Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006023.1 Hibiscus syriacus cultivar Beakdansim tig00014213_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: 1315283
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:817337 original size:2 final size:2
Alignment explanation
Indices: 817330--817400 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
817320 GGCGCTCTAA
817330 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
817372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
817401 AAGAAAGGGT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:819042 original size:38 final size:38
Alignment explanation
Indices: 818987--819272 Score: 423
Period size: 38 Copynumber: 7.6 Consensus size: 38
818977 CATATAACGC
* *
818987 ATATAATATATAATTTTGAAAACATTTTTTGAATATAT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATAT
*
819025 ATATAATGTATAGTTTTGAAAACATTTTTTGAAAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATAT
* *
819063 ATATAGTATATAGTTTTGAAAACATTTTTCGAAAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATAT
* *
819101 ATATAATATATAGTTTTGAAAACATTTTTCGAGAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATAT
* * *
819139 ATAAAATATATAGATTTAAAAACA-TTTTTG-AAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATAT
*
819175 ATATAATATATAGTTTTGAAAACTTTTTTTGAAAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATAT
* **
819213 ATATAATATATAGTTTTGAAAACACTTTTCAAAAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATAT
*
819251 ATATAATATATACTTTTGAAAA
1 ATATAATATATAGTTTTGAAAA
819273 GCGTATATAA
Statistics
Matches: 224, Mismatches: 22, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
36 25 0.11
37 11 0.05
38 188 0.84
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (38 bp):
ATATAATATATAGTTTTGAAAACATTTTTTGAAAATAT
Found at i:819110 original size:112 final size:111
Alignment explanation
Indices: 818987--819272 Score: 419
Period size: 112 Copynumber: 2.5 Consensus size: 111
818977 CATATAACGC
* * *
818987 ATATAATATATAATTTTGAAAACATTTTTTGAATATATATATAATGTATAGTTTTGAAAACATTT
1 ATATAATATATAGTTTTGAAAACATTTTTCGAA-ATATATATAATATATAGTTTTGAAAACA-TT
*
819052 TTTGAAAATATATATAGTATATAGTTTTGAAAACATTTTTCGAAAATAT
64 TTTG-AAATATATATAATATATAGTTTTGAAAACATTTTTCGAAAATAT
* * *
819101 ATATAATATATAGTTTTGAAAACATTTTTCGAGAATATATAAAATATATAGATTTAAAAACATTT
1 ATATAATATATAGTTTTGAAAACATTTTTCGA-AATATATATAATATATAGTTTTGAAAACATTT
* *
819166 TTGAAATATATATAATATATAGTTTTGAAAACTTTTTTTGAAAATAT
65 TTGAAATATATATAATATATAGTTTTGAAAACATTTTTCGAAAATAT
* * *
819213 ATATAATATATAGTTTTGAAAACACTTTTCAAAAATATATATAATATATACTTTTGAAAA
1 ATATAATATATAGTTTTGAAAACATTTTTC-GAAATATATATAATATATAGTTTTGAAAA
819273 GCGTATATAA
Statistics
Matches: 155, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
112 93 0.60
113 7 0.05
114 54 0.35
115 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (111 bp):
ATATAATATATAGTTTTGAAAACATTTTTCGAAATATATATAATATATAGTTTTGAAAACATTTT
TGAAATATATATAATATATAGTTTTGAAAACATTTTTCGAAAATAT
Found at i:819346 original size:18 final size:17
Alignment explanation
Indices: 819320--819375 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
819310 GAGAACACAT
819320 TTTATATTATATTTTTTA
1 TTTA-ATTATATTTTTTA
*
819338 TTTACATTATATTTATTA
1 TTTA-ATTATATTTTTTA
819356 TTT-ATT-TATTTATTTA
1 TTTAATTATATTT-TTTA
819372 TTTA
1 TTTA
819376 TTTTGTTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 5 0.15
16 9 0.27
18 19 0.58
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTAATTATATTTTTTA
Found at i:819354 original size:4 final size:4
Alignment explanation
Indices: 819324--819378 Score: 60
Period size: 4 Copynumber: 13.2 Consensus size: 4
819314 ACACATTTTA
819324 TATT ATATT T-TT TATT TACATT ATATT TA-T TATT TATT TATT TATT
1 TATT -TATT TATT TATT T--ATT -TATT TATT TATT TATT TATT TATT
819370 TATT TATT T
1 TATT TATT T
819379 TGTTTACTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
3 6 0.13
4 28 0.62
5 7 0.16
6 3 0.07
7 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:826262 original size:46 final size:45
Alignment explanation
Indices: 826193--826316 Score: 155
Period size: 46 Copynumber: 2.8 Consensus size: 45
826183 AATAAAATCT
*
826193 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACC-AAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCTAAATA
* *
826237 CTTACCATTTAAATTCCATAAGCTCGT-AGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCTAAATA
* * *
826283 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
826317 GCATGGTTAC
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
43 13 0.19
44 19 0.27
45 14 0.20
46 24 0.34
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCTAAATA
Found at i:826460 original size:40 final size:40
Alignment explanation
Indices: 826416--826537 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
826406 ACCGTAGTGC
826416 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
826456 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
826496 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
826536 TA
1 TA
826538 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:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:830345 original size:2 final size:2
Alignment explanation
Indices: 830327--830385 Score: 86
Period size: 2 Copynumber: 29.5 Consensus size: 2
830317 TTATGCTCAT
830327 TA TA TGA TA TGA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA
1 TA TA T-A TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
830370 TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA T
830386 GGATGACAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.04
2 47 0.89
3 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:830372 original size:25 final size:26
Alignment explanation
Indices: 830333--830385 Score: 99
Period size: 25 Copynumber: 2.1 Consensus size: 26
830323 TCATTATATG
830333 ATATGATATATATATATATATATTAT
1 ATATGATATATATATATATATATTAT
830359 ATAT-ATATATATATATATATATTAT
1 ATATGATATATATATATATATATTAT
830384 AT
1 AT
830386 GGATGACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
ATATGATATATATATATATATATTAT
Found at i:830799 original size:2 final size:2
Alignment explanation
Indices: 830776--830829 Score: 81
Period size: 2 Copynumber: 25.5 Consensus size: 2
830766 TTATGCTCAT
830776 TA TA TGA TA TGA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA T-A TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
830819 TA TA TA TA TA T
1 TA TA TA TA TA T
830830 GGATGACAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 43 0.88
3 6 0.12
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:830813 original size:443 final size:438
Alignment explanation
Indices: 829988--830874 Score: 1579
Period size: 443 Copynumber: 2.0 Consensus size: 438
829978 CCAAAACTTA
829988 AGGATCATTTCAACAAAATGGAAGGGTTGGGGTGATGGATGCTGATGAAATGAATGTCCTAATAT
1 AGGATCATTTCAACAAAATGGAAGGGTTGGGGTGATGGATGCTGATGAAATGAATGTCCTAATAT
830053 GCACTGTAAGGTAGTGCCTACCATCCTGCACTAAGTATCTCAATATACACTTTAGTGTTAAATCG
66 GCACTGTAAGGTAGTGCCTACCATCCTGCACTAAGTATCTCAATATACACTTTAGTGTTAAATCG
830118 AATATGCAGCATGCTGCTGGACTCTATGACATGCCAACTGTACCTTTGTCCCACAATGACCTAAT
131 AATATGCAGCATGCTGCTGGACTCTATGACATGCCAACTGTACCTTTGTCCCACAATGACCTAAT
830183 TGAGCATATATTTAATATTTATTCATTCATGACAATGTATCATATAATACAACATTGGGCAGTTT
196 TGAGCATATATTTAATATTTATTCATTCATGACAATGTATCATATAAT--AACATTGGGCAGTTT
830248 ATACTTGAATAACATTCATATCATATACACTATTAATCAATGCATTTTATTTTTCCCTTATATGT
259 ATACTTGAATAACATTCATATCATATACACTATTAATCAATGCATTTTATTTTTCCCTTATATGT
*
830313 AATATTATGCTCATTATATGATATG-ATATATATATATATATATTATATATATATATATATATAT
324 AATATTATGCTCATTATATGATATGAATATAGATATATAT-TA-TATATATATATATATATATAT
830377 ATATTATATGGATGACAATAGGTCAGGTCGGATTTTTGCTTGCTCTGACTTCG
387 ATA-TATATGGATGACAATAGGTCAGGTCGGATTTTTGCTTGCTCTGACTTCG
830430 AGGATCATTTCAACAAAATGGAAGGGTTGGGGTGATGGATGCTGATGAAATGAAGTGTCCTAATA
1 AGGATCATTTCAACAAAATGGAAGGGTTGGGGTGATGGATGCTGATGAAATGAA-TGTCCTAATA
830495 TGCACTGTAAGGTAGTGCCTACCATCCTGCACTAAGTATC-CTAATATACACTTTAGTGTTAAAT
65 TGCACTGTAAGGTAGTGCCTACCATCCTGCACTAAGTATCTC-AATATACACTTTAGTGTTAAAT
830559 CGAATATGCAGCATGCTGCTGGACTCTATGACATGCCAACTGTACCTTTGTCCCACAATGACCTA
129 CGAATATGCAGCATGCTGCTGGACTCTATGACATGCCAACTGTACCTTTGTCCCACAATGACCTA
830624 ATTGAGCATATATTTAATATTTATTTCATTCATGACAATGTATATCAATATAAT-ACATTGGGCA
194 ATTGAGCATATATTTAATATTTA-TTCATTCATGACAATG--TATC-ATATAATAACATTGGGCA
830688 GTTTATACTTGAAATAACATTCATATCATATATCACTATTAATCAATGCATTTTATTTTTCATCC
255 GTTTATACTTG-AATAACATTCATATCATATA-CACTATTAATCAATGCATTTTA-TTTT--TCC
830753 CTTATATGTAATATTATGCTCATTATATGATATG-ATAT-GATATATA-TATATATATATATATA
315 CTTATATGTAATATTATGCTCATTATATGATATGAATATAGATATATATTATATATATATATATA
830815 TATATATATATATATGGATGACAATAGGTCAGGTCGGATTTTTGCTTGCTCTGACTTCG
380 TATATATATATATATGGATGACAATAGGTCAGGTCGGATTTTTGCTTGCTCTGACTTCG
830874 A
1 A
830875 CCCGATATAA
Statistics
Matches: 433, Mismatches: 1, Indels: 20
0.95 0.00 0.04
Matches are distributed among these distances:
442 55 0.13
443 160 0.37
444 87 0.20
445 44 0.10
446 28 0.06
447 11 0.03
448 7 0.02
449 41 0.09
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (438 bp):
AGGATCATTTCAACAAAATGGAAGGGTTGGGGTGATGGATGCTGATGAAATGAATGTCCTAATAT
GCACTGTAAGGTAGTGCCTACCATCCTGCACTAAGTATCTCAATATACACTTTAGTGTTAAATCG
AATATGCAGCATGCTGCTGGACTCTATGACATGCCAACTGTACCTTTGTCCCACAATGACCTAAT
TGAGCATATATTTAATATTTATTCATTCATGACAATGTATCATATAATAACATTGGGCAGTTTAT
ACTTGAATAACATTCATATCATATACACTATTAATCAATGCATTTTATTTTTCCCTTATATGTAA
TATTATGCTCATTATATGATATGAATATAGATATATATTATATATATATATATATATATATATAT
ATATGGATGACAATAGGTCAGGTCGGATTTTTGCTTGCTCTGACTTCG
Found at i:831124 original size:19 final size:20
Alignment explanation
Indices: 831100--831150 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
831090 AATGACCAAT
831100 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
831119 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
831139 AAAATCGCAACG
1 AAAATCGCAACG
831151 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:831144 original size:20 final size:20
Alignment explanation
Indices: 831100--831294 Score: 90
Period size: 20 Copynumber: 9.6 Consensus size: 20
831090 AATGACCAAT
* *
831100 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
831119 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
831139 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
831159 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
831179 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
831200 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
831223 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
831243 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
831263 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
*
831283 AGAATCGCAACG
1 AAAATCGCAACG
831295 TTGAAAATAA
Statistics
Matches: 138, Mismatches: 29, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
19 17 0.12
20 94 0.68
21 14 0.10
23 13 0.09
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:831411 original size:6 final size:6
Alignment explanation
Indices: 831400--831473 Score: 141
Period size: 6 Copynumber: 12.5 Consensus size: 6
831390 GACACGTATT
831400 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
831448 ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
831474 CGAGACGAGA
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.07
6 63 0.93
ACGTcount: A:0.32, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:832179 original size:6 final size:6
Alignment explanation
Indices: 832158--832207 Score: 86
Period size: 6 Copynumber: 8.7 Consensus size: 6
832148 TCTCGTCTCG
832158 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
832204 GGTC
1 GGTC
832208 ATACATGTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.23
6 34 0.77
ACGTcount: A:0.00, C:0.18, G:0.52, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:832309 original size:20 final size:20
Alignment explanation
Indices: 832284--832327 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
832274 TTTTTAACTA
832284 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGACCGTTGCGATT
* *
832304 TTCTTTTTAGCGTTGCGATT
1 TTCTTTTGACCGTTGCGATT
832324 TTCT
1 TTCT
832328 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.18, G:0.18, T:0.55
Consensus pattern (20 bp):
TTCTTTTGACCGTTGCGATT
Found at i:832336 original size:20 final size:20
Alignment explanation
Indices: 832294--832651 Score: 180
Period size: 20 Copynumber: 17.6 Consensus size: 20
832284 TTCTTTTGAC
*** *
832294 CGTTGCGATTTTCTTTTTAG
1 CGTTGCGATTTTCTAAATCG
832314 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
832334 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
832354 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * *
832374 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
832394 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
832414 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
832437 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
832457 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
832477 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
832497 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
832517 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
832540 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* ***
832561 CGTTGCGATTTTTTTTTTAC-
1 CGTTGCGATTTTCTAAAT-CG
*** **
832581 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTAAATCG
832601 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
832621 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
832640 CGTTGCGATTTT
1 CGTTGCGATTTT
832652 ATTGGTCATT
Statistics
Matches: 282, Mismatches: 47, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
19 17 0.06
20 218 0.77
21 15 0.05
22 4 0.01
23 28 0.10
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:832360 original size:40 final size:40
Alignment explanation
Indices: 832316--832526 Score: 260
Period size: 40 Copynumber: 5.2 Consensus size: 40
832306 CTTTTTAGCG
* * * *
832316 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
* * *
832356 TTGCGATTCTCTCAGTCGCGTTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
* * *
832396 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGATTCTCTCAATCGCATTGCGA--TTC-TCTCAATCGCA
* * *
832439 TTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
* *
832479 TTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
832519 TTGCGATT
1 TTGCGATT
832527 TTCTTCTAAA
Statistics
Matches: 154, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
40 116 0.75
41 3 0.02
42 3 0.02
43 32 0.21
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.36
Consensus pattern (40 bp):
TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
Found at i:832463 original size:83 final size:83
Alignment explanation
Indices: 832351--832506 Score: 231
Period size: 83 Copynumber: 1.9 Consensus size: 83
832341 ATTCTCTCAG
* * * * * * * *
832351 TCGCATTGCGATTCTCTCAGTCGCGTTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TCGCATTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCA
832416 TTGCGATTTTCTTCTAAA
66 TTGCGATTTTCTTCTAAA
*
832434 TCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCA
1 TCGCATTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCA
832499 TTGCGATT
66 TTGCGATT
832507 CTATCAATCG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
83 64 1.00
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.36
Consensus pattern (83 bp):
TCGCATTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCA
TTGCGATTTTCTTCTAAA
Found at i:832483 original size:103 final size:103
Alignment explanation
Indices: 832324--832547 Score: 358
Period size: 103 Copynumber: 2.2 Consensus size: 103
832314 CGTTGCGATT
* * * * * * *
832324 TTCTAAATCGCGTTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCGTTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
* * *
832389 AGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTC
66 AATCGCATTGCGATTCTATCAATCGCATTGCGATTTTC
832427 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
832492 AATCGCATTGCGATTCTATCAATCGCATTGCGATTTTC
66 AATCGCATTGCGATTCTATCAATCGCATTGCGATTTTC
832530 TTCTAAATCGCGTTGCGA
1 TTCTAAATCGCGTTGCGA
832548 ACTTGGAAGC
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.36
Consensus pattern (103 bp):
TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
AATCGCATTGCGATTCTATCAATCGCATTGCGATTTTC
Found at i:832641 original size:19 final size:20
Alignment explanation
Indices: 832601--832651 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
832591 TTCTTTTTAA
*
832601 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
832621 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
832640 CGTTGCGATTTT
1 CGTTGCGATTTT
832652 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:835600 original size:36 final size:36
Alignment explanation
Indices: 835529--835647 Score: 163
Period size: 36 Copynumber: 3.3 Consensus size: 36
835519 ATCCCATTAT
* **
835529 CATTTTTC-AACAAACATCAACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
835565 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
835601 CA-TTTTCAAAGAAACA-TTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
835635 CATATTTTCAAAG
1 CAT-TTTTCAAAG
835648 TTGGTTACCA
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
34 20 0.27
35 14 0.19
36 22 0.29
37 19 0.25
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.29
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:835626 original size:34 final size:35
Alignment explanation
Indices: 835548--835647 Score: 148
Period size: 34 Copynumber: 2.8 Consensus size: 35
835538 ACAAACATCA
*
835548 ACCAAACTTTGAAAAACTATTTTTCAAAGAAACATTT
1 ACCAAACTTTG-AAAACCA-TTTTCAAAGAAACATTT
835585 ACCAAACTTTGAAAACCATTTTCAAAGAAACA-TT
1 ACCAAACTTTGAAAACCATTTTCAAAGAAACATTT
835619 ACCAAACTTTGAAAACCATATTTTCAAAG
1 ACCAAACTTTGAAAACC--ATTTTCAAAG
835648 TTGGTTACCA
Statistics
Matches: 60, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
34 19 0.32
35 14 0.23
36 16 0.27
37 11 0.18
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.29
Consensus pattern (35 bp):
ACCAAACTTTGAAAACCATTTTCAAAGAAACATTT
Found at i:840217 original size:37 final size:36
Alignment explanation
Indices: 840170--840276 Score: 171
Period size: 35 Copynumber: 2.9 Consensus size: 36
840160 TTTTTAACAC
* *
840170 ACATCTACCAAACTTTGAAAAACTATTTTTCAAAGAA
1 ACATTTACCAAACTTTG-AAAACCATTTTTCAAAGAA
840207 ACATTTACCAAACTTTGAAAACCA-TTTTCAAAGAA
1 ACATTTACCAAACTTTGAAAACCATTTTTCAAAGAA
840242 ACATTTACCAAACTTTGAAAACCATTTTTTCAAAG
1 ACATTTACCAAACTTTGAAAACCA-TTTTTCAAAG
840277 TTGGTTACCA
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
35 35 0.53
36 6 0.09
37 25 0.38
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.31
Consensus pattern (36 bp):
ACATTTACCAAACTTTGAAAACCATTTTTCAAAGAA
Found at i:840232 original size:21 final size:21
Alignment explanation
Indices: 840208--840268 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
840198 TTCAAAGAAA
840208 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
840229 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
840243 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
840264 CATTT
1 CATTT
840269 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:840285 original size:35 final size:36
Alignment explanation
Indices: 840175--840303 Score: 142
Period size: 35 Copynumber: 3.6 Consensus size: 36
840165 AACACACATC
* *
840175 TACCAAACTTTGAAAAAC-TATTTTTCAAAGAAACATT
1 TACCAAACTTTGAAAACCAT-TTTTTCAAAG-AACAGT
*
840212 TACCAAACTTTGAAAACCA--TTTTCAAAGAAACATT
1 TACCAAACTTTGAAAACCATTTTTTCAAAG-AACAGT
***
840247 TACCAAACTTTGAAAACCATTTTTTCAAAG-TTGGT
1 TACCAAACTTTGAAAACCATTTTTTCAAAGAACAGT
840282 TACCAAAC-TTGAAAACCATTTT
1 TACCAAACTTTGAAAACCATTTT
840304 AATACTTTCA
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
34 14 0.17
35 44 0.52
37 26 0.31
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.33
Consensus pattern (36 bp):
TACCAAACTTTGAAAACCATTTTTTCAAAGAACAGT
Found at i:843577 original size:15 final size:15
Alignment explanation
Indices: 843560--843589 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
843550 ATCTTTCTTT
843560 CCCGTTCTGGATTTTC
1 CCCG-TCTGGATTTTC
843576 CCCGTCTGGATTTT
1 CCCGTCTGGATTTT
843590 GATCTGCCAT
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:0.07, C:0.30, G:0.20, T:0.43
Consensus pattern (15 bp):
CCCGTCTGGATTTTC
Found at i:844837 original size:37 final size:36
Alignment explanation
Indices: 844778--844897 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
844768 ATCCCATTAT
* *
844778 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
844814 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
*
844850 CA-TTTTCAAAGAAACATTTACCAAACTCTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
844885 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
844898 TTGGTTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 34 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:844853 original size:21 final size:20
Alignment explanation
Indices: 844829--844889 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
844819 TTCAAAGAAA
844829 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAAC-TTGAAAAC
*
844850 CATTT-TCAAA---G-AAA-
1 CATTTACCAAACTTGAAAAC
844864 CATTTACCAAACTCTGAAAAC
1 CATTTACCAAACT-TGAAAAC
844885 CATTT
1 CATTT
844890 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.23, G:0.05, T:0.30
Consensus pattern (20 bp):
CATTTACCAAACTTGAAAAC
Found at i:847815 original size:3 final size:3
Alignment explanation
Indices: 847807--847875 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
847797 AATTAATTCA
847807 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
847855 ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
847876 TTGTAAATTG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:848945 original size:20 final size:20
Alignment explanation
Indices: 848892--848945 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
848882 TCATCTCATT
* *
848892 AAAAAGAACACAAAAAAGAG
1 AAAAAGAAGAGAAAAAAGAG
*
848912 AAAAAAAAGGAGAAAAATAGAG
1 AAAAAGAA-GAGAAAAA-AGAG
848934 AAAAAGAA-AGAA
1 AAAAAGAAGAGAA
848946 TAGTCACCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.39
21 6 0.21
22 11 0.39
ACGTcount: A:0.76, C:0.04, G:0.19, T:0.02
Consensus pattern (20 bp):
AAAAAGAAGAGAAAAAAGAG
Found at i:849024 original size:3 final size:3
Alignment explanation
Indices: 849016--849070 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
849006 AGGTAATTCT
849016 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
849064 TTA TTA T
1 TTA TTA T
849071 ATTTATTTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:849202 original size:3 final size:3
Alignment explanation
Indices: 849194--849250 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
849184 AGGGTTCTCG
849194 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
849242 ATT ATT ATT
1 ATT ATT ATT
849251 GAAATGACCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:849444 original size:3 final size:3
Alignment explanation
Indices: 849436--849464 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
849426 GGACAACCAT
849436 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
849465 TTGGTCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:849797 original size:45 final size:46
Alignment explanation
Indices: 849717--849807 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
849707 TTTGCCACTT
849717 GCTTTTTTTAATTTGATTTTGTTTTGTTATTTTTTTTCATTTATTA
1 GCTTTTTTTAATTTGATTTTGTTTTGTTATTTTTTTTCATTTATTA
849763 GCTTTTTTTAATTTGATTTTGTTTTGTTA-TTTTTTTCATTTATTA
1 GCTTTTTTTAATTTGATTTTGTTTTGTTATTTTTTTTCATTTATTA
849808 ATATAATTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 16 0.36
46 29 0.64
ACGTcount: A:0.15, C:0.04, G:0.09, T:0.71
Consensus pattern (46 bp):
GCTTTTTTTAATTTGATTTTGTTTTGTTATTTTTTTTCATTTATTA
Found at i:856490 original size:31 final size:32
Alignment explanation
Indices: 856416--856489 Score: 93
Period size: 30 Copynumber: 2.4 Consensus size: 32
856406 TAAGAGTGTG
*
856416 CTCATAATAAAAATTATTGGAAAAAGATAGAC
1 CTCATAATAAAAAGTATTGGAAAAAGATAGAC
*
856448 CTC-TAATAAAAAGTATT-GAAAAA-ATTATA-
1 CTCATAATAAAAAGTATTGGAAAAAGA-TAGAC
856477 CTCATAATAAAAA
1 CTCATAATAAAAA
856490 ATAAATATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 4 0.11
30 18 0.47
31 13 0.34
32 3 0.08
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.27
Consensus pattern (32 bp):
CTCATAATAAAAAGTATTGGAAAAAGATAGAC
Found at i:861000 original size:20 final size:20
Alignment explanation
Indices: 860971--861073 Score: 136
Period size: 20 Copynumber: 5.1 Consensus size: 20
860961 ATAAACGTGA
*
860971 TTTTAGTTTCGCGTTGCAAT
1 TTTTATTTTCGCGTTGCAAT
*
860991 TTTTATTTTCGCGTTGCGAT
1 TTTTATTTTCGCGTTGCAAT
*
861011 TTTCATGTTT-GCGTTGCAAT
1 TTTTAT-TTTCGCGTTGCAAT
* *
861031 TTTCATTTTCGCGTTGCGAT
1 TTTTATTTTCGCGTTGCAAT
861051 TTTTATTTTCGCGTTGCGAAT
1 TTTTATTTTCGCGTTGC-AAT
861072 TT
1 TT
861074 AAGTTTCAGA
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.86
21 7 0.10
ACGTcount: A:0.13, C:0.16, G:0.19, T:0.52
Consensus pattern (20 bp):
TTTTATTTTCGCGTTGCAAT
Found at i:861027 original size:40 final size:40
Alignment explanation
Indices: 860969--861073 Score: 153
Period size: 40 Copynumber: 2.6 Consensus size: 40
860959 CAATAAACGT
*
860969 GATTTTA-GTTTCGCGTTGCAATTTTTATTTTCGCGTTGC
1 GATTTTATGTTTCGCGTTGCAATTTTCATTTTCGCGTTGC
861008 GATTTTCATGTTT-GCGTTGCAATTTTCATTTTCGCGTTGC
1 GATTTT-ATGTTTCGCGTTGCAATTTTCATTTTCGCGTTGC
861048 GATTTTTAT-TTTCGCGTTGCGAATTT
1 GA-TTTTATGTTTCGCGTTGC-AATTT
861074 AAGTTTCAGA
Statistics
Matches: 60, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
39 9 0.15
40 38 0.63
41 13 0.22
ACGTcount: A:0.13, C:0.15, G:0.20, T:0.51
Consensus pattern (40 bp):
GATTTTATGTTTCGCGTTGCAATTTTCATTTTCGCGTTGC
Found at i:863155 original size:21 final size:21
Alignment explanation
Indices: 863129--863189 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
863119 TTGCCCTATC
*
863129 ATCGTTCAAGAGGCGCCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
863150 ATCGTTCAAGAGGCCCCT-CT
1 ATCGTTCAAGAGGCCCCTCCT
*
863170 CATC-ATCGAAGAGGCCCCTC
1 -ATCGTTC-AAGAGGCCCCTC
863190 TCACCATTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 4 0.11
21 31 0.89
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:863202 original size:21 final size:21
Alignment explanation
Indices: 863154--863203 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
863144 CCTCCTATCG
*
863154 TTCAAGAGGCCCCTCTCATCA
1 TTCAAGAGGCCCCTCTCACCA
863175 -TCGAAGAGGCCCCTCTCACCA
1 TTC-AAGAGGCCCCTCTCACCA
863196 TTCAAGAG
1 TTCAAGAG
863204 ACCCTGTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 22 0.85
22 2 0.08
ACGTcount: A:0.26, C:0.36, G:0.18, T:0.20
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCTCACCA
Found at i:864748 original size:20 final size:20
Alignment explanation
Indices: 864723--864775 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
864713 TCGTTGTGAT
864723 AGTCAAATTCGCAACGCAAA
1 AGTCAAATTCGCAACGCAAA
*
864743 AGTCAAATTCGCAACGTAAA
1 AGTCAAATTCGCAACGCAAA
864763 AGTCAAATTCGCA
1 AGTCAAATTCGCA
864776 TTGCGATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.19
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCAAA
Found at i:864861 original size:74 final size:74
Alignment explanation
Indices: 864679--864861 Score: 240
Period size: 74 Copynumber: 2.5 Consensus size: 74
864669 GTACACTTTT
* ** *
864679 GCAACGCGAAAGTCAAATTCGCGTTGTGATTTTCTCGTTGTGATAGTCAAATTCGCAACGCAAAA
1 GCAACGCGAAAGTCAAATTCGCGTTGTGATTTTCGCGTTACGATAGTCAAATTCGCAACACAAAA
864744 GTCAAATTC
66 GTCAAATTC
** * * * * **
864753 GCAACGTAAAAGTCAAATTCGCATTGCGATTTTCGCGTTACGATAGTCAAATTTGCAATATTAAA
1 GCAACGCGAAAGTCAAATTCGCGTTGTGATTTTCGCGTTACGATAGTCAAATTCGCAACACAAAA
*
864818 GTTAAATTC
66 GTCAAATTC
*
864827 GCAACGCGAAAGTCAAATTCGCGTTGTGAATTTCG
1 GCAACGCGAAAGTCAAATTCGCGTTGTGATTTTCG
864862 GTTTGCGATT
Statistics
Matches: 91, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
74 91 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (74 bp):
GCAACGCGAAAGTCAAATTCGCGTTGTGATTTTCGCGTTACGATAGTCAAATTCGCAACACAAAA
GTCAAATTC
Found at i:864895 original size:21 final size:20
Alignment explanation
Indices: 864864--864933 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
864854 GAATTTCGGT
864864 TTGCG-ATTTTAATTTTTGCG
1 TTGCGAATTTTAA-TTTTGCG
864884 TTGCGAATTTTAATTTTGCG
1 TTGCGAATTTTAATTTTGCG
* * * * *
864904 TTACGAATTTGACTTTCGCA
1 TTGCGAATTTTAATTTTGCG
864924 TTGCGAATTT
1 TTGCGAATTT
864934 AACTTTCACA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 36 0.84
21 7 0.16
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.49
Consensus pattern (20 bp):
TTGCGAATTTTAATTTTGCG
Found at i:865219 original size:18 final size:18
Alignment explanation
Indices: 865196--865231 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
865186 AAGCCGGTTG
*
865196 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
865214 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
865232 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:868390 original size:29 final size:28
Alignment explanation
Indices: 868348--868507 Score: 182
Period size: 29 Copynumber: 5.7 Consensus size: 28
868338 GAACCGACCC
*
868348 GACACTTTGGGAATTATTTTGAAAAAGGT
1 GACATTTTGGGAATTATTTTGAAAAA-GT
868377 GACATTTTGGGAATTATTTTGAAAAATGT
1 GACATTTTGGGAATTATTTTGAAAAA-GT
*
868406 GACATTTTGGGAACTATTTTG-AAAAGT
1 GACATTTTGGGAATTATTTTGAAAAAGT
* * *
868433 GACATTTTGGG-ATTTTTTTAAAAACAAT
1 GACATTTTGGGAATTATTTTGAAAA-AGT
* * *
868461 GACATTCTGGTAATTATTTTTAAAACA-T
1 GACATTTTGGGAATTATTTTGAAAA-AGT
*
868489 GACATTTTGAGAATTATTT
1 GACATTTTGGGAATTATTT
868508 GTAAAACTTT
Statistics
Matches: 114, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
26 6 0.05
27 16 0.14
28 32 0.28
29 60 0.53
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (28 bp):
GACATTTTGGGAATTATTTTGAAAAAGT
Found at i:868442 original size:27 final size:29
Alignment explanation
Indices: 868348--868555 Score: 178
Period size: 29 Copynumber: 7.3 Consensus size: 29
868338 GAACCGACCC
*
868348 GACACTTTGGGAATTATTTTGAAAAAGGT
1 GACATTTTGGGAATTATTTTGAAAAAGGT
*
868377 GACATTTTGGGAATTATTTTGAAAAATGT
1 GACATTTTGGGAATTATTTTGAAAAAGGT
*
868406 GACATTTTGGGAACTATTTTG-AAAA-GT
1 GACATTTTGGGAATTATTTTGAAAAAGGT
* **
868433 GACATTTTGGG-ATT-TTTTTAAAAACAAT
1 GACATTTTGGGAATTATTTTGAAAAA-GGT
* * *
868461 GACATTCTGGTAATTATTTTTAAAACA--T
1 GACATTTTGGGAATTATTTTGAAAA-AGGT
* ***
868489 GACATTTTGAGAATTA-TTTGTAAAACTTT
1 GACATTTTGGGAATTATTTTG-AAAAAGGT
* * *
868518 GATATTTTGGTAATTATTTTTAATAAAGGT
1 GACATTTTGGGAATTATTTTGAA-AAAGGT
*
868548 GATATTTT
1 GACATTTT
868556 TGTAGTTTTC
Statistics
Matches: 148, Mismatches: 20, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
25 4 0.03
26 6 0.04
27 16 0.11
28 32 0.22
29 66 0.45
30 23 0.16
31 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (29 bp):
GACATTTTGGGAATTATTTTGAAAAAGGT
Found at i:868540 original size:57 final size:55
Alignment explanation
Indices: 868348--868537 Score: 186
Period size: 55 Copynumber: 3.4 Consensus size: 55
868338 GAACCGACCC
* *
868348 GACACTTTGGGAATTATTTTGAAAAAGGTGACATTTTGGGAATTATTTTGAAAAA-TGT
1 GACATTTTGGGAATTATTTTGAAAAA--TGACATTTT-GGAATTATTTT-AAAAACTAT
* * * * *
868406 GACATTTTGGGAACTATTTTGAAAAGTGACATTTTGGGATTTTTTTAAAAACAAT
1 GACATTTTGGGAATTATTTTGAAAAATGACATTTTGGAATTATTTTAAAAACTAT
* * * *
868461 GACATTCTGGTAATTATTTTTAAAACATGACATTTTGAGAATTATTTGT-AAAACTTT
1 GACATTTTGGGAATTATTTTGAAAA-ATGACATTTTG-GAATTATTT-TAAAAACTAT
* *
868518 GATATTTTGGTAATTATTTT
1 GACATTTTGGGAATTATTTT
868538 TAATAAAGGT
Statistics
Matches: 110, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
54 5 0.05
55 31 0.28
56 19 0.17
57 31 0.28
58 24 0.22
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (55 bp):
GACATTTTGGGAATTATTTTGAAAAATGACATTTTGGAATTATTTTAAAAACTAT
Found at i:875886 original size:29 final size:29
Alignment explanation
Indices: 875844--876055 Score: 202
Period size: 29 Copynumber: 7.3 Consensus size: 29
875834 ACCCGACCCA
*
875844 GTGATATTTTGGGAATTATTTTGAAAAAG
1 GTGACATTTTGGGAATTATTTTGAAAAAG
*
875873 GTGACATTTTGGGAATTATTTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAG
*
875902 GTGACATTTTGGGAATTA-TTT-AAAAAA
1 GTGACATTTTGGGAATTATTTTGAAAAAG
* *
875929 GTGACATTTTGGGAATT-TTTTTAAAAATA
1 GTGACATTTTGGGAATTATTTTGAAAAA-G
* * *
875958 GTGACATTCTGGTAATTATTGTT-AAAATG
1 GTGACATTTTGGGAATTATT-TTGAAAAAG
* *
875987 ATGAAATTTTGGGAATTA-TTTGTAAAACA-
1 GTGACATTTTGGGAATTATTTTG-AAAA-AG
* * * *
876016 ATGATATTTTGGTAATTATTTTTAATAAAG
1 GTGACATTTTGGGAATTATTTTGAA-AAAG
*
876046 GTGATATTTT
1 GTGACATTTT
876056 TATAATTTTC
Statistics
Matches: 156, Mismatches: 16, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
27 27 0.17
28 9 0.06
29 98 0.63
30 20 0.13
31 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.19, T:0.43
Consensus pattern (29 bp):
GTGACATTTTGGGAATTATTTTGAAAAAG
Found at i:875996 original size:85 final size:87
Alignment explanation
Indices: 875843--876045 Score: 256
Period size: 85 Copynumber: 2.4 Consensus size: 87
875833 GACCCGACCC
* * * *
875843 AGTGATATTTTGGGAATTATTTTGAAAAAGGTGACATTTTGGGAATTATTTTGAAAAATGTGACA
1 AGTGATATTTTGGGAATTATTTTTAAAAAAGTGACATTCTGGGAATTATTTT-AAAAATGTGAAA
875908 TTTTGGGAATTA-TT-TAAAA-A
65 TTTTGGGAATTATTTGTAAAACA
* *
875928 AGTGACATTTTGGGAATT-TTTTTAAAAATAGTGACATTCTGGTAATTATTGTT-AAAATGATGA
1 AGTGATATTTTGGGAATTATTTTTAAAAA-AGTGACATTCTGGGAATTATT-TTAAAAATG-TGA
875991 AATTTTGGGAATTATTTGTAAAACA
63 AATTTTGGGAATTATTTGTAAAACA
* *
876016 A-TGATATTTTGGTAATTATTTTTAATAAAG
1 AGTGATATTTTGGGAATTATTTTTAAAAAAG
876046 GTGATATTTT
Statistics
Matches: 102, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
84 15 0.15
85 51 0.50
86 4 0.04
87 21 0.21
88 11 0.11
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (87 bp):
AGTGATATTTTGGGAATTATTTTTAAAAAAGTGACATTCTGGGAATTATTTTAAAAATGTGAAAT
TTTGGGAATTATTTGTAAAACA
Found at i:876001 original size:58 final size:57
Alignment explanation
Indices: 875843--876055 Score: 227
Period size: 58 Copynumber: 3.7 Consensus size: 57
875833 GACCCGACCC
* *
875843 AGTGATATTTTGGGAATTATTTTGAAAAAGGTGACATTTTGGGAATTATTTTGAAAAAT
1 AGTGACATTTTGGGAATTATTTT-AAAAA-GTGACATTTTGGGAATTATTTTTAAAAAT
*
875902 -GTGACATTTTGGGAATTATTTAAAAAAGTGACATTTTGGGAATT-TTTTTAAAAAT
1 AGTGACATTTTGGGAATTATTTTAAAAAGTGACATTTTGGGAATTATTTTTAAAAAT
* * * * *
875957 AGTGACATTCTGGTAATTATTGTTAAAATGATGAAATTTTGGGAATTATTTGTAAAACA-
1 AGTGACATTTTGGGAATTATT-TTAAAAAG-TGACATTTTGGGAATTATTTTTAAAA-AT
* * *
876016 A-TGATATTTTGGTAATTATTTTTAATAAAGGTGATATTTT
1 AGTGACATTTTGGGAATTA-TTTTAA-AAA-GTGACATTTT
876056 TATAATTTTC
Statistics
Matches: 133, Mismatches: 13, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
55 10 0.08
56 35 0.26
57 11 0.08
58 54 0.41
59 21 0.16
60 2 0.02
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.43
Consensus pattern (57 bp):
AGTGACATTTTGGGAATTATTTTAAAAAGTGACATTTTGGGAATTATTTTTAAAAAT
Found at i:878732 original size:20 final size:20
Alignment explanation
Indices: 878709--878775 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
878699 CGAAAATCGA
*
878709 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTATGT
878729 GTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTTATGT
*
878749 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTATGT
878769 GTTGCGA
1 GTTGCGA
878776 TTTACATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.16, C:0.12, G:0.27, T:0.45
Consensus pattern (20 bp):
GTTGCGAATTTGACTTATGT
Found at i:878793 original size:40 final size:41
Alignment explanation
Indices: 878670--878800 Score: 128
Period size: 40 Copynumber: 3.3 Consensus size: 41
878660 ACTAAAACCT
* * * * *
878670 GTTGCGAAATTAAATTC-GTGTTGCGAATTCGA-AAATCGA
1 GTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTAATCGA
* * *
878709 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTAT-GT
1 GTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTAATCGA
*
878749 GTTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACATAATCGC
1 GTTGCGAATTTGACTTCTGTGTTGCGAATTTGAC-TAATCGA
*
878789 GTTGCAAATTTG
1 GTTGCGAATTTG
878801 GAAACTGGGT
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
38 2 0.03
39 20 0.26
40 52 0.68
41 2 0.03
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.40
Consensus pattern (41 bp):
GTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTAATCGA
Found at i:883099 original size:26 final size:26
Alignment explanation
Indices: 883042--883120 Score: 103
Period size: 26 Copynumber: 3.2 Consensus size: 26
883032 AAAAAATATA
*
883042 ATATATATA-TATATAATATAAAATT
1 ATATATAAACTATATAATATAAAATT
*
883067 ATATATAAACTATATAACTATATAATT
1 ATATATAAACTATATAA-TATAAAATT
883094 AT-TATAAACTATAT-ATAT-AAATT
1 ATATATAAACTATATAATATAAAATT
883117 ATAT
1 ATAT
883121 TTATGTGAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
23 6 0.12
24 4 0.08
25 9 0.19
26 19 0.40
27 10 0.21
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATATAAACTATATAATATAAAATT
Found at i:883120 original size:9 final size:9
Alignment explanation
Indices: 883068--883108 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
883058 TATAAAATTA
883068 TATATAAAC
1 TATATAAAC
883077 TATAT-AAC
1 TATATAAAC
*
883085 TATAT-AAT
1 TATATAAAC
883093 TATTATAAAC
1 TA-TATAAAC
883103 TATATA
1 TATATA
883109 TATAAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 12 0.43
9 12 0.43
10 4 0.14
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (9 bp):
TATATAAAC
Found at i:883194 original size:18 final size:18
Alignment explanation
Indices: 883047--883210 Score: 84
Period size: 18 Copynumber: 8.6 Consensus size: 18
883037 ATATAATATA
* *
883047 TATATATATAATATAAAAT
1 TATATATATATTAT-AAAC
* *
883066 TATATATAAACTATATAAC
1 TATATATATATTATA-AAC
883085 TATATA-ATTATTATAAAC
1 TATATATA-TATTATAAAC
**
883103 TATATATATAAATTAT-ATT
1 TATATATAT--ATTATAAAC
* *
883122 TATGTGAACAATATATATAAAC
1 TATAT--A-TATAT-TATAAAC
*
883144 TATGTATATAAAATTATAAAC
1 TA--TATAT-ATATTATAAAC
*
883165 TATATTTATATTATAAAC
1 TATATATATATTATAAAC
883183 TATATCAT-TATTATAAGA-
1 TATAT-ATATATTATAA-AC
883201 TATATATATA
1 TATATATATA
883211 AATTATGTTA
Statistics
Matches: 112, Mismatches: 17, Indels: 33
0.69 0.10 0.20
Matches are distributed among these distances:
17 2 0.02
18 42 0.38
19 37 0.33
20 7 0.06
21 13 0.12
22 9 0.08
24 2 0.02
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (18 bp):
TATATATATATTATAAAC
Found at i:883251 original size:15 final size:15
Alignment explanation
Indices: 883037--883364 Score: 101
Period size: 15 Copynumber: 22.3 Consensus size: 15
883027 ATTGAAAAAA
*
883037 ATATA-ATATATA-T
1 ATATATATATAAACT
883050 ATATATAATATAAA--
1 ATATAT-ATATAAACT
883064 AT-TATATATAAACT
1 ATATATATATAAACT
*
883078 ATATA-ACTATATA--
1 ATATATA-TATAAACT
883091 AT-TAT-TATAAAC-
1 ATATATATATAAACT
*
883103 -TATATATATAAATT
1 ATATATATATAAACT
* * *
883117 ATATTTATGTGAAC-
1 ATATATATATAAACT
883131 A-ATATATATAAACT
1 ATATATATATAAACT
883145 ATGTATATAAAATTATAAACT
1 A--TATAT---A-TATAAACT
883166 ATATTTATATTATAAACT
1 ATA--TATA-TATAAACT
*
883184 ATATCAT-TATTATAA-G
1 ATAT-ATATA-TA-AACT
*
883200 ATATATATATAAATT
1 ATATATATATAAACT
* * *
883215 ATGT-TAATGTGAAC-
1 ATATAT-ATATAAACT
883229 -TATATATATAAAC-
1 ATATATATATAAACT
*
883242 -TATGTATATAAACT
1 ATATATATATAAACT
* *
883256 ATATATGTATAACCT
1 ATATATATATAAACT
* * * *
883271 ATAAAAAGTATATAGT
1 ATATATA-TATAAACT
* * * **
883287 TTATAAAATATTATTT
1 ATAT-ATATATAAACT
*
883303 ATAT-TATATATA-T
1 ATATATATATAAACT
*
883316 ATATATATATATA-T
1 ATATATATATAAACT
883330 ATATATATATAAACT
1 ATATATATATAAACT
*
883345 ATATATGTATAAACT
1 ATATATATATAAACT
883360 ATATA
1 ATATA
883365 AAATATATAG
Statistics
Matches: 237, Mismatches: 43, Indels: 68
0.68 0.12 0.20
Matches are distributed among these distances:
11 6 0.03
12 12 0.05
13 50 0.21
14 36 0.15
15 71 0.30
16 23 0.10
17 11 0.05
18 13 0.05
19 2 0.01
20 1 0.00
21 12 0.05
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.43
Consensus pattern (15 bp):
ATATATATATAAACT
Found at i:883314 original size:2 final size:2
Alignment explanation
Indices: 883302--883417 Score: 82
Period size: 2 Copynumber: 59.0 Consensus size: 2
883292 AAATATTATT
*
883302 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
883343 CTA TA TA TG TA TA AA CTA TA TA -A AA TA TA TA GTT TA TA TG T-
1 -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
883384 TA TA -A TT TA TA T- TA -A TA TA GTA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
883418 CATTAGATTA
Statistics
Matches: 90, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
1 6 0.07
2 79 0.88
3 5 0.06
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:883488 original size:15 final size:15
Alignment explanation
Indices: 883470--883506 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
883460 TTTATTACTT
883470 TATATAGTTTATATA
1 TATATAGTTTATATA
883485 TATATAGTTTATATA
1 TATATAGTTTATATA
883500 TACTATA
1 TA-TATA
883507 CATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:883536 original size:7 final size:7
Alignment explanation
Indices: 883524--883595 Score: 65
Period size: 7 Copynumber: 10.4 Consensus size: 7
883514 TATATATACA
883524 TTAGGGT
1 TTAGGGT
883531 TTAGGG-
1 TTAGGGT
*
883537 TTATGGT
1 TTAGGGT
*
883544 TTAGTGT
1 TTAGGGT
883551 TTAGGGT
1 TTAGGGT
**
883558 TTAAAGT
1 TTAGGGT
883565 TTAGGGT
1 TTAGGGT
* *
883572 TTATGAT
1 TTAGGGT
*
883579 TTAAGGT
1 TTAGGGT
*
883586 TTAAGGT
1 TTAGGGT
883593 TTA
1 TTA
883596 TATAAACTAT
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
6 5 0.10
7 47 0.90
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (7 bp):
TTAGGGT
Found at i:883568 original size:21 final size:21
Alignment explanation
Indices: 883524--883595 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 21
883514 TATATATACA
*
883524 TTAGGGTTTAGGG-TTATGGT
1 TTAGGGTTTAGGGTTTAAGGT
* *
883544 TTAGTGTTTAGGGTTTAAAGT
1 TTAGGGTTTAGGGTTTAAGGT
* *
883565 TTAGGGTTTATGATTTAAGGT
1 TTAGGGTTTAGGGTTTAAGGT
*
883586 TTAAGGTTTA
1 TTAGGGTTTA
883596 TATAAACTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 12 0.28
21 31 0.72
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (21 bp):
TTAGGGTTTAGGGTTTAAGGT
Found at i:897109 original size:7 final size:7
Alignment explanation
Indices: 897099--897162 Score: 65
Period size: 8 Copynumber: 8.6 Consensus size: 7
897089 AAAATTTAAA
897099 AAAAAAT
1 AAAAAAT
897106 AAAAAAT
1 AAAAAAT
897113 AAAAAATT
1 AAAAAA-T
897121 AAAAAAT
1 AAAAAAT
*
897128 AAAAAAAG
1 -AAAAAAT
*
897136 AGAAAAAG
1 A-AAAAAT
897144 AGAAAAAT
1 A-AAAAAT
*
897152 TAAAAAT
1 AAAAAAT
897159 AAAA
1 AAAA
897163 GAAAAATAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
7 24 0.48
8 26 0.52
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:897109 original size:8 final size:8
Alignment explanation
Indices: 897098--897173 Score: 59
Period size: 8 Copynumber: 9.5 Consensus size: 8
897088 AAAAATTTAA
897098 AAAAAAAT
1 AAAAAAAT
897106 -AAAAAAT
1 AAAAAAAT
897113 -AAAAAAT
1 AAAAAAAT
*
897120 TAAAAAAT
1 AAAAAAAT
*
897128 AAAAAAAG
1 AAAAAAAT
* *
897136 AGAAAAAG
1 AAAAAAAT
*
897144 AGAAAAATT
1 A-AAAAAAT
897153 AAAAATAA-
1 AAAAA-AAT
897161 AAGAAAAAT
1 AA-AAAAAT
897170 AAAA
1 AAAA
897174 GGGGGTTCAA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
7 14 0.25
8 31 0.55
9 11 0.20
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:897118 original size:15 final size:15
Alignment explanation
Indices: 897098--897162 Score: 76
Period size: 15 Copynumber: 4.3 Consensus size: 15
897088 AAAAATTTAA
897098 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
*
897113 AAAAAATTAAAAAAT
1 AAAAAAATAAAAAAT
* *
897128 AAAAAAAGAGAAAAAG
1 AAAAAAATA-AAAAAT
* *
897144 AGAAAAATTAAAAAT
1 AAAAAAATAAAAAAT
897159 AAAA
1 AAAA
897163 GAAAAATAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
15 29 0.73
16 11 0.28
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:897142 original size:32 final size:31
Alignment explanation
Indices: 897095--897173 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 31
897085 ATGAAAAATT
*
897095 TAAAAAAAAATAAAAA-ATAAAAAATTAAAAAA
1 TAAAAAAAAAGAAAAAGA-AAAAAATT-AAAAA
* *
897127 TAAAAAAAGAGAAAAAGAGAAAAATTAAAAA
1 TAAAAAAAAAGAAAAAGAAAAAAATTAAAAA
*
897158 TAAAAGAAAAATAAAA
1 TAAAA-AAAAAGAAAA
897174 GGGGGTTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 10 0.25
32 29 0.73
33 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (31 bp):
TAAAAAAAAAGAAAAAGAAAAAAATTAAAAA
Found at i:898499 original size:37 final size:37
Alignment explanation
Indices: 898445--898520 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
898435 AAACAATTTA
898445 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA-TC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACTC
898481 ATCTATAAGCCTTCACGGAAGAGTAGTGAAGCAAACTC
1 ATCT-TAAGCCTTCACGGAAGAGTAGTGAAGCAAACTC
898519 AT
1 AT
898521 TTTATGAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 4 0.11
37 30 0.79
38 4 0.11
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (37 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACTC
Found at i:898612 original size:55 final size:55
Alignment explanation
Indices: 898535--899224 Score: 710
Period size: 55 Copynumber: 12.6 Consensus size: 55
898525 TGAAGATCGG
* *
898535 GTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTAAAGATTGTTCTA
1 GTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGA
* * ** * *
898590 -TTCCTATACTCTCTCATA-GAATA-AGGAGCAGATACATTTGTTGAAGATTGTTCAA
1 GTT-CTATACTCTCTGA-AGGAATAGA-GAGCGGACCCGTTTGTTGAAGATTGTTCGA
*
898645 GTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTT-GA
1 GTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGA
* * *
898699 GTCCTATACTCTCTGATA-GAATAGGGAGTGGACCCGTTTGTTGAAGATTGTTCGA
1 GTTCTATACTCTCTGA-AGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGA
** * * *
898754 GTTCTATACTCTCTGAAGGAATAGAGAGCATACCCATTTGTTGAAGATTTTTCAA
1 GTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGA
898809 GTT-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGTTCGA
1 GTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGTTCGA
* * * * *
898863 GTTTTATACTCTCTGAAGGAATAGGGAACGGACCCGTTTGTTGAAGAATGTCCGA
1 GTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGA
* * *
898918 GTCCTATACTCTCTGATA-GAATAGAGAGTGGACCCGTTT-TATGAAGATTATTCGA
1 GTTCTATACTCTCTGA-AGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGTTCGA
*
898973 GTTCTATACTCTCTGAAGGAATAGAGAGCGTACCCGTTT-TATGAAGATTGTTCGA
1 GTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGTTCGA
* * *
899028 GTTATATACTTTCTGAAGGAATAGAGAGCGAACCCGTTT-TATGAAGATTGTTCGA
1 GTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGTTCGA
* * * * * *
899083 G-TCTTATACTCCCTGAACGAATAGGGAGC-AAGCACGTTTGCTGAAGATTGTTCGA
1 GTTC-TATACTCTCTGAAGGAATAGAGAGCGGA-CCCGTTTGTTGAAGATTGTTCGA
* * * * *** ** * *
899138 G-TCTTATACTCCCTCAACGAATAGGGAATAGACAAGTTTGCTGAAGATTGTGT-TA
1 GTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT-TCGA
* *
899193 GTAT-TATACTCCCTGAAGGAATAGGGAGCGGA
1 GT-TCTATACTCTCTGAAGGAATAGAGAGCGGA
899225 TCCATCATTC
Statistics
Matches: 545, Mismatches: 68, Indels: 44
0.83 0.10 0.07
Matches are distributed among these distances:
53 1 0.00
54 104 0.19
55 431 0.79
56 8 0.01
57 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (55 bp):
GTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGA
Found at i:898810 original size:164 final size:165
Alignment explanation
Indices: 898535--899112 Score: 755
Period size: 164 Copynumber: 3.5 Consensus size: 165
898525 TGAAGATCGG
* *
898535 GTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTAAAGATTGTTCTA-TTCCTATAC
1 GTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTT-CTATAC
* ** *
898599 TCTCTCATAGAATA-AGGAGCAGATACATTTGTTGAAGATTGTTCAAGTTCTATACTCTCTGAAG
65 TCTCTGATAGAATAGA-GAGCAGACCCATTTGTTGAAGATTATTCAAGTTCTATACTCTCTGAAG
898663 GAATAGAGAGCGGACCCG-TTTATTGAAGATTGTT-GA
129 GAATAGAGAGCGGACCCGTTTTA-TGAAGATTGTTCGA
* * *
898699 GTCCTATACTCTCTGATA-GAATAGGGAGTGGACCCGTTTGTTGAAGATTGTTCGAGTTCTATAC
1 GTTCTATACTCTCTGA-AGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTTCTATAC
* *
898763 TCTCTGA-AGGAATAGAGAGCATACCCATTTGTTGAAGATTTTTCAAGTT-TATACTCTCTGAAG
65 TCTCTGATA-GAATAGAGAGCAGACCCATTTGTTGAAGATTATTCAAGTTCTATACTCTCTGAAG
898826 GAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGA
129 GAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGA
* * * * * *
898863 GTTTTATACTCTCTGAAGGAATAGGGAACGGACCCGTTTGTTGAAGAATGTCCGAGTCCTATACT
1 GTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTTCTATACT
** * *
898928 CTCTGATAGAATAGAGAGTGGACCCGTTT-TATGAAGATTATTCGAGTTCTATACTCTCTGAAGG
66 CTCTGATAGAATAGAGAGCAGACCCATTTGT-TGAAGATTATTCAAGTTCTATACTCTCTGAAGG
*
898992 AATAGAGAGCGTACCCGTTTTATGAAGATTGTTCGA
130 AATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGA
* * *
899028 GTTATATACTTTCTGAAGGAATAGAGAGCGAACCCGTTT-TATGAAGATTGTTCGAG-TCTTATA
1 GTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGTTCGAGTTC-TATA
* *
899091 CTCCCTGA-ACGAATAGGGAGCA
64 CTCTCTGATA-GAATAGAGAGCA
899113 AGCACGTTTG
Statistics
Matches: 365, Mismatches: 36, Indels: 25
0.86 0.08 0.06
Matches are distributed among these distances:
163 46 0.13
164 197 0.54
165 122 0.33
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (165 bp):
GTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTTCTATACT
CTCTGATAGAATAGAGAGCAGACCCATTTGTTGAAGATTATTCAAGTTCTATACTCTCTGAAGGA
ATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGA
Found at i:906536 original size:20 final size:19
Alignment explanation
Indices: 906511--906552 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
906501 AAATTTTCTA
906511 TTCCCTCTAAATTTCCCAAT
1 TTCCCTCTAAA-TTCCCAAT
*
906531 TTCCCTCTAAATTCTCAAT
1 TTCCCTCTAAATTCCCAAT
906550 TTC
1 TTC
906553 TCTATATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.24, C:0.33, G:0.00, T:0.43
Consensus pattern (19 bp):
TTCCCTCTAAATTCCCAAT
Found at i:906551 original size:19 final size:19
Alignment explanation
Indices: 906511--906565 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 19
906501 AAATTTTCTA
*
906511 TTCCCTCTAAATTTCCCAAT
1 TTCCCTCTAAA-TTCTCAAT
906531 TTCCCTCTAAATTCTCAAT
1 TTCCCTCTAAATTCTCAAT
*
906550 TT--CTCTATATTCTCAA
1 TTCCCTCTAAATTCTCAA
906566 AATTTCCTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 13 0.39
19 9 0.27
20 11 0.33
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (19 bp):
TTCCCTCTAAATTCTCAAT
Found at i:906924 original size:23 final size:24
Alignment explanation
Indices: 906898--906947 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
906888 TTATTTTTTC
906898 TTTATATAAATTAAAATATA-TAA
1 TTTATATAAATTAAAATATATTAA
*
906921 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAAATATATTAA
906945 TTT
1 TTT
906948 TCCTTTGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAAATATATTAA
Found at i:907226 original size:16 final size:16
Alignment explanation
Indices: 907207--907241 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
907197 TCATTTACAA
*
907207 GTCATGTTAAAAACAG
1 GTCAGGTTAAAAACAG
*
907223 GTCAGGTTGAAAACAG
1 GTCAGGTTAAAAACAG
907239 GTC
1 GTC
907242 GGGTAATACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (16 bp):
GTCAGGTTAAAAACAG
Found at i:907486 original size:7 final size:7
Alignment explanation
Indices: 907476--907628 Score: 147
Period size: 7 Copynumber: 21.7 Consensus size: 7
907466 AAAATGATGA
907476 AAAAATG
1 AAAAATG
*
907483 AAAAGA-A
1 AAAA-ATG
907490 AAAAATGG
1 AAAAAT-G
907498 AAAAAATG
1 -AAAAATG
907506 AAAAATG
1 AAAAATG
907513 -AAAATG
1 AAAAATG
907519 AAAAATG
1 AAAAATG
907526 AAAAATG
1 AAAAATG
907533 AAAAATG
1 AAAAATG
907540 AAAAATG
1 AAAAATG
*
907547 AAAAAAATA
1 --AAAAATG
907556 AAAAATG
1 AAAAATG
907563 AAAAATG
1 AAAAATG
907570 AAAAATG
1 AAAAATG
*
907577 AAAAAAG
1 AAAAATG
*
907584 AATAAAGAG
1 AA-AAA-TG
*
907593 AAAAATA
1 AAAAATG
907600 AAAAATG
1 AAAAATG
907607 --AAAT-
1 AAAAATG
*
907611 AAAAAAG
1 AAAAATG
907618 AAAAAT-
1 AAAAATG
907624 AAAAA
1 AAAAA
907629 GGGGGTTCAA
Statistics
Matches: 124, Mismatches: 10, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
5 4 0.03
6 15 0.12
7 81 0.65
8 8 0.06
9 16 0.13
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:907491 original size:22 final size:25
Alignment explanation
Indices: 907477--907581 Score: 73
Period size: 23 Copynumber: 4.4 Consensus size: 25
907467 AAATGATGAA
**
907477 AAAATG-AAAA-GAAAAAAATGGAA
1 AAAATGAAAAATGAAAATGATGGAA
***
907500 AAAATGAAAAATGAAAATGAAAAATGA
1 AAAATGAAAAATGAAAATGATGGA--A
*
907527 AAAATGAAAAATGAAAA--ATGAAA
1 AAAATGAAAAATGAAAATGATGGAA
*
907550 AAAATAAAAAATGAAAA--AT-G-A
1 AAAATGAAAAATGAAAATGATGGAA
907571 AAAATGAAAAA
1 AAAATGAAAAA
907582 AGAATAAAGA
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
21 11 0.16
23 25 0.37
24 4 0.06
25 10 0.15
27 18 0.26
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.12
Consensus pattern (25 bp):
AAAATGAAAAATGAAAATGATGGAA
Found at i:907512 original size:30 final size:31
Alignment explanation
Indices: 907455--907614 Score: 169
Period size: 30 Copynumber: 5.2 Consensus size: 31
907445 CGCTTGAAGA
907455 AAAAAAATGAAAAAATGATGAAAAAATG-AAAA-G
1 AAAAAAATG-AAAAA--ATG-AAAAATGAAAAATG
907488 AAAAAAATGGAAAAAATGAAAAATG-AAAATG
1 AAAAAAAT-GAAAAAATGAAAAATGAAAAATG
907519 --AAAAATG-AAAAATGAAAAATGAAAAATG
1 AAAAAAATGAAAAAATGAAAAATGAAAAATG
907547 AAAAAAAT-AAAAAATGAAAAATGAAAAATG
1 AAAAAAATGAAAAAATGAAAAATGAAAAATG
*
907577 -AAAAAA-GAATAAAGA-GAAAAATAAAAAATG
1 AAAAAAATGAA-AAA-ATGAAAAATGAAAAATG
907607 AAATAAAA
1 AAA-AAAA
907615 AAGAAAAATA
Statistics
Matches: 115, Mismatches: 1, Indels: 23
0.83 0.01 0.17
Matches are distributed among these distances:
27 14 0.12
28 7 0.06
29 14 0.12
30 55 0.48
31 7 0.06
32 4 0.03
33 13 0.11
34 1 0.01
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.12
Consensus pattern (31 bp):
AAAAAAATGAAAAAATGAAAAATGAAAAATG
Found at i:907520 original size:44 final size:43
Alignment explanation
Indices: 907457--907629 Score: 107
Period size: 44 Copynumber: 4.0 Consensus size: 43
907447 CTTGAAGAAA
907457 AAAAATGAAAAAATGATGAAAAAATGAAAA-GAAAAAAATGGAAAA-AA
1 AAAAATG-AAAAA--ATGAAAAAATGAAAATG--AAAAAT-GAAAAGAA
907504 TGAAAAATG--AAAATG-AAAAATGAAAAATGAAAAATGAAAAATGAA
1 --AAAAATGAAAAAATGAAAAAATG-AAAATGAAAAATG-AAAA-GAA
* *
907549 AAAAAT-AAAAAATG-AAAAATGAAAAATGAAAAAAGAATAAAGAG
1 AAAAATGAAAAAATGAAAAAATG-AAAATGAAAAATG-A-AAAGAA
* *
907593 AAAAAT-AAAAAATGAAATAA--AAAA-GAAAAATAAAAAG
1 AAAAATGAAAAAATGAAAAAATGAAAATGAAAAATGAAAAG
907630 GGGGTTCAAG
Statistics
Matches: 110, Mismatches: 5, Indels: 28
0.77 0.03 0.20
Matches are distributed among these distances:
39 4 0.04
40 1 0.01
41 6 0.05
42 5 0.05
43 23 0.21
44 51 0.46
45 10 0.09
46 3 0.03
49 7 0.06
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (43 bp):
AAAAATGAAAAAATGAAAAAATGAAAATGAAAAATGAAAAGAA
Found at i:907625 original size:37 final size:36
Alignment explanation
Indices: 907498--907627 Score: 115
Period size: 37 Copynumber: 3.5 Consensus size: 36
907488 AAAAAAATGG
907498 AAAAAATGAAAAATGAAAATGAAAAATGAAAAATGAAAAAT
1 AAAAAA-GAAAAAT-AAAA-GAAAAATGAAAAATG--AAAT
* *
907539 GAAAAATGAAAAA-AATA-AAAAATGAAAAATGAAA-
1 -AAAAAAGAAAAATAAAAGAAAAATGAAAAATGAAAT
* *
907573 AATGAAAA-AAGAATAAAGAGAAAAATAAAAAATGAAAT
1 AA--AAAAGAAAAATAAA-AGAAAAATGAAAAATGAAAT
907611 AAAAAAGAAAAATAAAA
1 AAAAAAGAAAAATAAAA
907628 AGGGGGTTCA
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
33 2 0.03
34 4 0.05
35 8 0.11
36 6 0.08
37 38 0.51
38 2 0.03
39 3 0.04
41 6 0.08
42 5 0.07
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (36 bp):
AAAAAAGAAAAATAAAAGAAAAATGAAAAATGAAAT
Found at i:908958 original size:37 final size:37
Alignment explanation
Indices: 908899--908974 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
908889 AAACAATTTA
908899 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA-TC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACTC
*
908935 ATCTATAAGTCTTCACGGAAGAGTAGTGAAGCAAACTC
1 ATCT-TAAGCCTTCACGGAAGAGTAGTGAAGCAAACTC
908973 AT
1 AT
908975 TTTATGAAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
36 4 0.11
37 29 0.78
38 4 0.11
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (37 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACTC
Found at i:909053 original size:55 final size:55
Alignment explanation
Indices: 908985--909738 Score: 815
Period size: 55 Copynumber: 13.7 Consensus size: 55
908975 TTTATGAAGA
* * *
908985 TCGAGTTATATACTCTCTGAAGGAATAGAGAGCTGACCCATTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* * * *
909040 TCGAGTCCTATACTCTCTGATA-GAATAGGGAGCGGAACCATTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGA-AGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* ** *
909095 TCAAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACATGTTTCTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
*
909150 TCGAAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTT-TATGAAGATTGT
1 TCG-AGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGT
** *
909206 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAAACTCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* * * * *
909261 TCGAGTTCTATACTCTCTCAAGAAATATATAGAGCGGATCCGTTT-TATGAAGACTGT
1 TCGAGTTCTATACTCTCTGAAG-GA-ATAGAGAGCGGACCCGTTTGT-TGAAGATTGT
*
909318 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGAGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* * * **
909373 TTGAGTCCTATACTCTCTGATA-GAATAGGGAGCATACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGA-AGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
*
909428 TCGAGTTCTATACTCACTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGT
* * **
909483 TCAAGTTCTATACTCTCTGAAGGAATAGAGAGTGGACCTATTT-TATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGT
* * * *
909538 TCGAGTTCTATACTCTCTGAAGAAATAGAGAGTGAACCCGTTT-TATAAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGT
* * * * ** * * *
909593 TCGAGTTTTATACTCCCTGAACGAATAGGGAGCAAACACGTTTGCTAAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* * * * ** * * *
909648 TCGAG-TCTTATACTCCCTGAACGAATAGGGAACAAACACGTTTGCTGAAGATTTT
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
** * * *
909703 TTTAG-TCTTATTCTCTCTGAATGAATAGGGAGCGGA
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGA
909739 TCCATCATTC
Statistics
Matches: 609, Mismatches: 76, Indels: 28
0.85 0.11 0.04
Matches are distributed among these distances:
54 4 0.01
55 503 0.83
56 58 0.10
57 44 0.07
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
Found at i:912517 original size:20 final size:20
Alignment explanation
Indices: 912483--912535 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
912473 CCATCTTCTC
*
912483 AAATTTTTCTA-TTCCCTCT
1 AAATTTTTCAATTTCCCTCT
912502 AAATTTTTCAATTTCCCTCT
1 AAATTTTTCAATTTCCCTCT
*
912522 AAA-TTCTCAATTTC
1 AAATTTTTCAATTTC
912536 TCTATATTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.26, C:0.25, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATTTTTCAATTTCCCTCT
Found at i:912554 original size:19 final size:17
Alignment explanation
Indices: 912498--912548 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
912488 TTTCTATTCC
*
912498 CTCTAAATTTTTCAATTT
1 CTCTAAA-TTCTCAATTT
912516 CCCTCTAAATTCTCAATTT
1 --CTCTAAATTCTCAATTT
*
912535 CTCTATATTCTCAA
1 CTCTAAATTCTCAA
912549 AATTTCCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 13 0.45
19 9 0.31
20 7 0.24
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.47
Consensus pattern (17 bp):
CTCTAAATTCTCAATTT
Found at i:913193 original size:16 final size:16
Alignment explanation
Indices: 913162--913211 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
913152 CAGATCATTT
*
913162 ACAGGTCATG-TAAAA
1 ACAGGTCAGGTTAAAA
*
913177 ACATGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* *
913193 ATAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
913209 ACA
1 ACA
913212 AGTCGGGTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 8 0.29
16 20 0.71
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:916420 original size:27 final size:26
Alignment explanation
Indices: 916370--916422 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
916360 GTCTGACGCG
*
916370 ACAGTTTCTAGAAGGTCCAATCAGCA
1 ACAGTTTCTAGAAGATCCAATCAGCA
* *
916396 ACAGTTTTCTAGAAGATCTAGTCAGCA
1 ACAG-TTTCTAGAAGATCCAATCAGCA
916423 CCTTCTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (26 bp):
ACAGTTTCTAGAAGATCCAATCAGCA
Found at i:916705 original size:19 final size:19
Alignment explanation
Indices: 916652--916713 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
916642 ATTTTTTTTC
* *
916652 TTTTCTTTTCAAGTATTCAT
1 TTTTATTTT-AAGTTTTCAT
* **
916672 TTTCATTTTTTGTTTTCAT
1 TTTTATTTTAAGTTTTCAT
916691 TTTTATTTTAAGTTTT-AT
1 TTTTATTTTAAGTTTTCAT
916709 TTTTA
1 TTTTA
916714 AACATGCTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
18 7 0.21
19 20 0.59
20 7 0.21
ACGTcount: A:0.18, C:0.08, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTATTTTAAGTTTTCAT
Found at i:926400 original size:15 final size:16
Alignment explanation
Indices: 926380--926417 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
926370 TTATCCTTCA
926380 ATTTTTTATTCTCTTT
1 ATTTTTTATTCTCTTT
926396 ATTTTTTATTCTCTTT
1 ATTTTTTATTCTCTTT
926412 ATTTTT
1 ATTTTT
926418 CTTTAAATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTTTATTCTCTTT
Found at i:927159 original size:20 final size:20
Alignment explanation
Indices: 927131--927196 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
927121 TCCAAATTCG
* *
927131 CAACGCGAATCTGTAAATCA
1 CAACACGAATTTGTAAATCA
927151 CAACACGAATTTGTAAATCA
1 CAACACGAATTTGTAAATCA
*
927171 CAACACGAATTTGTAAATCG
1 CAACACGAATTTGTAAATCA
927191 CAACAC
1 CAACAC
927197 AGAAGTCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.42, C:0.24, G:0.12, T:0.21
Consensus pattern (20 bp):
CAACACGAATTTGTAAATCA
Found at i:927211 original size:20 final size:19
Alignment explanation
Indices: 927188--927366 Score: 191
Period size: 20 Copynumber: 9.0 Consensus size: 19
927178 AATTTGTAAA
*
927188 TCGCAACACAGAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
927208 TCGCAACGCGATAGTCAAAT
1 TCGCAACGCGA-AGTCAAAT
* *
927228 TCGCAACACAAAGTCAAAT
1 TCGCAACGCGAAGTCAAAT
927247 TCGCAACGCGATAGTCAAAT
1 TCGCAACGCGA-AGTCAAAT
927267 TCGCAACGCGATAGTCAAAT
1 TCGCAACGCGA-AGTCAAAT
* * *
927287 TCACAACACAAAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
927307 TCGCAACGCGAATTTGT-AAA-
1 TCGCAACGCGAA---GTCAAAT
*
927327 TCGCAACACAGAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
927347 TCGCAACGCGATAGTCAAAT
1 TCGCAACGCGA-AGTCAAAT
927367 GTTTTTACGC
Statistics
Matches: 136, Mismatches: 13, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
18 2 0.01
19 26 0.19
20 99 0.73
21 7 0.05
22 2 0.01
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.18
Consensus pattern (19 bp):
TCGCAACGCGAAGTCAAAT
Found at i:927331 original size:60 final size:59
Alignment explanation
Indices: 927200--927353 Score: 224
Period size: 60 Copynumber: 2.6 Consensus size: 59
927190 GCAACACAGA
927200 AGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAGTCAAATTCGCAACGCGAT
*
927259 AGTCAAATTCGCAACGCGATAGTCAAATTCACAACACAAAAGTCAAATTCGCAACGCGAATT
1 AGTCAAATTCGCAACGCGATAGTCAAATTCGCAACAC-AAAGTCAAATTCGCAACGCG-A-T
* *
927321 TGT-AAA-TCGCAACACAGA-AGTCAAATTCGCAAC
1 AGTCAAATTCGCAACGC-GATAGTCAAATTCGCAAC
927354 GCGATAGTCA
Statistics
Matches: 87, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
59 36 0.41
60 42 0.48
61 6 0.07
62 3 0.03
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.19
Consensus pattern (59 bp):
AGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAGTCAAATTCGCAACGCGAT
Found at i:930136 original size:21 final size:20
Alignment explanation
Indices: 930112--930179 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
930102 CTTATCATGG
930112 AAGAGTCCCCTCACACCGTTC
1 AAGAGTCCCCTC-CACCGTTC
* * *
930133 AAGAGGCCCCTGTCATCGTTC
1 AAGAGTCCCCT-CCACCGTTC
*
930154 AAGAGGTCCCGC-CCGCCGTTC
1 AAGA-GTCCC-CTCCACCGTTC
930175 AAGAG
1 AAGAG
930180 CCCGATTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
20 1 0.03
21 31 0.84
22 4 0.11
23 1 0.03
ACGTcount: A:0.22, C:0.37, G:0.24, T:0.18
Consensus pattern (20 bp):
AAGAGTCCCCTCCACCGTTC
Found at i:932064 original size:18 final size:18
Alignment explanation
Indices: 932041--932076 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
932031 AAGCCGGTTG
*
932041 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
932059 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
932077 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:934350 original size:24 final size:24
Alignment explanation
Indices: 934316--934369 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
934306 ACATGCAATC
934316 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
934340 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
934364 ATCAAA
1 ATCAAA
934370 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:934512 original size:12 final size:12
Alignment explanation
Indices: 934490--934528 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
934480 GAAAAGGTTG
934490 TGTGTTTTGATAT
1 TGTG-TTTGATAT
934503 TGTGTTTGATAT
1 TGTGTTTGATAT
*
934515 TGTGTTTGGTAT
1 TGTGTTTGATAT
934527 TG
1 TG
934529 GAAATGTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 21 0.84
13 4 0.16
ACGTcount: A:0.13, C:0.00, G:0.28, T:0.59
Consensus pattern (12 bp):
TGTGTTTGATAT
Found at i:935299 original size:19 final size:19
Alignment explanation
Indices: 935277--935366 Score: 85
Period size: 19 Copynumber: 4.6 Consensus size: 19
935267 TAAATTCGTA
935277 TTGCGAATTTGAAATTCAG
1 TTGCGAATTTGAAATTCAG
*
935296 TTGCGAATTTGAAATTCCG
1 TTGCGAATTTGAAATTCAG
* *
935315 CATTGCGAATTTG-ACTTCTGTG
1 --TTGCGAATTTGAAATTC--AG
*
935337 TTGCG-ATTTACAAATTCAG
1 TTGCGAATTT-GAAATTCAG
935356 TTGCGAATTTG
1 TTGCGAATTTG
935367 GCTTAGTATT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
19 28 0.49
20 13 0.23
21 15 0.26
22 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (19 bp):
TTGCGAATTTGAAATTCAG
Found at i:936115 original size:17 final size:17
Alignment explanation
Indices: 936093--936139 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
936083 ACTTGAAAAT
936093 AAATAATTAAAAAGTTC
1 AAATAATTAAAAAGTTC
*
936110 AAATAATTAAAAAGTTG
1 AAATAATTAAAAAGTTC
* *
936127 AAAAAAATAAAAA
1 AAATAATTAAAAA
936140 TAAAAAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.23
Consensus pattern (17 bp):
AAATAATTAAAAAGTTC
Found at i:936341 original size:8 final size:8
Alignment explanation
Indices: 936328--936356 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
936318 AAAAAAGGAA
936328 TGAATTTT
1 TGAATTTT
936336 TGAATTTT
1 TGAATTTT
936344 TGAATTTT
1 TGAATTTT
936352 TGAAT
1 TGAAT
936357 CGAATAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:937223 original size:42 final size:42
Alignment explanation
Indices: 937176--937274 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
937166 GATATACCTA
* *
937176 TCATCATTCAAGAGGCGCCTC-CTATCGTTCAAAAGGCCCCTC
1 TCATCATTCAAGAGGCCCCTCTC-ACCGTTCAAAAGGCCCCTC
* * *
937218 TCATCA-TCGAAGAGTCCCCTCTCACCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAGGCCCCTCTCACCGTTCAAAAGGCCCCTC
*
937260 TCATCGTTCAAGAGG
1 TCATCATTCAAGAGG
937275 TCCCGCCCGC
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
41 2 0.04
42 42 0.89
43 3 0.06
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCTCTCACCGTTCAAAAGGCCCCTC
Found at i:937251 original size:21 final size:21
Alignment explanation
Indices: 937182--937294 Score: 86
Period size: 21 Copynumber: 5.4 Consensus size: 21
937172 CCTATCATCA
* *
937182 TTCAAGAGGCGCCTC-CTATCG
1 TTCAAGAGGCCCCTCTC-ACCG
* *
937203 TTCAAAAGGCCCCTCTCATC-
1 TTCAAGAGGCCCCTCTCACCG
* *
937223 ATCGAAGAGTCCCCTCTCACCG
1 TTC-AAGAGGCCCCTCTCACCG
* *
937245 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCCTCTCACCG
* * * *
937266 TTCAAGAGGTCCCGCCCGCCG
1 TTCAAGAGGCCCCTCTCACCG
937287 TTCAAGAG
1 TTCAAGAG
937295 CCCGATTCAC
Statistics
Matches: 73, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
20 2 0.03
21 68 0.93
22 3 0.04
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCTCACCG
Found at i:939178 original size:18 final size:18
Alignment explanation
Indices: 939155--939190 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
939145 AAGCCGGTTG
*
939155 TGATTGGGATCTTGATTT
1 TGATTGCGATCTTGATTT
*
939173 TGATTGCGATTTTGATTT
1 TGATTGCGATCTTGATTT
939191 CCTTTTGCTT
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:0.17, C:0.06, G:0.25, T:0.53
Consensus pattern (18 bp):
TGATTGCGATCTTGATTT
Found at i:939976 original size:24 final size:24
Alignment explanation
Indices: 939942--939991 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
939932 CCATCACATC
939942 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
939966 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
939990 AT
1 AT
939992 TAAATTTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:940142 original size:12 final size:12
Alignment explanation
Indices: 940121--940154 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
940111 GGTTGTGGGT
*
940121 TTTGAGATTGTG
1 TTTGATATTGTG
940133 TTTGATATTGTG
1 TTTGATATTGTG
*
940145 TTTGGTATTG
1 TTTGATATTG
940155 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:940742 original size:14 final size:15
Alignment explanation
Indices: 940706--940743 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
940696 GAAATCATTG
940706 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
940721 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
940736 AAAAATTA
1 AAAAATTA
940744 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:940900 original size:19 final size:19
Alignment explanation
Indices: 940876--940927 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
940866 TACATAAAAC
940876 ATTTGTGTTACGAAACTAA
1 ATTTGTGTTACGAAACTAA
*
940895 ATTTGTGTTGCGAAACTAA
1 ATTTGTGTTACGAAACTAA
* *
940914 ATTCGTGTTTCGAA
1 ATTTGTGTTACGAA
940928 TTTGAAATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (19 bp):
ATTTGTGTTACGAAACTAA
Found at i:940942 original size:19 final size:19
Alignment explanation
Indices: 940920--940956 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
940910 CTAAATTCGT
*
940920 GTTTCGAATTTGAAATTCA
1 GTTTCGAATTTAAAATTCA
940939 GTTTCGAATTTAAAATTC
1 GTTTCGAATTTAAAATTC
940957 CGCATTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (19 bp):
GTTTCGAATTTAAAATTCA
Found at i:940986 original size:20 final size:19
Alignment explanation
Indices: 940961--941071 Score: 109
Period size: 20 Copynumber: 5.6 Consensus size: 19
940951 AAATTCCGCA
940961 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACT-TCGCG
*
940981 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTC-GCG
941001 TTGCG-ATTT-ACAAATTCGCG
1 TTGCGAATTTGAC---TTCGCG
* * *
941021 TTGCGAAATTGGAGTTCTCG
1 TTGCG-AATTTGACTTCGCG
941041 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGAC-TTCGCG
941061 TTGCGAATTTG
1 TTGCGAATTTG
941072 TTGGTCATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
18 2 0.03
19 12 0.16
20 54 0.72
21 3 0.04
22 3 0.04
23 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (19 bp):
TTGCGAATTTGACTTCGCG
Found at i:940990 original size:60 final size:61
Alignment explanation
Indices: 940915--941052 Score: 142
Period size: 60 Copynumber: 2.3 Consensus size: 61
940905 CGAAACTAAA
* * *
940915 TTCGTGTTTCGAATTTGAAATTCAGT-TT-CGAATTTA-AAATTCCGCATTGCG-AATTTGAC
1 TTCGCGTTGCGAATTTGAAATTCAGTGTTGCG-ATTTACAAATT-CGCATTGCGAAATTGGAC
* * * *
940974 TATCGCGTTGCGAATTTG-ACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGAAATTGGAG
1 T-TCGCGTTGCGAATTTGAAATTCAGTGTTGCGATTTACAAATTCGCATTGCGAAATTGGAC
*
941035 TTCTCGTTGCGAATTTGA
1 TTCGCGTTGCGAATTTGA
941053 CTTTCGCGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
59 7 0.11
60 44 0.68
61 14 0.22
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (61 bp):
TTCGCGTTGCGAATTTGAAATTCAGTGTTGCGATTTACAAATTCGCATTGCGAAATTGGAC
Found at i:941005 original size:40 final size:39
Alignment explanation
Indices: 940961--941071 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 39
940951 AAATTCCGCA
*
940961 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCT-CG
* * *
941001 TTGCG-ATTT-ACAAATTCGCGTTGCGAAATTGGAGTTCTCG
1 TTGCGAATTTGAC-TA-TCGCGTTGCG-AATTTGACTTCTCG
*
941041 TTGCGAATTTGACTTTCGCGTTGCGAATTTG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTG
941072 TTGGTCATTT
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
38 2 0.03
39 10 0.17
40 31 0.53
41 14 0.24
42 2 0.03
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (39 bp):
TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTCG
Found at i:942949 original size:17 final size:17
Alignment explanation
Indices: 942927--942959 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
942917 CTTGAAAAAT
942927 AAATAATTAAAAAGTTC
1 AAATAATTAAAAAGTTC
942944 AAATAATTAAAAAGTT
1 AAATAATTAAAAAGTT
942960 GAAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (17 bp):
AAATAATTAAAAAGTTC
Found at i:943446 original size:31 final size:33
Alignment explanation
Indices: 943405--943499 Score: 99
Period size: 31 Copynumber: 3.0 Consensus size: 33
943395 GATCCTTAAC
*
943405 GTTATCGATTCGTTCAATTTTAGTCCCT-AA-T
1 GTTATTGATTCGTTCAATTTTAGTCCCTCAACT
* * *
943436 GTTATTGATTCATTCGATTTTAGTCTCTCAACT
1 GTTATTGATTCGTTCAATTTTAGTCCCTCAACT
* *
943469 GTTAAATCA-T-GTTCAATTTTAGTCCCTCAAC
1 GTT-ATTGATTCGTTCAATTTTAGTCCCTCAAC
943500 AATGTTAAGA
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
31 24 0.46
32 20 0.38
33 5 0.10
34 3 0.06
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (33 bp):
GTTATTGATTCGTTCAATTTTAGTCCCTCAACT
Found at i:945997 original size:14 final size:14
Alignment explanation
Indices: 945978--946006 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
945968 CTTAATTCAA
945978 TATTTTACTTGCTT
1 TATTTTACTTGCTT
945992 TATTTTACTTGCTT
1 TATTTTACTTGCTT
946006 T
1 T
946007 TTAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TATTTTACTTGCTT
Found at i:946557 original size:2 final size:2
Alignment explanation
Indices: 946550--946583 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
946540 TTTTATACAC
946550 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
946584 GTTCGCAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:946657 original size:36 final size:37
Alignment explanation
Indices: 946596--946749 Score: 165
Period size: 37 Copynumber: 4.1 Consensus size: 37
946586 TCGCAAACGG
*
946596 TTTTTGAAAATACGTATATAATATATAATTTTTAAAACA
1 TTTTTG-AAATAC-TATATAATATATAGTTTTTAAAACA
946635 TTTTTGAAA-ACTATATAATATATAGTTTTTAAAACA
1 TTTTTGAAATACTATATAATATATAGTTTTTAAAACA
* *
946671 TTTTAGAATATA-TATATAATATATAGTTTTTAAAAAA
1 TTTTTGAA-ATACTATATAATATATAGTTTTTAAAACA
* *
946708 TATTTTGGAAAT-TTATAT-ATGATAT-GTTTTTGAAAATA
1 T-TTTT-GAAATACTATATAAT-ATATAGTTTTT-AAAACA
946746 TTTT
1 TTTT
946750 ATTATTATTT
Statistics
Matches: 103, Mismatches: 5, Indels: 16
0.83 0.04 0.13
Matches are distributed among these distances:
36 31 0.30
37 39 0.38
38 24 0.23
39 9 0.09
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (37 bp):
TTTTTGAAATACTATATAATATATAGTTTTTAAAACA
Found at i:946696 original size:37 final size:36
Alignment explanation
Indices: 946610--946705 Score: 149
Period size: 36 Copynumber: 2.6 Consensus size: 36
946600 TGAAAATACG
* *
946610 TATATAATATATAATTTTTAAAACATTTTTGAAAAC
1 TATATAATATATAGTTTTTAAAACATTTTAGAAAAC
946646 TATATAATATATAGTTTTTAAAACATTTTAGAATATA-
1 TATATAATATATAGTTTTTAAAACATTTTAGAA-A-AC
946683 TATATAATATATAGTTTTTAAAA
1 TATATAATATATAGTTTTTAAAA
946706 AATATTTTGG
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
36 31 0.55
37 24 0.43
38 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTAGAAAAC
Found at i:946725 original size:75 final size:73
Alignment explanation
Indices: 946610--946750 Score: 187
Period size: 73 Copynumber: 1.9 Consensus size: 73
946600 TGAAAATACG
*
946610 TATATAATATATAATTTTTAAAACATTTTTGAAAACTATATAAT-ATATAGTTTTT-AAAACATT
1 TATATAATATATAATTTTTAAAAAATTTTTGAAAACTATAT-ATGATAT-GTTTTTGAAAACATT
946673 TTAGAATATA
64 TTAGAATATA
* ** *
946683 TATATAATATATAGTTTTTAAAAAATATTTTGGAAATTTATATATGATATGTTTTTGAAAATATT
1 TATATAATATATAATTTTTAAAAAAT-TTTT-GAAAACTATATATGATATGTTTTTGAAAACATT
946748 TTA
64 TTA
946751 TTATTATTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
73 24 0.41
74 12 0.20
75 23 0.39
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (73 bp):
TATATAATATATAATTTTTAAAAAATTTTTGAAAACTATATATGATATGTTTTTGAAAACATTTT
AGAATATA
Found at i:946737 original size:37 final size:36
Alignment explanation
Indices: 946610--946749 Score: 146
Period size: 36 Copynumber: 3.8 Consensus size: 36
946600 TGAAAATACG
*
946610 TATATAATATATAATTTTTAAAACAT-TTTTGAAA-A
1 TATATAATATATAGTTTTTAAAA-ATATTTTGAAATA
*
946645 CTATATAATATATAGTTTTTAAAACAT-TTTAGAATATA
1 -TATATAATATATAGTTTTTAAAA-ATATTTTGAA-ATA
*
946683 TATATAATATATAGTTTTTAAAAAATATTTTGGAAATT
1 TATATAATATATAGTTTTT-AAAAATATTTT-GAAATA
*
946721 TATAT-ATGATAT-GTTTTTGAAAATATTTT
1 TATATAAT-ATATAGTTTTTAAAAATATTTT
946750 ATTATTATTT
Statistics
Matches: 93, Mismatches: 5, Indels: 12
0.85 0.05 0.11
Matches are distributed among these distances:
36 41 0.44
37 30 0.32
38 19 0.20
39 3 0.03
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAAATATTTTGAAATA
Found at i:946752 original size:5 final size:5
Alignment explanation
Indices: 946744--946777 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
946734 TTTTTGAAAA
946744 TATTT TATTAT TA-TT TATTT TATTT TATTT TATT
1 TATTT TATT-T TATTT TATTT TATTT TATTT TATT
946778 ATTTATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 3 0.11
5 21 0.78
6 3 0.11
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:946764 original size:15 final size:14
Alignment explanation
Indices: 946744--946789 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 14
946734 TTTTTGAAAA
946744 TATTTTATTATTATT
1 TATTTTATT-TTATT
946759 TATTTTATTTTATT
1 TATTTTATTTTATT
*
946773 T-TATTA-TTTATT
1 TATTTTATTTTATT
946785 TATTT
1 TATTT
946790 ATTATGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 7 0.25
13 6 0.21
14 6 0.21
15 9 0.32
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTTATTTTATT
Found at i:946779 original size:22 final size:19
Alignment explanation
Indices: 946744--946794 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
946734 TTTTTGAAAA
946744 TATTTTATTATTATTTATTT
1 TATTTTATTATTATTTA-TT
946764 TATTTTATTTTATTATTTATT
1 TATTTTA--TTATTATTTATT
946785 TA-TTTATTAT
1 TATTTTATTAT
946795 GTTTTTTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.14
20 11 0.38
21 4 0.14
22 10 0.34
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (19 bp):
TATTTTATTATTATTTATT
Found at i:946790 original size:15 final size:15
Alignment explanation
Indices: 946747--946794 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 15
946737 TTGAAAATAT
946747 TTTATTA-TTATTTA
1 TTTATTATTTATTTA
*
946761 -TT-TTATTT-TAT-
1 TTTATTATTTATTTA
946772 TTTATTATTTATTTA
1 TTTATTATTTATTTA
946787 TTTATTAT
1 TTTATTAT
946795 GTTTTTTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
12 7 0.26
13 10 0.37
14 2 0.07
15 8 0.30
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTATTATTTATTTA
Found at i:946799 original size:25 final size:25
Alignment explanation
Indices: 946743--946799 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
946733 GTTTTTGAAA
946743 ATATTTTATTATTATTTATTTTATT
1 ATATTTTATTATTATTTATTTTATT
*
946768 TTATTTTATTATTTATTTA-TTTATT
1 ATATTTTATTA-TTATTTATTTTATT
*
946793 ATGTTTT
1 ATATTTT
946800 TTGCAGGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 21 0.75
26 7 0.25
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (25 bp):
ATATTTTATTATTATTTATTTTATT
Found at i:947841 original size:13 final size:13
Alignment explanation
Indices: 947823--947847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
947813 TTATTATTAA
947823 TATTTTTATTTTT
1 TATTTTTATTTTT
947836 TATTTTTATTTT
1 TATTTTTATTTT
947848 AGTATTATTA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TATTTTTATTTTT
Found at i:947909 original size:7 final size:8
Alignment explanation
Indices: 947888--947929 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
947878 AAAATTAATT
947888 TATTTTTC
1 TATTTTTC
947896 TATTTTTC
1 TATTTTTC
947904 TATTTTTTC
1 TA-TTTTTC
*
947913 TATTTTTT
1 TATTTTTC
*
947921 TCTTTTTC
1 TATTTTTC
947929 T
1 T
947930 TCTCTTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
8 22 0.73
9 8 0.27
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (8 bp):
TATTTTTC
Done.