Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008540.1 Hibiscus syriacus cultivar Beakdansim tig00111429_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: 255285
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:235766 original size:14 final size:13
Alignment explanation
Indices: 235512--235766 Score: 94
Period size: 14 Copynumber: 19.7 Consensus size: 13
235502 TATATTAATA
235512 ATATAATACTA-AT
1 ATATAATA-TACAT
*
235525 ATATAATATATA-
1 ATATAATATACAT
*
235537 ACTATATATATATAT
1 A-TATA-ATATACAT
*
235552 ATATAATATATA-
1 ATATAATATACAT
*
235564 ATATAACTATATTAT
1 ATATAA-TATA-CAT
*
235579 ATATAATAATAAAT
1 ATATAAT-ATACAT
*
235593 ATATATTATA-AT
1 ATATAATATACAT
*
235605 ATATAA-ATATA-
1 ATATAATATACAT
*
235616 ATATAATAT-TAT
1 ATATAATATACAT
* *
235628 ATTATATTATAATAT
1 A-TATAATAT-ACAT
*
235643 ATATAATAGA-AT
1 ATATAATATACAT
235655 AGTATAATAT--AT
1 A-TATAATATACAT
*
235667 A-ATACTATA-AT
1 ATATAATATACAT
* *
235678 ATATAAGACTATAT
1 ATATAATA-TACAT
235692 A-AT-ATATAGCAT
1 ATATAATATA-CAT
*
235704 ATACT-ATATAAAT
1 ATA-TAATATACAT
235717 ACTATAATATACA-
1 A-TATAATATACAT
*
235730 ATATAAAATA-AT
1 ATATAATATACAT
235742 ATATAGAATATAGCAT
1 ATAT--AATATA-CAT
*
235758 ATATTATAT
1 ATATAATAT
235767 GAAAGAATCC
Statistics
Matches: 196, Mismatches: 17, Indels: 57
0.73 0.06 0.21
Matches are distributed among these distances:
10 6 0.03
11 17 0.09
12 47 0.24
13 52 0.27
14 54 0.28
15 14 0.07
16 6 0.03
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATAATATACAT
Found at i:236728 original size:23 final size:22
Alignment explanation
Indices: 236702--236774 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
236692 AACATGCCAC
236702 AAAGGCAGAGATAAATGTGTCGT
1 AAAGGCAGAGATAAAT-TGTCGT
* * **
236725 AAAGGCAAAGA-ACA-TGTCAC
1 AAAGGCAGAGATAAATTGTCGT
*
236745 AAAGACAGAGATAAATATGTCGT
1 AAAGGCAGAGATAAAT-TGTCGT
236768 AAAGGCA
1 AAAGGCA
236775 AAGAATATGT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
20 13 0.35
21 2 0.05
22 2 0.05
23 20 0.54
ACGTcount: A:0.47, C:0.12, G:0.25, T:0.16
Consensus pattern (22 bp):
AAAGGCAGAGATAAATTGTCGT
Found at i:236746 original size:43 final size:43
Alignment explanation
Indices: 236692--236794 Score: 170
Period size: 43 Copynumber: 2.4 Consensus size: 43
236682 GGTAGAGAAA
* * *
236692 AACATGCCACAAAGGCAGAGATAAATGTGTCGTAAAGGCAAAG
1 AACATGTCACAAAGACAGAGATAAATATGTCGTAAAGGCAAAG
236735 AACATGTCACAAAGACAGAGATAAATATGTCGTAAAGGCAAAG
1 AACATGTCACAAAGACAGAGATAAATATGTCGTAAAGGCAAAG
*
236778 AATATGTCACAAAGACA
1 AACATGTCACAAAGACA
236795 TAACTATTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.48, C:0.16, G:0.21, T:0.16
Consensus pattern (43 bp):
AACATGTCACAAAGACAGAGATAAATATGTCGTAAAGGCAAAG
Found at i:236748 original size:20 final size:20
Alignment explanation
Indices: 236725--236791 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
236715 AATGTGTCGT
*
236725 AAAGGCAAAGAACATGTCAC
1 AAAGGCAAAGAATATGTCAC
* * **
236745 AAAGACAGAGATAAATATGTCGT
1 AAAGGCA-A-A-GAATATGTCAC
236768 AAAGGCAAAGAATATGTCAC
1 AAAGGCAAAGAATATGTCAC
236788 AAAG
1 AAAG
236792 ACATAACTAT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 2 0.06
23 13 0.37
ACGTcount: A:0.51, C:0.13, G:0.21, T:0.15
Consensus pattern (20 bp):
AAAGGCAAAGAATATGTCAC
Found at i:243402 original size:3 final size:3
Alignment explanation
Indices: 243394--243451 Score: 73
Period size: 3 Copynumber: 18.3 Consensus size: 3
243384 CGGGTCTTTT
243394 TTA TTA TTA TT- TATA TATA TTTA TTA TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA T-TA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA
243442 TTA TTA TTA T
1 TTA TTA TTA T
243452 GTTTATTAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 1 0.02
3 40 0.78
4 9 0.18
5 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:243457 original size:9 final size:8
Alignment explanation
Indices: 243397--243459 Score: 53
Period size: 9 Copynumber: 7.8 Consensus size: 8
243387 GTCTTTTTTA
243397 TTATTA-T
1 TTATTATT
243404 TTATATATAT
1 TTAT-TAT-T
243414 TTATTATT
1 TTATTATT
243422 ATTATTATT
1 -TTATTATT
243431 ATTATTA-T
1 -TTATTATT
243439 TTATTA--
1 TTATTATT
243445 TTATTATGT
1 TTATTAT-T
243454 TTATTA
1 TTATTA
243460 ATTACATATT
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
6 6 0.12
7 10 0.20
8 4 0.08
9 24 0.49
10 5 0.10
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (8 bp):
TTATTATT
Found at i:245054 original size:22 final size:22
Alignment explanation
Indices: 245029--245072 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
245019 TCAAACGGTG
*
245029 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
245051 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
245073 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:246537 original size:33 final size:33
Alignment explanation
Indices: 246458--246529 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
246448 TGGGTAGATT
246458 GCATGTCCGGGTAGGATTGTTATTTAATTGAAA
1 GCATGTCCGGGTAGGATTGTTATTTAATTGAAA
246491 GCATGTCCGGGTAGGATTGTTATTTAATTGAAA
1 GCATGTCCGGGTAGGATTGTTATTTAATTGAAA
246524 GCATGT
1 GCATGT
246530 TTGGGTAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (33 bp):
GCATGTCCGGGTAGGATTGTTATTTAATTGAAA
Found at i:250248 original size:4 final size:4
Alignment explanation
Indices: 250239--250286 Score: 68
Period size: 4 Copynumber: 13.0 Consensus size: 4
250229 AAAAGTATAC
250239 ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT AC-- ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
250283 ACAT
1 ACAT
250287 GATACATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 4 0.10
4 36 0.90
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:250258 original size:18 final size:18
Alignment explanation
Indices: 250235--250286 Score: 104
Period size: 18 Copynumber: 2.9 Consensus size: 18
250225 CGAGAAAAGT
250235 ATACACATACATACATAC
1 ATACACATACATACATAC
250253 ATACACATACATACATAC
1 ATACACATACATACATAC
250271 ATACACATACATACAT
1 ATACACATACATACAT
250287 GATACATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (18 bp):
ATACACATACATACATAC
Found at i:250286 original size:14 final size:14
Alignment explanation
Indices: 250243--250285 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
250233 GTATACACAT
250243 ACATACATACATAC
1 ACATACATACATAC
250257 ACATACATACATAC
1 ACATACATACATAC
* *
250271 ATACACATACATAC
1 ACATACATACATAC
250285 A
1 A
250286 TGATACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (14 bp):
ACATACATACATAC
Found at i:250859 original size:34 final size:36
Alignment explanation
Indices: 250775--250872 Score: 128
Period size: 36 Copynumber: 2.8 Consensus size: 36
250765 TCGTTTCCTC
* *
250775 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAAACAAATTTTGTCTCGCTTGAGACAATATCTCT
** *
250811 AAAAACAAATTTTGTCTCATTTGAGACTATATCT-T
1 AAAAACAAATTTTGTCTCGCTTGAGACAATATCTCT
*
250846 -AAAGCAAATTTTGTCTCGCTTGAGACA
1 AAAAACAAATTTTGTCTCGCTTGAGACA
250873 TCATTTTCTC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
34 23 0.43
35 1 0.02
36 29 0.55
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (36 bp):
AAAAACAAATTTTGTCTCGCTTGAGACAATATCTCT
Found at i:251166 original size:29 final size:29
Alignment explanation
Indices: 251124--251355 Score: 174
Period size: 29 Copynumber: 8.0 Consensus size: 29
251114 TTTCTCTTGA
251124 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
*
251153 AAAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
* *
251182 AAATATCTTTGAG-TTGTTTCTTTTG---
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
* * **
251207 AAAAATCTTTGAGTCTATTTATTTTGAA-
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
* *** * *
251235 ACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG-A-
1 A-AAA-------ATCT-TTGAGTTTGTTCCTTTTGAAT
*
251271 AAAAATCTTTGAGTTTGTTCATTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
*
251300 AAAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
* *
251329 AAATATCTTTGAG-TTGTTTCTTTTGAA
1 AAAAATCTTTGAGTTTGTTCCTTTTGAA
251356 AATCTTTGAG
Statistics
Matches: 163, Mismatches: 26, Indels: 29
0.75 0.12 0.13
Matches are distributed among these distances:
25 12 0.07
26 9 0.06
27 12 0.07
28 29 0.18
29 80 0.49
35 3 0.02
36 5 0.03
37 13 0.08
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.47
Consensus pattern (29 bp):
AAAAATCTTTGAGTTTGTTCCTTTTGAAT
Found at i:251232 original size:54 final size:54
Alignment explanation
Indices: 251120--251366 Score: 128
Period size: 57 Copynumber: 4.3 Consensus size: 54
251110 ACAGTTTCTC
* * *
251120 TTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTGAAAAAATCTTTGAGTTTGTTCCTTTTG-A-AAAAATCTTGGAGTCTATTCATT
* * *
251176 TTGAATAAATATCTTTGAG-TTGTTTCTTTTG-AAAAATCTTTGAGTCTATTTATT
1 TTGAA-AAA-ATCTTTGAGTTTGTTCCTTTTGAAAAAATCTTGGAGTCTATTCATT
*** * * * * *
251230 TTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCATT
1 TTGAAA-AAA--------TCT-TTGAGTTTGTTCCTTTTGAAAAAATCTTGGAGTCTATTCATT
* * *
251294 TTGAATAAAAATCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGT-TGTTTC-TT
1 TTG-A-AAAAATCTTTGAGTTTGTTCCTTTTGAA-AAA-ATCTTGGAGTCT-ATTCATT
251351 TTG--AAAATCTTTGAGT
1 TTGAAAAAATCTTTGAGT
251367 CTATTATTTT
Statistics
Matches: 152, Mismatches: 20, Indels: 41
0.71 0.09 0.19
Matches are distributed among these distances:
53 14 0.09
54 25 0.16
56 19 0.12
57 26 0.17
58 22 0.14
61 3 0.02
62 5 0.03
63 9 0.06
64 23 0.15
65 4 0.03
66 2 0.01
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.47
Consensus pattern (54 bp):
TTGAAAAAATCTTTGAGTTTGTTCCTTTTGAAAAAATCTTGGAGTCTATTCATT
Found at i:251257 original size:147 final size:145
Alignment explanation
Indices: 251094--251426 Score: 600
Period size: 147 Copynumber: 2.3 Consensus size: 145
251084 AAAACGATTT
*
251094 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAAT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCATTTTGAATAAAAAT
251159 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
66 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTG-AAAATCTTTGAGTCTA
251224 TTTATTTTGAAACAAAG
130 -TTATTTTGAAACAAAG
251241 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCATTTTGAATAAAAAT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCATTTTGAATAAAAAT
251306 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAATCTTTGAGTCTAT
66 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAATCTTTGAGTCTAT
251371 TATTTTGAAACAAAG
131 TATTTTGAAACAAAG
* *
251386 TTTTGTCTCTCTTGAGACA-ATT-TCGTG-AAAAATCTTTGAGT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGT
251427 CTGAAACAAA
Statistics
Matches: 183, Mismatches: 3, Indels: 5
0.96 0.02 0.03
Matches are distributed among these distances:
142 14 0.08
143 4 0.02
144 2 0.01
145 35 0.19
146 16 0.09
147 112 0.61
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (145 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCATTTTGAATAAAAAT
CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAATCTTTGAGTCTAT
TATTTTGAAACAAAG
Found at i:251360 original size:24 final size:25
Alignment explanation
Indices: 251271--251366 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 25
251261 TTTCTCTTGA
*
251271 AAAAATCTTTGAGTTTGTTCATTTTG
1 AAAAATCTTTGAG-TTGTTCCTTTTG
*
251297 AATAAAAATCTTGGAGTTTGTTCCTTTTG
1 ---AAAAATCTTTGAG-TTGTTCCTTTTG
*
251326 AATAAATATCTTTGAGTTGTTTCTTTTG
1 -A-AAA-ATCTTTGAGTTGTTCCTTTTG
251354 -AAAATCTTTGAGT
1 AAAAATCTTTGAGT
251367 CTATTATTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
24 10 0.17
25 3 0.05
27 1 0.02
28 14 0.23
29 32 0.53
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (25 bp):
AAAAATCTTTGAGTTGTTCCTTTTG
Found at i:251498 original size:28 final size:28
Alignment explanation
Indices: 251467--251535 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
251457 ATTTTGTGAA
*
251467 AAAAAAATCTTTGAGATTGTTTCTTTTG
1 AAAAAAATCTTTGAGATTGTTTCTTTGG
*
251495 AAAAAAATCTTTGAGTTTGTTTCTTTGG
1 AAAAAAATCTTTGAGATTGTTTCTTTGG
251523 AAACAAAAT-TTTG
1 AAA-AAAATCTTTG
251536 TCTCTCTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.43
Consensus pattern (28 bp):
AAAAAAATCTTTGAGATTGTTTCTTTGG
Found at i:251564 original size:37 final size:37
Alignment explanation
Indices: 251513--251639 Score: 117
Period size: 37 Copynumber: 3.6 Consensus size: 37
251503 CTTTGAGTTT
251513 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
** * * * *
251550 GTTTCTTTTAAAACAAAA------ATCT-TTGAGTTT
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
251580 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* *
251617 ATTTCTTTTGAAA-AAAATCTTTG
1 GTTTCTTTGGAAACAAAAT-TTTG
251640 AATCTGTTTC
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
30 21 0.31
31 3 0.04
36 8 0.12
37 36 0.53
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (37 bp):
GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
Found at i:251572 original size:67 final size:65
Alignment explanation
Indices: 251480--251704 Score: 285
Period size: 67 Copynumber: 3.4 Consensus size: 65
251470 AAAATCTTTG
*
251480 AGATTGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
*
251545 AGATAGTTTCTTTTAAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1 AGATAGTTTCTTTT-GAA-AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
251610 TA
64 TA
* * * * *
251612 AGATAATTTCTTTTGAAAAAAATCTTTGAATCTGTTTCTCTT--AAA-ATGAATTTTGTATCTCT
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCT-TTGGAAACA-AAATTTTGTCTCTCT
*
251674 TG
64 TA
* * **
251676 AGACAGTTTCTCTTGAAGTAAATCTTTGA
1 AGATAGTTTCTTTTGAAAAAAATCTTTGA
251705 ATATGTTCAT
Statistics
Matches: 142, Mismatches: 14, Indels: 9
0.86 0.08 0.05
Matches are distributed among these distances:
63 1 0.01
64 41 0.29
65 33 0.23
66 6 0.04
67 61 0.43
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (65 bp):
AGATAGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
Found at i:251584 original size:95 final size:93
Alignment explanation
Indices: 251429--251602 Score: 242
Period size: 95 Copynumber: 1.8 Consensus size: 93
251419 CTTTGAGTCT
* * *
251429 GAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAAAATCTTTGAGATTGTTTCTTTT
1 GAAACAAAATTTTGTCTCTCTTAAGACAATTTTGTGAAAAAAAAATCTTTGAGATTGTTTCTTTG
251494 GAAA-AAAATCTTTGAGTTTGTTTCTTTG
66 GAAACAAAAT-TTTGAGTTTGTTTCTTTG
* * * * *
251522 GAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTTTTAAAACAAAAATCTTTGAGTTTGTTTCTT
1 GAAACAAAATTTTGTCTCTCTTAAGACAATTT-TGTGAAAA-AAAAATCTTTGAGATTGTTTCTT
251587 TGGAAACAAAATTTTG
64 TGGAAACAAAATTTTG
251603 TCTCTCTTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
93 28 0.40
94 6 0.09
95 31 0.44
96 5 0.07
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (93 bp):
GAAACAAAATTTTGTCTCTCTTAAGACAATTTTGTGAAAAAAAAATCTTTGAGATTGTTTCTTTG
GAAACAAAATTTTGAGTTTGTTTCTTTG
Found at i:251934 original size:120 final size:119
Alignment explanation
Indices: 251751--251974 Score: 258
Period size: 120 Copynumber: 1.9 Consensus size: 119
251741 TTAACAAAAT
* * *
251751 CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTCTCTCTTGAGACAGTTTCTAATAAAAAAC
1 CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTAATAAAAAA-
251816 TAA-CTTTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGATGTGATC
65 -AATC-TTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGATC
* ** ** *
251871 CATCTTTGAGTCTGTTTCTTTTGAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTTTTGAAAA
1 CATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTATCTCTT-AAGACAATTTCTAATAAAAA
* * * *
251934 AAATCTTTGAGTTTGTTTCCTTTGAAGCAAAATTTTGTCTC
64 AAATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTC
251975 TCGAGACAAC
Statistics
Matches: 87, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
118 22 0.25
119 19 0.22
120 42 0.48
121 4 0.05
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (119 bp):
CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTAATAAAAAAA
ATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGATC
Found at i:251951 original size:64 final size:63
Alignment explanation
Indices: 251872--251996 Score: 178
Period size: 64 Copynumber: 2.0 Consensus size: 63
251862 GATGTGATCC
* *
251872 ATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAAAAA
* * * **
251936 ATCTTTGAGTTTGTTTCCTTTGAAGCAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
251997 TACCCACATT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
63 19 0.35
64 35 0.65
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (63 bp):
ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAA
Found at i:252041 original size:40 final size:40
Alignment explanation
Indices: 251978--252057 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
251968 TTGTCTCTCG
251978 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
* * *
252018 AGACAATTTCTTTT-AAAACTACCCACCTTTGAGATTGTTT
1 AGACAACTTCTTTTGAAAA-TACCCACATTTGAGATCGTTT
252058 TTATTAAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
Found at i:252135 original size:31 final size:30
Alignment explanation
Indices: 252100--252160 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 30
252090 GTTTCTCTAG
*
252100 AAATACAAA-ATCTTTGAGTTTGTTTCACTTT
1 AAATA-AAACATCTTTGAG-TCGTTTCACTTT
*
252131 AAATAAAACCATTTTTGAGTCGTTTCACTT
1 AAATAAAA-CATCTTTGAGTCGTTTCACTT
252161 GAAACATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 3 0.12
31 15 0.58
32 8 0.31
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (30 bp):
AAATAAAACATCTTTGAGTCGTTTCACTTT
Found at i:252485 original size:36 final size:34
Alignment explanation
Indices: 252434--252529 Score: 95
Period size: 36 Copynumber: 2.7 Consensus size: 34
252424 TTTGAGAAAA
* * * *
252434 ATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTACC
1 ATCTTTGAATCTGTTTCTTT-GAAACAAAA-TAAAC
*
252470 ATCTTTGAATCTGTTTCCCTTGAAACAAAATAAAC
1 ATCTTTGAATCTGTTT-CTTTGAAACAAAATAAAC
252505 ATCTTTGAGATC-GTTTCTCTTGAAA
1 ATCTTTGA-ATCTGTTTCT-TTGAAA
252530 TGAATTTTGT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
34 1 0.02
35 21 0.41
36 26 0.51
37 3 0.06
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (34 bp):
ATCTTTGAATCTGTTTCTTTGAAACAAAATAAAC
Found at i:252521 original size:35 final size:36
Alignment explanation
Indices: 252455--252529 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
252445 TGTTTCTTTG
* *
252455 GAAACAAAATTTACCATCTTTGAATCTGTTTCCCTT
1 GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
*
252491 GAAACAAAA-TAAACATCTTTGAGATC-GTTTCTCTT
1 GAAACAAAATTAAACATCTTTGA-ATCTGTTTCCCTT
252526 GAAA
1 GAAA
252530 TGAATTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (36 bp):
GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
Found at i:253144 original size:133 final size:134
Alignment explanation
Indices: 252899--253211 Score: 495
Period size: 133 Copynumber: 2.3 Consensus size: 134
252889 CATAGGAACC
252899 GTGTCATCCCCTGACCAGATCTCCTCATCATGTAGGAGCCATGTCAACCATAGATAACCAGCCGT
1 GTGTCATCCCCTGACCAGATCTCCTCATCATGTAGGAGCCATGTCAACCATAGATAACCAGCCGT
* *
252964 CCTCATCACGTAGGAACCGTGTTATCGCCCTACCTAAAGATGTCCAGAACTCTTCATCACGTATG
66 CCTCATCACGTAGGAACCGTGTTATCACCCTACCTAAAGATGACCAGAACTCTTCATCACGTATG
253029 AGCA
131 AGCA
* * * *
253033 GTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTCATCC-TAGATAACCAGCCGT
1 GTGTCATCCCCTGACCAGATCTCCTCATCATGTAGGAGCCATGTCAACCATAGATAACCAGCCGT
* *
253097 CCTCATCACGTAGGAATCGTGTTATCACTCCT-CCTAAAGATGACCAGAACTCTTCATCATGTAT
66 CCTCATCACGTAGGAACCGTGTTATCAC-CCTACCTAAAGATGACCAGAACTCTTCATCACGTAT
253161 GAGCA
130 GAGCA
* * * *
253166 GTGTCATCCCTTGACCAGATTTCCTCATCATGTAGGAACCTTGTCA
1 GTGTCATCCCCTGACCAGATCTCCTCATCATGTAGGAGCCATGTCA
253212 CTTTTAGACG
Statistics
Matches: 164, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
133 116 0.71
134 48 0.29
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (134 bp):
GTGTCATCCCCTGACCAGATCTCCTCATCATGTAGGAGCCATGTCAACCATAGATAACCAGCCGT
CCTCATCACGTAGGAACCGTGTTATCACCCTACCTAAAGATGACCAGAACTCTTCATCACGTATG
AGCA
Found at i:253412 original size:3 final size:3
Alignment explanation
Indices: 253404--253457 Score: 90
Period size: 3 Copynumber: 17.3 Consensus size: 3
253394 CCGGGTCTTT
253404 TTA TTA TTA TTA TATA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
253451 TTA TTA T
1 TTA TTA T
253458 GTTTATTAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 44 0.90
4 4 0.08
5 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Done.