Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold15
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: 4011073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 11440 characters in sequence are not A, C, G, or T
File 17 of 25
Found at i:2624044 original size:14 final size:14
Alignment explanation
Indices: 2624027--2624075 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
2624017 ATCTTTATCA
* *
2624027 AAAATATTTGTGTC
1 AAAATACTTATGTC
*
2624041 AAAATACTTATGTT
1 AAAATACTTATGTC
*
2624055 AAAAGCACTTATGTC
1 AAAA-TACTTATGTC
2624070 AAAATA
1 AAAATA
2624076 TTTCTATTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (14 bp):
AAAATACTTATGTC
Found at i:2624096 original size:23 final size:24
Alignment explanation
Indices: 2624066--2624114 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
2624056 AAAGCACTTA
*
2624066 TGTCAAAATATTTCTATTAA-AAG
1 TGTCAAAATATTTCTACTAAGAAG
2624089 TGTCAAAATATTTCTACTAAGAAG
1 TGTCAAAATATTTCTACTAAGAAG
2624113 TG
1 TG
2624115 CATGACAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (24 bp):
TGTCAAAATATTTCTACTAAGAAG
Found at i:2624342 original size:3 final size:3
Alignment explanation
Indices: 2624334--2624371 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2624324 TAGATTAAGT
2624334 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2624372 TGCTGATGAA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2627143 original size:29 final size:29
Alignment explanation
Indices: 2627101--2627161 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
2627091 ATATATTTGC
*
2627101 ATCTTGGGTAACACATTAGTTTGGGTATG
1 ATCTTGGGTAACACATCAGTTTGGGTATG
2627130 ATCTTGGGTAACACATCAGTTTGGGTATG
1 ATCTTGGGTAACACATCAGTTTGGGTATG
2627159 ATC
1 ATC
2627162 AAATTGTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (29 bp):
ATCTTGGGTAACACATCAGTTTGGGTATG
Found at i:2628496 original size:57 final size:57
Alignment explanation
Indices: 2628408--2628527 Score: 197
Period size: 57 Copynumber: 2.1 Consensus size: 57
2628398 TTTATGGATG
* *
2628408 ATGCTACTAAGGATAGTTTTAAATTGGAGTGTCTTACTTT-TCGCATGTCCAAGGCCA
1 ATGCTACTAAGGATAGTTTTAAATTGAAGTGTCTTA-TTTCTCACATGTCCAAGGCCA
*
2628465 ATGCTACTAAGGATAGTTTTAAATTGAAGTGTCTTATTTCTCACATGTCCAAGGCTA
1 ATGCTACTAAGGATAGTTTTAAATTGAAGTGTCTTATTTCTCACATGTCCAAGGCCA
2628522 ATGCTA
1 ATGCTA
2628528 TTCTTAACAT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
56 3 0.05
57 56 0.95
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (57 bp):
ATGCTACTAAGGATAGTTTTAAATTGAAGTGTCTTATTTCTCACATGTCCAAGGCCA
Found at i:2632892 original size:80 final size:77
Alignment explanation
Indices: 2632700--2632973 Score: 212
Period size: 80 Copynumber: 3.4 Consensus size: 77
2632690 CTCTCGGAAG
** * * * * *
2632700 AGATGAAAAAATTCAATGCTTTAGAAGTAAAAATGGGGTTAGAGTATCTCATCGAAAATGGTAAG
1 AGATG-AAAAATTCAATATTTTAGAAGTAAAAA-CGGGTTGGAGTATCTCCTCG-AAATGATGAG
*
2632765 GTTAGAGTATCCTCTA
63 GTTGGAGTATCC-CTA
* * ** * * *
2632781 AGATGAATATTTTGATGTTTTGGAAAATAAAAACGGTGTTGGAGTATC-CCTCAGAAATGATGAG
1 AGATGAAAAATTCAATATTTTAG-AAGTAAAAACGG-GTTGGAGTATCTCCTC-GAAATGATGAG
*
2632845 ATTGGAGTATCCCTA
63 GTTGGAGTATCCCTA
* *
2632860 GAGATGAAGAAATTCAATATTTTAGAAGTAAAAACGAGATTGGAGTATCTCCTCGAAATTGATGG
1 -AGATGAA-AAATTCAATATTTTAGAAGTAAAAACG-GGTTGGAGTATCTCCTCGAAA-TGATGA
2632925 GGTTGGTA-TATCTCCTA
62 GGTTGG-AGTATC-CCTA
** *
2632942 AGAT-AAAAATTTTGATATTTTAGAAGGAAAAA
1 AGATGAAAAA-TTCAATATTTTAGAAGTAAAAA
2632974 TTTAAAAATT
Statistics
Matches: 155, Mismatches: 27, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
79 6 0.04
80 87 0.56
81 57 0.37
82 5 0.03
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.30
Consensus pattern (77 bp):
AGATGAAAAATTCAATATTTTAGAAGTAAAAACGGGTTGGAGTATCTCCTCGAAATGATGAGGTT
GGAGTATCCCTA
Found at i:2635301 original size:39 final size:40
Alignment explanation
Indices: 2635247--2635322 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
2635237 AATATATTGA
*
2635247 TACATTTAGGTCAAAAACC-AGAATGTATCAATACAACGG
1 TACATTTAGGTCAAAAACCTAAAATGTATCAATACAACGG
*
2635286 TACATTTGGGTCAAAAACCTAAAATGTATCAATACAA
1 TACATTTAGGTCAAAAACCTAAAATGTATCAATACAA
2635323 TGAAAAATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 18 0.53
40 16 0.47
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25
Consensus pattern (40 bp):
TACATTTAGGTCAAAAACCTAAAATGTATCAATACAACGG
Found at i:2635409 original size:20 final size:21
Alignment explanation
Indices: 2635381--2635432 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
2635371 ACATGGTCCT
*
2635381 GTATTGATACATT-CACTTA-A
1 GTATCGATACATTAC-CTTATA
*
2635401 GTATCGATACATTACCTTATT
1 GTATCGATACATTACCTTATA
2635422 GTATCGATACA
1 GTATCGATACA
2635433 AATTGTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
GTATCGATACATTACCTTATA
Found at i:2636496 original size:20 final size:20
Alignment explanation
Indices: 2636471--2636509 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2636461 GATGGAGATG
*
2636471 ATATGGATCGTAAAAAATAC
1 ATATGGATCATAAAAAATAC
*
2636491 ATATGGATCATATAAAATA
1 ATATGGATCATAAAAAATA
2636510 AGGCATCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (20 bp):
ATATGGATCATAAAAAATAC
Found at i:2636731 original size:21 final size:20
Alignment explanation
Indices: 2636707--2636755 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2636697 TTCTACAATT
*
2636707 TGTATCGATATAACAAGTTAA
1 TGTATCGATAT-ACAAGTGAA
* *
2636728 TGTATCAATATATAAGTGAA
1 TGTATCGATATACAAGTGAA
2636748 TGTATCGA
1 TGTATCGA
2636756 CACATAAGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATATACAAGTGAA
Found at i:2646143 original size:13 final size:13
Alignment explanation
Indices: 2646103--2646149 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
2646093 ATATATTTTA
2646103 TTATTAACTAATTT
1 TTATTAA-TAATTT
* *
2646117 TTAAT-GTAAGTTT
1 TTATTAATAA-TTT
2646130 TTATTAATAATTT
1 TTATTAATAATTT
2646143 TTATTAA
1 TTATTAA
2646150 ATTAAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
12 3 0.11
13 17 0.63
14 7 0.26
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (13 bp):
TTATTAATAATTT
Found at i:2648391 original size:20 final size:20
Alignment explanation
Indices: 2648366--2648436 Score: 133
Period size: 20 Copynumber: 3.5 Consensus size: 20
2648356 ATTGGGCTCA
*
2648366 ATGTATTGATACATTTCACC
1 ATGTATCGATACATTTCACC
2648386 ATGTATCGATACATTTCACC
1 ATGTATCGATACATTTCACC
2648406 ATGTATCGATACATTTCACC
1 ATGTATCGATACATTTCACC
2648426 ATGTATCGATA
1 ATGTATCGATA
2648437 TAATGTATTG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTTCACC
Found at i:2648548 original size:13 final size:13
Alignment explanation
Indices: 2648530--2648556 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2648520 TACCAAGAAC
2648530 ATGTATCGATACA
1 ATGTATCGATACA
2648543 ATGTATCGATACA
1 ATGTATCGATACA
2648556 A
1 A
2648557 AGCAATATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2648553 original size:32 final size:33
Alignment explanation
Indices: 2648512--2648575 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
2648502 CAATTCAGTG
*
2648512 TGTATCGATACCAAG-AACATGTATCGATACAA
1 TGTATCGATACAAAGCAACATGTATCGATACAA
*
2648544 TGTATCGATACAAAGCAATATGTATCGATACA
1 TGTATCGATACAAAGCAACATGTATCGATACA
2648576 TCTAGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.27
Consensus pattern (33 bp):
TGTATCGATACAAAGCAACATGTATCGATACAA
Found at i:2650958 original size:51 final size:52
Alignment explanation
Indices: 2650828--2650966 Score: 167
Period size: 51 Copynumber: 2.7 Consensus size: 52
2650818 ATTTACCTGC
* * *
2650828 ATGTATCGATA-CATTGAAGAATATATCGATAAATTTGGGTCAAAAATTCAGA
1 ATGTATCGATACCA-TGAAGAATGTATCGATACATTTGGGTCAAAAACTCAGA
* * *
2650880 ATGTATCGATACAATAAAGAATGTATCGATACATTAT-GGTC-AAAACTCATA
1 ATGTATCGATACCATGAAGAATGTATCGATACATT-TGGGTCAAAAACTCAGA
* *
2650931 ATGTATCAATACCATGAAGAGTGTATCGATACATTT
1 ATGTATCGATACCATGAAGAATGTATCGATACATTT
2650967 TCATTTCAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
50 1 0.01
51 39 0.52
52 33 0.44
53 2 0.03
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (52 bp):
ATGTATCGATACCATGAAGAATGTATCGATACATTTGGGTCAAAAACTCAGA
Found at i:2651156 original size:20 final size:21
Alignment explanation
Indices: 2651115--2651167 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 21
2651105 TGAAACTTTG
2651115 TATCGATACATTCAAAAAATA
1 TATCGATACATTCAAAAAATA
*
2651136 TATCGATACATT-AAGAAATA
1 TATCGATACATTCAAAAAATA
2651156 TATCGATACATT
1 TATCGATACATT
2651168 TAGGCAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (21 bp):
TATCGATACATTCAAAAAATA
Found at i:2651591 original size:26 final size:25
Alignment explanation
Indices: 2651562--2651619 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
2651552 TATTTTTTAA
*
2651562 AAAAATATTACTAAAATAATGCTAAT
1 AAAAATA-GACTAAAATAATGCTAAT
* *
2651588 AAAAACGAGACTAAAATAATGTTAAT
1 AAAAA-TAGACTAAAATAATGCTAAT
*
2651614 ACAAAT
1 AAAAAT
2651620 GGGATTATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
26 25 0.96
27 1 0.04
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.26
Consensus pattern (25 bp):
AAAAATAGACTAAAATAATGCTAAT
Found at i:2652350 original size:21 final size:22
Alignment explanation
Indices: 2652325--2652372 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
2652315 AAATTTAAGT
2652325 TATAAAATATATT-AATATAAA
1 TATAAAATATATTAAATATAAA
* *
2652346 TATAAAATGTATTAAATATTAA
1 TATAAAATATATTAAATATAAA
2652368 TATAA
1 TATAA
2652373 CATCCTTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TATAAAATATATTAAATATAAA
Found at i:2655127 original size:16 final size:17
Alignment explanation
Indices: 2655108--2655141 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2655098 AAAATTTTAA
*
2655108 TATTTTTTAATT-ATTT
1 TATTTTTAAATTAATTT
2655124 TATTTTTAAATTAATTT
1 TATTTTTAAATTAATTT
2655141 T
1 T
2655142 TAATATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTTAAATTAATTT
Found at i:2655298 original size:23 final size:22
Alignment explanation
Indices: 2655272--2655329 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
2655262 ATACTTTATT
2655272 TATTTGATATTTA-AATTTTTAAA
1 TATTT-ATATTTATAA-TTTTAAA
*
2655295 TATTAAATATTTATAATTTTAAA
1 TATT-TATATTTATAATTTTAAA
2655318 -ATTTATATTTAT
1 TATTTATATTTAT
2655330 TTATAGACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
21 8 0.26
22 3 0.10
23 18 0.58
24 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTTATATTTATAATTTTAAA
Found at i:2655300 original size:15 final size:16
Alignment explanation
Indices: 2655282--2655324 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2655272 TATTTGATAT
*
2655282 TTAAATTTTTA-AATA
1 TTAAATATTTATAATA
*
2655297 TTAAATATTTATAATT
1 TTAAATATTTATAATA
2655313 TTAAA-ATTTATA
1 TTAAATATTTATA
2655325 TTTATTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 17 0.68
16 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATATTTATAATA
Found at i:2656163 original size:16 final size:16
Alignment explanation
Indices: 2656130--2656164 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2656120 AACCAGATCG
* *
2656130 AAAATGATTTGAATTT
1 AAAATGATTTAAACTT
2656146 AAAATGATTTAAACTT
1 AAAATGATTTAAACTT
2656162 AAA
1 AAA
2656165 GCGACTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (16 bp):
AAAATGATTTAAACTT
Found at i:2658988 original size:15 final size:15
Alignment explanation
Indices: 2658968--2658997 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2658958 TAGTGAATTT
2658968 TGAACCTAAATGATC
1 TGAACCTAAATGATC
2658983 TGAACCTAAATGATC
1 TGAACCTAAATGATC
2658998 CAAGTGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (15 bp):
TGAACCTAAATGATC
Found at i:2659280 original size:2 final size:2
Alignment explanation
Indices: 2659273--2659299 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2659263 TTCAGCGATG
2659273 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 T
2659300 TGGAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2667554 original size:2 final size:2
Alignment explanation
Indices: 2667547--2667583 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2667537 TTCTATAAAC
2667547 AT 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 AT A
2667584 GACACAGCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2668306 original size:298 final size:298
Alignment explanation
Indices: 2667770--2668365 Score: 933
Period size: 298 Copynumber: 2.0 Consensus size: 298
2667760 CAAATAAGTT
* * *
2667770 ACTAACACATGAAATTTATTTTCAAATTTTAACCATAACAAGAGAATGATGAATAAATATTCAAA
1 ACTAACACATGAAAGTCATTTTCAAATTTTAACCATAACAAGAGAATGATGAATAAACATTCAAA
* *
2667835 AGTAAAACCTAGCTAAAATCGTGGTCCAAACTAAAGCGAATAAGAATGCCCATTAATATTTCATG
66 AGTAAAACCTAGCCAAAATCGTGGTCCAAACTAAAGCGAATAAGAATGCCCATTAATATCTCATG
** ** * *
2667900 TAAAAAATTCGAAAGGTAGTTTGTATTGAAAAGATTATAAATTTCAATCATGTTTTAGTTTGTTT
131 TAAAAAATTCGAAAGGTAAATCATATTGAAAAGATTATAAATTTCAACCACGTTTTAGTTTGTTT
* *
2667965 AATTTTCTTTTATTAATTATCCATTTATTTAAAATAAATTTAATACATGTTTAATAAATATACTA
196 AATTTTCTTTTATTAATTATCCATTTAATTAAAATAAATTTAATAAATGTTTAATAAATATACTA
**
2668030 AAAATAAAATTATATAACATGCATTTATGATCTGAACA
261 AAAATAAAATTATATAACACACATTTATGATCTGAACA
* *
2668068 ACTAACATATGAAAGTCATTTTCAAATTTTAACTATAACAAGAGAATGATGAATAAACATTCAAA
1 ACTAACACATGAAAGTCATTTTCAAATTTTAACCATAACAAGAGAATGATGAATAAACATTCAAA
* *
2668133 AGTAAAACCTAGCCAAAATCGTAGGTCCAAACTAAAGTGAATAAGAATGCCCCTTAATATCTCAT
66 AGTAAAACCTAGCCAAAATCGT-GGTCCAAACTAAAGCGAATAAGAATGCCCATTAATATCTCAT
* *
2668198 GTAAAAAATTTGGAAGGTAAATCATATTGAAAAGATTATAAATTTCAACCACGTTTTAGTTTGTT
130 GTAAAAAATTCGAAAGGTAAATCATATTGAAAAGATTATAAATTTCAACCACGTTTTAGTTTGTT
* * *
2668263 TAATTTT-TTTTATTAATTATCCGTTTAATTAAAATAAATTTAATAAATTTTTGATAAATATACT
195 TAATTTTCTTTTATTAATTATCCATTTAATTAAAATAAATTTAATAAATGTTTAATAAATATACT
* * *
2668327 AAAGATAAAGTTATATAACACATATTTATGATCTGAACA
260 AAAAATAAAATTATATAACACACATTTATGATCTGAACA
2668366 CCGCAGTCAG
Statistics
Matches: 270, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
298 167 0.62
299 103 0.38
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.35
Consensus pattern (298 bp):
ACTAACACATGAAAGTCATTTTCAAATTTTAACCATAACAAGAGAATGATGAATAAACATTCAAA
AGTAAAACCTAGCCAAAATCGTGGTCCAAACTAAAGCGAATAAGAATGCCCATTAATATCTCATG
TAAAAAATTCGAAAGGTAAATCATATTGAAAAGATTATAAATTTCAACCACGTTTTAGTTTGTTT
AATTTTCTTTTATTAATTATCCATTTAATTAAAATAAATTTAATAAATGTTTAATAAATATACTA
AAAATAAAATTATATAACACACATTTATGATCTGAACA
Found at i:2669327 original size:31 final size:32
Alignment explanation
Indices: 2669258--2669328 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
2669248 TTTTAAAATA
*
2669258 TAAATAATATATATTTTAATATTTATACTATG
1 TAAATTATATATATTTTAATATTTATACTATG
*
2669290 -ATATTATATATA-TTT-ATATTTTATA-TGATG
1 TAAATTATATATATTTTAATA-TTTATACT-ATG
2669320 TAAATTATA
1 TAAATTATA
2669329 CGATATACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
29 4 0.12
30 12 0.36
31 17 0.52
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (32 bp):
TAAATTATATATATTTTAATATTTATACTATG
Found at i:2670032 original size:17 final size:16
Alignment explanation
Indices: 2670006--2670037 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2669996 TCCATTTTTA
2670006 TTAATAAATATAATAC
1 TTAATAAATATAATAC
2670022 TTAATTAAATATAATA
1 TTAA-TAAATATAATA
2670038 ATAATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAATAAATATAATAC
Found at i:2670531 original size:20 final size:19
Alignment explanation
Indices: 2670508--2670576 Score: 77
Period size: 18 Copynumber: 3.6 Consensus size: 19
2670498 AATGAGGTAC
*
2670508 ATTTAAACAAATAAATATTT
1 ATTTAAAAAAATAAA-ATTT
* *
2670528 ATTTTAAAAAATAAAAATT
1 ATTTAAAAAAATAAAATTT
* *
2670547 ATGTAAAAAAAT-TAATTT
1 ATTTAAAAAAATAAAATTT
2670565 ATTTAAAAAAAT
1 ATTTAAAAAAAT
2670577 TCTTATTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
18 15 0.37
19 13 0.32
20 13 0.32
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (19 bp):
ATTTAAAAAAATAAAATTT
Found at i:2671338 original size:40 final size:40
Alignment explanation
Indices: 2671278--2671358 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
2671268 AAGTTTTTTT
*
2671278 TTTTTTTTTTCTTTTTCTCCCTGCCTGCTTCCCGCAACAA
1 TTTTTTTTTTCTTTTCCTCCCTGCCTGCTTCCCGCAACAA
2671318 TTTTTTTTTTCTTTTCCTCCCTGCCTGCTTCCCGCAACAA
1 TTTTTTTTTTCTTTTCCTCCCTGCCTGCTTCCCGCAACAA
2671358 T
1 T
2671359 CCCTCCATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.10, C:0.33, G:0.07, T:0.49
Consensus pattern (40 bp):
TTTTTTTTTTCTTTTCCTCCCTGCCTGCTTCCCGCAACAA
Found at i:2674561 original size:15 final size:15
Alignment explanation
Indices: 2674528--2674570 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2674518 AAAATCTAAT
** *
2674528 AAATAATTTATTTAT
1 AAATAATTTATAAAA
2674543 AAATAATTTATAAAA
1 AAATAATTTATAAAA
2674558 AAATTAATTTATA
1 AAA-TAATTTATA
2674571 TCGTGATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATAATTTATAAAA
Found at i:2675495 original size:16 final size:16
Alignment explanation
Indices: 2675476--2675519 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
2675466 TTTGTATGTG
2675476 AAAAAATTTGAATTAA
1 AAAAAATTTGAATTAA
*
2675492 AAAAAATTT-AAATAA
1 AAAAAATTTGAATTAA
*
2675507 AAAAAGTTTGAAT
1 AAAAAATTTGAAT
2675520 CCGAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (16 bp):
AAAAAATTTGAATTAA
Found at i:2679037 original size:26 final size:26
Alignment explanation
Indices: 2679008--2679061 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
2678998 AAAGGTGCAT
*
2679008 TTTAGGGATAGGCTAGTCATTTCATA
1 TTTAGCGATAGGCTAGTCATTTCATA
*
2679034 TTTAGCGATAGGCTAGTTATTTCATA
1 TTTAGCGATAGGCTAGTCATTTCATA
2679060 TT
1 TT
2679062 ATTATCGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (26 bp):
TTTAGCGATAGGCTAGTCATTTCATA
Found at i:2680121 original size:13 final size:13
Alignment explanation
Indices: 2680080--2680127 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
2680070 CCGTTACAAG
2680080 CAATGTATCGATA
1 CAATGTATCGATA
2680093 CAAT-T-TC-AT-
1 CAATGTATCGATA
2680102 C-ATGTATCGATA
1 CAATGTATCGATA
*
2680114 CAATGTATTGATA
1 CAATGTATCGATA
2680127 C
1 C
2680128 TTTATCCCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
8 2 0.07
9 2 0.07
10 4 0.14
11 4 0.14
12 2 0.07
13 15 0.52
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2680229 original size:19 final size:19
Alignment explanation
Indices: 2680178--2680234 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
2680168 CTGCCAATCT
*
2680178 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAC
* * *
2680198 CATTGTATTGATATAATGAG
1 CA-TGTATCGATACAATGAC
2680218 CATGTATCGATACAATG
1 CATGTATCGATACAATG
2680235 TATCGATACA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 13 0.43
20 6 0.20
21 11 0.37
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:2680237 original size:13 final size:13
Alignment explanation
Indices: 2680219--2680245 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2680209 TATAATGAGC
2680219 ATGTATCGATACA
1 ATGTATCGATACA
2680232 ATGTATCGATACA
1 ATGTATCGATACA
2680245 A
1 A
2680246 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2687905 original size:17 final size:17
Alignment explanation
Indices: 2687878--2687919 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
2687868 TTTTCGATAG
2687878 AATTTTTAAATGTAT-A
1 AATTTTTAAATGTATCA
*
2687894 AATTTTTAAAATTTATCA
1 AATTTTT-AAATGTATCA
2687912 AATATTTT
1 AAT-TTTT
2687920 CATTAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 7 0.32
18 4 0.18
19 4 0.18
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
AATTTTTAAATGTATCA
Found at i:2694170 original size:11 final size:10
Alignment explanation
Indices: 2694154--2694210 Score: 53
Period size: 11 Copynumber: 5.4 Consensus size: 10
2694144 AGGCAATGTA
2694154 AAAAAAATAAC
1 AAAAAAA-AAC
2694165 AAAAAAACAAC
1 AAAAAAA-AAC
*
2694176 AAAACAAAAAT
1 AAAA-AAAAAC
2694187 AAAAAAATAA-
1 AAAAAAA-AAC
*
2694197 AAACAAAAAC
1 AAAAAAAAAC
2694207 AAAA
1 AAAA
2694211 GGAAAAGGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 2 0.05
10 12 0.31
11 22 0.56
12 3 0.08
ACGTcount: A:0.84, C:0.11, G:0.00, T:0.05
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:2694170 original size:14 final size:14
Alignment explanation
Indices: 2694167--2694205 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2694157 AAAATAACAA
*
2694167 AAAAACAACAAAAC
1 AAAAACAAAAAAAC
* *
2694181 AAAAATAAAAAAAT
1 AAAAACAAAAAAAC
2694195 AAAAACAAAAA
1 AAAAACAAAAA
2694206 CAAAAGGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.85, C:0.10, G:0.00, T:0.05
Consensus pattern (14 bp):
AAAAACAAAAAAAC
Found at i:2694173 original size:8 final size:9
Alignment explanation
Indices: 2694156--2694210 Score: 55
Period size: 8 Copynumber: 6.4 Consensus size: 9
2694146 GCAATGTAAA
2694156 AAAAATAAC
1 AAAAATAAC
2694165 AAAAA-AAC
1 AAAAATAAC
*
2694173 AACAA-AAC
1 AAAAATAAC
2694181 AAAAATAA-
1 AAAAATAAC
2694189 AAAAATAA-
1 AAAAATAAC
*
2694197 AAACAAAAAC
1 AAA-AATAAC
2694207 AAAA
1 AAAA
2694211 GGAAAAGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
8 25 0.62
9 12 0.30
10 3 0.08
ACGTcount: A:0.84, C:0.11, G:0.00, T:0.05
Consensus pattern (9 bp):
AAAAATAAC
Found at i:2694184 original size:25 final size:26
Alignment explanation
Indices: 2694156--2694210 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
2694146 GCAATGTAAA
*
2694156 AAAAATAACAAAAA-AACAAC-AAAAC
1 AAAAATAA-AAAAATAAAAACAAAAAC
2694181 AAAAATAAAAAAATAAAAACAAAAAC
1 AAAAATAAAAAAATAAAAACAAAAAC
2694207 AAAA
1 AAAA
2694211 GGAAAAGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 13 0.48
26 9 0.33
ACGTcount: A:0.84, C:0.11, G:0.00, T:0.05
Consensus pattern (26 bp):
AAAAATAAAAAAATAAAAACAAAAAC
Found at i:2694190 original size:20 final size:20
Alignment explanation
Indices: 2694152--2694210 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
2694142 AAAGGCAATG
2694152 TAAAAA-AAATAACAAAAAAA
1 TAAAAACAAA-AACAAAAAAA
* *
2694172 CAACAAAACAAAAATAAAAAAA
1 -TA-AAAACAAAAACAAAAAAA
2694194 TAAAAACAAAAACAAAA
1 TAAAAACAAAAACAAAA
2694211 GGAAAAGGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 14 0.44
21 2 0.06
22 13 0.41
23 3 0.09
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (20 bp):
TAAAAACAAAAACAAAAAAA
Found at i:2695323 original size:31 final size:30
Alignment explanation
Indices: 2695288--2695386 Score: 81
Period size: 31 Copynumber: 3.1 Consensus size: 30
2695278 TGATGATATC
2695288 CCTAGTTAACTCTTTTTGACTTAGGTTTTAT
1 CCTAGTT-ACTCTTTTTGACTTAGGTTTTAT
* * **
2695319 CCTAGTTACTCTTAGTTGACTATATTGATTTTGC
1 CCTAGTTACTCTT-TTTGACT-TA--GGTTTTAT
* * *
2695353 CCTAGTTGTCTCTTTTTGACTTATGTTTCAT
1 CCTAGTT-ACTCTTTTTGACTTAGGTTTTAT
2695384 CCT
1 CCT
2695387 GGTCACCCTT
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
30 6 0.12
31 19 0.37
32 2 0.04
33 2 0.04
34 18 0.35
35 5 0.10
ACGTcount: A:0.17, C:0.19, G:0.13, T:0.51
Consensus pattern (30 bp):
CCTAGTTACTCTTTTTGACTTAGGTTTTAT
Found at i:2695398 original size:65 final size:65
Alignment explanation
Indices: 2695287--2695839 Score: 383
Period size: 65 Copynumber: 8.5 Consensus size: 65
2695277 CTGATGATAT
* * * * * *
2695287 CCCTAGTTAACTCTTTTTGACTTAGGTTTTATCCTAGTTACTCTTAGTTGACTATATTGA-TTTT
1 CCCTAGTCAAC-CTTTTTGACTTAGGTTTCATCCTGGTCACCCTTAGTTGACTATATTCAGTTTT
2695351 G
65 G
*** *
2695352 CCCTAGTTGTCTCTTTTTGACTTATGTTTCATCCTGGTCACCCTTAGTTGA-TGATA-TCAGTTT
1 CCCTAGTCAAC-CTTTTTGACTTAGGTTTCATCCTGGTCACCCTTAGTTGACT-ATATTCAGTTT
*
2695415 TT
64 TG
** ** * * * *
2695417 CCCTAGTCAATCCTTTTTTGACTTAGGTTTTGTTTTGGTCACCTTTCGTTGATTATA-TCA-ATT
1 CCCTAGTCAA-CC-TTTTTGACTTAGGTTTCATCCTGGTCACCCTTAGTTGACTATATTCAGTTT
2695480 TG
64 TG
* * * * *
2695482 CCTTGGTCAACCCTTTTTTGACTTAGATTTCATCCTGGTTACCCTCAGTTGACTATATT-AGTTT
1 CCCTAGTCAA-CC-TTTTTGACTTAGGTTTCATCCTGGTCACCCTTAGTTGACTATATTCAGTTT
**
2695546 CA
64 TG
* * * * * *
2695548 CCCTGGTCAACCTATTTTGACTTAGATTTCATCTTGGTCACCTTTAGTTGACTATATTGA-TTTC
1 CCCTAGTCAACCT-TTTTGACTTAGGTTTCATCCTGGTCACCCTTAGTTGACTATATTCAGTTTT
*
2695612 A
65 G
* * ** * * * * *
2695613 CCATGGTCAAGCCTTTTCAACTTAGATTTTATCCTAGT-ATCCTTAGTTGTCTATA-TCAGTTTT
1 CCCTAGTCAA-CCTTTTTGACTTAGGTTTCATCCTGGTCACCCTTAGTTGACTATATTCAGTTTT
2695676 G
65 G
** * ** * * *
2695677 CCCTAGTCAACTCCTTTTCAATTTAGGTTTTGTCCTTGTCACCTTTAGTTGACTATGTT-AGTTT
1 CCCTAGTCAA--CCTTTTTGACTTAGGTTTCATCCTGGTCACCCTTAGTTGACTATATTCAGTTT
*
2695741 TA
64 TG
* *
2695743 CCTTAGTCAACCTTTTTCGACTTAGGTTTCATCCTGGTCGCCCTTAGTTGACTATA-TC-GATTT
1 CCCTAGTCAACCTTTTT-GACTTAGGTTTCATCCTGGTCACCCTTAGTTGACTATATTCAG-TTT
2695806 TG
64 TG
* * *
2695808 CCCTGGTCAACCCCTTTTGGATTTAGGTTTCA
1 CCCTAGTCAA--CCTTTTTGACTTAGGTTTCA
2695840 ACTAGTTACC
Statistics
Matches: 388, Mismatches: 81, Indels: 37
0.77 0.16 0.07
Matches are distributed among these distances:
63 2 0.01
64 37 0.10
65 247 0.64
66 94 0.24
67 8 0.02
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.45
Consensus pattern (65 bp):
CCCTAGTCAACCTTTTTGACTTAGGTTTCATCCTGGTCACCCTTAGTTGACTATATTCAGTTTTG
Found at i:2695526 original size:31 final size:31
Alignment explanation
Indices: 2695485--2695589 Score: 95
Period size: 31 Copynumber: 3.3 Consensus size: 31
2695475 CAATTTGCCT
*
2695485 TGGTCAACCCTTTTTTGACTTAGATTTCATCC
1 TGGTC-ACCCTATTTTGACTTAGATTTCATCC
* * * *
2695517 TGGTTACCCTCA-GTTGACTATATTAGTTTCACCC
1 TGGTCACCCT-ATTTTGACT-TA-GA-TTTCATCC
* *
2695551 TGGTCAACCTATTTTGACTTAGATTTCATCT
1 TGGTCACCCTATTTTGACTTAGATTTCATCC
2695582 TGGTCACC
1 TGGTCACC
2695590 TTTAGTTGAC
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
31 24 0.43
32 7 0.12
33 4 0.07
34 21 0.38
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (31 bp):
TGGTCACCCTATTTTGACTTAGATTTCATCC
Found at i:2695568 original size:34 final size:34
Alignment explanation
Indices: 2695530--2695628 Score: 84
Period size: 31 Copynumber: 3.0 Consensus size: 34
2695520 TTACCCTCAG
*
2695530 TTGACTATATTAGTTTCACCCTGGTCAACCTATT-
1 TTGACTATATTAGTTTCACCATGGTCAACCT-TTA
* * *
2695564 TTGACT-TA-GA-TTTCATCTTGGTC-ACCTTTA
1 TTGACTATATTAGTTTCACCATGGTCAACCTTTA
2695594 GTTGACTATATT-GATTTCACCATGGTCAAGCCTTT
1 -TTGACTATATTAG-TTTCACCATGGTCAA-CCTTT
2695629 TCAACTTAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
29 2 0.04
30 4 0.08
31 17 0.33
32 3 0.06
33 2 0.04
34 17 0.33
35 1 0.02
36 5 0.10
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.42
Consensus pattern (34 bp):
TTGACTATATTAGTTTCACCATGGTCAACCTTTA
Found at i:2695599 original size:31 final size:31
Alignment explanation
Indices: 2695499--2695600 Score: 91
Period size: 31 Copynumber: 3.2 Consensus size: 31
2695489 CAACCCTTTT
* * *
2695499 TTGACTTAGATTTCATCCTGGTTACCCTCAG
1 TTGACTTAGATTTCATCCTGGTCACCTTTAG
* *
2695530 TTGACTATATTAGTTTCACCCTGGTCAACCTATT--
1 TTGACT-TA-GA-TTTCATCCTGGTC-ACCT-TTAG
*
2695564 TTGACTTAGATTTCATCTTGGTCACCTTTAG
1 TTGACTTAGATTTCATCCTGGTCACCTTTAG
2695595 TTGACT
1 TTGACT
2695601 ATATTGATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
29 2 0.04
30 4 0.07
31 23 0.41
32 3 0.05
33 3 0.05
34 17 0.30
35 3 0.05
36 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (31 bp):
TTGACTTAGATTTCATCCTGGTCACCTTTAG
Found at i:2695647 original size:130 final size:128
Alignment explanation
Indices: 2695364--2695837 Score: 451
Period size: 130 Copynumber: 3.6 Consensus size: 128
2695354 CTAGTTGTCT
*
2695364 CTTTTT-GACTTATG-TTTCATCCTGGTCACCCTTAGTTGA-TGATATCAGTTTTTCCCTAGTCA
1 CTTTTTCGACTTA-GATTTCATCCTGGTCACCCTTAGTTGACT-ATATCAGTTTTACCCTAGTCA
* * * * *
2695426 ATCCTTTTTTGACTTAGGTTTTGTTTTGGTCACCTTTCGTTGATTATATCAATTTGCCTTGGTCA
64 ATCC-TTTTTGACTTAGGTTTTGTCTTGGTCACCTTTAGTTGACTATAT-TATTTACCTTGGTCA
2695491 ACC
127 A-C
* * * * * *
2695494 CTTTTTTGACTTAGATTTCATCCTGGTTACCCTCAGTTGACTATATTAGTTTCACCCTGGTCAA-
1 CTTTTTCGACTTAGATTTCATCCTGGTCACCCTTAGTTGACTATATCAGTTTTACCCTAGTCAAT
* ** *
2695558 CCTATTTTGACTTAGATTTCATCTTGGTCACCTTTAGTTGACTATATTGATTTCACCATGGTCAA
66 CCT-TTTTGACTTAGGTTTTGTCTTGGTCACCTTTAGTTGACTATATT-ATTT-ACCTTGGTCAA
2695623 GC
128 -C
* * * * * *
2695625 C-TTTTCAACTTAGATTTTATCCTAGT-ATCCTTAGTTGTCTATATCAGTTTTGCCCTAGTCAAC
1 CTTTTTCGACTTAGATTTCATCCTGGTCACCCTTAGTTGACTATATCAGTTTTACCCTAGTCAA-
** * * *
2695688 TCCTTTTCAATTTAGGTTTTGTCCTT-GTCACCTTTAGTTGACTATGTTAGTTTTACCTTAGTCA
65 TCCTTTTTGACTTAGGTTTTGT-CTTGGTCACCTTTAGTTGACTATATTA--TTTACCTTGGTCA
2695752 AC
127 AC
* * * *
2695754 CTTTTTCGACTTAGGTTTCATCCTGGTCGCCCTTAGTTGACTATATC-GATTTTGCCCTGGTCAA
1 CTTTTTCGACTTAGATTTCATCCTGGTCACCCTTAGTTGACTATATCAG-TTTTACCCTAGTCAA
* * *
2695818 CCCCTTTTGGATTTAGGTTT
65 -TCCTTTTTGACTTAGGTTT
2695838 CAACTAGTTA
Statistics
Matches: 283, Mismatches: 47, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
129 33 0.12
130 135 0.48
131 114 0.40
132 1 0.00
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.45
Consensus pattern (128 bp):
CTTTTTCGACTTAGATTTCATCCTGGTCACCCTTAGTTGACTATATCAGTTTTACCCTAGTCAAT
CCTTTTTGACTTAGGTTTTGTCTTGGTCACCTTTAGTTGACTATATTATTTACCTTGGTCAAC
Found at i:2699256 original size:52 final size:52
Alignment explanation
Indices: 2699185--2699306 Score: 208
Period size: 52 Copynumber: 2.3 Consensus size: 52
2699175 TGAAATTTTA
* * *
2699185 CCTGCTTGTATCGATACATTTCATATTGTATCGATACATTTGGGCAAATTTG
1 CCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTG
*
2699237 CCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTG
1 CCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTG
2699289 CCTGCATGTATCGATACA
1 CCTGCATGTATCGATACA
2699307 AAAATCAATG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (52 bp):
CCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTG
Found at i:2699319 original size:52 final size:52
Alignment explanation
Indices: 2699185--2699327 Score: 182
Period size: 52 Copynumber: 2.8 Consensus size: 52
2699175 TGAAATTTTA
* ** * *
2699185 CCTGCTTGTATCGATACATTTCATATTGTATCGATACATTTGGGCAAATTTG
1 CCTGCATGTATCGATACAAATCATAGTGTATCGATACATCTGGGCAAATTTG
* **
2699237 CCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTG
1 CCTGCATGTATCGATACAAATCATAGTGTATCGATACATCTGGGCAAATTTG
2699289 CCTGCATGTATCGATACAAAAATCA-A-TGTATCGATACAT
1 CCTGCATGTATCGATAC--AAATCATAGTGTATCGATACAT
2699328 TTTCTTGGCA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 77 0.94
53 1 0.01
54 4 0.05
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
CCTGCATGTATCGATACAAATCATAGTGTATCGATACATCTGGGCAAATTTG
Found at i:2699382 original size:19 final size:18
Alignment explanation
Indices: 2699358--2699454 Score: 70
Period size: 19 Copynumber: 5.8 Consensus size: 18
2699348 AGCGATACAT
2699358 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
2699377 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
2699390 TGTATTGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
2699409 TTTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
2699422 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
2699441 TGTATCAATACAAA
1 TGTATCGATACAAA
2699455 TCGTTGAAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 25
0.67 0.05 0.27
Matches are distributed among these distances:
13 20 0.33
14 2 0.03
16 4 0.07
18 3 0.05
19 32 0.52
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:2699391 original size:32 final size:32
Alignment explanation
Indices: 2699350--2699452 Score: 170
Period size: 32 Copynumber: 3.2 Consensus size: 32
2699340 AGCTTCATAG
*
2699350 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
* *
2699382 CGATACATTGTATTGATACAACACTTATTTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
2699414 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
2699446 CAATACA
1 CGATACA
2699453 AATCGTTGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:2701107 original size:13 final size:13
Alignment explanation
Indices: 2701089--2701113 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2701079 CTATTCATAA
2701089 TGTATCGATACAC
1 TGTATCGATACAC
2701102 TGTATCGATACA
1 TGTATCGATACA
2701114 TGAACAGTGA
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:2701132 original size:10 final size:10
Alignment explanation
Indices: 2701113--2701200 Score: 68
Period size: 10 Copynumber: 8.4 Consensus size: 10
2701103 GTATCGATAC
*
2701113 ATGAACAGTG
1 ATGAATAGTG
2701123 ATGAATAGTG
1 ATGAATAGTG
* * *
2701133 ATGTATCGCTAC
1 ATGAATAG-T-G
2701145 ATGAATAGTG
1 ATGAATAGTG
2701155 ATGAATAGTG
1 ATGAATAGTG
* * *
2701165 ATGTATTGATAC
1 ATGAATAG-T-G
*
2701177 ATGAACAGTG
1 ATGAATAGTG
2701187 ATGAATAGTG
1 ATGAATAGTG
2701197 ATGA
1 ATGA
2701201 GCAGTGAGAT
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
10 44 0.75
11 4 0.07
12 11 0.19
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.30
Consensus pattern (10 bp):
ATGAATAGTG
Found at i:2701146 original size:32 final size:32
Alignment explanation
Indices: 2701102--2701199 Score: 169
Period size: 32 Copynumber: 3.1 Consensus size: 32
2701092 ATCGATACAC
2701102 TGTATCGATACATGAACAGTGATGAATAGTGA
1 TGTATCGATACATGAACAGTGATGAATAGTGA
* *
2701134 TGTATCGCTACATGAATAGTGATGAATAGTGA
1 TGTATCGATACATGAACAGTGATGAATAGTGA
*
2701166 TGTATTGATACATGAACAGTGATGAATAGTGA
1 TGTATCGATACATGAACAGTGATGAATAGTGA
2701198 TG
1 TG
2701200 AGCAGTGAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.31
Consensus pattern (32 bp):
TGTATCGATACATGAACAGTGATGAATAGTGA
Found at i:2702335 original size:181 final size:182
Alignment explanation
Indices: 2702074--2702405 Score: 603
Period size: 181 Copynumber: 1.8 Consensus size: 182
2702064 TTCCTTAAAC
* *
2702074 ATTGAAAGTGAATTTGTTATTGAATTAAATTAAATTAATCATATGAAATTTTATTTCAAATACTT
1 ATTGAAAGTGAATTCGTTATTGAATTAAATTAAATTAATCATATAAAATTTTATTTCAAATACTT
*
2702139 AATTTTTAATTTTTACAATTTAAGCCTTCTAATTAACTTTTATGGTATAATTTTACATAATATAG
66 AATTTTTAATTTTTACAATTTAAGCCTTCTAATTAACTTTTATAGTATAATTTTACATAATATAG
2702204 ACAAATATCACAC-AATTTTTCTAAAACTTAACTGATGTCCTGGATGACATA
131 ACAAATATCACACAAATTTTTCTAAAACTTAACTGATGTCCTGGATGACATA
* *
2702255 ATTGAAGGTGAATTCGTTATTGAATTAAATTAAATTGATCATATAAAATTTTATTTCAAATACTT
1 ATTGAAAGTGAATTCGTTATTGAATTAAATTAAATTAATCATATAAAATTTTATTTCAAATACTT
*
2702320 AATTTTTAATTTTTACAATTTAAGCCTTCTAATTAACTTTTATAGTATAATTTTACATAATATAT
66 AATTTTTAATTTTTACAATTTAAGCCTTCTAATTAACTTTTATAGTATAATTTTACATAATATAG
2702385 ACAAATATCACACAAATTTTT
131 ACAAATATCACACAAATTTTT
2702406 TTGAATTTAA
Statistics
Matches: 144, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
181 137 0.95
182 7 0.05
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (182 bp):
ATTGAAAGTGAATTCGTTATTGAATTAAATTAAATTAATCATATAAAATTTTATTTCAAATACTT
AATTTTTAATTTTTACAATTTAAGCCTTCTAATTAACTTTTATAGTATAATTTTACATAATATAG
ACAAATATCACACAAATTTTTCTAAAACTTAACTGATGTCCTGGATGACATA
Found at i:2703936 original size:19 final size:20
Alignment explanation
Indices: 2703888--2703959 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
2703878 ACACCCAGAT
*
2703888 GTATCGATACATATTGCTTA
1 GTATCGATACATATTGATTA
* * *
2703908 GTATCAATACATGTTTATTA
1 GTATCGATACATATTGATTA
2703928 -TATCGATACATCA-TGAATT-
1 GTATCGATACAT-ATTG-ATTA
2703947 GTATCGATACATA
1 GTATCGATACATA
2703960 AAAGTGACAG
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
19 12 0.29
20 30 0.71
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (20 bp):
GTATCGATACATATTGATTA
Found at i:2704026 original size:14 final size:14
Alignment explanation
Indices: 2704007--2704061 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
2703997 ATTACTGTTC
* *
2704007 ATCACTGTTTATGT
1 ATCACTATTCATGT
2704021 ATCACTATTCATGT
1 ATCACTATTCATGT
2704035 ATCACTATTC----
1 ATCACTATTCATGT
2704045 ATCACTATTCATGT
1 ATCACTATTCATGT
2704059 ATC
1 ATC
2704062 GATACAGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 10 0.29
14 25 0.71
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (14 bp):
ATCACTATTCATGT
Found at i:2706208 original size:21 final size:21
Alignment explanation
Indices: 2706184--2706235 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2706174 GAACTAGAGG
**
2706184 AGAAAATGAATGAGTTGGAAA
1 AGAAAATGAATGAGTTACAAA
**
2706205 AGAAAACAAATGAGTTACAAA
1 AGAAAATGAATGAGTTACAAA
2706226 ATGAAAATGA
1 A-GAAAATGA
2706236 TGAATTAACT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.58, C:0.04, G:0.21, T:0.17
Consensus pattern (21 bp):
AGAAAATGAATGAGTTACAAA
Found at i:2709596 original size:19 final size:20
Alignment explanation
Indices: 2709551--2709601 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2709541 ACACCCAGAT
2709551 GTATCGATACATATTGCTTA
1 GTATCGATACATATTGCTTA
*
2709571 GTATCGATACATGTT-CATTA
1 GTATCGATACATATTGC-TTA
2709591 -TATCGATACAT
1 GTATCGATACAT
2709602 CATGAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
GTATCGATACATATTGCTTA
Found at i:2713719 original size:22 final size:21
Alignment explanation
Indices: 2713675--2713720 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2713665 AGCAATGAGT
**
2713675 TTATATTATAAAAATTATTTA
1 TTATATTATAAAAATTAAGTA
*
2713696 TTATATTATTGAAAATTAAGTA
1 TTATATTA-TAAAAATTAAGTA
2713718 TTA
1 TTA
2713721 AATATAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (21 bp):
TTATATTATAAAAATTAAGTA
Found at i:2717191 original size:10 final size:11
Alignment explanation
Indices: 2717172--2717204 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
2717162 TTATTTTATT
2717172 TTTTTATAAAA
1 TTTTTATAAAA
2717183 TTTTT-TAAAA
1 TTTTTATAAAA
2717193 TTTTATATAAAA
1 TTTT-TATAAAA
2717205 AATTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.45
11 6 0.30
12 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTTATAAAA
Found at i:2723307 original size:27 final size:29
Alignment explanation
Indices: 2723271--2723324 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
2723261 ATAATTATTT
*
2723271 TTATTAAAAATAA-AT-AATATTTATTAC
1 TTATTAAAAATAATATGAATATATATTAC
*
2723298 TTATTCAAAATAATATGAATATATATT
1 TTATTAAAAATAATATGAATATATATT
2723325 TATTAGAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 12 0.52
28 2 0.09
29 9 0.39
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (29 bp):
TTATTAAAAATAATATGAATATATATTAC
Found at i:2726084 original size:26 final size:26
Alignment explanation
Indices: 2726048--2726097 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
2726038 TATGAGTAAG
2726048 TTTGAATTAAACTTTCAATTTTTAAT
1 TTTGAATTAAACTTTCAATTTTTAAT
* *
2726074 TTTGAATTAAATTTTTAATTTTTA
1 TTTGAATTAAACTTTCAATTTTTA
2726098 TTCATTATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (26 bp):
TTTGAATTAAACTTTCAATTTTTAAT
Found at i:2727050 original size:34 final size:34
Alignment explanation
Indices: 2727004--2727188 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
2726994 GTAAAAACCA
*
2727004 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2727038 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
2727072 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2727106 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2727140 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2727173 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
2727189 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2731281 original size:19 final size:19
Alignment explanation
Indices: 2731254--2731316 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2731244 TCACGTGTAC
* *
2731254 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
2731273 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
2731292 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
2731311 AGTACC
1 AGTACC
2731317 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:2731669 original size:34 final size:34
Alignment explanation
Indices: 2731623--2731718 Score: 122
Period size: 34 Copynumber: 2.8 Consensus size: 34
2731613 GTAAAAACCA
* *
2731623 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGAAACCTACCAAATCAC
*
2731657 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-AAACCTACCAAATCAC
* * *
2731691 CCATTTAATCAATAATGGTAAGCTACCA
1 CCATTTAATCAACAATGGAAACCTACCA
2731719 CATACGAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
33 3 0.06
34 46 0.87
35 4 0.08
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (34 bp):
CCATTTAATCAACAATGGAAACCTACCAAATCAC
Found at i:2734737 original size:20 final size:20
Alignment explanation
Indices: 2734701--2734739 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2734691 CGTATATTCA
*
2734701 TTTTATATCATATTTTAATT
1 TTTTATATCATAGTTTAATT
2734721 TTTTATAATCAT-GTTTAAT
1 TTTTAT-ATCATAGTTTAAT
2734740 ATTATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTATATCATAGTTTAATT
Found at i:2735456 original size:15 final size:15
Alignment explanation
Indices: 2735436--2735483 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
2735426 TTTAAAAATA
2735436 TAAAATAATTTAATT
1 TAAAATAATTTAATT
*
2735451 TAAAATAATTAAATT
1 TAAAATAATTTAATT
2735466 TAAAATTAA-TTAATT
1 TAAAA-TAATTTAATT
2735481 TAA
1 TAA
2735484 TTCATCTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 27 0.90
16 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAAATAATTTAATT
Found at i:2735872 original size:16 final size:16
Alignment explanation
Indices: 2735824--2735875 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
2735814 ATATTAATAA
* * *
2735824 TATTTATTATCAATAT
1 TATTTATCATTAACAT
2735840 TATTT-TCA-TAACA-
1 TATTTATCATTAACAT
2735853 TATTTATCATTAACAT
1 TATTTATCATTAACAT
2735869 TATTTAT
1 TATTTAT
2735876 GATTGTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 5 0.17
14 6 0.20
15 7 0.23
16 12 0.40
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (16 bp):
TATTTATCATTAACAT
Found at i:2740048 original size:31 final size:31
Alignment explanation
Indices: 2739986--2740045 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
2739976 TTATATATAT
* *
2739986 AAATTTTAATATGTTAATAATTTTTATTTAC
1 AAATTTTAATATATTAATAATTTGTATTTAC
**
2740017 AAATTTTAATATATTTGTACATTTGTATT
1 AAATTTTAATATATTAATA-ATTTGTATT
2740046 ACATTAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 16 0.67
32 8 0.33
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (31 bp):
AAATTTTAATATATTAATAATTTGTATTTAC
Found at i:2741676 original size:14 final size:14
Alignment explanation
Indices: 2741657--2741689 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2741647 AATTTAAATT
2741657 TTAAATTCTTTAA-A
1 TTAAATT-TTTAATA
2741671 TTAAATTTTTAATA
1 TTAAATTTTTAATA
2741685 TTAAA
1 TTAAA
2741690 AATTTAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAAATTTTTAATA
Found at i:2741739 original size:3 final size:3
Alignment explanation
Indices: 2741731--2741779 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
2741721 TGAGAAATTG
2741731 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2741779 A
1 A
2741780 ATATTATTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2743986 original size:13 final size:13
Alignment explanation
Indices: 2743968--2743992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2743958 CATATTGCTT
2743968 TGTATCGATACAG
1 TGTATCGATACAG
2743981 TGTATCGATACA
1 TGTATCGATACA
2743993 TGATTTTGGT
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2745714 original size:12 final size:12
Alignment explanation
Indices: 2745699--2745736 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
2745689 AACCATCAAA
*
2745699 GATGATGAAGAT
1 GATGATGTAGAT
*
2745711 GATGATGTTGAT
1 GATGATGTAGAT
2745723 GATGATGTAGAT
1 GATGATGTAGAT
2745735 GA
1 GA
2745737 AGTTGACTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (12 bp):
GATGATGTAGAT
Found at i:2749909 original size:21 final size:21
Alignment explanation
Indices: 2749883--2749924 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2749873 AGCTACTGCC
2749883 AAGGAAATGTATCAATACATT
1 AAGGAAATGTATCAATACATT
* *
2749904 AAGGAAGTGTATCGATACATT
1 AAGGAAATGTATCAATACATT
2749925 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCAATACATT
Found at i:2749929 original size:13 final size:13
Alignment explanation
Indices: 2749911--2749936 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2749901 ATTAAGGAAG
2749911 TGTATCGATACAT
1 TGTATCGATACAT
2749924 TGTATCGATACAT
1 TGTATCGATACAT
2749937 CGATCTTTGT
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:2752346 original size:52 final size:52
Alignment explanation
Indices: 2752289--2752415 Score: 193
Period size: 52 Copynumber: 2.4 Consensus size: 52
2752279 TCAATTGTTT
*
2752289 ATAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTCC
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCC
* * *
2752340 TTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC
1 -ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCC
*
2752393 ACAATCGGGGATACTCCAACCCC
1 ATAATCGGGGATACTCCAACCCC
2752416 ATTATTTCTG
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
52 52 0.78
53 15 0.22
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (52 bp):
ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCC
Found at i:2752491 original size:79 final size:79
Alignment explanation
Indices: 2752347--2752521 Score: 237
Period size: 79 Copynumber: 2.2 Consensus size: 79
2752337 TCCTTTAATC
* *
2752347 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAAC-CCGATTTCATTTCCAAAAACACCAATTTTTCACAACCGGGGATACTCCAA
*
2752412 CCCCATTA-TTTCTGA
65 CCCCATTATTTTC-AA
* * * *
2752427 GGGGATACTCCAATCCCGATTTCATTTCC-TAATCATCTATTTTTCACAACCGGGGATACTCCAA
1 GGGGATACTCCAA-CCCGATTTCATTTCCAAAAACACCAATTTTTCACAACCGGGGATACTCCAA
*
2752491 CCCCGTTATTTTCAA
65 CCCCATTATTTTCAA
2752506 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
2752522 CGTTATTATC
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
78 3 0.04
79 51 0.60
80 30 0.35
81 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (79 bp):
GGGGATACTCCAACCCGATTTCATTTCCAAAAACACCAATTTTTCACAACCGGGGATACTCCAAC
CCCATTATTTTCAA
Found at i:2754428 original size:31 final size:31
Alignment explanation
Indices: 2754393--2754459 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
2754383 GTATTCAATC
*
2754393 TCAAATTT-CATTAATTCTTTTTCAAATTTT-A
1 TCAAATTTACATCAATTC-TTTTC-AATTTTCA
*
2754424 TCAAATTTACATCATTTCTTTTCAATTTTCA
1 TCAAATTTACATCAATTCTTTTCAATTTTCA
2754455 TCAAA
1 TCAAA
2754460 ATCTTCATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 6 0.19
31 19 0.59
32 7 0.22
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (31 bp):
TCAAATTTACATCAATTCTTTTCAATTTTCA
Found at i:2756338 original size:21 final size:23
Alignment explanation
Indices: 2756290--2756344 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
2756280 GTTTTAGTGT
2756290 TTAA-AGGGAGCATTAAATTTTCA
1 TTAAGAGGGAGCA-TAAATTTTCA
2756313 TTAAGAGGGAGCA-AAATTTT-A
1 TTAAGAGGGAGCATAAATTTTCA
*
2756334 TTAAGGGGGAG
1 TTAAGAGGGAG
2756345 TTATATATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 11 0.37
22 7 0.23
23 4 0.13
24 8 0.27
ACGTcount: A:0.38, C:0.05, G:0.27, T:0.29
Consensus pattern (23 bp):
TTAAGAGGGAGCATAAATTTTCA
Found at i:2756959 original size:20 final size:22
Alignment explanation
Indices: 2756923--2756963 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
2756913 AAAGGTCAAA
2756923 ACCCTAGAAAGTATCGATACAG
1 ACCCTAGAAAGTATCGATACAG
2756945 ACCC-AGAAA-TATCGATACA
1 ACCCTAGAAAGTATCGATACA
2756964 TATTGCTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 5 0.26
22 4 0.21
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.17
Consensus pattern (22 bp):
ACCCTAGAAAGTATCGATACAG
Found at i:2756990 original size:13 final size:13
Alignment explanation
Indices: 2756972--2756996 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2756962 CATATTGCTT
2756972 TGTATCGATACAG
1 TGTATCGATACAG
2756985 TGTATCGATACA
1 TGTATCGATACA
2756997 CAATGAATTG
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2759243 original size:31 final size:28
Alignment explanation
Indices: 2759205--2759262 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
2759195 ATCGGTGTTC
2759205 CGAAAATAAAATTGGGGTTGGAGTATCCCTT
1 CGAAAATAAAA---GGGTTGGAGTATCCCTT
*
2759236 CGAAAATAACAGGGTTGGAGTATCCCT
1 CGAAAATAAAAGGGTTGGAGTATCCCT
2759263 AATTATAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 16 0.62
31 10 0.38
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (28 bp):
CGAAAATAAAAGGGTTGGAGTATCCCTT
Found at i:2759330 original size:79 final size:79
Alignment explanation
Indices: 2759185--2759340 Score: 206
Period size: 79 Copynumber: 2.0 Consensus size: 79
2759175 AGTATGCTCG
* * * *
2759185 ATTATGGAAAATCGGTGTTCCGAAAATAAAATTGGGGTTGGAGTATCCCTTCGAAAATAACAGGG
1 ATTATAGAAAATCGGTATTCCGAAAATAAAATCGGGATTGGAGTATCCCTTCGAAAATAACAGGG
**
2759250 TTGGAGTATCCCTA
66 TTAAAGTATCCCTA
** **
2759264 ATTATAGAAAATCGGTATTTTGAAAATAAAATCGGGATTGGAGTATTCCC-TCGAAAATAATGGG
1 ATTATAGAAAATCGGTATTCCGAAAATAAAATCGGGATTGGAGTA-TCCCTTCGAAAATAACAGG
2759328 GTTAAAGTATCCC
65 GTTAAAGTATCCC
2759341 CGATTGTGAG
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
79 62 0.94
80 4 0.06
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (79 bp):
ATTATAGAAAATCGGTATTCCGAAAATAAAATCGGGATTGGAGTATCCCTTCGAAAATAACAGGG
TTAAAGTATCCCTA
Found at i:2759371 original size:79 final size:79
Alignment explanation
Indices: 2759206--2759368 Score: 177
Period size: 79 Copynumber: 2.1 Consensus size: 79
2759196 TCGGTGTTCC
* * ** *
2759206 GAAAATAAAATTGGGGTTGGAGTATCCCTTCGAAAATAACAGGGTTGGAGTATCCCTAATTATAG
1 GAAAATAAAATCGGGATTGGAGTATCCCTTCGAAAATAACAGGGTTAAAGTATCCCCAATTATAG
* *
2759271 AAAATCGGTATTTT
66 AAAATCGATATTTA
** * *
2759285 GAAAATAAAATCGGGATTGGAGTATTCCC-TCGAAAATAATGGGGTTAAAGTATCCCCGATTGT-
1 GAAAATAAAATCGGGATTGGAGTA-TCCCTTCGAAAATAACAGGGTTAAAGTATCCCCAATTATA
*
2759348 GAGAAATTGATGATTTA
65 GA-AAATCGAT-ATTTA
2759365 GAAA
1 GAAA
2759369 TAAGGCCGGG
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
78 2 0.03
79 55 0.80
80 12 0.17
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (79 bp):
GAAAATAAAATCGGGATTGGAGTATCCCTTCGAAAATAACAGGGTTAAAGTATCCCCAATTATAG
AAAATCGATATTTA
Found at i:2759432 original size:50 final size:51
Alignment explanation
Indices: 2759325--2759442 Score: 150
Period size: 50 Copynumber: 2.3 Consensus size: 51
2759315 CGAAAATAAT
* * ** *
2759325 GGGGTTAAAGTATCCCCGATTGTGAGAAATTGATGATTTAGAAATAAGGCC
1 GGGGTTGAAGTATCCCTGATTGTGAGAAATCAATGATTTAGAAATAAAGCC
*
2759376 GGGGTTGAAGTATCCCTGATTGTGA-AAATCAAT-ATTTTGGAAATAAAGCC
1 GGGGTTGAAGTATCCCTGATTGTGAGAAATCAATGA-TTTAGAAATAAAGCC
*
2759426 GGGGTTGGAGTATCCCT
1 GGGGTTGAAGTATCCCT
2759443 TCGGAAATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
49 1 0.02
50 35 0.59
51 23 0.39
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.29
Consensus pattern (51 bp):
GGGGTTGAAGTATCCCTGATTGTGAGAAATCAATGATTTAGAAATAAAGCC
Found at i:2759501 original size:28 final size:28
Alignment explanation
Indices: 2759427--2759501 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 28
2759417 AATAAAGCCG
*
2759427 GGGTTGGAGTATCCCTTCG--GAAATAACG
1 GGGTTGGAGTATCCC--CGATGAAATAACA
*
2759455 GGGTTAGAGTATCCCCGATGAAATAACA
1 GGGTTGGAGTATCCCCGATGAAATAACA
2759483 GGGTTGGAGTATCCCCGAT
1 GGGTTGGAGTATCCCCGAT
2759502 TGTGAAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 2 0.05
28 40 0.95
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGATGAAATAACA
Found at i:2759544 original size:50 final size:51
Alignment explanation
Indices: 2759485--2759581 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
2759475 AAATAACAGG
*
2759485 GTTGGAGTATCCCCGATTGT-GAAAATTGATGTTTT-GAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAAAATTGATGTTTTAG-AAATAAAATCGGA
2759535 GTTGGAGTATCCCCGATTATGGAAAATTGATGTTTTAGAAATAAAAT
1 GTTGGAGTATCCCCGATTATGGAAAATTGATGTTTTAGAAATAAAAT
2759582 TAAGGTTAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
50 19 0.43
51 24 0.55
52 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGGAAAATTGATGTTTTAGAAATAAAATCGGA
Found at i:2759594 original size:51 final size:49
Alignment explanation
Indices: 2759484--2759599 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 49
2759474 GAAATAACAG
* **
2759484 GGTTGGAGTATCCCCGATTGTGAAAATTGATGTTTTGAAAATAAAATCG
1 GGTTGGAGTATCCCCGATTATGAAAATTGATGTTTTGAAAATAAAATAA
2759533 GAGTTGGAGTATCCCCGATTATGGAAAATTGATGTTTT-AGAAATAAAATTAA
1 G-GTTGGAGTATCCCCGATTAT-GAAAATTGATGTTTTGA-AAATAAAA-TAA
*
2759585 GGTTAGAGTATCCCC
1 GGTTGGAGTATCCCC
2759600 TCAAAAATAG
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
49 1 0.02
50 20 0.34
51 36 0.61
52 2 0.03
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (49 bp):
GGTTGGAGTATCCCCGATTATGAAAATTGATGTTTTGAAAATAAAATAA
Found at i:2759594 original size:157 final size:157
Alignment explanation
Indices: 2759333--2759630 Score: 339
Period size: 157 Copynumber: 1.9 Consensus size: 157
2759323 ATGGGGTTAA
** * * *
2759333 AGTATCCCCGATTGTGAGAAATTGATGATTTAGAAATAAGGCCGGGGTTGAAGTATCCCTGATTG
1 AGTATCCCCGATTGTGAGAAATTGATGATTTAGAAATAAAACCGGAGTTGAAGTATCCCCGATTA
* * ** * * **
2759398 TGAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCTTCGGAAATAACGGGGTTAGA
66 TGAAAATCAATATTTTAGAAATAAAACCAAGGTTAGAGTATCCCCTCAAAAATAACGGGGTTAGA
* *
2759463 GTATCCCCGATGAAATAACAGGGTTGG
131 ATACCCCCGATGAAATAACAGGGTTGG
* * *
2759490 AGTATCCCCGATTGTGA-AAATTGATG-TTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATT
1 AGTATCCCCGATTGTGAGAAATTGATGATTTAG-AAATAAAACCGGAGTTGAAGTATCCCCGATT
** * ** * *
2759553 ATGGAAAATTGATGTTTTAGAAATAAAATTAAGGTTAGAGTATCCCCTCAAAAATAGCGGGGTTG
65 AT-GAAAATCAATATTTTAGAAATAAAACCAAGGTTAGAGTATCCCCTCAAAAATAACGGGGTTA
2759618 GAATACCCCCGAT
129 GAATACCCCCGAT
2759631 TGTAAAAAAT
Statistics
Matches: 114, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
155 4 0.04
156 35 0.31
157 75 0.66
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (157 bp):
AGTATCCCCGATTGTGAGAAATTGATGATTTAGAAATAAAACCGGAGTTGAAGTATCCCCGATTA
TGAAAATCAATATTTTAGAAATAAAACCAAGGTTAGAGTATCCCCTCAAAAATAACGGGGTTAGA
ATACCCCCGATGAAATAACAGGGTTGG
Found at i:2762040 original size:20 final size:20
Alignment explanation
Indices: 2762017--2762084 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
2762007 CATTGTAAAA
2762017 TGTATCGATACAATGAGCAG
1 TGTATCGATACAATGAGCAG
2762037 TGTATCGATAC-AT------
1 TGTATCGATACAATGAGCAG
2762050 TGTATCGATACAATGAGCAG
1 TGTATCGATACAATGAGCAG
2762070 TGTATCGATACAATG
1 TGTATCGATACAATG
2762085 TATCGATACA
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.27
14 2 0.05
19 2 0.05
20 26 0.63
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (20 bp):
TGTATCGATACAATGAGCAG
Found at i:2762055 original size:13 final size:13
Alignment explanation
Indices: 2762037--2762061 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2762027 CAATGAGCAG
2762037 TGTATCGATACAT
1 TGTATCGATACAT
2762050 TGTATCGATACA
1 TGTATCGATACA
2762062 ATGAGCAGTG
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:2762088 original size:13 final size:13
Alignment explanation
Indices: 2762070--2762099 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2762060 CAATGAGCAG
2762070 TGTATCGATACAA
1 TGTATCGATACAA
2762083 TGTATCGATACAA
1 TGTATCGATACAA
2762096 TGTA
1 TGTA
2762100 AAATGTATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2762172 original size:33 final size:33
Alignment explanation
Indices: 2762015--2762177 Score: 158
Period size: 33 Copynumber: 5.1 Consensus size: 33
2762005 TACATTGTAA
* *
2762015 AATGTATCGATACAATGAGCAGTGTATCGATAC
1 AATGTATCGATACAATGAACAATGTATCGATAC
* * *
2762048 ATTGTATCGATACAATGAGCAGTGTATCGATAC
1 AATGTATCGATACAATGAACAATGTATCGATAC
2762081 AATGTATCGATACAATGTAA-AATGTATCGATAC
1 AATGTATCGATACAATG-AACAATGTATCGATAC
* ** * **
2762114 -ATCT-GGGTAAACCCTG---AATGTATCGATAC
1 AATGTATCG-ATACAATGAACAATGTATCGATAC
*
2762143 AATGTATCAATACAATGAACAATGTATCGATAC
1 AATGTATCGATACAATGAACAATGTATCGATAC
2762176 AA
1 AA
2762178 ATTGTGAAAA
Statistics
Matches: 106, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
29 13 0.12
30 8 0.08
31 1 0.01
32 8 0.08
33 75 0.71
34 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (33 bp):
AATGTATCGATACAATGAACAATGTATCGATAC
Found at i:2762177 original size:13 final size:13
Alignment explanation
Indices: 2762130--2762159 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2762120 GTAAACCCTG
*
2762130 AATGTATCGATAC
1 AATGTATCAATAC
2762143 AATGTATCAATAC
1 AATGTATCAATAC
2762156 AATG
1 AATG
2762160 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (13 bp):
AATGTATCAATAC
Found at i:2765709 original size:6 final size:6
Alignment explanation
Indices: 2765698--2765729 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
2765688 CTATAATTCT
2765698 CTATCA CTATCA CTATCA CTATCA CTATCA CT
1 CTATCA CTATCA CTATCA CTATCA CTATCA CT
2765730 TGAAGATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (6 bp):
CTATCA
Found at i:2768756 original size:2 final size:2
Alignment explanation
Indices: 2768749--2768778 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2768739 TAAAAACAAG
2768749 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2768779 TCAAACATCA
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):
GA
Found at i:2771356 original size:15 final size:15
Alignment explanation
Indices: 2771338--2771374 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2771328 TTATTCTTAG
2771338 ATTATTTAATTAAAA-
1 ATTATTT-ATTAAAAT
2771353 ATTATTTATTAAAAT
1 ATTATTTATTAAAAT
2771368 ATTATTT
1 ATTATTT
2771375 TTATATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTATTTATTAAAAT
Found at i:2772142 original size:32 final size:31
Alignment explanation
Indices: 2772100--2772179 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 31
2772090 AATTAAAATC
2772100 AATTTTAATTTATTAAATATATCAAAATCGAA
1 AATTTTAATTTATTAAATATATCAAAATC-AA
* * *
2772132 TATTTTAATTTATTAAATGTATTAAAATCAA
1 AATTTTAATTTATTAAATATATCAAAATCAA
*
2772163 AATTTTCAATTCATTAA
1 AATTTT-AATTTATTAA
2772180 TTTTATCTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 7 0.17
32 35 0.83
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (31 bp):
AATTTTAATTTATTAAATATATCAAAATCAA
Found at i:2776505 original size:13 final size:13
Alignment explanation
Indices: 2776487--2776511 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2776477 ATAATGCACA
2776487 GTATCGATACATT
1 GTATCGATACATT
2776500 GTATCGATACAT
1 GTATCGATACAT
2776512 GACCACTGTA
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):
GTATCGATACATT
Found at i:2776508 original size:33 final size:32
Alignment explanation
Indices: 2776466--2776528 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
2776456 CACCTTCAGA
*
2776466 TGTATCGATACATAATGCACAGTATCGATACAT
1 TGTATCGATACATAA-CCACAGTATCGATACAT
* *
2776499 TGTATCGATACATGACCACTGTATCGATAC
1 TGTATCGATACATAACCACAGTATCGATAC
2776529 TTGCAAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (32 bp):
TGTATCGATACATAACCACAGTATCGATACAT
Found at i:2776618 original size:13 final size:13
Alignment explanation
Indices: 2776600--2776625 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2776590 ACATACAAGA
2776600 TGTATCGATACAT
1 TGTATCGATACAT
2776613 TGTATCGATACAT
1 TGTATCGATACAT
2776626 GACCAAATGT
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:2776621 original size:32 final size:33
Alignment explanation
Indices: 2776580--2776647 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2776570 CTTTAACTGT
2776580 TTGTATCGATACAT-A-CAAGATGTATCGATACA
1 TTGTATCGATACATGACCAA-ATGTATCGATACA
*
2776612 TTGTATCGATACATGACCAAATGTATCGATGCA
1 TTGTATCGATACATGACCAAATGTATCGATACA
2776645 TTG
1 TTG
2776648 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 16 0.48
34 3 0.09
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAATGTATCGATACA
Found at i:2785306 original size:13 final size:13
Alignment explanation
Indices: 2785288--2785312 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2785278 ATAATGCACA
2785288 GTATCGATACATT
1 GTATCGATACATT
2785301 GTATCGATACAT
1 GTATCGATACAT
2785313 GACCACTGTA
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):
GTATCGATACATT
Found at i:2785309 original size:33 final size:32
Alignment explanation
Indices: 2785267--2785329 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
2785257 CACCTTTAGA
*
2785267 TGTATCGATACATAATGCACAGTATCGATACAT
1 TGTATCGATACATAA-CCACAGTATCGATACAT
* *
2785300 TGTATCGATACATGACCACTGTATCGATAC
1 TGTATCGATACATAACCACAGTATCGATAC
2785330 TTGCAAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (32 bp):
TGTATCGATACATAACCACAGTATCGATACAT
Found at i:2785422 original size:32 final size:33
Alignment explanation
Indices: 2785381--2785448 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 33
2785371 CCTTAACTGT
2785381 TTGTATCGATACAT-A-CAAGATGTATCA-ATACA
1 TTGTATCGATACATGACCAA-ATGTAT-AGATACA
2785413 TTGTATCGATACATGACCAAATGTATAGATACA
1 TTGTATCGATACATGACCAAATGTATAGATACA
2785446 TTG
1 TTG
2785449 GCTTGTAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
32 15 0.45
33 15 0.45
34 3 0.09
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAATGTATAGATACA
Found at i:2786198 original size:15 final size:15
Alignment explanation
Indices: 2786178--2786208 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2786168 AGCTTTCATA
2786178 AATTCAGAAAGTGGG
1 AATTCAGAAAGTGGG
2786193 AATTCAGAAAGTGGG
1 AATTCAGAAAGTGGG
2786208 A
1 A
2786209 CAGTGCGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.32, T:0.19
Consensus pattern (15 bp):
AATTCAGAAAGTGGG
Found at i:2788495 original size:19 final size:20
Alignment explanation
Indices: 2788468--2788521 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
2788458 ATATTATGCT
**
2788468 TTATATCGATACATGTTC-A
1 TTATATCGATACATGCACAA
*
2788487 TTGTATCGATACATGCACAA
1 TTATATCGATACATGCACAA
2788507 TTATATCGATACATG
1 TTATATCGATACATG
2788522 AAACTGGAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (20 bp):
TTATATCGATACATGCACAA
Found at i:2792595 original size:20 final size:20
Alignment explanation
Indices: 2792570--2792611 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2792560 TTTATGAATC
2792570 TAACCCCTCCGAAAGGAAAG
1 TAACCCCTCCGAAAGGAAAG
2792590 TAACCCCTCCGAAAGGAAAG
1 TAACCCCTCCGAAAGGAAAG
2792610 TA
1 TA
2792612 TCTTTTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.29, G:0.19, T:0.12
Consensus pattern (20 bp):
TAACCCCTCCGAAAGGAAAG
Found at i:2794975 original size:19 final size:20
Alignment explanation
Indices: 2794948--2794986 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2794938 CTTAAAATTT
2794948 CATCAA-TTTTACATCAAAA
1 CATCAATTTTTACATCAAAA
* *
2794967 CATCTATTTTTTCATCAAAA
1 CATCAATTTTTACATCAAAA
2794987 TCTTCGACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (20 bp):
CATCAATTTTTACATCAAAA
Found at i:2801501 original size:32 final size:32
Alignment explanation
Indices: 2801465--2801529 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
2801455 ACTTATTCCT
2801465 TAGTAATTTCATTTTAGATCTTATATTCTTAC
1 TAGTAATTTCATTTTAGATCTTATATTCTTAC
2801497 TAGTAATTTCATTTTAGATCTTATATTCTTAC
1 TAGTAATTTCATTTTAGATCTTATATTCTTAC
2801529 T
1 T
2801530 TAATTCATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.54
Consensus pattern (32 bp):
TAGTAATTTCATTTTAGATCTTATATTCTTAC
Found at i:2806117 original size:13 final size:14
Alignment explanation
Indices: 2806089--2806117 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2806079 AAAAATAAAT
2806089 AAATCAAAATTTAA
1 AAATCAAAATTTAA
2806103 AAATCAAAA-TTAA
1 AAATCAAAATTTAA
2806116 AA
1 AA
2806118 TTTTGTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATCAAAATTTAA
Found at i:2807278 original size:2 final size:2
Alignment explanation
Indices: 2807271--2807315 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2807261 TTCAGGTTCG
2807271 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
2807313 AT A
1 AT A
2807316 GGAAACTGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2809205 original size:2 final size:2
Alignment explanation
Indices: 2809198--2809223 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2809188 CAGAGTGGGA
2809198 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
2809224 GTGTGTGTGT
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:2809228 original size:2 final size:2
Alignment explanation
Indices: 2809223--2809260 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2809213 TATATATATA
2809223 TG TG TG TG TG TG 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 TG TG TG TG TG TG
2809261 CATTCTCTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2814573 original size:4 final size:4
Alignment explanation
Indices: 2814564--2814589 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2814554 AGGAAATGGG
2814564 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
2814590 AGAAAAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:2818113 original size:41 final size:42
Alignment explanation
Indices: 2818036--2818125 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 42
2818026 TAGGTGTTGT
*
2818036 TTGT-GGTTTTATTTTAGGTGCTATAGGTATTTTTAGG-GTA
1 TTGTAGGTTCTATTTTAGGTGCTATAGGTATTTTTAGGAGTA
* *
2818076 TTGTAGGTTCTATTTTAGGTGCTATATGT-TTTATTAGGAGTG
1 TTGTAGGTTCTATTTTAGGTGCTATAGGTATTT-TTAGGAGTA
2818118 TTGTAGGT
1 TTGTAGGT
2818126 ATTTTTGGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 7 0.16
41 27 0.61
42 10 0.23
ACGTcount: A:0.18, C:0.03, G:0.28, T:0.51
Consensus pattern (42 bp):
TTGTAGGTTCTATTTTAGGTGCTATAGGTATTTTTAGGAGTA
Found at i:2818187 original size:62 final size:62
Alignment explanation
Indices: 2818056--2818187 Score: 167
Period size: 62 Copynumber: 2.1 Consensus size: 62
2818046 ATTTTAGGTG
* * *
2818056 CTATAGGTATTTTTAGGGTATTGTAGGTTCTATTTTAGGTGCTATATGTTTTATTAGGAGTG
1 CTATAGGTATTTTTAGGGTATTGTAGGTTCTATCTTAGGTGCTATAGGTTTTATTAGGAGTA
* * * * * *
2818118 TTGTAGGTATTTTTGGGGTATTGTAGGTTCTATCTTAGGTGCTCTAGGTTTTGTTTGG-GATA
1 CTATAGGTATTTTTAGGGTATTGTAGGTTCTATCTTAGGTGCTATAGGTTTTATTAGGAG-TA
2818180 CTATAGGT
1 CTATAGGT
2818188 GTTGGTTTAG
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
61 1 0.02
62 57 0.98
ACGTcount: A:0.18, C:0.06, G:0.28, T:0.48
Consensus pattern (62 bp):
CTATAGGTATTTTTAGGGTATTGTAGGTTCTATCTTAGGTGCTATAGGTTTTATTAGGAGTA
Found at i:2818309 original size:32 final size:32
Alignment explanation
Indices: 2818268--2818332 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
2818258 TCTTGTGTGA
2818268 ACTCTTCTTGTAAAGATAAAGTTGAGTAGAAT
1 ACTCTTCTTGTAAAGATAAAGTTGAGTAGAAT
*
2818300 ACTCTTCTTGTAAAGATAAATTTGAGTAGAAT
1 ACTCTTCTTGTAAAGATAAAGTTGAGTAGAAT
2818332 A
1 A
2818333 TGGCTTTCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.35
Consensus pattern (32 bp):
ACTCTTCTTGTAAAGATAAAGTTGAGTAGAAT
Done.