Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 39
Found at i:643880 original size:35 final size:35
Alignment explanation
Indices: 643834--643908 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
643824 AGAATACTTT
*
643834 AATTTAGGGTTTAGAATATAATTGAAATATTTTGG
1 AATTTAGGGTTTAGAATATAATTGAAATATTTTAG
* *
643869 AATTTAGGGTTTAGAATATAATTGAAGTGTTTTAG
1 AATTTAGGGTTTAGAATATAATTGAAATATTTTAG
643904 AATTT
1 AATTT
643909 TGAACATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATATAATTGAAATATTTTAG
Found at i:647985 original size:3 final size:3
Alignment explanation
Indices: 647977--648028 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
647967 AATTTTTCGT
** *
647977 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA TTAA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
648023 TTA TTA
1 TTA TTA
648029 CAAGCCCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 40 0.95
4 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:649341 original size:15 final size:15
Alignment explanation
Indices: 649321--649370 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
649311 ATCCATTAGT
649321 TTTTAATATTATTAC
1 TTTTAATATTATTAC
* *
649336 TTTTAAT-TTCTTTC
1 TTTTAATATTATTAC
649350 ATTTTAATTATTATTA-
1 -TTTTAA-TATTATTAC
649366 TTTTA
1 TTTTA
649371 TTTTATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 5 0.18
15 18 0.64
16 1 0.04
17 4 0.14
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTAATATTATTAC
Found at i:649438 original size:20 final size:22
Alignment explanation
Indices: 649350--649438 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 22
649340 AATTTCTTTC
*
649350 ATTTTAATTATTA-TTAT-TTT
1 ATTTTAATTATTACTTATGATT
649370 ATTTT-ATTATTACGTT-TGATAT
1 ATTTTAATTATTAC-TTATGAT-T
649392 ATGTTTAAATTATTATCTTCATGATT
1 AT-TTT-AATTATTA-CTT-ATGATT
*
649418 ATTTT-ATTATTA-TTATTATT
1 ATTTTAATTATTACTTATGATT
649438 A
1 A
649439 AGTTATATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 20
0.72 0.03 0.25
Matches are distributed among these distances:
19 7 0.12
20 12 0.21
21 5 0.09
22 3 0.05
23 10 0.18
25 12 0.21
26 4 0.07
27 4 0.07
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.62
Consensus pattern (22 bp):
ATTTTAATTATTACTTATGATT
Found at i:649458 original size:14 final size:15
Alignment explanation
Indices: 649441--649473 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
649431 TATTATTAAG
649441 TTATATAA-ATATAT
1 TTATATAATATATAT
*
649455 TTATATAATATTTAT
1 TTATATAATATATAT
649470 TTAT
1 TTAT
649474 TTATTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATAATATATAT
Found at i:653450 original size:6 final size:6
Alignment explanation
Indices: 653439--653469 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
653429 GAATGGCAAC
653439 GGGTCG GGGTCG GGGTCG GGGTCG GGG-CG GG
1 GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GG
653470 TTTTGCTCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.00, C:0.16, G:0.71, T:0.13
Consensus pattern (6 bp):
GGGTCG
Found at i:653650 original size:25 final size:25
Alignment explanation
Indices: 653622--653672 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
653612 AATATTTTAT
653622 ATATAAT-TAATATAAAAAATATAAA
1 ATATAATAT-ATATAAAAAATATAAA
* **
653647 ATATTATATATATAATTAATATAAA
1 ATATAATATATATAAAAAATATAAA
653672 A
1 A
653673 AATATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
ATATAATATATATAAAAAATATAAA
Found at i:653657 original size:34 final size:34
Alignment explanation
Indices: 653610--653694 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
653600 CCCGAACCCG
*
653610 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
653644 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
653678 AAAATATTATATATATA
1 AAAATATTATATATATA
653695 TAATCGGGGC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:654331 original size:11 final size:11
Alignment explanation
Indices: 654317--654342 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
654307 GACTCTCAAT
654317 AATCTCTGAAG
1 AATCTCTGAAG
654328 AATCTCTGAAG
1 AATCTCTGAAG
654339 AATC
1 AATC
654343 GACCATTCGA
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:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (11 bp):
AATCTCTGAAG
Found at i:657294 original size:2 final size:2
Alignment explanation
Indices: 657287--657314 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
657277 ATCCTATCCC
657287 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
657315 ATAGAAAATT
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):
TA
Found at i:661395 original size:15 final size:16
Alignment explanation
Indices: 661377--661410 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
661367 TATGAACATC
661377 AAATAAAATAACAA-A
1 AAATAAAATAACAATA
*
661392 AAATAGAATAACAATA
1 AAATAAAATAACAATA
661408 AAA
1 AAA
661411 ATAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (16 bp):
AAATAAAATAACAATA
Found at i:663102 original size:3 final size:3
Alignment explanation
Indices: 663094--663175 Score: 157
Period size: 3 Copynumber: 27.7 Consensus size: 3
663084 GTATATTGTA
663094 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
663142 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
663176 ATATAAAAGA
Statistics
Matches: 78, Mismatches: 0, Indels: 2
0.98 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 76 0.97
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:663391 original size:43 final size:44
Alignment explanation
Indices: 663336--663448 Score: 110
Period size: 40 Copynumber: 2.7 Consensus size: 44
663326 GACGACACTG
* *
663336 CTCATACATGATGAAGAGGTCTGGTCATCTAAGGGA-GACACGA
1 CTCATACGTGATGAAGAGATCTGGTCATCTAAGGGATGACACGA
* * * * *
663379 TTCCTACGTGATGAGGAAATCTGG---TC-AAGGGATGACACGG
1 CTCATACGTGATGAAGAGATCTGGTCATCTAAGGGATGACACGA
* *
663419 CTCATACGCGATGAAGAGTTCTGGTCATCT
1 CTCATACGTGATGAAGAGATCTGGTCATCT
663449 TTAAGAAGGG
Statistics
Matches: 52, Mismatches: 13, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
39 6 0.12
40 26 0.50
43 20 0.38
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (44 bp):
CTCATACGTGATGAAGAGATCTGGTCATCTAAGGGATGACACGA
Found at i:663606 original size:134 final size:134
Alignment explanation
Indices: 663362--663673 Score: 525
Period size: 134 Copynumber: 2.3 Consensus size: 134
663352 AGGTCTGGTC
** ** *
663362 ATCTAAGGGAGACACGATTCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACG
1 ATCTAAGGTTGACACGGCTCCTACGTGATGAGGAAGTCTGGTCAAGGGATGACACGGCTCATACG
663427 CGATGAAGAGTTCTGGTCATCTTTAAGAAGGGTGATAACTAGGTTCCTACGTAATAAGGACGGCT
66 CGATGAAGAGTTCTGGTCATCTTTAAGAAGGGTGATAACTAGGTTCCTACGTAATAAGGACGGCT
663492 GATT
131 GATT
* * *
663496 ATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGAGGGATGACACGTCTCATACG
1 ATCTAAGGTTGACACGGCTCCTACGTGATGAGGAAGTCTGGTCAAGGGATGACACGGCTCATACG
* * *
663561 CGATGAAGAGTTCTGGTCATCTTTAAGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCT
66 CGATGAAGAGTTCTGGTCATCTTTAAGAAGGGTGATAACTAGGTTCCTACGTAATAAGGACGGCT
663626 GATT
131 GATT
663630 ATCTAAGGTTGACACGGCTCCTACGTGATGAGGAAGTCTGGTCA
1 ATCTAAGGTTGACACGGCTCCTACGTGATGAGGAAGTCTGGTCA
663674 GTTGATGTTG
Statistics
Matches: 165, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
134 165 1.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (134 bp):
ATCTAAGGTTGACACGGCTCCTACGTGATGAGGAAGTCTGGTCAAGGGATGACACGGCTCATACG
CGATGAAGAGTTCTGGTCATCTTTAAGAAGGGTGATAACTAGGTTCCTACGTAATAAGGACGGCT
GATT
Found at i:664639 original size:16 final size:16
Alignment explanation
Indices: 664618--664653 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
664608 TCCTTTATTT
664618 ATTTTTC-TTCTTTTTC
1 ATTTTTCATT-TTTTTC
664634 ATTTTTCATTTTTTTC
1 ATTTTTCATTTTTTTC
664650 ATTT
1 ATTT
664654 CCCTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.89
17 2 0.11
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (16 bp):
ATTTTTCATTTTTTTC
Found at i:664664 original size:15 final size:16
Alignment explanation
Indices: 664646--664675 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
664636 TTTTCATTTT
664646 TTTCATTTCC-CTTTA
1 TTTCATTTCCTCTTTA
664661 TTTCATTTCCTCTTT
1 TTTCATTTCCTCTTT
664676 TTTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.10, C:0.27, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTCATTTCCTCTTTA
Found at i:676123 original size:15 final size:16
Alignment explanation
Indices: 676105--676138 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
676095 TATGAACATC
676105 AAATAAAATAACAA-A
1 AAATAAAATAACAATA
*
676120 AAATAGAATAACAATA
1 AAATAAAATAACAATA
676136 AAA
1 AAA
676139 ATAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (16 bp):
AAATAAAATAACAATA
Found at i:677825 original size:3 final size:3
Alignment explanation
Indices: 677817--677885 Score: 113
Period size: 3 Copynumber: 22.7 Consensus size: 3
677807 GTATATTGTA
677817 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
677863 AAT AAAT AAT AAT AAT AA- AAT AA
1 AAT -AAT AAT AAT AAT AAT AAT AA
677886 ATATAAAAGA
Statistics
Matches: 63, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.03
3 55 0.87
4 6 0.10
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:680806 original size:22 final size:22
Alignment explanation
Indices: 680780--680836 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
680770 ATAATCAATT
*
680780 ATAACAAATTTATTTAGTCACA
1 ATAACAAATTTATTTAGTCAAA
* *
680802 ATAACATATTAAATTTAGTCAAA
1 ATAACAAATT-TATTTAGTCAAA
680825 ATAA-AAATTTAT
1 ATAACAAATTTAT
680837 GTTAAATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 2 0.07
22 13 0.45
23 14 0.48
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (22 bp):
ATAACAAATTTATTTAGTCAAA
Found at i:681037 original size:32 final size:32
Alignment explanation
Indices: 680935--681025 Score: 114
Period size: 32 Copynumber: 2.9 Consensus size: 32
680925 ATTTCTCATT
* * * **
680935 ATAAAAAATTGTGACAAATAATATTTTTTCACA
1 ATAAAAAATTATAACAAA-ATTATTTAGTCACA
680968 ATAAAAAATTATAACAAAATTATTTAGTCACA
1 ATAAAAAATTATAACAAAATTATTTAGTCACA
681000 ATAAAAAATTATAA-AAAA-TATTTAGT
1 ATAAAAAATTATAACAAAATTATTTAGT
681026 GACGAAATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
30 8 0.15
31 4 0.08
32 25 0.47
33 16 0.30
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (32 bp):
ATAAAAAATTATAACAAAATTATTTAGTCACA
Found at i:684249 original size:29 final size:29
Alignment explanation
Indices: 684116--684472 Score: 187
Period size: 31 Copynumber: 11.9 Consensus size: 29
684106 TATTCTTATA
*
684116 ATATTTTAAAATTAAGATAAAAATAAAATAT
1 ATATTTT-AAGTTAAGATAAAAAT-AAATAT
*
684147 ATCTTTTTTAA-TTAAGATAAAAATAAA-AT
1 A--TATTTTAAGTTAAGATAAAAATAAATAT
* * *
684176 AT-TTTAAAATTAAAATAAGAAA-AATATAT
1 ATATTTTAAGTTAAGATAA-AAATAA-ATAT
* *
684205 ATATATATATATTTAA-ATAAAAATAGAATAT
1 ATAT-TTTA-AGTTAAGATAAAAATA-AATAT
* *
684236 ATATTTTAAGTTAAAATAATAATAAATA-
1 ATATTTTAAGTTAAGATAAAAATAAATAT
* * * * *
684264 ATACTTAAATTATTAAAATTAATAATATAATAT
1 ATATTTTAA--GTTAAGA-TAAAAATA-AATAT
* *** *
684297 ATGTGACAATTTAAGATAAAAATAAA-AT
1 ATATTTTAAGTTAAGATAAAAATAAATAT
*
684325 ACATTTTTAAAAGTTAAGATAAAAATTAAATAT
1 ATA-TTTT--AAGTTAAGATAAAAA-TAAATAT
* *
684358 ATATTTTTAAGTTAAGATAAGATTAAA-AT
1 ATA-TTTTAAGTTAAGATAAAAATAAATAT
*
684387 ATATTTTTTAGTTAAGAT-AAAATAAA-AT
1 ATA-TTTTAAGTTAAGATAAAAATAAATAT
* * *
684415 ATATTTTTTAGTGAAGATAAGAATAAA-AT
1 ATA-TTTTAAGTTAAGATAAAAATAAATAT
*
684444 ATATTTAATAAGTTAAATATAAAAATAAA
1 ATATTT--TAAGTT-AAGATAAAAATAAA
684473 AAGTTTTTTT
Statistics
Matches: 262, Mismatches: 38, Indels: 52
0.74 0.11 0.15
Matches are distributed among these distances:
26 5 0.02
27 11 0.04
28 42 0.16
29 50 0.19
30 39 0.15
31 81 0.31
32 16 0.06
33 18 0.07
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (29 bp):
ATATTTTAAGTTAAGATAAAAATAAATAT
Found at i:684296 original size:61 final size:62
Alignment explanation
Indices: 684174--684298 Score: 141
Period size: 61 Copynumber: 2.0 Consensus size: 62
684164 TAAAAATAAA
* *
684174 ATATTTTAAAATTAAAATAAGAAAAATATATATATATATATATTTAAATAAAAATAGAATAT
1 ATATTTTAAAATTAAAATAAGAAAAATATATATATAAATATATTAAAATAAAAATAGAATAT
* * * *
684236 ATATTTT-AAGTTAAAATAATAATAAATA-ATACT-TAAAT-TATTAAAATTAATAATATAATAT
1 ATATTTTAAAATTAAAATAAGAA-AAATATATA-TATAAATATATTAAAA-TAAAAATAGAATAT
684297 AT
1 AT
684299 GTGACAATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
60 7 0.13
61 34 0.63
62 13 0.24
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (62 bp):
ATATTTTAAAATTAAAATAAGAAAAATATATATATAAATATATTAAAATAAAAATAGAATAT
Found at i:684379 original size:36 final size:32
Alignment explanation
Indices: 684308--684422 Score: 93
Period size: 29 Copynumber: 3.8 Consensus size: 32
684298 TGTGACAATT
*
684308 TAAGATAAAAA-TAAAATACATTTTTAAAAGT
1 TAAGATAAAAATTAAAATACATTTTTAAAAGA
* *
684339 TAAGATAAAAATTAAATATATATTTTT--AAGT
1 TAAGATAAAAATTAAA-ATACATTTTTAAAAGA
* * * *
684370 TAAGAT-AAGATTAAAATATATTTTT--TAGT
1 TAAGATAAAAATTAAAATACATTTTTAAAAGA
*
684399 TAAGAT-AAAA-TAAAATATATTTTT
1 TAAGATAAAAATTAAAATACATTTTT
684423 TAGTGAAGAT
Statistics
Matches: 78, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
28 14 0.18
29 22 0.28
30 8 0.10
31 21 0.27
32 4 0.05
33 9 0.12
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.40
Consensus pattern (32 bp):
TAAGATAAAAATTAAAATACATTTTTAAAAGA
Found at i:684442 original size:57 final size:61
Alignment explanation
Indices: 684309--684449 Score: 191
Period size: 57 Copynumber: 2.4 Consensus size: 61
684299 GTGACAATTT
* * *
684309 AAGATAAAAATAAAATACATTTTTAAAAGTTAAGATAAAAATTAAATATATATTTTTAAGTT
1 AAGATAAGAATAAAATATATTTTT-AAAGTTAAGATAAAAATTAAATATATATTTTTAAGTG
* * *
684371 AAGATAAGATTAAAATATATTTTT-TAGTTAAGAT-AAAA-TAAA-ATATATTTTTTAGTG
1 AAGATAAGAATAAAATATATTTTTAAAGTTAAGATAAAAATTAAATATATATTTTTAAGTG
684428 AAGATAAGAATAAAATATATTT
1 AAGATAAGAATAAAATATATTT
684450 AATAAGTTAA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
57 34 0.47
58 4 0.06
59 4 0.06
60 9 0.12
62 21 0.29
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.38
Consensus pattern (61 bp):
AAGATAAGAATAAAATATATTTTTAAAGTTAAGATAAAAATTAAATATATATTTTTAAGTG
Found at i:684480 original size:57 final size:58
Alignment explanation
Indices: 684309--684480 Score: 156
Period size: 57 Copynumber: 2.9 Consensus size: 58
684299 GTGACAATTT
* * * *
684309 AAGATAAAAATAAAATACATTTTTAA-AAGTTAAGATAAAAATTAAATATATATTTTTAAGTT
1 AAGATAAGAATAAAAT--ATATTTAATAAGTTAAGATAAAAAATAAA-A-A-ATTTTTAAGTG
* * * *
684371 AAGATAAGATTAAAATATATTT-TTTAGTTAAGAT--AAAATAAAATATATTTTTTAGTG
1 AAGATAAGAATAAAATATATTTAATAAGTTAAGATAAAAAATAAAA-A-ATTTTTAAGTG
*
684428 AAGATAAGAATAAAATATATTTAATAAGTTAA-ATATAAAAATAAAAAGTTTTT
1 AAGATAAGAATAAAATATATTTAATAAGTTAAGATA-AAAAATAAAAAATTTTT
684481 TTAAATAAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
57 36 0.39
58 19 0.20
59 1 0.01
60 23 0.25
62 14 0.15
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (58 bp):
AAGATAAGAATAAAATATATTTAATAAGTTAAGATAAAAAATAAAAAATTTTTAAGTG
Found at i:685124 original size:51 final size:52
Alignment explanation
Indices: 684938--685248 Score: 536
Period size: 52 Copynumber: 6.0 Consensus size: 52
684928 AAAACCCAAA
* *
684938 AGGTAGGGGAAAGTCAGGTCAAATTTAGAAGAACAAGGAAATTGTTTAACAT
1 AGGTAGGGGAAAGTCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACAT
684990 AGGTAGGGGAAAGTCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACAT
1 AGGTAGGGGAAAGTCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACAT
685042 AGGTAGGGGAAAGTCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACAT
1 AGGTAGGGGAAAGTCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACAT
*
685094 AGGTA-GGGAAAGTCAGGTCAAATTTGGAAGAACAAGGAAGTTTTTTAACAT
1 AGGTAGGGGAAAGTCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACAT
* *
685145 AGGTAGGGGAAAGTAAGGTCAAATTTGGAAGAATAAGGAAGTTGTTTAACAT
1 AGGTAGGGGAAAGTCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACAT
* * *
685197 A-GTAGGGGAAAGTCATGTCAAATTTGGAAGAATAAGAAAGTTGTTTAACAT
1 AGGTAGGGGAAAGTCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACAT
685248 A
1 A
685249 TAATCAAAGG
Statistics
Matches: 249, Mismatches: 9, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
51 98 0.39
52 151 0.61
ACGTcount: A:0.40, C:0.07, G:0.29, T:0.24
Consensus pattern (52 bp):
AGGTAGGGGAAAGTCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACAT
Found at i:685157 original size:103 final size:104
Alignment explanation
Indices: 684938--685248 Score: 536
Period size: 103 Copynumber: 3.0 Consensus size: 104
684928 AAAACCCAAA
* *
684938 AGGTAGGGGAAAGTCAGGTCAAATTTAGAAGAACAAGGAAATTGTTTAACATAGGTAGGGGAAAG
1 AGGTAGGGGAAAGTCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACATAGGTAGGGGAAAG
685003 TCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACAT
66 TCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACAT
685042 AGGTAGGGGAAAGTCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACATAGGTA-GGGAAAG
1 AGGTAGGGGAAAGTCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACATAGGTAGGGGAAAG
*
685106 TCAGGTCAAATTTGGAAGAACAAGGAAGTTTTTTAACAT
66 TCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACAT
* *
685145 AGGTAGGGGAAAGTAAGGTCAAATTTGGAAGAATAAGGAAGTTGTTTAACATA-GTAGGGGAAAG
1 AGGTAGGGGAAAGTCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACATAGGTAGGGGAAAG
* * *
685209 TCATGTCAAATTTGGAAGAATAAGAAAGTTGTTTAACAT
66 TCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACAT
685248 A
1 A
685249 TAATCAAAGG
Statistics
Matches: 197, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
102 3 0.02
103 139 0.71
104 55 0.28
ACGTcount: A:0.40, C:0.07, G:0.29, T:0.24
Consensus pattern (104 bp):
AGGTAGGGGAAAGTCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACATAGGTAGGGGAAAG
TCAGGTCAAATTTGGAAGAACAAGGAAGTTGTTTAACAT
Found at i:690926 original size:98 final size:98
Alignment explanation
Indices: 690816--691349 Score: 265
Period size: 98 Copynumber: 5.4 Consensus size: 98
690806 TTACTGGAAC
* *
690816 TAAATAATTTTGTTACAATTTGTTATTGTGA-AATAATATTATTTGTCACAATTATTTATAATAA
1 TAAATAAATTTGTTACAATTTGTTATTGTGATAA-AATATTATTTGTCAAAATTATTTATAATAA
*
690880 GAAATTTATATTTGTTATAATTTGTTATTTTGAT
65 GAAATTTATATTTGTTATAATTTGTTATTGTGAT
** * ** * * * * *
690914 TAAATAAATTTGTCCCAATTT-TTCATTTTGATAAAATA-T-TGGGACAAAATAAATT-TGA-CA
1 TAAATAAATTTGTTACAATTTGTT-ATTGTGATAAAATATTATTTGTCAAAATTATTTATAATAA
* * * * * *
690974 TAATTTTTTACTATGATAAAACTTAGCGTGTTATTGTGAT
65 GAAATTTATA-TTTGTTATAA-TT----TGTTATTGTGAT
* * * * * *
691014 TAAATCATTTTGTTACAATTTGTTATTGTGA-AAGAATATTACTTGTCATAATTTTTTATAATGA
1 TAAATAAATTTGTTACAATTTGTTATTGTGATAA-AATATTATTTGTCAAAATTATTTATAATAA
* * *
691078 GAAATTAATATTTGTTAT-ATATTATTATTTTGAT
65 GAAATTTATATTTGTTATAAT-TTGTTATTGTGAT
* * * * * * *
691112 TAAATAAATTTTTTATAATTTTTTATT-TCGATAAAATA-T-TGTGACAAAATAAATTTGA-CAT
1 TAAATAAATTTGTTACAATTTGTTATTGT-GATAAAATATTATTTGTCAAAAT-TATTT-ATAAT
* * * *
691173 AA-AATTTTAT-TTTGACTA-AATTTACTATGTTATTGTAAC
63 AAGAAATTTATATTTG-TTATAA--T--T-TGTTATTGTGAT
* * * * * *
691212 TAAATAAATTTGTTACACTCTGTTATTGTGA-AAGAATATTATTTGTCATAATTTTTTAT-TTCG
1 TAAATAAATTTGTTACAATTTGTTATTGTGATAA-AATATTATTTGTCAAAATTATTTATAAT-A
* * * * *
691275 AGGAATTAATATTTGTTATAAATTGTTATTATGAC
64 AGAAATTTATATTTGTTATAATTTGTTATTGTGAT
* * * * *
691310 TAAATAAATTTGTCAAAAGTTGTTATTATGAGAAAATATT
1 TAAATAAATTTGTTACAATTTGTTATTGTGATAAAATATT
691350 GTGACGAAAT
Statistics
Matches: 312, Mismatches: 89, Indels: 70
0.66 0.19 0.15
Matches are distributed among these distances:
94 8 0.03
95 13 0.04
96 28 0.09
97 11 0.04
98 109 0.35
99 12 0.04
100 76 0.24
101 10 0.03
102 25 0.08
103 13 0.04
104 7 0.02
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.47
Consensus pattern (98 bp):
TAAATAAATTTGTTACAATTTGTTATTGTGATAAAATATTATTTGTCAAAATTATTTATAATAAG
AAATTTATATTTGTTATAATTTGTTATTGTGAT
Found at i:691160 original size:198 final size:196
Alignment explanation
Indices: 690813--691414 Score: 726
Period size: 198 Copynumber: 3.0 Consensus size: 196
690803 TTTTTACTGG
* * *
690813 AACTAAATAATTTTGTTACAATTTGTTATTGTGAAATAATATTATTTGTCACAATTATTTATAAT
1 AACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCATAATTTTTTATAAT
* * ** *
690878 AAGAAATTTATATTTGTTATAATTTGTTATTTTGATTAAATAAATTTGTCCCAATTTTTCATTTT
66 GAGAAATTAATATTTGTTATAA-TTGTTATTTTGATTAAATAAATTTGTCAAAATTTTTTA-TTT
* * *
690943 GATAAAATATTGGGACAAAATAAATTTGACATAATTTTTTACTATGA-TAAAACTTAGC-GTGTT
129 GATAAAATATTGTGACAAAATAAATTTGACATAAATTTTTACTATGACT-AAACTTA-CTATGTT
691006 ATTGT
192 ATTGT
* * * *
691011 GATTAAATCATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCATAATTTTTTATAAT
1 AACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCATAATTTTTTATAAT
* * * *
691076 GAGAAATTAATATTTGTTATATATTATTATTTTGATTAAATAAATTTTTTATAATTTTTTATTTC
66 GAGAAATTAATATTTGTTATA-ATTGTTATTTTGATTAAATAAATTTGTCAAAATTTTTTATTT-
* * * *
691141 GATAAAATATTGTGACAAAATAAATTTGACATAAAATTTTATTTTGACTAAATTTACTATGTTAT
129 GATAAAATATTGTGACAAAATAAATTTGACATAAATTTTTACTATGACTAAACTTACTATGTTAT
691206 TGT
194 TGT
* * * *
691209 AACTAAATAAATTTGTTACACTCTGTTATTGTGAAAGAATATTATTTGTCATAATTTTTTAT-TT
1 AACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCATAATTTTTTATAAT
* * * * *
691273 CGAGGAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGTTGTTATTA
66 -GAGAAATTAATATTTGTTAT-AATTGTTATTTTGATTAAATAAATTTGTCAAAATTTTTTATT-
* * * * * * *
691338 TGAGAAAATATTGTGACGAAATAAATTTAACATAAATTTTTA-TTTTAGCTAAATTTAATATGTT
128 TGATAAAATATTGTGACAAAATAAATTTGACATAAATTTTTACTATGA-CTAAACTTACTATGTT
691402 ATTGT
192 ATTGT
*
691407 GACTAAAT
1 AACTAAAT
691415 GCATGATTTA
Statistics
Matches: 350, Mismatches: 46, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
197 9 0.03
198 337 0.96
199 4 0.01
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (196 bp):
AACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCATAATTTTTTATAAT
GAGAAATTAATATTTGTTATAATTGTTATTTTGATTAAATAAATTTGTCAAAATTTTTTATTTGA
TAAAATATTGTGACAAAATAAATTTGACATAAATTTTTACTATGACTAAACTTACTATGTTATTG
T
Found at i:694152 original size:48 final size:47
Alignment explanation
Indices: 694084--694260 Score: 202
Period size: 44 Copynumber: 3.8 Consensus size: 47
694074 ATAAAATCTT
* *
694084 TTACCATTT--ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
** *
694129 TTACTGTTTAAAATTCCATAAGCTCGTAAGCTTATATTTTTTTCCAATATAC
1 TTACCATTT-AAATTCCATAAGCTCGTAAGC-T-TA--TTTTACCAATATAC
*
694181 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
* *
694228 TTGCCA-TT--ATTCCAAAAGCTCGTAAGCTTATTT
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTT
694261 GTATGCTTAC
Statistics
Matches: 114, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
44 24 0.21
45 7 0.06
46 2 0.02
47 17 0.15
48 18 0.16
49 3 0.03
50 3 0.03
51 21 0.18
52 19 0.17
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (47 bp):
TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:694409 original size:40 final size:40
Alignment explanation
Indices: 694365--694486 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
694355 ACCGTAGTGC
694365 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
694405 TACACATAAGGTCGTGCCCACCATATATACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
694445 TACACATAAGGTCGTGCCCACCATATACATCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
694485 TA
1 TA
694487 TAAACCTGCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:701138 original size:48 final size:47
Alignment explanation
Indices: 701074--701250 Score: 175
Period size: 44 Copynumber: 3.8 Consensus size: 47
701064 ATAAAATCTT
* * *
701074 TTACCATTT--ATCCCATAAGCTCCTAAGCTTATTTTACCAAAATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
* *
701119 TTACCGTTTAAAATTCCATAAGCTCGTAAGCTTATATTGTTTTCCAATATAC
1 TTACCATTT-AAATTCCATAAGCTCGTAAGC-T-TA-T-TTTACCAATATAC
* * *
701171 TTACCATTTAAATTCCTTAAGCTCGTATGCTTATTTTACCCATATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
* * *
701218 TTGCCA-TT--ATTCCAAAAGCTCATAAGCTTATTT
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTT
701251 GTATGCTTAC
Statistics
Matches: 110, Mismatches: 15, Indels: 15
0.79 0.11 0.11
Matches are distributed among these distances:
44 21 0.19
45 8 0.07
46 2 0.02
47 16 0.15
48 18 0.16
49 3 0.03
50 3 0.03
51 20 0.18
52 19 0.17
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.40
Consensus pattern (47 bp):
TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:701195 original size:51 final size:53
Alignment explanation
Indices: 701105--701204 Score: 150
Period size: 51 Copynumber: 1.9 Consensus size: 53
701095 CCTAAGCTTA
*
701105 TTTTACCAAAATACTTACCGTTTAAAATTCCATAAGCTCGTAAGCTTATATTG
1 TTTTACCAAAATACTTACCATTTAAAATTCCATAAGCTCGTAAGCTTATATTG
* * *
701158 TTTT-CCAATATACTTACCATTT-AAATTCCTTAAGCTCGTATGCTTAT
1 TTTTACCAAAATACTTACCATTTAAAATTCCATAAGCTCGTAAGCTTAT
701205 TTTACCCATA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 23 0.53
52 16 0.37
53 4 0.09
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (53 bp):
TTTTACCAAAATACTTACCATTTAAAATTCCATAAGCTCGTAAGCTTATATTG
Found at i:701399 original size:40 final size:40
Alignment explanation
Indices: 701355--701516 Score: 306
Period size: 40 Copynumber: 4.0 Consensus size: 40
701345 ACCGTAGTGC
701355 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
701395 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
701435 TACACATAAGGTCGTACCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
701475 TACACATAAGGTCGTGCCCACCATATACATCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
701515 TA
1 TA
701517 TAAACCTGCA
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 119 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:704913 original size:406 final size:411
Alignment explanation
Indices: 704255--705036 Score: 1030
Period size: 406 Copynumber: 1.9 Consensus size: 411
704245 AATTTTTTTA
* * *
704255 TAGTATAATTTTTCATAATGATTGAAATATATAACTAAAAAATAATTGCTTACAAAAAACTTGAA
1 TAGTATAATTTTTCATAATGATTGAAATATATAACGAAAAAAAAATTGATTACAAAAAACTTGAA
704320 TTTTATTATCTAATGTGATAATTTTTTCTATAACAATAACTATAAATTATAATTACAAAACTTAT
66 TTTTATTATCTAATGTGATAATTTTTTCTATAACAATAAC--------ATAATTACAAAACTTAT
* * * *
704385 CAATATAGCTTTTTGAAACAAAAAAATGAAGAAAAATATTTATCAAAATATATGTTATTACCATA
123 CAATATAACTTTTTGAAACAAAAAAATGAAGAAAAATAGTTATCAAAATATATGCTATCACCATA
* * *
704450 ATTAAAATTTATAACTACAAGTATAATTTCTCACAAAAATGTGAATACCATTATTTTTTGTGACA
188 ATTAAAATTTATAACTACAAATATAATTTCTCACAAAAACGTGAATACAATTATTTTTTGTGACA
704515 ATGTTTTTTGTAATAATTA-TATACACTTATAGTTACAAAA-AT-TTACTATATGA-TTTTTTGG
253 ATGTTTTTTGTAATAATTATTA-ACACTTATAGTTACAAAATATATTACTATATGACTTTTTTGG
* * *
704576 TGC-AAAAAAATATGGTGGAAAATCTTTATGACAATATATTTTGTTACTATATAACATTTTTTAC
317 CGCAAAAAAAATATGGAGGAAAATCTTTATGACAATATATTTTGTCACTATATAACATTTTTTAC
704640 AGTAAAAAAAATAAGGAGAAATGTTTATGC
382 AGTAAAAAAAATAAGGAGAAATGTTTATGC
* * *
704670 TAGTATAATTTTTCATAATGATT-ATATTATATAAGGACAAAAAAAATTTATTACAAAAAACTTG
1 TAGTATAATTTTTCATAATGATTGA-AATATATAACGA-AAAAAAAATTGATTACAAAAAACTTG
* * * * *
704734 AATTTTATTATTTGATGTGATACTTTTTTTTATAACAATAAC-T-A-TA-AAAA-TTGTCAATAT
64 AATTTTATTATCTAATGTGATAATTTTTTCTATAACAATAACATAATTACAAAACTTATCAATAT
* * *
704794 AAC-TTTTGAAACAAAAAAGTGGAGAAAAATAGTTATGACAATTAATATATGCTATCACTATAAT
129 AACTTTTTGAAACAAAAAAATGAAGAAAAATAGTTAT--CAA--AATATATGCTATCACCATAAT
* * *
704858 TAAAATTTATAACTACAAATATAATTTGTCACAAAAACGTGAATATAATTATTTTTTGTGAGAAT
190 TAAAATTTATAACTACAAATATAATTTCTCACAAAAACGTGAATACAATTATTTTTTGTGACAAT
* * * * *
704923 GTTTTTTGTAATAATTATTAATACTTATAGTTATAAAATTTATTACTATATTACTTTTTTTGCGC
255 GTTTTTTGTAATAATTATTAACACTTATAGTTACAAAATATATTACTATATGACTTTTTTGGCGC
* * *
704988 AAAAAAAATATGGAGGGAAATTTTTGTGACAATATATTTTGTCACTATA
320 AAAAAAAATATGGAGGAAAATCTTTATGACAATATATTTTGTCACTATA
705037 ACTAAAACAT
Statistics
Matches: 321, Mismatches: 35, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
402 30 0.09
403 11 0.03
404 7 0.02
405 2 0.01
406 111 0.35
407 4 0.01
408 10 0.03
409 9 0.03
410 43 0.13
414 1 0.00
415 32 0.10
416 61 0.19
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (411 bp):
TAGTATAATTTTTCATAATGATTGAAATATATAACGAAAAAAAAATTGATTACAAAAAACTTGAA
TTTTATTATCTAATGTGATAATTTTTTCTATAACAATAACATAATTACAAAACTTATCAATATAA
CTTTTTGAAACAAAAAAATGAAGAAAAATAGTTATCAAAATATATGCTATCACCATAATTAAAAT
TTATAACTACAAATATAATTTCTCACAAAAACGTGAATACAATTATTTTTTGTGACAATGTTTTT
TGTAATAATTATTAACACTTATAGTTACAAAATATATTACTATATGACTTTTTTGGCGCAAAAAA
AATATGGAGGAAAATCTTTATGACAATATATTTTGTCACTATATAACATTTTTTACAGTAAAAAA
AATAAGGAGAAATGTTTATGC
Found at i:707223 original size:44 final size:44
Alignment explanation
Indices: 707160--707259 Score: 148
Period size: 44 Copynumber: 2.3 Consensus size: 44
707150 GCAACCCAAC
* **
707160 AGTATCGACACCTATCAAGGAGTATCGATACTACTATGTGTAGT
1 AGTATCGATACCTATCAAGGAGTATCGATACTACTATGTAAAGT
*
707204 AGTATCGATACC-ATCCAAGGAGTATTGATACTACTATGTAAAGT
1 AGTATCGATACCTAT-CAAGGAGTATCGATACTACTATGTAAAGT
707248 AGTATCGATACC
1 AGTATCGATACC
707260 GGTCATGATA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 2 0.04
44 49 0.96
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (44 bp):
AGTATCGATACCTATCAAGGAGTATCGATACTACTATGTAAAGT
Found at i:707257 original size:24 final size:24
Alignment explanation
Indices: 707180--707258 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 24
707170 CCTATCAAGG
**
707180 AGTATCGATACTACTATGTGTAGT
1 AGTATCGATACTACTATGTAAAGT
** *
707204 AGTATCGATAC--C-AT-CCAAGG
1 AGTATCGATACTACTATGTAAAGT
*
707224 AGTATTGATACTACTATGTAAAGT
1 AGTATCGATACTACTATGTAAAGT
707248 AGTATCGATAC
1 AGTATCGATAC
707259 CGGTCATGAT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
20 12 0.29
21 2 0.05
22 2 0.05
23 2 0.05
24 24 0.57
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (24 bp):
AGTATCGATACTACTATGTAAAGT
Found at i:709550 original size:18 final size:18
Alignment explanation
Indices: 709529--709563 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
709519 AAAACAATAT
709529 AATTAAATAAAAAACAAC
1 AATTAAATAAAAAACAAC
*
709547 AATTAAATCAAAAACAA
1 AATTAAATAAAAAACAA
709564 ATATTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.17
Consensus pattern (18 bp):
AATTAAATAAAAAACAAC
Found at i:709928 original size:20 final size:20
Alignment explanation
Indices: 709903--709954 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
709893 CCCGACAGGT
709903 AGTATCGGTACTCCTCGAGG
1 AGTATCGGTACTCCTCGAGG
709923 AGTATCGGTACTCCTCGAGG
1 AGTATCGGTACTCCTCGAGG
*
709943 AGTATCGATACT
1 AGTATCGGTACT
709955 TTAAGGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (20 bp):
AGTATCGGTACTCCTCGAGG
Found at i:719091 original size:16 final size:17
Alignment explanation
Indices: 719066--719098 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
719056 GTTACAGGCT
*
719066 AAAATATATAACTTTTA
1 AAAATATATAAATTTTA
719083 AAAAT-TATAAATTTTA
1 AAAATATATAAATTTTA
719099 GTCCCTACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATATATAAATTTTA
Found at i:720702 original size:43 final size:43
Alignment explanation
Indices: 720649--720878 Score: 223
Period size: 43 Copynumber: 5.3 Consensus size: 43
720639 GCGTTTGAGA
* * *
720649 AGAA-AAACACCGTAAAAGGTTGATATTTATAGCGGCATTTTT
1 AGAACAAACGCCGCAAAAGGTTGATATCTATAGCGGCATTTTT
* * * * * *
720691 AGAACAAACACCACAAAAGGTCGATATATATAGTGGCGTTTTT
1 AGAACAAACGCCGCAAAAGGTTGATATCTATAGCGGCATTTTT
* * * *
720734 -GAAACAGACGCCGCAAAAGGTCGATATCTATAACGACATTTTT
1 AG-AACAAACGCCGCAAAAGGTTGATATCTATAGCGGCATTTTT
*
720777 AGAACAAACGCCGCAAAAGGTTGATATATATATAGCGGCATTTTT
1 AGAACAAACGCCGCAAAAGGTTG--ATATCTATAGCGGCATTTTT
* * * * *
720822 GGAACAAATGCTGCAAAAGGTT-AGATCTATAGCGGCGTTTTT
1 AGAACAAACGCCGCAAAAGGTTGATATCTATAGCGGCATTTTT
*
720864 TGATACAAACGCCGC
1 AGA-ACAAACGCCGC
720879 TAATTACCTT
Statistics
Matches: 154, Mismatches: 28, Indels: 11
0.80 0.15 0.06
Matches are distributed among these distances:
42 24 0.16
43 93 0.60
44 1 0.01
45 36 0.23
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (43 bp):
AGAACAAACGCCGCAAAAGGTTGATATCTATAGCGGCATTTTT
Found at i:722400 original size:78 final size:77
Alignment explanation
Indices: 722289--722444 Score: 285
Period size: 78 Copynumber: 2.0 Consensus size: 77
722279 AAAACTTCTC
* *
722289 ACCTTGGCTATGGGCTTCAGCAGCTTTCTGGAGAAGAGAAGAGTTCACGATGATTCTAAAAAAAA
1 ACCTTGGCTATGGGCTTCAACAGCTTTCTGGAGAAGAGAAGAGTTCACGATGATTAT-AAAAAAA
722354 CAAATCTCCAATT
65 CAAATCTCCAATT
722367 ACCTTGGCTATGGGCTTCAACAGCTTTCTGGAGAAGAGAAGAGTTCACGATGATTATAAAAAAAC
1 ACCTTGGCTATGGGCTTCAACAGCTTTCTGGAGAAGAGAAGAGTTCACGATGATTATAAAAAAAC
722432 AAATCTCCAATT
66 AAATCTCCAATT
722444 A
1 A
722445 TTAACCTTTA
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
77 21 0.28
78 55 0.72
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (77 bp):
ACCTTGGCTATGGGCTTCAACAGCTTTCTGGAGAAGAGAAGAGTTCACGATGATTATAAAAAAAC
AAATCTCCAATT
Found at i:724576 original size:42 final size:43
Alignment explanation
Indices: 724462--724646 Score: 178
Period size: 43 Copynumber: 4.3 Consensus size: 43
724452 CCGCTAAAGT
** * * *
724462 TAGCGGCGTTTGAGAAGAAAAACACCGCAAAAGGTTGATATCTA
1 TAGCGGCGTTTTTGAA-ACAAACACCGCAAAAGGTCGATATATA
* *
724506 TAGGGGCATTTTTTG-AACAAACACCGCAAAAGGTCGATATATA
1 TAGCGGC-GTTTTTGAAACAAACACCGCAAAAGGTCGATATATA
* * *
724549 TA-CGGCGTTTTTGAAACATACGCCGCAAAAGGTCGATATCTA
1 TAGCGGCGTTTTTGAAACAAACACCGCAAAAGGTCGATATATA
* * * *
724591 TAACGACGTTTTT-ATAACAAACACCGCAAAAGTTAGATATATA
1 TAGCGGCGTTTTTGA-AACAAACACCGCAAAAGGTCGATATATA
* *
724634 TATCAGCGTTTTT
1 TAGCGGCGTTTTT
724647 TTATACAAAC
Statistics
Matches: 116, Mismatches: 21, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
41 6 0.05
42 31 0.27
43 68 0.59
44 7 0.06
45 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27
Consensus pattern (43 bp):
TAGCGGCGTTTTTGAAACAAACACCGCAAAAGGTCGATATATA
Found at i:724630 original size:85 final size:86
Alignment explanation
Indices: 724486--724646 Score: 227
Period size: 85 Copynumber: 1.9 Consensus size: 86
724476 AAGAAAAACA
* ** * *
724486 CCGCAAAAGGTTGATATCTATAGGGGCATTTTTTGAACAAACACCGCAAAAGGTCGATATATATA
1 CCGCAAAAGGTCGATATCTATAACGACATTTTTTGAACAAACACCGCAAAAGGTAGATATATATA
*
724551 -CGGCGTTTTTGAAACATACG
66 TCAGCGTTTTTGAAACATACG
* *
724571 CCGCAAAAGGTCGATATCTATAACGACGTTTTTAT-AACAAACACCGCAAAAGTTAGATATATAT
1 CCGCAAAAGGTCGATATCTATAACGACATTTTT-TGAACAAACACCGCAAAAGGTAGATATATAT
724635 ATCAGCGTTTTT
65 ATCAGCGTTTTT
724647 TTATACAAAC
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
85 56 0.85
86 10 0.15
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (86 bp):
CCGCAAAAGGTCGATATCTATAACGACATTTTTTGAACAAACACCGCAAAAGGTAGATATATATA
TCAGCGTTTTTGAAACATACG
Found at i:736623 original size:36 final size:35
Alignment explanation
Indices: 736577--736662 Score: 121
Period size: 30 Copynumber: 2.6 Consensus size: 35
736567 GGGGAATGTT
736577 GGTAATGCTCATTGAATATTGATATTGGAAAATTA
1 GGTAATGCTCATTGAATATTGATATTGGAAAATTA
736612 GGTAAATGCTCATTG---A---ATATTGGAAAATTA
1 GGT-AATGCTCATTGAATATTGATATTGGAAAATTA
736642 GGTAATGCTCATTGAATATTG
1 GGTAATGCTCATTGAATATTG
736663 GAAAATAGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
29 11 0.25
30 17 0.39
32 1 0.02
33 1 0.02
35 3 0.07
36 11 0.25
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (35 bp):
GGTAATGCTCATTGAATATTGATATTGGAAAATTA
Found at i:736680 original size:28 final size:29
Alignment explanation
Indices: 736594--736702 Score: 168
Period size: 29 Copynumber: 3.8 Consensus size: 29
736584 CTCATTGAAT
736594 ATTG-ATATTGGAAAATTAGGTAAATGCTC
1 ATTGAATATTGGAAAATTAGGT-AATGCTC
736623 ATTGAATATTGGAAAATTAGGTAATGCTC
1 ATTGAATATTGGAAAATTAGGTAATGCTC
736652 ATTGAATATTGGAAAA-TAGGTAATGCTC
1 ATTGAATATTGGAAAATTAGGTAATGCTC
* **
736680 ATTTAATATTTAAAAATTAGGTA
1 ATTGAATATTGGAAAATTAGGTA
736703 TTTCCACTAG
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
28 25 0.33
29 33 0.44
30 17 0.23
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (29 bp):
ATTGAATATTGGAAAATTAGGTAATGCTC
Found at i:736688 original size:57 final size:58
Alignment explanation
Indices: 736594--736702 Score: 168
Period size: 57 Copynumber: 1.9 Consensus size: 58
736584 CTCATTGAAT
*
736594 ATTGATATTGGAAAATTAGGTAAATGCTCATTGAATATTGGAAAATTAGGTAATGCTC
1 ATTGATATTGGAAAATTAGGTAAATGCTCATTGAATATTGAAAAATTAGGTAATGCTC
* *
736652 ATTGAATATTGGAAAA-TAGGT-AATGCTCATTTAATATTTAAAAATTAGGTA
1 ATTG-ATATTGGAAAATTAGGTAAATGCTCATTGAATATTGAAAAATTAGGTA
736703 TTTCCACTAG
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
57 27 0.57
58 9 0.19
59 11 0.23
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (58 bp):
ATTGATATTGGAAAATTAGGTAAATGCTCATTGAATATTGAAAAATTAGGTAATGCTC
Found at i:743687 original size:20 final size:20
Alignment explanation
Indices: 743664--743772 Score: 57
Period size: 20 Copynumber: 5.4 Consensus size: 20
743654 GAACTTCAAT
743664 TTCGCAACACAGTTTCCAAA
1 TTCGCAACACAGTTTCCAAA
**
743684 TTCGCAACTTAGTTTCTGC-AA
1 TTCGCAACACAGTTTC--CAAA
*
743705 -TCGCAACGC-GATTTCCAAA
1 TTCGCAACACAG-TTTCCAAA
* **
743724 TTCACAAC-GTGATTTCCAAA
1 TTCGCAACACAG-TTTCCAAA
* *
743744 TTCACAACACGGAATTT-CAAA
1 TTCGCAACAC--AGTTTCCAAA
743765 TTCGCAAC
1 TTCGCAAC
743773 TCGATTTCTG
Statistics
Matches: 70, Mismatches: 10, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
18 1 0.01
19 3 0.04
20 49 0.70
21 13 0.19
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (20 bp):
TTCGCAACACAGTTTCCAAA
Found at i:743766 original size:21 final size:22
Alignment explanation
Indices: 743714--743772 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 22
743704 ATCGCAACGC
743714 GATTTCCAAATTCAC-A-ACGT
1 GATTTCCAAATTCACAACACGT
743734 GATTTCCAAATTCACAACACG-
1 GATTTCCAAATTCACAACACGT
*
743755 GAATTT-CAAATTCGCAAC
1 G-ATTTCCAAATTCACAAC
743773 TCGATTTCTG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
20 15 0.43
21 13 0.37
22 7 0.20
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.27
Consensus pattern (22 bp):
GATTTCCAAATTCACAACACGT
Found at i:743787 original size:41 final size:40
Alignment explanation
Indices: 743715--743801 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 40
743705 TCGCAACGCG
743715 ATTTCCAAATTCACAACGTGATTTCCAAATTCACAACACGGA
1 ATTT-CAAATTCACAACGTGATTTCCAAATTCACAACAC-GA
* ** * *
743757 ATTTCAAATTCGCAAC-TCGATTTCTGAATTCGCAACGCGA
1 ATTTCAAATTCACAACGT-GATTTCCAAATTCACAACACGA
743797 ATTTC
1 ATTTC
743802 TTTTTCGCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
40 8 0.21
41 27 0.69
42 4 0.10
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.30
Consensus pattern (40 bp):
ATTTCAAATTCACAACGTGATTTCCAAATTCACAACACGA
Found at i:743788 original size:20 final size:21
Alignment explanation
Indices: 743696--743802 Score: 71
Period size: 20 Copynumber: 5.2 Consensus size: 21
743686 CGCAACTTAG
743696 TTTCTGCAA-TCGCAACGCG-A
1 TTTCTG-AATTCGCAACGCGAA
** * *
743716 TTTCCAAATTCACAACGTG-A
1 TTTCTGAATTCGCAACGCGAA
** * *
743736 TTTCCAAATTCACAACACGGAA
1 TTTCTGAATTCGCAACGC-GAA
* *
743758 TTTC-AAATTCGCAACTCG-A
1 TTTCTGAATTCGCAACGCGAA
743777 TTTCTGAATTCGCAACGCGAA
1 TTTCTGAATTCGCAACGCGAA
743798 TTTCT
1 TTTCT
743803 TTTTCGCAAC
Statistics
Matches: 72, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
19 7 0.10
20 42 0.58
21 18 0.25
22 5 0.07
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (21 bp):
TTTCTGAATTCGCAACGCGAA
Found at i:743841 original size:20 final size:20
Alignment explanation
Indices: 743785--743833 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
743775 GATTTCTGAA
* *
743785 TTCGCAACGCGAA-TTTCTTT
1 TTCGCAACAC-AAGTTTCCTT
743805 TTCGCAACACAAGTTTCCTT
1 TTCGCAACACAAGTTTCCTT
743825 TTCGCAACA
1 TTCGCAACA
743834 AGATTTTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (20 bp):
TTCGCAACACAAGTTTCCTT
Found at i:743867 original size:40 final size:40
Alignment explanation
Indices: 743806--743901 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 40
743796 AATTTCTTTT
* * * *
743806 TCGCAACAC-AAGTTTCCTTTTCGCAACAAGATTTTCTAAA
1 TCGCAACACGAA-TTTTCTTTTCACAACAAGATTGTCGAAA
* ** *
743846 TCGCAACACGAATTTTGTTTTCACAACTCGATTGTCGAAT
1 TCGCAACACGAATTTTCTTTTCACAACAAGATTGTCGAAA
743886 TCGCAACACGAATTTT
1 TCGCAACACGAATTTT
743902 AATTTTGCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 45 0.96
41 2 0.04
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (40 bp):
TCGCAACACGAATTTTCTTTTCACAACAAGATTGTCGAAA
Found at i:744056 original size:22 final size:22
Alignment explanation
Indices: 744031--744084 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
744021 CTCTCCGGCA
*
744031 ACATCCGTTCCTATATCCAGCG
1 ACATCCGTTCCTATATCCAACG
744053 ACATCCGTTCCTATATCCAACG
1 ACATCCGTTCCTATATCCAACG
744075 ACATCC-TTCC
1 ACATCCGTTCC
744085 CCATCTCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.24, C:0.39, G:0.09, T:0.28
Consensus pattern (22 bp):
ACATCCGTTCCTATATCCAACG
Found at i:744890 original size:23 final size:24
Alignment explanation
Indices: 744826--744892 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
744816 GTGAGTACTA
*
744826 GTCAATATTCGAAATTTGATCTTG
1 GTCAATACTCGAAATTTGATCTTG
* *
744850 GTCAATACCCGAACTTTGATCTTG
1 GTCAATACTCGAAATTTGATCTTG
*
744874 GTCAA-ACTCGAATTTTGAT
1 GTCAATACTCGAAATTTGAT
744893 GATGTTTCAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
23 12 0.32
24 26 0.68
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.37
Consensus pattern (24 bp):
GTCAATACTCGAAATTTGATCTTG
Found at i:747191 original size:18 final size:18
Alignment explanation
Indices: 747157--747192 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
747147 AAGCAAAAGG
**
747157 AAATCAAAATTGTAATCA
1 AAATCAAAATTCCAATCA
747175 AAATCAAAATTCCAATCA
1 AAATCAAAATTCCAATCA
747193 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.17, G:0.03, T:0.25
Consensus pattern (18 bp):
AAATCAAAATTCCAATCA
Found at i:747505 original size:20 final size:20
Alignment explanation
Indices: 747480--747518 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
747470 TGCGATTGTT
747480 GCGAAAGTCAAATTCGAAAC
1 GCGAAAGTCAAATTCGAAAC
747500 GCGAAAGTCAAATTCGAAA
1 GCGAAAGTCAAATTCGAAA
747519 TGCAAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGAAAC
Found at i:747586 original size:49 final size:49
Alignment explanation
Indices: 747520--747636 Score: 171
Period size: 49 Copynumber: 2.4 Consensus size: 49
747510 AATTCGAAAT
* * * *
747520 GCAAAAATGACAACGCGAATTTGACTTTCGCGTTGTGAATTTGACTTTC
1 GCAAAAATCACAACGCGAATTTAACGTTCGCGTTGCGAATTTGACTTTC
*
747569 GCAATAATCACAACGCGAATTTAACGTTCGCGTTGCGAATTTGACTTTC
1 GCAAAAATCACAACGCGAATTTAACGTTCGCGTTGCGAATTTGACTTTC
* *
747618 GCAACAATCACAAAGCGAA
1 GCAAAAATCACAACGCGAA
747637 AATCGCAACG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 61 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (49 bp):
GCAAAAATCACAACGCGAATTTAACGTTCGCGTTGCGAATTTGACTTTC
Found at i:749171 original size:21 final size:21
Alignment explanation
Indices: 749145--749223 Score: 113
Period size: 21 Copynumber: 3.8 Consensus size: 21
749135 CATGTGAATC
*
749145 GGCCTCTTGAATGGTGGGAGG
1 GGCCTCTTGAATGATGGGAGG
* *
749166 GGCCTCTTGAACGATGAGAGG
1 GGCCTCTTGAATGATGGGAGG
*
749187 GGCCTCTTGAATGATAGGAGG
1 GGCCTCTTGAATGATGGGAGG
*
749208 GGCCTCTTGAACGATG
1 GGCCTCTTGAATGATG
749224 ACAGGTGAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.20, C:0.18, G:0.39, T:0.23
Consensus pattern (21 bp):
GGCCTCTTGAATGATGGGAGG
Found at i:749207 original size:42 final size:42
Alignment explanation
Indices: 749145--749224 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
749135 CATGTGAATC
* *
749145 GGCCTCTTGAATGGTGGGAGGGGCCTCTTGAACGATGAGAGG
1 GGCCTCTTGAATGATAGGAGGGGCCTCTTGAACGATGAGAGG
749187 GGCCTCTTGAATGATAGGAGGGGCCTCTTGAACGATGA
1 GGCCTCTTGAATGATAGGAGGGGCCTCTTGAACGATGA
749225 CAGGTGAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.21, C:0.17, G:0.39, T:0.23
Consensus pattern (42 bp):
GGCCTCTTGAATGATAGGAGGGGCCTCTTGAACGATGAGAGG
Found at i:749389 original size:4 final size:4
Alignment explanation
Indices: 749368--749413 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
749358 GGGCCGCTAA
* * *
749368 AAAT AAAT TAAT ACAT AAAT AAGT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
749414 TGCCGAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:749859 original size:42 final size:42
Alignment explanation
Indices: 749800--749898 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 42
749790 GTGATGGAAT
* * * *
749800 AGGTGATGGCTCTCGGTGTGGAGGTGTATAATCGGCTTGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
*
749842 AGGTGATGGATCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
*
749884 AGGTCATGGCTCTCG
1 AGGTGATGGCTCTCG
749899 AAGTGGGGGT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.17, C:0.18, G:0.36, T:0.28
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
Found at i:751417 original size:20 final size:20
Alignment explanation
Indices: 751394--751476 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 20
751384 TTTGAAACTT
*
751394 AAATTCACAACACGAAAATG
1 AAATTCACAACACGAAAATA
* *
751414 AAATTCGCAACGCGAAAATA
1 AAATTCACAACACGAAAATA
** * *
751434 AAATTCGTAACGCGAAACTA
1 AAATTCACAACACGAAAATA
* * *
751454 AAA-TCGCAACGCGAAACTA
1 AAATTCACAACACGAAAATA
751473 AAAT
1 AAAT
751477 CGCGTTGCGA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
19 18 0.32
20 38 0.68
ACGTcount: A:0.51, C:0.20, G:0.13, T:0.16
Consensus pattern (20 bp):
AAATTCACAACACGAAAATA
Found at i:751487 original size:19 final size:19
Alignment explanation
Indices: 751418--751479 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
751408 AAAATGAAAT
*
751418 TCGCAACGCGAAAATAAAA
1 TCGCAACGCGAAACTAAAA
*
751437 TTCGTAACGCGAAACTAAAA
1 -TCGCAACGCGAAACTAAAA
751457 TCGCAACGCGAAACTAAAA
1 TCGCAACGCGAAACTAAAA
751476 TCGC
1 TCGC
751480 GTTGCGAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.15
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:751876 original size:22 final size:22
Alignment explanation
Indices: 751841--751909 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
751831 ATAGAGGGGG
* * *
751841 GTCGCCGGATATGGGGACGAAT
1 GTCGCCAGAGATGGGGACGGAT
*
751863 GTCGCCAGAGATGGGGATGGAT
1 GTCGCCAGAGATGGGGACGGAT
751885 GTCGCCAGAGATGGGGACGGAT
1 GTCGCCAGAGATGGGGACGGAT
751907 GTC
1 GTC
751910 ACCGTAGAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.22, C:0.17, G:0.43, T:0.17
Consensus pattern (22 bp):
GTCGCCAGAGATGGGGACGGAT
Found at i:762065 original size:66 final size:66
Alignment explanation
Indices: 761957--762107 Score: 239
Period size: 66 Copynumber: 2.3 Consensus size: 66
761947 TCTTAGGAGG
* * *
761957 CCAGAATTTAAGAAGTGATCATAACCTGTTGATTCCCAGTGTGTCAAGATCAAACTACGCCGGTG
1 CCAGAATTTAAGAAGAGGTCATAACCAGTTGATTCCCAGTGTGTCAAGATCAAACTACGCCGGTG
762022 A
66 A
* *
762023 CCAGAATTTAAGAAGAGGTCATAACCAGTTGATTTCCGGTGTGTCAAGATCAAACTACGCCGGTG
1 CCAGAATTTAAGAAGAGGTCATAACCAGTTGATTCCCAGTGTGTCAAGATCAAACTACGCCGGTG
*
762088 G
66 A
*
762089 CCAGAATTTAAGAGGAGGT
1 CCAGAATTTAAGAAGAGGT
762108 GAGCCAAGAT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 78 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (66 bp):
CCAGAATTTAAGAAGAGGTCATAACCAGTTGATTCCCAGTGTGTCAAGATCAAACTACGCCGGTG
A
Found at i:762200 original size:111 final size:111
Alignment explanation
Indices: 762001--762203 Score: 334
Period size: 111 Copynumber: 1.8 Consensus size: 111
761991 CCCAGTGTGT
* * * *
762001 CAAGATCAAACTACGCCGGTGACCAGAATTTAAGAAGAGGTCATAACCAGTTGATTTCCGGTGTG
1 CAAGATCAAACTACGCCCGTGACCAGAATTTAAGAAGAGATCATAACCAGTTGATTTCCAGCGTG
* *
762066 TCAAGATCAAACTACGCCGGTGGCCAGAATTTAAGAGGAGGTGAGC
66 TCAAGATCAAACCACGCCAGTGGCCAGAATTTAAGAGGAGGTGAGC
* *
762112 CAAGATCAATCTACGCCCGTGGCCAGAATTTAAGAAGAGATCATAACCAGTTGATTTCCAGCGTG
1 CAAGATCAAACTACGCCCGTGACCAGAATTTAAGAAGAGATCATAACCAGTTGATTTCCAGCGTG
762177 TCAAGATCAAACCACGCCAGTGGCCAG
66 TCAAGATCAAACCACGCCAGTGGCCAG
762204 TTTTTGCTGA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 84 1.00
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (111 bp):
CAAGATCAAACTACGCCCGTGACCAGAATTTAAGAAGAGATCATAACCAGTTGATTTCCAGCGTG
TCAAGATCAAACCACGCCAGTGGCCAGAATTTAAGAGGAGGTGAGC
Found at i:764207 original size:82 final size:83
Alignment explanation
Indices: 764069--764235 Score: 282
Period size: 82 Copynumber: 2.0 Consensus size: 83
764059 TGATTTTCAT
*
764069 GTAATGTATGATGGTTTTTTTCTAATAGTTTGGGGTGATTATAAGATAATATCTGTTCAAAATTT
1 GTAATGTATGATGGTTTTTTTCTAATAGTCTGGGGTGATTATAAGATAATATCTGTTCAAAATTT
764134 TTGTTAGCCAATGATAAC
66 TTGTTAGCCAATGATAAC
* * * *
764152 GTAATGTATGCTTG-TTTTTTCTATTAGTCTGTGGTGATTATAAGATAATATCTGTTCAAAATTT
1 GTAATGTATGATGGTTTTTTTCTAATAGTCTGGGGTGATTATAAGATAATATCTGTTCAAAATTT
764216 TTGTTAGCCAATGATAAC
66 TTGTTAGCCAATGATAAC
764234 GT
1 GT
764236 CTACACACAC
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
82 67 0.85
83 12 0.15
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (83 bp):
GTAATGTATGATGGTTTTTTTCTAATAGTCTGGGGTGATTATAAGATAATATCTGTTCAAAATTT
TTGTTAGCCAATGATAAC
Found at i:765356 original size:25 final size:25
Alignment explanation
Indices: 765295--765392 Score: 90
Period size: 25 Copynumber: 3.7 Consensus size: 25
765285 TCTTTTTTAG
*
765295 TTAAGATAAAAATAAAATATATTTTT
1 TTAA-ATAAAAATAAAATATATATTT
*
765321 AAATTAAAATAAGAATAAAATATATATTT
1 ---TT-AAATAAAAATAAAATATATATTT
*
765350 TTAAATAAAAATAGAATATATA-TT
1 TTAAATAAAAATAAAATATATATTT
* *
765374 TTAAGTTAAAATAATAATA
1 TTAAATAAAAATAA-AATA
765393 AATAATACTT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
24 13 0.22
25 22 0.37
26 2 0.03
29 21 0.35
30 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
TTAAATAAAAATAAAATATATATTT
Found at i:765386 original size:30 final size:29
Alignment explanation
Indices: 765253--765583 Score: 269
Period size: 30 Copynumber: 11.2 Consensus size: 29
765243 TATTCTTATA
* *
765253 ATATTTTAAAATTAAGATAAAAATAAAAT
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
*
765282 ATATCTTTTTTAGTTAAGATAAAAATAAAAT
1 ATA--TTTTTAAGTTAAGATAAAAATAAAAT
* * *
765313 ATATTTTTAAATTAAAATAAGAATAAAAT
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
* *
765342 ATATATTT---TTAA-ATAAAAATAGAAT
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
* *
765367 ATATATTTTAAGTTAAAATAATAAT-AAAT
1 ATAT-TTTTAAGTTAAGATAAAAATAAAAT
** * * * *
765396 AATACTTAATAATTTAAGGTAAGAATATAAT
1 -ATA-TTTTTAAGTTAAGATAAAAATAAAAT
* * * **
765427 ATATTTAATAATTTAA-ATTAATAATGTAAT
1 ATATTT-TTAAGTTAAGA-TAAAAATAAAAT
**
765457 ATATGTAATAAGTTAAGATAAAAATAAAAT
1 ATAT-TTTTAAGTTAAGATAAAAATAAAAT
*
765487 ATATTTTTAAAAGTTAAGATAAAAATAAAAA
1 ATATTTTT--AAGTTAAGATAAAAATAAAAT
* * *
765518 ATATTTTTTAGTTAAGATAAGAATAACAT
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
*
765547 ATATTTAATAAGTTAAGATAAAAATAAAAT
1 ATATTT-TTAAGTTAAGATAAAAATAAAAT
765577 ATATTTT
1 ATATTTT
765584 AAAAAAAATT
Statistics
Matches: 244, Mismatches: 41, Indels: 34
0.76 0.13 0.11
Matches are distributed among these distances:
25 15 0.06
26 7 0.03
29 66 0.27
30 96 0.39
31 60 0.25
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (29 bp):
ATATTTTTAAGTTAAGATAAAAATAAAAT
Found at i:769119 original size:19 final size:20
Alignment explanation
Indices: 769069--769121 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
769059 TCATTTTCAT
769069 TTTCATTTTTATCCGGATGA
1 TTTCATTTTTATCCGGATGA
*
769089 TTTCATTTTTATCCGGATGG
1 TTTCATTTTTATCCGGATGA
769109 TTTCA-TTTTATCC
1 TTTCATTTTTATCC
769122 AACCCGTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 8 0.25
20 24 0.75
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.53
Consensus pattern (20 bp):
TTTCATTTTTATCCGGATGA
Found at i:770443 original size:18 final size:18
Alignment explanation
Indices: 770416--770496 Score: 90
Period size: 18 Copynumber: 4.5 Consensus size: 18
770406 TCACGGAATG
*
770416 TAAGATTACCGGTGGGAA
1 TAAGATTACCAGTGGGAA
*
770434 TAAAATTACCAGTGGGAA
1 TAAGATTACCAGTGGGAA
* *
770452 TAGGATTACCAGTGAGAA
1 TAAGATTACCAGTGGGAA
* * **
770470 TAGGATTACCGGCAGGAA
1 TAAGATTACCAGTGGGAA
770488 TAAGATTAC
1 TAAGATTAC
770497 TGAGAATGTT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.22
Consensus pattern (18 bp):
TAAGATTACCAGTGGGAA
Found at i:775314 original size:18 final size:18
Alignment explanation
Indices: 775291--775341 Score: 102
Period size: 18 Copynumber: 2.8 Consensus size: 18
775281 CAACCTCACT
775291 ATGACAATAGAAATGGAA
1 ATGACAATAGAAATGGAA
775309 ATGACAATAGAAATGGAA
1 ATGACAATAGAAATGGAA
775327 ATGACAATAGAAATG
1 ATGACAATAGAAATG
775342 ATAATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.55, C:0.06, G:0.22, T:0.18
Consensus pattern (18 bp):
ATGACAATAGAAATGGAA
Found at i:776129 original size:3 final size:3
Alignment explanation
Indices: 776121--776170 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
776111 TTATGAGAAT
776121 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
776169 AT
1 AT
776171 GTTCCCAGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:777620 original size:79 final size:80
Alignment explanation
Indices: 777511--777721 Score: 228
Period size: 79 Copynumber: 2.6 Consensus size: 80
777501 CATCATGTAG
* * * * *
777511 CACGTCTTGCACTCATATTAAACAAAACAACATGTTTATCCTTTATTTTAATTA-ACTCATGTGT
1 CACGTCTTGCACTCTTATTCAACATAACAACATGTTTATCATTTATTTTAATTACACTCATGTGC
* *
777575 ATTCCCATTGTTAAA
66 ATTCACATTGATAAA
* * * *
777590 CACGTCTTGCACTCTTATTCAACATGACAACATGTTTTTCATTTAATTATAATTACCATTCATGT
1 CACGTCTTGCACTCTTATTCAACATAACAACATGTTTATCATTT-ATTTTAATTA-CACTCATGT
*
777655 GCATTCACATTGATAAG
64 GCATTCACATTGATAAA
* * * *
777672 TACGTTTTTGCA-TTTATATTCAACATAACAACATGTTTATCATTTGTTTT
1 CACG-TCTTGCACTCT-TATTCAACATAACAACATGTTTATCATTTATTTT
777722 GTTAAATTCA
Statistics
Matches: 108, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
79 38 0.35
80 9 0.08
82 28 0.26
83 33 0.31
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.42
Consensus pattern (80 bp):
CACGTCTTGCACTCTTATTCAACATAACAACATGTTTATCATTTATTTTAATTACACTCATGTGC
ATTCACATTGATAAA
Found at i:777821 original size:53 final size:53
Alignment explanation
Indices: 777689--777821 Score: 178
Period size: 53 Copynumber: 2.5 Consensus size: 53
777679 TTGCATTTAT
* *
777689 ATTCAACATAACAACATGTTTATCATTTGTTTTGTTAAATTCACGTGCACTCAC
1 ATTC-ACATAACAGCATGTTTATCATTTGTTTTGTTAAATTCACGTGCACCCAC
* *
777743 ATTTACATAACAGCATGTTCATCATTTGTTTTTGTT-AATTCACGTGCACCCAC
1 ATTCACATAACAGCATGTTTATCATTTG-TTTTGTTAAATTCACGTGCACCCAC
* * *
777796 ATTCACTTTACAGCATGTTTTTCATT
1 ATTCACATAACAGCATGTTTATCATT
777822 ATCACTCATG
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
53 59 0.86
54 10 0.14
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (53 bp):
ATTCACATAACAGCATGTTTATCATTTGTTTTGTTAAATTCACGTGCACCCAC
Found at i:779719 original size:2 final size:2
Alignment explanation
Indices: 779712--779745 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
779702 GTTAACTTGC
779712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
779746 TCATAAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:779809 original size:2 final size:2
Alignment explanation
Indices: 779804--779863 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
779794 TATCTCTTGC
779804 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
779846 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
779864 GTGTGTGTAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:780208 original size:3 final size:3
Alignment explanation
Indices: 780200--780242 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
780190 TGTTGAAAAG
780200 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
780243 ATTTCACTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:782302 original size:26 final size:26
Alignment explanation
Indices: 782271--782323 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
782261 AAGTTCGTCT
782271 CATAACATAAAATCATACATCCATCC
1 CATAACATAAAATCATACATCCATCC
782297 CATAACATAAAATCATACATCCATCC
1 CATAACATAAAATCATACATCCATCC
782323 C
1 C
782324 TGACTGTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (26 bp):
CATAACATAAAATCATACATCCATCC
Found at i:784585 original size:3 final size:3
Alignment explanation
Indices: 784577--784619 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
784567 ATTATTTATT
*
784577 TAA TAA TAA TAA TAA TAA TAA AACA TAA TAA TAA TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA T-AA TAA TA
784620 TAAGTAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 31 0.86
4 5 0.14
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:784627 original size:13 final size:13
Alignment explanation
Indices: 784577--784628 Score: 65
Period size: 13 Copynumber: 4.1 Consensus size: 13
784567 ATTATTTATT
784577 TAATAATAAT-AA
1 TAATAATAATAAA
784589 TAATAATAA-AACA
1 TAATAATAATAA-A
784602 TAATAATAATAAA
1 TAATAATAATAAA
784615 TAAT-ATAAGTAAA
1 TAATAATAA-TAAA
784628 T
1 T
784629 GAGAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
12 14 0.39
13 20 0.56
14 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:785198 original size:124 final size:124
Alignment explanation
Indices: 785046--785384 Score: 536
Period size: 124 Copynumber: 2.7 Consensus size: 124
785036 AGTAATGAAT
* * *
785046 TCAAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* *
785111 TCTCATTATGAACTTTCTCTAGAAAAGTGGATGCTGATCTATCTCCTTCTGTGATAGAG
66 TCTCATTATGAACTTTCTCTGGAAAAGTGGATGCTGATCTATCTCCTTCTGGGATAGAG
** *
785170 TCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * *
785235 TTTTATTATGAACTTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGGGATAGAG
66 TCTCATTATGAACTTTCTCTGGAAAAGTGGATGCTGATCTATCTCCTTCTGGGATAGAG
* *
785294 TCAAACAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTA
1 TCAAAC-AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
785358 TTCTCATTATGAACTTTCTCTGGAAAA
65 TTCTCATTATGAACTTTCTCTGGAAAA
785385 ATTAATCCAT
Statistics
Matches: 194, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
124 152 0.78
125 42 0.22
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (124 bp):
TCAAACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTTTCTCTGGAAAAGTGGATGCTGATCTATCTCCTTCTGGGATAGAG
Found at i:786570 original size:18 final size:18
Alignment explanation
Indices: 786544--786583 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
786534 ATGTTTATAT
786544 AAAACAAATTGAATTTCA
1 AAAACAAATTGAATTTCA
*
786562 AAAATAAATTGAATTTCA
1 AAAACAAATTGAATTTCA
786580 AAAA
1 AAAA
786584 GATAAACTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAACAAATTGAATTTCA
Found at i:786952 original size:18 final size:17
Alignment explanation
Indices: 786931--786969 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
786921 TTGACCCTCC
786931 TTTTCTATTTTATTATTT
1 TTTTCT-TTTTATTATTT
* *
786949 TTTTCTTTTTTTTCTTT
1 TTTTCTTTTTATTATTT
786966 TTTT
1 TTTT
786970 TTCATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTCTTTTTATTATTT
Found at i:786959 original size:10 final size:9
Alignment explanation
Indices: 786946--786970 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
786936 TATTTTATTA
786946 TTTTTTTCT
1 TTTTTTTCT
786955 TTTTTTTCT
1 TTTTTTTCT
786964 TTTTTTT
1 TTTTTTT
786971 TCATTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:786971 original size:10 final size:10
Alignment explanation
Indices: 786946--786979 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
786936 TATTTTATTA
786946 TTTTTTTC-T
1 TTTTTTTCTT
786955 TTTTTTTCTT
1 TTTTTTTCTT
786965 TTTTTTTCATT
1 TTTTTTTC-TT
786976 TTTT
1 TTTT
786980 CTTATTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.35
10 9 0.39
11 6 0.26
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:786977 original size:18 final size:19
Alignment explanation
Indices: 786931--786982 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
786921 TTGACCCTCC
* *
786931 TTTTCTATTTTAT-TATTT
1 TTTTCTATTTTTTCTTTTT
*
786949 TTTTCTTTTTTTTCTTTTT
1 TTTTCTATTTTTTCTTTTT
786968 TTTTC-ATTTTTTCTT
1 TTTTCTATTTTTTCTT
786983 ATTCAAGCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 20 0.69
19 9 0.31
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTCTATTTTTTCTTTTT
Found at i:794343 original size:15 final size:15
Alignment explanation
Indices: 794325--794356 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
794315 TGAATAATAA
*
794325 ATGTATGCAAAATGC
1 ATGTATGCAAAAGGC
794340 ATGTATGCAAAAGGC
1 ATGTATGCAAAAGGC
794355 AT
1 AT
794357 TGATCCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (15 bp):
ATGTATGCAAAAGGC
Found at i:797583 original size:21 final size:20
Alignment explanation
Indices: 797552--797593 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
797542 ATAATACTTG
797552 AAAATAAAATA-ACAATATAA
1 AAAATAAAATATAC-ATATAA
797572 AAAATAATAATATACATATAA
1 AAAATAA-AATATACATATAA
797593 A
1 A
797594 TATTATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 11 0.55
22 2 0.10
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATAAAATATACATATAA
Found at i:797630 original size:28 final size:28
Alignment explanation
Indices: 797572--797632 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
797562 AACAATATAA
*
797572 AAAATAATAATATACATATAAATATTATG
1 AAAATAATAATATA-ATATAAAAATTATG
*
797601 AAAATAATAAGTAT-ATATAAAAATTTTG
1 AAAATAATAA-TATAATATAAAAATTATG
797629 AAAA
1 AAAA
797633 GAAAGAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 16 0.55
29 10 0.34
30 3 0.10
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAATAATAATATAATATAAAAATTATG
Found at i:799850 original size:3 final size:3
Alignment explanation
Indices: 799842--799890 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
799832 ATTATTTATT
*
799842 TAA TAA TAA TAA T-A TAA -CA TAA TAA TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
799886 TAA TA
1 TAA TA
799891 TAAGTAAATG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 3 0.07
3 35 0.85
4 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:799870 original size:22 final size:22
Alignment explanation
Indices: 799842--799890 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
799832 ATTATTTATT
799842 TAATAATAATAAT-ATAACATAA
1 TAATAATAATAATAATAACA-AA
*
799864 TAATAATAATAATAATAATAAA
1 TAATAATAATAATAATAACAAA
799886 TAATA
1 TAATA
799891 TAAGTAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TAATAATAATAATAATAACAAA
Found at i:799898 original size:13 final size:13
Alignment explanation
Indices: 799842--799899 Score: 70
Period size: 13 Copynumber: 4.6 Consensus size: 13
799832 ATTATTTATT
799842 TAAT-AATAATAA
1 TAATAAATAATAA
799854 T-ATAACATAATAA
1 TAATAA-ATAATAA
799867 TAAT-AATAATAA
1 TAATAAATAATAA
799879 TAATAAATAAT-A
1 TAATAAATAATAA
799891 TAAGTAAAT
1 TAA-TAAAT
799900 GAGAAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
11 2 0.05
12 17 0.41
13 20 0.49
14 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (13 bp):
TAATAAATAATAA
Found at i:801093 original size:3 final size:3
Alignment explanation
Indices: 801085--801780 Score: 1143
Period size: 3 Copynumber: 238.7 Consensus size: 3
801075 AGGCCAAACT
801085 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
801133 GAA GAA GAA GAA -AA GAA GAA GAA -AA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
801179 GAA GAA G-A GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-A
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
801225 GAA GAA GAA GAA GAA -AA G-A GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
801271 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
801319 GAA GAA GAA GAA -AA GAA GAA GAA GAA GAA G-A GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
801365 GAA GAA GAA GAA G-A GAA GAA GAC GAA GAA GAA GAA GAA GAAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA
*
801410 GAA -AA GAA TAA GAA GAA GAA GAA GAA GAA G-A GAA GAA GAA GAAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA
801454 GAA G-A GAGA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -AA
1 GAA GAA GA-A GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
801498 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
801546 GAA GAA GAA GAA GAA GAA GAA G-A GAA GAA GAA -AGA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA
* * *
801590 GAA GAA GAA -AC GAA GAA GAA CAA GAA GAA G-A GAA GAC GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
801636 GAA -AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-A GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
801681 GAA GAA -AA -AA GAA GAA GAA GAA GAA -AA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
801726 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -AA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
801773 GAA GAA GA
1 GAA GAA GA
801781 TGAATTGATC
Statistics
Matches: 656, Mismatches: 10, Indels: 54
0.91 0.01 0.08
Matches are distributed among these distances:
2 46 0.07
3 600 0.91
4 10 0.02
ACGTcount: A:0.67, C:0.01, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:806926 original size:18 final size:18
Alignment explanation
Indices: 806903--806963 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
806893 CTGCAATCGA
*
806903 TTCATCCTCCTTCGGTTG
1 TTCATCCTCCTTCGGTCG
* *
806921 TTCATCCTTCTTCTGTCG
1 TTCATCCTCCTTCGGTCG
806939 TTCA-CCTCCTTCGGTCG
1 TTCATCCTCCTTCGGTCG
806956 ATTCATCC
1 -TTCATCC
806964 ACCGTAGAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
17 11 0.31
18 23 0.64
19 2 0.06
ACGTcount: A:0.08, C:0.36, G:0.13, T:0.43
Consensus pattern (18 bp):
TTCATCCTCCTTCGGTCG
Found at i:809367 original size:15 final size:16
Alignment explanation
Indices: 809335--809373 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
809325 AAAGCCTCTT
809335 AATCATTCAGACTGCTA
1 AATCATTCAGA-TGCTA
809352 AATCATTCAG-TGCTA
1 AATCATTCAGATGCTA
*
809367 AACCATT
1 AATCATT
809374 TAGTTTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.52
17 10 0.48
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (16 bp):
AATCATTCAGATGCTA
Found at i:809465 original size:2 final size:2
Alignment explanation
Indices: 809458--809519 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
809448 CTCAATGACC
809458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
809500 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
809520 GTGTGTGTAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:812577 original size:22 final size:22
Alignment explanation
Indices: 812552--812598 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
812542 ACAATAAATT
*
812552 TTTTACACATAAACGTAAATCA
1 TTTTACACATAAACGTAAATAA
812574 TTTTACACATAAACGTAAATAA
1 TTTTACACATAAACGTAAATAA
812596 TTT
1 TTT
812599 AAATAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (22 bp):
TTTTACACATAAACGTAAATAA
Found at i:812882 original size:29 final size:29
Alignment explanation
Indices: 812823--812882 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
812813 TTTTTTTACT
* *
812823 GGTTGAGAGGATTATTGTAGTAGTTTCTA
1 GGTTGAGAGGAATATTGTAGGAGTTTCTA
812852 GGTTGAGAGGAATA-TGTGAGAGAGTTT-TA
1 GGTTGAGAGGAATATTGT-AG-GAGTTTCTA
812881 GG
1 GG
812883 GGGAAGGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 3 0.11
29 19 0.70
30 5 0.19
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.35
Consensus pattern (29 bp):
GGTTGAGAGGAATATTGTAGGAGTTTCTA
Found at i:815684 original size:3 final size:3
Alignment explanation
Indices: 815676--815710 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
815666 AATTTTTAAA
*
815676 ATT ATT ATT AATA ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT A
815711 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.93
4 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:815690 original size:22 final size:22
Alignment explanation
Indices: 815665--815712 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
815655 TTTTTTCATT
*
815665 TAATTTTTAAAATTATTATTAA
1 TAATTATTAAAATTATTATTAA
** *
815687 TAATTATTATTATTATTATTAT
1 TAATTATTAAAATTATTATTAA
815709 TAAT
1 TAAT
815713 ATATATATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TAATTATTAAAATTATTATTAA
Found at i:815718 original size:2 final size:2
Alignment explanation
Indices: 815711--815736 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
815701 ATTATTATTA
815711 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
815737 TATTTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:816627 original size:7 final size:7
Alignment explanation
Indices: 816615--816644 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
816605 TGAGAGAGAG
816615 AATGAAA
1 AATGAAA
816622 AATGAAA
1 AATGAAA
816629 AATGAAA
1 AATGAAA
816636 AATGAAA
1 AATGAAA
816643 AA
1 AA
816645 ATTGTCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AATGAAA
Found at i:817304 original size:2 final size:2
Alignment explanation
Indices: 817293--817334 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
817283 ATATCCTGCT
817293 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
817334 T
1 T
817335 TTACTTCATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:822853 original size:10 final size:9
Alignment explanation
Indices: 822827--822851 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
822817 AAAAAAAGAT
822827 GAAAAAAGG
1 GAAAAAAGG
822836 GAAAAAAGG
1 GAAAAAAGG
822845 GAAAAAA
1 GAAAAAA
822852 AGAAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (9 bp):
GAAAAAAGG
Found at i:826130 original size:54 final size:54
Alignment explanation
Indices: 826066--826383 Score: 415
Period size: 54 Copynumber: 5.9 Consensus size: 54
826056 GAAATCTGGG
* *
826066 CAGAAGCCACAGGAAATGATGAATATGTTGTTAAATGTTTTACGAACCTCTAGA
1 CAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACCTCTAGA
* * * * *
826120 CAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATATTTTATGAACATCTATG-
1 CAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACCTCTA-GA
* * *
826174 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACCTCTGGA
1 CAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACCTCTAGA
* * * * *
826228 CAGAAGCCACAAGAAAAGATGAATGTGTTATCAAATGTTTTACGAACATCTGTGA
1 CAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACCTCT-AGA
* * * *
826283 -AGAAACCACAGGAAATGATAAATGTGTTGTCAAATGTTTTACGAATCTCTGGA
1 CAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACCTCTAGA
* *
826336 CAGAAGCCACAGGAAATGATGAACGTGTTGTCAAATATTTTACGAACC
1 CAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACC
826384 AGTTATTCTG
Statistics
Matches: 227, Mismatches: 33, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
53 3 0.01
54 221 0.97
55 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (54 bp):
CAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACCTCTAGA
Found at i:826254 original size:108 final size:108
Alignment explanation
Indices: 826065--826382 Score: 501
Period size: 108 Copynumber: 2.9 Consensus size: 108
826055 AGAAATCTGG
* * * *
826065 GCAGAAGCCACAGGAAATGATGAATATGTTGTTAAATGTTTTACGAACCTCTAGACAGAAGCCAC
1 GCAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACCTCTGGACAGAAGCCAC
*
826130 AAGAAAAGATGAATGTGTTGTCAAATATTTTATGAACATCTAT
66 AAGAAAAGATGAATGTGTTGTCAAATATTTTACGAACATCTAT
*
826173 GCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACCTCTGGACAGAAGCCAC
1 GCAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACCTCTGGACAGAAGCCAC
* * *
826238 AAGAAAAGATGAATGTGTTATCAAATGTTTTACGAACATCTGT
66 AAGAAAAGATGAATGTGTTGTCAAATATTTTACGAACATCTAT
* * *
826281 GAAGAAACCACAGGAAATGATAAATGTGTTGTCAAATGTTTTACGAATCTCTGGACAGAAGCCAC
1 GCAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACCTCTGGACAGAAGCCAC
* * *
826346 AGGAAATGATGAACGTGTTGTCAAATATTTTACGAAC
66 AAGAAAAGATGAATGTGTTGTCAAATATTTTACGAAC
826383 CAGTTATTCT
Statistics
Matches: 192, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 192 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (108 bp):
GCAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACCTCTGGACAGAAGCCAC
AAGAAAAGATGAATGTGTTGTCAAATATTTTACGAACATCTAT
Found at i:826761 original size:22 final size:22
Alignment explanation
Indices: 826735--826825 Score: 121
Period size: 22 Copynumber: 4.1 Consensus size: 22
826725 CTACATTTAC
*
826735 ATTCTTCAAAAATGATAGATTT
1 ATTCTTCAAAGATGATAGATTT
*
826757 ATTCTTCAAAGATGATAGATTC
1 ATTCTTCAAAGATGATAGATTT
826779 ATTCTTCAAAGATGATAGATTCT
1 ATTCTTCAAAGATGATAGATT-T
* * *
826802 CTT-TTCAAAGATGAAAGCTTT
1 ATTCTTCAAAGATGATAGATTT
826823 ATT
1 ATT
826826 GGATTTCTAC
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
21 3 0.05
22 56 0.92
23 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (22 bp):
ATTCTTCAAAGATGATAGATTT
Found at i:827620 original size:76 final size:76
Alignment explanation
Indices: 827489--828379 Score: 1459
Period size: 76 Copynumber: 11.8 Consensus size: 76
827479 CTATAGTGCA
*
827489 TGATGTTTTCAAAGCCTTTGGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
*
827554 CAGGAGCTTTT
66 CGGGAGCTTTT
827565 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGAT-TCTTTCAAAAAGCCT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATGT-TTTCAAAAAGCCT
827629 TCGGGAGCTTTT
65 TCGGGAGCTTTT
*
827641 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
*
827706 CGGGAGATTTT
66 CGGGAGCTTTT
* * *
827717 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGAAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
827782 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
827793 TGATGTTTTCAAAGCCTTTGGGTTATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
*
827858 CGGAAGCTTTT
66 CGGGAGCTTTT
* * *
827869 TGATGTTTTCAAAACCTTCGGGTAATTTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
827934 CGGGAGCTTTT
66 CGGGAGCTTTT
*
827945 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
*
828010 CGGGAGCTTTA
66 CGGGAGCTTTT
* *
828021 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
828086 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
828097 TGATGTTTTCAAAGGCTTCAGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
828162 CGGGAGCTTTT
66 CGGGAGCTTTT
828173 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
828238 CGGGAGCTTTT
66 CGGGAGCTTTT
* * * * *
828249 TGATGTTTTTAAAACCTCCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
828312 CGGGAGCTTTT
66 CGGGAGCTTTT
* ** * * *
828323 TGA--TATTCAAAGCCTTCGGGGTCATCCATAAGACCTACAGTGCAAGATGTTTTCAAA
1 TGATGTTTTCAAAGCCTTC-GGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAA
828380 TGAGATTTTA
Statistics
Matches: 763, Mismatches: 48, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
72 10 0.01
73 30 0.04
74 20 0.03
75 5 0.01
76 697 0.91
77 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (76 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
CGGGAGCTTTT
Found at i:829630 original size:3 final size:3
Alignment explanation
Indices: 829622--829702 Score: 117
Period size: 3 Copynumber: 26.0 Consensus size: 3
829612 TATTTTTAAA
829622 ATT ATT ATT ATT ATT ATT AATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
829668 ATT ATT AAT ATT ATAT AAT ATAT ATT ATT ATT ATT
1 ATT ATT ATT ATT AT-T ATT AT-T ATT ATT ATT ATT
829703 TAAATAATTA
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
3 63 0.89
4 8 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:831208 original size:5 final size:5
Alignment explanation
Indices: 831198--831226 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
831188 ATTCATATAT
831198 TCGGG TCGGG TCGGG TCGGG TCGGG TCGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGG
831227 ATGAAACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.21, G:0.59, T:0.21
Consensus pattern (5 bp):
TCGGG
Found at i:831596 original size:196 final size:199
Alignment explanation
Indices: 831394--831787 Score: 643
Period size: 196 Copynumber: 2.0 Consensus size: 199
831384 TTTTATTATT
*
831394 TCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCT
1 TCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCG
* *
831459 GGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTTGGGTCAG-GTTTTTTTAATTGTGATATTC
66 GGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTC-GTGTTTTTTTAAGTGTGATATTC
* *
831523 GGGTC-G-GGTCGGGTTCGGGTTTAGGATGAAAAAAACCGGACCGACCCG-AAAATATATATAAT
130 GGGTCGGAGGTCGGGTTCGGGTTTAGGATGAAAAAAACCAGACCGACCCGAAAAAAATATATAAT
831585 TCGGG
195 TCGGG
*
831590 TCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGATACTTTATTTTGTTCG
1 TCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCG
* *
831655 GGTTGGGTTTTTTAAGTGTGATATTTGGGTCGAGTCGGGTCGTGTTTTTTTAAGTGTGATATTCG
66 GGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCGTGTTTTTTTAAGTGTGATATTCG
*
831720 GGTCGGGTCAGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCAGACCGACCCGAAAAAAATATATA
131 GGTC-GG--AGGTCGGGTTCGGGTTTAGGATGAAAAAAACCAGACCGACCCGAAAAAAATATATA
831785 ATT
193 ATT
831788 TTACCTTATA
Statistics
Matches: 182, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
195 1 0.01
196 126 0.69
198 1 0.01
201 40 0.22
202 14 0.08
ACGTcount: A:0.21, C:0.13, G:0.31, T:0.35
Consensus pattern (199 bp):
TCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCG
GGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCGTGTTTTTTTAAGTGTGATATTCG
GGTCGGAGGTCGGGTTCGGGTTTAGGATGAAAAAAACCAGACCGACCCGAAAAAAATATATAATT
CGGG
Found at i:831693 original size:37 final size:37
Alignment explanation
Indices: 831652--831738 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 37
831642 TTTATTTTGT
* *
831652 TCGGGTTGGGTTTTTTAAGTGTGATATTTGGGTCGAG
1 TCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAG
* *
831689 TCGGGTCGTGTTTTTTTAAGTGTGATATTCGGGTCGGG
1 TCGGGTCG-GGTTTTTTAAGTGTGATATTCGGGTCGAG
*
831727 TCAGGTCGGGTT
1 TCGGGTCGGGTT
831739 CGGGTTTAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 10 0.23
38 33 0.77
ACGTcount: A:0.11, C:0.09, G:0.38, T:0.41
Consensus pattern (37 bp):
TCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAG
Found at i:835537 original size:20 final size:21
Alignment explanation
Indices: 835491--835551 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
835481 TTCCCCTGTG
*
835491 GGGGGAATCAGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
835514 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
835534 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
835552 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 3 0.09
23 12 0.34
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:838220 original size:43 final size:43
Alignment explanation
Indices: 838172--838258 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
838162 AATTGTTCTA
838172 ATGCTTCATCTTTAGTATTTAAAAATAGAACCCAAGTATATCT
1 ATGCTTCATCTTTAGTATTTAAAAATAGAACCCAAGTATATCT
838215 ATGCTTCATCTTTAGTATTTAAAAATAGAACCCAAGTATATCT
1 ATGCTTCATCTTTAGTATTTAAAAATAGAACCCAAGTATATCT
838258 A
1 A
838259 GAATAGTCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (43 bp):
ATGCTTCATCTTTAGTATTTAAAAATAGAACCCAAGTATATCT
Found at i:839447 original size:22 final size:21
Alignment explanation
Indices: 839407--839446 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
839397 AAGTTTGTTT
839407 TCATTTTTAAATTTTAAAACA
1 TCATTTTTAAATTTTAAAACA
*
839428 TCATTTTTATATTTTAAAA
1 TCATTTTTAAATTTTAAAA
839447 ATAATTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (21 bp):
TCATTTTTAAATTTTAAAACA
Found at i:839453 original size:20 final size:21
Alignment explanation
Indices: 839409--839453 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
839399 GTTTGTTTTC
*
839409 ATTTTTAAATTTTAAAACATC
1 ATTTTTAAATTTTAAAACATA
*
839430 ATTTTTATATTTTAAAA-ATA
1 ATTTTTAAATTTTAAAACATA
839450 ATTT
1 ATTT
839454 CTCATAATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTTTAAATTTTAAAACATA
Found at i:841905 original size:16 final size:16
Alignment explanation
Indices: 841886--841924 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
841876 ATTGGATTTA
841886 AATTCCTACAGATTCC
1 AATTCCTACAGATTCC
841902 AATTCCTACAGATTCC
1 AATTCCTACAGATTCC
841918 AATTCCT
1 AATTCCT
841925 TCAAAGATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (16 bp):
AATTCCTACAGATTCC
Found at i:842083 original size:25 final size:23
Alignment explanation
Indices: 842061--842106 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
842051 TTTATTTGCA
842061 ATATTATTTTATTATTACTTTTG
1 ATATTATTTTATTATTACTTTTG
*
842084 ATATATATTTAAATTATTACTTT
1 ATAT-TATTT-TATTATTACTTT
842107 CATTATCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 5 0.25
25 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (23 bp):
ATATTATTTTATTATTACTTTTG
Done.