Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold24
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: 3006277
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.30
Warning! 383161 characters in sequence are not A, C, G, or T
File 18 of 19
Found at i:2640252 original size:27 final size:27
Alignment explanation
Indices: 2640192--2640253 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
2640182 AAATCACATA
* **
2640192 TAATTTTAAAATTTAAATAAATTAATT
1 TAATTTTAAAAATTAAATAAATTAACC
* *
2640219 TAATTTTAAAAATTAATTCAATTAACC
1 TAATTTTAAAAATTAAATAAATTAACC
*
2640246 TACTTTTA
1 TAATTTTA
2640254 TATAAAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (27 bp):
TAATTTTAAAAATTAAATAAATTAACC
Found at i:2640527 original size:9 final size:9
Alignment explanation
Indices: 2640452--2640526 Score: 53
Period size: 9 Copynumber: 8.2 Consensus size: 9
2640442 TTTAAAAAAA
2640452 AATTAAATT
1 AATTAAATT
* *
2640461 GATTAAATA
1 AATTAAATT
* *
2640470 AATTTATTT
1 AATTAAATT
*
2640479 TATTAAATTT
1 AATTAAA-TT
*
2640489 TATTAAAATT
1 AATT-AAATT
2640499 AATTAAATT
1 AATTAAATT
* *
2640508 AATTGAATA
1 AATTAAATT
2640517 AATT-AATT
1 AATTAAATT
2640525 AA
1 AA
2640527 AATCAATTGA
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
8 5 0.10
9 32 0.63
10 11 0.22
11 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (9 bp):
AATTAAATT
Found at i:2644503 original size:29 final size:30
Alignment explanation
Indices: 2644441--2644497 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2644431 CTCTTTAGAC
* *
2644441 GTAAATTACAGATTAAAAGTTTATTTAATA
1 GTAAATTAAAGATTAAAAGCTTATTTAATA
2644471 GTAAATTAAAGATT-AAAGCTTATTTAA
1 GTAAATTAAAGATTAAAAGCTTATTTAA
2644498 ATGTAATAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.39
Consensus pattern (30 bp):
GTAAATTAAAGATTAAAAGCTTATTTAATA
Found at i:2650133 original size:5 final size:5
Alignment explanation
Indices: 2650112--2650152 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
2650102 CATGTATTTT
2650112 TTATA TT-TA TT-TA TTATA TTATA TTATAA TTATAA TTATA T
1 TTATA TTATA TTATA TTATA TTATA TTAT-A TTAT-A TTATA T
2650153 CTAAAATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 8 0.24
5 15 0.44
6 11 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:2650210 original size:24 final size:24
Alignment explanation
Indices: 2650183--2650241 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
2650173 ATAAATTTTA
2650183 TATTTATTAATAAT-TTTTAAGTAT
1 TATTT-TTAATAATATTTTAAGTAT
* *
2650207 TATTTTTTAATTATATTTTAATTAT
1 TA-TTTTTAATAATATTTTAAGTAT
2650232 T-TTTTTAATA
1 TATTTTTAATA
2650242 TGTTTAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 8 0.27
24 9 0.30
25 13 0.43
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TATTTTTAATAATATTTTAAGTAT
Found at i:2650232 original size:25 final size:24
Alignment explanation
Indices: 2650183--2650241 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
2650173 ATAAATTTTA
*
2650183 TATTTATTAATAATTTTTAAGTAT
1 TATTTTTTAATAATTTTTAAGTAT
* *
2650207 TATTTTTTAATTATATTTTAATTA-
1 TATTTTTTAATAAT-TTTTAAGTAT
2650231 T-TTTTTTAATA
1 TATTTTTTAATA
2650242 TGTTTAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 9 0.30
24 13 0.43
25 8 0.27
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TATTTTTTAATAATTTTTAAGTAT
Found at i:2650236 original size:11 final size:11
Alignment explanation
Indices: 2650205--2650236 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2650195 ATTTTTAAGT
2650205 ATTATTTTTTA
1 ATTATTTTTTA
*
2650216 ATTATATTTTA
1 ATTATTTTTTA
2650227 ATTATTTTTT
1 ATTATTTTTT
2650237 TAATATGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTATTTTTTA
Found at i:2650897 original size:2 final size:2
Alignment explanation
Indices: 2650890--2650938 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
2650880 TTTCTGTTCC
*
2650890 AT AT AT AT AT AT AT AT TT 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
2650932 AT AT AT A
1 AT AT AT A
2650939 GAGGTATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2651170 original size:24 final size:24
Alignment explanation
Indices: 2651141--2651199 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
2651131 ATAGTATTGA
*
2651141 TTTA-TTTAAAAAAATTATATAATT
1 TTTATTTTAAAAAAATTAT-CAATT
*
2651165 TTTATTTTTAAAAAATTATCAATT
1 TTTATTTTAAAAAAATTATCAATT
2651189 TTT-TCTTTAAA
1 TTTAT-TTTAAA
2651200 CCCTAGCCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 1 0.03
24 16 0.53
25 13 0.43
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTATTTTAAAAAAATTATCAATT
Found at i:2651183 original size:25 final size:24
Alignment explanation
Indices: 2651141--2651199 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
2651131 ATAGTATTGA
* *
2651141 TTTA-TTTAAAAAAATTATATAATT
1 TTTATTTTTAAAAAATTAT-CAATT
2651165 TTTATTTTTAAAAAATTATCAATT
1 TTTATTTTTAAAAAATTATCAATT
*
2651189 TTT-TCTTTAAA
1 TTTATTTTTAAA
2651200 CCCTAGCCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.23
24 11 0.35
25 13 0.42
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTATTTTTAAAAAATTATCAATT
Found at i:2651346 original size:21 final size:20
Alignment explanation
Indices: 2651322--2651360 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2651312 ATAAAATAAT
2651322 TAATGATTATTATTTTGTTAA
1 TAATG-TTATTATTTTGTTAA
*
2651343 TAATGTTTTTATTTTGTT
1 TAATGTTATTATTTTGTT
2651361 TTCAACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (20 bp):
TAATGTTATTATTTTGTTAA
Found at i:2651721 original size:30 final size:30
Alignment explanation
Indices: 2651686--2651747 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
2651676 ATTTTGTTTG
* *
2651686 ATATATATCTATATGTAT-TTATAATTTTTA
1 ATATAT-TATATATGTATCTTATAATTATTA
* *
2651716 ATATATTATATATTTATCTTTTAATTATTA
1 ATATATTATATATGTATCTTATAATTATTA
2651746 AT
1 AT
2651748 TAAATTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (30 bp):
ATATATTATATATGTATCTTATAATTATTA
Found at i:2651754 original size:24 final size:23
Alignment explanation
Indices: 2651711--2651755 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
2651701 TATTTATAAT
*
2651711 TTTTAATATATTATATATTTATC
1 TTTTAATATATTATAAATTTATC
2651734 TTTTAAT-TATTAATTAAATTTA
1 TTTTAATATATT-A-TAAATTTA
2651756 ATATATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTAATATATTATAAATTTATC
Found at i:2653173 original size:35 final size:35
Alignment explanation
Indices: 2653107--2653173 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
2653097 AAATCATTAT
2653107 AATTTTAAAAATAATAAAATTATATAATATGAATA
1 AATTTTAAAAATAATAAAATTATATAATATGAATA
*
2653142 AATTATTAAAAATAATATAA-TATATAATATGA
1 AATT-TTAAAAATAATAAAATTATATAATATGA
2653174 TGTGAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 16 0.53
36 14 0.47
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (35 bp):
AATTTTAAAAATAATAAAATTATATAATATGAATA
Found at i:2654461 original size:2 final size:2
Alignment explanation
Indices: 2654454--2654479 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2654444 ATCATAATGA
2654454 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
2654480 CCTTTTTTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2664989 original size:43 final size:43
Alignment explanation
Indices: 2664942--2665028 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
2664932 ACTATGAGAC
*
2664942 CCCCAAATCTCAATCGTACATCAACCAACAAC-AGCAAGACAGG
1 CCCCAAATCTCAATCATACATCAACCAACAACAAG-AAGACAGG
* * *
2664985 CCCCAAATTTCAATCATGCGTCAACCAACAACAAGAAGACAGG
1 CCCCAAATCTCAATCATACATCAACCAACAACAAGAAGACAGG
2665028 C
1 C
2665029 TTATCTCATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 37 0.95
44 2 0.05
ACGTcount: A:0.41, C:0.33, G:0.13, T:0.13
Consensus pattern (43 bp):
CCCCAAATCTCAATCATACATCAACCAACAACAAGAAGACAGG
Found at i:2665273 original size:2 final size:2
Alignment explanation
Indices: 2665255--2665300 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
2665245 GTGGCTGCCA
* * *
2665255 AT AT TT AT AT TT AT AT AT AC 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
2665297 AT AT
1 AT AT
2665301 TCATCCGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2665949 original size:22 final size:21
Alignment explanation
Indices: 2665907--2665951 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2665897 AAAACGATTA
* * *
2665907 TTAAAAATAATTTTTTATATT
1 TTAAAAATAAATATTGATATT
2665928 TTAAAAATAAATATTGATTATT
1 TTAAAAATAAATATTGA-TATT
2665950 TT
1 TT
2665952 TAATTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTAAAAATAAATATTGATATT
Found at i:2666847 original size:20 final size:20
Alignment explanation
Indices: 2666810--2666848 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2666800 AATAAAATTT
* **
2666810 ATTAATTTTTTATTTTAAAA
1 ATTAATTTATTAAGTTAAAA
2666830 ATTAATTTATTAAGTTAAA
1 ATTAATTTATTAAGTTAAA
2666849 TATCTAGATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
ATTAATTTATTAAGTTAAAA
Found at i:2672221 original size:2 final size:2
Alignment explanation
Indices: 2672216--2672240 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2672206 ATATATATAT
2672216 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
2672241 TAGAACTGGG
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2682479 original size:26 final size:24
Alignment explanation
Indices: 2682432--2682479 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
2682422 AAAGTTAATT
*
2682432 AAAAATTATTTATTTATCATTTAA
1 AAAAATTATTTATATATCATTTAA
*
2682456 AAAAATATATTTAATATATTATTT
1 AAAAAT-TATTT-ATATATCATTT
2682480 TTACTGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 5 0.25
26 9 0.45
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
AAAAATTATTTATATATCATTTAA
Found at i:2686515 original size:28 final size:31
Alignment explanation
Indices: 2686484--2686554 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 31
2686474 ATAAAAAATT
*
2686484 TTAAGTTTTATTT-AAAA-TTTAAA-TTTAA
1 TTAAATTTTATTTTAAAATTTTAAAGTTTAA
2686512 TTAAATTTTATTTTTAAAATTTTAAAGTTTAA
1 TTAAATTTTA-TTTTAAAATTTTAAAGTTTAA
*
2686544 TTTAATATTTA
1 TTAAAT-TTTA
2686555 AGTTTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 9 0.25
29 3 0.08
30 4 0.11
31 6 0.17
32 10 0.28
33 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (31 bp):
TTAAATTTTATTTTAAAATTTTAAAGTTTAA
Found at i:2687064 original size:21 final size:22
Alignment explanation
Indices: 2687035--2687090 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 22
2687025 ATCTTAGATG
* *
2687035 AAATATAAAATTATTTTA-CAA
1 AAATTTAAAATTATGTTATCAA
*
2687056 AAATTT-AAATT-TGTTATTAA
1 AAATTTAAAATTATGTTATCAA
2687076 AAATTTAAATATTAT
1 AAATTTAAA-ATTAT
2687091 AATATTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 4 0.14
20 13 0.46
21 7 0.25
22 3 0.11
23 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
AAATTTAAAATTATGTTATCAA
Found at i:2687172 original size:22 final size:21
Alignment explanation
Indices: 2687123--2687180 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
2687113 AATTATCATT
2687123 ATAATT-TTTTATTTTT-TAA
1 ATAATTATTTTATTTTTATAA
2687142 AT--TTATTTTATTTTTATAAA
1 ATAATTATTTTATTTTTAT-AA
*
2687162 ATAATTATTTTATTATTAT
1 ATAATTATTTTATTTTTAT
2687181 TTTATTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
17 2 0.06
18 10 0.30
19 3 0.09
20 4 0.12
22 14 0.42
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
ATAATTATTTTATTTTTATAA
Found at i:2690183 original size:6 final size:6
Alignment explanation
Indices: 2690172--2690212 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
2690162 TTTTGGTGAA
*
2690172 GCCATT GCCATT GCCATT GCCATT GCCGTT GCC-TT GCCATT
1 GCCATT GCCATT GCCATT GCCATT GCCATT GCCATT GCCATT
2690213 CATACAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.12, C:0.34, G:0.20, T:0.34
Consensus pattern (6 bp):
GCCATT
Found at i:2693479 original size:21 final size:22
Alignment explanation
Indices: 2693453--2693506 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
2693443 AAAAATAAAA
*
2693453 AAATTATAAATATTAA-AATTT
1 AAATTATAAATATTAATAAATT
*
2693474 AAATTAAAAATATTAATTAAATT
1 AAATTATAAATATTAA-TAAATT
2693497 AAATT-TAAAT
1 AAATTATAAAT
2693507 TTCATAGCGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.54
22 4 0.14
23 9 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATTATAAATATTAATAAATT
Found at i:2693505 original size:24 final size:21
Alignment explanation
Indices: 2693426--2693501 Score: 63
Period size: 21 Copynumber: 3.7 Consensus size: 21
2693416 TTTTTGTTAC
*
2693426 ATTAAAAATTATAATTTAAAA-
1 ATTAAAAATTA-AATTAAAAAT
*
2693447 A-T-AAAA--AAATTATAAAT
1 ATTAAAAATTAAATTAAAAAT
*
2693464 ATTAAAATTTAAATTAAAAAT
1 ATTAAAAATTAAATTAAAAAT
2693485 ATTAATTAAATTAAATT
1 ATTAA--AAATTAAATT
2693502 TAAATTTCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
16 7 0.16
17 2 0.05
18 1 0.02
19 7 0.16
20 1 0.02
21 16 0.37
23 9 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTAAAAATTAAATTAAAAAT
Found at i:2693506 original size:29 final size:28
Alignment explanation
Indices: 2693426--2693507 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 28
2693416 TTTTTGTTAC
*
2693426 ATTA-AAAATTATAATTTAAAAATAAAAAA
1 ATTATAAAATTA-AATTT-AAATTAAAAAA
*
2693455 ATTATAAATATTAAAATTTAAATTAAAAAT
1 ATTATAAA-ATT-AAATTTAAATTAAAAAA
*
2693485 ATTAATTAAATTAAATTTAAATT
1 ATT-ATAAAATTAAATTTAAATT
2693508 TCATAGCGGG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
29 15 0.33
30 18 0.39
31 12 0.26
32 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
ATTATAAAATTAAATTTAAATTAAAAAA
Found at i:2695215 original size:23 final size:24
Alignment explanation
Indices: 2695170--2695225 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
2695160 TTTAATATAA
* *
2695170 TATATTTAAAATTTTATATTTTTTTG
1 TATATTTAAAA--TTATACTTTTTCG
2695196 TATATTTAAAA-TATACTTTTTCG
1 TATATTTAAAATTATACTTTTTCG
2695219 TATATTT
1 TATATTT
2695226 GTCAAAAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 17 0.61
26 11 0.39
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (24 bp):
TATATTTAAAATTATACTTTTTCG
Found at i:2701397 original size:18 final size:19
Alignment explanation
Indices: 2701353--2701398 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2701343 TTATTATATC
2701353 AATTAAAAATATTATTTTT
1 AATTAAAAATATTATTTTT
* *
2701372 TA-TATAAATATATATTTTT
1 AATTAAAAATAT-TATTTTT
2701391 AATTAAAA
1 AATTAAAA
2701399 TTAAAATTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTAAAAATATTATTTTT
Found at i:2702372 original size:23 final size:24
Alignment explanation
Indices: 2702345--2702390 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
2702335 ATAATTCAAT
* *
2702345 ATTAAAATTTAT-ATTTTATTTTA
1 ATTAAAATTAATCATTATATTTTA
*
2702368 ATTAATATTAATCATTATATTTT
1 ATTAAAATTAATCATTATATTTT
2702391 TAAAATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTAAAATTAATCATTATATTTTA
Found at i:2706433 original size:21 final size:20
Alignment explanation
Indices: 2706409--2706456 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
2706399 TCTCATTCAA
*
2706409 ATATTTTTAAAATTATTTAAT
1 ATATTTTTAAAA-TAATTAAT
*
2706430 ATATTATTTATAATAATTAAT
1 ATATT-TTTAAAATAATTAAT
2706451 A-ATTTT
1 ATATTTT
2706457 ATTTATGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.08
20 3 0.12
21 13 0.54
22 6 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTTTTAAAATAATTAAT
Found at i:2706439 original size:22 final size:22
Alignment explanation
Indices: 2706408--2706461 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
2706398 ATCTCATTCA
*
2706408 AATATT-TTTAAAATTATTTAAT
1 AATATTATTTAAAA-TAATTAAT
*
2706430 -ATATTATTTATAATAATTAAT
1 AATATTATTTAAAATAATTAAT
*
2706451 AATTTTATTTA
1 AATATTATTTA
2706462 TGTGTATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATATTATTTAAAATAATTAAT
Found at i:2706710 original size:14 final size:13
Alignment explanation
Indices: 2706675--2706710 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2706665 ATCACGGTTA
2706675 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
*
2706688 TTTTATTTTTTTT
1 TTTTCTTTTTTTT
*
2706701 TTTTCCTTTT
1 TTTTCTTTTT
2706711 CAAGTACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:2707268 original size:3 final size:3
Alignment explanation
Indices: 2707260--2707290 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2707250 GAGTCCATAG
2707260 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2707291 AGAGAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2710085 original size:16 final size:18
Alignment explanation
Indices: 2710056--2710106 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
2710046 CATATACATA
*
2710056 TATATATATATATAATTTT
1 TATATTTAT-TATAATTTT
2710075 T-TATTT-TTATAATTTT
1 TATATTTATTATAATTTT
2710091 TATATTTATT-TAATTT
1 TATATTTATTATAATTT
2710107 AATTATTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 10 0.34
17 12 0.41
18 6 0.21
19 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATATTTATTATAATTTT
Found at i:2710092 original size:15 final size:16
Alignment explanation
Indices: 2710060--2710099 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
2710050 TACATATATA
*
2710060 TATATATATAATTTTT
1 TATATTTATAATTTTT
*
2710076 TATTTTTATAA-TTTT
1 TATATTTATAATTTTT
2710091 TATATTTAT
1 TATATTTAT
2710100 TTAATTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATATTTATAATTTTT
Found at i:2710243 original size:21 final size:23
Alignment explanation
Indices: 2710201--2710243 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
2710191 TTTTTAACAA
**
2710201 TAATATATATATGATAGTATTTT
1 TAATATATATATGATAACATTTT
2710224 TAAT-TAT-TATGATAACATTT
1 TAATATATATATGATAACATTT
2710244 AAAATATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 3 0.17
23 4 0.22
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (23 bp):
TAATATATATATGATAACATTTT
Found at i:2710795 original size:3 final size:3
Alignment explanation
Indices: 2710787--2710835 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
2710777 TACACAAATG
* *
2710787 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AAA ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2710835 A
1 A
2710836 AAAATCCATG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:2711059 original size:3 final size:3
Alignment explanation
Indices: 2711053--2711087 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2711043 TAATGATAAT
2711053 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
2711088 TAAAAGATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:2711413 original size:3 final size:3
Alignment explanation
Indices: 2711405--2711448 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2711395 AAAGAATATG
2711405 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2711449 ACTTGTGTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2711774 original size:2 final size:2
Alignment explanation
Indices: 2711761--2711794 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2711751 TTCTCACGCA
*
2711761 CT CT CA CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2711795 ATATATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:2711799 original size:2 final size:2
Alignment explanation
Indices: 2711794--2711833 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2711784 TCTCTCTCTC
2711794 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2711834 AAACAATCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2712671 original size:3 final size:3
Alignment explanation
Indices: 2712623--2712651 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2712613 TAAGTATCTG
2712623 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2712652 AGCAACTAAT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2713092 original size:3 final size:3
Alignment explanation
Indices: 2713086--2713124 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2713076 ACCAATGCAT
2713086 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
2713125 CTGCAGCTTC
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2723081 original size:20 final size:22
Alignment explanation
Indices: 2723064--2723116 Score: 92
Period size: 20 Copynumber: 2.5 Consensus size: 22
2723054 GTTATTAATG
2723064 TTATTAATATTATTTTAAGTAA
1 TTATTAATATTATTTTAAGTAA
2723086 TTATTAATA--ATTTTAAGTAA
1 TTATTAATATTATTTTAAGTAA
2723106 TTATTAATATT
1 TTATTAATATT
2723117 TAGTATCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 20 0.69
22 9 0.31
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (22 bp):
TTATTAATATTATTTTAAGTAA
Found at i:2723106 original size:10 final size:11
Alignment explanation
Indices: 2723078--2723112 Score: 56
Period size: 10 Copynumber: 3.4 Consensus size: 11
2723068 TAATATTATT
2723078 TTAAGTAATTA
1 TTAAGTAATTA
2723089 TTAA-TAATT-
1 TTAAGTAATTA
2723098 TTAAGTAATTA
1 TTAAGTAATTA
2723109 TTAA
1 TTAA
2723113 TATTTAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.18
10 10 0.45
11 8 0.36
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (11 bp):
TTAAGTAATTA
Found at i:2730691 original size:2 final size:2
Alignment explanation
Indices: 2730679--2730718 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2730669 TTTCTCATCC
*
2730679 AT AT AT CT 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
2730719 CATTGTTACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2732012 original size:37 final size:37
Alignment explanation
Indices: 2731971--2732044 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
2731961 GATCTGCTCA
2731971 TTGGGATTATAATTTGGAGGTTTGATATTGAAGCTGT
1 TTGGGATTATAATTTGGAGGTTTGATATTGAAGCTGT
2732008 TTGGGATTATAATTTGGAGGTTTGATATTGAAGCTGT
1 TTGGGATTATAATTTGGAGGTTTGATATTGAAGCTGT
2732045 CTTTCGGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.03, G:0.30, T:0.43
Consensus pattern (37 bp):
TTGGGATTATAATTTGGAGGTTTGATATTGAAGCTGT
Found at i:2735683 original size:3 final size:3
Alignment explanation
Indices: 2735675--2735699 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2735665 GAGAAATTGT
2735675 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
2735700 GGAACTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2737585 original size:1 final size:1
Alignment explanation
Indices: 2737579--2737605 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
2737569 CCTGGAAACC
2737579 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
2737606 GATAAACCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2746920 original size:23 final size:23
Alignment explanation
Indices: 2746892--2746936 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2746882 TGGAATCATA
2746892 AAAATAATCTGAAACAAATAGAT
1 AAAATAATCTGAAACAAATAGAT
2746915 AAAATAATCTGAAACAAATAGA
1 AAAATAATCTGAAACAAATAGA
2746937 CATAGAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.20
Consensus pattern (23 bp):
AAAATAATCTGAAACAAATAGAT
Found at i:2749944 original size:22 final size:21
Alignment explanation
Indices: 2749919--2749976 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
2749909 ATTTTGTTAA
2749919 ATTATATTATTAAATTTTTATT
1 ATTATATTATTAAATTTTT-TT
*
2749941 ATTA-ATAAATTAAA-TTTTTT
1 ATTATAT-TATTAAATTTTTTT
*
2749961 ATTAATTTTATTAAAT
1 ATT-ATATTATTAAAT
2749977 AAAATTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
20 5 0.17
21 13 0.45
22 11 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTATATTATTAAATTTTTTT
Found at i:2749978 original size:30 final size:34
Alignment explanation
Indices: 2749915--2749992 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 34
2749905 TTTAATTTTG
2749915 TTAAATTATATTATTAAATTTTTATTATTAAT-AAA
1 TTAAATT-TATTATTAAATTTTTATTA-TAATAAAA
*
2749950 TTAAATTTTTTATT-AA-TTTTATTA-AATAAAA
1 TTAAATTTATTATTAAATTTTTATTATAATAAAA
2749981 TT-AATTTATTAT
1 TTAAATTTATTAT
2749993 ATATACATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 12 0.30
31 5 0.12
32 8 0.20
33 2 0.05
34 6 0.15
35 7 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (34 bp):
TTAAATTTATTATTAAATTTTTATTATAATAAAA
Found at i:2750889 original size:2 final size:2
Alignment explanation
Indices: 2750884--2750916 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2750874 ATATATATAT
2750884 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2750917 TGGTCTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2756101 original size:6 final size:6
Alignment explanation
Indices: 2756090--2756116 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2756080 TAAATAAAGC
2756090 TTGATT TTGATT TTGATT TTGATT TTG
1 TTGATT TTGATT TTGATT TTGATT TTG
2756117 GTGAATTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.19, T:0.67
Consensus pattern (6 bp):
TTGATT
Found at i:2760703 original size:21 final size:21
Alignment explanation
Indices: 2760677--2760716 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2760667 TGCCTTCTTC
2760677 TTCTTGACCTTGTAAGACCTT
1 TTCTTGACCTTGTAAGACCTT
2760698 TTCTTGACCTTGTAAGACC
1 TTCTTGACCTTGTAAGACC
2760717 CCATCCAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (21 bp):
TTCTTGACCTTGTAAGACCTT
Found at i:2762567 original size:2 final size:2
Alignment explanation
Indices: 2762560--2762585 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2762550 TTGAAGTTGG
2762560 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
2762586 CACATCTTTG
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:2763958 original size:2 final size:2
Alignment explanation
Indices: 2763945--2763978 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2763935 AAACTACAAA
*
2763945 AT AT AC 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
2763979 GGACTTCAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2764625 original size:2 final size:2
Alignment explanation
Indices: 2764620--2764649 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2764610 ATATATATAT
2764620 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2764650 GTGGGTGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2764783 original size:7 final size:7
Alignment explanation
Indices: 2764771--2764804 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
2764761 TTTTCCACCA
2764771 TAGCCAT
1 TAGCCAT
2764778 TAGCCAT
1 TAGCCAT
2764785 TAGCCAT
1 TAGCCAT
2764792 TAGCCAT
1 TAGCCAT
2764799 TAGCCA
1 TAGCCA
2764805 GGCTGATCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (7 bp):
TAGCCAT
Found at i:2765269 original size:32 final size:32
Alignment explanation
Indices: 2765199--2765270 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
2765189 ATACGATATG
* *
2765199 AAATTATA-ATAATAAATATATAAATATGTCA
1 AAATTATATAAAATAAATATATAAATATGTAA
*
2765230 AATTTATATAAAATAAAT-TATTAAAATAT-TAA
1 AAATTATATAAAATAAATATA-T-AAATATGTAA
2765262 AAATTATAT
1 AAATTATAT
2765271 TTAATTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
31 9 0.26
32 19 0.56
33 6 0.18
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (32 bp):
AAATTATATAAAATAAATATATAAATATGTAA
Found at i:2765663 original size:3 final size:3
Alignment explanation
Indices: 2765655--2765688 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2765645 GCTAACATCC
2765655 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2765689 TTGATGTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2766035 original size:3 final size:3
Alignment explanation
Indices: 2766027--2766060 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2766017 TACATCAACA
2766027 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2766061 CACCAATGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2766490 original size:32 final size:30
Alignment explanation
Indices: 2766441--2766499 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
2766431 TAATTTGATT
*
2766441 TTTTTAAATTTAAATATTATTGATTTAAATAA
1 TTTTTAAATTCAAATATTA--GATTTAAATAA
2766473 TTTTTAAA-TCAAGATATTAGATTTAAA
1 TTTTTAAATTCAA-ATATTAGATTTAAA
2766500 ATTTATGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 8 0.32
31 3 0.12
32 14 0.56
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (30 bp):
TTTTTAAATTCAAATATTAGATTTAAATAA
Found at i:2770647 original size:2 final size:2
Alignment explanation
Indices: 2770640--2770673 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2770630 AGATAGGTAA
2770640 AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2770674 AACAAAGAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2772984 original size:5 final size:5
Alignment explanation
Indices: 2772974--2773005 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
2772964 CACAAAAGGT
2772974 GGCTA GGCTA GGCTA GGCTA GGCTA GGCTA GG
1 GGCTA GGCTA GGCTA GGCTA GGCTA GGCTA GG
2773006 GGCTAGCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.44, T:0.19
Consensus pattern (5 bp):
GGCTA
Found at i:2773657 original size:2 final size:2
Alignment explanation
Indices: 2773650--2773684 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2773640 TGTCTCAGAA
*
2773650 AG AG AG AG AG AG CG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2773685 TGATTTCGTC
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2775997 original size:2 final size:2
Alignment explanation
Indices: 2775992--2776017 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2775982 TATATATATA
2775992 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
2776018 ATCTGATTTG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2776471 original size:2 final size:2
Alignment explanation
Indices: 2776428--2776452 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2776418 AGTACATTAC
2776428 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 A
2776453 ATACTTCCAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2777869 original size:45 final size:43
Alignment explanation
Indices: 2777815--2777910 Score: 140
Period size: 46 Copynumber: 2.2 Consensus size: 43
2777805 TATATATATT
2777815 ATAAATTTTAAT-TTTTTAATAATTTATAAAATATGAAATATTTA
1 ATAAATTTTAATATTTTTAATAATTTATAAAATAT-AAAT-TTTA
*
2777859 GATAAATTTTAATATTTTTAATAATTTATAATATATAAATTTTA
1 -ATAAATTTTAATATTTTTAATAATTTATAAAATATAAATTTTA
*
2777903 ATATATTT
1 ATAAATTT
2777911 ATATTTAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
43 7 0.15
44 4 0.08
45 16 0.33
46 21 0.44
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (43 bp):
ATAAATTTTAATATTTTTAATAATTTATAAAATATAAATTTTA
Found at i:2777882 original size:19 final size:20
Alignment explanation
Indices: 2777855--2777892 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2777845 ATATGAAATA
2777855 TTTAGATAAATTT-TAATATT
1 TTTAGAT-AATTTATAATATT
2777875 TTTA-ATAATTTATAATAT
1 TTTAGATAATTTATAATAT
2777893 ATAAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTAGATAATTTATAATATT
Found at i:2778363 original size:2 final size:2
Alignment explanation
Indices: 2778351--2778398 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
2778341 GCCGCCATCT
*
2778351 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2778393 TC TC TC
1 TC TC TC
2778399 GGCACTATTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:2781109 original size:2 final size:2
Alignment explanation
Indices: 2781102--2781143 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2781092 TTGTTAGAAA
2781102 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2781144 GGATTAAGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2784517 original size:21 final size:20
Alignment explanation
Indices: 2784482--2784526 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
2784472 ATAGTAAATA
*
2784482 AAAAAATAATTAATGATGTT
1 AAAAAATAATTAATGATGAT
* *
2784502 AAAAAATATTTAAATGTTGAT
1 AAAAAATAATT-AATGATGAT
2784523 AAAA
1 AAAA
2784527 TATTAACGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (20 bp):
AAAAAATAATTAATGATGAT
Found at i:2785489 original size:16 final size:16
Alignment explanation
Indices: 2785451--2785491 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2785441 AAACATATTA
*
2785451 AATTAAAATTAAAATT
1 AATTAAATTTAAAATT
*
2785467 AACTAAATTTAAAATT
1 AATTAAATTTAAAATT
*
2785483 ATTTAAATT
1 AATTAAATT
2785492 CAAATAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTAAATTTAAAATT
Found at i:2785971 original size:20 final size:20
Alignment explanation
Indices: 2785948--2785991 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2785938 AACTAATAAA
2785948 ATAAAAT-TATAACTATTATT
1 ATAAAATATATAACTA-TATT
*
2785968 ATAAAATATATAATTATATT
1 ATAAAATATATAACTATATT
2785988 ATAA
1 ATAA
2785992 TAAAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAAAATATATAACTATATT
Found at i:2786664 original size:18 final size:18
Alignment explanation
Indices: 2786616--2786678 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
2786606 AGAATTGAGT
*
2786616 AAATTTTATTAATAATAA
1 AAATTTTTTTAATAATAA
* *
2786634 AAATATTTATAATAATAA
1 AAATTTTTTTAATAATAA
** *
2786652 TGATTTTTTTAAT--TTA
1 AAATTTTTTTAATAATAA
2786668 AAATTTTTTTA
1 AAATTTTTTTA
2786679 TATTAATTAT
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
16 11 0.31
18 24 0.69
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
AAATTTTTTTAATAATAA
Found at i:2786706 original size:13 final size:13
Alignment explanation
Indices: 2786672--2786707 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2786662 AATTTAAAAT
2786672 TTTTTTATATTAA
1 TTTTTTATATTAA
* *
2786685 TTATCTATATTAA
1 TTTTTTATATTAA
2786698 TTTTTTATAT
1 TTTTTTATAT
2786708 CTGTATTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTTTATATTAA
Found at i:2786717 original size:29 final size:27
Alignment explanation
Indices: 2786669--2786725 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
2786659 TTTAATTTAA
*
2786669 AATTTTTTTATATTAATTATCTATATT
1 AATTTTTTTATATTAATTATATATATT
* *
2786696 AATTTTTTATATCTGTATTTATATATATT
1 AATTTTTT-TATAT-TAATTATATATATT
2786725 A
1 A
2786726 TATATAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.32
28 4 0.16
29 13 0.52
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (27 bp):
AATTTTTTTATATTAATTATATATATT
Found at i:2786753 original size:13 final size:13
Alignment explanation
Indices: 2786737--2786761 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2786727 ATATAAATTA
2786737 TAAATATTTTTAC
1 TAAATATTTTTAC
2786750 TAAATATTTTTA
1 TAAATATTTTTA
2786762 TTTTAAAAAT
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:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTTTTAC
Found at i:2787644 original size:2 final size:2
Alignment explanation
Indices: 2787639--2787667 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2787629 TTGTGTGTGC
2787639 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
2787668 AATTATAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2791683 original size:2 final size:2
Alignment explanation
Indices: 2791670--2791702 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2791660 GAGTAGATAC
*
2791670 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2791703 AAATAAACTC
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2792390 original size:2 final size:2
Alignment explanation
Indices: 2792385--2792413 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2792375 TATCCATCTA
2792385 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 T
2792414 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2792804 original size:2 final size:2
Alignment explanation
Indices: 2792782--2792824 Score: 50
Period size: 2 Copynumber: 20.0 Consensus size: 2
2792772 TCATTCATAC
*
2792782 TA TA CTA TA CTA TA CTA TA TA TA TA TA TA TA TA TT TA TA TA TA
1 TA TA -TA TA -TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2792825 AATCCTACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 30 0.83
3 6 0.17
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2795891 original size:2 final size:2
Alignment explanation
Indices: 2795884--2795913 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2795874 TGATAGCTTA
*
2795884 AT AT AT AT AT TT 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
2795914 CTATGTTGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2797206 original size:2 final size:2
Alignment explanation
Indices: 2797199--2797247 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2797189 AACATTATGA
2797199 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
2797241 AT AT AT A
1 AT AT AT A
2797248 AATGCGTGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2800464 original size:50 final size:50
Alignment explanation
Indices: 2800389--2800488 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
2800379 CAAATAGAGG
* *
2800389 ATGTCATAATCCTCTTCTCAGACTAGCATGTCTGTTGCTGAAAGTTCATT
1 ATGTCATAACCCTCTTCTCAGACTAGCATGTCTGTTGCTGAAAGGTCATT
2800439 ATGTCATAACCCTCTTCTCAGACTAGCATGTCTGTTGCTGAAAGGTCATT
1 ATGTCATAACCCTCTTCTCAGACTAGCATGTCTGTTGCTGAAAGGTCATT
2800489 TACTTTTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (50 bp):
ATGTCATAACCCTCTTCTCAGACTAGCATGTCTGTTGCTGAAAGGTCATT
Found at i:2802893 original size:2 final size:2
Alignment explanation
Indices: 2802886--2802925 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2802876 ATATAGAAGG
2802886 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2802926 GCTATTAGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2803602 original size:2 final size:2
Alignment explanation
Indices: 2803586--2803620 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2803576 ACTGTGTATT
*
2803586 TA TA GA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2803621 GCTAGATAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2806963 original size:2 final size:2
Alignment explanation
Indices: 2806956--2806998 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2806946 TCCAAAATAC
2806956 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
2806998 A
1 A
2806999 ACACTGAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2807092 original size:20 final size:20
Alignment explanation
Indices: 2807055--2807095 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2807045 AACACAGATT
*
2807055 CATATTATTTTACTTATATC
1 CATATTATTTTACATATATC
* *
2807075 CATATTGTTTTAGATATATC
1 CATATTATTTTACATATATC
2807095 C
1 C
2807096 CTATATATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.51
Consensus pattern (20 bp):
CATATTATTTTACATATATC
Found at i:2807743 original size:48 final size:48
Alignment explanation
Indices: 2807668--2807763 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
2807658 ATCTTTGCCT
*
2807668 TTTTCTTAATTAATTAAGCTATACATCTATGTTAATAAAAACATATCA
1 TTTTATTAATTAATTAAGCTATACATCTATGTTAATAAAAACATATCA
2807716 TTTTATTAATTAATTAAGCTATACATCTATGTTAATAAAAACATATCA
1 TTTTATTAATTAATTAAGCTATACATCTATGTTAATAAAAACATATCA
2807764 ACTTAGTTGC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (48 bp):
TTTTATTAATTAATTAAGCTATACATCTATGTTAATAAAAACATATCA
Found at i:2808470 original size:2 final size:2
Alignment explanation
Indices: 2808463--2808491 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2808453 GCTTTTAATC
2808463 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
2808492 ATTAATTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2808599 original size:6 final size:7
Alignment explanation
Indices: 2808584--2808613 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2808574 ATCTCACATC
2808584 TTTTGTT
1 TTTTGTT
2808591 TTTTGTT
1 TTTTGTT
2808598 TTTTGTT
1 TTTTGTT
*
2808605 TTTTCTT
1 TTTTGTT
2808612 TT
1 TT
2808614 GGGTGCATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (7 bp):
TTTTGTT
Found at i:2809077 original size:2 final size:2
Alignment explanation
Indices: 2809070--2809098 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2809060 GGCAAGTGTA
2809070 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
2809099 CAGACTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2810942 original size:3 final size:3
Alignment explanation
Indices: 2810936--2810973 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2810926 ATAATAATAA
2810936 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2810974 AATATCCTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2811335 original size:3 final size:3
Alignment explanation
Indices: 2811327--2811378 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
2811317 TGGGTGGACT
2811327 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
2811375 TTA T
1 TTA T
2811379 GTCTTTAAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2811885 original size:1 final size:1
Alignment explanation
Indices: 2811881--2811912 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
2811871 AAAAAAAAAA
*
2811881 GGGGGGGCGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
2811913 CAAATTTCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:2818956 original size:2 final size:2
Alignment explanation
Indices: 2818949--2818982 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2818939 AATCTCTGTC
2818949 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
2818983 GAGATGAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2835538 original size:21 final size:22
Alignment explanation
Indices: 2835509--2835554 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2835499 TGTTCAGACA
** *
2835509 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2835531 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2835552 AGT
1 AGT
2835555 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2841827 original size:117 final size:115
Alignment explanation
Indices: 2841649--2841859 Score: 262
Period size: 117 Copynumber: 1.8 Consensus size: 115
2841639 TGTTGATTTC
* * * **
2841649 TTTCTTATCTTTATTGTGTTTCTTTCTTCTTTGATGACCCAAAATTAATAAATTACGATTATAAT
1 TTTCTTATCTTGATTGTGTTTCTTTCTTCTTTAATAACCCAAAATTAATAAATTAAAATTATAAT
* *
2841714 T-TCATTTGTATTAGCATTTTTTAATAATACGAAAACCAAAGGTTACTTTT
66 TCT-ATTTATATTAACATTTTTTAATAATACGAAAACCAAAGGTTACTTTT
* * * * *
2841764 TTTCTTATCTTGCTTTTGTTTCTTTTTTTCTTTCAATAACTCAAAATTAGTAAATTAAAATTATA
1 TTTCTTATCTTGATTGTGTTTC-TTTCTTCTTT-AATAACCCAAAATTAATAAATTAAAATTATA
* *
2841829 ATTCTATTTATATTAATATTTTTTAGTAATA
64 ATTCTATTTATATTAACATTTTTTAATAATA
2841860 TTATTTTTAA
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
115 19 0.24
116 9 0.11
117 50 0.63
118 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (115 bp):
TTTCTTATCTTGATTGTGTTTCTTTCTTCTTTAATAACCCAAAATTAATAAATTAAAATTATAAT
TCTATTTATATTAACATTTTTTAATAATACGAAAACCAAAGGTTACTTTT
Found at i:2841962 original size:18 final size:18
Alignment explanation
Indices: 2841933--2841972 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
2841923 AACTTAGATA
*
2841933 AAAAATAGTTAATATTAAT
1 AAAAATAGTTAAT-TAAAT
2841952 AAAAATA-TTAATTAAAT
1 AAAAATAGTTAATTAAAT
2841969 AAAA
1 AAAA
2841973 TTTAGATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 5 0.25
19 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAAATAGTTAATTAAAT
Found at i:2843522 original size:6 final size:6
Alignment explanation
Indices: 2843511--2843541 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2843501 GGCTACCTAC
*
2843511 GGCTAT GGCTAT GGCTAT GGCTAT GGTTAT G
1 GGCTAT GGCTAT GGCTAT GGCTAT GGCTAT G
2843542 CTGCTCTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.13, G:0.35, T:0.35
Consensus pattern (6 bp):
GGCTAT
Found at i:2844839 original size:3 final size:3
Alignment explanation
Indices: 2844831--2844863 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2844821 TACATTACAT
2844831 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2844864 CTACTAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2851645 original size:27 final size:27
Alignment explanation
Indices: 2851615--2851669 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
2851605 TGTCAGTATA
2851615 ATAAATTGACTATCCATGGATTTGGGT
1 ATAAATTGACTATCCATGGATTTGGGT
*
2851642 ATAAATTGAGTATCCATGGATTTGGGT
1 ATAAATTGACTATCCATGGATTTGGGT
2851669 A
1 A
2851670 AGTAAAGACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (27 bp):
ATAAATTGACTATCCATGGATTTGGGT
Found at i:2855111 original size:1 final size:1
Alignment explanation
Indices: 2855105--2855130 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2855095 GTCAAAACAG
2855105 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
2855131 CACCCCCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2857985 original size:2 final size:2
Alignment explanation
Indices: 2857980--2858004 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2857970 CTTCGTAAAC
2857980 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 A
2858005 GTCAGTTCCC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2866195 original size:16 final size:16
Alignment explanation
Indices: 2866171--2866201 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2866161 AAAGTTAATA
2866171 ATTTAAATTTAAAATT
1 ATTTAAATTTAAAATT
*
2866187 ATTTGAATTTAAAAT
1 ATTTAAATTTAAAAT
2866202 AGCTTGAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
ATTTAAATTTAAAATT
Found at i:2866208 original size:16 final size:16
Alignment explanation
Indices: 2866176--2866217 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2866166 TAATAATTTA
*
2866176 AATTTAAAATTATTTG
1 AATTTAAAATTACTTG
2866192 AATTTAAAA-TAGCTTG
1 AATTTAAAATTA-CTTG
2866208 AATTTGAAAA
1 AATTT-AAAA
2866218 AGTTTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 2 0.09
16 17 0.74
17 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (16 bp):
AATTTAAAATTACTTG
Found at i:2866227 original size:16 final size:16
Alignment explanation
Indices: 2866208--2866253 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
2866198 AAATAGCTTG
*
2866208 AATTTGAAAAAGTTTA
1 AATTTGAAAAAATTTA
*
2866224 AATTCGAAAAAATTTA
1 AATTTGAAAAAATTTA
2866240 AATTT-AAAAGAATT
1 AATTTGAAAA-AATT
2866254 CGAACTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.35
Consensus pattern (16 bp):
AATTTGAAAAAATTTA
Found at i:2866262 original size:16 final size:16
Alignment explanation
Indices: 2866243--2866278 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2866233 AAATTTAAAT
2866243 TTAAAAGAATTCGAAC
1 TTAAAAGAATTCGAAC
*
2866259 TTAAAAGAATTCGAAT
1 TTAAAAGAATTCGAAC
2866275 TTAA
1 TTAA
2866279 GACTGATCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (16 bp):
TTAAAAGAATTCGAAC
Found at i:2867520 original size:24 final size:23
Alignment explanation
Indices: 2867484--2867531 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
2867474 TTTAGTTAAG
*
2867484 ATTAAATGGATTTTTAAATATTTT
1 ATTAAATAGATTTTTAAAT-TTTT
*
2867508 ATTAAATATATTTTTAAATTTTT
1 ATTAAATAGATTTTTAAATTTTT
2867531 A
1 A
2867532 AAATTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
ATTAAATAGATTTTTAAATTTTT
Found at i:2867759 original size:30 final size:30
Alignment explanation
Indices: 2867658--2867782 Score: 91
Period size: 30 Copynumber: 4.3 Consensus size: 30
2867648 TCAATATGAT
* *
2867658 TATAATAATAAA-TTATTTAAAAATTAATTA
1 TATAATAA-AAATTTACTTAAAAATTAATAA
* ** * *
2867688 TATATATAAATATAGACTT--TAATAAATAA
1 TATA-ATAAAAATTTACTTAAAAATTAATAA
* *
2867717 -ATAAT-TAAATTTA-TTAAAAATGTAATAG
1 TATAATAAAAATTTACTTAAAAAT-TAATAA
2867745 TATAATAAAAATTTACTTAAAAATTAATAA
1 TATAATAAAAATTTACTTAAAAATTAATAA
*
2867775 TTTAATAA
1 TATAATAA
2867783 TTTACTTTTT
Statistics
Matches: 70, Mismatches: 17, Indels: 16
0.68 0.17 0.16
Matches are distributed among these distances:
25 2 0.03
26 4 0.06
27 5 0.07
28 7 0.10
29 12 0.17
30 25 0.36
31 15 0.21
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (30 bp):
TATAATAAAAATTTACTTAAAAATTAATAA
Found at i:2869073 original size:13 final size:13
Alignment explanation
Indices: 2869057--2869104 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
2869047 AAATTTAATT
2869057 AAAAGTAATATGA
1 AAAAGTAATATGA
*
2869070 AAAATTAATAT-A
1 AAAAGTAATATGA
2869082 AAAA-TAATATGA
1 AAAAGTAATATGA
* *
2869094 ATATGTAATAT
1 AAAAGTAATAT
2869105 ATAATAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 6 0.20
12 8 0.27
13 16 0.53
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
AAAAGTAATATGA
Found at i:2869083 original size:24 final size:23
Alignment explanation
Indices: 2869045--2869121 Score: 77
Period size: 23 Copynumber: 3.2 Consensus size: 23
2869035 ACAATACAGA
2869045 AAAAATTTAAT-TAAAAGTAATATG
1 AAAAA-TTAATATAAAA-TAATATG
2869069 AAAAATTAATATAAAAATAATATG
1 AAAAATTAATAT-AAAATAATATG
* *
2869093 -AATATGTAATATATAATAATATG
1 AAAAAT-TAATATAAAATAATATG
2869116 CAAAAA
1 -AAAAA
2869122 AAATTATTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
23 19 0.42
24 19 0.42
25 7 0.16
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.31
Consensus pattern (23 bp):
AAAAATTAATATAAAATAATATG
Found at i:2869453 original size:14 final size:14
Alignment explanation
Indices: 2869436--2869505 Score: 50
Period size: 14 Copynumber: 4.7 Consensus size: 14
2869426 ATCTATACTA
2869436 TATTTTTTATAATT
1 TATTTTTTATAATT
* *
2869450 TATTTTTTAAAAATA
1 TATTTTTT-ATAATT
* *
2869465 TATATTTTAAAATT
1 TATTTTTTATAATT
* *
2869479 TAATCTTTATTAATT
1 TATTTTTTA-TAATT
2869494 TAATATTTTTAT
1 T-AT-TTTTTAT
2869506 TAAGTTTTAA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
14 19 0.45
15 16 0.38
16 2 0.05
17 5 0.12
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTTTTTATAATT
Found at i:2869560 original size:14 final size:16
Alignment explanation
Indices: 2869541--2869572 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
2869531 ACTTAATTTT
2869541 TAATATT-TATAT-TA
1 TAATATTATATATATA
2869555 TAATATTATATATATA
1 TAATATTATATATATA
2869571 TA
1 TA
2869573 TGTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATATTATATATATA
Found at i:2871665 original size:18 final size:17
Alignment explanation
Indices: 2871626--2871669 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2871616 TCCCAAAGCT
*
2871626 TTTTTTTTTCTTCTATC
1 TTTTTTTTTCTTCTACC
* *
2871643 ATTTTTTTTCTCTCTCCC
1 TTTTTTTTTCT-TCTACC
2871661 TTTTTTTTT
1 TTTTTTTTT
2871670 TATAAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTTTTTCTTCTACC
Found at i:2871957 original size:2 final size:2
Alignment explanation
Indices: 2871950--2871985 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2871940 TAAGAGACTT
*
2871950 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2871986 AACCAAGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Done.