Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold361
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: 439703
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 26097 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:126 original size:24 final size:24
Alignment explanation
Indices: 98--174 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
88 ATAAGATAAC
* * *
98 TTAAAATAATAATACCTAATAGCT
1 TTAAAACAATAATACATAATAGAT
* * *
122 TTAAAACAACAATACATAATAAAA
1 TTAAAACAATAATACATAATAGAT
*
146 TTAAAACAATTATACATAATAGAT
1 TTAAAACAATAATACATAATAGAT
170 TTAAA
1 TTAAA
175 TGAATGTACA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (24 bp):
TTAAAACAATAATACATAATAGAT
Found at i:1171 original size:22 final size:25
Alignment explanation
Indices: 1140--1194 Score: 80
Period size: 23 Copynumber: 2.3 Consensus size: 25
1130 AAAAAGTGTA
1140 TTTTCGTTTTT-CTCTTATTT-TCT
1 TTTTCGTTTTTGCTCTTATTTCTCT
*
1163 TTTTC-TTTTTGCTGTTATTTCTCT
1 TTTTCGTTTTTGCTCTTATTTCTCT
1187 TTTTCGTT
1 TTTTCGTT
1195 CCTTTTTGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 5 0.18
23 13 0.46
24 8 0.29
25 2 0.07
ACGTcount: A:0.04, C:0.16, G:0.07, T:0.73
Consensus pattern (25 bp):
TTTTCGTTTTTGCTCTTATTTCTCT
Found at i:2501 original size:164 final size:164
Alignment explanation
Indices: 2323--3198 Score: 1752
Period size: 164 Copynumber: 5.3 Consensus size: 164
2313 ATATATATAT
2323 ATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGA
1 ATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGA
2388 CAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGA
66 CAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGA
2453 CAAAATTAATATTTTTCCCTAGTTAATTTGAAAC
131 CAAAATTAATATTTTTCCCTAGTTAATTTGAAAC
2487 ATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGA
1 ATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGA
2552 CAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGA
66 CAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGA
2617 CAAAATTAATATTTTTCCCTAGTTAATTTGAAAC
131 CAAAATTAATATTTTTCCCTAGTTAATTTGAAAC
2651 ATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGA
1 ATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGA
2716 CAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGA
66 CAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGA
2781 CAAAATTAATATTTTTCCCTAGTTAATTTGAAAC
131 CAAAATTAATATTTTTCCCTAGTTAATTTGAAAC
2815 ATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGA
1 ATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGA
2880 CAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGA
66 CAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGA
2945 CAAAATTAATATTTTTCCCTAGTTAATTTGAAAC
131 CAAAATTAATATTTTTCCCTAGTTAATTTGAAAC
2979 ATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGA
1 ATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGA
3044 CAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGA
66 CAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGA
3109 CAAAATTAATATTTTTCCCTAGTTAATTTGAAAC
131 CAAAATTAATATTTTTCCCTAGTTAATTTGAAAC
3143 ATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTT
1 ATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTT
3199 CCTCAAAAGT
Statistics
Matches: 712, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 712 1.00
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (164 bp):
ATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGA
CAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGA
CAAAATTAATATTTTTCCCTAGTTAATTTGAAAC
Found at i:2836 original size:328 final size:328
Alignment explanation
Indices: 2222--3198 Score: 1774
Period size: 328 Copynumber: 2.9 Consensus size: 328
2212 AATTAATATT
* ** * * ** *
2222 AGATATCGTTTAATCAAATATATCTCATAAAACTAACAAATATTTTTCCAATGATGAAAAAATTA
1 AGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGACAAAATTA
* *
2287 ATATTTTTCCCTAGTTTGAAATATATATATATATATATATATATGCAATACTTTTCCCCTCATTT
66 ATATTTTTCCCTAG-TT---A-AT-T-T-GA-A-ACATATATATGCAATACTTTTCCCCTCATTT
2352 GAAATTTTGCATGCTTCTACCAATCTTTTAACAAGACAATGTCAAGATATGGTTTAATCAAATAT
121 GAAATTTTGCATGCTTCTACCAATCTTTTAACAAGACAATGTCAAGATATGGTTTAATCAAATAT
2417 ATCTTGTAAAATTAACAAATATTTTTCTAACAATGACAAAATTAATATTTTTCCCTAGTTAATTT
186 ATCTTGTAAAATTAACAAATATTTTTCTAACAATGACAAAATTAATATTTTTCCCTAGTTAATTT
2482 GAAACATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAA
251 GAAACATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAA
2547 CAAGACAATGTCA
316 CAAGACAATGTCA
2560 AGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGACAAAATTA
1 AGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGACAAAATTA
2625 ATATTTTTCCCTAGTTAATTTGAAACATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGC
66 ATATTTTTCCCTAGTTAATTTGAAACATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGC
2690 ATGCTTCTACCAATCTTTTAACAAGACAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAA
131 ATGCTTCTACCAATCTTTTAACAAGACAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAA
2755 ATTAACAAATATTTTTCTAACAATGACAAAATTAATATTTTTCCCTAGTTAATTTGAAACATATA
196 ATTAACAAATATTTTTCTAACAATGACAAAATTAATATTTTTCCCTAGTTAATTTGAAACATATA
2820 TATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGACAATG
261 TATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGACAATG
2885 TCA
326 TCA
2888 AGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGACAAAATTA
1 AGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGACAAAATTA
2953 ATATTTTTCCCTAGTTAATTTGAAACATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGC
66 ATATTTTTCCCTAGTTAATTTGAAACATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGC
3018 ATGCTTCTACCAATCTTTTAACAAGACAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAA
131 ATGCTTCTACCAATCTTTTAACAAGACAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAA
3083 ATTAACAAATATTTTTCTAACAATGACAAAATTAATATTTTTCCCTAGTTAATTTGAAACATATA
196 ATTAACAAATATTTTTCTAACAATGACAAAATTAATATTTTTCCCTAGTTAATTTGAAACATATA
3148 TATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTT
261 TATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTT
3199 CCTCAAAAGT
Statistics
Matches: 629, Mismatches: 10, Indels: 10
0.97 0.02 0.02
Matches are distributed among these distances:
328 549 0.87
329 1 0.00
330 1 0.00
331 1 0.00
332 1 0.00
333 2 0.00
334 1 0.00
337 2 0.00
338 71 0.11
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (328 bp):
AGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGACAAAATTA
ATATTTTTCCCTAGTTAATTTGAAACATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGC
ATGCTTCTACCAATCTTTTAACAAGACAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAA
ATTAACAAATATTTTTCTAACAATGACAAAATTAATATTTTTCCCTAGTTAATTTGAAACATATA
TATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGACAATG
TCA
Found at i:3163 original size:492 final size:500
Alignment explanation
Indices: 2222--3198 Score: 1790
Period size: 492 Copynumber: 2.0 Consensus size: 500
2212 AATTAATATT
**
2222 AGATATCGTTTAATCAAATATATCTCATAAAACTAACAAATATTTTTCCAATGATGAAAAAATTA
1 AGATATCGTTTAATCAAATATATCTCATAAAACTAACAAATATTTTTCCAACAATGAAAAAATTA
* *
2287 ATATTTTTCCCTAGTTTGAAATATATATATATATATATATATATGCAATACTTTTCCCCTCATTT
66 ATATTTTTCCCTAGTTT--AATATATATAGATATACATATATATGCAATACTTTTCCCCTCATTT
2352 GAAATTTTGCATGCTTCTACCAATCTTTTAACAAGACAATGTCAAGATATGGTTTAATCAAATAT
129 GAAATTTTGCATGCTTCTACCAATCTTTTAACAAGACAATGTCAAGATATGGTTTAATCAAATAT
2417 ATCTTGTAAAATTAACAAATATTTTTCTAACAATGACAAAATTAATATTTTTCCCTAGTTAATTT
194 ATCTTGTAAAATTAACAAATATTTTTCTAACAATGACAAAATTAATATTTTTCCCTAGTTAATTT
2482 GAAACATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAA
259 GAAACATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAA
2547 CAAGACAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAAC
324 CAAGACAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAAC
2612 AATGACAAAATTAATATTTTTCCCTAGTTAATTTGAAACATATATATGCAATACTTTTCCCCTCA
389 AATGACAAAATTAATATTTTTCCCTAGTTAATTTGAAACATATATATGCAATACTTTTCCCCTCA
2677 TTTGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGACAATGTCA
454 TTTGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGACAATGTCA
* ** * * *
2724 AGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAATGACAAAATTA
1 AGATATCGTTTAATCAAATATATCTCATAAAACTAACAAATATTTTTCCAACAATGAAAAAATTA
2789 ATATTTTTCCCTAG-TT-A-AT-T-T-GA-A-ACATATATATGCAATACTTTTCCCCTCATTTGA
66 ATATTTTTCCCTAGTTTAATATATATAGATATACATATATATGCAATACTTTTCCCCTCATTTGA
2846 AATTTTGCATGCTTCTACCAATCTTTTAACAAGACAATGTCAAGATATGGTTTAATCAAATATAT
131 AATTTTGCATGCTTCTACCAATCTTTTAACAAGACAATGTCAAGATATGGTTTAATCAAATATAT
2911 CTTGTAAAATTAACAAATATTTTTCTAACAATGACAAAATTAATATTTTTCCCTAGTTAATTTGA
196 CTTGTAAAATTAACAAATATTTTTCTAACAATGACAAAATTAATATTTTTCCCTAGTTAATTTGA
2976 AACATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACA
261 AACATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACA
3041 AGACAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAA
326 AGACAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAA
3106 TGACAAAATTAATATTTTTCCCTAGTTAATTTGAAACATATATATGCAATACTTTTCCCCTCATT
391 TGACAAAATTAATATTTTTCCCTAGTTAATTTGAAACATATATATGCAATACTTTTCCCCTCATT
3171 TGAAATTTTGCATGCTTCTACCAATCTT
456 TGAAATTTTGCATGCTTCTACCAATCTT
3199 CCTCAAAAGT
Statistics
Matches: 465, Mismatches: 10, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
492 385 0.83
493 1 0.00
494 1 0.00
495 1 0.00
496 1 0.00
497 2 0.00
498 1 0.00
501 2 0.00
502 71 0.15
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (500 bp):
AGATATCGTTTAATCAAATATATCTCATAAAACTAACAAATATTTTTCCAACAATGAAAAAATTA
ATATTTTTCCCTAGTTTAATATATATAGATATACATATATATGCAATACTTTTCCCCTCATTTGA
AATTTTGCATGCTTCTACCAATCTTTTAACAAGACAATGTCAAGATATGGTTTAATCAAATATAT
CTTGTAAAATTAACAAATATTTTTCTAACAATGACAAAATTAATATTTTTCCCTAGTTAATTTGA
AACATATATATGCAATACTTTTCCCCTCATTTGAAATTTTGCATGCTTCTACCAATCTTTTAACA
AGACAATGTCAAGATATGGTTTAATCAAATATATCTTGTAAAATTAACAAATATTTTTCTAACAA
TGACAAAATTAATATTTTTCCCTAGTTAATTTGAAACATATATATGCAATACTTTTCCCCTCATT
TGAAATTTTGCATGCTTCTACCAATCTTTTAACAAGACAATGTCA
Found at i:3749 original size:25 final size:25
Alignment explanation
Indices: 3720--3770 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
3710 AAAAAACTAT
*
3720 ATTAATTAACAGTTCATTATCTAAA
1 ATTAATTAACAGTTCATTATATAAA
3745 ATTAATTAACAGTTCATTATATAAA
1 ATTAATTAACAGTTCATTATATAAA
3770 A
1 A
3771 GAGTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (25 bp):
ATTAATTAACAGTTCATTATATAAA
Found at i:3995 original size:18 final size:17
Alignment explanation
Indices: 3963--3996 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3953 GATTTCATGA
*
3963 ATTTTTTTATTTTTTGT
1 ATTTTTTTATGTTTTGT
3980 ATTTTTTTGATGTTTTG
1 ATTTTTTT-ATGTTTTG
3997 AAAAAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (17 bp):
ATTTTTTTATGTTTTGT
Found at i:5898 original size:42 final size:42
Alignment explanation
Indices: 5839--5933 Score: 172
Period size: 42 Copynumber: 2.3 Consensus size: 42
5829 AATTAAAGTT
*
5839 AGCTGCTGTTTGAAGTCTTTTAGGTGACCATTCAGTCAAGGG
1 AGCTGCTGTTTGAAGTCTTTTAGGTGACCATTCAGCCAAGGG
*
5881 AGCTGTTGTTTGAAGTCTTTTAGGTGACCATTCAGCCAAGGG
1 AGCTGCTGTTTGAAGTCTTTTAGGTGACCATTCAGCCAAGGG
5923 AGCTGCTGTTT
1 AGCTGCTGTTT
5934 CATGCTTCCA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (42 bp):
AGCTGCTGTTTGAAGTCTTTTAGGTGACCATTCAGCCAAGGG
Found at i:9550 original size:27 final size:27
Alignment explanation
Indices: 9520--9594 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
9510 CGCCAATGGG
*
9520 ATTGGCGGCACCAAAGGTGCCAA-AGCA
1 ATTGGCGGCACCAATGGTGCCAATA-CA
** *
9547 ATTGGTTGCACCAATGGTGCCAATACC
1 ATTGGCGGCACCAATGGTGCCAATACA
9574 ATTGGCGGCACCAATGGTGCC
1 ATTGGCGGCACCAATGGTGCC
9595 GTATTGATTG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 40 0.98
28 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATACA
Found at i:9730 original size:11 final size:10
Alignment explanation
Indices: 9693--9731 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
9683 AGTTGCTGCG
*
9693 GAAAAAAAGA
1 GAAAAAGAGA
9703 GAAAAAGAGA
1 GAAAAAGAGA
9713 GAAAAAGAGGA
1 GAAAAAGA-GA
9724 GAAAAAGA
1 GAAAAAGA
9732 AGGTATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
GAAAAAGAGA
Found at i:9795 original size:19 final size:21
Alignment explanation
Indices: 9757--9795 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
9747 AACAATTGAT
*
9757 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
9778 TATATT-TT-TTAATATTTT
1 TATATTGTTGTTAATATTTT
9796 TTGTTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:9824 original size:33 final size:33
Alignment explanation
Indices: 9786--9890 Score: 99
Period size: 33 Copynumber: 3.2 Consensus size: 33
9776 TGTATATTTT
9786 TTAATATTTTTTGTTTTACTTTATTTATTAAGA
1 TTAATATTTTTTGTTTTACTTTATTTATTAAGA
**** ***
9819 TTAATAAAACTTGTTGTTA-TTT-TTGTA-TATTTT
1 TTAATATTTTTTGTT-TTACTTTATT-TATTA-AGA
9852 TTAATATTTTTTGTTTTACTTTATTTATTAAGA
1 TTAATATTTTTTGTTTTACTTTATTTATTAAGA
9885 TTAATA
1 TTAATA
9891 AAACTCAAAA
Statistics
Matches: 52, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
32 7 0.13
33 38 0.73
34 7 0.13
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.62
Consensus pattern (33 bp):
TTAATATTTTTTGTTTTACTTTATTTATTAAGA
Found at i:9869 original size:66 final size:68
Alignment explanation
Indices: 9761--9895 Score: 256
Period size: 66 Copynumber: 2.0 Consensus size: 68
9751 ATTGATTATA
9761 TTGTTGTTATTATTTTGTATATTTTTTAATATTTTTTGTTTTACTTTATTTATTAAGATTAATAA
1 TTGTTGTTATTATTTTGTATATTTTTTAATATTTTTTGTTTTACTTTATTTATTAAGATTAATAA
9826 AAC
66 AAC
9829 TTGTTGTTA-T-TTTTGTATATTTTTTAATATTTTTTGTTTTACTTTATTTATTAAGATTAATAA
1 TTGTTGTTATTATTTTGTATATTTTTTAATATTTTTTGTTTTACTTTATTTATTAAGATTAATAA
9892 AAC
66 AAC
9895 T
1 T
9896 CAAAATAATA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
66 57 0.85
67 1 0.01
68 9 0.13
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.62
Consensus pattern (68 bp):
TTGTTGTTATTATTTTGTATATTTTTTAATATTTTTTGTTTTACTTTATTTATTAAGATTAATAA
AAC
Found at i:17517 original size:41 final size:42
Alignment explanation
Indices: 17430--17516 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
17420 CCATTTTTTC
17430 TTTTCGTATTTTATGTTTTCTTAAATAAATTTTTTTGTCATT
1 TTTTCGTATTTTATGTTTTCTTAAATAAATTTTTTTGTCATT
*
17472 TTTTCGTATTTTATGTTTTCTTAAATAATTTTTTTTGTCATT
1 TTTTCGTATTTTATGTTTTCTTAAATAAATTTTTTTGTCATT
17514 TTT
1 TTT
17517 CTTTTAATGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (42 bp):
TTTTCGTATTTTATGTTTTCTTAAATAAATTTTTTTGTCATT
Found at i:17784 original size:28 final size:31
Alignment explanation
Indices: 17739--17923 Score: 78
Period size: 28 Copynumber: 6.2 Consensus size: 31
17729 AAAATACCCT
17739 TTTTTTTTTCCTTCCTTC-CCTCTTCTTCTTC
1 TTTTTTTTTCCTTCCTTCTCCT-TTCTTCTTC
*
17770 TTTTTTTTT-C-T-CTTCTCCTTTCTTTTTC
1 TTTTTTTTTCCTTCCTTCTCCTTTCTTCTTC
* * *
17798 TTTCCTTCTTT-CTTTCTT-T--TTTCTTCTCC
1 TTT--TTTTTTCCTTCCTTCTCCTTTCTTCTTC
** *
17827 TTTCCTTTT-CTT-CTTCTTTCTTTC-T-TTC
1 TTTTTTTTTCCTTCCTTC-TCCTTTCTTCTTC
* *
17855 TTTTTTTCTCTTCTCCTT-TCCTTTTCTTTCCTTC
1 TTTTTTTTTCCT-TCCTTCTCC-TTTC-TT-CTTC
* * *
17889 TTTTTCTTT-CTTTCATCTCCTTTC-T-TTC
1 TTTTTTTTTCCTTCCTTCTCCTTTCTTCTTC
17917 TTTTTTT
1 TTTTTTT
17924 CTTTCTTTCT
Statistics
Matches: 117, Mismatches: 19, Indels: 39
0.67 0.11 0.22
Matches are distributed among these distances:
26 3 0.03
27 6 0.05
28 33 0.28
29 19 0.16
30 17 0.15
31 14 0.12
32 11 0.09
33 4 0.03
34 10 0.09
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (31 bp):
TTTTTTTTTCCTTCCTTCTCCTTTCTTCTTC
Found at i:17785 original size:18 final size:18
Alignment explanation
Indices: 17762--17899 Score: 73
Period size: 18 Copynumber: 7.1 Consensus size: 18
17752 CCTTCCCTCT
17762 TCTTCTTCTTTTTTTTTC
1 TCTTCTTCTTTTTTTTTC
* *
17780 TCTTCTCCTTTCTTTTTC
1 TCTTCTTCTTTTTTTTTC
*
17798 T-TTCCTTCTTTCTTTCTTTTT
1 TCTT-CTTC-TT-TTT-TTTTC
*
17819 TCTTCTCCTTTCCTTTTCTTC
1 TCTTCTTCTTT--TTTT-TTC
17840 TTCTTTCTTTCTTTCTTTTTTTC
1 -TC-TTC-TTC-TT-TTTTTTTC
* **
17863 TCTTCTCCTTTCCTTTTC
1 TCTTCTTCTTTTTTTTTC
*
17881 T-TTCCTTCTTTTTCTTTC
1 TCTT-CTTCTTTTTTTTTC
17899 T
1 T
17900 TTCATCTCCT
Statistics
Matches: 91, Mismatches: 15, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
17 4 0.04
18 38 0.42
19 5 0.05
20 8 0.09
21 15 0.16
22 6 0.07
23 6 0.07
24 6 0.07
25 2 0.02
26 1 0.01
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
TCTTCTTCTTTTTTTTTC
Found at i:17789 original size:34 final size:34
Alignment explanation
Indices: 17737--17855 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 34
17727 AAAAAATACC
* * *
17737 CTTTTTTTTT-TCCT-TCCTTCCCTCTTCTTCTT
1 CTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTCTT
*
17769 CTTTTTTTTTCTCTTCTCCTTTCTTTTTCTTTCCTT
1 CTTTTTTTTTCTCTTCTCCTTTCCTTTTC-TT-CTT
*
17805 CTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTCTT
1 C-TT-TTT-TTTTCTCTTCTCCTTTCCTTTTCTTCTT
17842 CTTTCTTTCTTTCT
1 CTTT-TTT-TTTCT
17856 TTTTTTCTCT
Statistics
Matches: 71, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
32 10 0.14
33 3 0.04
34 10 0.14
35 4 0.06
36 12 0.17
37 6 0.08
38 5 0.07
39 21 0.30
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (34 bp):
CTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTCTT
Found at i:17794 original size:4 final size:4
Alignment explanation
Indices: 17767--17940 Score: 118
Period size: 4 Copynumber: 43.8 Consensus size: 4
17757 CCTCTTCTTC
* *
17767 TTCT TT-T TT-T TTCT CTTC- TCCT TTC- TT-T TTCT TTCC TTCT TTCT
1 TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
17811 TTCT TT-T TTCT TCTCCT TTCCT TT-T CTTC- TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT T-T-CT TT-CT TTCT -TTCT TTCT TTCT TTCT TTCT
* * *
17856 TTTT TTCT CTTC- TCCT TTCCTT TTCT TTCC TTC- TT-T TTCT TTCT TTCAT
1 TTCT TTCT -TTCT TTCT TT-C-T TTCT TTCT TTCT TTCT TTCT TTCT TTC-T
* *
17905 CTCCT TTCT TTCT TTTT TTCT TTCT TTCT TTCT TTC
1 -TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
17941 CCTCTCCTTC
Statistics
Matches: 138, Mismatches: 13, Indels: 38
0.73 0.07 0.20
Matches are distributed among these distances:
3 25 0.18
4 88 0.64
5 17 0.12
6 8 0.06
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (4 bp):
TTCT
Found at i:17825 original size:44 final size:44
Alignment explanation
Indices: 17760--17939 Score: 181
Period size: 42 Copynumber: 4.3 Consensus size: 44
17750 TTCCTTCCCT
*
17760 CTTC-TTC-TTCTTTTTTTTTCT-CTTCTCCTTTCTTTTTCTTTC
1 CTTCTTTCTTTCTTTTTTCTTCTCCTT-TCCTTTCTTTTTCTTTC
*
17802 CTTCTTTCTTTCTTTTTTCTTCTCCTTTCC-TT-TTCTTC-TTC
1 CTTCTTTCTTTCTTTTTTCTTCTCCTTTCCTTTCTTTTTCTTTC
* *
17843 TTTCTTTCTTTC-TTTTT-TTCT-CTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTCTTTCTTTTTTCTTCTCCTT-TCCTTTCTTTTTCTTTC
*
17885 CTTC-TT-TTTCTTTCTTTCATCTCCTTT-CTTTC-TTTT-TTTC
1 CTTCTTTCTTTCTTT-TTTCTTCTCCTTTCCTTTCTTTTTCTTTC
*
17925 TTTCTTTCTTTCTTT
1 CTTCTTTCTTTCTTT
17940 CCCTCTCCTT
Statistics
Matches: 117, Mismatches: 8, Indels: 26
0.77 0.05 0.17
Matches are distributed among these distances:
38 3 0.03
39 7 0.06
40 18 0.15
41 28 0.24
42 30 0.26
43 9 0.08
44 19 0.16
45 3 0.03
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (44 bp):
CTTCTTTCTTTCTTTTTTCTTCTCCTTTCCTTTCTTTTTCTTTC
Found at i:17849 original size:49 final size:47
Alignment explanation
Indices: 17789--17935 Score: 152
Period size: 44 Copynumber: 3.3 Consensus size: 47
17779 CTCTTCTCCT
*
17789 TTCTT-TTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTC
1 TTCTTCTTTCTTT--TTCTTTCTTTCTTTTCTCTTCTCCTTTCCTTTTC
17837 TTCTTCTTTC--TTTCTTTCTTT-TTTTCTCTTCTCCTTTCCTTTTC
1 TTCTTCTTTCTTTTTCTTTCTTTCTTTTCTCTTCTCCTTTCCTTTTC
* * * *
17881 -T-TTCCTTCTTTTTCTTTCTTTCATCTC-CTT-T-CTTT-CTTTTT
1 TTCTTCTTTCTTTTTCTTTCTTTCTTTTCTCTTCTCCTTTCCTTTTC
17922 TTCTTTCTTTCTTT
1 TTC-TTCTTTCTTT
17936 CTTTCCCTCT
Statistics
Matches: 86, Mismatches: 6, Indels: 18
0.78 0.05 0.16
Matches are distributed among these distances:
41 5 0.06
42 11 0.13
43 2 0.02
44 45 0.52
45 13 0.15
47 1 0.01
48 5 0.06
49 4 0.05
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (47 bp):
TTCTTCTTTCTTTTTCTTTCTTTCTTTTCTCTTCTCCTTTCCTTTTC
Found at i:18112 original size:23 final size:23
Alignment explanation
Indices: 18086--18130 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
18076 GTTTTTTTTG
*
18086 ATATATTTTGGTAAATAAAAAAT
1 ATATATTTTAGTAAATAAAAAAT
18109 ATATATTTTAGTAAATAAAAAA
1 ATATATTTTAGTAAATAAAAAA
18131 AAGTTATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (23 bp):
ATATATTTTAGTAAATAAAAAAT
Found at i:24299 original size:15 final size:16
Alignment explanation
Indices: 24279--24310 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
24269 ATGTAAACAG
24279 ATTTGAAAAT-AATGA
1 ATTTGAAAATGAATGA
24294 ATTTGAAAATGAATGA
1 ATTTGAAAATGAATGA
24310 A
1 A
24311 AAGGGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (16 bp):
ATTTGAAAATGAATGA
Found at i:27938 original size:14 final size:15
Alignment explanation
Indices: 27909--27940 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
27899 AAAAACATCA
27909 TAATTTTATCTATTT
1 TAATTTTATCTATTT
27924 TAATTTTAT-TATTT
1 TAATTTTATCTATTT
27938 TAA
1 TAA
27941 CTATAACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTATCTATTT
Found at i:29166 original size:88 final size:88
Alignment explanation
Indices: 29055--29405 Score: 542
Period size: 88 Copynumber: 4.0 Consensus size: 88
29045 GATAAGACTG
* * * * * * *
29055 GTGTCTTCGATCTACTTCGCTGTCGGTGCATGAAGGCAAAATCTGCTATCTTCAAACTGCTCCGC
1 GTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCGC
29120 TGCAACCCAGGGAGGCAAGGCTA
66 TGCAACCCAGGGAGGCAAGGCTA
* *
29143 GTGTCTTCGATCTGCTTCACTGTCAGTATAGGAAGGCAAGATCTGCTATCTTCAGCCTGCTCCGC
1 GTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCGC
29208 TGCAACCCAGGGAGGCAAGGCTA
66 TGCAACCCAGGGAGGCAAGGCTA
* *
29231 GTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAGCCTGCTCCGC
1 GTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCGC
*
29296 TGCAACCCAGGGAGGCAACGCTA
66 TGCAACCCAGGGAGGCAAGGCTA
* * *
29319 GTGTCTTCGATCTGCTTCACTGTCAGTACAGGAATGG-AAGATCTGCTATTTTCAGCTTGCTCCG
1 GTGTCTTCGATCTGCTTCACTGTCAGTACAGGAA-GGCAAGATCTGCTATCTTCAACCTGCTCCG
*
29383 CTGCAACTCAGGGAGGCAAGGCT
65 CTGCAACCCAGGGAGGCAAGGCT
29406 TTGTGATTTT
Statistics
Matches: 247, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
88 245 0.99
89 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.26
Consensus pattern (88 bp):
GTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCGC
TGCAACCCAGGGAGGCAAGGCTA
Found at i:29180 original size:44 final size:44
Alignment explanation
Indices: 29127--29352 Score: 158
Period size: 44 Copynumber: 5.1 Consensus size: 44
29117 CGCTGCAACC
*
29127 CAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTA
1 CAGGAAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTA
* * * * * * ***
29171 TAGGAAGGCAAGATCT-GCTATCTTC-AGCCTGCTCCGCTG-CAACC
1 CAGGAAGGCAAG-GCTAG-TGTCTTCGA-TCTGCTTCACTGTCAGTA
*
29215 CAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTA
1 CAGGAAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTA
* * * * * * ***
29259 CAGGAAGGCAAGATCT-GCTATTTTC-AGCCTGCTCCGCTG-CAACC
1 CAGGAAGGCAAG-GCTAG-TGTCTTCGA-TCTGCTTCACTGTCAGTA
* *
29303 CAGGGAGGCAACGCTAGTGTCTTCGATCTGCTTCACTGTCAGTA
1 CAGGAAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTA
29347 CAGGAA
1 CAGGAA
29353 TGGAAGATCT
Statistics
Matches: 128, Mismatches: 42, Indels: 24
0.66 0.22 0.12
Matches are distributed among these distances:
43 33 0.26
44 62 0.48
45 33 0.26
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.25
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTA
Found at i:30229 original size:28 final size:28
Alignment explanation
Indices: 30172--30235 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 28
30162 GATTTCGCGG
*
30172 AAAATGGCCCATTCCGGTAAATAATCAA
1 AAAATGGCCCATTCCGGTAAATAATAAA
* *
30200 AAAATCGGCCCATTTCGGTAAAT-TTAAA
1 AAAAT-GGCCCATTCCGGTAAATAATAAA
30228 AAAATGGC
1 AAAATGGC
30236 TTTTTTTGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 3 0.09
28 13 0.41
29 16 0.50
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (28 bp):
AAAATGGCCCATTCCGGTAAATAATAAA
Found at i:33623 original size:15 final size:16
Alignment explanation
Indices: 33591--33631 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
33581 ATCTTTATAC
*
33591 TTTA-ATTTTGTTATT
1 TTTAGATTTTGTTAAT
33606 TTTAGATTTT-TTAAT
1 TTTAGATTTTGTTAAT
33621 TTTAGAATTTT
1 TTTAG-ATTTT
33632 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (16 bp):
TTTAGATTTTGTTAAT
Found at i:37455 original size:103 final size:101
Alignment explanation
Indices: 37337--37667 Score: 461
Period size: 102 Copynumber: 3.2 Consensus size: 101
37327 CCAGTGATTC
*
37337 GGGGAATCAACACTTAGCAACCCCTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAACACTTAGCAACCCCTTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACC
37402 ACCAATGATTCGGAGAATCAGCACTTAGCAACCCCTT
66 ACCAATGATTCGG-GAATCAGCACTTAGCAACCCCTT
* * * *
37439 AGGGGAATCAGCACTTAGCAACCCCATTCACATTTAAA-ATACGGTGGGATCAGCACTTAGCAAC
1 -GGGGAATCAACACTTAGCAACCCCTTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAAC
* *
37503 CACCAATGAATCGGGGAATCAGCACTTAGCAATCCCTT
65 CACCAATGATTC-GGGAATCAGCACTTAGCAACCCCTT
* * * *
37541 TGGGAATCAACACTTAGCAACCCCCTTT-ATATTCAAAGATACGGTGGAATCAGCATTTTGCAAC
1 GGGGAATCAACACTTAGCAA-CCCCTTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAAC
* *
37605 CACCAATGAGTTAGGGAATCAGCACCTAGCAACCCCTT
65 CACCAATGA-TTCGGGAATCAGCACTTAGCAACCCCTT
37643 GGGGGAATCAGA-ACTTAGCAACCCC
1 -GGGGAATCA-ACACTTAGCAACCCC
37668 CTTTATATTC
Statistics
Matches: 202, Mismatches: 20, Indels: 13
0.86 0.09 0.06
Matches are distributed among these distances:
101 25 0.12
102 122 0.60
103 54 0.27
104 1 0.00
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (101 bp):
GGGGAATCAACACTTAGCAACCCCTTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACC
ACCAATGATTCGGGAATCAGCACTTAGCAACCCCTT
Found at i:62492 original size:74 final size:74
Alignment explanation
Indices: 62371--62517 Score: 294
Period size: 74 Copynumber: 2.0 Consensus size: 74
62361 ACAGGCTCCA
62371 CCTAACACTGGTCATTACAGCAACGGTCTGTTGTTGGATGATGTAAGTTCATTTCTGCTTTACAT
1 CCTAACACTGGTCATTACAGCAACGGTCTGTTGTTGGATGATGTAAGTTCATTTCTGCTTTACAT
62436 TTTATCTTG
66 TTTATCTTG
62445 CCTAACACTGGTCATTACAGCAACGGTCTGTTGTTGGATGATGTAAGTTCATTTCTGCTTTACAT
1 CCTAACACTGGTCATTACAGCAACGGTCTGTTGTTGGATGATGTAAGTTCATTTCTGCTTTACAT
62510 TTTATCTT
66 TTTATCTT
62518 TCTTATGTAG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (74 bp):
CCTAACACTGGTCATTACAGCAACGGTCTGTTGTTGGATGATGTAAGTTCATTTCTGCTTTACAT
TTTATCTTG
Found at i:68407 original size:21 final size:22
Alignment explanation
Indices: 68376--68421 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
68366 TTGAATTCAA
* *
68376 AACCTTAAAACCTCGAGCCTTG
1 AACCTTAAAACCTCGAACATTG
68398 AACC-TAAAACCTCGAACATTG
1 AACCTTAAAACCTCGAACATTG
68419 AAC
1 AAC
68422 ACCGAACACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.39, C:0.30, G:0.11, T:0.20
Consensus pattern (22 bp):
AACCTTAAAACCTCGAACATTG
Found at i:68972 original size:23 final size:25
Alignment explanation
Indices: 68946--68991 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
68936 TATTACCTAT
68946 TAGATCAT-ATAT-ATTTTTAAAAA
1 TAGATCATAATATAATTTTTAAAAA
*
68969 TAGATCATAATTTAATTTTTAAA
1 TAGATCATAATATAATTTTTAAA
68992 TCATAGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 3 0.15
25 9 0.45
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (25 bp):
TAGATCATAATATAATTTTTAAAAA
Found at i:75237 original size:18 final size:17
Alignment explanation
Indices: 75205--75243 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
75195 AATTTTTAAT
* *
75205 TTATAAATTATAAAAGA
1 TTATAAATAATAAAAAA
75222 TTATAAATAAATAAAAAA
1 TTATAAAT-AATAAAAAA
75240 TTAT
1 TTAT
75244 TTTAGGACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TTATAAATAATAAAAAA
Found at i:77017 original size:48 final size:48
Alignment explanation
Indices: 76946--77064 Score: 195
Period size: 48 Copynumber: 2.5 Consensus size: 48
76936 TTATGGAAAA
*
76946 TTATATGAGTGCTAGATAGGAGCAGTACAATATTGGTTTGAACTCGTG
1 TTATATAAGTGCTAGATAGGAGCAGTACAATATTGGTTTGAACTCGTG
*
76994 TTATATAAGTGCTAGATAGGAGCATTACAATATTGGTTTGAACTCGTG
1 TTATATAAGTGCTAGATAGGAGCAGTACAATATTGGTTTGAACTCGTG
*
77042 TTATTTAAGTGTCT-GATAGGAGC
1 TTATATAAGTG-CTAGATAGGAGC
77065 TTTAATAATC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
48 65 0.97
49 2 0.03
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.35
Consensus pattern (48 bp):
TTATATAAGTGCTAGATAGGAGCAGTACAATATTGGTTTGAACTCGTG
Found at i:88780 original size:16 final size:17
Alignment explanation
Indices: 88741--88790 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
88731 AATCAAAATA
88741 AAAAAAGAATAATAAGAGT
1 AAAAAA-AA-AATAAGAGT
*
88760 AAAAACAAAATAAGA-T
1 AAAAAAAAAATAAGAGT
*
88776 AAAAAAAAAACAAGA
1 AAAAAAAAAATAAGA
88791 CAAACTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.50
17 7 0.25
18 2 0.07
19 5 0.18
ACGTcount: A:0.76, C:0.04, G:0.10, T:0.10
Consensus pattern (17 bp):
AAAAAAAAAATAAGAGT
Found at i:91535 original size:2 final size:2
Alignment explanation
Indices: 91528--91560 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
91518 GGATGCAGTA
91528 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 A
91561 CATTATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:98674 original size:20 final size:19
Alignment explanation
Indices: 98620--98677 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 19
98610 TGTCAATTCA
98620 AAAATAATTAAATAAATTATT
1 AAAAT-ATTAAA-AAATTATT
* *
98641 AAAAAATAATAAAAATTAATT
1 AAAATATTA-AAAAATT-ATT
98662 AAAATATTAAAAAATT
1 AAAATATTAAAAAATT
98678 TATGAACTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATATTAAAAAATTATT
Found at i:100884 original size:30 final size:30
Alignment explanation
Indices: 100840--100902 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
100830 GCTTAACAAG
100840 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
100870 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
100900 CAA
1 CAA
100903 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:107282 original size:9 final size:9
Alignment explanation
Indices: 107268--107304 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
107258 TATAGTTTGA
107268 TATTCGAAT
1 TATTCGAAT
107277 TATTCGAAT
1 TATTCGAAT
*
107286 TATTCGAGT
1 TATTCGAAT
107295 TATTCGAAT
1 TATTCGAAT
107304 T
1 T
107305 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:113103 original size:21 final size:21
Alignment explanation
Indices: 113077--113117 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
113067 GCCTAAAATT
* *
113077 TGAATTTGATTGAATTGAATA
1 TGAATTTCATTAAATTGAATA
113098 TGAATTTCATTAAATTGAAT
1 TGAATTTCATTAAATTGAAT
113118 TAAATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (21 bp):
TGAATTTCATTAAATTGAATA
Found at i:115862 original size:18 final size:17
Alignment explanation
Indices: 115839--115877 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
115829 TTTTATAAAT
115839 TGTGAATT-ATATCTGATA
1 TGTGAATTAATAT-TGA-A
115857 TGTGAATTAATATTGAA
1 TGTGAATTAATATTGAA
115874 TGTG
1 TGTG
115878 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.44
Consensus pattern (17 bp):
TGTGAATTAATATTGAA
Found at i:116120 original size:23 final size:23
Alignment explanation
Indices: 116089--116164 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
116079 AGTGTTATTG
116089 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
116112 TTCAGTGGTAGCTACGGTTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
116135 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
116158 ATCAGTG
1 ATCAGTG
116165 TGGCACTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:119289 original size:21 final size:23
Alignment explanation
Indices: 119263--119312 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
119253 TTTTTTGCTA
119263 TATTAT-ATTA-T-TTGTTATTAT
1 TATTATGATTATTGTTGTTA-TAT
119284 TATTATGATTATTGTTGTTATAT
1 TATTATGATTATTGTTGTTATAT
119307 TATTAT
1 TATTAT
119313 TATACTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.23
22 4 0.15
23 10 0.38
24 6 0.23
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (23 bp):
TATTATGATTATTGTTGTTATAT
Found at i:119523 original size:21 final size:21
Alignment explanation
Indices: 119499--119539 Score: 73
Period size: 21 Copynumber: 1.9 Consensus size: 21
119489 ATATTTTACA
119499 TTTTATACATATATATATATAT
1 TTTTATA-ATATATATATATAT
119521 TTTTATAATATATATATAT
1 TTTTATAATATATATATAT
119540 TCATACACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTATAATATATATATATAT
Found at i:121686 original size:25 final size:25
Alignment explanation
Indices: 121652--121701 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
121642 TACATATTGT
* *
121652 ATATATAAAT-AATTATATTTATTTA
1 ATATAAAAATAAATTA-ATGTATTTA
121677 ATATAAAAATAAATTAATGTATTTA
1 ATATAAAAATAAATTAATGTATTTA
121702 TTTATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
ATATAAAAATAAATTAATGTATTTA
Found at i:125828 original size:1 final size:1
Alignment explanation
Indices: 125822--125852 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
125812 ACAATTGAAG
125822 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
125853 CTGTTCTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:130604 original size:29 final size:27
Alignment explanation
Indices: 130538--130604 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 27
130528 GAGTCTCACG
*
130538 TGTATAATTGCATCAAATTAAGATTTA
1 TGTATAATTGCATCAAATTAAAATTTA
*
130565 TGTATACAATTGTACATTAAATTAAAATTTA
1 TGTAT--AATTG--CATCAAATTAAAATTTA
130596 TGTATAATT
1 TGTATAATT
130605 TAGAACTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 5 0.15
29 9 0.26
31 20 0.59
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (27 bp):
TGTATAATTGCATCAAATTAAAATTTA
Found at i:130993 original size:14 final size:14
Alignment explanation
Indices: 130974--131000 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
130964 GTGACTAAAT
130974 TATAAATTTTAACA
1 TATAAATTTTAACA
130988 TATAAATTTTAAC
1 TATAAATTTTAAC
131001 TTGAGGATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
TATAAATTTTAACA
Found at i:137425 original size:74 final size:74
Alignment explanation
Indices: 137304--137457 Score: 290
Period size: 74 Copynumber: 2.1 Consensus size: 74
137294 TTCTTTATAC
137304 GAGAGTGGTCAATTGGATTCTCTTGTATTAATTTATTTTGTTCGGTACACTAAGTGGATATGTGT
1 GAGAGTGGTCAATTGGATTCTCTTGTATTAATTTATTTTGTTCGGTACACTAAGTGGATATGTGT
*
137369 CATTTAAGG
66 CATCTAAGG
137378 GAGAGTGGTCAATTGGATTCTCTTGTATTAATTTATTTTGTTCGGTACACTAAGTGGATATGTGT
1 GAGAGTGGTCAATTGGATTCTCTTGTATTAATTTATTTTGTTCGGTACACTAAGTGGATATGTGT
137443 CATCTAAGG
66 CATCTAAGG
*
137452 GTGAGT
1 GAGAGT
137458 AAACTTAAAC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41
Consensus pattern (74 bp):
GAGAGTGGTCAATTGGATTCTCTTGTATTAATTTATTTTGTTCGGTACACTAAGTGGATATGTGT
CATCTAAGG
Found at i:145915 original size:38 final size:38
Alignment explanation
Indices: 145864--145940 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
145854 CTCAATTTCA
*
145864 ACTTCAACTCAACCATGAGAGTCATGTTCATTTTTACT
1 ACTTCAACTCAACCATGAGAATCATGTTCATTTTTACT
*
145902 ACTTCAGCTCAACCATGAGAATCATGTTCATTTTTACT
1 ACTTCAACTCAACCATGAGAATCATGTTCATTTTTACT
145940 A
1 A
145941 GGAAATAGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.36
Consensus pattern (38 bp):
ACTTCAACTCAACCATGAGAATCATGTTCATTTTTACT
Found at i:153165 original size:31 final size:31
Alignment explanation
Indices: 153130--153189 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
153120 CTACTTTTGA
*
153130 CAATTAATCTTCGAAGTATAATATAATAAAC
1 CAATTAATCTACGAAGTATAATATAATAAAC
*
153161 CAATTCATCTACGAAGTATAATATAATAA
1 CAATTAATCTACGAAGTATAATATAATAA
153190 TCTATCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (31 bp):
CAATTAATCTACGAAGTATAATATAATAAAC
Found at i:159826 original size:15 final size:14
Alignment explanation
Indices: 159806--159846 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
159796 TAGACTTTGC
159806 TTTCTTTTTTTTCTT
1 TTTCTTTTTTTT-TT
159821 TTTCTTTTTTTTTT
1 TTTCTTTTTTTTTT
*
159835 TTGACTTTTTTT
1 TT-TCTTTTTTT
159847 GTTATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.85
Consensus pattern (14 bp):
TTTCTTTTTTTTTT
Found at i:164362 original size:15 final size:15
Alignment explanation
Indices: 164342--164375 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
164332 TTAATCATAA
164342 TTAATTAATAAAAAC
1 TTAATTAATAAAAAC
* *
164357 TTAATTAATTAAACC
1 TTAATTAATAAAAAC
164372 TTAA
1 TTAA
164376 GTGTAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAATTAATAAAAAC
Found at i:166647 original size:32 final size:32
Alignment explanation
Indices: 166591--166651 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
166581 CTTAGGCAAC
* *
166591 TTTGGCTAATGAAAAAGCGGCACATGGCATGT
1 TTTGGCCAATGAAAAAACGGCACATGGCATGT
* *
166623 TTTGGCCAATGAAAAAATGTCACATGGCA
1 TTTGGCCAATGAAAAAACGGCACATGGCA
166652 ATTAATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (32 bp):
TTTGGCCAATGAAAAAACGGCACATGGCATGT
Found at i:175302 original size:15 final size:15
Alignment explanation
Indices: 175282--175346 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 15
175272 ATACTACAAA
175282 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
175297 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
* *
175314 AAATATTTAGTATTAAA
1 --ATATTTATTATTAAT
*
175331 ATA-TTACTATTAAT
1 ATATTTATTATTAAT
175345 AT
1 AT
175347 TTTCAATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
14 11 0.28
15 12 0.30
16 1 0.03
17 7 0.17
18 1 0.03
19 8 0.20
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:180972 original size:29 final size:30
Alignment explanation
Indices: 180915--180978 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
180905 ATTACTCAAT
*
180915 TATTAGTAAATTTATTTTTGGTCACCCAAC
1 TATTAGTAAATTTAGTTTTGGTCACCCAAC
* *
180945 TATTAGTAAATTT-GTTTTGGTCATCCAAT
1 TATTAGTAAATTTAGTTTTGGTCACCCAAC
180974 TATTA
1 TATTA
180979 AAAGTTACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (30 bp):
TATTAGTAAATTTAGTTTTGGTCACCCAAC
Found at i:189446 original size:11 final size:12
Alignment explanation
Indices: 189421--189451 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
189411 GCGTTTAATA
*
189421 TTTAATTATTTT
1 TTTAAATATTTT
189433 TTTAAATATTTT
1 TTTAAATATTTT
189445 TTTAAAT
1 TTTAAAT
189452 TATAGTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTAAATATTTT
Found at i:189754 original size:24 final size:24
Alignment explanation
Indices: 189727--189785 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
189717 ATTGTAAATC
*
189727 AATAAAATTAATACAA-ATTTTTAA
1 AATAAAATTAACACAATA-TTTTAA
*
189751 AATAAAATTAGCACAATATTTTAA
1 AATAAAATTAACACAATATTTTAA
189775 AATAATAATTA
1 AATAA-AATTA
189786 TAAATTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 25 0.81
25 6 0.19
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (24 bp):
AATAAAATTAACACAATATTTTAA
Found at i:189986 original size:5 final size:5
Alignment explanation
Indices: 189976--190006 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
189966 GTATTACAAT
189976 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
190007 AATAAATGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:190249 original size:21 final size:21
Alignment explanation
Indices: 190196--190249 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
190186 CCCTCTTAGA
* *
190196 TTCATATTTTTATCTTATTTTT
1 TTCA-ATTTTTAACTTATTTTC
**
190218 TTCAAGATTTAACTTATTTTC
1 TTCAATTTTTAACTTATTTTC
*
190239 TTCACTTTTTA
1 TTCAATTTTTA
190250 TATATGAGAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.22, C:0.13, G:0.02, T:0.63
Consensus pattern (21 bp):
TTCAATTTTTAACTTATTTTC
Found at i:191410 original size:4 final size:4
Alignment explanation
Indices: 191401--191434 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
191391 ATATACCTAA
191401 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
191435 TTGCGGGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:196633 original size:24 final size:24
Alignment explanation
Indices: 196605--196655 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
196595 CTTTATATAT
196605 TTTTTATAATTTTT-TAAAAAATAAA
1 TTTTTA-AATTTTTAT-AAAAATAAA
*
196630 TTTTTAAATTTTTATAAATATAAA
1 TTTTTAAATTTTTATAAAAATAAA
196654 TT
1 TT
196656 AAAATTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTTTAAATTTTTATAAAAATAAA
Found at i:196863 original size:224 final size:225
Alignment explanation
Indices: 196462--196874 Score: 819
Period size: 224 Copynumber: 1.8 Consensus size: 225
196452 GCACATAAAT
196462 TTGAAACCATATATATTTGAAAATTTTTTCAAAGCAAAATAATAATAAAATACGTATGATAAACT
1 TTGAAACCATATATATTTGAAAATTTTTTCAAAGCAAAATAATAATAAAATACGTATGATAAACT
196527 CAAATAATTAATTAACTTATTTAGATCCTAAAATTATTATTCTAGACAGTTTTTAATTTTTTAAT
66 CAAATAATTAATTAACTTATTTAGATCCTAAAATTATTATTCTAGACAGTTTTTAATTTTTTAAT
196592 TTTCTTTATATATTTTTTATAATTTTTTAAAAAATAAATTTTTAAATTTTTATAAATATAAATTA
131 TTTCTTTATATATTTTTTATAATTTTTTAAAAAATAAATTTTTAAATTTTTATAAATATAAATTA
196657 AAATTTTGTTGCAGCATAACTAATTTCATA
196 AAATTTTGTTGCAGCATAACTAATTTCATA
196687 TTGAAACCAT-TATATTTGAAAATTTTTTCAAAGCAAAATAATAATAAAATACGTATGATAAACT
1 TTGAAACCATATATATTTGAAAATTTTTTCAAAGCAAAATAATAATAAAATACGTATGATAAACT
196751 CAAATAATTAATTAACTTATTTAGATCCTAAAATTATTATTCTAGACAGTTTTTAATTTTTTAAT
66 CAAATAATTAATTAACTTATTTAGATCCTAAAATTATTATTCTAGACAGTTTTTAATTTTTTAAT
196816 TTTCTTTATATATTTTTTATAATTTTTTAAAAAATAAATTTTTAAATTTTTATAAATAT
131 TTTCTTTATATATTTTTTATAATTTTTTAAAAAATAAATTTTTAAATTTTTATAAATAT
196875 TTTGAATCTT
Statistics
Matches: 188, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
224 178 0.95
225 10 0.05
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (225 bp):
TTGAAACCATATATATTTGAAAATTTTTTCAAAGCAAAATAATAATAAAATACGTATGATAAACT
CAAATAATTAATTAACTTATTTAGATCCTAAAATTATTATTCTAGACAGTTTTTAATTTTTTAAT
TTTCTTTATATATTTTTTATAATTTTTTAAAAAATAAATTTTTAAATTTTTATAAATATAAATTA
AAATTTTGTTGCAGCATAACTAATTTCATA
Found at i:196891 original size:19 final size:19
Alignment explanation
Indices: 196849--196904 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
196839 TTTTTAAAAA
*
196849 ATAAAT-TTTTAAATTTTT
1 ATAAATATTTTGAATTTTT
196867 ATAAATATTTTGAATCTTTT
1 ATAAATATTTTGAAT-TTTT
*
196887 A-AAATTATTCTGAATTTT
1 ATAAA-TATTTTGAATTTT
196905 CTTTTTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 6 0.18
19 13 0.39
20 14 0.42
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (19 bp):
ATAAATATTTTGAATTTTT
Found at i:204350 original size:28 final size:28
Alignment explanation
Indices: 204306--204386 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 28
204296 TAAATAATTT
204306 TATATT-TCATTTATTAAAACTTTATA-TA
1 TATATTAT-ATTTATTAAAA-TTTATATTA
* * *
204334 TATCTTATATTTTTTAATATTTATATTA
1 TATATTATATTTATTAAAATTTATATTA
204362 TATATTATATATTATTATAAATTTA
1 TATATTATAT-TTATTA-AAATTTA
204387 GTTTTTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
27 6 0.14
28 25 0.58
29 6 0.14
30 6 0.14
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (28 bp):
TATATTATATTTATTAAAATTTATATTA
Found at i:209029 original size:29 final size:29
Alignment explanation
Indices: 208996--209052 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
208986 CTAAAGGCTT
*
208996 GCCTATAAGGT-TTCACATGCAAGGGGTTC
1 GCCTAT-AGGTGTTCACATACAAGGGGTTC
*
209025 GCCTATAGGTGTTCGCATACAAGGGGTT
1 GCCTATAGGTGTTCACATACAAGGGGTT
209053 TACATGCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (29 bp):
GCCTATAGGTGTTCACATACAAGGGGTTC
Found at i:211247 original size:25 final size:25
Alignment explanation
Indices: 211186--211266 Score: 83
Period size: 25 Copynumber: 3.1 Consensus size: 25
211176 GCAAGTATGA
*
211186 AATTGAAAATAAAAATATTAATAATT
1 AATT-AAAATAAAATTATTAATAATT
211212 AAATTAGAAATAAAATTATTTAATAATT
1 -AATTA-AAATAAAATTA-TTAATAATT
* *
211240 AATT-AAATAGAATTAATTAGTAATT
1 AATTAAAATAAAATT-ATTAATAATT
211265 AA
1 AA
211267 ATTGATTAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
25 19 0.40
26 2 0.04
27 18 0.38
28 9 0.19
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (25 bp):
AATTAAAATAAAATTATTAATAATT
Found at i:212648 original size:36 final size:35
Alignment explanation
Indices: 212554--212651 Score: 90
Period size: 36 Copynumber: 2.7 Consensus size: 35
212544 GCGCGGAGCT
* *
212554 CATATTACTTTGGACATACCGATGAAGTGCGGATCA
1 CATATTACTTTGGACATACCAATG-AGTGCGGAACA
* * ** *
212590 CACATTACTTCGGTTTATACCAATGAG-GCGTGAAACG
1 CATATTACTTTGG-ACATACCAATGAGTGCG-G-AACA
212627 CATATTACTTTGGACATACCAATGA
1 CATATTACTTTGGACATACCAATGA
212652 TGCATTAGGT
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
35 3 0.06
36 24 0.50
37 21 0.44
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (35 bp):
CATATTACTTTGGACATACCAATGAGTGCGGAACA
Found at i:213503 original size:2 final size:2
Alignment explanation
Indices: 213467--213491 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
213457 ATGTACATAC
213467 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
213492 CACTCCTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:218523 original size:11 final size:11
Alignment explanation
Indices: 218507--218532 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
218497 TGTGAATTTA
218507 AAAAAAAAAAG
1 AAAAAAAAAAG
218518 AAAAAAAAAAG
1 AAAAAAAAAAG
218529 AAAA
1 AAAA
218533 GGAAGATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:222764 original size:22 final size:23
Alignment explanation
Indices: 222739--222781 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
222729 ACTAATGTTC
*
222739 AATTTGGCACTTG-ATTTTTTCT
1 AATTTGACACTTGAATTTTTTCT
*
222761 AATTTGATACTTGAATTTTTT
1 AATTTGACACTTGAATTTTTT
222782 TGCCCTGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.23, C:0.09, G:0.12, T:0.56
Consensus pattern (23 bp):
AATTTGACACTTGAATTTTTTCT
Found at i:223313 original size:531 final size:531
Alignment explanation
Indices: 222271--223334 Score: 1871
Period size: 531 Copynumber: 2.0 Consensus size: 531
222261 TGCTACTACT
* *
222271 GTGATCGTTTGTTGTTGTATCCTGGGAGACAGACGTCTAACGTTACTCAAAGCATCGAGGAGTGG
1 GTGATCGTTTGTTGTTGTATCCTGGGAGACAGACGTCCAACGTTACTCAAAGCATCGAGGAGAGG
* * * * *
222336 ATGAATTTGTCTTAAGGAAACTGTTTATATAGGCATCAACAAAATTCTTCTTCTAATTTTTAACT
66 ACGAATTTGTCTTAAAGAAACAGTTTATACAGGCATCAACAAAATTCTTCTTCTAATTTTCAACT
* *
222401 TTGTTCGATTACAAGTATTCTGTTGCGTTACTGCTACTGCGTTGTATTGCATTGTCATTGTTACT
131 TTGTTCGATTACAAGTATTCTGTTGCGTTACTGCCACTGCATTGTATTGCATTGTCATTGTTACT
*
222466 GACATATTAATACTATATACGACATCAGATTTTCTTATAGGTTTCAATCAAGGTGAAGCTAGAAA
196 GACATATTAATACTATATACGACATCAGATTTTCTTATAGGTTCCAATCAAGGTGAAGCTAGAAA
*
222531 ATTTGTTTGGGGACTGAAATTAAGTTGTATATATTTTACGATAGAAAAAATACAATTTCACAATT
261 ATTTGTTTGAGGACTGAAATTAAGTTGTATATATTTTACGATAGAAAAAATACAATTTCACAATT
* * * *
222596 TTAATAGCCTATACTTTTTTTTTATAAATTTTAAAGGATTAAATCAATTTTTTAACATTTTGATT
326 TTAATAGCATATACTATATTTTTATAAATTTTAAAGGATTAAATCAAATTTTTAACATTTTGATT
*
222661 TAAAATTTTATAAATTATAAAAAGGCCTAAATGGAATTTTTTTTTATTTTAAGGGGTCGGGGCAT
391 TAAAATTTTATAAATTATAAAAAGGCCTAAATGGAATATTTTTTTATTTTAAGGGGTCGGGGCAT
* *
222726 GCCACTAATGTTCAATTTGGCACTTGATTTTTTCTAATTTGATACTTGAATTTTTTTGCCCTGGT
456 GCCACTAATGTTCAAATTGGCACCTGATTTTTTCTAATTTGATACTTGAATTTTTTTGCCCTGGT
222791 TAAATACCAAA
521 TAAATACCAAA
* *
222802 GTGATCTTTTGTTGTTGTATCCTGGGAGACAGACGTCCAACGTTACTTAAAGCATCGAGGAGAGG
1 GTGATCGTTTGTTGTTGTATCCTGGGAGACAGACGTCCAACGTTACTCAAAGCATCGAGGAGAGG
222867 ACGAATTTGTCTTAAAGAAACAGTTTATACAGGCATCAACAAAATTCTTCTTCTAATTTTCAACT
66 ACGAATTTGTCTTAAAGAAACAGTTTATACAGGCATCAACAAAATTCTTCTTCTAATTTTCAACT
222932 TTGTTCGATTACAAGTATTCTGTTGCGTTACTGCCACTGCATTGTATTGCATTGTCATTGTTACT
131 TTGTTCGATTACAAGTATTCTGTTGCGTTACTGCCACTGCATTGTATTGCATTGTCATTGTTACT
222997 GACATATTAATACTATATACGACATCAGATTTTCTTATAGGTTCCAATCAAGGTGAAGCTAGAAA
196 GACATATTAATACTATATACGACATCAGATTTTCTTATAGGTTCCAATCAAGGTGAAGCTAGAAA
* * *
223062 TTTTGTTTGAGGACTGAAATTAAGTTGTATATATTTTACGATAGAAAAAATACAATTTCTCCATT
261 ATTTGTTTGAGGACTGAAATTAAGTTGTATATATTTTACGATAGAAAAAATACAATTTCACAATT
*
223127 TTAATAGCATATA-TATATTTTTATAAATTTTAAAGGATTAAATCAAATTTTTATCATTTTGATT
326 TTAATAGCATATACTATATTTTTATAAATTTTAAAGGATTAAATCAAATTTTTAACATTTTGATT
*
223191 TAAAATTTTATAAATTATAAAAAGGCCTAAATGAGAA-ATTTTTTTATTTTAGGGGGTCGGGGCA
391 TAAAATTTTATAAATTATAAAAAGGCCTAAATG-GAATATTTTTTTATTTTAAGGGGTCGGGGCA
223255 TGCCACTAATGTTCAAATTGGCACCTGATTTTTTCTAATTTGATACTTGAATTTTTTTTGCCCTG
455 TGCCACTAATGTTCAAATTGGCACCTGATTTTTTCTAATTTGATACTTGAA-TTTTTTTGCCCTG
223320 GTTAAATACCAAA
519 GTTAAATACCAAA
223333 GT
1 GT
223335 TTAAATTCTA
Statistics
Matches: 506, Mismatches: 25, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
530 154 0.30
531 352 0.70
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (531 bp):
GTGATCGTTTGTTGTTGTATCCTGGGAGACAGACGTCCAACGTTACTCAAAGCATCGAGGAGAGG
ACGAATTTGTCTTAAAGAAACAGTTTATACAGGCATCAACAAAATTCTTCTTCTAATTTTCAACT
TTGTTCGATTACAAGTATTCTGTTGCGTTACTGCCACTGCATTGTATTGCATTGTCATTGTTACT
GACATATTAATACTATATACGACATCAGATTTTCTTATAGGTTCCAATCAAGGTGAAGCTAGAAA
ATTTGTTTGAGGACTGAAATTAAGTTGTATATATTTTACGATAGAAAAAATACAATTTCACAATT
TTAATAGCATATACTATATTTTTATAAATTTTAAAGGATTAAATCAAATTTTTAACATTTTGATT
TAAAATTTTATAAATTATAAAAAGGCCTAAATGGAATATTTTTTTATTTTAAGGGGTCGGGGCAT
GCCACTAATGTTCAAATTGGCACCTGATTTTTTCTAATTTGATACTTGAATTTTTTTGCCCTGGT
TAAATACCAAA
Found at i:228913 original size:16 final size:16
Alignment explanation
Indices: 228894--228925 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
228884 AACACGAAGG
228894 GTCAAATGCTGCCATT
1 GTCAAATGCTGCCATT
228910 GTCAAATGCTGCCATT
1 GTCAAATGCTGCCATT
228926 AAAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (16 bp):
GTCAAATGCTGCCATT
Found at i:241432 original size:7 final size:7
Alignment explanation
Indices: 241420--241461 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
241410 TATGATGCAT
241420 GCAATGG
1 GCAATGG
241427 GCAATGG
1 GCAATGG
241434 GCAATGG
1 GCAATGG
241441 GCAATGG
1 GCAATGG
241448 GCAATGG
1 GCAATGG
241455 GCAATGG
1 GCAATGG
241462 CTGTATTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.43, T:0.14
Consensus pattern (7 bp):
GCAATGG
Found at i:253027 original size:3 final size:3
Alignment explanation
Indices: 253019--253057 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
253009 TGTCTTGAGG
253019 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
253058 NNNNNNNNNN
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:253911 original size:35 final size:35
Alignment explanation
Indices: 253858--253930 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
253848 TTGGTGTCCA
* * * *
253858 TTGCATATTAGATGTACAAACACTTAACATATTTG
1 TTGCATATCAAATCTACAAACACCTAACATATTTG
253893 TTGCATATCAAATCTACAAACACCTAACATATTTG
1 TTGCATATCAAATCTACAAACACCTAACATATTTG
253928 TTG
1 TTG
253931 TTATGTCACC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (35 bp):
TTGCATATCAAATCTACAAACACCTAACATATTTG
Found at i:264637 original size:64 final size:64
Alignment explanation
Indices: 264561--264688 Score: 213
Period size: 64 Copynumber: 2.0 Consensus size: 64
264551 ATCTACATTA
* *
264561 ATTTCACGTAAGTGTTATCAAAGGTTTAA-TTTCATAATATGGTTGAGATTAAAGCTAATAATGG
1 ATTTCACATAAGTGTTATCAAAGG-TTAATTTTCATAATATGGCTGAGATTAAAGCTAATAATGG
*
264625 ATTTCACATAAGTGTTATCAAAGGTTAATTTTCATAATATGGCTGAGATTAGAGCTAATAATGG
1 ATTTCACATAAGTGTTATCAAAGGTTAATTTTCATAATATGGCTGAGATTAAAGCTAATAATGG
264689 GCCGATTTCG
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 4 0.07
64 56 0.93
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.37
Consensus pattern (64 bp):
ATTTCACATAAGTGTTATCAAAGGTTAATTTTCATAATATGGCTGAGATTAAAGCTAATAATGG
Found at i:268858 original size:58 final size:59
Alignment explanation
Indices: 268779--268895 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 59
268769 TTGTTGATGA
268779 AGTTAAGGGTTTTCTTTGGCCAAAAATAAAGTTGAAGTTTTGATTGCCTTGGCTTGGTC
1 AGTTAAGGGTTTTCTTTGGCCAAAAATAAAGTTGAAGTTTTGATTGCCTTGGCTTGGTC
268838 AGTTAAGGG-TTTCTTTGGCCAAAAATAAAGTTGAAGTTTTGATTGCCTTGGCTTGGTC
1 AGTTAAGGGTTTTCTTTGGCCAAAAATAAAGTTGAAGTTTTGATTGCCTTGGCTTGGTC
268896 TTCTTCTTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 49 0.84
59 9 0.16
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (59 bp):
AGTTAAGGGTTTTCTTTGGCCAAAAATAAAGTTGAAGTTTTGATTGCCTTGGCTTGGTC
Found at i:270229 original size:91 final size:91
Alignment explanation
Indices: 270082--270289 Score: 310
Period size: 91 Copynumber: 2.3 Consensus size: 91
270072 TTGATTTTAG
* *
270082 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* *
270147 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
270174 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
270239 TGTAATAATTATTATTTTAAATTATA
66 TGTAATAATTATTATTTTAAATTATA
* * * *
270265 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
270290 GTTATAATTA
Statistics
Matches: 106, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
91 87 0.82
92 19 0.18
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:270256 original size:47 final size:46
Alignment explanation
Indices: 270114--270257 Score: 106
Period size: 47 Copynumber: 3.1 Consensus size: 46
270104 ATTATTAAGA
*
270114 ATTTTATGAAATTATATATCATTATTAAATTATATTTAAT-ATTAATT
1 ATTTTATGAAATTATATATTATTATTAAATTATA-TTAATAATT-ATT
* * ** *
270161 ATTTTA--AATTGTATAAATTCATATAAGAAAATT-TATT-ATCAA-GA--
1 ATTTTATGAAAT-TATATATT-AT-T-ATTAAATTATATTAAT-AATTATT
270205 ATTTTATGAAATTATATATTATTATTAAATTATATGTAATAATTATT
1 ATTTTATGAAATTATATATTATTATTAAATTATAT-TAATAATTATT
270252 ATTTTA
1 ATTTTA
270258 AATTATACAA
Statistics
Matches: 72, Mismatches: 11, Indels: 28
0.65 0.10 0.25
Matches are distributed among these distances:
42 6 0.08
43 4 0.06
44 11 0.15
45 13 0.18
46 12 0.17
47 16 0.22
48 4 0.06
49 6 0.08
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (46 bp):
ATTTTATGAAATTATATATTATTATTAAATTATATTAATAATTATT
Found at i:270264 original size:44 final size:43
Alignment explanation
Indices: 270122--270264 Score: 105
Period size: 44 Copynumber: 3.2 Consensus size: 43
270112 GAATTTTATG
*
270122 AAATTATATATCATTATTAAATTATATTTAAT-ATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATT-ATTATTTT
* ** ** *
270166 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATTATTATT-TT
270213 AAATTATATATTATTATTAAATTATATGTAATAATTATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATTATTATTTT
270257 AAATTATA
1 AAATTATA
270265 CAAATTCATA
Statistics
Matches: 74, Mismatches: 13, Indels: 24
0.67 0.12 0.22
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 20 0.27
45 12 0.16
46 11 0.15
47 11 0.15
48 4 0.05
49 6 0.08
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATTATTATTTT
Found at i:270453 original size:15 final size:15
Alignment explanation
Indices: 270443--270483 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
270433 TAAATTCATG
270443 ATAT-TTTAATTATA
1 ATATATTTAATTATA
*
270457 ATATATTTAATAATA
1 ATATATTTAATTATA
270472 AT-TATGTTAATT
1 ATATAT-TTAATT
270484 TATATTTTAN
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATATTTAATTATA
Found at i:270627 original size:14 final size:15
Alignment explanation
Indices: 270605--270640 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
270595 NNNNNNNNNT
*
270605 TATTAAATTAT-ATA
1 TATTTAATTATAATA
270619 TATTTAATTATAATA
1 TATTTAATTATAATA
270634 TATTTAA
1 TATTTAA
270641 CAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:270894 original size:16 final size:16
Alignment explanation
Indices: 270869--270922 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
270859 TTGATTTGCT
*
270869 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
270885 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
270901 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
270917 AATACA
1 ATTACA
270923 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.26, C:0.35, G:0.04, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:271020 original size:16 final size:16
Alignment explanation
Indices: 270999--271038 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
270989 ATATAGTCTA
*
270999 TTTGAGTTAGGATAAT
1 TTTGAGTTAAGATAAT
*
271015 TTTGAGTTAAGATAGT
1 TTTGAGTTAAGATAAT
*
271031 TTCGAGTT
1 TTTGAGTT
271039 CATGTAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.45
Consensus pattern (16 bp):
TTTGAGTTAAGATAAT
Found at i:288369 original size:31 final size:31
Alignment explanation
Indices: 288302--288369 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
288292 TGAAAAACTT
* * * *
288302 AAAGTTCAGGCCTCAACGTGAGAACAATTGC
1 AAAGTTCAGGCCCCAACATGAGAACAAGTAC
*
288333 AAAGTTCAGGCCCCAATATGAGAACAAGTAC
1 AAAGTTCAGGCCCCAACATGAGAACAAGTAC
*
288364 CAAGTT
1 AAAGTT
288370 TAGGAACTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (31 bp):
AAAGTTCAGGCCCCAACATGAGAACAAGTAC
Found at i:297579 original size:6 final size:6
Alignment explanation
Indices: 297568--297593 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
297558 TTTTATTGCC
297568 AATGCT AATGCT AATGCT AATGCT AA
1 AATGCT AATGCT AATGCT AATGCT AA
297594 GTGCCAGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (6 bp):
AATGCT
Found at i:304187 original size:30 final size:30
Alignment explanation
Indices: 304107--304187 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 30
304097 AATATGTATG
* *
304107 ATTGAATCAAATTAAAGTTTTATGTATACA
1 ATTGAACCAAATTAAAGTTTCATGTATACA
* ** * *
304137 TTTGAACCACAACCAAAGTTTCATGTGTATA
1 ATTGAACCA-AATTAAAGTTTCATGTATACA
*
304168 ATTGCACCAAATTAAAGTTT
1 ATTGAACCAAATTAAAGTTT
304188 ACGTACCAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
30 16 0.41
31 23 0.59
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.36
Consensus pattern (30 bp):
ATTGAACCAAATTAAAGTTTCATGTATACA
Found at i:305236 original size:27 final size:25
Alignment explanation
Indices: 305198--305251 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 25
305188 CACTTACATC
* * *
305198 TTTTATTAATTTGACTTTTATTCTT
1 TTTTATTAATTTCACCTTTAATCTT
305223 TTTTAGTTAAATTTCACCTTTAATCTT
1 TTTTA-TT-AATTTCACCTTTAATCTT
305250 TT
1 TT
305252 AAAAAGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.21
26 2 0.08
27 17 0.71
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTATTAATTTCACCTTTAATCTT
Found at i:313871 original size:57 final size:57
Alignment explanation
Indices: 313778--313889 Score: 145
Period size: 57 Copynumber: 2.0 Consensus size: 57
313768 CATGCACCCA
** * * *
313778 AAAAATAATTTGGATTAAGGGCGTAAAAAGCACTCAAA-TTTAAAAAAATAATAAATT
1 AAAAATAATTACGATTAAGGACATAAAAAACACTCAAACTTTAAAAAAA-AATAAATT
* *
313835 AAAAATAATTACGATTAAGGATATAAAAAACTCTCAAACTTTAAAAAAAAATAAA
1 AAAAATAATTACGATTAAGGACATAAAAAACACTCAAACTTTAAAAAAAAATAAA
313890 ACAGAAGCTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
57 37 0.79
58 10 0.21
ACGTcount: A:0.58, C:0.08, G:0.09, T:0.25
Consensus pattern (57 bp):
AAAAATAATTACGATTAAGGACATAAAAAACACTCAAACTTTAAAAAAAAATAAATT
Found at i:315644 original size:2 final size:2
Alignment explanation
Indices: 315637--315663 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
315627 TTTACGGCAC
315637 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
315664 TTAACATGTA
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:315874 original size:6 final size:6
Alignment explanation
Indices: 315863--315887 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
315853 CCAGCAGGCC
315863 TGTATA TGTATA TGTATA TGTATA T
1 TGTATA TGTATA TGTATA TGTATA T
315888 ATGCCTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TGTATA
Found at i:332275 original size:14 final size:14
Alignment explanation
Indices: 332248--332291 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
332238 TTTACAACAC
*
332248 ATACGAATAAATAT
1 ATACAAATAAATAT
* *
332262 TTACAAATATATAT
1 ATACAAATAAATAT
332276 ATACAAATACAATAT
1 ATACAAATA-AATAT
332291 A
1 A
332292 CCAGTAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (14 bp):
ATACAAATAAATAT
Found at i:333017 original size:3 final size:3
Alignment explanation
Indices: 332968--333000 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
332958 AATATACATG
332968 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
333001 CACAATGCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:337630 original size:13 final size:14
Alignment explanation
Indices: 337600--337632 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
337590 CAATATTATT
337600 ATATTAATAATAAA
1 ATATTAATAATAAA
*
337614 ATATTAAT-ATCAA
1 ATATTAATAATAAA
337627 ATATTA
1 ATATTA
337633 TCTATTGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATTAATAATAAA
Found at i:337926 original size:20 final size:18
Alignment explanation
Indices: 337884--337932 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 18
337874 ATCCTCACCC
337884 TTAATATTTTCTACTCAT
1 TTAATATTTTCTACTCAT
*
337902 TTAATTTTTTCTACTCATCT
1 TTAATATTTTCTACTCA--T
337922 TTAATATTTTC
1 TTAATATTTTC
337933 AATCTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 16 0.59
20 11 0.41
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATATTTTCTACTCAT
Found at i:338437 original size:18 final size:17
Alignment explanation
Indices: 338414--338447 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
338404 TTTATTTTTA
338414 TTTTTAAATTTTAAAATG
1 TTTTT-AATTTTAAAATG
*
338432 TTTTTATTTTTAAAAT
1 TTTTTAATTTTAAAAT
338448 AATTTTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTTAATTTTAAAATG
Found at i:340657 original size:24 final size:22
Alignment explanation
Indices: 340630--340687 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 22
340620 TTTTTATTAA
340630 AATATTTATATATAAGCACATTGT
1 AATATTTATATATAAGCAC-TT-T
*
340654 AATATTATATATTATAATCACTTT
1 AATATT-TATA-TATAAGCACTTT
340678 AAT-TTTATAT
1 AATATTTATAT
340688 GTTATAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 1 0.03
22 4 0.13
23 2 0.06
24 10 0.32
25 6 0.19
26 8 0.26
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.48
Consensus pattern (22 bp):
AATATTTATATATAAGCACTTT
Found at i:348233 original size:77 final size:78
Alignment explanation
Indices: 348138--348293 Score: 305
Period size: 77 Copynumber: 2.0 Consensus size: 78
348128 TATAAAAAAA
348138 TATTAAAAAACTTAAAATTATTTAAAAATAAGAATTTTATATAAAAATTCTAATGAAATAAAATC
1 TATTAAAAAACTTAAAATTATTTAAAAATAAGAATTTTATATAAAAATTCTAATGAAATAAAATC
348203 TCTAATACGTTGT
66 TCTAATACGTTGT
348216 TATTAAAAAA-TTAAAATTATTTAAAAATAAGAATTTTATATAAAAATTCTAATGAAATAAAATC
1 TATTAAAAAACTTAAAATTATTTAAAAATAAGAATTTTATATAAAAATTCTAATGAAATAAAATC
348280 TCTAATACGTTGT
66 TCTAATACGTTGT
348293 T
1 T
348294 GTTGAAGAAC
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 68 0.87
78 10 0.13
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (78 bp):
TATTAAAAAACTTAAAATTATTTAAAAATAAGAATTTTATATAAAAATTCTAATGAAATAAAATC
TCTAATACGTTGT
Found at i:348321 original size:77 final size:77
Alignment explanation
Indices: 348138--348322 Score: 282
Period size: 77 Copynumber: 2.4 Consensus size: 77
348128 TATAAAAAAA
*
348138 TATTAAAAAACTTAAAATTATTTAAAAATAAGAATTTTATATAAAAATTCTAATGAAATAAAATC
1 TATTAAAAAAC-TAAAATTATATAAAAATAAGAATTTTATATAAAAATTCTAATGAAATAAAATC
348203 TCTAATACGTTGT
65 TCTAATACGTTGT
* *
348216 TATTAAAAAATTAAAATTATTTAAAAATAAGAATTTTATATAAAAATTCTAATGAAATAAAATCT
1 TATTAAAAAACTAAAATTATATAAAAATAAGAATTTTATATAAAAATTCTAATGAAATAAAATCT
348281 CTAATACGTTGT
66 CTAATACGTTGT
* * * *
348293 TGTTGAAGAACTAATA-TATATAAGAAATAA
1 TATTAAAAAACTAAAATTATATAA-AAATAA
348323 AGATATTTAT
Statistics
Matches: 99, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
76 6 0.06
77 83 0.84
78 10 0.10
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.36
Consensus pattern (77 bp):
TATTAAAAAACTAAAATTATATAAAAATAAGAATTTTATATAAAAATTCTAATGAAATAAAATCT
CTAATACGTTGT
Found at i:349215 original size:26 final size:26
Alignment explanation
Indices: 349162--349215 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
349152 TAAACTAAAA
**
349162 TTTTTAAAAGTATTTCTCAAAATTAC
1 TTTTTAAAAGTATTTCTCAAAAGCAC
* * *
349188 TTTTTTAAAGTATTTTTGAAAAGCAC
1 TTTTTAAAAGTATTTCTCAAAAGCAC
349214 TT
1 TT
349216 CTCAAAAGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.48
Consensus pattern (26 bp):
TTTTTAAAAGTATTTCTCAAAAGCAC
Found at i:350967 original size:11 final size:11
Alignment explanation
Indices: 350953--351007 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
350943 TAATTTTTAA
350953 TTTTAAAATAT
1 TTTTAAAATAT
350964 TTTTAAAATACT
1 TTTTAAAATA-T
* *
350976 TTTT-TATTAT
1 TTTTAAAATAT
*
350986 TTTTTAAATAT
1 TTTTAAAATAT
350997 TTTTAAAATAT
1 TTTTAAAATAT
351008 ATATATTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 5 0.14
11 27 0.73
12 5 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:351019 original size:33 final size:32
Alignment explanation
Indices: 350947--351028 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 32
350937 TATTTTTAAT
* *
350947 TTTTAATTTTAAAATATTTTTAAAATACTTTT
1 TTTTATTTTTAAAATATTTTTAAAATACTTTA
*
350979 TTATTATTTTTTAAATATTTTTAAAATA-TATATA
1 TT-TTATTTTTAAAATATTTTTAAAATACT-T-TA
351013 TTTTATTTTTAAAATA
1 TTTTATTTTTAAAATA
351029 AAATTTTGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
32 3 0.07
33 37 0.86
34 3 0.07
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (32 bp):
TTTTATTTTTAAAATATTTTTAAAATACTTTA
Found at i:358270 original size:14 final size:13
Alignment explanation
Indices: 358250--358315 Score: 51
Period size: 14 Copynumber: 4.8 Consensus size: 13
358240 TTGCAATTTG
358250 ATTCTCAATTTCTT
1 ATTCTCAATTT-TT
*
358264 GTTCTCAATCTTTT
1 ATTCTCAAT-TTTT
**
358278 ATTCTCAATTGTCA
1 ATTCTCAATT-TTT
*
358292 ATTCTCGATTTTTT
1 ATTCTC-AATTTTT
*
358306 ATTCTAAATT
1 ATTCTCAATT
358316 CCCAATTTCA
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
13 4 0.10
14 31 0.77
15 5 0.12
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.55
Consensus pattern (13 bp):
ATTCTCAATTTTT
Found at i:358296 original size:28 final size:28
Alignment explanation
Indices: 358265--358341 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
358255 CAATTTCTTG
* * **
358265 TTCTCAATCTTTTATTCTCAATTGTCAA
1 TTCTCAATTTTTTATTCTAAATTCCCAA
*
358293 TTCTCGATTTTTTATTCTAAATTCCCAA
1 TTCTCAATTTTTTATTCTAAATTCCCAA
*
358321 TT-TCAATTTTTT-TTTTAAATT
1 TTCTCAATTTTTTATTCTAAATT
358342 TTTCTAAATC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 8 0.19
27 9 0.21
28 25 0.60
ACGTcount: A:0.25, C:0.17, G:0.03, T:0.56
Consensus pattern (28 bp):
TTCTCAATTTTTTATTCTAAATTCCCAA
Found at i:358506 original size:52 final size:52
Alignment explanation
Indices: 358440--358544 Score: 158
Period size: 52 Copynumber: 2.0 Consensus size: 52
358430 TAACAAACGG
* *
358440 TAAGAAAATGTTATTAAATTATTTAATTTT-AATCAGTTAGTTATTATGATGT
1 TAAGAAAATATTATTAAATTATTTAATTTTAAAT-AGTTAATTATTATGATGT
* *
358492 TAAGAAACTATTATTAAATTATTTAATTTTAAATAGTTAATTATTATGTTGT
1 TAAGAAAATATTATTAAATTATTTAATTTTAAATAGTTAATTATTATGATGT
358544 T
1 T
358545 TAGATTATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 45 0.94
53 3 0.06
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.50
Consensus pattern (52 bp):
TAAGAAAATATTATTAAATTATTTAATTTTAAATAGTTAATTATTATGATGT
Found at i:362665 original size:6 final size:6
Alignment explanation
Indices: 362654--362702 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
362644 TCTGAAATCG
362654 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
362702 A
1 A
362703 ACTTGTTCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:364328 original size:13 final size:13
Alignment explanation
Indices: 364306--364336 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
364296 TTTTATTTCG
*
364306 AATAACTAAGGAA
1 AATAAATAAGGAA
364319 AATAAATAAGGAA
1 AATAAATAAGGAA
364332 AATAA
1 AATAA
364337 TGATTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.13, T:0.16
Consensus pattern (13 bp):
AATAAATAAGGAA
Found at i:368413 original size:21 final size:21
Alignment explanation
Indices: 368387--368441 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
368377 AACAGCGGTG
*
368387 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
368408 GCGGTGAGATTAGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
368429 GCGGTGAGATTAG
1 GCGGTGAGATTAG
368442 AAATAATGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:378098 original size:13 final size:13
Alignment explanation
Indices: 378080--378141 Score: 79
Period size: 13 Copynumber: 4.8 Consensus size: 13
378070 TTCTTCATTG
378080 CTTTTGAAAAGTA
1 CTTTTGAAAAGTA
378093 CTTTTGAAAAGTA
1 CTTTTGAAAAGTA
* *
378106 CTGTGGAAAAGTA
1 CTTTTGAAAAGTA
* *
378119 CTTTTGAGAAGTG
1 CTTTTGAAAAGTA
*
378132 TTTTTGAAAA
1 CTTTTGAAAA
378142 TTTTGAGTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.37
Consensus pattern (13 bp):
CTTTTGAAAAGTA
Found at i:380104 original size:72 final size:71
Alignment explanation
Indices: 380014--380186 Score: 231
Period size: 72 Copynumber: 2.4 Consensus size: 71
380004 AAAATCACAT
* * *
380014 ATAAACAACTATTGATAAAACTAATTTAGTAAAAAATAAGTAGAATATAAATTCAATATCTAAAG
1 ATAAACAACTATTGATAAAACTAATTTAG-AAAAAATAAGTAGAACATAAATTCAATATCCAAAA
380079 ACCAAAC
65 ACCAAAC
* * * *
380086 ATAAACAACTTTTAATAAAACTAGATTTCA-CATAAATAAGTAGAACATAAATTCAATATCCAAA
1 ATAAACAACTATTGATAAAACTA-ATTT-AGAAAAAATAAGTAGAACATAAATTCAATATCCAAA
380150 AACCAAAC
64 AACCAAAC
* *
380158 ATAAATAACTATTGATAAAACTAGTTTAG
1 ATAAACAACTATTGATAAAACTAATTTAG
380187 CATTGTTGTT
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
70 1 0.01
71 3 0.03
72 78 0.90
73 4 0.05
74 1 0.01
ACGTcount: A:0.54, C:0.13, G:0.06, T:0.27
Consensus pattern (71 bp):
ATAAACAACTATTGATAAAACTAATTTAGAAAAAATAAGTAGAACATAAATTCAATATCCAAAAA
CCAAAC
Found at i:380634 original size:18 final size:18
Alignment explanation
Indices: 380613--380660 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
380603 TCCATCAATT
380613 TGAACATCATTTAAAATG
1 TGAACATCATTTAAAATG
380631 TGAACATCATTTAAAATG
1 TGAACATCATTTAAAATG
*
380649 TAAACATCATTT
1 TGAACATCATTT
380661 CTCATATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.35
Consensus pattern (18 bp):
TGAACATCATTTAAAATG
Found at i:383214 original size:25 final size:25
Alignment explanation
Indices: 383136--383208 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 25
383126 AGAGGAACAA
* *
383136 AGCACCAGCAGAGGAACAAATAACC
1 AGCACCAGTAGAGGAACAAAGAACC
* *
383161 AACACCAGTAGAAGAACAAAGAACC
1 AGCACCAGTAGAGGAACAAAGAACC
*
383186 AGCACCAGTAGAGGATCAAAGAA
1 AGCACCAGTAGAGGAACAAAGAA
383209 GTAGCAGAGG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.51, C:0.23, G:0.21, T:0.05
Consensus pattern (25 bp):
AGCACCAGTAGAGGAACAAAGAACC
Found at i:383704 original size:44 final size:46
Alignment explanation
Indices: 383617--383707 Score: 132
Period size: 44 Copynumber: 2.0 Consensus size: 46
383607 CTAAAAAACA
*
383617 ATTAACAATATCATTGAAAAACAAAAAAAAAATTATTAATTTATTTT
1 ATTAACAATATAATT-AAAAACAAAAAAAAAATTATTAATTTATTTT
* *
383664 ATTAACAATATAATT-AAAA-AATAATAAAATTATTAATTTATTTT
1 ATTAACAATATAATTAAAAACAAAAAAAAAATTATTAATTTATTTT
383708 TATTGGTAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
44 23 0.56
45 4 0.10
47 14 0.34
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (46 bp):
ATTAACAATATAATTAAAAACAAAAAAAAAATTATTAATTTATTTT
Found at i:385409 original size:26 final size:24
Alignment explanation
Indices: 385380--385473 Score: 84
Period size: 26 Copynumber: 3.8 Consensus size: 24
385370 GGGCTCACCA
385380 CAGCTCGTATGAGCTTACCTATATAT
1 CAGCTCGTATGAGCTTACCT-T-TAT
** *
385406 CAGCTTTTATGAGCTTACCGTT-T
1 CAGCTCGTATGAGCTTACCTTTAT
*
385429 CAGCTCG-ATAGAGCTTATCGTTTAT
1 CAGCTCGTAT-GAGCTTA-CCTTTAT
*
385454 CAGCTCGGAATGAGCTTACC
1 CAGCTC-GTATGAGCTTACC
385474 GATCATGGCT
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
22 2 0.04
23 13 0.24
24 4 0.07
25 9 0.16
26 25 0.45
27 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (24 bp):
CAGCTCGTATGAGCTTACCTTTAT
Found at i:385680 original size:20 final size:20
Alignment explanation
Indices: 385638--385681 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
385628 GATGAATTAT
* * *
385638 TGTTGATATGTATAAGTTGC
1 TGTTGATACGGATAAATTGC
*
385658 TGTTGATACGGATAAATTTC
1 TGTTGATACGGATAAATTGC
385678 TGTT
1 TGTT
385682 ATTACTGATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (20 bp):
TGTTGATACGGATAAATTGC
Found at i:386031 original size:117 final size:118
Alignment explanation
Indices: 385870--386104 Score: 463
Period size: 117 Copynumber: 2.0 Consensus size: 118
385860 TATATGATTT
385870 ATATGAATTGACGAATGAATTTGGAGGCTAAAAGAATGTTATGTGTTTGGTTTCATCTTTATGAA
1 ATATGAATTGACGAATGAATTTGGAGGCTAAAAGAATGTTATGTGTTTGGTTTCATCTTTATGAA
385935 TGGATGAATATATGGATGTGAAATGAATAACTTGTGAATGGTGATGTGAATAG
66 TGGATGAATATATGGATGTGAAATGAATAACTTGTGAATGGTGATGTGAATAG
385988 ATATGAATTG-CGAATGAATTTGGAGGCTAAAAGAATGTTATGTGTTTGGTTTCATCTTTATGAA
1 ATATGAATTGACGAATGAATTTGGAGGCTAAAAGAATGTTATGTGTTTGGTTTCATCTTTATGAA
386052 TGGATGAATATATGGATGTGAAATGAATAACTTGTGAATGGTGATGTGAATAG
66 TGGATGAATATATGGATGTGAAATGAATAACTTGTGAATGGTGATGTGAATAG
386105 GTTTTTTGGA
Statistics
Matches: 117, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
117 107 0.91
118 10 0.09
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (118 bp):
ATATGAATTGACGAATGAATTTGGAGGCTAAAAGAATGTTATGTGTTTGGTTTCATCTTTATGAA
TGGATGAATATATGGATGTGAAATGAATAACTTGTGAATGGTGATGTGAATAG
Found at i:405268 original size:41 final size:41
Alignment explanation
Indices: 405223--405305 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
405213 CAAAACATAA
405223 CTCACCCTACTCCAACAGACAATCTTAAACATCTACGAAAT
1 CTCACCCTACTCCAACAGACAATCTTAAACATCTACGAAAT
*
405264 CTCACCCTACTCTAACAGACAATCTTAAACATCTACGAAAT
1 CTCACCCTACTCCAACAGACAATCTTAAACATCTACGAAAT
405305 C
1 C
405306 ATCGATGCCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.34, G:0.05, T:0.23
Consensus pattern (41 bp):
CTCACCCTACTCCAACAGACAATCTTAAACATCTACGAAAT
Found at i:405287 original size:23 final size:23
Alignment explanation
Indices: 405223--405288 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 23
405213 CAAAACATAA
*
405223 CTCACCCTACTCCAACAGACAAT
1 CTCACCCTACTCTAACAGACAAT
* **
405246 CTTAAAC-A-TCT-AC-GA-AAT
1 CTCACCCTACTCTAACAGACAAT
405264 CTCACCCTACTCTAACAGACAAT
1 CTCACCCTACTCTAACAGACAAT
405287 CT
1 CT
405289 TAAACATCTA
Statistics
Matches: 31, Mismatches: 7, Indels: 10
0.65 0.15 0.21
Matches are distributed among these distances:
18 7 0.23
19 3 0.10
20 5 0.16
21 4 0.13
22 3 0.10
23 9 0.29
ACGTcount: A:0.36, C:0.36, G:0.05, T:0.23
Consensus pattern (23 bp):
CTCACCCTACTCTAACAGACAAT
Found at i:407384 original size:183 final size:184
Alignment explanation
Indices: 407190--407687 Score: 748
Period size: 183 Copynumber: 2.6 Consensus size: 184
407180 TCAAAGACAT
* * *
407190 ATACATACATATATATATGCAAAATGATATTTAAGAAAAACCCAAAGAGGTGATTAATGTAAAAC
1 ATACATACATATATATATGCAAAATGATATTTAAG-AAAACCCAAAGAGCTGGTTAATGTAAACC
*
407255 TTAAGACAGATCACAAATATCACTTAATAACTAAGATGGCAGAAAGGAATATCAAAGTAAAAAGG
65 TTAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATATCAAAGTAAAAAGG
407320 GTCATCAATGGCTGTCATGCAATGTGAGGCACATATTAAGGACATACCTGC-AA-
130 GTCATCAATGGCTGTCATGCAATGTGAGGCACATATTAAGGACATACCTGCAAAC
* *
407373 ATACATACATATATATATGCAAAATGATATTTAAGGAAAACCCAAAGCGCTGGTTAATGGAAACC
1 ATACATACATATATATATGCAAAATGATATTTAA-GAAAACCCAAAGAGCTGGTTAATGTAAACC
407438 TTAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATATCAAAGTAAAAAGG
65 TTAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATATCAAAGTAAAAAGG
* *
407503 GTTATCAATGGCTGTCATGCAATGTGAGGCACATATTAAGGCCATACCTGCAAATGC
130 GTCATCAATGGCTGTCATGCAATGTGAGGCACATATTAAGGACATACCTGCAAA--C
*
407560 ATACATATATATATGCAAATATATATGCAAAATGATATTTAATGAAAACCCAAAGAGCTGGTTAA
1 ATAC------ATA--CATATATATATGCAAAATGATATTTAA-GAAAACCCAAAGAGCTGGTTAA
* * * *
407625 TGTAAACCTTAAGACAGATCACAGATATCACTTAATAATTAAGATGGAAGCAAGGTATATCAA
57 TGTAAACCTTAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATATCAA
407688 GTATCAATGG
Statistics
Matches: 286, Mismatches: 16, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
183 171 0.60
184 3 0.01
187 4 0.01
193 3 0.01
195 105 0.37
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (184 bp):
ATACATACATATATATATGCAAAATGATATTTAAGAAAACCCAAAGAGCTGGTTAATGTAAACCT
TAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATATCAAAGTAAAAAGGG
TCATCAATGGCTGTCATGCAATGTGAGGCACATATTAAGGACATACCTGCAAAC
Found at i:407597 original size:14 final size:12
Alignment explanation
Indices: 407566--407590 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
407556 ATGCATACAT
407566 ATATATATGCAA
1 ATATATATGCAA
407578 ATATATATGCAA
1 ATATATATGCAA
407590 A
1 A
407591 ATGATATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
ATATATATGCAA
Done.