Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009443.1 Hibiscus syriacus cultivar Beakdansim tig00113507_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: 131245
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:18 original size:4 final size:4
Alignment explanation
Indices: 1--78 Score: 113
Period size: 4 Copynumber: 19.0 Consensus size: 4
1 TGTA TGTA -GCTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TG-TA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
49 TGTCTA TGTA TGTA TGTA TGTG TGTA TGTA
1 TG--TA TGTA TGTA TGTA TGTA TGTA TGTA
79 CACTAAGATT
Statistics
Matches: 68, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
3 1 0.01
4 62 0.91
5 1 0.01
6 4 0.06
ACGTcount: A:0.23, C:0.03, G:0.26, T:0.49
Consensus pattern (4 bp):
TGTA
Found at i:150 original size:2 final size:2
Alignment explanation
Indices: 143--190 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
133 GGTGATAGTA
*
143 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
184 -T AT AT AT
1 AT AT AT AT
191 TTATTATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:191 original size:10 final size:11
Alignment explanation
Indices: 143--197 Score: 62
Period size: 10 Copynumber: 5.2 Consensus size: 11
133 GGTGATAGTA
143 ATATATATA-T
1 ATATATATATT
153 ATATATATA-T
1 ATATATATATT
163 ATATATATA-T
1 ATATATATATT
*
173 AGATATATTATT
1 ATATATA-TATT
*
185 ATATATTTATT
1 ATATATATATT
196 AT
1 AT
198 TATTTTCACA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
10 26 0.65
11 8 0.20
12 6 0.15
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (11 bp):
ATATATATATT
Found at i:195 original size:14 final size:14
Alignment explanation
Indices: 143--200 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
133 GGTGATAGTA
143 ATATATATA-TA-T
1 ATATATATATTATT
155 ATATATATATATATAT
1 ATATATATAT-TAT-T
*
171 ATAGATATATTATT
1 ATATATATATTATT
*
185 ATATATTTATTATT
1 ATATATATATTATT
199 AT
1 AT
201 TTTCACACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
12 9 0.23
14 17 0.44
15 3 0.08
16 10 0.26
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
ATATATATATTATT
Found at i:291 original size:3 final size:3
Alignment explanation
Indices: 283--321 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
273 TAAGGGGTTA
283 TAT TAT TAT T-T TAT TA- TAT TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
322 ATAAATAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.18
3 27 0.82
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:322 original size:11 final size:11
Alignment explanation
Indices: 283--323 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
273 TAAGGGGTTA
283 TATTATTATT-T
1 TATTA-TATTAT
294 TATTATATTAT
1 TATTATATTAT
305 TATTATATTAT
1 TATTATATTAT
316 TATTATAT
1 TATTATAT
324 AAATAAAGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 4 0.14
11 25 0.86
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATTATATTAT
Found at i:6534 original size:31 final size:31
Alignment explanation
Indices: 6496--6557 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
6486 AAGTGTTCTA
6496 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
*
6527 TACGAGCTGTGGTGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
6558 ATGCGCCATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.15, G:0.39, T:0.24
Consensus pattern (31 bp):
TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
Found at i:7043 original size:88 final size:88
Alignment explanation
Indices: 6934--7114 Score: 353
Period size: 88 Copynumber: 2.1 Consensus size: 88
6924 TGTTTCAAAT
*
6934 TTTAAAATAATTAGGGTTGAGGACCAATAACATATGATGAATATGGATGTTCTTCATGTGATATT
1 TTTATAATAATTAGGGTTGAGGACCAATAACATATGATGAATATGGATGTTCTTCATGTGATATT
6999 GATATCTACCTAGAGTATCATTC
66 GATATCTACCTAGAGTATCATTC
7022 TTTATAATAATTAGGGTTGAGGACCAATAACATATGATGAATATGGATGTTCTTCATGTGATATT
1 TTTATAATAATTAGGGTTGAGGACCAATAACATATGATGAATATGGATGTTCTTCATGTGATATT
7087 GATATCTACCTAGAGTATCATTC
66 GATATCTACCTAGAGTATCATTC
7110 TTTAT
1 TTTAT
7115 GTAATTTTTA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 92 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (88 bp):
TTTATAATAATTAGGGTTGAGGACCAATAACATATGATGAATATGGATGTTCTTCATGTGATATT
GATATCTACCTAGAGTATCATTC
Found at i:10035 original size:19 final size:22
Alignment explanation
Indices: 10013--10068 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 22
10003 TTAATACTTT
10013 AAAATAA-TTTTTTAT-ACC-C
1 AAAATAATTTTTTTATCACCTC
10032 AAAATAATTTTTTTATCACCTC
1 AAAATAATTTTTTTATCACCTC
*
10054 AAAATATTCTTTTTT
1 AAAATAAT-TTTTTT
10069 TAAATTGACA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 7 0.22
20 8 0.25
21 3 0.09
22 8 0.25
23 6 0.19
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAATAATTTTTTTATCACCTC
Found at i:10066 original size:22 final size:19
Alignment explanation
Indices: 10013--10067 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 19
10003 TTAATACTTT
*
10013 AAAATAATTTTTTATACCC
1 AAAATATTTTTTTATACCC
10032 AAAATAATTTTTTTATCACCTC
1 AAAAT-ATTTTTTTAT-ACC-C
10054 AAAATATTCTTTTT
1 AAAATATT-TTTTT
10068 TTAAATTGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 5 0.16
20 9 0.29
21 6 0.19
22 11 0.35
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATATTTTTTTATACCC
Found at i:19092 original size:2 final size:2
Alignment explanation
Indices: 19085--19119 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
19075 TCACATTGAG
*
19085 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19120 GGGTTTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:23512 original size:17 final size:16
Alignment explanation
Indices: 23490--23561 Score: 76
Period size: 15 Copynumber: 4.5 Consensus size: 16
23480 CAGTGTCCCG
*
23490 ACCCGGATTTTATGGGT
1 ACCCGGATTTT-CGGGT
23507 ACCCGG-TTTTCGGGT
1 ACCCGGATTTTCGGGT
23522 ACCCGGATTTTGCGGGT
1 ACCCGGATTTT-CGGGT
* *
23539 ACCCGTA-TATCGGGT
1 ACCCGGATTTTCGGGT
*
23554 ACCTGGAT
1 ACCCGGAT
23562 GCGTTTGCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
15 20 0.43
16 10 0.21
17 17 0.36
ACGTcount: A:0.15, C:0.24, G:0.31, T:0.31
Consensus pattern (16 bp):
ACCCGGATTTTCGGGT
Found at i:23531 original size:32 final size:32
Alignment explanation
Indices: 23490--23561 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
23480 CAGTGTCCCG
* *
23490 ACCCGGATTTTATGGGTACCCGGT-TTTCGGGT
1 ACCCGGATTTTACGGGTACCC-GTATATCGGGT
*
23522 ACCCGGATTTTGCGGGTACCCGTATATCGGGT
1 ACCCGGATTTTACGGGTACCCGTATATCGGGT
*
23554 ACCTGGAT
1 ACCCGGAT
23562 GCGTTTGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 2 0.06
32 33 0.94
ACGTcount: A:0.15, C:0.24, G:0.31, T:0.31
Consensus pattern (32 bp):
ACCCGGATTTTACGGGTACCCGTATATCGGGT
Found at i:26749 original size:77 final size:80
Alignment explanation
Indices: 26645--26839 Score: 261
Period size: 84 Copynumber: 2.4 Consensus size: 80
26635 TAAATCCATG
*
26645 AAGGTGAAAATGGTTGTTAGCAAGCTGACATGCAT-ACATACATGGATCCATTTGTTCCGA-TTT
1 AAGGTGAAAATGGTTGTTAGCAAGCTGACATGCATAACATACATGGATCCATGTGTTCCGAGTTT
**
26708 TTTTGACAAAATGCA
66 TTCAGACAAAATGCA
*
26723 AAGGTGAAAATGG-TGTTAGCAAGCTGACACGCATACACACACATACATGGATCCATGTGTTCCG
1 AAGGTGAAAATGGTTGTTAGCAAGCTGACATGCAT----A-ACATACATGGATCCATGTGTTCCG
*
26787 AGTTTTTCAGACAAAATGTA
61 AGTTTTTCAGACAAAATGCA
**
26807 ACTGTGAAAATGGTTGTTAGCAAGCTGACATGC
1 AAGGTGAAAATGGTTGTTAGCAAGCTGACATGC
26840 GCGCGCGCGT
Statistics
Matches: 101, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
77 20 0.20
78 13 0.13
83 24 0.24
84 26 0.26
85 18 0.18
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (80 bp):
AAGGTGAAAATGGTTGTTAGCAAGCTGACATGCATAACATACATGGATCCATGTGTTCCGAGTTT
TTCAGACAAAATGCA
Found at i:26879 original size:89 final size:85
Alignment explanation
Indices: 26647--26913 Score: 246
Period size: 89 Copynumber: 3.2 Consensus size: 85
26637 AATCCATGAA
* * * **
26647 GGTGAAAATGGTTGTTAGCAAGCTGACATG------CATACATACATGGATCCATTTGTTCCGA-
1 GGTGAAAATGGTTGTTAGCAAGCTGACACGCACACACACACATACATAGATCCACGTGTTCCGAG
** * *
26705 TTTTTTTGACAAAATGCAAA
66 TTTTTCAGACAAAATGTAAC
* * *
26725 GGTGAAAATGG-TGTTAGCAAGCTGACACGCATACACACACATACATGGATCCATGTGTTCCGAG
1 GGTGAAAATGGTTGTTAGCAAGCTGACACGCACACACACACATACATAGATCCACGTGTTCCGAG
26789 TTTTTCAGACAAAATGTAAC
66 TTTTTCAGACAAAATGTAAC
* * * * *
26809 TGTGAAAATGGTTGTTAGCAAGCTGACATGCGCGCGCGCGTACACATGCATAGATCCACGTGTTC
1 GGTGAAAATGGTTGTTAGCAAGCTGACA--CGCACACAC--ACACATACATAGATCCACGTGTTC
* * *
26874 TGAGTTTTTCTGACACAATGTAAC
62 CGAGTTTTTCAGACAAAATGTAAC
26898 GGTG-AAATCGGTTGTT
1 GGTGAAAAT-GGTTGTT
26914 TGTAGGGACT
Statistics
Matches: 157, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
77 17 0.11
78 11 0.07
83 26 0.17
84 26 0.17
85 16 0.10
87 5 0.03
88 4 0.03
89 52 0.33
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (85 bp):
GGTGAAAATGGTTGTTAGCAAGCTGACACGCACACACACACATACATAGATCCACGTGTTCCGAG
TTTTTCAGACAAAATGTAAC
Found at i:35186 original size:121 final size:121
Alignment explanation
Indices: 34971--35276 Score: 425
Period size: 121 Copynumber: 2.5 Consensus size: 121
34961 TAAATTATGT
* * * *
34971 ATTTAGTACTTAAACTATCAATTTTGGTCCATTTTAGTACCTAGACTTTCATTTTTTTCAAAATC
1 ATTTAGTACCTAAACTATCAATTTTGGTCCATTTTAGTACCTAAACTTTCAATTTTTTCAAAACC
* * *
35036 ATATCTAACATTTAATTTTCATTTCATTTTAGCACCCACCATTAAAAACTTAACGTC
66 ATACCTAACATTTAATTATCATTTCATTTTAGCACCCACCATTAAAAACTTAAC-AC
* * *
35093 -TTTAGTACCTAAACTATCAATTTTAGTCTATTTTAGTACCTAAACTTTTAATTTTTTCAAAACC
1 ATTTAGTACCTAAACTATCAATTTTGGTCCATTTTAGTACCTAAACTTTCAATTTTTTCAAAACC
* ** * ***
35157 TTACCTAATGTTTAGTTATCATTTCATTTTAGCACCTGTCATTAAAAACTTAACAC
66 ATACCTAACATTTAATTATCATTTCATTTTAGCACCCACCATTAAAAACTTAACAC
* *
35213 ATTTAGTACCTAAACTATCAGTTTTGGTCCATTTTAGTACATAAACTTTCAATTTTTTCAAAAC
1 ATTTAGTACCTAAACTATCAATTTTGGTCCATTTTAGTACCTAAACTTTCAATTTTTTCAAAAC
35277 TTAACGTTTA
Statistics
Matches: 161, Mismatches: 22, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
120 1 0.01
121 160 0.99
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.43
Consensus pattern (121 bp):
ATTTAGTACCTAAACTATCAATTTTGGTCCATTTTAGTACCTAAACTTTCAATTTTTTCAAAACC
ATACCTAACATTTAATTATCATTTCATTTTAGCACCCACCATTAAAAACTTAACAC
Found at i:36088 original size:20 final size:21
Alignment explanation
Indices: 36065--36111 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
36055 AAATTATTTA
36065 AATATATAA-ACAATTAAAAC
1 AATATATAATACAATTAAAAC
* *
36085 AATA-AAAATACAATTAGAAC
1 AATATATAATACAATTAAAAC
36105 AATATAT
1 AATATAT
36112 TTAAAAGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.14
20 18 0.82
21 1 0.05
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
AATATATAATACAATTAAAAC
Found at i:37400 original size:3 final size:3
Alignment explanation
Indices: 37392--37566 Score: 244
Period size: 3 Copynumber: 57.7 Consensus size: 3
37382 TTATTTATTA
*
37392 AAT AAT AAT AAT ATAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
* **
37439 AAAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GCT AAT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
37485 AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
37533 AAT AAT GAT AAT AAT ATT AAT AAT -AT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
37567 AATGGATAAA
Statistics
Matches: 152, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.01
3 141 0.93
4 9 0.06
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:38111 original size:113 final size:113
Alignment explanation
Indices: 37864--38423 Score: 949
Period size: 113 Copynumber: 4.9 Consensus size: 113
37854 GATATCAAAC
* *
37864 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * * *
37929 CATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACA
66 -ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
*
37978 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
38043 ATGAACTTTCTCTAGAAAAGATGATCCACCAAATGATGGATTCAGGCA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
38091 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
38156 ATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGCA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
38204 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
38269 ATGAACTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
38317 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
38382 ATGAACTTTCTCTGGTAATGATGATCCATCAAATGATGAATT
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATT
38424 TGAATCTTTG
Statistics
Matches: 421, Mismatches: 25, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
113 359 0.85
114 62 0.15
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
Found at i:39059 original size:52 final size:52
Alignment explanation
Indices: 38981--39850 Score: 1471
Period size: 52 Copynumber: 16.7 Consensus size: 52
38971 CACTTCTTCG
* * *
38981 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCCATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
39033 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTTTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
39085 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
39137 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
39189 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
* *
39241 GATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGTTTTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
39293 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
39345 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
*
39397 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
39449 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
* *
39501 GATCAGATAACTCAAAAAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
39553 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
* *
39605 GATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
39657 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
*
39709 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
39761 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
39813 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
39851 TGAGCACATA
Statistics
Matches: 775, Mismatches: 33, Indels: 20
0.94 0.04 0.02
Matches are distributed among these distances:
51 5 0.01
52 765 0.99
53 5 0.01
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.24
Consensus pattern (52 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
Found at i:40803 original size:1 final size:1
Alignment explanation
Indices: 40792--40827 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
40782 CCTTGACCCC
* *
40792 TTTTTTCTTTTTCTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40828 CAAGCATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:52245 original size:20 final size:21
Alignment explanation
Indices: 52222--52268 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
52212 AAATTATTTA
52222 AATATATAA-ACAATTAAAAC
1 AATATATAATACAATTAAAAC
* *
52242 AATA-AAAATACAATTAGAAC
1 AATATATAATACAATTAAAAC
52262 AATATAT
1 AATATAT
52269 TTAAAAGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.14
20 18 0.82
21 1 0.05
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
AATATATAATACAATTAAAAC
Found at i:53558 original size:3 final size:3
Alignment explanation
Indices: 53550--53731 Score: 256
Period size: 3 Copynumber: 59.7 Consensus size: 3
53540 TTATTTATTA
*
53550 AAT AAT AAT AAT ATAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
* **
53597 AAAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GCT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
53643 AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT ATT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
53691 ATT AAT AAT GAT AAT AAT AAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
53732 AATGGATAAA
Statistics
Matches: 158, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
3 149 0.94
4 9 0.06
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:53862 original size:19 final size:19
Alignment explanation
Indices: 53820--53865 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
53810 TTATACTAAC
* *
53820 AATTTGATAAGTTTAAGAA
1 AATTTGATAAGATTAAAAA
* *
53839 TATTTTATAAGATTAAAAA
1 AATTTGATAAGATTAAAAA
53858 AATTTGAT
1 AATTTGAT
53866 GACCAAAACA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (19 bp):
AATTTGATAAGATTAAAAA
Found at i:56410 original size:19 final size:21
Alignment explanation
Indices: 56376--56420 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
56366 ATTAAATCTC
56376 TATTTTATTGAATAAAAATAA
1 TATTTTATTGAATAAAAATAA
* *
56397 TATTTT-TT-AATAAATATAT
1 TATTTTATTGAATAAAAATAA
56416 TATTT
1 TATTT
56421 CGGGTCGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
20 2 0.09
21 6 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTTTATTGAATAAAAATAA
Found at i:61149 original size:54 final size:54
Alignment explanation
Indices: 61067--61171 Score: 183
Period size: 54 Copynumber: 1.9 Consensus size: 54
61057 GTTATTTTAA
61067 ACATCAAAATAACGTCATTAAAATGCCATCGTTTCAATATAACATCCACATTAG
1 ACATCAAAATAACGTCATTAAAATGCCATCGTTTCAATATAACATCCACATTAG
* * *
61121 ACATCAAAGTAACGTCATTAAAATGCCATCGTTTTAATATGACATCCACAT
1 ACATCAAAATAACGTCATTAAAATGCCATCGTTTCAATATAACATCCACAT
61172 CAGCACCTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.29
Consensus pattern (54 bp):
ACATCAAAATAACGTCATTAAAATGCCATCGTTTCAATATAACATCCACATTAG
Found at i:67725 original size:22 final size:22
Alignment explanation
Indices: 67698--67742 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
67688 TGCATCTCTC
67698 GATCGTCGATTACCGTCAAGAG
1 GATCGTCGATTACCGTCAAGAG
67720 GATCGTCGATTACCGTCAAGAG
1 GATCGTCGATTACCGTCAAGAG
67742 G
1 G
67743 TACTAGACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (22 bp):
GATCGTCGATTACCGTCAAGAG
Found at i:72381 original size:13 final size:15
Alignment explanation
Indices: 72353--72384 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
72343 AATTTTATTT
72353 AATTATATAAATTAA
1 AATTATATAAATTAA
72368 AATTA-ATAAA-TAA
1 AATTATATAAATTAA
72381 AATT
1 AATT
72385 TTCAATCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 5 0.29
15 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTATATAAATTAA
Found at i:84102 original size:31 final size:31
Alignment explanation
Indices: 84062--84147 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 31
84052 AAAAGTTCAT
* *
84062 TAAATTTAATGATCACTT-TGTAACAGTTTGA
1 TAAATTTAATGACCA-TTCTGTAACAGTTAGA
*
84093 TAAAATTAATGACCATTCTGTAACAGTTAGA
1 TAAATTTAATGACCATTCTGTAACAGTTAGA
* *
84124 TAAATTTAATGACTATTTTGTAAC
1 TAAATTTAATGACCATTCTGTAAC
84148 TTTTGAAAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
30 2 0.04
31 46 0.96
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (31 bp):
TAAATTTAATGACCATTCTGTAACAGTTAGA
Found at i:85955 original size:2 final size:2
Alignment explanation
Indices: 85948--85972 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
85938 TAACGATTCT
85948 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
85973 GCTCATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:87465 original size:16 final size:18
Alignment explanation
Indices: 87429--87466 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
87419 AAAAATAGAT
*
87429 TTTTTTATATTAATAATA
1 TTTTTTATATTAATAAAA
87447 TTTTTTAT-TTAA-AAAA
1 TTTTTTATATTAATAAAA
87463 TTTT
1 TTTT
87467 AAAAATACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 4 0.21
18 8 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTTATATTAATAAAA
Found at i:87550 original size:14 final size:16
Alignment explanation
Indices: 87526--87565 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
87516 TTACAATCCA
87526 AACACTTAAAAA-TAT
1 AACACTTAAAAACTAT
87541 AACA-TTAAAAACTAT
1 AACACTTAAAAACTAT
87556 AAACACTTAA
1 -AACACTTAA
87566 TTTTAACGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.32
15 7 0.32
16 4 0.18
17 4 0.18
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (16 bp):
AACACTTAAAAACTAT
Found at i:98955 original size:14 final size:14
Alignment explanation
Indices: 98936--98966 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
98926 TTTTAATTTT
*
98936 TAAAATCAATTGAA
1 TAAAATCAATTAAA
98950 TAAAATCAATTAAA
1 TAAAATCAATTAAA
98964 TAA
1 TAA
98967 TATTATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.29
Consensus pattern (14 bp):
TAAAATCAATTAAA
Found at i:99793 original size:2 final size:2
Alignment explanation
Indices: 99786--99813 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
99776 AAGTTTGGGG
99786 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
99814 GTATTTGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:100397 original size:2 final size:2
Alignment explanation
Indices: 100390--100417 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
100380 AATTAGACCA
100390 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
100418 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107145 original size:10 final size:10
Alignment explanation
Indices: 107130--107229 Score: 79
Period size: 10 Copynumber: 10.3 Consensus size: 10
107120 CCGGTTTTCA
107130 ACCGGTTCTG
1 ACCGGTTCTG
* *
107140 ACCGGTTTTCA
1 ACCGGTTCT-G
107151 ACCGGTTCTG
1 ACCGGTTCTG
107161 ACCGGTT-TG
1 ACCGGTTCTG
*
107170 ACCGGTT-TCA
1 ACCGGTTCT-G
107180 ACCGGTTC-G
1 ACCGGTTCTG
107189 AACCGGTT-TG
1 -ACCGGTTCTG
107199 ACCGG-TCTG
1 ACCGGTTCTG
*
107208 AATCGGTT-TG
1 -ACCGGTTCTG
107218 ACCGG-TCTG
1 ACCGGTTCTG
107227 ACC
1 ACC
107230 CGACCCGACC
Statistics
Matches: 73, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
8 2 0.03
9 26 0.36
10 36 0.49
11 9 0.12
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.29
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:107145 original size:21 final size:21
Alignment explanation
Indices: 107109--107168 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
107099 GGCTGCTGGA
*
107109 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTGACCGGTTTTC
107129 AACCGGTTCTGACCGGTTTTC
1 AACCGGTTCTGACCGGTTTTC
107150 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTGACCGGTTT
107169 GACCGGTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 8 0.21
21 30 0.79
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTGACCGGTTTTC
Found at i:107175 original size:19 final size:19
Alignment explanation
Indices: 107111--107229 Score: 84
Period size: 19 Copynumber: 6.1 Consensus size: 19
107101 CTGCTGGAAA
* * *
107111 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
* *
107131 CCGGTTCTGACCGGTTTTCAA
1 CCGGTT-TGACCGGTTCT-GA
107152 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
107171 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
107191 CCGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
*
107210 TCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
107228 CC
1 CC
107230 CGACCCGACC
Statistics
Matches: 88, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
18 5 0.06
19 39 0.44
20 15 0.17
21 29 0.33
ACGTcount: A:0.15, C:0.28, G:0.27, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:107236 original size:5 final size:5
Alignment explanation
Indices: 107226--107288 Score: 72
Period size: 5 Copynumber: 11.8 Consensus size: 5
107216 TGACCGGTCT
* *
107226 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCC GACCGTT GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACCC GACC--C GACCC
107275 GACCC GACCC GACC
1 GACCC GACCC GACC
107289 GTTGACCGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
5 42 0.84
7 8 0.16
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.06
Consensus pattern (5 bp):
GACCC
Found at i:107252 original size:22 final size:22
Alignment explanation
Indices: 107248--107295 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
107238 CCGTTGACCC
107248 GACCCGACCCGACCCGACCGTT
1 GACCCGACCCGACCCGACCGTT
107270 GACCCGACCCGACCCGACCGTT
1 GACCCGACCCGACCCGACCGTT
107292 GACC
1 GACC
107296 GTTGACCGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.08
Consensus pattern (22 bp):
GACCCGACCCGACCCGACCGTT
Found at i:107258 original size:27 final size:27
Alignment explanation
Indices: 107226--107302 Score: 127
Period size: 27 Copynumber: 2.8 Consensus size: 27
107216 TGACCGGTCT
107226 GACCCGACCCGACCGTTGACCCGACCC
1 GACCCGACCCGACCGTTGACCCGACCC
107253 GACCCGACCCGACCGTTGACCCGACCC
1 GACCCGACCCGACCGTTGACCCGACCC
*
107280 GACCCGACCGTTGACCGTTGACC
1 GACCCGACC--CGACCGTTGACC
107303 GTTGACCATT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 36 0.77
29 11 0.23
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.10
Consensus pattern (27 bp):
GACCCGACCCGACCGTTGACCCGACCC
Found at i:107295 original size:17 final size:17
Alignment explanation
Indices: 107225--107283 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 17
107215 TTGACCGGTC
107225 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
107242 TGACCCGA--C--CC--
1 TGACCCGACCCGACCGT
107253 -GACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
107269 TGACCCGACCCGACC
1 TGACCCGACCCGACC
107284 CGACCGTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
10 7 0.20
12 1 0.03
13 2 0.06
14 2 0.06
15 1 0.03
17 22 0.63
ACGTcount: A:0.19, C:0.51, G:0.22, T:0.08
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:107297 original size:7 final size:7
Alignment explanation
Indices: 107285--107315 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
107275 GACCCGACCC
107285 GACCGTT
1 GACCGTT
107292 GACCGTT
1 GACCGTT
107299 GACCGTT
1 GACCGTT
*
107306 GACCATT
1 GACCGTT
107313 GAC
1 GAC
107316 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:114503 original size:10 final size:9
Alignment explanation
Indices: 114468--114559 Score: 76
Period size: 10 Copynumber: 9.6 Consensus size: 9
114458 GCTGCTGGAA
*
114468 ACCGGTTTA
1 ACCGGTTTG
*
114477 ACCGGTTTTCA
1 ACCGG-TTT-G
114488 ACCGGTTCTG
1 ACCGGTT-TG
114498 ACCGGTTTG
1 ACCGGTTTG
*
114507 ACCGGTTTCA
1 ACCGGTTT-G
*
114517 ACCGGTTCG
1 ACCGGTTTG
114526 AACCGGTTTG
1 -ACCGGTTTG
*
114536 ACCGGTCTG
1 ACCGGTTTG
*
114545 AATCGGTTTG
1 -ACCGGTTTG
114555 ACCGG
1 ACCGG
114560 GTCTGACCCG
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
9 27 0.40
10 34 0.50
11 7 0.10
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:114512 original size:19 final size:19
Alignment explanation
Indices: 114469--114567 Score: 78
Period size: 19 Copynumber: 5.1 Consensus size: 19
114459 CTGCTGGAAA
* * *
114469 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
114489 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
114508 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
114528 CCGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
* *
114547 TCGGTTTGACCGGGTCTGA
1 CCGGTTTGACCGGTTCTGA
114566 CC
1 CC
114568 CGACCCGACC
Statistics
Matches: 67, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
18 3 0.04
19 37 0.55
20 19 0.28
21 8 0.12
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.29
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:114530 original size:29 final size:30
Alignment explanation
Indices: 114467--114541 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
114457 GGCTGCTGGA
*
114467 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
114498 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
114526 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
114542 CTGAATCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:114574 original size:5 final size:5
Alignment explanation
Indices: 114564--114643 Score: 70
Period size: 5 Copynumber: 14.8 Consensus size: 5
114554 GACCGGGTCT
* *
114564 GACCC GACCC GACCGTT GACCC GACCC GACCGTT GACCC GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACC--C GACCC GACCC GACCC
* *
114613 GACCC GACCGTT GACCC GACTC GACCC GACC
1 GACCC GACC--C GACCC GACCC GACCC GACC
114644 GTTGACCGTT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
5 49 0.80
7 12 0.20
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.09
Consensus pattern (5 bp):
GACCC
Found at i:114590 original size:22 final size:22
Alignment explanation
Indices: 114564--114650 Score: 115
Period size: 22 Copynumber: 4.0 Consensus size: 22
114554 GACCGGGTCT
114564 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
* *
114586 GACCCGACCGTTGACC--CGACCC
1 GACCCGACC--CGACCGTTGACCC
114608 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
114630 GACTCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
114651 GTTGACCGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
20 4 0.07
22 48 0.86
24 4 0.07
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.10
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:114622 original size:27 final size:27
Alignment explanation
Indices: 114581--114657 Score: 118
Period size: 27 Copynumber: 2.8 Consensus size: 27
114571 CCCGACCGTT
114581 GACCCGACCCGACCGTTGACCCGACCC
1 GACCCGACCCGACCGTTGACCCGACCC
*
114608 GACCCGACCCGACCGTTGACCCGACTC
1 GACCCGACCCGACCGTTGACCCGACCC
*
114635 GACCCGACCGTTGACCGTTGACC
1 GACCCGACC--CGACCGTTGACC
114658 GTTGACCATT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 35 0.76
29 11 0.24
ACGTcount: A:0.18, C:0.47, G:0.23, T:0.12
Consensus pattern (27 bp):
GACCCGACCCGACCGTTGACCCGACCC
Found at i:114638 original size:17 final size:17
Alignment explanation
Indices: 114563--114611 Score: 98
Period size: 17 Copynumber: 2.9 Consensus size: 17
114553 TGACCGGGTC
114563 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
114580 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
114597 TGACCCGACCCGACC
1 TGACCCGACCCGACC
114612 CGACCCGACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.18, C:0.49, G:0.22, T:0.10
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:114652 original size:7 final size:7
Alignment explanation
Indices: 114640--114670 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
114630 GACTCGACCC
114640 GACCGTT
1 GACCGTT
114647 GACCGTT
1 GACCGTT
114654 GACCGTT
1 GACCGTT
*
114661 GACCATT
1 GACCGTT
114668 GAC
1 GAC
114671 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:117627 original size:23 final size:23
Alignment explanation
Indices: 117601--117645 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
117591 TTAAATTATA
*
117601 TATAAAATTTTAAAAAATAAAAG
1 TATAAAATTTTAAAAAAGAAAAG
* *
117624 TATATATTTTTAAAAAAGAAAA
1 TATAAAATTTTAAAAAAGAAAA
117646 CACATAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (23 bp):
TATAAAATTTTAAAAAAGAAAAG
Found at i:117657 original size:23 final size:22
Alignment explanation
Indices: 117605--117658 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
117595 ATTATATATA
* **
117605 AAATTTTAAAAAATAAAAGTAT
1 AAATTTTAAAAAAGAAAAACAT
*
117627 ATATTTTTAAAAAAGAAAACACAT
1 A-AATTTTAAAAAAGAAAA-ACAT
117651 AAATTTTA
1 AAATTTTA
117659 TATAACCCCT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 1 0.04
23 21 0.84
24 3 0.12
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (22 bp):
AAATTTTAAAAAAGAAAAACAT
Found at i:120026 original size:23 final size:23
Alignment explanation
Indices: 119981--120026 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
119971 GGTTGAGATC
* * *
119981 AATAAAATTTTAGGGTGGGCACA
1 AATAAAATTTAAGGGTAGACACA
120004 AATAAAATTTAAGGGTAGACACA
1 AATAAAATTTAAGGGTAGACACA
120027 TCAGTAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.24
Consensus pattern (23 bp):
AATAAAATTTAAGGGTAGACACA
Found at i:120556 original size:14 final size:16
Alignment explanation
Indices: 120530--120561 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
120520 TTTTTATCCC
120530 AATCTCAAACCC-TAA
1 AATCTCAAACCCTTAA
120545 AATCTC-AACCCTTAA
1 AATCTCAAACCCTTAA
120560 AA
1 AA
120562 CCCAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (16 bp):
AATCTCAAACCCTTAA
Found at i:120577 original size:21 final size:23
Alignment explanation
Indices: 120536--120590 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
120526 TCCCAATCTC
*
120536 AAACCCTAAAATCTCAACCCTTA
1 AAACCCTAAAATATCAACCCTTA
120559 AAACCC-AAAATAT-AACCCTT-
1 AAACCCTAAAATATCAACCCTTA
*
120579 AAACCCTCAAAT
1 AAACCCTAAAAT
120591 TTTCAATCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 6 0.21
21 11 0.38
22 6 0.21
23 6 0.21
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (23 bp):
AAACCCTAAAATATCAACCCTTA
Found at i:126872 original size:29 final size:28
Alignment explanation
Indices: 126810--126873 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
126800 TAGATACTCC
*
126810 ATAAT-AAATAAATAAAAGAACTTAATTT
1 ATAATAAAATAAATAAAAGAAC-GAATTT
*
126838 AAAATAAAATAAAATAAAAGAA-GAATATT
1 ATAATAAAAT-AAATAAAAGAACGAAT-TT
126867 ATAATAA
1 ATAATAA
126874 TTATCTCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 7 0.23
29 12 0.40
30 11 0.37
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (28 bp):
ATAATAAAATAAATAAAAGAACGAATTT
Found at i:128178 original size:23 final size:23
Alignment explanation
Indices: 128145--128191 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
128135 TTCAGAAGAA
128145 AAGCTTCTTAGATTTTATGTTTT
1 AAGCTTCTTAGATTTTATGTTTT
*
128168 AAGCTTTTTAGATTTTATGTTTT
1 AAGCTTCTTAGATTTTATGTTTT
128191 A
1 A
128192 CTTTTATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.23, C:0.06, G:0.13, T:0.57
Consensus pattern (23 bp):
AAGCTTCTTAGATTTTATGTTTT
Done.