Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014850.1 Kokia drynarioides strain JFW-HI SEQ_129893, 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: 775807
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 814 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:456241 original size:301 final size:294
Alignment explanation
Indices: 455547--456282 Score: 770
Period size: 301 Copynumber: 2.4 Consensus size: 294
455537 AGGAAGTGAC
* *
455547 AAAAAACAAGGCAATTAGAGTAAAGGGTATCGAAATAAAATTGAAAAAAAAAAACAC-AAACCCA
1 AAAAAACAAGGCAATTAGACTAAAGGGTATTGAAATAAAATTG----AAAAAAACACTAAACCCA
* **
455611 GAGTCAAGAACACCATGAAAGATCAAATGCTCAAGCGAATAACCAATAAAACAGA-GATTTTCAG
62 AAGTCAAGAACA-CACCAAAGATCAAATGCTCAAGCGAATAACCAATAAAACA-ATGATTTTCAG
* ** *
455675 CAAAATTAGAGATATGAAGTTAAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTTGA
125 C-AAA-TAGAGATAAGAAGAAAAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTAGA
* * * **
455740 AAAAAAAAACCTAACTCATAGCCAAGAACACCATGAAAGATCAAATGCTCAAACGAACAACCAAT
188 AAAAAAAAACCAAACCCAGAGCCAAGAACACCACCAAAGATCAAATGCTCAAACGAACAACCAAT
* * * *
455805 AAAACAATTATTTTCAGCAAAATCGAGCTAGGAAGTTTTTTA
253 AAAACAATGATTTTCAGCAAAATCAAGCTAGGAAGTTGTTAA
* * * * *
455847 AAAATACAAGGCAATTAGACTAAAGAGTATTGAGATAAAATTGAAAAAAA-A-TAAAACCTAA-T
1 AAAAAACAAGGCAATTAGACTAAAGGGTATTGAAATAAAATTGAAAAAAACACTAAACCCAAAGT
* * *
455909 CCAGAGCCAAAAACACCATGAAAGATCAAATGTTCAAGCGAATAACCAATAAAACAATGGTTTTC
66 -CA-AG---AACACACC---AAAGATCAAATGCTCAAGCGAATAACCAATAAAACAATGATTTTC
* *
455974 AGCGAAATCGA-ACTAAGAAGAAAAAAAAACAAGGCAATTTGAGTAAAGGGTATTGAAATAAATT
123 AGC-AAATAGAGA-TAAGAAG-AAAAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATT
* * * *
456038 AGAAAAAAAAAAAACACAAAAACCCAGAGCCAAGAATC-TCACCCAAGCTCCAATGCTCAAACGA
185 AG--AAAAAAAAAAC-C--AAACCCAGAGCCAAGAA-CACCACCAAAGATCAAATGCTCAAACGA
* *
456102 ACAACCAATAAAACAATGATTTTCAGCAAATTCAAGCTATG-AG-TGTTAA
244 ACAACCAATAAAACAATGATTTTCAGCAAAATCAAGCTAGGAAGTTGTTAA
* * *
456151 AAAAAACAAGGCAATTATACTAAAGGGAATTGAAATAAAATCGAAAAAACACACTAAACCCAAAG
1 AAAAAACAAGGCAATTAGACTAAAGGGTATTGAAATAAAATTGAAAAAA-ACACTAAACCCAAAG
* * * * * *
456216 TCAAGAATCTCACCAAAGCTCAAATGCTCAAACAAACAACCAAAAACAACAATGATTTTCAGCAA
65 TCAAGAA-CACACCAAAGATCAAATGCTCAAGCGAATAACCAATAA-AACAATGATTTTCAGCAA
456281 AT
128 AT
456283 TCTAGCTGGG
Statistics
Matches: 360, Mismatches: 52, Indels: 47
0.78 0.11 0.10
Matches are distributed among these distances:
294 1 0.00
295 9 0.03
296 9 0.03
298 2 0.01
299 4 0.01
300 48 0.13
301 118 0.33
302 15 0.04
303 13 0.04
304 52 0.14
305 3 0.01
306 74 0.21
307 11 0.03
308 1 0.00
ACGTcount: A:0.52, C:0.16, G:0.14, T:0.18
Consensus pattern (294 bp):
AAAAAACAAGGCAATTAGACTAAAGGGTATTGAAATAAAATTGAAAAAAACACTAAACCCAAAGT
CAAGAACACACCAAAGATCAAATGCTCAAGCGAATAACCAATAAAACAATGATTTTCAGCAAATA
GAGATAAGAAGAAAAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTAGAAAAAAAAA
ACCAAACCCAGAGCCAAGAACACCACCAAAGATCAAATGCTCAAACGAACAACCAATAAAACAAT
GATTTTCAGCAAAATCAAGCTAGGAAGTTGTTAA
Found at i:457711 original size:9 final size:9
Alignment explanation
Indices: 457697--457724 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
457687 AAAACCGTTT
457697 AGTTAGGTA
1 AGTTAGGTA
457706 AGTTAGGTA
1 AGTTAGGTA
457715 AGTTAGGTA
1 AGTTAGGTA
457724 A
1 A
457725 ATAATACTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (9 bp):
AGTTAGGTA
Found at i:462725 original size:60 final size:60
Alignment explanation
Indices: 462661--462809 Score: 228
Period size: 60 Copynumber: 2.5 Consensus size: 60
462651 GACAAAATTA
* *
462661 AATAGTTGGGTGACCATTTTGTAACTTTTTATAGCTAGGTGACCAAAAAAGAAATGTACT
1 AATAGTTGAGTGACCATTTTGTAACTTTTCATAGCTAGGTGACCAAAAAAGAAATGTACT
* * *
462721 AATAGTTGAGTGACCTTTTTGTAACTTTTCATAGCTAGGTGACCAAATAAGAAATTTACT
1 AATAGTTGAGTGACCATTTTGTAACTTTTCATAGCTAGGTGACCAAAAAAGAAATGTACT
**
462781 -ATAGTTGAGTGATTATTTTGTAACTTTTC
1 AATAGTTGAGTGACCATTTTGTAACTTTTC
462810 TTAGTTGGGT
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 26 0.32
60 55 0.68
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (60 bp):
AATAGTTGAGTGACCATTTTGTAACTTTTCATAGCTAGGTGACCAAAAAAGAAATGTACT
Found at i:470219 original size:31 final size:29
Alignment explanation
Indices: 470146--470227 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
470136 AGAAATGGAT
*
470146 CAAAA-CAAAATTTTACATATAAAATTACA
1 CAAAACCAAAA-TTCACATATAAAATTACA
* *
470175 CACAATCAAAATTCACATATAAAATTACA
1 CAAAACCAAAATTCACATATAAAATTACA
*
470204 CATTAAACCAAAATTCATATATAA
1 CA--AAACCAAAATTCACATATAA
470228 TTTTAAAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
29 23 0.51
30 5 0.11
31 17 0.38
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (29 bp):
CAAAACCAAAATTCACATATAAAATTACA
Found at i:472106 original size:21 final size:21
Alignment explanation
Indices: 472076--472115 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
472066 TAGTATTTTT
472076 TTTTTAAAATTTGTGTTAAAG
1 TTTTTAAAATTTGTGTTAAAG
* *
472097 TTTTTCAAATTTGTTTTAA
1 TTTTTAAAATTTGTGTTAA
472116 TTTGATTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (21 bp):
TTTTTAAAATTTGTGTTAAAG
Found at i:473931 original size:223 final size:229
Alignment explanation
Indices: 473484--474246 Score: 770
Period size: 223 Copynumber: 3.3 Consensus size: 229
473474 TATCAAGATT
* * * * *
473484 TTGAGACTACCCC-TTCAAGATTTTGTTGTCCATACATAACCATGAATTTAGCCTTTATTTATTT
1 TTGAGAGT-CCCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAACTTAGCCTTTATTTA-CT
* * * * * * * *
473548 CCCC------CTAAAATCCGTCAAATTTCATAAAAAGTCCCTCTATCAGTTGTGTTTTT-CACAA
64 CCCCTATATAATAAAATCGGTCAAATCTCATAGAAACTCCCTCTATTATTTGTTTTTTTCCACAA
* * * * *
473606 GTTTTAGTCTCTCTACTATAATTTGATCATTTCTTGGGTGAGTGGAGAGCATCGAGTCAAGTTAC
129 -ATTTAGTCTTTCTACTATAAGTT-ATCA-TTC-----T-AATGGAGAGTATCGAGTCAAGTTAC
* * * *
473671 AACTCAGGAGAGTGGAATTGTATCAACAAAATTTGAATAATGGTTA
185 AATTCAGGAGAGTGG-ATTATATCAACAAAGTTTGAATAATGGTCA
* * *
473717 TTGAGAGTTCCCTTTCAAGATTTTGTTGTCCAAATATAACCACT-AATTTAGCTTTTATTTA-TC
1 TTGAGAGTCCCCTTTCAAGATTTTGTTGTCCAAATATAACCA-TGAACTTAGCCTTTATTTACTC
473780 CCCTTATATAATAAAATCGGTCAAATCTCATAGAAACTCCCTCTATTATTT-TTTTTTT-CACAA
65 CCC-TATATAATAAAATCGGTCAAATCTCATAGAAACTCCCTCTATTATTTGTTTTTTTCCACAA
* * * *
473843 ATTTAGT-TTCTCTACTGT-AGTT-TGA-T-T-ATGGAGAGTATCGAGTCAAGTTACAGTTCAAG
129 ATTTAGTCTT-TCTACTATAAGTTATCATTCTAATGGAGAGTATCGAGTCAAGTTACAATTCAGG
473902 AGAGTGAGATTATATCAACAAAGTTTGAATAATGGTCA
193 AGAGTG-GATTATATCAACAAAGTTTGAATAATGGTCA
* ***
473940 TTGAGAGTGCCCTTTCAAGATTTTGTTGTCCATGGATAACCATGAACTTAGCCTTTATTTACTCC
1 TTGAGAGTCCCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAACTTAGCCTTTATTTACTCC
* * *
474005 CCTATATAATAAAATGGGTCAAATTTCATAGAAAGTCCCTCTATTATTTGTTTTTTTCCACAAAT
66 CCTATATAATAAAATCGGTCAAATCTCATAGAAACTCCCTCTATTATTTGTTTTTTTCCACAAAT
* *
474070 TTAGTCTTTCTACTATAATTTAATCATTTCTTTCGTGAATGGAGGGTATCGAGTCAAGTTACAAT
131 TTAGTCTTTCTACTATAAGTT-ATCA-----TTC-T-AATGGAGAGTATCGAGTCAAGTTACAAT
*
474135 TCAGGAGAGTGGGATTATATCAACAAAGTTTGAATGATGGTCA
188 TCAGGAGAGT-GGATTATATCAACAAAGTTTGAATAATGGTCA
* * * * * *
474178 TTGAGAGTCCCCTTTCAAGATTTTGTTGTTCAAATATAACCGTGAATTTAGCCTTCATGTATTCC
1 TTGAGAGTCCCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAACTTAGCCTTTATTTACTCC
474243 CCTA
66 CCTA
474247 AAATCGATCA
Statistics
Matches: 448, Mismatches: 52, Indels: 55
0.81 0.09 0.10
Matches are distributed among these distances:
222 1 0.00
223 157 0.35
224 13 0.03
225 20 0.04
226 5 0.01
228 2 0.00
231 6 0.01
232 3 0.01
233 52 0.12
234 2 0.00
235 4 0.01
236 14 0.03
237 11 0.02
238 157 0.35
239 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (229 bp):
TTGAGAGTCCCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAACTTAGCCTTTATTTACTCC
CCTATATAATAAAATCGGTCAAATCTCATAGAAACTCCCTCTATTATTTGTTTTTTTCCACAAAT
TTAGTCTTTCTACTATAAGTTATCATTCTAATGGAGAGTATCGAGTCAAGTTACAATTCAGGAGA
GTGGATTATATCAACAAAGTTTGAATAATGGTCA
Found at i:478557 original size:29 final size:29
Alignment explanation
Indices: 478515--478575 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
478505 GGACGGAACT
478515 ATGCGTGATGACTCGATTCAATCGGTTCA
1 ATGCGTGATGACTCGATTCAATCGGTTCA
*
478544 ATGCGTGATGACTCGATTCAATCTGTTCA
1 ATGCGTGATGACTCGATTCAATCGGTTCA
478573 ATG
1 ATG
478576 TACTGGGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (29 bp):
ATGCGTGATGACTCGATTCAATCGGTTCA
Found at i:483327 original size:27 final size:27
Alignment explanation
Indices: 483297--483356 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
483287 GACCAAAAAT
*
483297 CAATTTGAATTAAGAATAACAATTTTA
1 CAATTTGAATTAAGAATAACAACTTTA
483324 CAATTTGAATTAAGAATAACAACTTTA
1 CAATTTGAATTAAGAATAACAACTTTA
483351 CAATTT
1 CAATTT
483357 TTAATGACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (27 bp):
CAATTTGAATTAAGAATAACAACTTTA
Found at i:485448 original size:44 final size:44
Alignment explanation
Indices: 485398--485488 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
485388 TTGTCTTCTA
485398 TACGTTAAATGTCGACACGGATATAATGTGAATCAAATTTTAAG
1 TACGTTAAATGTCGACACGGATATAATGTGAATCAAATTTTAAG
485442 TACGTTAAATGTCGACACGGATATAATGTGAATCAAATTTTAAG
1 TACGTTAAATGTCGACACGGATATAATGTGAATCAAATTTTAAG
485486 TAC
1 TAC
485489 ATATGTATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (44 bp):
TACGTTAAATGTCGACACGGATATAATGTGAATCAAATTTTAAG
Found at i:502820 original size:17 final size:17
Alignment explanation
Indices: 502789--502823 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
502779 TATTTTGACC
**
502789 TTTTAAATTTTTAAAAA
1 TTTTAAATTAATAAAAA
502806 TTTTAAATTAATAAAAA
1 TTTTAAATTAATAAAAA
502823 T
1 T
502824 AAAATTACAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTAAATTAATAAAAA
Found at i:503265 original size:20 final size:20
Alignment explanation
Indices: 503228--503266 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
503218 TATTTAAGTA
* **
503228 TAATTTTTTAAATTTATTTT
1 TAATTTATTAAAAATATTTT
503248 TAATTTATTAAAAATATTT
1 TAATTTATTAAAAATATTT
503267 ATTTTAATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TAATTTATTAAAAATATTTT
Found at i:507651 original size:12 final size:11
Alignment explanation
Indices: 507610--507650 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
507600 TAAATTTTAA
*
507610 TTTAAAAGTTT
1 TTTAAAATTTT
*
507621 TTTAATATATTT
1 TTTAAAAT-TTT
507633 TTTAAAATTTT
1 TTTAAAATTTT
507644 TTTAAAA
1 TTTAAAA
507651 AATAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (11 bp):
TTTAAAATTTT
Found at i:509778 original size:32 final size:32
Alignment explanation
Indices: 509729--509789 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
509719 GTAACGTTTA
*
509729 GATTTTTTTGTTGAATTTCTAGTGATTTTTTC
1 GATTTTTTTGTTAAATTTCTAGTGATTTTTTC
* * *
509761 GATTTTTTTTTTAAATTTTTAGTGCTTTT
1 GATTTTTTTGTTAAATTTCTAGTGATTTT
509790 AAGTGATAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.16, C:0.05, G:0.13, T:0.66
Consensus pattern (32 bp):
GATTTTTTTGTTAAATTTCTAGTGATTTTTTC
Found at i:510442 original size:4 final size:4
Alignment explanation
Indices: 510433--510460 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
510423 TCTACGTACA
510433 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
510461 CACGTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:528485 original size:2 final size:2
Alignment explanation
Indices: 528476--528505 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
528466 TTTTCTTCTG
528476 TA TA -A 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 TA TA TA T
528506 GATGTAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:535468 original size:14 final size:15
Alignment explanation
Indices: 535442--535470 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
535432 AGGTTCAACT
535442 ATTAATATTGTTAAA
1 ATTAATATTGTTAAA
535457 ATTAAT-TTGTTAAA
1 ATTAATATTGTTAAA
535471 TTCAAGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
ATTAATATTGTTAAA
Found at i:535563 original size:14 final size:15
Alignment explanation
Indices: 535546--535574 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
535536 ATATCAAATC
535546 AAAAAA-TTTAACAG
1 AAAAAATTTTAACAG
535560 AAAAAATTTTAACAG
1 AAAAAATTTTAACAG
535575 TGTTAACAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (15 bp):
AAAAAATTTTAACAG
Found at i:536314 original size:25 final size:23
Alignment explanation
Indices: 536286--536331 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
536276 TTTTTTTCAA
*
536286 AAAATTATATAAAAACTAAAAATAC
1 AAAA-TAT-TAAAAACAAAAAATAC
*
536311 AAAATATTATAAACAAAAAAT
1 AAAATATTAAAAACAAAAAAT
536332 TGTAATTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 3 0.16
25 4 0.21
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAATATTAAAAACAAAAAATAC
Found at i:541671 original size:16 final size:16
Alignment explanation
Indices: 541650--541688 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
541640 TTTTGGTTTG
541650 GGTTTGGGTCATTTCA
1 GGTTTGGGTCATTTCA
* * *
541666 GGTTTGAGTCTTTTCG
1 GGTTTGGGTCATTTCA
541682 GGTTTGG
1 GGTTTGG
541689 TTTTGAGTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.08, C:0.10, G:0.36, T:0.46
Consensus pattern (16 bp):
GGTTTGGGTCATTTCA
Found at i:545485 original size:22 final size:22
Alignment explanation
Indices: 545460--545513 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
545450 CAAACGAAAC
545460 AAACGGAGAGTACCGAAGTACT
1 AAACGGAGAGTACCGAAGTACT
545482 AAACGGAGAGTACCGAAGTACT
1 AAACGGAGAGTACCGAAGTACT
* *
545504 TAACAGAGAG
1 AAACGGAGAG
545514 CACATAAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.43, C:0.17, G:0.28, T:0.13
Consensus pattern (22 bp):
AAACGGAGAGTACCGAAGTACT
Found at i:545556 original size:23 final size:23
Alignment explanation
Indices: 545530--545672 Score: 131
Period size: 23 Copynumber: 6.4 Consensus size: 23
545520 AGTGCTGGGT
545530 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
545553 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
* *
545572 -AC--TGAGCACACAAAGTGTTA
1 AACAGAGAGCACACAAAGTGCTA
* *
545592 ATCAGAGAGCACACGAAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
*
545616 TAACAGAGAGCACA-AGACGTGCTA
1 -AACAGAGAGCACACA-AAGTGCTA
*
545640 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
545663 ATCAGAGAGC
1 AACAGAGAGC
545673 GCGCTAGCGT
Statistics
Matches: 96, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
16 10 0.10
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
23 58 0.60
24 3 0.03
25 18 0.19
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:545598 original size:39 final size:39
Alignment explanation
Indices: 545536--545610 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
545526 GGGTAACAGA
*
545536 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* * *
545575 GAGCACACAAAGTGTTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
545611 GCTAATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:560896 original size:6 final size:6
Alignment explanation
Indices: 560885--560933 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
560875 TAAGTCCCTT
* * * *
560885 ACATAC ACATAC ACATAC ACATAC ACGTAC ACGTAC ACGTAC ACGTAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
560933 A
1 A
560934 TACATCCTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.43, C:0.33, G:0.08, T:0.16
Consensus pattern (6 bp):
ACATAC
Found at i:560908 original size:18 final size:18
Alignment explanation
Indices: 560885--560933 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
560875 TAAGTCCCTT
*
560885 ACATACACATACACATAC
1 ACATACACGTACACATAC
*
560903 ACATACACGTACACGTAC
1 ACATACACGTACACATAC
*
560921 ACGTACACGTACA
1 ACATACACGTACA
560934 TACATCCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.43, C:0.33, G:0.08, T:0.16
Consensus pattern (18 bp):
ACATACACGTACACATAC
Found at i:571955 original size:17 final size:18
Alignment explanation
Indices: 571933--571970 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
571923 CCGGACCCCT
571933 TTTAAATTTATTTT-AAA
1 TTTAAATTTATTTTCAAA
571950 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTCAAA
571968 TTT
1 TTT
571971 TAAAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAAATTTATTTTCAAA
Found at i:573822 original size:30 final size:29
Alignment explanation
Indices: 573786--574111 Score: 207
Period size: 30 Copynumber: 10.9 Consensus size: 29
573776 CTCTGGAGGT
*
573786 CCCTAAATTGTCCAAAAATTCCATTTTTGA-
1 CCCTAAACT-TCCAAAAATTCCATTTTT-AC
**
573816 CCCTAAAACTTCCAAAAATTATATTTTTAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
** *
573846 CCCCGAAC-TCTCAAAAAATCCATTTTTAAC
1 CCCTAAACTTC-CAAAAATTCCATTTTT-AC
* * **
573876 CCCAAAACTTCCAAAAGTTAAATTTTTA-
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
*
573904 CCCTCGAACTTCCAAAAATTCCATTTTTGAC
1 CCCT-AAACTTCCAAAAATTCCATTTTT-AC
* * * * *
573935 CTCAAAACTTCTAAAATTTACCCTTTTTTAC
1 CCCTAAACTTCCAAAAATT--CCATTTTTAC
* * *
573966 CCCCAAACCTCCAAAAATTCTATTTTTGAC
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* * *
573996 CTCGAAACTTTCAAAAATTACCATTTTTACC
1 CCCTAAACTTCCAAAAATT-CCATTTTTA-C
** * *
574027 CCCCGAA-TGTCCAAAAACTCCATTTTGAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAC
* *
574056 CTCGAAAC-TCTCAAAAATTACCA-TTTTAC
1 CCCTAAACTTC-CAAAAATT-CCATTTTTAC
574085 CCCTAAA-TGTCCAAAAATTCCATTTTT
1 CCCTAAACT-TCCAAAAATTCCATTTTT
574112 TATCCCGATT
Statistics
Matches: 226, Mismatches: 50, Indels: 41
0.71 0.16 0.13
Matches are distributed among these distances:
28 10 0.04
29 77 0.34
30 88 0.39
31 44 0.19
32 7 0.03
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAC
Found at i:573890 original size:59 final size:61
Alignment explanation
Indices: 573796--574111 Score: 312
Period size: 59 Copynumber: 5.3 Consensus size: 61
573786 CCCTAAATTG
*
573796 TCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTA-TATTTTTACCCCCGAACTC
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACTATTTTTACCCCCGAACTC
* * * * *
573856 T-CAAAAAATCCATTTTTAACCCCAAAACTTCCAAAAGTTA-AATTTTTACCCTCGAACT-
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACTATTTTTACCCCCGAACTC
* * * *
573914 TCCAAAAATTCCATTTTTGACCTCAAAACTTCTAAAATTTACCCT-TTTTTACCCCCAAAC-C
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTA--CTATTTTTACCCCCGAACTC
* * * * * *
573975 TCCAAAAATTCTATTTTTGACCTCGAAACTTTCAAAAATTACCATTTTTACCCCCCGAA-TG
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACTATTTTTA-CCCCCGAACTC
* * * * * * *
574036 TCCAAAAACTCCA-TTTTGACCTCGAAAC-TCTCAAAAATTACCA-TTTTA-CCCCTAAATG
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTC-CAAAAATTACTATTTTTACCCCCGAACTC
574094 TCCAAAAATTCCATTTTT
1 TCCAAAAATTCCATTTTT
574112 TATCCCGATT
Statistics
Matches: 218, Mismatches: 27, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
57 6 0.03
58 15 0.07
59 96 0.44
60 34 0.16
61 67 0.31
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (61 bp):
TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACTATTTTTACCCCCGAACTC
Found at i:575638 original size:7 final size:8
Alignment explanation
Indices: 575623--575648 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
575613 TTAAAAATTC
575623 ATAAAAAA
1 ATAAAAAA
575631 ATAAAAAA
1 ATAAAAAA
575639 ATAAAAAA
1 ATAAAAAA
575647 AT
1 AT
575649 TTGATTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
ATAAAAAA
Found at i:582856 original size:132 final size:129
Alignment explanation
Indices: 582605--582870 Score: 327
Period size: 132 Copynumber: 2.0 Consensus size: 129
582595 ACCCAAGACG
* *
582605 CCATTAGTTAAGATAGGAAAGACCCTTGCCACCAGTAACTAATCATCCGCATTCTATAGGCCAAG
1 CCATTAGTTAAGATAAGAAAGACCCTTGCCACCAGTAACTAATCATCCACATTCTATAGGCCAAG
* * * *
582670 GGGATAGATGTTGACCACGAGTTTTAAAGTTGCTTCATACCCAATGTGAGGATCGAA-CCTCGA
66 GGGATAGATGTTGACCACGAGTTTTAAAGCTGCTCCATACCCAAGGCGAGGATCGAACCCTCGA
* * * * * * * *
582733 CCATTAGTTATGGTAAGAAAGATCTTTGCCACCAGTAACTAATCTTTCACATTGTGTAGGCTCAT
1 CCATTAGTTAAGATAAGAAAGACCCTTGCCACCAGTAACTAATCATCCACATTCTATAGGC-C--
** * *
582798 TAAGGGGATAGATGTTGGTCACGAGTTTTAAAGCTGCTCCATACCTAAGGCGATGATCGAACCCT
63 -AAGGGGATAGATGTTGACCACGAGTTTTAAAGCTGCTCCATACCCAAGGCGAGGATCGAACCCT
582863 CGA
127 CGA
582866 CCATT
1 CCATT
582871 GATTAAGTTA
Statistics
Matches: 115, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
128 51 0.44
129 1 0.01
132 52 0.45
133 11 0.10
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (129 bp):
CCATTAGTTAAGATAAGAAAGACCCTTGCCACCAGTAACTAATCATCCACATTCTATAGGCCAAG
GGGATAGATGTTGACCACGAGTTTTAAAGCTGCTCCATACCCAAGGCGAGGATCGAACCCTCGA
Found at i:584922 original size:8 final size:8
Alignment explanation
Indices: 584909--584949 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
584899 TGAAGAAGGT
584909 TATACATA
1 TATACATA
584917 TATACATA
1 TATACATA
*
584925 CATACATA
1 TATACATA
*
584933 TATATATA
1 TATACATA
*
584941 TATATATA
1 TATACATA
584949 T
1 T
584950 GATTTTCAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (8 bp):
TATACATA
Found at i:600867 original size:20 final size:20
Alignment explanation
Indices: 600831--600872 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
600821 TTATTTTAAT
*
600831 AAAATTTGAAAGTAAAAGAG
1 AAAATTTGAAAGCAAAAGAG
*
600851 AAAATTTTG-AAGCAAAATAG
1 AAAA-TTTGAAAGCAAAAGAG
600871 AA
1 AA
600873 GAAGAAGCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.60, C:0.02, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAATTTGAAAGCAAAAGAG
Found at i:601617 original size:17 final size:17
Alignment explanation
Indices: 601575--601617 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
601565 CTAGCTTGAA
* **
601575 TTTTAGATTTTTTATTT
1 TTTTAGATATTTTAAAT
601592 TTTTA-ATATTTTAAAT
1 TTTTAGATATTTTAAAT
601608 TTTTAGATAT
1 TTTTAGATAT
601618 ATTTTTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (17 bp):
TTTTAGATATTTTAAAT
Found at i:606882 original size:16 final size:17
Alignment explanation
Indices: 606848--606882 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
606838 TGATAGATAT
*
606848 ATTTATTTTATAAGTAA
1 ATTTATTTTATAAGAAA
606865 ATTTATTTT-TAAGAAA
1 ATTTATTTTATAAGAAA
606881 AT
1 AT
606883 GCAATATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (17 bp):
ATTTATTTTATAAGAAA
Found at i:607212 original size:18 final size:18
Alignment explanation
Indices: 607185--607219 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
607175 TTTCTTTTAC
*
607185 CATAATTTATACATAATA
1 CATAACTTATACATAATA
*
607203 CATAACTTATGCATAAT
1 CATAACTTATACATAAT
607220 GCAGGGACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (18 bp):
CATAACTTATACATAATA
Found at i:622384 original size:25 final size:24
Alignment explanation
Indices: 622347--622396 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
622337 CAGTATTTAT
* * *
622347 ATAATATTCAAACAATAACAATAAA
1 ATAATAGTAAAACAACAACAA-AAA
622372 ATAATAGTAAAACAACAACAAAAA
1 ATAATAGTAAAACAACAACAAAAA
622396 A
1 A
622397 GGAAGTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.68, C:0.12, G:0.02, T:0.18
Consensus pattern (24 bp):
ATAATAGTAAAACAACAACAAAAA
Found at i:631845 original size:23 final size:23
Alignment explanation
Indices: 631819--631863 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
631809 GAGCTTGCTA
*
631819 GGTGTACGTATAAAAATATATAT
1 GGTGTAAGTATAAAAATATATAT
*
631842 GGTGTAAGTATAACAATATATA
1 GGTGTAAGTATAAAAATATATA
631864 CACACGCACA
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:0.44, C:0.04, G:0.18, T:0.33
Consensus pattern (23 bp):
GGTGTAAGTATAAAAATATATAT
Found at i:634314 original size:20 final size:21
Alignment explanation
Indices: 634286--634333 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
634276 CACAAAAAAT
634286 ATATATATAATTTTAT-ATTA
1 ATATATATAATTTTATAATTA
* *
634306 ATATTTATATTTTTATAATTA
1 ATATATATAATTTTATAATTA
*
634327 ATTTATA
1 ATATATA
634334 AATAGACTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATATATAATTTTATAATTA
Found at i:643472 original size:33 final size:33
Alignment explanation
Indices: 643430--643527 Score: 187
Period size: 33 Copynumber: 3.0 Consensus size: 33
643420 AAAAAACCCA
643430 TTATGGAATTCATACTCAACCAGCTAATTCACT
1 TTATGGAATTCATACTCAACCAGCTAATTCACT
*
643463 TTATGGAATTCATACTTAACCAGCTAATTCACT
1 TTATGGAATTCATACTCAACCAGCTAATTCACT
643496 TTATGGAATTCATACTCAACCAGCTAATTCAC
1 TTATGGAATTCATACTCAACCAGCTAATTCAC
643528 AAAGCAAAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (33 bp):
TTATGGAATTCATACTCAACCAGCTAATTCACT
Found at i:645893 original size:26 final size:26
Alignment explanation
Indices: 645853--645904 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
645843 TAAGGATACC
* *
645853 TTAATTATAGTTTCTTATTCTACAAG
1 TTAATTATAGATTCTTACTCTACAAG
* *
645879 TTAATTTTAGATTCTTGCTCTACAAG
1 TTAATTATAGATTCTTACTCTACAAG
645905 ACTAAAACCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (26 bp):
TTAATTATAGATTCTTACTCTACAAG
Found at i:655515 original size:8 final size:8
Alignment explanation
Indices: 655502--655533 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
655492 TCGAGAAAAA
655502 ATAATTTT
1 ATAATTTT
655510 ATAATTTT
1 ATAATTTT
655518 ATAATTTT
1 ATAATTTT
655526 -TAATTTT
1 ATAATTTT
655533 A
1 A
655534 ATTAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATAATTTT
Found at i:655523 original size:16 final size:15
Alignment explanation
Indices: 655502--655533 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
655492 TCGAGAAAAA
655502 ATAATTTTATAATTTT
1 ATAATTTT-TAATTTT
655518 ATAATTTTTAATTTT
1 ATAATTTTTAATTTT
655533 A
1 A
655534 ATTAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATAATTTTTAATTTT
Found at i:656526 original size:22 final size:22
Alignment explanation
Indices: 656487--656529 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
656477 CCACTCTGAC
*
656487 TCTTTCCTTCCTATTCCTTCCT
1 TCTTTCCTTCCTACTCCTTCCT
656509 TCTTTCCTTCACT-CTCCTTCC
1 TCTTTCCTTC-CTACTCCTTCC
656530 ATTTCCTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.05, C:0.44, G:0.00, T:0.51
Consensus pattern (22 bp):
TCTTTCCTTCCTACTCCTTCCT
Found at i:657664 original size:22 final size:22
Alignment explanation
Indices: 657638--657687 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
657628 ATGGAGCTGG
*
657638 TTTTT-AACTCTTTTTTTTTTTT
1 TTTTTGAA-TCTTTTTTGTTTTT
*
657660 TTTTTGTATCTTTTTTGTTTTT
1 TTTTTGAATCTTTTTTGTTTTT
*
657682 TGTTTG
1 TTTTTG
657688 CTAATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.06, C:0.06, G:0.08, T:0.80
Consensus pattern (22 bp):
TTTTTGAATCTTTTTTGTTTTT
Found at i:657696 original size:23 final size:20
Alignment explanation
Indices: 657648--657698 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
657638 TTTTTAACTC
*
657648 TTTTTTTTTTTTTTTTTGTA
1 TTTTTTTTTTTTTGTTTGTA
657668 TCTTTTTTGTTTTTTGTTTGCTAA
1 T-TTTTTT-TTTTTTGTTTG-T-A
657692 TTTTTTT
1 TTTTTTT
657699 ACTTGCTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.04
21 6 0.23
22 10 0.38
23 7 0.27
24 2 0.08
ACGTcount: A:0.06, C:0.04, G:0.08, T:0.82
Consensus pattern (20 bp):
TTTTTTTTTTTTTGTTTGTA
Found at i:658191 original size:241 final size:240
Alignment explanation
Indices: 657768--658247 Score: 793
Period size: 241 Copynumber: 2.0 Consensus size: 240
657758 AAATCATAAC
* *
657768 TGAATGTAATATCAACTTTTTGATGTGCTAAGGATGTGTTTTGTGGCCGATTGAGCTTGAGCTCA
1 TGAATGTAATATCAACTTTTTGATGTGCTAAGGATGTCTTTTGTCGCCGATTGAGCTTGAGCTCA
657833 GTTAGCACTTAGAGGTGGTTTCGATTCGATTGTGCTTAAGTGCGAATCATTCTCCTATTTAAGAG
66 GTTAGCACTTAGAGGTGGTTTCGATTCGATTGTGCTTAAGTGCGAATCATTCTCCTATTTAAGAG
* *
657898 TTTGGGGTATGAATAGTGGTAGAAATTGTATAAAAAAAGTATGCGTTTTGTATCATTCTCCTATT
131 TTTGAGGTATGAATAGTGGTAGAAATTGTATAAAAAAAGTATGAGTTTTGTATCATTCTCCTATT
* *
657963 CAAGAGTTTGGGGTATGAATATTAGTAGAAATTCTATAACAAAAAT
196 CAAGAGTTCGGGGTATGAATAGTAGTAGAAATTCTATAA-AAAAAT
* *
658009 TGAATGTAATATTAA-TTTGTTGATGTGCTAAGGATGTCTTTTTTCGCCGATTGAGCTTGAGCTC
1 TGAATGTAATATCAACTTT-TTGATGTGCTAAGGATGTCTTTTGTCGCCGATTGAGCTTGAGCTC
* * *
658073 AGTTAGCACTGT-GAGGTGGTTTCGGTTTGATTGTGCTTAAGTGCGTATCATTCTCCTATTTAAG
65 AGTTAGCACT-TAGAGGTGGTTTCGATTCGATTGTGCTTAAGTGCGAATCATTCTCCTATTTAAG
658137 AGTTTGAGGTATGAATAGTGGTAGAAATTGTATAAAAAAAGTATGAGTTTTGTATCATTCTCCTA
129 AGTTTGAGGTATGAATAGTGGTAGAAATTGTATAAAAAAAGTATGAGTTTTGTATCATTCTCCTA
* * *
658202 TTTAAGAGTTCGGGGTATGGATAGTAGTAGAAATTGTATAAAAAAA
194 TTCAAGAGTTCGGGGTATGAATAGTAGTAGAAATTCTATAAAAAAA
658248 GTATGGTTGT
Statistics
Matches: 223, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
240 8 0.04
241 214 0.96
242 1 0.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.38
Consensus pattern (240 bp):
TGAATGTAATATCAACTTTTTGATGTGCTAAGGATGTCTTTTGTCGCCGATTGAGCTTGAGCTCA
GTTAGCACTTAGAGGTGGTTTCGATTCGATTGTGCTTAAGTGCGAATCATTCTCCTATTTAAGAG
TTTGAGGTATGAATAGTGGTAGAAATTGTATAAAAAAAGTATGAGTTTTGTATCATTCTCCTATT
CAAGAGTTCGGGGTATGAATAGTAGTAGAAATTCTATAAAAAAAT
Found at i:658233 original size:71 final size:71
Alignment explanation
Indices: 658117--658252 Score: 236
Period size: 71 Copynumber: 1.9 Consensus size: 71
658107 GCTTAAGTGC
* *
658117 GTATCATTCTCCTATTTAAGAGTTTGAGGTATGAATAGTGGTAGAAATTGTATAAAAAAAGTATG
1 GTATCATTCTCCTATTTAAGAGTTCGAGGTATGAATAGTAGTAGAAATTGTATAAAAAAAGTATG
658182 AGTTTT
66 AGTTTT
* *
658188 GTATCATTCTCCTATTTAAGAGTTCGGGGTATGGATAGTAGTAGAAATTGTATAAAAAAAGTATG
1 GTATCATTCTCCTATTTAAGAGTTCGAGGTATGAATAGTAGTAGAAATTGTATAAAAAAAGTATG
658253 GTTGTCATCC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (71 bp):
GTATCATTCTCCTATTTAAGAGTTCGAGGTATGAATAGTAGTAGAAATTGTATAAAAAAAGTATG
AGTTTT
Found at i:662498 original size:22 final size:21
Alignment explanation
Indices: 662473--662521 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
662463 AAATCCGTTC
* * *
662473 ATATTATTTTTTATTTTTTTAA
1 ATATTATATTATATTATTTT-A
662495 ATATTTATATTATATTATTTTA
1 ATA-TTATATTATATTATTTTA
662517 ATATT
1 ATATT
662522 TAATAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.09
22 7 0.30
23 14 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATATTATATTATATTATTTTA
Found at i:663980 original size:21 final size:20
Alignment explanation
Indices: 663912--663980 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
663902 TTTATTTGAT
*
663912 TAAAAAAATAATTTTAAAAA
1 TAAAAAAATAAATTTAAAAA
** * *
663932 TATTAAATTATATTTAAAAA
1 TAAAAAAATAAATTTAAAAA
** *
663952 CCATAAAATAAATTATAAAAA
1 TAAAAAAATAAATT-TAAAAA
663973 TAAAAAAA
1 TAAAAAAA
663981 CCCCAAAAGA
Statistics
Matches: 35, Mismatches: 13, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
20 24 0.69
21 11 0.31
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAAAAATAAATTTAAAAA
Found at i:665773 original size:13 final size:13
Alignment explanation
Indices: 665755--665780 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
665745 GATAAATATC
665755 TATAATTAGAAGG
1 TATAATTAGAAGG
665768 TATAATTAGAAGG
1 TATAATTAGAAGG
665781 GAAATCTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (13 bp):
TATAATTAGAAGG
Found at i:683928 original size:24 final size:24
Alignment explanation
Indices: 683883--683928 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
683873 GGAAAAATCA
* *
683883 TTTTATCTTTTTAATTTCTTTTAT
1 TTTTATCTTTTTAAATTATTTTAT
683907 TTTTAT-TTTTTAAAATTATTTT
1 TTTTATCTTTTT-AAATTATTTT
683929 TAGTTGTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTTATCTTTTTAAATTATTTTAT
Found at i:684352 original size:20 final size:21
Alignment explanation
Indices: 684329--684367 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
684319 AAATTCAGGT
*
684329 TTTTTGAAAAA-ATAAAATTA
1 TTTTTAAAAAAGATAAAATTA
684349 TTTTTAAAAAAGATAAAAT
1 TTTTTAAAAAAGATAAAAT
684368 GAGCAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
TTTTTAAAAAAGATAAAATTA
Found at i:686408 original size:2 final size:2
Alignment explanation
Indices: 686396--686430 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
686386 TAGACTAAAT
*
686396 TA TA GA TA TA 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 TA TA TA TA TA T
686431 TAGAGGTTTT
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:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:696424 original size:14 final size:14
Alignment explanation
Indices: 696405--696446 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
696395 TATTAATAAT
696405 TTTTATATTTTTTA
1 TTTTATATTTTTTA
696419 TTTTAT-TTTATTTA
1 TTTTATATTT-TTTA
*
696433 TTTTTTCATTTTTT
1 TTTTAT-ATTTTTT
696447 TTCCATGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 3 0.12
14 15 0.62
15 3 0.12
16 3 0.12
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTATATTTTTTA
Found at i:696848 original size:28 final size:27
Alignment explanation
Indices: 696817--696872 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
696807 TTTCCCATTA
* *
696817 TACTTTCTTTCGTTTTCCTTTTTTTCTT
1 TACTTTATTTCATTTTCC-TTTTTTCTT
*
696845 TACTTTATTTTATTTTCCTTTTTTCTT
1 TACTTTATTTCATTTTCCTTTTTTCTT
696872 T
1 T
696873 TTCTCATCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (27 bp):
TACTTTATTTCATTTTCCTTTTTTCTT
Found at i:697016 original size:2 final size:2
Alignment explanation
Indices: 697009--697040 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
696999 ACGTCTTCTT
697009 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
697041 CTTTCGTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:699897 original size:13 final size:13
Alignment explanation
Indices: 699879--699903 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
699869 TCACGAACTC
699879 AAATAAATAAAAT
1 AAATAAATAAAAT
699892 AAATAAATAAAA
1 AAATAAATAAAA
699904 AGAGAAGAGA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:710535 original size:2 final size:2
Alignment explanation
Indices: 710522--710556 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
710512 GAAAAAGAGA
*
710522 AT AT AT AG 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
710557 AGTTTTAAGT
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:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:718684 original size:13 final size:13
Alignment explanation
Indices: 718668--718696 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
718658 TTTGTTGGTT
718668 TTTTTTATTTTTA
1 TTTTTTATTTTTA
718681 TTTTTTATTTTTA
1 TTTTTTATTTTTA
718694 TTT
1 TTT
718697 GAACGGCTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:718927 original size:30 final size:30
Alignment explanation
Indices: 718893--718952 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
718883 TTTAAAACCC
*
718893 TAATAAAAATTTT-CTCATAATTTTTA-ATTA
1 TAAT-AAAATTTTAC-CATAATATTTACATTA
*
718923 TAATATAATTTTACCATAATATTTACATTA
1 TAATAAAATTTTACCATAATATTTACATTA
718953 ATTGTAGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.48
Consensus pattern (30 bp):
TAATAAAATTTTACCATAATATTTACATTA
Found at i:721700 original size:33 final size:33
Alignment explanation
Indices: 721663--721729 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
721653 TATTGATGAA
*
721663 TGTGGGTTCATTTTTTGTAATTCTTTTTTGTGT
1 TGTGGGTTAATTTTTTGTAATTCTTTTTTGTGT
*
721696 TGTGGGTTAATTTTTTGTATTTCTTTTTTGTGT
1 TGTGGGTTAATTTTTTGTAATTCTTTTTTGTGT
721729 T
1 T
721730 TTTTTACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.09, C:0.04, G:0.21, T:0.66
Consensus pattern (33 bp):
TGTGGGTTAATTTTTTGTAATTCTTTTTTGTGT
Found at i:726191 original size:44 final size:44
Alignment explanation
Indices: 726128--726211 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
726118 TGAGCTCGAG
* *
726128 CTATCGGTTGTGTTAAATTCAAGCATTGTAATAATTGATTTGAT
1 CTATCAGTTGTGTTAAATTCAAGCATCGTAATAATTGATTTGAT
726172 CTATCAGTTGTGTTAAATTCAAGCATCGTAATAATTGATT
1 CTATCAGTTGTGTTAAATTCAAGCATCGTAATAATTGATT
726212 CGAACGGCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.42
Consensus pattern (44 bp):
CTATCAGTTGTGTTAAATTCAAGCATCGTAATAATTGATTTGAT
Found at i:733017 original size:19 final size:19
Alignment explanation
Indices: 732995--733032 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
732985 TAACTTTTTC
*
732995 ATATATTATTATATTTTAA
1 ATATATTATCATATTTTAA
733014 ATATATTATCATATTTTAA
1 ATATATTATCATATTTTAA
733033 CATACTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATATTATCATATTTTAA
Found at i:733214 original size:25 final size:25
Alignment explanation
Indices: 733168--733230 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 25
733158 ACAAAGCTAT
* *
733168 TTTATA-TTAAAAATATTGTTATAG
1 TTTATACTAAAAAATATTGTTATAA
* * *
733192 TTTCTACTAAAAAATGTTTTTATAA
1 TTTATACTAAAAAATATTGTTATAA
*
733217 TTTATATTAAAAAA
1 TTTATACTAAAAAA
733231 GTTAAAAATA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 5 0.16
25 26 0.84
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (25 bp):
TTTATACTAAAAAATATTGTTATAA
Found at i:738018 original size:11 final size:11
Alignment explanation
Indices: 738002--738027 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
737992 GACGGTGAGA
738002 TTTTTTTATTT
1 TTTTTTTATTT
738013 TTTTTTTATTT
1 TTTTTTTATTT
738024 TTTT
1 TTTT
738028 ACATTTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTATTT
Found at i:740645 original size:105 final size:105
Alignment explanation
Indices: 740461--740694 Score: 362
Period size: 105 Copynumber: 2.2 Consensus size: 105
740451 TCATAAACGG
* * *
740461 TGATCACAGTATTATTTCAAGGCCAATTTATGGAAATGTTAAAATAATTGTCTTTACGCTTGTTG
1 TGATCACAGTATTATTTC-TGG-CAATTTATGGAAATGTTAAAACAATTGTCTTTACACTTGTTG
* * **
740526 CTTCCATTACAAGCAACTCAATCATTTTCACCAGTCCATTGT
64 CTTCCATTACAAGCAACTCAATCAATTTCACCAATCCATCAT
*
740568 TGATCACAGTATTACTTCTGGCAATTTATGGAAATGTTAAAACAATTGTCTTTACACTTGTTGCT
1 TGATCACAGTATTATTTCTGGCAATTTATGGAAATGTTAAAACAATTGTCTTTACACTTGTTGCT
740633 TCCATTACAAGCAACTCAATCAATTTCACCAATCCATCAT
66 TCCATTACAAGCAACTCAATCAATTTCACCAATCCATCAT
740673 TGATCACA-TAATTATTTCTGGC
1 TGATCACAGT-ATTATTTCTGGC
740695 CGATTTATCT
Statistics
Matches: 117, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
104 1 0.01
105 97 0.83
106 2 0.02
107 17 0.15
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (105 bp):
TGATCACAGTATTATTTCTGGCAATTTATGGAAATGTTAAAACAATTGTCTTTACACTTGTTGCT
TCCATTACAAGCAACTCAATCAATTTCACCAATCCATCAT
Found at i:742464 original size:190 final size:191
Alignment explanation
Indices: 742122--742486 Score: 635
Period size: 190 Copynumber: 1.9 Consensus size: 191
742112 TTATATGAAA
*
742122 AAAAAAAACTCAAAAAAAGTTAAAAATTGAGCACACCAGTGTCAAGTACATGCACCTAACATATC
1 AAAAAAAACTCAAAAAAAGTTAAAAATTGAGCACACCAGTGTCAAATACATGCACCTAACATATC
742187 CAACACCAACATTCGACTCCAATAGCAGACAGCATACTACGGTAGTCTTTACCTATGTTACTCAA
66 CAACACCAACATTCGACTCCAATAGCAGACAGCATACTACGGTAGTCTTTACCTATGTTACTCAA
742252 ACTCTTCATTTTTTAAAAGTATCAATGCTAGACACCAGTTTAGAAATCCTCCAATTATATG
131 ACTCTTCATTTTTTAAAAGTATCAATGCTAGACACCAGTTTAGAAATCCTCCAATTATATG
*
742313 AAAAATAACTC-AAAAAAGTTAAAAATTGAGCACACCAGTGTCAAATACATGCACCTAACATATC
1 AAAAAAAACTCAAAAAAAGTTAAAAATTGAGCACACCAGTGTCAAATACATGCACCTAACATATC
* *
742377 CAACACCAACATTCGAGTCCAATAGCAGACAGCATACTACGGTAGTCTTTACCTATGTTACTCGA
66 CAACACCAACATTCGACTCCAATAGCAGACAGCATACTACGGTAGTCTTTACCTATGTTACTCAA
* * * *
742442 ACTCTTCATTTTTCT-GAAGTATCGATGCTAGACGCTAGTTTAGAA
131 ACTCTTCATTTTT-TAAAAGTATCAATGCTAGACACCAGTTTAGAA
742487 CATGTATGAT
Statistics
Matches: 165, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
190 154 0.93
191 11 0.07
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (191 bp):
AAAAAAAACTCAAAAAAAGTTAAAAATTGAGCACACCAGTGTCAAATACATGCACCTAACATATC
CAACACCAACATTCGACTCCAATAGCAGACAGCATACTACGGTAGTCTTTACCTATGTTACTCAA
ACTCTTCATTTTTTAAAAGTATCAATGCTAGACACCAGTTTAGAAATCCTCCAATTATATG
Found at i:744154 original size:17 final size:17
Alignment explanation
Indices: 744132--744170 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
744122 CTTCACCTTG
*
744132 ACAAGAA-TTCTCTACGA
1 ACAAGAACTT-TCAACGA
744149 ACAAGAACTTTCAACGA
1 ACAAGAACTTTCAACGA
744166 ACAAG
1 ACAAG
744171 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (17 bp):
ACAAGAACTTTCAACGA
Found at i:754676 original size:46 final size:46
Alignment explanation
Indices: 754605--754693 Score: 151
Period size: 46 Copynumber: 1.9 Consensus size: 46
754595 TTTCATCTCT
* * *
754605 GTATTAATGTTATGTGGTGAGAGAACTTAGCAAGTCTCTAGTCTTG
1 GTATTAATGTTACGTGGTGAAAGAACCTAGCAAGTCTCTAGTCTTG
754651 GTATTAATGTTACGTGGTGAAAGAACCTAGCAAGTCTCTAGTC
1 GTATTAATGTTACGTGGTGAAAGAACCTAGCAAGTCTCTAGTC
754694 CTATTATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (46 bp):
GTATTAATGTTACGTGGTGAAAGAACCTAGCAAGTCTCTAGTCTTG
Found at i:754835 original size:31 final size:29
Alignment explanation
Indices: 754799--754865 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
754789 ATGTTTTATA
754799 ATGGTACATGTACTTTTATAAAATATCTAAT
1 ATGGTACATGTA-TTTTA-AAAATATCTAAT
* ** * *
754830 GTGGTATTTGTATTTTAAAAATGTTTAAT
1 ATGGTACATGTATTTTAAAAATATCTAAT
754859 ATGGTAC
1 ATGGTAC
754866 GTTAACTATC
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
29 15 0.52
30 5 0.17
31 9 0.31
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (29 bp):
ATGGTACATGTATTTTAAAAATATCTAAT
Found at i:754858 original size:29 final size:31
Alignment explanation
Indices: 754807--754864 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
754797 TAATGGTACA
*
754807 TGTACTTTTATAAAATATCTAATGTGGTATT
1 TGTACTTTTATAAAATATCTAATATGGTATT
* *
754838 TGTA-TTTTA-AAAATGTTTAATATGGTA
1 TGTACTTTTATAAAATATCTAATATGGTA
754865 CGTTAACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.62
30 5 0.21
31 4 0.17
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (31 bp):
TGTACTTTTATAAAATATCTAATATGGTATT
Found at i:758512 original size:197 final size:197
Alignment explanation
Indices: 758177--758567 Score: 514
Period size: 197 Copynumber: 2.0 Consensus size: 197
758167 GACTATGATA
* * * * * * *
758177 GTGGTATGTTTTTGGATCAGTATCGTGTTTGGTTGAATGCTCTTTATTCTTTCGAGCATATATTT
1 GTGGTATGCTTTTAGATCACTATCATCTTTGGTTGAATGCTCTTCATGCTTTCGAGCATATATTT
* * * ** * *
758242 GAATGTCTGTGTATTCTCAATCGTTATATTGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
66 CAATGTCAGTGTAATCTCAATCGTTATAAAGTCTATCGAGGATGTAGGTTGAATCCTTTATATAT
* * * *
758307 TAAATCCAACATTGTCTCCAAAAACAATGAGTAATTAAATTGAATGG-CATGGTAAGAAGATTGG
131 TAAATCCAACATTATCTCAAAAAACAATGAGTAATTAAATGGAATGGTC-TGATAAGAAGATTGG
758371 GTT
195 GTT
* * *
758374 GTGGTATGCTTTTAGATCACTTTCATCTTTGGTTGAATGCTCTTCATGCTTTTGAGCATATGTTT
1 GTGGTATGCTTTTAGATCACTATCATCTTTGGTTGAATGCTCTTCATGCTTTCGAGCATATATTT
* * * * *
758439 CTATGTCAGTGTAATCTCAATTGTTGTAAAGTCTGTCGAGGATGTAGGTTGAATCCTTTATATGT
66 CAATGTCAGTGTAATCTCAATCGTTATAAAGTCTATCGAGGATGTAGGTTGAATCCTTTATATAT
* *
758504 TAAATCCAACATTATCTCAAAAAACAGTGAGTGATTAAATGGAATGGTCTGATAAGAAGATTGG
131 TAAATCCAACATTATCTCAAAAAACAATGAGTAATTAAATGGAATGGTCTGATAAGAAGATTGG
758568 ATTGCATTTA
Statistics
Matches: 165, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
197 164 0.99
198 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (197 bp):
GTGGTATGCTTTTAGATCACTATCATCTTTGGTTGAATGCTCTTCATGCTTTCGAGCATATATTT
CAATGTCAGTGTAATCTCAATCGTTATAAAGTCTATCGAGGATGTAGGTTGAATCCTTTATATAT
TAAATCCAACATTATCTCAAAAAACAATGAGTAATTAAATGGAATGGTCTGATAAGAAGATTGGG
TT
Found at i:770213 original size:23 final size:23
Alignment explanation
Indices: 770187--770259 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
770177 GTTTGTTTGT
770187 TTAATATTCGTGAACATATTCAA
1 TTAATATTCGTGAACATATTCAA
*** * *
770210 TTAAGT-TAAATGAACATATTTAT
1 TTAA-TATTCGTGAACATATTCAA
*
770233 TTAATATTCGTGAATATATTCAA
1 TTAATATTCGTGAACATATTCAA
770256 TTAA
1 TTAA
770260 GTTAAATGAA
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.42
Consensus pattern (23 bp):
TTAATATTCGTGAACATATTCAA
Found at i:770272 original size:23 final size:23
Alignment explanation
Indices: 770197--770269 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
770187 TTAATATTCG
770197 TGAACATATTCAATTAAGTTAAA
1 TGAACATATTCAATTAAGTTAAA
* * ***
770220 TGAACATATTTATTTAA-TATTCG
1 TGAACATATTCAATTAAGT-TAAA
*
770243 TGAATATATTCAATTAAGTTAAA
1 TGAACATATTCAATTAAGTTAAA
770266 TGAA
1 TGAA
770270 TATGATAACA
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.40
Consensus pattern (23 bp):
TGAACATATTCAATTAAGTTAAA
Found at i:770410 original size:26 final size:26
Alignment explanation
Indices: 770354--770410 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
770344 AATAAACAAA
* *
770354 CAAATATGAACAGAGATTTATTTGTT
1 CAAACATGAACAGAGATTTATTTATT
770380 CAAACATGAACAGAGATTTATTTATT
1 CAAACATGAACAGAGATTTATTTATT
*
770406 TAAAC
1 CAAAC
770411 TCGATTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (26 bp):
CAAACATGAACAGAGATTTATTTATT
Found at i:773414 original size:209 final size:209
Alignment explanation
Indices: 772900--773929 Score: 1253
Period size: 209 Copynumber: 4.9 Consensus size: 209
772890 TGGTGAAATG
* *
772900 TGGGTATCGACGAGTT---AGAGTT-TAGTTTATGCTTATATTCTTTGAAACATGGTTAA-CTGG
1 TGGGTATCGACGAGTTACAAGAGTTCT-GTTTATGCTTATATTCTTCGAAACATGG-TAAGCTAG
* * * * * * * * * * *
772960 TTGGAATCTAAAGTTTTGTTATTAGAGTTTTGATTTAG-CCCATGATTCT-AAGAGTTATATTAT
64 TTGGAATCTAGAGTTTTGTTATCAAAGTTCT-ATTTTGACCTAAGATTCTGGA-ACTTTTGTTAT
* * * * **
773023 CAAAATTTTGATTATGATCACGATCTGTTAATGACACATGTGACTTATGTGAACTCGTATAAATT
127 CAAAATTCTGATTATGATCACAATCTGTTAATGATACATGTGACTTACGTGAACTCGTATAAACC
*
773088 TATTATGGTGATTACACA
192 CATTATGGTGATTACACA
* * *
773106 T-GGTATCGACGAGTTATAGGAGTTCTGTTTATGCTTATATTCTTCGAAACATGGCAAGCTAGTT
1 TGGGTATCGACGAGTTACAAGAGTTCTGTTTATGCTTATATTCTTCGAAACATGGTAAGCTAGTT
* * *
773170 GGAATCTAGAGTTTTATTATCTAAGTTCTATTTTGACCTAAGACTCTGGAACTTTTGTTATCAAA
66 GGAATCTAGAGTTTTGTTATCAAAGTTCTATTTTGACCTAAGATTCTGGAACTTTTGTTATCAAA
* *
773235 ATTTTGATTATGATCA-AGATCTGTTAATGATACATGTGACTTACGTGAACTCGTATAAATCCAT
131 ATTCTGATTATGATCACA-ATCTGTTAATGATACATGTGACTTACGTGAACTCGTATAAACCCAT
773299 TATGGTGATTACACA
195 TATGGTGATTACACA
*
773314 TGGGTATCGACGAGTTACAGGAGTTCTGTTTATGCTTATATTCTTCGAAACATGGTAAGCTAGTT
1 TGGGTATCGACGAGTTACAAGAGTTCTGTTTATGCTTATATTCTTCGAAACATGGTAAGCTAGTT
* * * * * *
773379 GGAATCTAGAGTTTTATTATCAAAGTTCCATTTTGAGCTAAAACTT-TGGGACTTTCGTTATCAA
66 GGAATCTAGAGTTTTGTTATCAAAGTTCTATTTTGACCTAAGA-TTCTGGAACTTTTGTTATCAA
* *
773443 AATTCTGATTATGATCACAATCTGTTAATGATACATGTGACTTACATGAACTCGGATAAACCCAT
130 AATTCTGATTATGATCACAATCTGTTAATGATACATGTGACTTACGTGAACTCGTATAAACCCAT
*
773508 TATGGTGATTAGACA
195 TATGGTGATTACACA
* * * * * *
773523 AGGGTATCGACAAGTTACAAGAGTTTTGTTTCTGCTTATATTCTTCGAAACATGATGAGCTAAG-
1 TGGGTATCGACGAGTTACAAGAGTTCTGTTTATGCTTATATTCTTCGAAACATGGTAAGCT-AGT
* * * * *
773587 TGGAATCTAAAGTTTTGTTATCATAGTTCTGTTTTGACCTAAGATTCT-GAGACTCTTATTATCA
65 TGGAATCTAGAGTTTTGTTATCAAAGTTCTATTTTGACCTAAGATTCTGGA-ACTTTTGTTATCA
* *
773651 AAATTCTGTTTATGATCACAATCTGTTAATGATACATGTGACTTA-GATGAAATCGTATAAACCC
129 AAATTCTGATTATGATCACAATCTGTTAATGATACATGTGACTTACG-TGAACTCGTATAAACCC
*
773715 ATTATGGTGATTAGACA
193 ATTATGGTGATTACACA
* * * * * * * *
773732 TGGGT-TCCTACGAGTTACAAGAGTTTTGTTTCTGCTTGTATTCTTCAAAACATGATGAGCTAAT
1 TGGGTAT-CGACGAGTTACAAGAGTTCTGTTTATGCTTATATTCTTCGAAACATGGTAAGCTAGT
* ** *
773796 TGGAATCTAGAGTTTTGTTATCATAA-TTCAATTTTGACCTAAGATTCTGGGGCTCTTGTTATCA
65 TGGAATCTAGAGTTTTGTTATCA-AAGTTCTATTTTGACCTAAGATTCTGGAACTTTTGTTATCA
* * *
773860 AAATTCTGATTATGATCACAATCTGTTACTGATACATGTGGCTTACGTGAACTCGTATAAACCTA
129 AAATTCTGATTATGATCACAATCTGTTAATGATACATGTGACTTACGTGAACTCGTATAAACCCA
773925 TTATG
194 TTATG
773930 ATGGTTTGCC
Statistics
Matches: 727, Mismatches: 77, Indels: 37
0.86 0.09 0.04
Matches are distributed among these distances:
205 14 0.02
206 1 0.00
207 7 0.01
208 159 0.22
209 539 0.74
210 7 0.01
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (209 bp):
TGGGTATCGACGAGTTACAAGAGTTCTGTTTATGCTTATATTCTTCGAAACATGGTAAGCTAGTT
GGAATCTAGAGTTTTGTTATCAAAGTTCTATTTTGACCTAAGATTCTGGAACTTTTGTTATCAAA
ATTCTGATTATGATCACAATCTGTTAATGATACATGTGACTTACGTGAACTCGTATAAACCCATT
ATGGTGATTACACA
Done.