Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, 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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 5 of 121
Found at i:405107 original size:15 final size:15
Alignment explanation
Indices: 405080--405121 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
405070 TTAACCTAAA
405080 TTCTTTTTT-TTTCT
1 TTCTTTTTTCTTTCT
*
405094 TTGTTTTTTCTTTCT
1 TTCTTTTTTCTTTCT
*
405109 TTCTATTTTCTTT
1 TTCTTTTTTCTTT
405122 TAATTCTTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (15 bp):
TTCTTTTTTCTTTCT
Found at i:405540 original size:13 final size:13
Alignment explanation
Indices: 405521--405551 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
405511 TTGTTTAATC
405521 GAAAATAATTTTT
1 GAAAATAATTTTT
*
405534 TAAAATAATTTTT
1 GAAAATAATTTTT
405547 GAAAA
1 GAAAA
405552 ATAACCTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (13 bp):
GAAAATAATTTTT
Found at i:405552 original size:14 final size:13
Alignment explanation
Indices: 405522--405555 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
405512 TGTTTAATCG
*
405522 AAAATAATTTTTT
1 AAAATAATTTTTA
405535 AAAATAATTTTTGA
1 AAAATAATTTTT-A
405549 AAAATAA
1 AAAATAA
405556 CCTTATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
AAAATAATTTTTA
Found at i:406070 original size:20 final size:20
Alignment explanation
Indices: 406019--406096 Score: 66
Period size: 20 Copynumber: 3.9 Consensus size: 20
406009 CTATTCAAAT
* * *
406019 AATACTAAAATAACTATTAA
1 AATACTAAAATTATTAATAA
* * *
406039 AATATTTAAAATTATTTATTA
1 AATA-CTAAAATTATTAATAA
* *
406060 ATTACTAAAATAATTAATAA
1 AATACTAAAATTATTAATAA
*
406080 AATACTAATATTATTAA
1 AATACTAAAATTATTAA
406097 AAATATAATT
Statistics
Matches: 43, Mismatches: 14, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
20 30 0.70
21 13 0.30
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
AATACTAAAATTATTAATAA
Found at i:406115 original size:22 final size:21
Alignment explanation
Indices: 406072--406132 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
406062 TACTAAAATA
* *
406072 ATTAATAAAATACTAATA-TT
1 ATTATTAAAATATTAATATTT
406092 ATTA--AAAATA-TAATTATTT
1 ATTATTAAAATATTAA-TATTT
406111 ATTATTAAAATATTAATATTT
1 ATTATTAAAATATTAATATTT
406132 A
1 A
406133 ATAATATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.08
18 8 0.22
19 6 0.17
20 4 0.11
21 12 0.33
22 3 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTATTAAAATATTAATATTT
Found at i:407923 original size:26 final size:26
Alignment explanation
Indices: 407886--407935 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
407876 CAAATAAAAT
407886 TTTTAATAAATTATTTAAATTGAATA
1 TTTTAATAAATTATTTAAATTGAATA
*
407912 TTTTAGAT-AATTATTTAGATTGAA
1 TTTTA-ATAAATTATTTAAATTGAA
407936 ATCAAAATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (26 bp):
TTTTAATAAATTATTTAAATTGAATA
Found at i:412720 original size:48 final size:48
Alignment explanation
Indices: 412654--412747 Score: 188
Period size: 48 Copynumber: 2.0 Consensus size: 48
412644 TTTTTGAGGA
412654 TAGTTAGAAGGCAGTCTCCCGGAATTTATAGCAAAAATGCTTATTTTT
1 TAGTTAGAAGGCAGTCTCCCGGAATTTATAGCAAAAATGCTTATTTTT
412702 TAGTTAGAAGGCAGTCTCCCGGAATTTATAGCAAAAATGCTTATTT
1 TAGTTAGAAGGCAGTCTCCCGGAATTTATAGCAAAAATGCTTATTT
412748 CATTTATATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (48 bp):
TAGTTAGAAGGCAGTCTCCCGGAATTTATAGCAAAAATGCTTATTTTT
Found at i:414318 original size:22 final size:22
Alignment explanation
Indices: 414292--414335 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
414282 TCTCTTGTCC
414292 CTTGTCCCTTTGGT-ATGTGCCT
1 CTTGTCCCTTT-GTAATGTGCCT
414314 CTTGTCCCTTTGTAATGTGCCT
1 CTTGTCCCTTTGTAATGTGCCT
414336 TATAGTCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.07, C:0.27, G:0.20, T:0.45
Consensus pattern (22 bp):
CTTGTCCCTTTGTAATGTGCCT
Found at i:418369 original size:18 final size:18
Alignment explanation
Indices: 418346--418394 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
418336 CAACTGAGTT
418346 TGAATAGTGCTAATTGGA
1 TGAATAGTGCTAATTGGA
418364 TGAATAGTGCTAATTGGA
1 TGAATAGTGCTAATTGGA
418382 TGAATAGTGCTAA
1 TGAATAGTGCTAA
418395 ATTCATGGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.33
Consensus pattern (18 bp):
TGAATAGTGCTAATTGGA
Found at i:418588 original size:253 final size:253
Alignment explanation
Indices: 418140--418638 Score: 989
Period size: 253 Copynumber: 2.0 Consensus size: 253
418130 TTTTGTTCTC
418140 AAATTCATGGTGATTTATGTGTTTTTGATACAAATTATGGCATGGATTTTGTAAATCTATGTGTT
1 AAATTCATGGTGATTTATGTGTTTTTGATACAAATTATGGCATGGATTTTGTAAATCTATGTGTT
418205 AATTACATGTTTAAAGGTTAATTACAAAAGAAAGCATCAAATTGGTTTTTAAATCGAAATATATC
66 AATTACATGTTTAAAGGTTAATTACAAAAGAAAGCATCAAATTGGTTTTTAAATCGAAATATATC
418270 CAAAACAGGTCAAATTTGACCCATTTAGGTAAGTTTGATCCAGTTGAAAGTAAGAGACAATAACC
131 CAAAACAGGTCAAATTTGACCCATTTAGGTAAGTTTGATCCAGTTGAAAGTAAGAGACAATAACC
418335 ACAACTGAGTTTGAATAGTGCTAATTGGATGAATAGTGCTAATTGGATGAATAGTGCT
196 ACAACTGAGTTTGAATAGTGCTAATTGGATGAATAGTGCTAATTGGATGAATAGTGCT
*
418393 AAATTCATGGTGATTTATGTGTTTTTGATGCAAATTATGGCATGGATTTTGTAAATCTATGTGTT
1 AAATTCATGGTGATTTATGTGTTTTTGATACAAATTATGGCATGGATTTTGTAAATCTATGTGTT
418458 AATTACATGTTTAAAGGTTAATTACAAAAGAAAGCATCAAATTGGTTTTTAAATCGAAATATATC
66 AATTACATGTTTAAAGGTTAATTACAAAAGAAAGCATCAAATTGGTTTTTAAATCGAAATATATC
418523 CAAAACAGGTCAAATTTGACCCATTTAGGTAAGTTTGATCCAGTTGAAAGTAAGAGACAATAACC
131 CAAAACAGGTCAAATTTGACCCATTTAGGTAAGTTTGATCCAGTTGAAAGTAAGAGACAATAACC
418588 ACAACTGAGTTTGAATAGTGCTAATTGGATGAATAGTGCTAATTGGATGAA
196 ACAACTGAGTTTGAATAGTGCTAATTGGATGAATAGTGCTAATTGGATGAA
418639 ATATTGAGTA
Statistics
Matches: 245, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
253 245 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (253 bp):
AAATTCATGGTGATTTATGTGTTTTTGATACAAATTATGGCATGGATTTTGTAAATCTATGTGTT
AATTACATGTTTAAAGGTTAATTACAAAAGAAAGCATCAAATTGGTTTTTAAATCGAAATATATC
CAAAACAGGTCAAATTTGACCCATTTAGGTAAGTTTGATCCAGTTGAAAGTAAGAGACAATAACC
ACAACTGAGTTTGAATAGTGCTAATTGGATGAATAGTGCTAATTGGATGAATAGTGCT
Found at i:418622 original size:18 final size:18
Alignment explanation
Indices: 418599--418638 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
418589 CAACTGAGTT
418599 TGAATAGTGCTAATTGGA
1 TGAATAGTGCTAATTGGA
418617 TGAATAGTGCTAATTGGA
1 TGAATAGTGCTAATTGGA
418635 TGAA
1 TGAA
418639 ATATTGAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.33
Consensus pattern (18 bp):
TGAATAGTGCTAATTGGA
Found at i:418822 original size:32 final size:30
Alignment explanation
Indices: 418786--418862 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 30
418776 ATAAAATATT
*
418786 TATTATATAATATTTATGCATGATTAAATAAG
1 TATTATAT-AT-TTTATGCACGATTAAATAAG
418818 TA-T-TATATTTTATGCACGATTAAATAAG
1 TATTATATATTTTATGCACGATTAAATAAG
418846 TA-T-TATATTTTATGCAC
1 TATTATATATTTTATGCAC
418863 ATGAATTTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
28 36 0.82
29 2 0.05
30 3 0.07
31 1 0.02
32 2 0.05
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.45
Consensus pattern (30 bp):
TATTATATATTTTATGCACGATTAAATAAG
Found at i:418831 original size:28 final size:28
Alignment explanation
Indices: 418798--418862 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
418788 TTATATAATA
*
418798 TTTATGCATGATTAAATAAGTATTATAT
1 TTTATGCACGATTAAATAAGTATTATAT
418826 TTTATGCACGATTAAATAAGTATTATAT
1 TTTATGCACGATTAAATAAGTATTATAT
418854 TTTATGCAC
1 TTTATGCAC
418863 ATGAATTTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (28 bp):
TTTATGCACGATTAAATAAGTATTATAT
Found at i:420467 original size:2 final size:2
Alignment explanation
Indices: 420460--420485 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
420450 ACATAATGTG
420460 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
420486 TTAAGAAACT
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:427159 original size:26 final size:26
Alignment explanation
Indices: 427123--427177 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
427113 CTTAAGCAGT
427123 TATAGGTATCCAAATGATCATTTAAC
1 TATAGGTATCCAAATGATCATTTAAC
427149 TATAGGTATCCAAATGATCATTTAAC
1 TATAGGTATCCAAATGATCATTTAAC
427175 TAT
1 TAT
427178 CTCTAACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (26 bp):
TATAGGTATCCAAATGATCATTTAAC
Found at i:427297 original size:30 final size:29
Alignment explanation
Indices: 427259--427319 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
427249 AAAGGGATAG
*
427259 TTTTGGGAAAAAAGCTTATCC-ATAAGTTT
1 TTTTGGG-AAAAAGCTTATCCAATAAGCTT
* *
427288 TTTTAGGGAACAAGCTTTTCCAATAAGCTT
1 TTTT-GGGAAAAAGCTTATCCAATAAGCTT
427318 TT
1 TT
427320 GAGAAGGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.39
Consensus pattern (29 bp):
TTTTGGGAAAAAGCTTATCCAATAAGCTT
Found at i:433444 original size:22 final size:22
Alignment explanation
Indices: 433413--433459 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
433403 TTTTCTATTC
* *
433413 TTAATTCTAGAGATATAAATAT
1 TTAATACTAGAGATACAAATAT
*
433435 TTAATACTAGTGATACAAATAT
1 TTAATACTAGAGATACAAATAT
433457 TTA
1 TTA
433460 CAGATTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (22 bp):
TTAATACTAGAGATACAAATAT
Found at i:436404 original size:20 final size:21
Alignment explanation
Indices: 436379--436424 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
436369 AATTGTAAAA
*
436379 ATTCACAAAT-AGTTTCAAAG
1 ATTCACAAATAAATTTCAAAG
436399 ATTCACAAATGAAATTTCAAAG
1 ATTCACAAAT-AAATTTCAAAG
436421 ATTC
1 ATTC
436425 TTAAGGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.43
22 13 0.57
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (21 bp):
ATTCACAAATAAATTTCAAAG
Found at i:436544 original size:19 final size:18
Alignment explanation
Indices: 436512--436553 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
436502 AGGTTTTGAG
*
436512 ATTTGCACAAATTTTCAAA
1 ATTTGCACAAA-TTTAAAA
436531 ATTTGCA-AACATTTAAAA
1 ATTTGCACAA-ATTTAAAA
436549 ATTTG
1 ATTTG
436554 AAAGACTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (18 bp):
ATTTGCACAAATTTAAAA
Found at i:436576 original size:18 final size:18
Alignment explanation
Indices: 436528--436576 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
436518 ACAAATTTTC
*
436528 AAAATTTGCAA-ACATTTA
1 AAAATTTGAAAGAC-TTTA
436546 AAAATTTGAAAGACTTTA
1 AAAATTTGAAAGACTTTA
* *
436564 AAGATTTGTAAGA
1 AAAATTTGAAAGA
436577 ATTCAAAGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (18 bp):
AAAATTTGAAAGACTTTA
Found at i:436700 original size:18 final size:17
Alignment explanation
Indices: 436679--436806 Score: 78
Period size: 17 Copynumber: 7.4 Consensus size: 17
436669 TAGATTGGTG
436679 AGAACTTAAAGATTCACA
1 AGAA-TTAAAGATTCACA
*
436697 AGAATTCAAAGATTCATA
1 AGAATT-AAAGATTCACA
* ** *
436715 AGAATTCAAAGGTTTGCG
1 AGAATT-AAAGATTCACA
* * **
436733 AGACTTTCAA-ATTTGCA
1 AGA-ATTAAAGATTCACA
* **
436750 AGACTTTTAGATTCACA
1 AGAATTAAAGATTCACA
*
436767 AGAATTGAAGATTCACA
1 AGAATTAAAGATTCACA
*
436784 AGAATGAAAGATTCACA
1 AGAATTAAAGATTCACA
*
436801 ATAATT
1 AGAATT
436807 CAAAACTTTG
Statistics
Matches: 85, Mismatches: 22, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
16 3 0.04
17 48 0.56
18 32 0.38
19 2 0.02
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (17 bp):
AGAATTAAAGATTCACA
Found at i:437070 original size:23 final size:22
Alignment explanation
Indices: 437044--437099 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
437034 ATTCAAATCC
437044 AAATTTAAAAAATTCACATTAAA
1 AAATTTAAAAAATTCACA-TAAA
* * *
437067 AAATTTTAGAGATTCACATAAA
1 AAATTTAAAAAATTCACATAAA
* *
437089 AGATTTCAAAA
1 AAATTTAAAAA
437100 CTCATATCCA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.30
Consensus pattern (22 bp):
AAATTTAAAAAATTCACATAAA
Found at i:438811 original size:45 final size:45
Alignment explanation
Indices: 438686--438813 Score: 170
Period size: 45 Copynumber: 2.8 Consensus size: 45
438676 AAGGCTAACA
* *
438686 AAAAATTTTAGAGATTCACATCCAAAATTCAAAGATTCTCATTTG
1 AAAAATTTTAGAGATTCACATCCAAAATTTAAAAATTCTCATTTG
* *
438731 AAAAA-TTTAG-GGTTTACATTCCAAAATTTAAAAAATTCTCATTTG
1 AAAAATTTTAGAGATTCACA-TCCAAAATTT-AAAAATTCTCATTTG
* *
438776 AAAAATTTTAGAGATTCACATCTAAAATTTGAAAATTC
1 AAAAATTTTAGAGATTCACATCCAAAATTTAAAAATTC
438814 AAGGATTTGC
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
43 6 0.08
44 14 0.20
45 31 0.44
46 14 0.20
47 6 0.08
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (45 bp):
AAAAATTTTAGAGATTCACATCCAAAATTTAAAAATTCTCATTTG
Found at i:449203 original size:14 final size:14
Alignment explanation
Indices: 449184--449225 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
449174 GATTTTATTT
*
449184 TATTTTAATTTTTC
1 TATTTTAATTTTTA
449198 TATTTT-ATTTTTA
1 TATTTTAATTTTTA
*
449211 GATTTTTAATTTTTA
1 TA-TTTTAATTTTTA
449226 CTTATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 7 0.29
14 10 0.42
15 7 0.29
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (14 bp):
TATTTTAATTTTTA
Found at i:449233 original size:28 final size:26
Alignment explanation
Indices: 449181--449261 Score: 78
Period size: 25 Copynumber: 3.1 Consensus size: 26
449171 TTTGATTTTA
*
449181 TTTTA-TTTTAATTTTT-CTATTTTAT
1 TTTTATTTTTAATTTTTACT-TATTAT
449206 TTTTAGATTTTTAATTTTTACTTATTAT
1 TTTT--ATTTTTAATTTTTACTTATTAT
* * *
449234 TATTATTTTT-ATCTTTAATTATTAT
1 TTTTATTTTTAATTTTTACTTATTAT
449259 TTT
1 TTT
449262 ACTTATGACT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
25 19 0.40
26 6 0.13
27 1 0.02
28 19 0.40
29 2 0.04
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (26 bp):
TTTTATTTTTAATTTTTACTTATTAT
Found at i:449243 original size:19 final size:19
Alignment explanation
Indices: 449219--449267 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
449209 TAGATTTTTA
*
449219 ATTTTTACTTATTATTATT
1 ATTTTTACTTATAATTATT
449238 ATTTTTATCTT-TAATTATT
1 ATTTTTA-CTTATAATTATT
449257 A-TTTTACTTAT
1 ATTTTTACTTAT
449268 GACTTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 3 0.11
18 6 0.22
19 15 0.56
20 3 0.11
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTTACTTATAATTATT
Found at i:463939 original size:334 final size:332
Alignment explanation
Indices: 463319--464603 Score: 1662
Period size: 334 Copynumber: 3.9 Consensus size: 332
463309 ACAAATTATT
** *
463319 GAAGGCGGCTTATAATAAAAGATGCCTTTAATAATCCAAGAAAA-TTTTTT-GAAAAATTATTAA
1 GAAGGCGTTTTATAATAAAAGATACCTTTAATAATCCAA-AAAATTTTTTTAGAAAAATTATTAA
* * ** * **
463382 AGGCGTTGTTATCTGAAAATAGCCTTTAGTAATTATATACAAACTATGATAGGAATTATTAAAAA
65 AGGCATTGTTTTCT-AAAACCGCCTTCAGTAATTATATACAAACTATGATAGGAATTATTAAAGG
** * * *
463447 TGTCTATCTTAAATATACGCCTTCAATAACAATGTTACAATTTGTGTAACGGTATATAAAAGGCA
129 CATCTATCTTAAATATACGCCTTCAATAACAGTGTTACAATTTGTGTAGCGGTATATAGAAGGCA
* *
463512 TTTTACAGTAGAAGAAGCCTTTAATAATTCCCAAAAATATTTAGTGGGAAAATTTTGAAGGCGTT
194 TTTTACAGTAGAAGACGCCTTTAATAATT-CCTAAAATATTTAGTGGGAAAATTTTGAAGGCGTT
* * * * *
463577 TTTTATTAACAAACAACTTCAATAATTGAAGGCGCCTTTTCTAATAAATACTTTCCATTACCATT
258 TGTTATTAACAAACACCTTCAGTAATTGAAGGCGCCTTTTCTAATAAATGCCTTCCATTACCATT
*
463642 GTGGTATGTC
323 GTGGTATATC
* * **
463652 GAATGCGTTTTATAATAAAAGATACCTTTAATAATTCAAAAAATTTTTTTTAGGGAAATTATTAA
1 GAAGGCGTTTTATAATAAAAGATACCTTTAATAATCCAAAAAA-TTTTTTTAGAAAAATTATTAA
* * * * *
463717 AGGCATAGTTTTTTGAAACCGCCTTCAATAATTATATACAAACTATGATAGAAATTATTAAAGGC
65 AGGCATTGTTTTCTAAAACCGCCTTCAGTAATTATATACAAACTATGATAGGAATTATTAAAGGC
* * * * * * *
463782 ATTTATCTTAAATATACGCCTTCAATAACGGTGTTATAATTTTTGTGGTGGTATATAGAAGGTAT
130 ATCTATCTTAAATATACGCCTTCAATAACAGTGTTACAATTTGTGTAGCGGTATATAGAAGGCAT
* ** * *
463847 TTTACAGTAGAAGACGCCTTTAATAATTCTTAAAATATTTAGTGAAAAAAATTTGAAGGCATTTT
195 TTTACAGTAGAAGACGCCTTTAATAATTCCTAAAATATTTAGTGGGAAAATTTTGAAGGC-GTTT
* * * * **
463912 GTTATTAACAAACGCCTTTAGTAATTGAAGGTGCCTTTTCTAATAAACGCCTTCCATTACCATCA
259 GTTATTAACAAACACCTTCAGTAATTGAAGGCGCCTTTTCTAATAAATGCCTTCCATTACCATTG
*
463977 TAGTATATC
324 TGGTATATC
* * * * * *
463986 GAAGGCATTTTATAACAAAAGACACCTTTAATAATCTGAAAAAATTTTATTAGGAAAATTATTAA
1 GAAGGCGTTTTATAATAAAAGATACCTTTAATAATC-CAAAAAATTTTTTTAGAAAAATTATTAA
* * *
464051 AGGCATTGTTTTCTAAAACCACATTCAGTAATTATATACAAACTATGATATGAATTATTAAAGGC
65 AGGCATTGTTTTCTAAAACCGCCTTCAGTAATTATATACAAACTATGATAGGAATTATTAAAGGC
* * * * * *
464116 ATCTATCTTAAATATATGCCTTCAATAACAGTGTTACAATTTGTGTGGTGATATATAGAAAGTAT
130 ATCTATCTTAAATATACGCCTTCAATAACAGTGTTACAATTTGTGTAGCGGTATATAGAAGGCAT
* * *
464181 TTTACAGTAGAAGACACCTTTACTAATTCCCAAAATATTTAGTGGGAAAATTTTGAAGGCGTTTG
195 TTTACAGTAGAAGACGCCTTTAATAATTCCTAAAATATTTAGTGGGAAAATTTTGAAGGCGTTTG
* * *
464246 TTATAAACAAACGCTTTCAGTAATTGAAGGCGCCTTTTCTAATAAATGCCTTCCATTACCATTGT
260 TTATTAACAAACACCTTCAGTAATTGAAGGCGCCTTTTCTAATAAATGCCTTCCATTACCATTGT
464311 GGTATATC
325 GGTATATC
* *
464319 GAAGGTGTTTTATAATAAAA-A-ACGCTTTTAATAATCCAAAAAAATTATTTTAGAAAAATTATT
1 GAAGGCGTTTTATAATAAAAGATAC-C-TTTAATAATCC-AAAAAATTTTTTTAGAAAAATTATT
* * *
464382 AAAGGCGTTGTTTTCTAAAACTGCCTTCAGTAATTATATACAAACTATTATAGGAATTATTAAAG
63 AAAGGCATTGTTTTCTAAAACCGCCTTCAGTAATTATATACAAACTATGATAGGAATTATTAAAG
* * * *
464447 GCATCTATCTTAAATATACGCTTTCAATAACAGTATTACAATTTATGTAGCAGTATATAGAAGGC
128 GCATCTATCTTAAATATACGCCTTCAATAACAGTGTTACAATTTGTGTAGCGGTATATAGAAGGC
* * * *
464512 ATTTTACAATAGAAGATGCCTTTAAGAATT-TTCAAAATATTTAGTGGGAAAATTTTGAAAGGCG
193 ATTTTACAGTAGAAGACGCCTTTAATAATTCCT-AAAATATTTAGTGGGAAAATTTTG-AAGGCG
*
464576 TTTGTTACTAACAAACACCTTCAGTAAT
256 TTTGTTATTAACAAACACCTTCAGTAAT
464604 AGATTACTAA
Statistics
Matches: 818, Mismatches: 124, Indels: 19
0.85 0.13 0.02
Matches are distributed among these distances:
331 2 0.00
332 6 0.01
333 342 0.42
334 441 0.54
335 27 0.03
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (332 bp):
GAAGGCGTTTTATAATAAAAGATACCTTTAATAATCCAAAAAATTTTTTTAGAAAAATTATTAAA
GGCATTGTTTTCTAAAACCGCCTTCAGTAATTATATACAAACTATGATAGGAATTATTAAAGGCA
TCTATCTTAAATATACGCCTTCAATAACAGTGTTACAATTTGTGTAGCGGTATATAGAAGGCATT
TTACAGTAGAAGACGCCTTTAATAATTCCTAAAATATTTAGTGGGAAAATTTTGAAGGCGTTTGT
TATTAACAAACACCTTCAGTAATTGAAGGCGCCTTTTCTAATAAATGCCTTCCATTACCATTGTG
GTATATC
Found at i:469382 original size:42 final size:41
Alignment explanation
Indices: 469335--469414 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 41
469325 ATACATTATA
*
469335 TTTTGATTTAATTAAATCG-ATATGTTCTTTATATATCTTAGG
1 TTTTGATTT-ATTAAATCGAAAATGTT-TTTATATATCTTAGG
* *
469377 TTTTGATTTCTTAAATTGAAAATGTTTTTATATATCTT
1 TTTTGATTTATTAAATCGAAAATGTTTTTATATATCTT
469415 CTGAACTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 19 0.56
42 15 0.44
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (41 bp):
TTTTGATTTATTAAATCGAAAATGTTTTTATATATCTTAGG
Found at i:475672 original size:35 final size:35
Alignment explanation
Indices: 475606--475681 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
475596 TGGCCATTAA
*
475606 ATAAAAACAAAATTAAATATAAAATATATAAAAAT
1 ATAAAAACAAAAATAAATATAAAATATATAAAAAT
*
475641 -TAAAAACTAAAAAT-AATAATAAAAT-TAATAAATAT
1 ATAAAAAC-AAAAATAAAT-ATAAAATAT-ATAAAAAT
475676 ATAAAA
1 ATAAAA
475682 TAATGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
34 11 0.31
35 19 0.54
36 5 0.14
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (35 bp):
ATAAAAACAAAAATAAATATAAAATATATAAAAAT
Found at i:475683 original size:25 final size:26
Alignment explanation
Indices: 475622--475691 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 26
475612 ACAAAATTAA
475622 ATATAAAATATATAAAAATTAAAAACT
1 ATATAAAATA-ATAAAAATTAAAAACT
*
475649 A-AAAATAATAAT-AAAATTAATAAA-T
1 ATATAA-AATAATAAAAATTAA-AAACT
475674 ATATAAAATAATGAAAAA
1 ATATAAAATAAT-AAAAA
475692 AAAAAGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
25 16 0.44
26 11 0.31
27 9 0.25
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (26 bp):
ATATAAAATAATAAAAATTAAAAACT
Found at i:476469 original size:3 final size:3
Alignment explanation
Indices: 476430--476458 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
476420 AACCAAAAAC
476430 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
476459 CAAGAGAAGA
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:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:477069 original size:2 final size:2
Alignment explanation
Indices: 477062--477096 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
477052 CAAACCGGTT
*
477062 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
477097 TATTTTGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:477367 original size:3 final size:3
Alignment explanation
Indices: 477359--477404 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
477349 TTAGCAACAA
477359 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
477405 GTTATTATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:481621 original size:27 final size:24
Alignment explanation
Indices: 481585--481644 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 24
481575 TTGGGACAAA
*
481585 TTTAGAAAAATTTTCTCATCTAAGAAT
1 TTTA-AAAAATTTAC-CATCTAA-AAT
*
481612 TTTATAAAAATTTACCATTTAAAAT
1 TTTA-AAAAATTTACCATCTAAAAT
481637 TTTAAAAA
1 TTTAAAAA
481645 TTTCATTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.13
25 7 0.23
26 6 0.20
27 13 0.43
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (24 bp):
TTTAAAAAATTTACCATCTAAAAT
Found at i:481705 original size:190 final size:188
Alignment explanation
Indices: 481340--481691 Score: 416
Period size: 190 Copynumber: 1.9 Consensus size: 188
481330 TTTGGAAAAG
* * * *
481340 AATATAATTATTTTTATTGAAATTTCATCTAAATTATTTCACTATTTGGGATATATTTAAAGAAA
1 AATATAATTATTATTATTGAAATTTCATCTAAATTATTTCACCATTTGGGACAAATTTAAAGAAA
* * * * * *
481405 TTTCTCACCTGGAGATTTCTTAAAAAATTTACCATTTGAAATTTCTAAGAATCTCCTCCTTGAAT
66 TTTCTCACCTGAAGAATTCTTAAAAAATTTACCATTTAAAATTTCTAAAAATCTCATCATTGAAT
*
481470 AATTAGTATTTAATTCCAAAATTTAATTTTTTATTTTTTATTTTTTAAAATTGAAAATA
131 AATTAGTATTTAATTCCAAAA-TAAATTTTTTATTTTTTATTTTTTAAAATTGAAAATA
481529 AATATTAATTATTATTATTGAAACTTTC-TCTAAATTA-TTCTACCATTTGGGACAAATTTAGAA
1 AATA-TAATTATTATTATTGAAA-TTTCATCTAAATTATTTC-ACCATTTGGGACAAATTTA-AA
* * *
481592 -AAATTTTCTCATCT-AAGAATT-TTATAAAAATTTACCATTTAAAATTT-TAAAAATTTCATTA
62 GAAA-TTTCTCACCTGAAGAATTCTTA-AAAAATTTACCATTTAAAATTTCTAAAAATCTCATCA
* * * *
481653 TTGGATAATTATTATTT-ATTCTAAAA-AAA-GTTTTATTTT
125 TTGAATAATTAGTATTTAATTCCAAAATAAATTTTTTATTTT
481692 GTTTTATATT
Statistics
Matches: 139, Mismatches: 18, Indels: 16
0.80 0.10 0.09
Matches are distributed among these distances:
185 9 0.06
186 2 0.01
188 8 0.06
189 34 0.24
190 71 0.51
191 15 0.11
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.46
Consensus pattern (188 bp):
AATATAATTATTATTATTGAAATTTCATCTAAATTATTTCACCATTTGGGACAAATTTAAAGAAA
TTTCTCACCTGAAGAATTCTTAAAAAATTTACCATTTAAAATTTCTAAAAATCTCATCATTGAAT
AATTAGTATTTAATTCCAAAATAAATTTTTTATTTTTTATTTTTTAAAATTGAAAATA
Found at i:482858 original size:44 final size:44
Alignment explanation
Indices: 482775--483003 Score: 169
Period size: 44 Copynumber: 5.2 Consensus size: 44
482765 AACATAAAAA
* * * **
482775 CTCCTTTAAACAAATGCTCTACAACTTTCAAGAAA-TAAAT-AAG
1 CTCCTCTAAACAAAGGCTCAACAACTTT-TGGAAACTAAATAAAG
* *
482818 TCTCCTCTAAACAAATGTTCAACAACTTTTGGAAACTAAATAAAG
1 -CTCCTCTAAACAAAGGCTCAACAACTTTTGGAAACTAAATAAAG
* ** * * * * * *
482863 CTTCTCTAAGTAGAGGCTTAATAAATTTTGAAAACTAAGTAAAG
1 CTCCTCTAAACAAAGGCTCAACAACTTTTGGAAACTAAATAAAG
* *
482907 CTCCTCTAAACAGAGGCTCAATGAA-TTTTGGAAACTAAATAAAG
1 CTCCTCTAAACAAAGGCTCAA-CAACTTTTGGAAACTAAATAAAG
** * * * * *
482951 CTTTTTTAAGCAAA-GCTCAACGACTTTTGGAAAATAAATAAGG
1 CTCCTCTAAACAAAGGCTCAACAACTTTTGGAAACTAAATAAAG
*
482994 CTTCTCTAAA
1 CTCCTCTAAA
483004 TAGAGGTTCA
Statistics
Matches: 146, Mismatches: 35, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
42 1 0.01
43 34 0.23
44 106 0.73
45 5 0.03
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (44 bp):
CTCCTCTAAACAAAGGCTCAACAACTTTTGGAAACTAAATAAAG
Found at i:482982 original size:43 final size:44
Alignment explanation
Indices: 482836--483002 Score: 174
Period size: 44 Copynumber: 3.8 Consensus size: 44
482826 AAACAAATGT
* *
482836 TCAACAACTTTTGGAAACTAAATAAAGCTTCTCTAAGTAGAGGC
1 TCAACAAATTTTGGAAACTAAATAAAGCTTCTCTAAGCAGAGGC
* * * * * *
482880 TTAATAAATTTTGAAAACTAAGTAAAGCTCCTCTAAACAGAGGC
1 TCAACAAATTTTGGAAACTAAATAAAGCTTCTCTAAGCAGAGGC
** * * *
482924 TCAATGAATTTTGGAAACTAAATAAAGCTTTTTTAAGCA-AAGC
1 TCAACAAATTTTGGAAACTAAATAAAGCTTCTCTAAGCAGAGGC
* * * *
482967 TCAACGACTTTTGGAAAATAAATAAGGCTTCTCTAA
1 TCAACAAATTTTGGAAACTAAATAAAGCTTCTCTAA
483003 ATAGAGGTTC
Statistics
Matches: 100, Mismatches: 23, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
43 33 0.33
44 67 0.67
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (44 bp):
TCAACAAATTTTGGAAACTAAATAAAGCTTCTCTAAGCAGAGGC
Found at i:484240 original size:7 final size:7
Alignment explanation
Indices: 484157--484230 Score: 58
Period size: 7 Copynumber: 10.4 Consensus size: 7
484147 TTATTTTTCC
*
484157 TTTCCTT
1 TTTCTTT
*
484164 TTTATTT
1 TTTCTTT
*
484171 TTTATTT
1 TTTCTTT
*
484178 TTGCTTT
1 TTTCTTT
*
484185 TTTATTTT
1 TTT-CTTT
**
484193 TTTCCCT
1 TTTCTTT
*
484200 TTTCTCT
1 TTTCTTT
*
484207 TTTCCTT
1 TTTCTTT
484214 TTTCTTT
1 TTTCTTT
484221 TTTCTTT
1 TTTCTTT
484228 TTT
1 TTT
484231 TTTCTTTTTT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
7 47 0.89
8 6 0.11
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.78
Consensus pattern (7 bp):
TTTCTTT
Found at i:488397 original size:16 final size:16
Alignment explanation
Indices: 488376--488407 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
488366 CACATTTTTA
488376 GTAGCTTTCACATATG
1 GTAGCTTTCACATATG
488392 GTAGCTTTCACATATG
1 GTAGCTTTCACATATG
488408 TGGTATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (16 bp):
GTAGCTTTCACATATG
Found at i:493336 original size:25 final size:26
Alignment explanation
Indices: 493304--493365 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
493294 TTCTCACCTA
*
493304 GAAATTTTATATAAATTT-ACCATTT
1 GAAATTTTATAAAAATTTCACCATTT
*
493329 GAAATTTT-TAAAAATTTCATCATTT
1 GAAATTTTATAAAAATTTCACCATTT
493354 GATAATTATTAT
1 GA-AATT-TTAT
493366 TTACTCTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 8 0.26
25 16 0.52
26 4 0.13
27 2 0.06
28 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.48
Consensus pattern (26 bp):
GAAATTTTATAAAAATTTCACCATTT
Found at i:493992 original size:11 final size:12
Alignment explanation
Indices: 493964--493995 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
493954 TTCAACCAAA
493964 TTCTA-AAAATT
1 TTCTAGAAAATT
493975 TTCTAGAAAATT
1 TTCTAGAAAATT
493987 TT-TAGAAAA
1 TTCTAGAAAA
493996 AAACTGCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (12 bp):
TTCTAGAAAATT
Found at i:500251 original size:26 final size:26
Alignment explanation
Indices: 500222--500284 Score: 101
Period size: 26 Copynumber: 2.4 Consensus size: 26
500212 TAAGTTTTCA
500222 ATTTAGGGTTTCGACCTT-AGGATTTT
1 ATTTAGGGTTTCGACCTTAAGG-TTTT
500248 ATTTAGGGTTTCGACCTTAAGGTTTT
1 ATTTAGGGTTTCGACCTTAAGGTTTT
*
500274 ATTTAAGGTTT
1 ATTTAGGGTTT
500285 TAATTTTAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 32 0.91
27 3 0.09
ACGTcount: A:0.21, C:0.10, G:0.22, T:0.48
Consensus pattern (26 bp):
ATTTAGGGTTTCGACCTTAAGGTTTT
Found at i:501658 original size:16 final size:15
Alignment explanation
Indices: 501633--501679 Score: 62
Period size: 16 Copynumber: 3.2 Consensus size: 15
501623 CTGCTCCCTC
501633 TTTCAATATTTCAAT
1 TTTCAATATTTCAAT
501648 TTTCTAATATTTCAAT
1 TTTC-AATATTTCAAT
*
501664 TTT-AA-ATTTAAAT
1 TTTCAATATTTCAAT
501677 TTT
1 TTT
501680 AAAATTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 10 0.33
14 2 0.07
15 4 0.13
16 14 0.47
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTCAATATTTCAAT
Found at i:501677 original size:13 final size:13
Alignment explanation
Indices: 501656--501714 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
501646 ATTTTCTAAT
*
501656 ATTTCAATTTTAA
1 ATTTAAATTTTAA
501669 ATTTAAATTTTAAA
1 ATTTAAATTTT-AA
*
501683 ATTTTAAGTTTTAA
1 A-TTTAAATTTTAA
* *
501697 TTTTTAATTTTATA
1 ATTTAAATTTTA-A
501711 ATTT
1 ATTT
501715 TATACGTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
13 19 0.51
14 9 0.24
15 9 0.24
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (13 bp):
ATTTAAATTTTAA
Found at i:501680 original size:7 final size:7
Alignment explanation
Indices: 501661--501716 Score: 62
Period size: 7 Copynumber: 8.0 Consensus size: 7
501651 CTAATATTTC
501661 AATTTTA
1 AATTTTA
501668 AA-TTTA
1 AATTTTA
501674 AATTTTAA
1 AATTTT-A
501682 AATTTTA
1 AATTTTA
*
501689 AGTTTT-
1 AATTTTA
*
501695 AATTTTT
1 AATTTTA
501702 AATTTTA
1 AATTTTA
501709 TAATTTTA
1 -AATTTTA
501717 TACGTTTATA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
6 11 0.26
7 17 0.40
8 14 0.33
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:501705 original size:28 final size:28
Alignment explanation
Indices: 501663--501716 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
501653 AATATTTCAA
501663 TTTTAAATTTAAATTTTAAAATTTTAAG
1 TTTTAAATTTAAATTTTAAAATTTTAAG
* * *
501691 TTTTAATTTTTAATTTTATAATTTTA
1 TTTTAAATTTAAATTTTAAAATTTTA
501717 TACGTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTAAATTTAAATTTTAAAATTTTAAG
Found at i:501738 original size:3 final size:3
Alignment explanation
Indices: 501730--501775 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
501720 GTTTATATAC
501730 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
501776 GAATGTGATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:502065 original size:15 final size:16
Alignment explanation
Indices: 502045--502077 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
502035 TATTTCCTTC
502045 TTTTTTTATTTTG-TT
1 TTTTTTTATTTTGATT
*
502060 TTTTTTTTTTTTGATT
1 TTTTTTTATTTTGATT
502076 TT
1 TT
502078 ATGATTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.88
Consensus pattern (16 bp):
TTTTTTTATTTTGATT
Found at i:502077 original size:14 final size:14
Alignment explanation
Indices: 502045--502114 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
502035 TATTTCCTTC
*
502045 TTTTTTTATTTTGTT
1 TTTTTTTATTTTG-A
*
502060 TTTTTTTTTTTTGA
1 TTTTTTTATTTTGA
* *
502074 TTTTATGATTTTGA
1 TTTTTTTATTTTGA
* **
502088 TTTTATGGTTTTGA
1 TTTTTTTATTTTGA
502102 TTTTATTTATTTT
1 TTTT-TTTATTTT
502115 TTCCTTTATT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
14 28 0.62
15 17 0.38
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (14 bp):
TTTTTTTATTTTGA
Found at i:502509 original size:35 final size:35
Alignment explanation
Indices: 502443--502562 Score: 143
Period size: 35 Copynumber: 3.4 Consensus size: 35
502433 ATATGACTAG
* * *
502443 AATTAAACCACT-AGCCGAAAAGTAAAGATGATCGA
1 AATTAAACC-CTAAGTCGAAAAATAAAAATGATCGA
* * * *
502478 GATTAAATCGTAAGTCGAGAAATAAAAATGATCGA
1 AATTAAACCCTAAGTCGAAAAATAAAAATGATCGA
502513 AATTAAACCCTAAGTCGAAAAATAAAAATGATCGA
1 AATTAAACCCTAAGTCGAAAAATAAAAATGATCGA
* *
502548 AACTAAACCATAAGT
1 AATTAAACCCTAAGT
502563 TTAAAAGTAA
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
34 1 0.01
35 70 0.99
ACGTcount: A:0.51, C:0.14, G:0.15, T:0.20
Consensus pattern (35 bp):
AATTAAACCCTAAGTCGAAAAATAAAAATGATCGA
Found at i:510343 original size:20 final size:19
Alignment explanation
Indices: 510318--510403 Score: 67
Period size: 20 Copynumber: 4.6 Consensus size: 19
510308 TCATGCAAAC
510318 ATGCAATTAAATATATAAT
1 ATGCAATTAAATATATAAT
*
510337 GATGCAAATAATAATATATAA-
1 -ATGC-AATTA-AATATATAAT
510358 AT--AATGT-AAT-TA-AAT
1 ATGCAAT-TAAATATATAAT
510373 ATGCAATTAAATATATAAT
1 ATGCAATTAAATATATAAT
*
510392 CATGCAAATAAA
1 -ATGCAATTAAA
510404 CATGCAATTA
Statistics
Matches: 53, Mismatches: 3, Indels: 20
0.70 0.04 0.26
Matches are distributed among these distances:
14 2 0.04
15 4 0.08
16 4 0.08
17 9 0.17
18 2 0.04
19 3 0.06
20 16 0.30
21 4 0.08
22 9 0.17
ACGTcount: A:0.55, C:0.06, G:0.07, T:0.33
Consensus pattern (19 bp):
ATGCAATTAAATATATAAT
Found at i:510409 original size:87 final size:87
Alignment explanation
Indices: 510314--510538 Score: 339
Period size: 87 Copynumber: 2.6 Consensus size: 87
510304 ATAATCATGC
* * *
510314 AAACATGCAATTAAATATATAATGATGCAAATAATAATATATAAATAATGTAATTAAATATGCAA
1 AAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAATAATGCAAATAAATATGCAA
*
510379 TTAAATATATAATCATGCAAAT
66 TTAAATATATAATCACGCAAAT
* * * *
510401 AAACATGCAATTAAATATAAAATCAAGCAAATAATAATATATAAATCATGCAAATAAATATGTAA
1 AAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAATAATGCAAATAAATATGCAA
*
510466 TTAAATATATAATTACGCAAAT
66 TTAAATATATAATCACGCAAAT
*
510488 AAACATGCAATTAAATATATAATCATGCAAAT-A-AATATATTAATAAT-CAAA
1 AAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAATAATGCAAA
510539 ACATTAAATA
Statistics
Matches: 125, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
84 4 0.03
85 12 0.10
86 1 0.01
87 108 0.86
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.30
Consensus pattern (87 bp):
AAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAATAATGCAAATAAATATGCAA
TTAAATATATAATCACGCAAAT
Found at i:510413 original size:32 final size:32
Alignment explanation
Indices: 510349--510522 Score: 186
Period size: 32 Copynumber: 5.7 Consensus size: 32
510339 TGCAAATAAT
* * * *
510349 AATATATAAATAATGTAATTAAATATGCAATTA
1 AATATAT-AATCATGCAAATAAACATGCAATTA
510382 AATATATAATCATGCAAATAAACATGCAATTA
1 AATATATAATCATGCAAATAAACATGCAATTA
* *
510414 AATATAAAATCAAGCAAAT--A-AT--AA-T-
1 AATATATAATCATGCAAATAAACATGCAATTA
* *
510439 -ATATA-AATCATGCAAATAAATATGTAATTA
1 AATATATAATCATGCAAATAAACATGCAATTA
* *
510469 AATATATAATTACGCAAATAAACATGCAATTA
1 AATATATAATCATGCAAATAAACATGCAATTA
510501 AATATATAATCATGCAAATAAA
1 AATATATAATCATGCAAATAAA
510523 TATATTAATA
Statistics
Matches: 119, Mismatches: 13, Indels: 19
0.79 0.09 0.13
Matches are distributed among these distances:
23 11 0.09
24 5 0.04
25 1 0.01
26 3 0.03
27 2 0.02
28 2 0.02
29 3 0.03
30 1 0.01
31 5 0.04
32 79 0.66
33 7 0.06
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.30
Consensus pattern (32 bp):
AATATATAATCATGCAAATAAACATGCAATTA
Found at i:510448 original size:55 final size:54
Alignment explanation
Indices: 510382--510489 Score: 162
Period size: 55 Copynumber: 2.0 Consensus size: 54
510372 TATGCAATTA
510382 AATATATAATCATGCAAATAAACATGCAATTAAATATAAAATCAAGCAAATAAT
1 AATATATAATCATGCAAATAAACATGCAATTAAATATAAAATCAAGCAAATAAT
* * * * *
510436 AATATATAAATCATGCAAATAAATATGTAATTAAATATATAATTACGCAAATAA
1 AATATAT-AATCATGCAAATAAACATGCAATTAAATATAAAATCAAGCAAATAA
510490 ACATGCAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
54 7 0.15
55 41 0.85
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.29
Consensus pattern (54 bp):
AATATATAATCATGCAAATAAACATGCAATTAAATATAAAATCAAGCAAATAAT
Found at i:510453 original size:23 final size:22
Alignment explanation
Indices: 510399--510458 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
510389 AATCATGCAA
*
510399 ATAAA-CATGC-AATTAAATAT
1 ATAAATCATGCAAATAAAATAT
*
510419 A-AAATCAAGCAAATAATAATAT
1 ATAAATCATGCAAATAA-AATAT
510441 ATAAATCATGCAAATAAA
1 ATAAATCATGCAAATAAA
510459 TATGTAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.09
20 5 0.15
21 4 0.12
22 7 0.21
23 14 0.42
ACGTcount: A:0.60, C:0.10, G:0.05, T:0.25
Consensus pattern (22 bp):
ATAAATCATGCAAATAAAATAT
Found at i:510509 original size:20 final size:20
Alignment explanation
Indices: 510486--510527 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
510476 AATTACGCAA
*
510486 ATAAACATGCAATTAAATAT
1 ATAAACATGCAAATAAATAT
*
510506 ATAATCATGCAAATAAATAT
1 ATAAACATGCAAATAAATAT
510526 AT
1 AT
510528 TAATAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.31
Consensus pattern (20 bp):
ATAAACATGCAAATAAATAT
Found at i:510533 original size:24 final size:24
Alignment explanation
Indices: 510506--510660 Score: 109
Period size: 24 Copynumber: 6.8 Consensus size: 24
510496 AATTAAATAT
510506 ATAATCATGCAAATAAATATATTA
1 ATAATCATGCAAATAAATATATTA
*
510530 ATAATCA--AAACATTAAATATATTA
1 ATAATCATGCAA-A-TAAATATATTA
** *
510554 ATAATCATGC-AATCGAT-TA-AA
1 ATAATCATGCAAATAAATATATTA
**
510575 TATAATCATATAAATAAATATATTA
1 -ATAATCATGCAAATAAATATATTA
510600 ATAATCATGC----AAATATATTA
1 ATAATCATGCAAATAAATATATTA
**
510620 ATCAATCACACAAAATAAATATA-T-
1 AT-AATCATGC-AAATAAATATATTA
510644 -TAATCATGCAAATAAAT
1 ATAATCATGCAAATAAAT
510661 TATCATGCAA
Statistics
Matches: 101, Mismatches: 16, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
20 12 0.12
21 15 0.15
22 18 0.18
23 10 0.10
24 36 0.36
25 3 0.03
26 7 0.07
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.32
Consensus pattern (24 bp):
ATAATCATGCAAATAAATATATTA
Found at i:510633 original size:21 final size:20
Alignment explanation
Indices: 510590--510633 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
510580 TCATATAAAT
**
510590 AAATATATTAATAATCATGC
1 AAATATATTAATAATCACAC
510610 AAATATATTAATCAATCACAC
1 AAATATATTAAT-AATCACAC
510631 AAA
1 AAA
510634 ATAAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.30
Consensus pattern (20 bp):
AAATATATTAATAATCACAC
Found at i:510636 original size:46 final size:43
Alignment explanation
Indices: 510520--510662 Score: 141
Period size: 46 Copynumber: 3.2 Consensus size: 43
510510 TCATGCAAAT
*
510520 AAATATATTAATAATCAAAACATTAAATATATTAATAATCATGC
1 AAATATATTAATAATCAAAA-AATAAATATATTAATAATCATGC
** *
510564 -AATCGATTAAATATAATCATATAAATAAATATATTAATAATCATGC
1 AAATATATT--A-ATAATCA-AAAAATAAATATATTAATAATCATGC
510610 AAATATATTAATCAATCACACAAAATAAATATA-T--TAATCATGC
1 AAATATATTAAT-AATCA-A-AAAATAAATATATTAATAATCATGC
*
510653 AAATAAATTA
1 AAATATATTA
510663 TCATGCAAGT
Statistics
Matches: 83, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
43 24 0.29
44 2 0.02
45 9 0.11
46 40 0.48
47 8 0.10
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (43 bp):
AAATATATTAATAATCAAAAAATAAATATATTAATAATCATGC
Found at i:510667 original size:16 final size:17
Alignment explanation
Indices: 510636--510670 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
510626 CACACAAAAT
*
510636 AAATATATTAATCATGC
1 AAATAAATTAATCATGC
510653 AAATAAATT-ATCATGC
1 AAATAAATTAATCATGC
510669 AA
1 AA
510671 GTATAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.31
Consensus pattern (17 bp):
AAATAAATTAATCATGC
Found at i:511662 original size:43 final size:43
Alignment explanation
Indices: 511601--512295 Score: 664
Period size: 42 Copynumber: 16.4 Consensus size: 43
511591 GCATTAAAAT
* * * *
511601 TTTTGGAAAATAAAATGCTCCCCCACAATTAAGACTTTGAAAC
1 TTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC
* * * * *
511644 TTTGGAAAACTAAAATGCTTCCCCATAACTGAGGCTTTGAAAA
1 TTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC
* * * *
511687 TTTTGAAAAATAAAACGTTCCTCTACAACTGAGGCTTTGAAAC
1 TTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC
* * * * *
511730 -ATT-AAAATATAAAATGCTCCCCCATAACTAAAGC-TTAAAAC
1 TTTTGAAAA-ATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC
* * * ** * * *
511771 TTTTGGAAAATAAAATACTTCCTTACAGCTGAGGCCTTAAAAC
1 TTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC
* *
511814 TTTAGAAAAATAAAATGCTCCCCCACAACTGAGACTTTGAAAC
1 TTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC
* * **
511857 TTTTGAAAAATAAAATGCT-CCCCAAAACTAAGTATTTGGAAA-
1 TTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTT-GAAAC
* * *
511899 -TTTGAAAAAATAAAATGCTCCCCCATAATTGAGGCTTTGGAA-
1 TTTTG-AAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC
*
511941 TTTTGGAAAAGTAAAATGCTCCCCCACAACTGAGGCTTTGAAAC
1 TTTT-GAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC
** * * *
511985 -TTTGAAAAATAAAACACTCCCACACAACTAAGGCTTTAAAAC
1 TTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC
* * * *
512027 TTTTG-AAAATAAAATACTCCCCTATAACCGAGGCTTTGAAAC
1 TTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC
** * * * * *
512069 -TTAAAAAAAAAAAATGCTTCCCCGCCACTAAGGCTTTGAAAC
1 TTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC
* * *
512111 TTTTG-AAAATAAAATGCTCCCCTACAATTAAGGCTTTGAAAC
1 TTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC
* *
512153 TTTTGAAAAATAAAATAG-TCCCTCACAATTGAGGCTTTGAAAC
1 TTTTGAAAAATAAAAT-GCTCCCCCACAACTGAGGCTTTGAAAC
* * * *
512196 TTTTG-AAAATAAAATACTCCCCCACAACTAAAGCTTTAAAAC
1 TTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC
* * *
512238 -TTTAAAAAATAAAATGCTCTCCCATAACTGAGGCTTTGAAAC
1 TTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC
512280 TTTTG-AAAATAAAATG
1 TTTTGAAAAATAAAATG
512296 AGATTATTTT
Statistics
Matches: 523, Mismatches: 111, Indels: 37
0.78 0.17 0.06
Matches are distributed among these distances:
41 19 0.04
42 271 0.52
43 231 0.44
44 2 0.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (43 bp):
TTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC
Found at i:511780 original size:85 final size:85
Alignment explanation
Indices: 511601--512295 Score: 701
Period size: 85 Copynumber: 8.2 Consensus size: 85
511591 GCATTAAAAT
* * * * * * *
511601 TTTTGGAAAATAAAATGCTCCCCCACAATTAAGACTTTGAAACTTTGGAAAACTAAAATGCTTCC
1 TTTT-GAAAATAAAATGCTCCCCTACAACTGAGGCTTTGAAACTTTGAAAAAATAAAATGCTCCC
* *
511666 CCATAACTGAGGCTTTGAAAA
65 CCACAACTGAGGCTTTGAAAC
* * * * *
511687 TTTTGAAAAATAAAACGTTCCTCTACAACTGAGGCTTTGAAACATT-AAAATATAAAATGCTCCC
1 TTTTG-AAAATAAAATGCTCCCCTACAACTGAGGCTTTGAAACTTTGAAAAAATAAAATGCTCCC
* * * *
511751 CCATAACTAAAGC-TTAAAAC
65 CCACAACTGAGGCTTTGAAAC
* * * * * *
511771 TTTTGGAAAATAAAATACTTCCTTACAGCTGAGGCCTTAAAACTTT-AGAAAAATAAAATGCTCC
1 TTTT-GAAAATAAAATGCTCCCCTACAACTGAGGCTTTGAAACTTTGA-AAAAATAAAATGCTCC
*
511835 CCCACAACTGAGACTTTGAAAC
64 CCCACAACTGAGGCTTTGAAAC
* * **
511857 TTTTGAAAAATAAAATGCTCCCC-AAAACTAAGTATTTGGAAA-TTTGAAAAAATAAAATGCTCC
1 TTTTG-AAAATAAAATGCTCCCCTACAACTGAGGCTTT-GAAACTTTGAAAAAATAAAATGCTCC
* * *
511920 CCCATAATTGAGGCTTTGGAA-
64 CCCACAACTGAGGCTTTGAAAC
* **
511941 TTTTGGAAAAGTAAAATGCTCCCCCACAACTGAGGCTTTGAAACTTTG-AAAAATAAAACACTCC
1 TTTT-GAAAA-TAAAATGCTCCCCTACAACTGAGGCTTTGAAACTTTGAAAAAATAAAATGCTCC
* * *
512005 CACACAACTAAGGCTTTAAAAC
64 CCCACAACTGAGGCTTTGAAAC
* * * * * *
512027 TTTTGAAAATAAAATACTCCCCTATAACCGAGGCTTTGAAAC-TTAAAAAAAAAAAATGCTTCCC
1 TTTTGAAAATAAAATGCTCCCCTACAACTGAGGCTTTGAAACTTTGAAAAAATAAAATGCTCCCC
* * *
512091 CGCCACTAAGGCTTTGAAAC
66 CACAACTGAGGCTTTGAAAC
* *
512111 TTTTGAAAATAAAATGCTCCCCTACAATTAAGGCTTTGAAACTTTTG-AAAAATAAAATAG-TCC
1 TTTTGAAAATAAAATGCTCCCCTACAACTGAGGCTTTGAAAC-TTTGAAAAAATAAAAT-GCTCC
* *
512174 CTCACAATTGAGGCTTTGAAAC
64 CCCACAACTGAGGCTTTGAAAC
* * * * * *
512196 TTTTGAAAATAAAATACTCCCCCACAACTAAAGCTTTAAAACTTT-AAAAAATAAAATGCTCTCC
1 TTTTGAAAATAAAATGCTCCCCTACAACTGAGGCTTTGAAACTTTGAAAAAATAAAATGCTCCCC
*
512260 CATAACTGAGGCTTTGAAAC
66 CACAACTGAGGCTTTGAAAC
512280 TTTTGAAAATAAAATG
1 TTTTGAAAATAAAATG
512296 AGATTATTTT
Statistics
Matches: 497, Mismatches: 94, Indels: 38
0.79 0.15 0.06
Matches are distributed among these distances:
83 3 0.01
84 194 0.39
85 215 0.43
86 85 0.17
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (85 bp):
TTTTGAAAATAAAATGCTCCCCTACAACTGAGGCTTTGAAACTTTGAAAAAATAAAATGCTCCCC
CACAACTGAGGCTTTGAAAC
Found at i:511805 original size:127 final size:127
Alignment explanation
Indices: 511607--512294 Score: 646
Period size: 127 Copynumber: 5.4 Consensus size: 127
511597 AAATTTTTGG
* * *
511607 AAAATAAAATGCTCCCCCACAA-TTAAGACTTTGAAAC-TTTGGAAAACTAAAATGCTTCCCCAT
1 AAAATAAAATGCTCCCCCACAACTAAAG-CTTTGAAACTTTTGGAAAA-TAAAATACTCCCCCAT
* * * * *
511670 AACTGAGGCTTTGAAAATTTTGAAAAATAAAACGTTCCTCTACAACTGAGGCTTTGAAACATTA
64 AACTGAGGCTTTGAAAATTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAACTTTA
* * * ** *
511734 AAATATAAAATGCTCCCCCATAACTAAAGC-TTAAAACTTTTGGAAAATAAAATACTTCCTTACA
1 AAA-ATAAAATGCTCCCCCACAACTAAAGCTTTGAAACTTTTGGAAAATAAAATACTCCCCCATA
* * * *
511798 GCTGAGGCCTT-AAAACTTTAGAAAAATAAAATGCTCCCCCACAACTGAGACTTTGAAACTTTTG
65 ACTGAGGCTTTGAAAA-TTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC-TTT-
511862 A
127 A
* * * *
511863 AAAATAAAATGCT-CCCCAAAACT-AAGTATTTGGAAA--TTTGAAAAAATAAAATGCTCCCCCA
1 AAAATAAAATGCTCCCCCACAACTAAAG-CTTT-GAAACTTTTG-GAAAATAAAATACTCCCCCA
* * *
511924 TAATTGAGGCTTTG-GAATTTTGGAAAAGTAAAATGCTCCCCCACAACTGAGGCTTTGAAACTTT
63 TAACTGAGGCTTTGAAAATTTT-GAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAACTTT
511988 GA
127 -A
** * * * *
511990 AAAATAAAACACTCCCACACAACTAAGGCTTTAAAACTTTT-GAAAATAAAATACTCCCCTATAA
1 AAAATAAAATGCTCCCCCACAACTAAAGCTTTGAAACTTTTGGAAAATAAAATACTCCCCCATAA
* * ** * * * * * *
512054 CCGAGGCTTTG-AAACTTAAAAAAAAAAAATGCTTCCCCGCCACTAAGGCTTTGAAACTTTTG
66 CTGAGGCTTTGAAAATTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAAC-TTTA
* * * * * * *
512116 AAAATAAAATGCTCCCCTACAATTAAGGCTTTGAAACTTTTGAAAAATAAAATAGTCCCTCACAA
1 AAAATAAAATGCTCCCCCACAACTAAAGCTTTGAAACTTTTGGAAAATAAAATACTCCCCCATAA
* * * * * *
512181 TTGAGGCTTTGAAACTTTTG-AAAATAAAATACTCCCCCACAACTAAAGCTTTAAAACTTTAA
66 CTGAGGCTTTGAAAATTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAACTTT-A
* * * *
512243 AAAATAAAATGCTCTCCCATAACTGAGGCTTTGAAACTTTT-GAAAATAAAAT
1 AAAATAAAATGCTCCCCCACAACTAAAGCTTTGAAACTTTTGGAAAATAAAAT
512295 GAGATTATTT
Statistics
Matches: 455, Mismatches: 86, Indels: 41
0.78 0.15 0.07
Matches are distributed among these distances:
126 87 0.19
127 232 0.51
128 120 0.26
129 16 0.04
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (127 bp):
AAAATAAAATGCTCCCCCACAACTAAAGCTTTGAAACTTTTGGAAAATAAAATACTCCCCCATAA
CTGAGGCTTTGAAAATTTTGAAAAATAAAATGCTCCCCCACAACTGAGGCTTTGAAACTTTA
Found at i:518957 original size:14 final size:14
Alignment explanation
Indices: 518935--518974 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
518925 TACTTAGATT
*
518935 ATGCTAAAATATTC
1 ATGCAAAAATATTC
*
518949 ATGCAAAAAT-GTC
1 ATGCAAAAATATTC
518962 ATGCAAAAATATT
1 ATGCAAAAATATT
518975 AATTATCATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (14 bp):
ATGCAAAAATATTC
Found at i:518985 original size:20 final size:20
Alignment explanation
Indices: 518960--518997 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
518950 TGCAAAAATG
*
518960 TCATGCAAAAATATTAATTA
1 TCATGCAAAAATAATAATTA
*
518980 TCATGCAATAATAATAAT
1 TCATGCAAAAATAATAAT
518998 CATATAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (20 bp):
TCATGCAAAAATAATAATTA
Found at i:519210 original size:20 final size:20
Alignment explanation
Indices: 519185--519224 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
519175 ATCACACAAA
*
519185 TAAATAAATTAATACTCATG
1 TAAATAAATTAATAATCATG
519205 TAAATAAATTAATAATCATG
1 TAAATAAATTAATAATCATG
519225 CAAGCAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (20 bp):
TAAATAAATTAATAATCATG
Found at i:519233 original size:20 final size:20
Alignment explanation
Indices: 519190--519233 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
519180 ACAAATAAAT
* * *
519190 AAATTAATACTCATGTAAAT
1 AAATTAATAATCATGCAAAC
*
519210 AAATTAATAATCATGCAAGC
1 AAATTAATAATCATGCAAAC
519230 AAAT
1 AAAT
519234 ATATTCATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (20 bp):
AAATTAATAATCATGCAAAC
Found at i:519233 original size:24 final size:24
Alignment explanation
Indices: 519206--519251 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
519196 ATACTCATGT
519206 AAATAAATTAATAATCATGCAAGC
1 AAATAAATTAATAATCATGCAAGC
* * *
519230 AAATATATTCATAATTATGCAA
1 AAATAAATTAATAATCATGCAA
519252 ACATGCAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (24 bp):
AAATAAATTAATAATCATGCAAGC
Found at i:519278 original size:20 final size:20
Alignment explanation
Indices: 519253--519330 Score: 102
Period size: 20 Copynumber: 3.8 Consensus size: 20
519243 ATTATGCAAA
519253 CATGCAATTAAATATATAAT
1 CATGCAATTAAATATATAAT
*
519273 CATGCAAATAATAATATATAAAT
1 CATGC-AATTA-AATATAT-AAT
*
519296 CATGCAATTAGATATATAAT
1 CATGCAATTAAATATATAAT
*
519316 CATGCAAATAAATAT
1 CATGCAATTAAATAT
519331 GCAATTAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
20 21 0.42
21 10 0.20
22 11 0.22
23 8 0.16
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.32
Consensus pattern (20 bp):
CATGCAATTAAATATATAAT
Found at i:519334 original size:32 final size:32
Alignment explanation
Indices: 519290--519362 Score: 112
Period size: 32 Copynumber: 2.2 Consensus size: 32
519280 ATAATAATAT
*
519290 ATAAATCATGCAATTAGATATATAA-TCATGCAA
1 ATAAAT-ATGCAATTAAATATA-AACTCATGCAA
519323 ATAAATATGCAATTAAATATAAACTCATGCAA
1 ATAAATATGCAATTAAATATAAACTCATGCAA
519355 ATAAATAT
1 ATAAATAT
519363 ATTAATAATC
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
31 2 0.05
32 30 0.79
33 6 0.16
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (32 bp):
ATAAATATGCAATTAAATATAAACTCATGCAA
Found at i:519354 original size:20 final size:19
Alignment explanation
Indices: 519253--519363 Score: 92
Period size: 20 Copynumber: 5.8 Consensus size: 19
519243 ATTATGCAAA
519253 CATGCAATTAAATATATAAT
1 CATGCAATTAAATATA-AAT
519273 CATGCAAATAATAATATATAAAT
1 CATGC-AAT--TAA-ATATAAAT
*
519296 CATGCAATTAGATATATAAT
1 CATGCAATTAAATATA-AAT
519316 CATGC-----AA-ATAAAT
1 CATGCAATTAAATATAAAT
519329 -ATGCAATTAAATATAAACT
1 CATGCAATTAAATATAAA-T
*
519348 CATGCAAATAAATATA
1 CATGCAATTAAATATA
519364 TTAATAATCA
Statistics
Matches: 75, Mismatches: 3, Indels: 26
0.72 0.03 0.25
Matches are distributed among these distances:
12 4 0.05
13 3 0.04
14 3 0.04
15 1 0.01
17 2 0.03
18 5 0.07
19 6 0.08
20 29 0.39
21 3 0.04
22 3 0.04
23 11 0.15
24 5 0.07
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (19 bp):
CATGCAATTAAATATAAAT
Found at i:519383 original size:24 final size:24
Alignment explanation
Indices: 519347--519482 Score: 122
Period size: 24 Copynumber: 5.8 Consensus size: 24
519337 AAATATAAAC
*
519347 TCATGCAAATAAATATATTAATAA
1 TCATACAAATAAATATATTAATAA
* *
519371 TCAAACAATTAAATATATTAATAA
1 TCATACAAATAAATATATTAATAA
* **
519395 TCATGCAAGCAAAT-TA--AATATA
1 TCATACAAATAAATATATTAATA-A
519417 CTCATACAAATAAATATATTAATAA
1 -TCATACAAATAAATATATTAATAA
* * *
519442 TCATGCAAAT--ATATTTTTA-AA
1 TCATACAAATAAATATATTAATAA
*
519463 TCACACAAATAAATATATTA
1 TCATACAAATAAATATATTA
519483 GGCAGACAAA
Statistics
Matches: 88, Mismatches: 17, Indels: 15
0.73 0.14 0.12
Matches are distributed among these distances:
21 14 0.16
22 8 0.09
23 19 0.22
24 42 0.48
25 1 0.01
26 4 0.05
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (24 bp):
TCATACAAATAAATATATTAATAA
Found at i:524482 original size:17 final size:16
Alignment explanation
Indices: 524460--524493 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
524450 AACTAACATG
*
524460 TAATTTATTTTGTTTAT
1 TAATTTATATT-TTTAT
524477 TAATTTATATTTTTAT
1 TAATTTATATTTTTAT
524493 T
1 T
524494 TATATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TAATTTATATTTTTAT
Found at i:529374 original size:13 final size:13
Alignment explanation
Indices: 529356--529380 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
529346 TAAAGTATGG
529356 TGACTCATCACTA
1 TGACTCATCACTA
529369 TGACTCATCACT
1 TGACTCATCACT
529381 TATTTAACAT
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:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (13 bp):
TGACTCATCACTA
Found at i:529422 original size:18 final size:18
Alignment explanation
Indices: 529388--529423 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
529378 ACTTATTTAA
**
529388 CATAAAGTAAAGGTGACT
1 CATAAAGTAAACATGACT
529406 CATAAAGTAAACATGACT
1 CATAAAGTAAACATGACT
529424 TGACTTAGAC
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:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (18 bp):
CATAAAGTAAACATGACT
Found at i:538143 original size:13 final size:13
Alignment explanation
Indices: 538125--538149 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
538115 TATAGTACGG
538125 TGACTCATCACTA
1 TGACTCATCACTA
538138 TGACTCATCACT
1 TGACTCATCACT
538150 TATTTGACAT
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:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (13 bp):
TGACTCATCACTA
Found at i:548001 original size:26 final size:25
Alignment explanation
Indices: 547984--548032 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
547974 GTTTTATTCT
*
547984 TTAGGGTTCTATTTAGGTTTCAACC
1 TTAGGGTTCTATTTAGGTTTTAACC
*
548009 TTAGGGTTTTATTTAGGGTTTTAA
1 TTAGGGTTCTATTTA-GGTTTTAA
548033 TTTTAGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.20, C:0.08, G:0.22, T:0.49
Consensus pattern (25 bp):
TTAGGGTTCTATTTAGGTTTTAACC
Found at i:548029 original size:12 final size:13
Alignment explanation
Indices: 547949--548031 Score: 57
Period size: 12 Copynumber: 6.4 Consensus size: 13
547939 AATCTTATGA
*
547949 TTTTA-TTTAGAG
1 TTTTACTTTAGGG
*
547961 TTTTGACTTTAAGG
1 TTTT-ACTTTAGGG
547975 TTTTATTCTTTAGGG
1 TTTTA--CTTTAGGG
*
547990 TTCTA-TTTA-GG
1 TTTTACTTTAGGG
* *
548001 TTTCAACCTTAGGG
1 TTT-TACTTTAGGG
548015 TTTTA-TTTAGGG
1 TTTTACTTTAGGG
548027 TTTTA
1 TTTTA
548032 ATTTTAGAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 14
0.71 0.12 0.18
Matches are distributed among these distances:
11 4 0.07
12 20 0.36
13 6 0.11
14 14 0.25
15 11 0.20
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.54
Consensus pattern (13 bp):
TTTTACTTTAGGG
Found at i:548038 original size:26 final size:25
Alignment explanation
Indices: 547954--548038 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 25
547944 TATGATTTTA
* *
547954 TTTAGAGTTTTGACTTTAAGGTTTTATT
1 TTTAGGGTTTT-A-TTT-AGGTTTTAAT
* * *
547982 CTTTAGGGTTCTATTTAGGTTTCAAC
1 -TTTAGGGTTTTATTTAGGTTTTAAT
*
548008 CTTAGGGTTTTATTTAGGGTTTTAAT
1 TTTAGGGTTTTATTTA-GGTTTTAAT
548034 TTTAG
1 TTTAG
548039 AATTTCATCT
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
25 14 0.31
26 18 0.40
27 3 0.07
28 1 0.02
29 9 0.20
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (25 bp):
TTTAGGGTTTTATTTAGGTTTTAAT
Found at i:548260 original size:3 final size:3
Alignment explanation
Indices: 548254--548375 Score: 92
Period size: 3 Copynumber: 41.7 Consensus size: 3
548244 AAAAAAATTG
* *
548254 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ACT ATT -TA ATGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
* * * * * * **
548301 -TT ATT ATT -TA ATA ATT TTT CAAT ATT -TA AGT AAA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
*
548344 ATT ATA ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
548376 AAAACTCGAT
Statistics
Matches: 94, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
2 6 0.06
3 87 0.93
4 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:550026 original size:33 final size:31
Alignment explanation
Indices: 549989--550060 Score: 83
Period size: 33 Copynumber: 2.3 Consensus size: 31
549979 CTTTCATTTC
* *
549989 TTTATTTTTATATATTATGGGCTTCCTTTTCTT
1 TTTATTTTT-TAAATTATGGGCTT-CTTTTATT
*
550022 TTTATTATTTTAAATTTTGGGCTTCTTTTATT
1 TTTATT-TTTTAAATTATGGGCTTCTTTTATT
550054 TTT-TTTT
1 TTTATTTT
550061 GCTTTTGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 2 0.06
31 2 0.06
32 10 0.29
33 18 0.51
34 3 0.09
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.68
Consensus pattern (31 bp):
TTTATTTTTTAAATTATGGGCTTCTTTTATT
Found at i:550116 original size:7 final size:7
Alignment explanation
Indices: 550104--550151 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
550094 GGCCTAAACT
550104 TTTTTTA
1 TTTTTTA
550111 TTTTTTA
1 TTTTTTA
*
550118 TATTATTA
1 T-TTTTTA
*
550126 TTTCTTAA
1 TTT-TTTA
550134 TTTTTTA
1 TTTTTTA
*
550141 TTTATTA
1 TTTTTTA
550148 TTTT
1 TTTT
550152 ATAAAAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 22 0.67
8 11 0.33
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTTA
Found at i:550237 original size:7 final size:7
Alignment explanation
Indices: 550222--550299 Score: 58
Period size: 6 Copynumber: 11.7 Consensus size: 7
550212 ATTTTCTAAT
*
550222 TTTTCAA
1 TTTTAAA
550229 TTTTAAA
1 TTTTAAA
550236 -TTTAAA
1 TTTTAAA
550242 -TTTAAA
1 TTTTAAA
550248 -TTTAAA
1 TTTTAAA
*
550254 TTTTTAAT
1 -TTTTAAA
*
550262 TTTTAAG
1 TTTTAAA
*
550269 TTTT-TA
1 TTTTAAA
* *
550275 TTTTTAT
1 TTTTAAA
550282 TTTTAAA
1 TTTTAAA
550289 TTTT-AA
1 TTTTAAA
550295 TTTTA
1 TTTTA
550300 TATTATTATT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
6 28 0.48
7 25 0.43
8 5 0.09
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:550265 original size:8 final size:7
Alignment explanation
Indices: 550212--550298 Score: 67
Period size: 7 Copynumber: 12.7 Consensus size: 7
550202 TTATTTGATT
550212 ATTTTCTA
1 ATTTT-TA
550220 ATTTTTCA
1 ATTTTT-A
550228 A-TTTTA
1 ATTTTTA
*
550234 A-ATTTA
1 ATTTTTA
*
550240 A-ATTTA
1 ATTTTTA
* *
550246 AATTTAA
1 ATTTTTA
550253 ATTTTTA
1 ATTTTTA
550260 ATTTTTA
1 ATTTTTA
550267 AGTTTTT-
1 A-TTTTTA
550274 ATTTTT-
1 ATTTTTA
550280 ATTTTTA
1 ATTTTTA
*
550287 AATTTTA
1 ATTTTTA
550294 ATTTT
1 ATTTT
550299 ATATTATTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
6 24 0.35
7 32 0.47
8 12 0.18
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.64
Consensus pattern (7 bp):
ATTTTTA
Found at i:550278 original size:20 final size:20
Alignment explanation
Indices: 550218--550299 Score: 85
Period size: 20 Copynumber: 4.1 Consensus size: 20
550208 GATTATTTTC
* *
550218 TAATTTTTCAATTTTAAATT
1 TAATTTTTAAATTTTAATTT
* *
550238 TAA-ATTTAAATTTAAATTTT
1 TAATTTTTAAATTTTAA-TTT
* *
550258 TAATTTTTAAGTTTTTATTT
1 TAATTTTTAAATTTTAATTT
*
550278 TTATTTTTAAATTTTAATTT
1 TAATTTTTAAATTTTAATTT
550298 TA
1 TA
550300 TATTATTATT
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
19 10 0.21
20 29 0.60
21 9 0.19
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (20 bp):
TAATTTTTAAATTTTAATTT
Found at i:550303 original size:27 final size:27
Alignment explanation
Indices: 550220--550309 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 27
550210 TTATTTTCTA
* * *
550220 ATTTTTCAATTTTAAA-TTTAAATTTAA
1 ATTTTT-ATTTTTAAATTTTAATTTTAT
** *
550247 ATTTAAATTTTTAATTTTTAAGTTTT-T
1 ATTTTTATTTTTAAATTTTAA-TTTTAT
550274 ATTTTTATTTTTAAATTTTAATTTTAT
1 ATTTTTATTTTTAAATTTTAATTTTAT
*
550301 ATTATTATT
1 ATTTTTATT
550310 ATTATTATTA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
26 11 0.22
27 36 0.72
28 3 0.06
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (27 bp):
ATTTTTATTTTTAAATTTTAATTTTAT
Found at i:550308 original size:3 final size:3
Alignment explanation
Indices: 550300--550338 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
550290 TTTAATTTTA
550300 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
550339 AACCATTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:552381 original size:29 final size:28
Alignment explanation
Indices: 552342--552396 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
552332 GTATAAGCTT
* *
552342 AAAAAAATATTTATTCATAATTTTTTTA
1 AAAAAAATATTAATTCATAATATTTTTA
552370 AAAAAAATTATTAATTCATAATATTTT
1 AAAAAAA-TATTAATTCATAATATTTT
552397 CCTTTGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (28 bp):
AAAAAAATATTAATTCATAATATTTTTA
Found at i:552396 original size:28 final size:28
Alignment explanation
Indices: 552342--552396 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
552332 GTATAAGCTT
* *
552342 AAAAAAATATTTATTCATAATTTTTTTA
1 AAAAAAATATTAATTCATAATTATTTTA
552370 AAAAAAATTATTAATTCATAA-TATTTT
1 AAAAAAA-TATTAATTCATAATTATTTT
552397 CCTTTGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (28 bp):
AAAAAAATATTAATTCATAATTATTTTA
Found at i:559568 original size:25 final size:25
Alignment explanation
Indices: 559539--559589 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
559529 CAAGGATATA
559539 ACCATCAATGTCAATATCAAATAAG
1 ACCATCAATGTCAATATCAAATAAG
559564 ACCATCAATGTCAATATCAAATAAG
1 ACCATCAATGTCAATATCAAATAAG
559589 A
1 A
559590 ATTTTTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.20, G:0.08, T:0.24
Consensus pattern (25 bp):
ACCATCAATGTCAATATCAAATAAG
Found at i:561789 original size:73 final size:72
Alignment explanation
Indices: 561665--561801 Score: 177
Period size: 73 Copynumber: 1.9 Consensus size: 72
561655 TTCCTTAACA
* ** *
561665 TTTTCACTTAATTTGGCTACTGGATAGAAAACCAATCGATCCAGTGTAAGGGGGATCGATTGGTT
1 TTTTCACTTAATTTAGCTACTGGATAGAAAACCAATCGATCCAGTCCAA-GGGGATCGATCGGTT
561730 CATTGATG
65 CATTGATG
* * * *
561738 TTTTCCCTTAATTTAGCTATTGGATGGAAAACCAATCGATCTTA-TCCAAGGGGATCGATCGGTT
1 TTTTCACTTAATTTAGCTACTGGATAGAAAACCAATCGATC-CAGTCCAAGGGGATCGATCGGTT
561802 TCACCCATAG
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
72 14 0.25
73 40 0.73
74 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (72 bp):
TTTTCACTTAATTTAGCTACTGGATAGAAAACCAATCGATCCAGTCCAAGGGGATCGATCGGTTC
ATTGATG
Found at i:568643 original size:22 final size:24
Alignment explanation
Indices: 568610--568653 Score: 58
Period size: 22 Copynumber: 1.9 Consensus size: 24
568600 TGTTGTACAG
568610 TTACATTTTTTA-ATG-AATTTAA
1 TTACATTTTTTACATGTAATTTAA
568632 TTAC-TTTCTTTACATGTAATTT
1 TTACATTT-TTTACATGTAATTT
568654 GTCTATTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 3 0.16
22 8 0.42
23 3 0.16
24 5 0.26
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.57
Consensus pattern (24 bp):
TTACATTTTTTACATGTAATTTAA
Found at i:572746 original size:17 final size:16
Alignment explanation
Indices: 572720--572764 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
572710 ATTAAAAAAT
572720 AAAAAT-TAAAAACTCA
1 AAAAATCTAAAAA-TCA
*
572736 AAAAATCTAAAAATCT
1 AAAAATCTAAAAATCA
572752 AAAAATCTAAAAA
1 AAAAATCTAAAAA
572765 AATGAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 21 0.78
17 6 0.22
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAAATCTAAAAATCA
Found at i:572772 original size:16 final size:16
Alignment explanation
Indices: 572713--572787 Score: 59
Period size: 16 Copynumber: 4.8 Consensus size: 16
572703 TTATCTAATT
572713 AAAAAATAAAAAT-T-
1 AAAAAATAAAAATCTA
*
572727 AAAAACTCAAAAAATCTA
1 AAAAAAT--AAAAATCTA
**
572745 AAAATCTAAAAATCTA
1 AAAAAATAAAAATCTA
*
572761 AAAAAATGAAAAAAC--
1 AAAAAAT-AAAAATCTA
572776 AAAAAATAAAAA
1 AAAAAATAAAAA
572788 CAAAAAACAA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
14 11 0.22
15 7 0.14
16 20 0.39
17 7 0.14
18 6 0.12
ACGTcount: A:0.75, C:0.08, G:0.01, T:0.16
Consensus pattern (16 bp):
AAAAAATAAAAATCTA
Found at i:572786 original size:13 final size:13
Alignment explanation
Indices: 572770--572799 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
572760 AAAAAAATGA
*
572770 AAAAACAAAAAAT
1 AAAAACAAAAAAC
572783 AAAAACAAAAAAC
1 AAAAACAAAAAAC
572796 AAAA
1 AAAA
572800 TGCTTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.87, C:0.10, G:0.00, T:0.03
Consensus pattern (13 bp):
AAAAACAAAAAAC
Found at i:574516 original size:14 final size:14
Alignment explanation
Indices: 574493--574519 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
574483 AAAAGAAACA
574493 GAAAAAAAAAGGAG
1 GAAAAAAAAAGGAG
574507 GAAAAAAAAAGGA
1 GAAAAAAAAAGGA
574520 TCAAAGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAAGGAG
Found at i:576492 original size:6 final size:6
Alignment explanation
Indices: 576444--576519 Score: 61
Period size: 6 Copynumber: 13.0 Consensus size: 6
576434 AGAAAAAATT
* * * * *
576444 TAAAAA TAGAAA TTAAAA TGAAAAA TAAAAGA GAGAAA GAAAAA T-AAAA
1 TAAAAA TAAAAA TAAAAA T-AAAAA TAAAA-A TAAAAA TAAAAA TAAAAA
576493 T-AAAA TAAAAA T--AAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
576520 GAAATTAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
4 4 0.07
5 10 0.18
6 34 0.60
7 9 0.16
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (6 bp):
TAAAAA
Found at i:576524 original size:16 final size:15
Alignment explanation
Indices: 576490--576524 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
576480 AAGAAAAATA
*
576490 AAATAAAATAAAAAT
1 AAATAAAATAAAAAG
576505 AAATAAAAATAAAAAG
1 AAAT-AAAATAAAAAG
576521 AAAT
1 AAAT
576525 TAATACAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (15 bp):
AAATAAAATAAAAAG
Found at i:576811 original size:14 final size:13
Alignment explanation
Indices: 576786--576810 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
576776 TAAGTAACAA
576786 AATTAAAAAAAAT
1 AATTAAAAAAAAT
576799 AATTAAAAAAAA
1 AATTAAAAAAAA
576811 ACACATGTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AATTAAAAAAAAT
Found at i:577198 original size:112 final size:111
Alignment explanation
Indices: 576970--577191 Score: 378
Period size: 108 Copynumber: 2.0 Consensus size: 111
576960 TAAAATCATT
*
576970 AAAAATATAGTAATTTTTTATTTTTTAATAAGAATTAGTTAAATTAAAAAATCAATTTGAAAATA
1 AAAAATATAGTAATTTTTTATTTTTTAATAAGAATTAGTTAAATTAAAAAA-CAATTTCAAAATA
577035 AAAGAAAAATCTGAAATATATTTAGTACATATATAAAAAAATTAGAA
65 AAAGAAAAATCTGAAATATATTTAGTACATATATAAAAAAATTAGAA
* *
577082 AAAAATATAGTAATTTTTTGTTTTTTAGTAAGAATTAGTTAAATT-AAAAA-AA-TTCAAAATAA
1 AAAAATATAGTAATTTTTTATTTTTTAATAAGAATTAGTTAAATTAAAAAACAATTTCAAAATAA
*
577144 AAGAAAATTCTGAAATATATTTAGTACATATATAAAAAAATTAGAA
66 AAGAAAAATCTGAAATATATTTAGTACATATATAAAAAAATTAGAA
577190 AA
1 AA
577192 TGAAAAAAGT
Statistics
Matches: 106, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
108 56 0.53
109 2 0.02
111 5 0.05
112 43 0.41
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (111 bp):
AAAAATATAGTAATTTTTTATTTTTTAATAAGAATTAGTTAAATTAAAAAACAATTTCAAAATAA
AAGAAAAATCTGAAATATATTTAGTACATATATAAAAAAATTAGAA
Found at i:577676 original size:2 final size:2
Alignment explanation
Indices: 577669--577694 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
577659 CAAATATTAA
577669 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
577695 TAAGTTTGAA
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:577760 original size:10 final size:10
Alignment explanation
Indices: 577747--577790 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
577737 AAAAATTAAA
577747 TTATATATTT
1 TTATATATTT
577757 TTAT-TAGTTT
1 TTATATA-TTT
577767 TTATATATTT
1 TTATATATTT
*
577777 TT-TAAATTT
1 TTATATATTT
577786 TTATA
1 TTATA
577791 AAATAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
9 10 0.33
10 18 0.60
11 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (10 bp):
TTATATATTT
Found at i:577786 original size:18 final size:19
Alignment explanation
Indices: 577741--577790 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
577731 ATTAAAAAAA
*
577741 ATTAAATTATATAT-TTTT
1 ATTAAATTTTATATATTTT
**
577759 ATTAGTTTTTATATATTTT
1 ATTAAATTTTATATATTTT
577778 -TTAAATTTT-TATA
1 ATTAAATTTTATATA
577791 AAATAAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 4 0.15
18 18 0.69
19 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTAAATTTTATATATTTT
Found at i:577835 original size:10 final size:10
Alignment explanation
Indices: 577820--577860 Score: 55
Period size: 10 Copynumber: 3.8 Consensus size: 10
577810 TATCTAAAAC
577820 TATTAAAATA
1 TATTAAAATA
577830 TATTAAAATTCA
1 TATTAAAA-T-A
577842 TATTAAAATA
1 TATTAAAATA
577852 TATATAAAA
1 TAT-TAAAA
577861 ATAAATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 12 0.43
11 7 0.25
12 9 0.32
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (10 bp):
TATTAAAATA
Found at i:577846 original size:12 final size:11
Alignment explanation
Indices: 577820--577862 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
577810 TATCTAAAAC
577820 TATTAAAA-TA
1 TATTAAAATTA
577830 TATTAAAATTCA
1 TATTAAAATT-A
577842 TATTAAAATATA
1 TATTAAAAT-TA
*
577854 TATAAAAAT
1 TATTAAAAT
577863 AAATTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 8 0.28
11 1 0.03
12 19 0.66
13 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
TATTAAAATTA
Found at i:579657 original size:9 final size:9
Alignment explanation
Indices: 579643--579668 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
579633 GTTGAAGTTG
579643 TAGTAGTAA
1 TAGTAGTAA
579652 TAGTAGTAA
1 TAGTAGTAA
579661 TAGTAGTA
1 TAGTAGTA
579669 GTGGTGCGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (9 bp):
TAGTAGTAA
Found at i:581870 original size:22 final size:22
Alignment explanation
Indices: 581844--581894 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
581834 CTTATCATAA
*
581844 ATAAGGATTTTTCATTCTTCAT
1 ATAAGGATCTTTCATTCTTCAT
*
581866 GTAAGGATCTTTCATTCTTCAT
1 ATAAGGATCTTTCATTCTTCAT
581888 ATAAGGA
1 ATAAGGA
581895 GAGGGAGGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (22 bp):
ATAAGGATCTTTCATTCTTCAT
Found at i:583359 original size:21 final size:21
Alignment explanation
Indices: 583305--583385 Score: 81
Period size: 21 Copynumber: 3.9 Consensus size: 21
583295 AATCAACTAA
* *
583305 ATCCCAAACTGATTTCTAACG
1 ATCCCAAACTGATCTCTAATG
* * **
583326 ATTCTAATTTGATCTCTAATG
1 ATCCCAAACTGATCTCTAATG
*
583347 ATCCCAAACTGATCTCCAATG
1 ATCCCAAACTGATCTCTAATG
* *
583368 ATCCCAATCTAATCTCTA
1 ATCCCAAACTGATCTCTA
583386 TCAATCTCAA
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.33
Consensus pattern (21 bp):
ATCCCAAACTGATCTCTAATG
Found at i:583383 original size:42 final size:42
Alignment explanation
Indices: 583305--583385 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
583295 AATCAACTAA
* * * * * *
583305 ATCCCAAACTGATTTCTAACGATTCTAATTTGATCTCTAATG
1 ATCCCAAACTGATCTCCAACGATCCCAATCTAATCTCTAATG
*
583347 ATCCCAAACTGATCTCCAATGATCCCAATCTAATCTCTA
1 ATCCCAAACTGATCTCCAACGATCCCAATCTAATCTCTA
583386 TCAATCTCAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.33
Consensus pattern (42 bp):
ATCCCAAACTGATCTCCAACGATCCCAATCTAATCTCTAATG
Found at i:583535 original size:14 final size:15
Alignment explanation
Indices: 583505--583537 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
583495 GTAGTATTCA
*
583505 CATACACTATTCATT
1 CATACACTATACATT
583520 CATACA-TATACATT
1 CATACACTATACATT
583534 CATA
1 CATA
583538 TAAACCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.36
Consensus pattern (15 bp):
CATACACTATACATT
Found at i:583901 original size:120 final size:121
Alignment explanation
Indices: 583735--583976 Score: 450
Period size: 120 Copynumber: 2.0 Consensus size: 121
583725 CTCAAACTAA
583735 TCTTCAACCAATTTTTTTAAAAATTTGAGTCAGCATTTTCAATAATCTCCATTTTTTACTTAAAT
1 TCTTCAACCAATTTTTTTAAAAATTTGAGTCAGCATTTTCAATAATCTCCATTTTTTACTTAAAT
*
583800 TTCATTAAACTATCATTCTTTATACTAGATATGCTTAACTTCACCTATAATGAAAG
66 TTCATTAAACTATCATTCTTTATACTAGATATGCTTAACTTCACCTACAATGAAAG
**
583856 TCTTCAACCAATTTTTTTTTAAATTTG-GTCAGCATTTTCAATAATCTCCATTTTTTACTTAAAT
1 TCTTCAACCAATTTTTTTAAAAATTTGAGTCAGCATTTTCAATAATCTCCATTTTTTACTTAAAT
583920 TTCATTAAACTATCATTCTTTATACTAGATATGCTTAACTTCACCTACAATGAAAG
66 TTCATTAAACTATCATTCTTTATACTAGATATGCTTAACTTCACCTACAATGAAAG
583976 T
1 T
583977 TTTGCAATCT
Statistics
Matches: 118, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
120 93 0.79
121 25 0.21
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.44
Consensus pattern (121 bp):
TCTTCAACCAATTTTTTTAAAAATTTGAGTCAGCATTTTCAATAATCTCCATTTTTTACTTAAAT
TTCATTAAACTATCATTCTTTATACTAGATATGCTTAACTTCACCTACAATGAAAG
Found at i:584379 original size:21 final size:21
Alignment explanation
Indices: 584345--584384 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
584335 TACCAAACTA
** *
584345 ATCTCTAATGATCCTAATTTG
1 ATCTCTAACAATCCCAATTTG
584366 ATCTCTAACAATCCCAATT
1 ATCTCTAACAATCCCAATT
584385 CAAATATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (21 bp):
ATCTCTAACAATCCCAATTTG
Found at i:584860 original size:16 final size:15
Alignment explanation
Indices: 584837--584877 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
584827 GGGTATCAAA
584837 AAAATTTTTTCTCTT
1 AAAATTTTTTCTCTT
584852 AAAA-TTTTTCTCTT
1 AAAATTTTTTCTCTT
584866 ACAAATCTTTTT
1 A-AAAT-TTTTT
584878 ATTTATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.48
15 7 0.30
17 5 0.22
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (15 bp):
AAAATTTTTTCTCTT
Found at i:589836 original size:2 final size:2
Alignment explanation
Indices: 589829--589869 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
589819 TCAGGACGGG
589829 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
589870 ATATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:589874 original size:2 final size:2
Alignment explanation
Indices: 589869--589893 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
589859 TCTCTCTCTC
589869 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
589894 CCTAATCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:595561 original size:2 final size:2
Alignment explanation
Indices: 595556--595588 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
595546 ATGATATATA
*
595556 TG TG TG TG TG TG TG TG CG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
595589 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.48, T:0.48
Consensus pattern (2 bp):
TG
Found at i:606593 original size:7 final size:7
Alignment explanation
Indices: 606581--606606 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
606571 AGAAGGGTTT
606581 GCAGTCG
1 GCAGTCG
606588 GCAGTCG
1 GCAGTCG
606595 GCAGTCG
1 GCAGTCG
606602 GCAGT
1 GCAGT
606607 TGCCTCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.27, G:0.42, T:0.15
Consensus pattern (7 bp):
GCAGTCG
Found at i:606767 original size:21 final size:21
Alignment explanation
Indices: 606740--606803 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
606730 TCGTAAAGTT
606740 TGTGGGCTTACCTAGGGGTTG
1 TGTGGGCTTACCTAGGGGTTG
*
606761 TTTGGG----CCTAGGGGTTG
1 TGTGGGCTTACCTAGGGGTTG
*
606778 TGTGGGCTTACCTAGGGATTG
1 TGTGGGCTTACCTAGGGGTTG
*
606799 AGTGG
1 TGTGG
606804 CCCATTTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 16 0.46
21 19 0.54
ACGTcount: A:0.11, C:0.12, G:0.44, T:0.33
Consensus pattern (21 bp):
TGTGGGCTTACCTAGGGGTTG
Found at i:606772 original size:17 final size:17
Alignment explanation
Indices: 606750--606784 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
606740 TGTGGGCTTA
*
606750 CCTAGGGGTTGTTTGGG
1 CCTAGGGGTTGTGTGGG
606767 CCTAGGGGTTGTGTGGG
1 CCTAGGGGTTGTGTGGG
606784 C
1 C
606785 TTACCTAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.14, G:0.49, T:0.31
Consensus pattern (17 bp):
CCTAGGGGTTGTGTGGG
Found at i:612436 original size:73 final size:74
Alignment explanation
Indices: 612296--612436 Score: 212
Period size: 73 Copynumber: 1.9 Consensus size: 74
612286 GACAAACTTC
* * * * *
612296 CACCTCCATTACATTAGTCCTGTCTCATAAAACATGAGAAGTAGAGGAAAGATAAAGAAATATAT
1 CACCTCCATTACATCACTCCTGTCTCATAAAACATGAGAACTAGAGGAAAGATAAACAAATAGAT
612361 AGAGGAAGA
66 AGAGGAAGA
* *
612370 CACCTCCATTACATCACTCCTGTCTCATGAAA-ATGAGAACTAGAGGAAAGATAAACCAATAGAT
1 CACCTCCATTACATCACTCCTGTCTCATAAAACATGAGAACTAGAGGAAAGATAAACAAATAGAT
612434 AGA
66 AGA
612437 CATAATTGAC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
73 31 0.52
74 29 0.48
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.21
Consensus pattern (74 bp):
CACCTCCATTACATCACTCCTGTCTCATAAAACATGAGAACTAGAGGAAAGATAAACAAATAGAT
AGAGGAAGA
Done.