Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold99
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: 1377724
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 13826 characters in sequence are not A, C, G, or T
File 10 of 10
Found at i:1321846 original size:33 final size:33
Alignment explanation
Indices: 1321804--1321870 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1321794 GCCAAGGAAA
***
1321804 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1321837 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1321870 T
1 T
1321871 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1324278 original size:51 final size:53
Alignment explanation
Indices: 1324209--1324549 Score: 217
Period size: 52 Copynumber: 6.5 Consensus size: 53
1324199 AGTTTCTCAA
* * * * *
1324209 TTCTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
1324260 TT-TTCTATAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * *
1324314 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAA-----T
* * * * *
1324372 TAT-TTC-CAA--GGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAAT
1 T-TCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* * * *
1324421 TT-TTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACGCCAATT
1 TTCTT-CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAA-T
* *
1324474 TTCCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
1324526 TT-TTCACAATCGAGGATACTCCAA
1 TTCTTCACAATCGGGGATACTCCAA
1324550 ACTCGTTATT
Statistics
Matches: 227, Mismatches: 37, Indels: 51
0.72 0.12 0.16
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 7 0.03
51 32 0.14
52 85 0.37
53 32 0.14
54 29 0.13
55 24 0.11
57 6 0.03
58 5 0.02
59 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:1324353 original size:27 final size:29
Alignment explanation
Indices: 1324323--1324398 Score: 113
Period size: 27 Copynumber: 2.7 Consensus size: 29
1324313 TTTCTTCACA
1324323 ATCGGGGATACTCCAACCCCGTTA-AT-C
1 ATCGGGGATACTCCAACCCCGTTATATCC
*
1324350 ATCGGGGATACTCCAACCCCGTTATTTCC
1 ATCGGGGATACTCCAACCCCGTTATATCC
*
1324379 A-AGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1324399 GTTTTATTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 24 0.53
28 19 0.42
29 2 0.04
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.21
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCGTTATATCC
Found at i:1324434 original size:107 final size:106
Alignment explanation
Indices: 1324272--1324664 Score: 316
Period size: 107 Copynumber: 3.7 Consensus size: 106
1324262 TTCTATAATC
* * * *
1324272 GGGGATACTCCAACTCTGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGGTTTTA-TTCC-AAAAACACCAATTT-TTCACAATCGAGGATACTCC
1324337 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCAA
63 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCAA
* * * *
1324381 GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTATTCCAAAAACACCAATTTTT-CACAATCGAGGATACTCCAA
* ** * * * ** * *
1324446 CCCCGGTTTTATTTTC---AAAACGCCAATTTTCCTTTA-AT-C--
65 CCCC-G-TTAATCATCGGGGATACTCCAA--CCCCGTTATTTCCAA
* * *
1324485 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTA-TTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAA
* * * * *
1324550 ACTCGTTATTTCATCGGGGATACTTCAACCCCGTTACTTTCGAA
65 CCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTA-TTTCCAA
* * * *** * * *
1324594 -GGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGAGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAAC
1324658 CCCGTTA
66 CCCGTTA
1324665 TTTTCGAGGG
Statistics
Matches: 219, Mismatches: 50, Indels: 32
0.73 0.17 0.11
Matches are distributed among these distances:
102 2 0.01
103 4 0.02
104 48 0.22
105 16 0.07
106 17 0.08
107 76 0.35
108 29 0.13
109 27 0.12
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.30
Consensus pattern (106 bp):
GGGGATACTCCAACCCCGGTTTTATTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAAC
CCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCAA
Found at i:1324581 original size:212 final size:212
Alignment explanation
Indices: 1324212--1324661 Score: 629
Period size: 212 Copynumber: 2.1 Consensus size: 212
1324202 TTCTCAATTC
* * *
1324212 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* * *
1324277 TACTCCAACTCTGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAACC
*
1324342 CGTTAATCATCGGGGATACTCCAACCCCGTTA-TTTCCAAGGGGATACTCCAACCCCGGTTTTAT
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTTCCAA-GGGATACTCCAACCCCGGCTTTAT
1324406 TGCTAAAACACTAATTTT
195 TGCTAAAACACTAATTTT
* * * *
1324424 TCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGG
1 TCCACAATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGG
*
1324489 ATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAAC
65 ATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAAC
* * * *
1324552 TCGTTATTTCATCGGGGATACTTCAACCCCGTTACTTTCGAAGGGATACTCCAACCCCGGCTTTA
130 CCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTTCCAAGGGATACTCCAACCCCGGCTTTA
* * * * * *
1324617 TTCCCAAAATATTGATTTC
194 TTGCTAAAACACTAATTTT
* *
1324636 T-CATAATTGAGGATACTCCAACCCCG
1 TCCACAATCGAGGATACTCCAACCCCG
1324662 TTATTTTCGA
Statistics
Matches: 210, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
211 49 0.23
212 120 0.57
213 41 0.20
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (212 bp):
TCCACAATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAACC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTTCCAAGGGATACTCCAACCCCGGCTTTATT
GCTAAAACACTAATTTT
Found at i:1324584 original size:28 final size:29
Alignment explanation
Indices: 1324534--1324590 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
1324524 ATTTTTCACA
*
1324534 ATCGAGGATACTCCAAACTCGTTA-TTTC
1 ATCGAGGATACTCCAAACCCGTTACTTTC
* * *
1324562 ATCGGGGATACTTCAACCCCGTTACTTTC
1 ATCGAGGATACTCCAAACCCGTTACTTTC
1324591 GAAGGGATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.32
Consensus pattern (29 bp):
ATCGAGGATACTCCAAACCCGTTACTTTC
Found at i:1327702 original size:14 final size:14
Alignment explanation
Indices: 1327683--1327712 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1327673 ACCTCTATCT
1327683 TCTTGTGCATGAGG
1 TCTTGTGCATGAGG
*
1327697 TCTTGTGCATTAGG
1 TCTTGTGCATGAGG
1327711 TC
1 TC
1327713 ATGGAACAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.17, G:0.30, T:0.40
Consensus pattern (14 bp):
TCTTGTGCATGAGG
Found at i:1328661 original size:19 final size:19
Alignment explanation
Indices: 1328637--1328692 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
1328627 TGTATTGATA
1328637 CATTGTATCGATACATGCT
1 CATTGTATCGATACATGCT
* *
1328656 CATTGTTTCGATACATACT
1 CATTGTATCGATACATGCT
1328675 CATTTGTATCGATACATG
1 CA-TTGTATCGATACATG
1328693 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:1334414 original size:12 final size:13
Alignment explanation
Indices: 1334388--1334413 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1334378 CACTAAGGGA
1334388 TACAAAATTTTTT
1 TACAAAATTTTTT
1334401 TACAAAATTTTTT
1 TACAAAATTTTTT
1334414 ATATTTCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TACAAAATTTTTT
Found at i:1334830 original size:181 final size:178
Alignment explanation
Indices: 1334490--1335006 Score: 660
Period size: 179 Copynumber: 2.8 Consensus size: 178
1334480 TATTTTTTAA
* * *
1334490 AAAATATTAATTTTAGAGAAATTGAATCTTTCTAAATTTTTAAATTTAATTTTTAATTTTGAAAA
1 AAAATATTAA-TTTAG-GAAATCGAATCTTTCTAAATTTTTAAATTTAACTTCTAATTTTGAAAA
** * * * * *
1334555 TTACATTTCGTACCCGATAGAAAACCAGGGGATATGAAAGATGTTATAAAAATTTTCATACCCCT
64 TTATGTTTCGTA-CCGATGGAAAACCAGGGGATACGAAAGGTGTTAAAAAAAATTTCATA-CCCT
*
1334620 ACGGAAAACCATAGGGATATGAAAACATAAACGACCTCATATTC-TTTTTTT
127 ACGGAAAACCATAGGAATATGAAAACATAAACGACCTCATATTCTTTTTTTT
* *
1334671 AAAATATTAATTTAGGAAACCGAATCTTTCTAAATTCTTAAATTTAACTTCTAATTTTGAAAATT
1 AAAATATTAATTTAGGAAATCGAATCTTTCTAAATTTTTAAATTTAACTTCTAATTTTGAAAATT
*
1334736 ATGTTTCGTATCCGATGGAAAACTAGGGGATACGAAAGGTGTTAAAAAAAAATTTCATACCCTTA
66 ATGTTTCGTA-CCGATGGAAAACCAGGGGATACGAAAGGTGTT-AAAAAAAATTTCATACCC-T-
1334801 ACGGAAAACCATAGGAATATGAAAACATAAACGACCTCATATTCTTTTTTTT
127 ACGGAAAACCATAGGAATATGAAAACATAAACGACCTCATATTCTTTTTTTT
* * * **
1334853 TAAATATTAGTTTAGGAAAATCGAATTTTTCTAAATTTTTAAATTTAACTTCTAATTTCAAAAAT
1 AAAATATTAATTTAGG-AAATCGAATCTTTCTAAATTTTTAAATTTAACTTCTAATTTTGAAAAT
* * * * * *
1334918 TATGTTTCGTACCTGACGGAAAAACCAAGAGATACGAAAAGTTTTTAAAAAAATTT-ATATCCCT
65 TATGTTTCGTACC-GATGG-AAAACCAGGGGATACGAAAGGTGTTAAAAAAAATTTCATA-CCCT
* * *
1334982 ACAGAAAACCATAAGAATATAAAAA
127 ACGGAAAACCATAGGAATATGAAAA
1335007 TGTGATCTAA
Statistics
Matches: 296, Mismatches: 32, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
179 84 0.28
180 19 0.06
181 75 0.25
182 27 0.09
183 71 0.24
184 20 0.07
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (178 bp):
AAAATATTAATTTAGGAAATCGAATCTTTCTAAATTTTTAAATTTAACTTCTAATTTTGAAAATT
ATGTTTCGTACCGATGGAAAACCAGGGGATACGAAAGGTGTTAAAAAAAATTTCATACCCTACGG
AAAACCATAGGAATATGAAAACATAAACGACCTCATATTCTTTTTTTT
Found at i:1335880 original size:32 final size:33
Alignment explanation
Indices: 1335814--1335942 Score: 98
Period size: 32 Copynumber: 4.1 Consensus size: 33
1335804 CTTGCTTTTC
* *
1335814 TCTTTTTGTTTCGGTTGCT-A-TTTTCTTTGTTT
1 TCTTCTTGTTTCGGTTGCTGATTTTTC-TTGCTT
1335846 TCTTCTTGTTTCGGTT-CTGATTTTTCTTGCTT
1 TCTTCTTGTTTCGGTTGCTGATTTTTCTTGCTT
* *
1335878 TCTCTCTT-TTT---TTGCTG-TTTCATCTT-TTT
1 TCT-TCTTGTTTCGGTTGCTGATTT-TTCTTGCTT
* *
1335907 TCTGCTTGTTTCGGTT-CTGGTTTTTTCTTGCTT
1 TCTTCTTGTTTCGGTTGCT-GATTTTTCTTGCTT
1335940 TCT
1 TCT
1335943 CTCTCTTTTG
Statistics
Matches: 78, Mismatches: 7, Indels: 23
0.72 0.06 0.21
Matches are distributed among these distances:
28 3 0.04
29 13 0.17
30 7 0.09
31 4 0.05
32 34 0.44
33 17 0.22
ACGTcount: A:0.02, C:0.18, G:0.15, T:0.65
Consensus pattern (33 bp):
TCTTCTTGTTTCGGTTGCTGATTTTTCTTGCTT
Found at i:1335898 original size:19 final size:20
Alignment explanation
Indices: 1335866--1335979 Score: 73
Period size: 20 Copynumber: 5.7 Consensus size: 20
1335856 TCGGTTCTGA
1335866 TTTTT-CTTGCTTTCTCTCTT
1 TTTTTGCTTG-TTTCTCTCTT
1335886 TTTTTGC-TGTTTCATCT-TT
1 TTTTTGCTTGTTTC-TCTCTT
*
1335905 TTTCTGCTTGTTTCGGT-TCTGGT
1 TTTTTGCTTGTTTC--TCTCT--T
1335928 TTTTT-CTTGCTTTCTCTC-T
1 TTTTTGCTTG-TTTCTCTCTT
* *
1335947 CTTTTGC-TGTTT-TGTCTT
1 TTTTTGCTTGTTTCTCTCTT
1335965 TTTTCTGCTTGTTTC
1 TTTT-TGCTTGTTTC
1335980 AGTTCTGTTC
Statistics
Matches: 74, Mismatches: 6, Indels: 27
0.69 0.06 0.25
Matches are distributed among these distances:
17 3 0.04
18 7 0.09
19 22 0.30
20 23 0.31
21 4 0.05
22 6 0.08
23 9 0.12
ACGTcount: A:0.01, C:0.20, G:0.13, T:0.66
Consensus pattern (20 bp):
TTTTTGCTTGTTTCTCTCTT
Found at i:1335916 original size:20 final size:18
Alignment explanation
Indices: 1335882--1335918 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
1335872 TTGCTTTCTC
1335882 TCTTTTTTTGCTGTTTCA
1 TCTTTTTTTGCTGTTTCA
1335900 TCTTTTTTCTGCTTGTTTC
1 TCTTTTTT-TGC-TGTTTC
1335919 GGTTCTGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 3 0.18
20 6 0.35
ACGTcount: A:0.03, C:0.19, G:0.11, T:0.68
Consensus pattern (18 bp):
TCTTTTTTTGCTGTTTCA
Found at i:1335968 original size:62 final size:62
Alignment explanation
Indices: 1335843--1335986 Score: 220
Period size: 61 Copynumber: 2.4 Consensus size: 62
1335833 ATTTTCTTTG
* *
1335843 TTTTCTTCTTGTTTCGGTTCT-GATTTTTCTTGCTTTCTCTCTTTTTTTGCTGTTTCATCTT
1 TTTTCTGCTTGTTTCGGTTCTGGATTTTTCTTGCTTTCTCTCTTCTTTTGCTGTTTCATCTT
* **
1335904 TTTTCTGCTTGTTTCGGTTCTGGTTTTTTCTTGCTTTCTCTC-TCTTTTGCTGTTTTGTCTT
1 TTTTCTGCTTGTTTCGGTTCTGGATTTTTCTTGCTTTCTCTCTTCTTTTGCTGTTTCATCTT
*
1335965 TTTTCTGCTTGTTTCAGTTCTG
1 TTTTCTGCTTGTTTCGGTTCTG
1335987 TTCTCTCCTT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
61 57 0.75
62 19 0.25
ACGTcount: A:0.02, C:0.19, G:0.15, T:0.64
Consensus pattern (62 bp):
TTTTCTGCTTGTTTCGGTTCTGGATTTTTCTTGCTTTCTCTCTTCTTTTGCTGTTTCATCTT
Found at i:1336637 original size:43 final size:43
Alignment explanation
Indices: 1336589--1336672 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
1336579 TAATGCCTGC
1336589 ATGCATGAAAT-AAACATTACGTAAAATGCATGCATGAAATGTA
1 ATGCATGAAATGAAA-ATTACGTAAAATGCATGCATGAAATGTA
* * *
1336632 ATGCATGAAATGCAAATTTCGTGAAATGCATGCATGAAATG
1 ATGCATGAAATGAAAATTACGTAAAATGCATGCATGAAATG
1336673 CATGCAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 35 0.95
44 2 0.05
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCATGAAATGAAAATTACGTAAAATGCATGCATGAAATGTA
Found at i:1336671 original size:13 final size:13
Alignment explanation
Indices: 1336612--1336678 Score: 71
Period size: 13 Copynumber: 4.8 Consensus size: 13
1336602 ACATTACGTA
1336612 AAATGCATGCATG
1 AAATGCATGCATG
*
1336625 AAATGTAATGCATG
1 AAATG-CATGCATG
* *
1336639 AAATGCAAATTTCGTG
1 AAATGC--A-TGCATG
1336655 AAATGCATGCATG
1 AAATGCATGCATG
1336668 AAATGCATGCA
1 AAATGCATGCA
1336679 ATATTTATTC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
13 20 0.45
14 13 0.30
15 1 0.02
16 10 0.23
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.25
Consensus pattern (13 bp):
AAATGCATGCATG
Found at i:1336738 original size:18 final size:18
Alignment explanation
Indices: 1336715--1336757 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1336705 GAGTTTTTTT
1336715 TTTTATATATATATATAC
1 TTTTATATATATATATAC
* * * *
1336733 TTTTATTTATTTATTTAT
1 TTTTATATATATATATAC
1336751 TTTTATA
1 TTTTATA
1336758 AATTTTAAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTATATATATATATAC
Found at i:1336775 original size:22 final size:22
Alignment explanation
Indices: 1336750--1336791 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1336740 TATTTATTTA
*
1336750 TTTTTATAAATTTTAAATAATT
1 TTTTTATAAATGTTAAATAATT
1336772 TTTTTATAAATGTTAAATAA
1 TTTTTATAAATGTTAAATAA
1336792 ACCAACGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTTTATAAATGTTAAATAATT
Found at i:1341480 original size:13 final size:13
Alignment explanation
Indices: 1341462--1341487 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1341452 CAATTTTTTG
1341462 TGTATCGATACAT
1 TGTATCGATACAT
1341475 TGTATCGATACAT
1 TGTATCGATACAT
1341488 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1341499 original size:32 final size:33
Alignment explanation
Indices: 1341442--1341505 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1341432 TACAAGCCAA
**
1341442 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1341475 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1341506 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1342570 original size:13 final size:13
Alignment explanation
Indices: 1342552--1342578 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1342542 ACATTATGCT
1342552 TTGTATCGATACA
1 TTGTATCGATACA
1342565 TTGTATCGATACA
1 TTGTATCGATACA
1342578 T
1 T
1342579 GCTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1342609 original size:20 final size:19
Alignment explanation
Indices: 1342562--1342614 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
1342552 TTGTATCGAT
*
1342562 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATAC
*
1342581 TCATTGTATCGATACATAC
1 ACATTGTATCGATACATAC
1342600 ACATTTGTATCGATA
1 ACA-TTGTATCGATA
1342615 GATTAAACTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (19 bp):
ACATTGTATCGATACATAC
Found at i:1342691 original size:20 final size:20
Alignment explanation
Indices: 1342648--1342699 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1342638 TAAGTGAAAT
* **
1342648 GTATCGATACATGGGACATT
1 GTATCGATACATGGGAAAAA
*
1342668 GTATCGATACATGGTAAAAA
1 GTATCGATACATGGGAAAAA
1342688 GTATCGATACAT
1 GTATCGATACAT
1342700 TGTGCCCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (20 bp):
GTATCGATACATGGGAAAAA
Found at i:1343048 original size:15 final size:15
Alignment explanation
Indices: 1343028--1343064 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
1343018 ACTTAGAGGC
1343028 AATTTTCGTTTGTAA
1 AATTTTCGTTTGTAA
1343043 AATTTTCGTTTGTAA
1 AATTTTCGTTTGTAA
1343058 AATTTTC
1 AATTTTC
1343065 TTGAGTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (15 bp):
AATTTTCGTTTGTAA
Found at i:1345113 original size:154 final size:152
Alignment explanation
Indices: 1344867--1345270 Score: 449
Period size: 154 Copynumber: 2.6 Consensus size: 152
1344857 CTAAGTGCAC
** *
1344867 ACCTTTGGCATAAAAGCGACCTGGTGACTATCTAGGACTT-GATCCTAGAAAAATTAACAAAATG
1 ACCTTTGGCATAAAAGCGACCTGGTGACTATCTAGGACTTAG-TTTTA-AAAAATTATCAAAATG
* * * * * *
1344931 TCCCTAGGATATACCTTCGATATAAAAGTATCTCGGTTATCC-TGAAGGATACAAAAAAATCATA
64 CCCCTAGG-TATACCTTCGACATGAAAGTATCTCAGTTA-CCTTAAAGGACACAAAAAAATCATA
*
1344995 AAAAGATGAA-CCTATCCTAAATATAT
127 AAAAGA-CAAGCCTATCCTAAATATAT
* *
1345021 ACCTTTGGCATAAAAGCAACCTGGTGACTATCTAGGACTTAGTTTTAAAAAATTATCAAAATACC
1 ACCTTTGGCATAAAAGCGACCTGGTGACTATCTAGGACTTAGTTTTAAAAAATTATCAAAATGCC
* **
1345086 CCTAAGGTATACCTTCGACGATGAAAGTATCTTAGTTACCTTAAAGGACACAAAAGGATCATAAA
66 CCT-AGGTATACCTTCGAC-ATGAAAGTATCTCAGTTACCTTAAAGGACACAAAAAAATCATAAA
* *
1345151 AAGACAAGCCTATTCTAAATGTAT
129 AAGACAAGCCTATCCTAAATATAT
* * * * * *
1345175 ACCTTTGGCATAAAAGTGACTTAGTGACTA-CATA-GAATTCAGTTCTAAAAAAATTATGAAAAT
1 ACCTTTGGCATAAAAGCGACCTGGTGACTATC-TAGGACTT-AGTT-TTAAAAAATTATCAAAAT
** *
1345238 GCCTGTAGGTATACCTTTGACATGAAAGTATCT
63 GCCCCTAGGTATACCTTCGACATGAAAGTATCT
1345271 TGGTCACCCT
Statistics
Matches: 214, Mismatches: 28, Indels: 17
0.83 0.11 0.07
Matches are distributed among these distances:
153 50 0.23
154 144 0.67
155 20 0.09
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.28
Consensus pattern (152 bp):
ACCTTTGGCATAAAAGCGACCTGGTGACTATCTAGGACTTAGTTTTAAAAAATTATCAAAATGCC
CCTAGGTATACCTTCGACATGAAAGTATCTCAGTTACCTTAAAGGACACAAAAAAATCATAAAAA
GACAAGCCTATCCTAAATATAT
Found at i:1346707 original size:97 final size:96
Alignment explanation
Indices: 1346473--1346708 Score: 271
Period size: 97 Copynumber: 2.4 Consensus size: 96
1346463 GTTAAAAAAC
* * * * * *
1346473 GGGTTGGAGTATCCCCTCGAAGGAATGGGGTTGGAGTATCCCTGATGATGATAATTTAGGCAAAA
1 GGGTTGGAGTATCCCCTCGAA-GAATGGGGTTGAAGTATCCCTAAAGATGACAATATAAGCAAAA
* *
1346538 ATAAGATTTAAATCTTGTCAAGTTTGAAAATG
65 ATAAGAATTAAATCTCGTCAAGTTTGAAAATG
* * * *
1346570 AGGTTGGAGTATCCCTTCAAAAGAATAGGGTT-AGAGTATCCCTAAAGATGACAATATAAGCAAA
1 GGGTTGGAGTATCCCCTC-GAAGAATGGGGTTGA-AGTATCCCTAAAGATGACAATATAAGCAAA
1346634 AATAAGAATTAAATCTCGAT-AAGTTT-AAAACTG
64 AATAAGAATTAAATCTCG-TCAAGTTTGAAAA-TG
* *
1346667 GGGTTCGAGTATCCCCTCGGAAGAATGGGGTTGAAATATCCC
1 GGGTTGGAGTATCCCCTC-GAAGAATGGGGTTGAAGTATCCC
1346709 CTGTGAATAA
Statistics
Matches: 115, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
96 4 0.03
97 107 0.93
98 4 0.03
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (96 bp):
GGGTTGGAGTATCCCCTCGAAGAATGGGGTTGAAGTATCCCTAAAGATGACAATATAAGCAAAAA
TAAGAATTAAATCTCGTCAAGTTTGAAAATG
Found at i:1349204 original size:20 final size:21
Alignment explanation
Indices: 1349179--1349222 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1349169 CAAGGTACAA
* *
1349179 TATCAATGCATTCACTTA-TG
1 TATCAATACATTAACTTATTG
1349199 TATCAATACATTAACTTATTG
1 TATCAATACATTAACTTATTG
1349220 TAT
1 TAT
1349223 TGATACAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (21 bp):
TATCAATACATTAACTTATTG
Found at i:1349981 original size:104 final size:105
Alignment explanation
Indices: 1349808--1350045 Score: 281
Period size: 104 Copynumber: 2.3 Consensus size: 105
1349798 GATATAATCC
* *
1349808 TAAGTTAGAAAAGGGTTGACCAGGGCGAAACTAAAAGTCAACAAATTTAAGGGGTTGATTAGGAC
1 TAAGTTAGAAAAGGGTTGACCAGGGCGAAACTAAAAGTCAACAAATTAAAGGGGTTGACTAGGAC
*
1349873 GAAACTAA-CAAGTCAA-TAAAAATGATTAGGATAAAACT
66 GAAACTAATAAAGTCAACTAAAAATGATTAGGATAAAACT
* * ** *
1349911 TAAGTTAGAAAAATGGTTGACCAGGGTGAAACTGTAAGTCAACAAGTTAAAGGGGTTGACTAGGG
1 TAAGTTAG-AAAAGGGTTGACCAGGGCGAAACTAAAAGTCAACAAATTAAAGGGGTTGACTA-GG
* * * *
1349976 A-GAAACTAATAAAGTCAACTAAAAGTGACTA-AAAAAAAC-
64 ACGAAACTAATAAAGTCAACTAAAAATGATTAGGATAAAACT
* *
1350015 TAA-TTAGAAAAGGTGTTAACCAGGGCAAAAC
1 TAAGTTAGAAAAGG-GTTGACCAGGGCGAAAC
1350046 AAATAAAACC
Statistics
Matches: 114, Mismatches: 16, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
102 5 0.04
103 26 0.23
104 57 0.50
105 16 0.14
106 10 0.09
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.21
Consensus pattern (105 bp):
TAAGTTAGAAAAGGGTTGACCAGGGCGAAACTAAAAGTCAACAAATTAAAGGGGTTGACTAGGAC
GAAACTAATAAAGTCAACTAAAAATGATTAGGATAAAACT
Found at i:1350142 original size:40 final size:39
Alignment explanation
Indices: 1350097--1350539 Score: 225
Period size: 40 Copynumber: 11.2 Consensus size: 39
1350087 ATCGATAAAT
*
1350097 CAACAAAGAGAAAAGGTTGACCGAGACAAAACTGACAAGC
1 CAACAAAGA-AAAAGGTTGACCGAGATAAAACTGACAAGC
* * * *
1350137 AAACAAAAAATAAAAGTTGA-CTAGGATAAAA-TCGACAAGC
1 CAACAAAGAA-AAAGGTTGACCGA-GATAAAACT-GACAAGC
* *
1350177 CAACAAAGAATAAAGGTTGACCAAGATAAAACCGACAA-C
1 CAACAAAGAA-AAAGGTTGACCGAGATAAAACTGACAAGC
* * *
1350216 CTAACAAA-AAATATAAGTTGA-CTAGGACAAAA-TCGACAAGC
1 C-AACAAAGAAA-A-AGGTTGACCGA-GATAAAACT-GACAAGC
* * * *
1350257 CAACAAAGAGTAAA-GTTGA-CTAGGACAAAACTGACATGC
1 CAACAAAGA-AAAAGGTTGACCGA-GATAAAACTGACAAGC
* *
1350296 CAACAAATAGTAAAA-GTTGACCGAGATAAAACTAACAAGC
1 CAAC-AA-AGAAAAAGGTTGACCGAGATAAAACTGACAAGC
* * *
1350336 CAATAAA-AAGTAAAGGTTGGCCGAGACAAAACTGACAAGC
1 CAACAAAGAA--AAAGGTTGACCGAGATAAAACTGACAAGC
* * * *
1350376 CAATAAAGAACAAAGGTTGACTG-GACAAAA-TCGACATGC
1 CAACAAAGAA-AAAGGTTGACCGAGATAAAACT-GACAAGC
* * * * ** * *
1350415 TAACAAATAGTAAAGCTTG-CTTAGGATAAAATTGATAAGC
1 CAACAAAGA-AAAAGGTTGACCGA-GATAAAACTGACAAGC
* * * *
1350455 CAACAAAGAATAAAGGTT-AACAAGGATGAAACTGACATGC
1 CAACAAAGAA-AAAGGTTGACCGA-GATAAAACTGACAAGC
* * *
1350495 AAACATAGAATAAAGGTTGACCG-GATAAAACCGACAAG-
1 CAACAAAGAA-AAAGGTTGACCGAGATAAAACTGACAAGC
1350533 CAACAAA
1 CAACAAA
1350540 AATTAAAGGA
Statistics
Matches: 314, Mismatches: 60, Indels: 60
0.72 0.14 0.14
Matches are distributed among these distances:
37 1 0.00
38 10 0.03
39 80 0.25
40 207 0.66
41 15 0.05
42 1 0.00
ACGTcount: A:0.50, C:0.17, G:0.18, T:0.15
Consensus pattern (39 bp):
CAACAAAGAAAAAGGTTGACCGAGATAAAACTGACAAGC
Found at i:1350171 original size:80 final size:80
Alignment explanation
Indices: 1350083--1350411 Score: 321
Period size: 80 Copynumber: 4.1 Consensus size: 80
1350073 TTGACCAAGG
* * *
1350083 CAAAATCGATAAATCAACAAAGAGAAAAGGTTGACCGAGACAAAACTGACAAGCAAACAAAAAAT
1 CAAAATCGACAAACCAACAAAGAGAAAAGGTTGACCGAGACAAAACTGACAAGCCAACAAAAAAT
1350148 AAAAGTTGACTAGGA
66 AAAAGTTGACTAGGA
* * * * *
1350163 TAAAATCGACAAGCCAACAAAGA-ATAAAGGTTGACCAAGATAAAACCGACAA-CCTAACAAAAA
1 CAAAATCGACAAACCAACAAAGAGA-AAAGGTTGACCGAGACAAAACTGACAAGCC-AACAAAAA
*
1350226 ATATAAGTTGACTAGGA
64 ATAAAAGTTGACTAGGA
* * * * * *
1350243 CAAAATCGACAAGCCAACAAAGAGTAAA-GTTGA-CTAGGACAAAACTGACATGCCAACAAATAG
1 CAAAATCGACAAACCAACAAAGAGAAAAGGTTGACCGA-GACAAAACTGACAAGCCAACAAAAAA
*
1350306 TAAAAGTTGAC-CGAGA
65 TAAAAGTTGACTAG-GA
* * * * * * * * *
1350322 TAAAA-CTAACAAGCCAATAAAAAGTAAAGGTTGGCCGAGACAAAACTGACAAGCCAATAAAGAA
1 CAAAATC-GACAAACCAACAAAGAGAAAAGGTTGACCGAGACAAAACTGACAAGCCAACAAAAAA
* *
1350386 CAAAGGTTGACT-GGA
65 TAAAAGTTGACTAGGA
1350401 CAAAATCGACA
1 CAAAATCGACA
1350412 TGCTAACAAA
Statistics
Matches: 205, Mismatches: 33, Indels: 23
0.79 0.13 0.09
Matches are distributed among these distances:
78 4 0.02
79 68 0.33
80 131 0.64
81 2 0.01
ACGTcount: A:0.51, C:0.17, G:0.18, T:0.14
Consensus pattern (80 bp):
CAAAATCGACAAACCAACAAAGAGAAAAGGTTGACCGAGACAAAACTGACAAGCCAACAAAAAAT
AAAAGTTGACTAGGA
Found at i:1350323 original size:119 final size:119
Alignment explanation
Indices: 1350108--1350515 Score: 366
Period size: 119 Copynumber: 3.4 Consensus size: 119
1350098 AACAAAGAGA
* * * *
1350108 AAAGGTTGACCGAGACAAAACTGACAAGCAAACAAAAAATAAAAGTTGACTAGGATAAAATCGAC
1 AAAGGTTGACAGAGACAAAACTGACAAGCCAACAAAGAAT-AAAGTTGACTAGGACAAAATCGAC
* * * * *
1350173 AAGCCAACAAAGAATAAAGGTTGACCAAGATAAAACCGACAA-CCTAACAAAAAAT
65 ATGCCAACAAATAGTAAAAGTTGACCAAGATAAAACCAACAAGCC-AACAAAAAAT
*
1350228 ATAA-GTTGACTAG-GACAAAA-TCGACAAGCCAACAAAGAGTAAAGTTGACTAGGACAAAA-CT
1 A-AAGGTTGAC-AGAGACAAAACT-GACAAGCCAACAAAGAATAAAGTTGACTAGGACAAAATC-
* * * *
1350289 GACATGCCAACAAATAGTAAAAGTTGACCGAGATAAAACTAACAAGCCAATAAAAAGT
62 GACATGCCAACAAATAGTAAAAGTTGACCAAGATAAAACCAACAAGCCAACAAAAAAT
* * * *
1350347 AAAGGTTGGCCGAGACAAAACTGACAAGCCAATAAAGAACAAAGGTTGACT-GGACAAAATCGAC
1 AAAGGTTGACAGAGACAAAACTGACAAGCCAACAAAGAATAAA-GTTGACTAGGACAAAATCGAC
* * * *** * *
1350411 ATGCTAACAAATAGT-AAAGCTTG-CTTAGGATAAAATTGATAAGCCAACAAAGAAT
65 ATGCCAACAAATAGTAAAAG-TTGAC-CAAGATAAAACCAACAAGCCAACAAAAAAT
* ** * * *
1350466 AAAGGTTAACA-AGGATGAAACTGACATGCAAACATAGAATAAAGGTTGAC
1 AAAGGTTGACAGA-GACAAAACTGACAAGCCAACAAAGAATAAA-GTTGAC
1350516 CGGATAAAAC
Statistics
Matches: 236, Mismatches: 39, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
118 10 0.04
119 183 0.78
120 40 0.17
121 3 0.01
ACGTcount: A:0.50, C:0.16, G:0.18, T:0.16
Consensus pattern (119 bp):
AAAGGTTGACAGAGACAAAACTGACAAGCCAACAAAGAATAAAGTTGACTAGGACAAAATCGACA
TGCCAACAAATAGTAAAAGTTGACCAAGATAAAACCAACAAGCCAACAAAAAAT
Found at i:1358690 original size:13 final size:13
Alignment explanation
Indices: 1358672--1358696 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1358662 CATAAAATGT
1358672 TGTATCGATACAA
1 TGTATCGATACAA
1358685 TGTATCGATACA
1 TGTATCGATACA
1358697 TATTTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1358712 original size:32 final size:33
Alignment explanation
Indices: 1358652--1358717 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
1358642 TTCAACGATG
1358652 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
** *
1358685 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1358717 T
1 T
1358718 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1358776 original size:13 final size:13
Alignment explanation
Indices: 1358758--1358782 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1358748 ATTACTCAAA
1358758 TGTATCGATACAT
1 TGTATCGATACAT
1358771 TGTATCGATACA
1 TGTATCGATACA
1358783 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1358846 original size:51 final size:52
Alignment explanation
Indices: 1358791--1358906 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
1358781 CACTGATCTT
*
1358791 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1358842 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1358894 TGTATCGATACAT
1 TGTATCGATACAT
1358907 ACAAGCAACT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 19 0.31
52 43 0.69
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1370537 original size:1 final size:1
Alignment explanation
Indices: 1370531--1370591 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
1370521 CCTCCAAACC
* * * * * * * *
1370531 AAAAAAAAAAAAACAAAAGAAAAAACAAACAAAAAAACAATAAAAAAAACAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1370592 GGGGGTCCGG
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.87, C:0.10, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:1370553 original size:12 final size:11
Alignment explanation
Indices: 1370534--1370591 Score: 80
Period size: 12 Copynumber: 4.9 Consensus size: 11
1370524 CCAAACCAAA
1370534 AAAAAAAAAAC
1 AAAAAAAAAAC
1370545 AAAAGAAAAAAC
1 AAAA-AAAAAAC
1370557 AAACAAAAAAAC
1 AAA-AAAAAAAC
1370569 AATAAAAAAAAC
1 AA-AAAAAAAAC
1370581 AAACAAAAAAA
1 AAA-AAAAAAA
1370592 GGGGGTCCGG
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.12
12 36 0.84
13 2 0.05
ACGTcount: A:0.86, C:0.10, G:0.02, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:1370555 original size:16 final size:16
Alignment explanation
Indices: 1370526--1370591 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
1370516 GGCGTCCTCC
*
1370526 AAACCAAAAAA-AAAA
1 AAACAAAAAAACAAAA
*
1370541 AAACAAAAGAAA-AAAC
1 AAACAAAA-AAACAAAA
1370557 AAACAAAAAAACAATAA
1 AAACAAAAAAACAA-AA
*
1370574 AAA-AAACAAACAAAA
1 AAACAAAAAAACAAAA
1370589 AAA
1 AAA
1370592 GGGGGTCCGG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
15 15 0.34
16 25 0.57
17 4 0.09
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.02
Consensus pattern (16 bp):
AAACAAAAAAACAAAA
Found at i:1370569 original size:24 final size:24
Alignment explanation
Indices: 1370537--1370591 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
1370527 AACCAAAAAA
1370537 AAAAAAACAA-AAGAAAAAACAAAC
1 AAAAAAACAATAA-AAAAAACAAAC
1370561 AAAAAAACAATAAAAAAAACAAAC
1 AAAAAAACAATAAAAAAAACAAAC
1370585 AAAAAAA
1 AAAAAAA
1370592 GGGGGTCCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 28 0.93
25 2 0.07
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.02
Consensus pattern (24 bp):
AAAAAAACAATAAAAAAAACAAAC
Found at i:1372092 original size:30 final size:29
Alignment explanation
Indices: 1372034--1372487 Score: 244
Period size: 30 Copynumber: 15.3 Consensus size: 29
1372024 CACCCTTCAA
* *
1372034 AAAGTCCACAAGTTAGTGGCACTTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA--TTTTTTTC
*
1372065 AAAGCCCACAAGTCGGTGGCATTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TTTTTTTC
***
1372095 GAAAGCCCACAAGTCAGTGGCA--ACCTTC
1 -AAAGCCCACAAGTCAGTGGCATTTTTTTC
** *
1372123 AAAGCCCACAAGTC-GTGGCCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGG-CA-TTTTTTTC
* * * * *
1372153 GAAGCCCACAAGTCGGCGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
* * * *
1372182 AAAGTCCACAAACTCCGTGGCACTCTTTTCTCTTTG
1 AAAGCCCAC-AAGTCAGTGGCA----TTT-T-TTTC
* * * * * * *
1372218 TAAGCTCATAACTCTA-TAGCACTCTTTTC
1 AAAGCCCACAAGTC-AGTGGCATTTTTTTC
* ***
1372247 --AGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
*
1372274 AAAAGCCCACAAGTCAGTGGCATATTTTTC
1 -AAAGCCCACAAGTCAGTGGCATTTTTTTC
*** *
1372304 AAAAGCCCACAAGTCAGTGGCA-ACCTTTA
1 -AAAGCCCACAAGTCAGTGGCATTTTTTTC
* *** *
1372333 AAAGCCCACAAGTTAGTGGCACCCTGTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
*
1372362 AAAAGCCCACAAGTCAGTGGCATATTTTTC
1 -AAAGCCCACAAGTCAGTGGCATTTTTTTC
1372392 AAAGCCCACAAGTC-GTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
***
1372420 GAAAGCCCACAAGTCAGTGGCA--ACCTTC
1 -AAAGCCCACAAGTCAGTGGCATTTTTTTC
* ** *
1372448 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TTTTTTTC
1372478 AAAGCCCACA
1 AAAGCCCACA
1372488 CAAGTCGGTG
Statistics
Matches: 335, Mismatches: 63, Indels: 51
0.75 0.14 0.11
Matches are distributed among these distances:
26 5 0.01
27 55 0.16
28 39 0.12
29 52 0.16
30 123 0.37
31 42 0.13
34 2 0.01
35 10 0.03
36 7 0.02
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATTTTTTTC
Found at i:1372349 original size:88 final size:86
Alignment explanation
Indices: 1372247--1372503 Score: 322
Period size: 88 Copynumber: 2.9 Consensus size: 86
1372237 CACTCTTTTC
1372247 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAAGTTAGTGGCACCC-TTTCAAAAGCCCACAAGTCAGTGGCATATTTTTC-AAAGCCC
1372312 ACAAGTCAGTGGCAACCTTT-AAA
64 ACAAGTC-GTGGCAACCTTTCAAA
1372335 AGCCCACAAGTTAGTGGCACCCTGTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAGCCCA
1 AGCCCACAAGTTAGTGGCACCCT-TTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAGCCCA
*** *
1372400 CAAGTCGTGGCATTTTTTTCGAA
65 CAAGTCGTGGCA-ACCTTTCAAA
* * * ** *
1372423 AGCCCACAAGTCAGTGGCAACC-TTC-AAAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCA
1 AGCCCACAAGTTAGTGGCACCCTTTCAAAAGCCCACAAGTCAGTGGCA-TATTTTTCAAAG-CC-
1372486 CACAAGTCGGTGGCAACC
63 CACAAGTC-GTGGCAACC
1372504 CTTCTAAGCC
Statistics
Matches: 149, Mismatches: 13, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
85 20 0.13
86 18 0.12
87 20 0.13
88 85 0.57
89 6 0.04
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (86 bp):
AGCCCACAAGTTAGTGGCACCCTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAGCCCAC
AAGTCGTGGCAACCTTTCAAA
Found at i:1372363 original size:58 final size:58
Alignment explanation
Indices: 1372247--1372503 Score: 293
Period size: 58 Copynumber: 4.4 Consensus size: 58
1372237 CACTCTTTTC
* * ***
1372247 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAA
1 AGCCCACAAGTCAGTGGCAACC-TTT-AAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
* *
1372307 AGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTTAGTGGCACCCTGTTCAAA
1 AGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
** * *** *
1372365 AGCCCACAAGTCAGTGGCATATTTTTCAAAGCCCACAAGTC-GTGGCATTTTTTTCGAA
1 AGCCCACAAGTCAGTGGCA-ACCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
* * *
1372423 AGCCCACAAGTCAGTGGCAACC-TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCAA
1 AGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
*
1372480 AGCCCACACAAGTCGGTGGCAACC
1 AG-CC-CACAAGTCAGTGGCAACC
1372504 CTTCTAAGCC
Statistics
Matches: 169, Mismatches: 24, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
56 16 0.09
57 16 0.09
58 80 0.47
59 37 0.22
60 20 0.12
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (58 bp):
AGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
Found at i:1372513 original size:30 final size:30
Alignment explanation
Indices: 1372251--1372515 Score: 127
Period size: 30 Copynumber: 9.0 Consensus size: 30
1372241 CTTTTCAGCC
*
1372251 CACAAGTTAGTGGC-ACCCTTTTCAAAAG-CC-
1 CACAAGTCAGTGGCAACCC--TTC-AAAGCCCA
***
1372281 CACAAGTCAGTGGCATATTTTTCAAAAG-CC-
1 CACAAGTCAGTGGCA-ACCCTTC-AAAGCCCA
* *
1372311 CACAAGTCAGTGGCAACCTTTAAAAG-CC-
1 CACAAGTCAGTGGCAACCCTTCAAAGCCCA
*
1372339 CACAAGTTAGTGGC-ACCCTGTTCAAAAG-CC-
1 CACAAGTCAGTGGCAACCC--TTC-AAAGCCCA
***
1372369 CACAAGTCAGTGGCATATTTTTCAAAG-CC-
1 CACAAGTCAGTGGCA-ACCCTTCAAAGCCCA
****
1372398 CACAAGTC-GTGGCATTTTTTTCGAAAG-CC-
1 CACAAGTCAGTGGCA-ACCCTTC-AAAGCCCA
1372427 CACAAGTCAGTGGCAA-CCTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCTTCAAAGCCCA
1372456 CA-AA-TCAGTGGC-ACCCTTTTCCAAAGCCCA
1 CACAAGTCAGTGGCAACCC--TT-CAAAGCCCA
* *
1372486 CACAAGTCGGTGGCAACCCTTCTAAGCCCA
1 CACAAGTCAGTGGCAACCCTTCAAAGCCCA
1372516 ATATAGCTGG
Statistics
Matches: 197, Mismatches: 20, Indels: 36
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.01
27 17 0.09
28 39 0.20
29 38 0.19
30 85 0.43
31 4 0.02
32 9 0.05
33 4 0.02
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.22
Consensus pattern (30 bp):
CACAAGTCAGTGGCAACCCTTCAAAGCCCA
Found at i:1372570 original size:49 final size:49
Alignment explanation
Indices: 1372508--1372744 Score: 308
Period size: 49 Copynumber: 4.9 Consensus size: 49
1372498 GCAACCCTTC
* *
1372508 TAAGCCCAATATAGCTGGCCTTGAATCACCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
1372557 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
*
1372606 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1372649 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTT
* * * *
1372701 T-AGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTT
1372745 TTCTCATCTT
Statistics
Matches: 168, Mismatches: 10, Indels: 18
0.86 0.05 0.09
Matches are distributed among these distances:
43 41 0.24
44 1 0.01
48 1 0.01
49 83 0.49
51 36 0.21
52 6 0.04
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
Found at i:1372661 original size:43 final size:43
Alignment explanation
Indices: 1372600--1372692 Score: 177
Period size: 43 Copynumber: 2.2 Consensus size: 43
1372590 TTGGCACCTT
1372600 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
*
1372643 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
1372686 CACCTTT
1 CACCTTT
1372693 TCCATCTTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (43 bp):
CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
Found at i:1372670 original size:22 final size:22
Alignment explanation
Indices: 1372602--1372670 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
1372592 GGCACCTTCA
1372602 CCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
* * *
1372624 CCTTGAA-TCAGCACAT-TGGC--A
1 CCTTTAAGTC--CA-ATATAGCTGG
1372645 CCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
1372667 CCTT
1 CCTT
1372671 GAATCAGCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
CCTTTAAGTCCAATATAGCTGG
Found at i:1372681 original size:92 final size:94
Alignment explanation
Indices: 1372554--1372744 Score: 307
Period size: 92 Copynumber: 2.0 Consensus size: 94
1372544 GCACCTTTAT
1372554 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TT-CACCTTTAAGTCCAATA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTCCACCTTT-AGTCCAATA
*
1372617 TAGCTGGCCTTGAATCAGCACATTGGCA-C
65 TAGCTGGCCTTGAATCAGCACATTGACATC
* * *
1372646 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAGTTCAATG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTTCCACCTTTAGTCCAATA
1372711 TAGCTGGCCTTGAATCAGCACATTGACATC
65 TAGCTGGCCTTGAATCAGCACATTGACATC
1372741 CTTT
1 CTTT
1372745 TTCTCATCTT
Statistics
Matches: 91, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
92 44 0.48
94 36 0.40
95 11 0.12
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (94 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTCCACCTTTAGTCCAATAT
AGCTGGCCTTGAATCAGCACATTGACATC
Found at i:1372723 original size:51 final size:54
Alignment explanation
Indices: 1372646--1372781 Score: 161
Period size: 51 Copynumber: 2.5 Consensus size: 54
1372636 ACATTGGCAC
* *
1372646 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CAT
1 CTTT-AGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* *
1372698 CTTTAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* * * *
1372752 CTTTATGCCCAATATCGTTGGCCGTGAATC
1 CTTTA-GTCCAATATAGCTGGCCTTGAATC
1372782 GACATATTGG
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
51 33 0.47
52 6 0.09
53 5 0.07
54 8 0.11
55 18 0.26
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (54 bp):
CTTTAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
Found at i:1373679 original size:13 final size:13
Alignment explanation
Indices: 1373661--1373685 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1373651 ATTACTCAAA
1373661 TGTATCGATACAT
1 TGTATCGATACAT
1373674 TGTATCGATACA
1 TGTATCGATACA
1373686 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1377527 original size:20 final size:20
Alignment explanation
Indices: 1377502--1377555 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1377492 TTTTACCCAG
1377502 ATGTATCGATACATTTCTCA
1 ATGTATCGATACATTTCTCA
1377522 ATGTATCGATACATTTCTCA
1 ATGTATCGATACATTTCTCA
*
1377542 ATGTATCGAAACAT
1 ATGTATCGATACAT
1377556 CCAGGCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTTCTCA
Done.