Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold78
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: 2238306
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 23262 characters in sequence are not A, C, G, or T
File 15 of 15
Found at i:2154469 original size:19 final size:19
Alignment explanation
Indices: 2154429--2154487 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
2154419 GAGATACATG
*
2154429 AAATTTATTTATATTATTATA
1 AAATTTATATA-ATT-TTATA
2154450 AAATTTA-ATCAATTTTATA
1 AAATTTATAT-AATTTTATA
**
2154469 ATTTTTATATAATTTTATA
1 AAATTTATATAATTTTATA
2154488 TTTATTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 19 0.58
20 6 0.18
21 8 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATTTATATAATTTTATA
Found at i:2154531 original size:29 final size:27
Alignment explanation
Indices: 2154480--2154539 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 27
2154470 TTTTTATATA
*
2154480 ATTTTATATTTATTTAATTTAAATGTAAT
1 ATTTTATATTTATTTAATATAAAT-T-AT
2154509 ATTTTATATTTTATTT-ATATAAATTAT
1 ATTTTATA-TTTATTTAATATAAATTAT
2154536 ATTT
1 ATTT
2154540 ATTGAGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 6 0.21
28 1 0.03
29 15 0.52
30 7 0.24
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
ATTTTATATTTATTTAATATAAATTAT
Found at i:2155757 original size:29 final size:30
Alignment explanation
Indices: 2155725--2155782 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
2155715 CAAATAATTC
* *
2155725 AAAATTAAAATTGATTGA-AAAATTTAATA
1 AAAATCAAAATTGAGTGACAAAATTTAATA
*
2155754 AAAATCAAAATTTAGTGACAAAATTTAAT
1 AAAATCAAAATTGAGTGACAAAATTTAAT
2155783 TAAACAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (30 bp):
AAAATCAAAATTGAGTGACAAAATTTAATA
Found at i:2155792 original size:29 final size:31
Alignment explanation
Indices: 2155742--2155812 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 31
2155732 AAATTGATTG
**
2155742 AAAAATTTAA-TAAAAATCAAAATTTAGTGA-
1 AAAAATTTAATTAAAAA-CAAAATAAAGTGAT
* *
2155772 CAAAATTTAATTAAACA-AAAATAAAGTGAT
1 AAAAATTTAATTAAAAACAAAATAAAGTGAT
2155802 AAAAATTTAAT
1 AAAAATTTAAT
2155813 ATCAAGTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
29 10 0.29
30 19 0.56
31 5 0.15
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.30
Consensus pattern (31 bp):
AAAAATTTAATTAAAAACAAAATAAAGTGAT
Found at i:2155833 original size:29 final size:29
Alignment explanation
Indices: 2155802--2155900 Score: 101
Period size: 30 Copynumber: 3.3 Consensus size: 29
2155792 ATAAAGTGAT
2155802 AAAAATTTAATATCAAGTTAAAATATAATA
1 AAAAATTTAATATCAA-TTAAAATATAATA
* *
2155832 AAAAATATTAAT-TAAAATAAAATATAATGA
1 AAAAAT-TTAATATCAATTAAAATATAAT-A
* * *
2155862 TAAATTTTAATATTCGATTAAAATATAATA
1 AAAAATTTAATA-TCAATTAAAATATAATA
*
2155892 ACAAATTTA
1 AAAAATTTA
2155901 CCCTTTTAAC
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
29 16 0.29
30 21 0.38
31 18 0.33
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAATTTAATATCAATTAAAATATAATA
Found at i:2155837 original size:60 final size:59
Alignment explanation
Indices: 2155773--2155900 Score: 163
Period size: 60 Copynumber: 2.1 Consensus size: 59
2155763 ATTTAGTGAC
2155773 AAAATTTAATTAAACA-AAAATA-AAGTGATAAAAATTTAATA-TCAAGTTAAAATATAATAA
1 AAAATTTAATTAAA-ATAAAATATAA-TGAT-AAAATTTAATATTCAA-TTAAAATATAATAA
* *
2155833 AAAATATTAATTAAAATAAAATATAATGATAAATTTTAATATTCGATTAAAATATAATAA
1 AAAAT-TTAATTAAAATAAAATATAATGATAAAATTTAATATTCAATTAAAATATAATAA
*
2155893 CAAATTTA
1 AAAATTTA
2155901 CCCTTTTAAC
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
59 3 0.05
60 34 0.56
61 22 0.36
62 2 0.03
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (59 bp):
AAAATTTAATTAAAATAAAATATAATGATAAAATTTAATATTCAATTAAAATATAATAA
Found at i:2156144 original size:23 final size:21
Alignment explanation
Indices: 2156101--2156144 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2156091 ATTTATTATT
* *
2156101 TTATTTATTTTTAATATATAA
1 TTATATATTTTTAATAAATAA
2156122 TTATATATTTTATAAATAAATAA
1 TTATATATTTT-T-AATAAATAA
2156145 AATTAATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 1 0.05
23 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATATATTTTTAATAAATAA
Found at i:2157010 original size:20 final size:19
Alignment explanation
Indices: 2156977--2157014 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
2156967 ATTAGATTAC
2156977 ATAAATATTAATAACAATA
1 ATAAATATTAATAACAATA
2156996 ATAAATATATAATAACAAT
1 ATAAATAT-TAATAACAAT
2157015 TAGAAATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAAATATTAATAACAATA
Found at i:2157021 original size:20 final size:19
Alignment explanation
Indices: 2156979--2157023 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
2156969 TAGATTACAT
*
2156979 AAATATTAATAACAATAAT
1 AAATATTAATAACAATAAG
*
2156998 AAATATATAATAACAATTAG
1 AAATAT-TAATAACAATAAG
2157018 AAATAT
1 AAATAT
2157024 CGTAAATATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
AAATATTAATAACAATAAG
Found at i:2157988 original size:19 final size:20
Alignment explanation
Indices: 2157953--2157990 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2157943 TAAAATTTTT
*
2157953 TTTTAAAAAATTAAATAAAA
1 TTTTAAAAAAATAAATAAAA
2157973 TTTTAAAAAAAT-AATAAA
1 TTTTAAAAAAATAAATAAA
2157991 TTGTTTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TTTTAAAAAAATAAATAAAA
Found at i:2158468 original size:18 final size:19
Alignment explanation
Indices: 2158441--2158484 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
2158431 TATATATTTA
* *
2158441 AAAATTAAA-TTTAAGTAT
1 AAAATAAAATTTTAAATAT
2158459 AAAATAAAATTTTAAATAT
1 AAAATAAAATTTTAAATAT
*
2158478 TAAATAA
1 AAAATAA
2158485 TAATATAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAATAAAATTTTAAATAT
Found at i:2158492 original size:32 final size:30
Alignment explanation
Indices: 2158437--2158500 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 30
2158427 TATTTATATA
*
2158437 TTTAAAAATTAAATTTAAGTATAAAATAAAAT
1 TTTAAAAATTAAATATAAGTAT--AATAAAAT
*
2158469 TTTAAATATTAAATAATAA-TATAATAAAAT
1 TTTAAAAATTAAAT-ATAAGTATAATAAAAT
2158499 TT
1 TT
2158501 AATTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 10 0.34
32 16 0.55
33 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
TTTAAAAATTAAATATAAGTATAATAAAAT
Found at i:2159166 original size:7 final size:8
Alignment explanation
Indices: 2159147--2159183 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
2159137 CTTTACTATT
*
2159147 TTTTTAAG
1 TTTTTAAA
2159155 TTTTTAAA
1 TTTTTAAA
2159163 TTTTTAAA
1 TTTTTAAA
*
2159171 TTTTTTAA
1 TTTTTAAA
2159179 TTTTT
1 TTTTT
2159184 TTATTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (8 bp):
TTTTTAAA
Found at i:2159167 original size:9 final size:9
Alignment explanation
Indices: 2159144--2159186 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
2159134 GAGCTTTACT
*
2159144 ATTTTTTTA
1 ATTTTTTAA
*
2159153 AGTTTTTAA
1 ATTTTTTAA
2159162 A-TTTTTAA
1 ATTTTTTAA
2159170 ATTTTTTAA
1 ATTTTTTAA
*
2159179 TTTTTTTA
1 ATTTTTTA
2159187 TTATTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
8 8 0.27
9 22 0.73
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:2159184 original size:8 final size:8
Alignment explanation
Indices: 2159146--2159195 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
2159136 GCTTTACTAT
2159146 TTTTTTAA
1 TTTTTTAA
*
2159154 GTTTTTAAA
1 -TTTTTTAA
*
2159163 TTTTTAAA
1 TTTTTTAA
2159171 TTTTTTAA
1 TTTTTTAA
*
2159179 TTTTTTTA
1 TTTTTTAA
2159187 TTATTTTAA
1 TT-TTTTAA
2159196 AAGAGATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
8 24 0.67
9 12 0.33
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (8 bp):
TTTTTTAA
Found at i:2162267 original size:30 final size:28
Alignment explanation
Indices: 2162222--2162280 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
2162212 ATAATATTAT
**
2162222 AATTATTATTTTATGATTTTAATTTTTA
1 AATTATTATTTTATGATAATAATTTTTA
2162250 AATTATTAATATTTATGATAATAATTTTTA
1 AATTATT-AT-TTTATGATAATAATTTTTA
2162280 A
1 A
2162281 TAATATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 7 0.26
29 2 0.07
30 18 0.67
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (28 bp):
AATTATTATTTTATGATAATAATTTTTA
Found at i:2163870 original size:21 final size:21
Alignment explanation
Indices: 2163829--2163870 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2163819 TGCAAAATTG
*
2163829 AAATATCTAAAAAATACAATA
1 AAATATCTAAAAAATAAAATA
*
2163850 AAATATC-AAAAATTTAAAATA
1 AAATATCTAAAAA-ATAAAATA
2163871 TAAAGATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATATCTAAAAAATAAAATA
Found at i:2164446 original size:41 final size:41
Alignment explanation
Indices: 2164389--2164472 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
2164379 GAAATTTCGT
2164389 TTATAAGTTGATTTATTATGGTAGGTTAAAAAAAATATTAA
1 TTATAAGTTGATTTATTATGGTAGGTTAAAAAAAATATTAA
*
2164430 TTATAAGTTGATTTATTATGGTAGGTTAAAAAACATATTAA
1 TTATAAGTTGATTTATTATGGTAGGTTAAAAAAAATATTAA
2164471 TT
1 TT
2164473 TTATAAAATG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.42, C:0.01, G:0.14, T:0.43
Consensus pattern (41 bp):
TTATAAGTTGATTTATTATGGTAGGTTAAAAAAAATATTAA
Found at i:2166110 original size:23 final size:24
Alignment explanation
Indices: 2166079--2166125 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2166069 ATAAATTCTT
* *
2166079 AATTAAAATTATA-TAAAAAATTA
1 AATTAAAATAAAATTAAAAAATTA
*
2166102 AATTCAAATAAAATTAAAAAATTA
1 AATTAAAATAAAATTAAAAAATTA
2166126 GCCTTTGCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTAAAATAAAATTAAAAAATTA
Found at i:2166374 original size:2 final size:2
Alignment explanation
Indices: 2166367--2166399 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2166357 TTGTTTTATG
*
2166367 AT AT AT AT AC AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2166400 GTATTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2166580 original size:11 final size:11
Alignment explanation
Indices: 2166563--2166634 Score: 51
Period size: 11 Copynumber: 6.5 Consensus size: 11
2166553 TGATACGTAC
2166563 ATTTATATTAT
1 ATTTATATTAT
*
2166574 TTTTATATTAT
1 ATTTATATTAT
*
2166585 AATTATATTA-
1 ATTTATATTAT
*
2166595 A--AATATTAT
1 ATTTATATTAT
2166604 ATATATATATTAAAT
1 AT-T-TATATT--AT
*
2166619 ATTTATATTGT
1 ATTTATATTAT
2166630 ATTTA
1 ATTTA
2166635 AAATTAAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
8 6 0.12
9 1 0.02
10 1 0.02
11 24 0.50
13 11 0.23
14 1 0.02
15 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:2166612 original size:21 final size:19
Alignment explanation
Indices: 2166578--2166632 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
2166568 TATTATTTTT
2166578 ATATTATA-ATTATATTAAA
1 ATATTATATATTATATT-AA
2166597 ATATTATATATATATATTAA
1 ATATTATATAT-TATATTAA
*
2166617 ATATT-TATATTGTATT
1 ATATTATATATTATATT
2166633 TAAAATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 5 0.15
19 13 0.39
20 9 0.27
21 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
ATATTATATATTATATTAA
Found at i:2166613 original size:13 final size:12
Alignment explanation
Indices: 2166565--2166615 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 12
2166555 ATACGTACAT
*
2166565 TTATATTAT-TT
1 TTATATTATATA
2166576 TTATATTATA-A
1 TTATATTATATA
*
2166587 TTATATTAAAATA
1 TTATATT-ATATA
2166600 TTATATATATATA
1 TTATAT-TATATA
2166613 TTA
1 TTA
2166616 AATATTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 16 0.48
12 2 0.06
13 14 0.42
14 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTATATTATATA
Found at i:2168363 original size:25 final size:24
Alignment explanation
Indices: 2168335--2168401 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 24
2168325 TATAATTTTA
* *
2168335 AATTTTTATCATTATTATTTATTAT
1 AATTTTTAT-AATAATATTTATTAT
*
2168360 AATTAATTATAATAATATTTATTAT
1 AATT-TTTATAATAATATTTATTAT
* *
2168385 ATATTTTAATTATAATA
1 A-ATTTTTATAATAATA
2168402 AATATAACGT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
25 27 0.79
26 7 0.21
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTTTTATAATAATATTTATTAT
Found at i:2168364 original size:13 final size:13
Alignment explanation
Indices: 2168335--2168400 Score: 57
Period size: 13 Copynumber: 5.2 Consensus size: 13
2168325 TATAATTTTA
*
2168335 AATT-TTTATCAT
1 AATTATTTATTAT
*
2168347 TATTATTTATTAT
1 AATTATTTATTAT
* *
2168360 AATTAATTATAAT
1 AATTATTTATTAT
2168373 AA-TATTTATTAT
1 AATTATTTATTAT
*
2168385 ATATT-TTAATTAT
1 A-ATTATTTATTAT
2168398 AAT
1 AAT
2168401 AAATATAACG
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
12 14 0.33
13 28 0.65
14 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (13 bp):
AATTATTTATTAT
Found at i:2168393 original size:28 final size:25
Alignment explanation
Indices: 2168350--2168402 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 25
2168340 TTATCATTAT
2168350 TATTTATTATAATTAATTATAATAA
1 TATTTATTATAATTAATTATAATAA
2168375 TATTTATTATATATTTTAATTATAATAA
1 TATTTATTATA-A--TTAATTATAATAA
2168403 ATATAACGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 11 0.44
26 1 0.04
28 13 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TATTTATTATAATTAATTATAATAA
Found at i:2171517 original size:16 final size:16
Alignment explanation
Indices: 2171496--2171535 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
2171486 ACCTGAATCC
*
2171496 AAATGATTTGAATTTA
1 AAATGATTTGAACTTA
*
2171512 AAATGATCTGAACTTA
1 AAATGATTTGAACTTA
2171528 AAATGATT
1 AAATGATT
2171536 CAAATCTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (16 bp):
AAATGATTTGAACTTA
Found at i:2173644 original size:34 final size:34
Alignment explanation
Indices: 2173606--2173701 Score: 95
Period size: 34 Copynumber: 2.8 Consensus size: 34
2173596 TAAATAAGTA
* *
2173606 ATTTGATAGTTTGTCATTGTTGACTAAAGGGATG
1 ATTTGATAGTTTGCCATTATTGACTAAAGGGATG
* * * * *
2173640 ATTTGTTGGTTTGCCATTATTGATTAAATGGCTG
1 ATTTGATAGTTTGCCATTATTGACTAAAGGGATG
* *
2173674 ATTT-AGTGGTTTACCATTATTGACTAAA
1 ATTTGA-TAGTTTGCCATTATTGACTAAA
2173702 TGGCTAAAAG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (34 bp):
ATTTGATAGTTTGCCATTATTGACTAAAGGGATG
Found at i:2173702 original size:34 final size:34
Alignment explanation
Indices: 2173620--2173706 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 34
2173610 GATAGTTTGT
* * * *
2173620 CATTGTTGACTAAAGGGATGATTTGTTGGTTTGC
1 CATTATTGACTAAATGGCTGATTTGTTGGTTTAC
*
2173654 CATTATTGATTAAATGGCTGATTTAG-TGGTTTAC
1 CATTATTGACTAAATGGCTGATTT-GTTGGTTTAC
2173688 CATTATTGACTAAATGGCT
1 CATTATTGACTAAATGGCT
2173707 AAAAGATAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 45 0.98
35 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.41
Consensus pattern (34 bp):
CATTATTGACTAAATGGCTGATTTGTTGGTTTAC
Found at i:2178216 original size:33 final size:34
Alignment explanation
Indices: 2178145--2178261 Score: 182
Period size: 34 Copynumber: 3.5 Consensus size: 34
2178135 AAGTGGGAGA
* * *
2178145 ATTGTTGACTAAATTGGTGATTTGATAGTTTGCT
1 ATTGTTGACTAAATGGGTGATTTGGTAGTTTGCC
2178179 ATTGTTGACTAAATGGGTGATTTGGT-GTTTGCC
1 ATTGTTGACTAAATGGGTGATTTGGTAGTTTGCC
* *
2178212 ATTGTTGACTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGACTAAATGGGTGATTTGGTAGTTTGCC
2178246 ATTGTTGACTAAATGG
1 ATTGTTGACTAAATGG
2178262 CTAAAAGATA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
33 32 0.41
34 46 0.59
ACGTcount: A:0.22, C:0.08, G:0.27, T:0.43
Consensus pattern (34 bp):
ATTGTTGACTAAATGGGTGATTTGGTAGTTTGCC
Found at i:2180244 original size:40 final size:39
Alignment explanation
Indices: 2180176--2180268 Score: 95
Period size: 41 Copynumber: 2.4 Consensus size: 39
2180166 AACTGATGTC
* ** *
2180176 TATATATTATTTAT-TTAT-ATTTTTAAAAAATTTTATATT
1 TATATATTATTTTTATTATAATTTAAAAAAAAATTTA-A-T
2180215 TAATATATTATTTTTATTA-AATTTAAAAAAAAATTTAAT
1 T-ATATATTATTTTTATTATAATTTAAAAAAAAATTTAAT
2180254 TATATATT-TTTTTAT
1 TATATATTATTTTTAT
2180269 ATATCACTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
37 7 0.15
38 7 0.15
39 3 0.06
40 13 0.28
41 17 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (39 bp):
TATATATTATTTTTATTATAATTTAAAAAAAAATTTAAT
Found at i:2182256 original size:30 final size:29
Alignment explanation
Indices: 2182182--2182256 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
2182172 GGTTAAATGA
*
2182182 ATTTTTT-TCAAACATTAAAAAAATAAAT
1 ATTTTTTCTCAAAAATTAAAAAAATAAAT
*
2182210 ATATTTTTCAT-AAAAATTTAAAAAATAAAT
1 AT-TTTTTC-TCAAAAATTAAAAAAATAAAT
2182240 ATTTTTTACTCAAAAAT
1 ATTTTTT-CTCAAAAAT
2182257 CTTTAACCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
28 2 0.05
29 11 0.28
30 26 0.65
31 1 0.03
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (29 bp):
ATTTTTTCTCAAAAATTAAAAAAATAAAT
Found at i:2183279 original size:17 final size:17
Alignment explanation
Indices: 2183257--2183298 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
2183247 GAGTTTTTAT
*
2183257 TTAGATATTTTTATTCG
1 TTAGATATTTTTATTAG
2183274 TTAGATA-TTTTATTAG
1 TTAGATATTTTTATTAG
2183290 TTATGATAT
1 TTA-GATAT
2183299 AAGATTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (17 bp):
TTAGATATTTTTATTAG
Found at i:2183286 original size:16 final size:16
Alignment explanation
Indices: 2183257--2183298 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
2183247 GAGTTTTTAT
*
2183257 TTAGATATTTTTATTCG
1 TTAGATA-TTTTATTAG
2183274 TTAGATATTTTATTAG
1 TTAGATATTTTATTAG
2183290 TTATGATAT
1 TTA-GATAT
2183299 AAGATTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (16 bp):
TTAGATATTTTATTAG
Found at i:2186608 original size:18 final size:17
Alignment explanation
Indices: 2186574--2186606 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2186564 GTGAAATTGA
2186574 AACAATAACGAAGAAAC
1 AACAATAACGAAGAAAC
2186591 AACATATAAC-AAGAAA
1 AACA-ATAACGAAGAAA
2186607 ACGCGTAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.67, C:0.15, G:0.09, T:0.09
Consensus pattern (17 bp):
AACAATAACGAAGAAAC
Found at i:2188515 original size:2 final size:2
Alignment explanation
Indices: 2188508--2188548 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2188498 GTTCACTCAT
2188508 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
2188549 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:2188553 original size:2 final size:2
Alignment explanation
Indices: 2188548--2188590 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
2188538 TCTCTCTCTC
* * *
2188548 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA CA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2188590 T
1 T
2188591 CTGAGTTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2193461 original size:24 final size:24
Alignment explanation
Indices: 2193395--2193469 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
2193385 TATTTTTATT
*
2193395 TAAAT-TTAAT-TATAA-AAATATA
1 TAAATATTAATATAAAATAAAT-TA
*
2193417 TAAATATTAATATAAAATAAATTT
1 TAAATATTAATATAAAATAAATTA
**
2193441 TAAATATTTAATAT-ATTTAAATTA
1 TAAATA-TTAATATAAAATAAATTA
2193465 TAAAT
1 TAAAT
2193470 TCAAGCTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
22 5 0.11
23 5 0.11
24 23 0.52
25 11 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAATATTAATATAAAATAAATTA
Found at i:2194735 original size:2 final size:2
Alignment explanation
Indices: 2194730--2194760 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2194720 AATGACAATT
2194730 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2194761 TTCAGCAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2195033 original size:3 final size:3
Alignment explanation
Indices: 2195025--2195065 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
2195015 GACGTCAATG
* *
2195025 AAT AAT AAT AAT AAT AAG AAT AAT AAT AAT CTAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT A
2195066 GTAAAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.94
4 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2195977 original size:28 final size:28
Alignment explanation
Indices: 2195918--2195973 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
2195908 GTCAAAATTT
* *
2195918 ATATAAAAATAATATAAAATATGACATT
1 ATATAAAAATAATATAAAATATAACATA
*
2195946 ATATAAAAATAATATAAAA-ATAATATA
1 ATATAAAAATAATATAAAATATAACATA
2195973 A
1 A
2195974 ATATGTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (28 bp):
ATATAAAAATAATATAAAATATAACATA
Found at i:2196010 original size:110 final size:110
Alignment explanation
Indices: 2195819--2196044 Score: 269
Period size: 110 Copynumber: 2.1 Consensus size: 110
2195809 AATTAAAATG
* * * * * *
2195819 TAATGTAAAATATAATATGATATAAAAAATATAAAAATTATATGAATGTATGAAAGTAATTAAAT
1 TAATATAAAATATAACATGATATAAAAAATATAAAAATAATATAAATATATAAAAGTAATTAAAT
*
2195884 ATATATAATATAAATTATTAATA-AGTCAAAATTTATATAAA-A-A
66 ATATACAATATAAATTATTAATACA-TCAAAATTTATATAAATATA
* * * *
2195927 TAATATAAAATATGACATTATATAAAAATAATATAAAAATAATATAAATATGTAAAAGTGATTAA
1 TAATATAAAATATAACATGATAT-AAAA-AATATAAAAATAATATAAATATATAAAAGTAATTAA
* * * *
2195992 ATTTATACAATCTGAATTATTAATACATTAAAATTTATATAAATATA
64 ATATATACAATATAAATTATTAATACATCAAAATTTATATAAATATA
2196039 TAATAT
1 TAATAT
2196045 TTTAATTATA
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
108 19 0.19
109 4 0.04
110 66 0.67
111 2 0.02
112 7 0.07
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.36
Consensus pattern (110 bp):
TAATATAAAATATAACATGATATAAAAAATATAAAAATAATATAAATATATAAAAGTAATTAAAT
ATATACAATATAAATTATTAATACATCAAAATTTATATAAATATA
Found at i:2196591 original size:16 final size:15
Alignment explanation
Indices: 2196548--2196592 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
2196538 TAGATTTGAA
2196548 TATTTTTATTATTATT
1 TATTTTTATTA-TATT
*
2196564 TATTTATA-TATATT
1 TATTTTTATTATATT
2196578 TATTTTTAATTATAT
1 TATTTTT-ATTATAT
2196593 AAATTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 12 0.48
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTTATTATATT
Found at i:2196598 original size:20 final size:21
Alignment explanation
Indices: 2196556--2196598 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2196546 AATATTTTTA
* *
2196556 TTATTATTTATTTATATATAT
1 TTATTATTTAATTATATAAAT
2196577 TTATT-TTTAATTATATAAAT
1 TTATTATTTAATTATATAAAT
2196597 TT
1 TT
2196599 TTAATATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATTATTTAATTATATAAAT
Found at i:2196670 original size:13 final size:13
Alignment explanation
Indices: 2196647--2196687 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
2196637 CATCGTGTTG
2196647 AAAGAGAGAAAAAA
1 AAAG-GAGAAAAAA
2196661 AAAGGAG-AAAAA
1 AAAGGAGAAAAAA
*
2196673 AAATGA-AAAAAA
1 AAAGGAGAAAAAA
2196685 AAA
1 AAA
2196688 TTTAACTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 18 0.72
13 3 0.12
14 4 0.16
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (13 bp):
AAAGGAGAAAAAA
Found at i:2197062 original size:76 final size:80
Alignment explanation
Indices: 2196938--2197090 Score: 206
Period size: 76 Copynumber: 2.0 Consensus size: 80
2196928 TTTTTATGCG
* * *
2196938 TTTGTATCATATCTCAATTTATCTTATGTCTCTATTTATTGATTATTCTGATTTAATTTAAAAAT
1 TTTGTATCATATCTCAATTTATCTTATGTCTCTAATAATTGATCATTCTGATTTAATTTAAAAAT
2197003 AACATCTATATTGTA
66 AACATCTATATTGTA
* * * *
2197018 TTTGTATCATGTCTCAA-TT-T-TT-TGTCTTTAATAATTGATCATTCTGATTTAATTTAGAAGT
1 TTTGTATCATATCTCAATTTATCTTATGTCTCTAATAATTGATCATTCTGATTTAATTTAAAAAT
*
2197079 AACATTTATATT
66 AACATCTATATT
2197091 ATACATATAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
76 44 0.68
77 2 0.03
78 1 0.02
79 2 0.03
80 16 0.25
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (80 bp):
TTTGTATCATATCTCAATTTATCTTATGTCTCTAATAATTGATCATTCTGATTTAATTTAAAAAT
AACATCTATATTGTA
Found at i:2201253 original size:76 final size:76
Alignment explanation
Indices: 2201127--2201279 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
2201117 GTTGTACAGA
2201127 GACATCCGAATGTCTTGGGATGAAATTCGAGAAAATAAATCAATTTTGGTAGCAACTGAAAATAC
1 GACATCCGAATGTCTTGGGATGAAATTCGAGAAAATAAATCAATTTTGGTAGCAACTGAAAATAC
2201192 GGGACAACATC
66 GGGACAACATC
2201203 GACATCCGAATGTCTTGGGATGAAATTCGAGAAAATAAATCAATTTTGGTAGCAACTGAAAATAC
1 GACATCCGAATGTCTTGGGATGAAATTCGAGAAAATAAATCAATTTTGGTAGCAACTGAAAATAC
2201268 GGGACAACATC
66 GGGACAACATC
2201279 G
1 G
2201280 TGCTGTCCCA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (76 bp):
GACATCCGAATGTCTTGGGATGAAATTCGAGAAAATAAATCAATTTTGGTAGCAACTGAAAATAC
GGGACAACATC
Found at i:2204279 original size:12 final size:12
Alignment explanation
Indices: 2204262--2204310 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
2204252 CATACTCTAT
2204262 TTTAAATAAATA
1 TTTAAATAAATA
2204274 TTTAAATAAATA
1 TTTAAATAAATA
**
2204286 AATAAAT-AATA
1 TTTAAATAAATA
2204297 TTT-AATAAA-A
1 TTTAAATAAATA
2204307 TTTA
1 TTTA
2204311 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
10 7 0.23
11 7 0.23
12 17 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TTTAAATAAATA
Found at i:2204343 original size:18 final size:17
Alignment explanation
Indices: 2204320--2204353 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
2204310 ATTTTTTATT
2204320 AAAATTAAATAAAATATA
1 AAAATTAAA-AAAATATA
2204338 AAAATTAAAAAAATAT
1 AAAATTAAAAAAATAT
2204354 CGTTAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATTAAAAAAATATA
Found at i:2204495 original size:17 final size:19
Alignment explanation
Indices: 2204475--2204521 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
2204465 TATTATTTTA
2204475 TAAAATTTATT-T-ATAAT
1 TAAAATTTATTATAATAAT
2204492 TAAAATTTATTAATAATAAT
1 TAAAATTTATT-ATAATAAT
2204512 TAAAATTTAT
1 TAAAATTTAT
2204522 AAAATAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.41
19 1 0.04
20 15 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAAATTTATTATAATAAT
Found at i:2204535 original size:20 final size:20
Alignment explanation
Indices: 2204487--2204536 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2204477 AAATTTATTT
* *
2204487 ATAATTAAAATTTATTAATA
1 ATAAATAAAATTTATAAATA
*
2204507 ATAATTAAAATTTATAAAATA
1 ATAAATAAAATTTAT-AAATA
2204528 A-AAATAAAA
1 ATAAATAAAA
2204537 AGCTCGAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAATAAAATTTATAAATA
Found at i:2204537 original size:21 final size:20
Alignment explanation
Indices: 2204493--2204537 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
2204483 ATTTATAATT
* * *
2204493 AAAATTTATTAATAATAATT
1 AAAATTTATAAATAAAAATA
2204513 AAAATTTATAAAATAAAAATA
1 AAAATTTAT-AAATAAAAATA
2204534 AAAA
1 AAAA
2204538 GCTCGAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATTTATAAATAAAAATA
Found at i:2207087 original size:3 final size:3
Alignment explanation
Indices: 2207079--2207104 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2207069 AGTGTTAGCA
2207079 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
2207105 AGAATTCGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2209016 original size:41 final size:41
Alignment explanation
Indices: 2208971--2209099 Score: 215
Period size: 41 Copynumber: 3.1 Consensus size: 41
2208961 TTTTAAAAAA
*
2208971 TAATTAAAATTAAATGATTAATTTTG-AAATTGTAATTTTGG
1 TAATTAAAATTAAATGATTAA-TTTGAAAATTGTAACTTTGG
2209012 TAATTAAAATTAAATGATTAATTTGAAAATTGTAACTTTGG
1 TAATTAAAATTAAATGATTAATTTGAAAATTGTAACTTTGG
* *
2209053 AAATTAAAATTAAATGATTAATTCGAAAATTGTAACTTTGG
1 TAATTAAAATTAAATGATTAATTTGAAAATTGTAACTTTGG
2209094 TAATTA
1 TAATTA
2209100 TTGCATGAAA
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
40 4 0.05
41 79 0.95
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (41 bp):
TAATTAAAATTAAATGATTAATTTGAAAATTGTAACTTTGG
Found at i:2212692 original size:19 final size:18
Alignment explanation
Indices: 2212665--2212700 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2212655 AGAAATCTTT
*
2212665 TTAATAAATTTTAATTAAC
1 TTAAAAAATTTT-ATTAAC
2212684 TTAAAAAATTTTATTAA
1 TTAAAAAATTTTATTAA
2212701 AATAATAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAAAAATTTTATTAAC
Found at i:2214297 original size:28 final size:29
Alignment explanation
Indices: 2214266--2214332 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
2214256 AGACCTTGTT
* *
2214266 AAATAACTTAAATGGCCCTAAAATAAT-A
1 AAATAACTAAAATAGCCCTAAAATAATGA
* * *
2214294 AAATTACTAAAATAGCCCTCAAATGATGA
1 AAATAACTAAAATAGCCCTAAAATAATGA
*
2214323 AAATTACTAA
1 AAATAACTAA
2214333 CCTGATAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
28 22 0.67
29 11 0.33
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.25
Consensus pattern (29 bp):
AAATAACTAAAATAGCCCTAAAATAATGA
Found at i:2215826 original size:35 final size:37
Alignment explanation
Indices: 2215787--2215859 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
2215777 TTTTGATTAA
2215787 ATTATGAAATAATTT-AAT-TAAAATAAAAAATTTTT
1 ATTATGAAATAATTTAAATATAAAATAAAAAATTTTT
* ** * *
2215822 ATTATTAAATTTTTTAAATATAAAATTATAAATTTTT
1 ATTATGAAATAATTTAAATATAAAATAAAAAATTTTT
2215859 A
1 A
2215860 ACTTTAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 12 0.39
36 3 0.10
37 16 0.52
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (37 bp):
ATTATGAAATAATTTAAATATAAAATAAAAAATTTTT
Found at i:2218555 original size:41 final size:40
Alignment explanation
Indices: 2218460--2218556 Score: 115
Period size: 41 Copynumber: 2.4 Consensus size: 40
2218450 TCTCTAATTA
*
2218460 AATTAAATTAATTAAGAGATAAATAAAGTAAATTTATCTCT
1 AATTAAATTAATTAAGAAATAAATAAAG-AAATTTATCTCT
* * * *
2218501 AACTAAATTAATTATGAAATAAATAAA-AGAGTTTATTTCT
1 AATTAAATTAATTAAGAAATAAATAAAGA-AATTTATCTCT
2218541 AATTAAATTAAATTAA
1 AATTAAATT-AATTAA
2218557 TTAAGAGATA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.02
40 17 0.36
41 29 0.62
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (40 bp):
AATTAAATTAATTAAGAAATAAATAAAGAAATTTATCTCT
Found at i:2218568 original size:41 final size:42
Alignment explanation
Indices: 2218446--2218568 Score: 126
Period size: 40 Copynumber: 2.9 Consensus size: 42
2218436 AAGAATCATT
2218446 TTTATCTCTAATTAAATTAAATTAATTAAGAGATAAATAAAGTAAA
1 TTTATCTCTAATTAAATTAAATTAATTAAGAGAT--A-AAAG-AAA
* * * * *
2218492 TTTATCTCTAACTAAATT-AATT-ATGAAATAAATAAAAG-AG
1 TTTATCTCTAATTAAATTAAATTAAT-TAAGAGATAAAAGAAA
*
2218532 TTTATTTCTAATTAAATTAAATTAATTAAGAGATAAA
1 TTTATCTCTAATTAAATTAAATTAATTAAGAGATAAA
2218569 CAATACCATG
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
40 17 0.27
41 12 0.19
42 6 0.09
43 1 0.02
44 2 0.03
45 9 0.14
46 17 0.27
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (42 bp):
TTTATCTCTAATTAAATTAAATTAATTAAGAGATAAAAGAAA
Found at i:2220702 original size:28 final size:27
Alignment explanation
Indices: 2220671--2220738 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
2220661 CAAGCTACCG
*
2220671 TTTTTGACAAACAAAAAAGAAACCACTA
1 TTTTTGACAAACAAAAAAG-AACCACCA
* * * *
2220699 TTTTTTACACACACAAAAGAATCACCA
1 TTTTTGACAAACAAAAAAGAACCACCA
2220726 TTTTTGACAAACA
1 TTTTTGACAAACA
2220739 TAAATGGTGA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
27 17 0.52
28 16 0.48
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (27 bp):
TTTTTGACAAACAAAAAAGAACCACCA
Found at i:2223503 original size:2 final size:2
Alignment explanation
Indices: 2223487--2223537 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
2223477 ATGCATGCAG
* * *
2223487 AT AT A- AT AC AT AT AT AT AT AT AT AT AT -T AC AG AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2223526 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2223538 TATGAACAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2225261 original size:32 final size:29
Alignment explanation
Indices: 2225189--2225328 Score: 95
Period size: 29 Copynumber: 4.6 Consensus size: 29
2225179 ATTTATCTTG
* *
2225189 AAAATTTATTTAAATATAAATTAAACGTTAA
1 AAAATTTATTT--AGATAAATTAAAAGTTAA
* * *
2225220 AAGACTTATTTTGATACAAGTTAAAAGATTAA
1 AAAATTTATTTAGATA-AA-TTAAAAG-TTAA
2225252 AAAATTTATTTAAGTATAAATTAAAAGTTAA
1 AAAATTTATTT-AG-ATAAATTAAAAGTTAA
* * * **
2225283 AAAA-ATATTTAAATATAATAAAAACATAA
1 AAAATTTATTTAGATA-AATTAAAAGTTAA
*
2225312 AAAA-TTATTTAAATAAA
1 AAAATTTATTTAGATAAA
2225329 ATAATAAAAT
Statistics
Matches: 89, Mismatches: 14, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
28 5 0.06
29 28 0.31
30 7 0.08
31 23 0.26
32 20 0.22
33 3 0.03
34 3 0.03
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAATTTATTTAGATAAATTAAAAGTTAA
Found at i:2225286 original size:31 final size:30
Alignment explanation
Indices: 2225189--2225353 Score: 138
Period size: 31 Copynumber: 5.4 Consensus size: 30
2225179 ATTTATCTTG
* *
2225189 AAAATTTATTTAAATATAAATTAAACGTTA
1 AAAAATTATTTAAATATAAATTAAAAGTTA
* ** * *
2225219 AAAGACTTATTTTGATACAAGTTAAAAGATTA
1 AAA-AATTATTTAAATATAAATTAAAAG-TTA
*
2225251 AAAAATTTATTTAAGTATAAATTAAAAGTTA
1 AAAAA-TTATTTAAATATAAATTAAAAGTTA
* * **
2225282 AAAAAATATTTAAATAT-AATAAAAACATA
1 AAAAATTATTTAAATATAAATTAAAAGTTA
*
2225311 AAAAATTATTTAAATA-AAATAATAAAATTTA
1 AAAAATTATTTAAATATAAAT--TAAAAGTTA
*
2225342 AAAACTT-TTTAA
1 AAAAATTATTTAA
2225354 TTATTTAAGC
Statistics
Matches: 107, Mismatches: 22, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
29 27 0.25
30 18 0.17
31 39 0.36
32 23 0.21
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAAATTATTTAAATATAAATTAAAAGTTA
Found at i:2225322 original size:63 final size:63
Alignment explanation
Indices: 2225189--2225344 Score: 160
Period size: 63 Copynumber: 2.5 Consensus size: 63
2225179 ATTTATCTTG
* ** ** * * *
2225189 AAAATTTATTTAAATATAAATTAAACGTTAAAAGACTTATTTTGATACAAGTTAAAAGATTAA
1 AAAATTTATTTAAATATAAATTAAAAGTTAAAAGAAATATTTAAATACAAGTAAAAACATAAA
* *
2225252 AAAATTTATTTAAGTATAAATTAAAAGTTAAAA-AAATATTTAAATATAA-TAAAAACAT-AA
1 AAAATTTATTTAAATATAAATTAAAAGTTAAAAGAAATATTTAAATACAAGTAAAAACATAAA
*
2225312 AAAA-TTATTTAAATA-AAATAATAAAATTTAAAA
1 AAAATTTATTTAAATATAAAT--TAAAAGTTAAAA
2225345 ACTTTTTAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
58 4 0.05
59 10 0.12
60 17 0.21
61 7 0.09
62 11 0.14
63 31 0.39
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (63 bp):
AAAATTTATTTAAATATAAATTAAAAGTTAAAAGAAATATTTAAATACAAGTAAAAACATAAA
Found at i:2225331 original size:29 final size:29
Alignment explanation
Indices: 2225249--2225332 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
2225239 GTTAAAAGAT
* * **
2225249 TAAAAAATTTATTTAAGTATAAATTAAAAGT
1 TAAAAAA-TTATTTAAATA-AAATAAAAACA
* *
2225280 TAAAAAAATATTTAAATATAATAAAAACA
1 TAAAAAATTATTTAAATAAAATAAAAACA
2225309 TAAAAAATTATTTAAATAAAATAA
1 TAAAAAATTATTTAAATAAAATAA
2225333 TAAAATTTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
29 29 0.64
30 9 0.20
31 7 0.16
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (29 bp):
TAAAAAATTATTTAAATAAAATAAAAACA
Found at i:2227704 original size:20 final size:20
Alignment explanation
Indices: 2227675--2227719 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2227665 AATCCTAAAC
* *
2227675 AAATTTAAAAGTAATCAATT
1 AAATTAAAAAATAATCAATT
**
2227695 AAATTAAAAAATTTTCAATT
1 AAATTAAAAAATAATCAATT
2227715 AAATT
1 AAATT
2227720 TTTTAATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (20 bp):
AAATTAAAAAATAATCAATT
Found at i:2233002 original size:20 final size:20
Alignment explanation
Indices: 2232951--2233002 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
2232941 ATATATCTCA
*
2232951 AATGTTTAATA-TTTTTTAT
1 AATGATTAATATTTTTTTAT
*
2232970 AATGGTTAA-ATTTTTTTAT
1 AATGATTAATATTTTTTTAT
2232989 AAAT-ATTAATATTT
1 -AATGATTAATATTT
2233003 AATTGTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 1 0.04
19 20 0.71
20 7 0.25
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (20 bp):
AATGATTAATATTTTTTTAT
Found at i:2233324 original size:2 final size:2
Alignment explanation
Indices: 2233317--2233351 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2233307 ATATAGACAA
2233317 AT AT AT 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 AT AT AT A
2233352 ACAGCCTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2234363 original size:22 final size:22
Alignment explanation
Indices: 2234338--2234403 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
2234328 AGATCAATTC
2234338 ATATTCAAGTCAATTGAGTTTA
1 ATATTCAAGTCAATTGAGTTTA
* *
2234360 ATATACGAA-TTAATTGAGTTTA
1 ATATTC-AAGTCAATTGAGTTTA
* * *
2234382 ACAATTCAAGCCAATGGAGTTT
1 A-TATTCAAGTCAATTGAGTTT
2234404 GACACTCAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
22 20 0.59
23 14 0.41
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (22 bp):
ATATTCAAGTCAATTGAGTTTA
Found at i:2237864 original size:19 final size:19
Alignment explanation
Indices: 2237833--2237873 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2237823 GAGGATATGG
*
2237833 ATAAATATTAGATTTAAAAA
1 ATAAATATTAGA-TAAAAAA
2237853 ATAAAT-TTAGATAAAAAA
1 ATAAATATTAGATAAAAAA
2237871 ATA
1 ATA
2237874 TCTATTTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 5 0.25
20 6 0.30
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
ATAAATATTAGATAAAAAA
Found at i:2237973 original size:17 final size:18
Alignment explanation
Indices: 2237951--2238013 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 18
2237941 AGTTCTTTTA
2237951 TTATAAAAATTATAT-TT
1 TTATAAAAATTATATATT
*
2237968 TTATAATATAATGATGTATATT
1 TTATAA-A-AAT--TATATATT
2237990 TTATAAAAATTATTATTATT
1 TTATAAAAATTA-TA-TATT
2238010 TTAT
1 TTAT
2238014 TTTACTAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
17 6 0.16
18 2 0.05
19 5 0.14
20 11 0.30
21 5 0.14
22 8 0.22
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTATAAAAATTATATATT
Done.