus pattern (182 bp):
ATAAAAAATTAAATTTGAGAGTTAAGTAATTAAATTAGGAGTAATTTGAAAGTTAAATAATTAAA
TCAAAATAATTAAAACTTCAGTGACCAAAACAAGAATGATAAGATAGTCGAGTGATTAATGATTG
AATTTACCCATAAAATATACCATGTTATAACAGTTGCTAAGTTTTTACCCCC
Found at i:104559 original size:15 final size:15
Alignment explanation
Indices: 104539--104572 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
104529 TATCAGCTTG
*
104539 TCTTCTTATTTTTCT
1 TCTTCTTATTTTTAT
*
104554 TCTTCTTCTTTTTAT
1 TCTTCTTATTTTTAT
104569 TCTT
1 TCTT
104573 AGGATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.74
Consensus pattern (15 bp):
TCTTCTTATTTTTAT
Found at i:104896 original size:9 final size:9
Alignment explanation
Indices: 104884--104910 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
104874 CTCACCGTAC
104884 TTTCAATTT
1 TTTCAATTT
104893 TTTCAATTT
1 TTTCAATTT
104902 TTTCAATTT
1 TTTCAATTT
104911 GCTCACTGAA
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:0.00, T:0.67
Consensus pattern (9 bp):
TTTCAATTT
Found at i:104980 original size:46 final size:46
Alignment explanation
Indices: 104930--105021 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
104920 ACTTTGTATA
** *
104930 TTGAATTTTTTTAATCACTCGGCCGTTTTCTCAGTTATACCATGAT
1 TTGAATTTTTTTAATCACTCAACCGTTTTCTCAGTTACACCATGAT
* *
104976 TTGAATTTTTTTAATCATTCAACCGTTTTCTCAGTTACACCGTGAT
1 TTGAATTTTTTTAATCACTCAACCGTTTTCTCAGTTACACCATGAT
105022 GATGTGGATT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.23, C:0.20, G:0.12, T:0.46
Consensus pattern (46 bp):
TTGAATTTTTTTAATCACTCAACCGTTTTCTCAGTTACACCATGAT
Found at i:105092 original size:28 final size:28
Alignment explanation
Indices: 105060--105115 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
105050 GACACACAGG
*
105060 ATTTACATTTAAAATAAAAGCTTCTTTT
1 ATTTACATTTAAAATAAAAGCTGCTTTT
*
105088 ATTTACATTTAAAATAAATGCTGCTTTT
1 ATTTACATTTAAAATAAAAGCTGCTTTT
105116 GCTTTACTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (28 bp):
ATTTACATTTAAAATAAAAGCTGCTTTT
Found at i:108161 original size:163 final size:163
Alignment explanation
Indices: 107891--108217 Score: 636
Period size: 163 Copynumber: 2.0 Consensus size: 163
107881 ATGGAGATAG
107891 GAACGGAAGAGGAGTTGACTTATATGATATAGATATATCCCTTTTTCGTTCGCGGTAGGAGAACT
1 GAACGGAAGAGGAGTTGACTTATATGATATAGATATATCCCTTTTTCGTTCGCGGTAGGAGAACT
107956 CTTGGTAGGAAACAACGATGTTGATACCTTGTGATTAGAAGGTCAAGAATTTGAGTTGTGGAAAC
66 CTTGGTAGGAAACAACGATGTTGATACCTTGTGATTAGAAGGTCAAGAATTTGAGTTGTGGAAAC
108021 AATCCTTTTAGTCTAACAACATCTCATGTAGTT
131 AATCCTTTTAGTCTAACAACATCTCATGTAGTT
*
108054 GAACGGAAGAGGAGTTGACTTATATGATATAGATATATCCCTTTTTCTTTCGCGGTAGGAGAACT
1 GAACGGAAGAGGAGTTGACTTATATGATATAGATATATCCCTTTTTCGTTCGCGGTAGGAGAACT
*
108119 CTTGGTAGGAAACAACGATGTTGATACCTTGTGATTAGAAGGTCAAGAGTTTGAGTTGTGGAAAC
66 CTTGGTAGGAAACAACGATGTTGATACCTTGTGATTAGAAGGTCAAGAATTTGAGTTGTGGAAAC
108184 AATCCTTTTAGTCTAACAACATCTCATGTAGTT
131 AATCCTTTTAGTCTAACAACATCTCATGTAGTT
108217 G
1 G
108218 CTTCAAGTCA
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 162 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (163 bp):
GAACGGAAGAGGAGTTGACTTATATGATATAGATATATCCCTTTTTCGTTCGCGGTAGGAGAACT
CTTGGTAGGAAACAACGATGTTGATACCTTGTGATTAGAAGGTCAAGAATTTGAGTTGTGGAAAC
AATCCTTTTAGTCTAACAACATCTCATGTAGTT
Found at i:112183 original size:14 final size:15
Alignment explanation
Indices: 112164--112192 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
112154 TAATTTAATT
112164 AAATTAAAT-TCTGA
1 AAATTAAATATCTGA
112178 AAATTAAATATCTGA
1 AAATTAAATATCTGA
112193 GTATTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (15 bp):
AAATTAAATATCTGA
Found at i:120397 original size:13 final size:11
Alignment explanation
Indices: 120369--120414 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
120359 AAAACACGTT
120369 TATA-ATAATA
1 TATATATAATA
* *
120379 TTTATACAATA
1 TATATATAATA
120390 TATATATAATA
1 TATATATAATA
120401 TATATA-AATA
1 TATATATAATA
120411 TATA
1 TATA
120415 AATATGTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 11 0.35
11 20 0.65
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
TATATATAATA
Found at i:120413 original size:8 final size:8
Alignment explanation
Indices: 120391--120429 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
120381 TATACAATAT
120391 ATATATAA
1 ATATATAA
120399 TATATATAA
1 -ATATATAA
120408 ATATATAA
1 ATATATAA
*
120416 ATATGTAA
1 ATATATAA
120424 ATATAT
1 ATATAT
120430 GTTCATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (8 bp):
ATATATAA
Found at i:121257 original size:99 final size:96
Alignment explanation
Indices: 121104--121294 Score: 249
Period size: 99 Copynumber: 1.9 Consensus size: 96
121094 AATTATTTAC
* * *
121104 TGACAGTCAGTCGCCCCTTCGCAGTAAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCATTCGT
1 TGACAGTCAGCCGCCCCTTCGCAGTAAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATC-TTCGC
*
121169 TGTGAAGTTGAAATTGACTCTGAAAGTTGTTTGT
65 TGTGAAGTTGAAATTGA-TATGAAA-TTGTTTGT
* * *
121203 TGACAATCAGCCGCCCCTTCGTC-GTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTCG
1 TGACAGTCAGCCGCCCCTTCG-CAGTAAAGTTGAGCTTGTGCTGTCTTGGGTCCAATAT-CTTCG
*
121267 CTGTGAAGTTGAAATTGGTTATGAAATT
64 CTGTGAAGTTGAAATT-GATATGAAATT
121295 AGGAAGCCCC
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
98 2 0.02
99 76 0.94
100 3 0.04
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (96 bp):
TGACAGTCAGCCGCCCCTTCGCAGTAAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCTTCGCT
GTGAAGTTGAAATTGATATGAAATTGTTTGT
Found at i:132971 original size:13 final size:13
Alignment explanation
Indices: 132953--132977 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
132943 ACAACTAATG
132953 AATAAATAAATAC
1 AATAAATAAATAC
132966 AATAAATAAATA
1 AATAAATAAATA
132978 AAAATAAAAT
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:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAATAAATAC
Found at i:134436 original size:15 final size:14
Alignment explanation
Indices: 134426--134460 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
134416 TTTATACAAT
134426 ATATATATATATAA
1 ATATATATATATAA
*
134440 TATATACATATATAA
1 -ATATATATATATAA
134455 ATATAT
1 ATATAT
134461 GTTCATTTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATATATATATAA
Found at i:134437 original size:8 final size:7
Alignment explanation
Indices: 134418--134459 Score: 50
Period size: 8 Copynumber: 5.9 Consensus size: 7
134408 TAATAATATT
*
134418 TATACAA
1 TATATAA
134425 TATATATA
1 TATATA-A
134433 TATATAA
1 TATATAA
134440 TATATACA
1 TATATA-A
134448 TATATAA
1 TATATAA
134455 -ATATA
1 TATATA
134460 TGTTCATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
6 5 0.16
7 13 0.41
8 14 0.44
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (7 bp):
TATATAA
Found at i:134863 original size:30 final size:29
Alignment explanation
Indices: 134822--134908 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 29
134812 TCTCATACAT
*
134822 ATGTCAGAATGGAGAATTTATCCTATGTAG
1 ATGTTAGAATGG-GAATTTATCCTATGTAG
* *
134852 ATGTTAGAATGGGGAGTTTATCCAATGTAG
1 ATGTTAGAAT-GGGAATTTATCCTATGTAG
134882 ATGTTAGAAATGGGAA-TTAGTCCTATG
1 ATGTTAG-AATGGGAATTTA-TCCTATG
134909 CAAAATCAGG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
29 3 0.06
30 41 0.84
31 5 0.10
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.33
Consensus pattern (29 bp):
ATGTTAGAATGGGAATTTATCCTATGTAG
Found at i:137477 original size:23 final size:23
Alignment explanation
Indices: 137451--137495 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
137441 CCCTCTAGAT
*
137451 TACACCAGGTAATATTAAAACGA
1 TACACCAGGTAATATCAAAACGA
*
137474 TACATCAGGTAATATCAAAACG
1 TACACCAGGTAATATCAAAACG
137496 TAAAAAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (23 bp):
TACACCAGGTAATATCAAAACGA
Found at i:137764 original size:30 final size:30
Alignment explanation
Indices: 137730--137810 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
137720 ATATAATCTC
137730 ATGCAGATGTCAAAACGGGGAATTTATCCT
1 ATGCAGATGTCAAAACGGGGAATTTATCCT
* * *** *
137760 ATGCAGATGCCAGAACATAGAGTTTATCCT
1 ATGCAGATGTCAAAACGGGGAATTTATCCT
137790 ATGCAGATGTCAAAACGGGGA
1 ATGCAGATGTCAAAACGGGGA
137811 CGAGATCCCA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (30 bp):
ATGCAGATGTCAAAACGGGGAATTTATCCT
Found at i:141109 original size:13 final size:14
Alignment explanation
Indices: 141079--141112 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
141069 TTCTATCATC
141079 TTAAATCTTAAGCT
1 TTAAATCTTAAGCT
141093 TTAAATCTTAA-CT
1 TTAAATCTTAAGCT
141106 TTAAATC
1 TTAAATC
141113 CTAAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (14 bp):
TTAAATCTTAAGCT
Found at i:141122 original size:14 final size:14
Alignment explanation
Indices: 141079--141130 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
141069 TTCTATCATC
* *
141079 TTAAATCTTAAGCT
1 TTAAATCCTAAACT
*
141093 TTAAAT-CTTAACT
1 TTAAATCCTAAACT
*
141106 TTAAATCCTAAATT
1 TTAAATCCTAAACT
*
141120 TTAAACCCTAA
1 TTAAATCCTAA
141131 CCTTAACCCT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
13 10 0.32
14 21 0.68
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (14 bp):
TTAAATCCTAAACT
Found at i:148450 original size:26 final size:26
Alignment explanation
Indices: 148395--148452 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
148385 TTGAGAGAAC
* *
148395 TTATTTATTATAAAAAAATTAAAATT
1 TTATTTATAATAAAAAAATTAAAATA
148421 TTATTTA-AATAAAAAAATATAAACA-A
1 TTATTTATAATAAAAAAAT-TAAA-ATA
148447 TTATTT
1 TTATTT
148453 CGTTATTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 10 0.36
26 17 0.61
27 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TTATTTATAATAAAAAAATTAAAATA
Found at i:153512 original size:30 final size:33
Alignment explanation
Indices: 153476--153553 Score: 94
Period size: 34 Copynumber: 2.5 Consensus size: 33
153466 AAGTAATATA
153476 TTAGCCC-AC-CTTCTTCC-TTTTTAACAGATT
1 TTAGCCCTACTCTTCTTCCTTTTTTAACAGATT
* *
153506 TTAGCCCTTCTTCTTCTTCCTTTTTTAATAGATT
1 TTAGCCCTAC-TCTTCTTCCTTTTTTAACAGATT
153540 TTAG-CCTA-TCTTCT
1 TTAGCCCTACTCTTCT
153554 CGAATAAGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 7 0.17
31 7 0.17
33 11 0.27
34 16 0.39
ACGTcount: A:0.17, C:0.27, G:0.06, T:0.50
Consensus pattern (33 bp):
TTAGCCCTACTCTTCTTCCTTTTTTAACAGATT
Found at i:153527 original size:33 final size:34
Alignment explanation
Indices: 153485--153553 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
153475 ATTAGCCCAC
153485 CTTCTTCC-TTTTTAACAGATTTTAGCCCT-TCTT
1 CTTCTTCCTTTTTTAACAGATTTTAG-CCTATCTT
*
153518 CTTCTTCCTTTTTTAATAGATTTTAGCCTATCTT
1 CTTCTTCCTTTTTTAACAGATTTTAGCCTATCTT
153552 CT
1 CT
153554 CGAATAAGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.16, C:0.25, G:0.06, T:0.54
Consensus pattern (34 bp):
CTTCTTCCTTTTTTAACAGATTTTAGCCTATCTT
Found at i:159327 original size:15 final size:15
Alignment explanation
Indices: 159304--159333 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
159294 ATTACTTGAT
159304 GAGAGGGAGCAGGCC
1 GAGAGGGAGCAGGCC
*
159319 GAGATGGAGCAGGCC
1 GAGAGGGAGCAGGCC
159334 AGAAGCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.20, G:0.50, T:0.03
Consensus pattern (15 bp):
GAGAGGGAGCAGGCC
Found at i:164028 original size:21 final size:21
Alignment explanation
Indices: 163986--164030 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
163976 TTTTGTTCGT
* * *
163986 TTGAAGGGGTATCGGTTTCCC
1 TTGAAGGGGTACCGATTCCCC
*
164007 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
164028 TTG
1 TTG
164031 CCCATAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Done.