Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009177.1 Hibiscus syriacus cultivar Beakdansim tig00112742_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: 392072
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:365155 original size:297 final size:295
Alignment explanation
Indices: 364583--365176 Score: 1017
Period size: 297 Copynumber: 2.0 Consensus size: 295
364573 TTTGAATACA
364583 AGCACGCAGTCTACTTCAACTGATTTTTTTGAAGACGGAATGGAATGGTTATGAACCTCCAGCAC
1 AGCACGCAGTCTACTTCAACTGATTTTTTTGAAGACGGAATGGAATGGTTATGAACCTCCAGCAC
* * *
364648 ATGATGTTTGATACATTTGGTTATAATTATGTTTTCAATGTTTTTGGGATCGACAATTGTTATAA
66 ATGATGTTAGAGACATTTGGTTATAATTATGTTTTCAATGTTTTTGGGATCAACAATTGTTATAA
*
364713 ATGTATCGAAACTTTATTGTGCACTTGGTTTTTAAAATATAGTATGGACAAAAATATATCGAAAC
131 ATGTATCGAAACTTTATTGTACACTTGGTTTTTAAAATATAGTATGGACAAAAATATATCGAAAC
*
364778 TTGATGTATTTGTGTCGATACTTCATGTATACATGTTTTCTCATAAACCGGTACATATAGACCGG
196 TTGATGTATTTGTGTCGATACTTCATGTATACATGTTTTCTCATAAACCGGTACATATAGACCAG
*
364843 TTACATTGTTAATTTACCTATTAAATTATAATTAT
261 TTACATTGCTAATTTACCTATTAAATTATAATTAT
*
364878 AGCACGTAGTCTACTTCAACTGAATTTTTTTGAAGACGGAATGGAATGGTTATGAACCTCCAGCA
1 AGCACGCAGTCTACTTCAACTG-ATTTTTTTGAAGACGGAATGGAATGGTTATGAACCTCCAGCA
* *
364943 CATGATGTTAGAGACATTTGGTTATAATTATGTTTTTCGATGTTTTTGGGATTAACAATTGTTAT
65 CATGATGTTAGAGACATTTGGTTATAATTATG-TTTTCAATGTTTTTGGGATCAACAATTGTTAT
* * * * *
365008 AAATGTATCGAAATTTTGTTGTACACTTGGTTTTTAAAATATAGTCTGGACAAAAATGTTTCGAA
129 AAATGTATCGAAACTTTATTGTACACTTGGTTTTTAAAATATAGTATGGACAAAAATATATCGAA
*
365073 ACTTGATGTATTTGTGTCGATACTTCATGTATACATGTTTTCTCATAAACCGGTACATTTAGACC
194 ACTTGATGTATTTGTGTCGATACTTCATGTATACATGTTTTCTCATAAACCGGTACATATAGACC
* *
365138 AGTTATATTGCTAATTTACCTATTACATTATAATTAT
259 AGTTACATTGCTAATTTACCTATTAAATTATAATTAT
365175 AG
1 AG
365177 TTTTCGAAGT
Statistics
Matches: 280, Mismatches: 17, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
295 21 0.08
296 72 0.26
297 187 0.67
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (295 bp):
AGCACGCAGTCTACTTCAACTGATTTTTTTGAAGACGGAATGGAATGGTTATGAACCTCCAGCAC
ATGATGTTAGAGACATTTGGTTATAATTATGTTTTCAATGTTTTTGGGATCAACAATTGTTATAA
ATGTATCGAAACTTTATTGTACACTTGGTTTTTAAAATATAGTATGGACAAAAATATATCGAAAC
TTGATGTATTTGTGTCGATACTTCATGTATACATGTTTTCTCATAAACCGGTACATATAGACCAG
TTACATTGCTAATTTACCTATTAAATTATAATTAT
Found at i:365474 original size:198 final size:198
Alignment explanation
Indices: 364964--366173 Score: 1576
Period size: 199 Copynumber: 6.1 Consensus size: 198
364954 AGACATTTGG
* ** * * *
364964 TTATAATTATGTTTTTCGATGTTTTTGGGATTAACAATTGTTATAAATGTATCGA-AATTTTGTT
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTATAAATGTATCGACACTTTT-TA
* * * * * * * *
365028 GTACACTTGGTTTTTAAAATATAGTCTGGACAAAAATGTTTCGAAACTTGATGTATTTGTGTCGA
65 GTGCACTTGG-TTTTGAAATACATTCTGGACAAAAA-GTATCGACACTTGTTATATTTGTGTCGA
** * * * * *
365093 TACTTCATGTATACATGTTTTCTCATAAACCGGTACATTTAGACCAGTTATA-TTGCTAATTTAC
128 TACTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACC-GTT-TACATGATAATTTAC
365157 CTATTACA
191 CTATTACA
* * * *
365165 TTATAATTATAG-TTTTCGAAGTTTTTGGGATCGACACTTGTTATATATGTATCTACACTTTTTA
1 TTATAATTAT-GTTTTTCGATGTTTTCGGGATCGACACTTGTTATAAATGTATCGACACTTTTTA
*
365229 GTGCACTTGGTTTTGAAATACATTCTGGAGAAAAAGTATCGACACTTGTTATATTTGTGTCGATA
65 GTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGATA
* *
365294 CTTTTTATACACATATTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTA
130 CTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATG-ATAATTTACCTA
365359 TTACA
194 TTACA
*
365364 TTATAATTATGTTTTTCGAT-TTTTCGGGATCGACACTTGTTTTAAATGTATCGACAC-TTTTAT
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTATAAATGTATCGACACTTTTTA-
* * *
365427 GTGCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTCTATTTGTGTCGATA
65 GTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGATA
* * * * *
365492 CTGTTTGTACACTTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGTTAATTTACCTA
130 CTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACA-TGATAATTTACCTA
365557 TTACA
194 TTACA
* * *
365562 TTATAATTATGGTTTTT-GATGTTTTTGGGATCGACACTTGTTATATATGTATCAACACTTTTTA
1 TTATAATTAT-GTTTTTCGATGTTTTCGGGATCGACACTTGTTATAAATGTATCGACACTTTTTA
* *
365626 GTGCACTTGGTTTTAAAATACAGTT-TGGAGAAAAAGTATCGACACTTGTTATATTTGTGTCGAT
65 GTGCACTTGGTTTTGAAATACA-TTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGAT
* *
365690 ACTTTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCT
129 ACTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATG-ATAATTTACCT
365755 ATTACA
193 ATTACA
*
365761 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACAC-TTTTAT
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTATAAATGTATCGACACTTTTTA-
* *
365825 GTGCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGACACTTG-T-TATTTGTGTCGATA
65 GTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGATA
* * ** * *
365888 CTGTTTGTACACATG-TTTCTCAAAAACCGGTATATTT--ACCGATTATTTTGCTAATTTACTTA
130 CTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTA-CATGATAATTTACCTA
365950 TTACA
194 TTACA
* * *
365955 TTATAATTATGGTTTTCGATGTTTT-TGGATC-ACACTTGTTAT--ATGTATTGACACTTTTTAG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
* * * * *
366016 TGCACTTGGATTTGAAATACAATATGGA-GAAAAGTATCGACACTTGTTAGATTTGTGTCGATAC
66 TGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGATAC
* *
366080 TTTTTGTATACATGTTTTCTCAAAAA-CAGTATATTTAGACCGTTTACATGAATAATTTACCTAT
131 TTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATG-ATAATTTACCTAT
366144 TACA
195 TACA
*
366148 TTATAATTATATTTTTCGATGTTTTC
1 TTATAATTATGTTTTTCGATGTTTTC
366174 AATACTTATA
Statistics
Matches: 892, Mismatches: 93, Indels: 55
0.86 0.09 0.05
Matches are distributed among these distances:
189 17 0.02
190 37 0.04
191 40 0.04
192 23 0.03
193 50 0.06
194 46 0.05
195 2 0.00
196 22 0.02
197 33 0.04
198 189 0.21
199 342 0.38
200 28 0.03
201 57 0.06
202 6 0.01
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (198 bp):
TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
TGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGATAC
TTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGATAATTTACCTATT
ACA
Found at i:366248 original size:20 final size:21
Alignment explanation
Indices: 366223--366261 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
366213 GTAGCGTTTT
366223 ACCGGTTTTGTCAT-TTTGGG
1 ACCGGTTTTGTCATATTTGGG
366243 ACCGGTTTTGTCATATTTG
1 ACCGGTTTTGTCATATTTG
366262 TACATGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.13, C:0.15, G:0.26, T:0.46
Consensus pattern (21 bp):
ACCGGTTTTGTCATATTTGGG
Found at i:374263 original size:20 final size:22
Alignment explanation
Indices: 374238--374295 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
374228 TTCCCCTTGA
374238 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
374258 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
374281 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
374296 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:374361 original size:64 final size:63
Alignment explanation
Indices: 374283--374423 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
374273 TCTTTAACAT
* * *
374283 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAATGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * *
374346 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
374410 GTGCATCGATGCAC
1 GTGCATCGATGCAC
374424 ATTGAATATG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 21 0.31
64 46 0.69
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:375256 original size:20 final size:20
Alignment explanation
Indices: 375233--375271 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
375223 TACTCAATCT
375233 TCGGCATGGAGACTAGTCCC
1 TCGGCATGGAGACTAGTCCC
*
375253 TCGGTATGGAGACTAGTCC
1 TCGGCATGGAGACTAGTCC
375272 ACCAACCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.23
Consensus pattern (20 bp):
TCGGCATGGAGACTAGTCCC
Found at i:375933 original size:2 final size:2
Alignment explanation
Indices: 375928--375962 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
375918 TTGTGTGTGA
375928 AT 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 AT A
375963 GTAAGATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:378287 original size:33 final size:32
Alignment explanation
Indices: 378224--378287 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
378214 GATTTTGAAA
*
378224 TTATTTTTCATGTATAATATAAAATTTTAAAT
1 TTATTTTTCATGTATAATATAAAATATTAAAT
*
378256 TTATTTTTCAT-TATAATCTTTAAAATATTAAA
1 TTATTTTTCATGTATAA--TATAAAATATTAAA
378288 AAAACTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 5 0.18
32 11 0.39
33 12 0.43
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (32 bp):
TTATTTTTCATGTATAATATAAAATATTAAAT
Found at i:378538 original size:20 final size:21
Alignment explanation
Indices: 378513--378564 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
378503 TTTTTCCAAT
*
378513 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
378533 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
378554 TCGCAATGCGA
1 TCGCAATGCGA
378565 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:378578 original size:20 final size:20
Alignment explanation
Indices: 378553--378653 Score: 105
Period size: 20 Copynumber: 5.0 Consensus size: 20
378543 AATTGGGAAA
378553 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
378573 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
378593 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
378614 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
378634 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
378654 TTCTCAACGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.03
20 51 0.75
21 13 0.19
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:378654 original size:20 final size:20
Alignment explanation
Indices: 378615--378667 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
378605 TAATACAAAA
* *
378615 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
378635 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
378655 TCTCAACGCGATT
1 TCGCAACGCGATT
378668 TACATAGCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:378666 original size:61 final size:61
Alignment explanation
Indices: 378550--378666 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
378540 GCGAATTGGG
* * * * *
378550 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
378611 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCTCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
378667 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:379246 original size:19 final size:19
Alignment explanation
Indices: 379222--379262 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
379212 CGAGAGAATT
*
379222 GCAACGCGAAATAAAAATC
1 GCAACGCGAAACAAAAATC
*
379241 GCAACGCGAAACCAAAATC
1 GCAACGCGAAACAAAAATC
379260 GCA
1 GCA
379263 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.27, G:0.17, T:0.07
Consensus pattern (19 bp):
GCAACGCGAAACAAAAATC
Found at i:379280 original size:19 final size:19
Alignment explanation
Indices: 379258--379403 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
379248 GAAACCAAAA
*
379258 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
379277 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
379296 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
379310 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
379329 TCGCGTTGC-A-ATTC---
1 TCGCGTTGCGATTTTCATT
* **
379343 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
379362 TCTGCGTTGCGATTCTCATT
1 TC-GCGTTGCGATTTTCATT
*
379382 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
379402 TC
1 TC
379404 AACCAAAAGA
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
14 17 0.17
15 1 0.01
16 5 0.05
17 6 0.06
18 1 0.01
19 40 0.40
20 29 0.29
21 2 0.02
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:379328 original size:33 final size:33
Alignment explanation
Indices: 379291--379378 Score: 149
Period size: 33 Copynumber: 2.6 Consensus size: 33
379281 GTTGCGATTT
379291 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
* *
379324 TCATTTCGCGTTGCAATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
379357 TCATTTCTGCGTTGCGATTCTC
1 TCATTTC-GCGTTGCGATTCTC
379379 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 38 0.75
34 13 0.25
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:381511 original size:21 final size:21
Alignment explanation
Indices: 381487--381553 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
381477 TCATTCCTCG
381487 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
381508 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
381529 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
381550 AGAG
1 AGAG
381554 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:381511 original size:42 final size:42
Alignment explanation
Indices: 381435--381553 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
381425 GACTCGCCTG
* * * *
381435 TCATCCCTC-AAGA-GTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCATTCAAGAGGCCACTA
* *
381477 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTCGAAGAGGT-CCCTCCCACCATTCAAGAGGCCACTA
* *
381519 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAG
381554 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
41 4 0.06
42 54 0.86
43 5 0.08
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAGGCCACTA
Found at i:382931 original size:14 final size:14
Alignment explanation
Indices: 382912--382943 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
382902 TTTAATTGAA
382912 TTGTAAAAGGTGAT
1 TTGTAAAAGGTGAT
*
382926 TTGTAAAAGTTGAT
1 TTGTAAAAGGTGAT
382940 TTGT
1 TTGT
382944 TTAATTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TTGTAAAAGGTGAT
Found at i:383121 original size:33 final size:33
Alignment explanation
Indices: 383084--383154 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
383074 AACGAGAGAA
383084 TCGCAACGCGAAAT-TAGCGTTGCGATTTTCATT
1 TCGCAACGCG-AATCTAGCGTTGCGATTTTCATT
** * **
383117 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCAACGCGAATCTAGCGTTGCGATTTTCATT
383150 TCGCA
1 TCGCA
383155 TTGCGATAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (33 bp):
TCGCAACGCGAATCTAGCGTTGCGATTTTCATT
Found at i:383127 original size:19 final size:19
Alignment explanation
Indices: 383103--383161 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
383093 GAAATTAGCG
383103 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
383122 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
383136 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
383155 TTGCGAT
1 TTGCGAT
383162 AGTAATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:385675 original size:24 final size:24
Alignment explanation
Indices: 385641--385694 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
385631 CTGAAACATC
*
385641 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
385665 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
385689 ATCAAA
1 ATCAAA
385695 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:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:386459 original size:20 final size:20
Alignment explanation
Indices: 386434--386484 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
386424 TGTATTATCT
*
386434 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAAAATCG
386454 CGTTGCGAAAGTCAAAATCG
1 CGTTGCGAAAGTCAAAATCG
*
386474 TGTTGCGAAAG
1 CGTTGCGAAAG
386485 GCAATCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (20 bp):
CGTTGCGAAAGTCAAAATCG
Found at i:386750 original size:19 final size:20
Alignment explanation
Indices: 386697--386766 Score: 108
Period size: 19 Copynumber: 3.5 Consensus size: 20
386687 ATTCATTTGA
386697 CTATCGCAACGCGAAAAATGG
1 CTATCGCAACGCG-AAAATGG
386718 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
386738 CTA-CGCAATGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
386756 CTATCGCAACG
1 CTATCGCAACG
386767 ACAAAATCGC
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.20
19 14 0.30
20 10 0.22
21 13 0.28
ACGTcount: A:0.34, C:0.26, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:386837 original size:19 final size:19
Alignment explanation
Indices: 386792--386856 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
386782 AAAATGAAAA
386792 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
386808 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
386825 TCGCATTGTGATTTTTATT
1 TCGCATTGCGATTTTCATT
386844 TCGCATTGCGATT
1 TCGCATTGCGATT
386857 CTCTCGTTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 11 0.27
16 3 0.07
17 3 0.07
19 24 0.59
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:387002 original size:14 final size:14
Alignment explanation
Indices: 386983--387019 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
386973 CATCAATTAA
386983 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
386997 ACAAATCATCTTTT
1 ACAAATCAACATTT
387011 ACAAATCAA
1 ACAAATCAA
387020 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:388901 original size:20 final size:20
Alignment explanation
Indices: 388878--388945 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
388868 GAAACTTAAA
388878 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
388898 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
* **
388918 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
388937 ATCGCAACG
1 ATCGCAACG
388946 ACAAAATCGC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 13 0.31
20 29 0.69
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:388953 original size:14 final size:14
Alignment explanation
Indices: 388934--388991 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
388924 ATGCGAAATG
388934 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
388948 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
388964 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
388980 AAAATCGCAACG
1 AAAATCGCAACG
388992 CGAAACCCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:388976 original size:32 final size:33
Alignment explanation
Indices: 388918--388996 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
388908 GAAAATGGCT
388918 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
388951 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
388983 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
388997 CCCAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:389025 original size:19 final size:18
Alignment explanation
Indices: 389003--389097 Score: 82
Period size: 19 Copynumber: 5.7 Consensus size: 18
388993 GAAACCCAAA
389003 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
389022 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
389038 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
*
389054 TCGCATTGCGA-TT--TG
1 TCGCATTGCGATTTCATT
389069 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
389086 TCGCATTGCGAT
1 TCGCATTGCGAT
389098 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
13 6 0.10
14 9 0.15
15 6 0.10
16 8 0.13
17 6 0.10
18 10 0.16
19 16 0.26
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:389055 original size:32 final size:33
Alignment explanation
Indices: 389008--389097 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
388998 CCAAATCGCA
*
389008 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
389041 TTGCGA-TTTCATTTCGCATTGCGA-TTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
389072 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
389098 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
31 13 0.24
32 35 0.65
33 6 0.11
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:389116 original size:20 final size:19
Alignment explanation
Indices: 389082--389136 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
389072 TTGCGATTTT
*
389082 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
389101 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
389121 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
389137 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:389641 original size:18 final size:18
Alignment explanation
Indices: 389615--389659 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
389605 GTCGATCAGA
*
389615 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
389633 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
389651 TGATGGCTC
1 TGATGGCTC
389660 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:391013 original size:18 final size:18
Alignment explanation
Indices: 390990--391065 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
390980 ACCGGTCACA
390990 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
391008 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
391025 ----TA-CCGACCCGTTG
1 ACCCGACCCGACCCGTTG
391038 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
391056 ACCCGACCCG
1 ACCCGACCCG
391066 TTGACCGTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
12 10 0.20
13 1 0.02
17 1 0.02
18 38 0.76
ACGTcount: A:0.17, C:0.50, G:0.21, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:391032 original size:12 final size:13
Alignment explanation
Indices: 391012--391071 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 13
391002 CCGTTGACCC
391012 GACCCGACCCGTT
1 GACCCGACCCGTT
*
391025 TA-CCGACCCGTT
1 GACCCGACCCGTT
391037 GACCCGACCCGACCCGTT
1 G-----ACCCGACCCGTT
391055 GACCCGACCCGTT
1 GACCCGACCCGTT
391068 GACC
1 GACC
391072 GTTGACCCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
12 10 0.26
13 17 0.44
17 1 0.03
18 11 0.28
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:391033 original size:30 final size:31
Alignment explanation
Indices: 390994--391071 Score: 140
Period size: 30 Copynumber: 2.5 Consensus size: 31
390984 GTCACAACCC
390994 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
391025 TA-CCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
391055 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
391072 GTTGACCCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 29 0.66
31 15 0.34
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:391075 original size:7 final size:7
Alignment explanation
Indices: 391063--391093 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
391053 TTGACCCGAC
391063 CCGTTGA
1 CCGTTGA
391070 CCGTTGA
1 CCGTTGA
*
391077 CCCTTGA
1 CCGTTGA
391084 CCGTTGA
1 CCGTTGA
391091 CCG
1 CCG
391094 GAGTTGACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.35, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:391085 original size:14 final size:15
Alignment explanation
Indices: 391047--391092 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
391037 GACCCGACCC
*
391047 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
391060 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
391075 GACCC-TTGACCGTT
1 GACCCGTTGACCGTT
391089 GACC
1 GACC
391093 GGAGTTGACC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 12 0.40
14 13 0.43
15 5 0.17
ACGTcount: A:0.15, C:0.39, G:0.24, T:0.22
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:391087 original size:21 final size:20
Alignment explanation
Indices: 390994--391093 Score: 77
Period size: 18 Copynumber: 4.9 Consensus size: 20
390984 GTCACAACCC
*
390994 GACCCGACCCGTTGACC--C
1 GACCCGACCCGTTGACCGTT
391012 GACCCGACCCGTTTACCGACCCGTT
1 GACCCGACCCG-TT---GA-CCGTT
391037 GACCCGACCC---GACCCGTT
1 GACCCGACCCGTTGA-CCGTT
391055 GACCCGACCCGTTGACCGTT
1 GACCCGACCCGTTGACCGTT
391075 GACCCTTGA-CCGTTGACCG
1 GACCC--GACCCGTTGACCG
391094 GAGTTGACCA
Statistics
Matches: 69, Mismatches: 1, Indels: 21
0.76 0.01 0.23
Matches are distributed among these distances:
18 29 0.42
19 2 0.03
20 10 0.14
21 12 0.17
22 4 0.06
23 2 0.03
25 10 0.14
ACGTcount: A:0.16, C:0.44, G:0.23, T:0.17
Consensus pattern (20 bp):
GACCCGACCCGTTGACCGTT
Done.