Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 11 of 259
Found at i:3125862 original size:25 final size:26
Alignment explanation
Indices: 3125834--3125885 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
3125824 GTAAATTAGA
*
3125834 TTTTT-TTTAA-TGGTTATAAGATTT
1 TTTTTGTTTAATTGATTATAAGATTT
3125858 TTTTTGTTTAATTGATTATAAGATTT
1 TTTTTGTTTAATTGATTATAAGATTT
3125884 TT
1 TT
3125886 GAAATATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.20
25 5 0.20
26 15 0.60
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.63
Consensus pattern (26 bp):
TTTTTGTTTAATTGATTATAAGATTT
Found at i:3130962 original size:13 final size:13
Alignment explanation
Indices: 3130946--3130971 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3130936 AATATATTAT
3130946 TTTATTAATTTAA
1 TTTATTAATTTAA
3130959 TTTATTAATTTAA
1 TTTATTAATTTAA
3130972 GAGTAGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTATTAATTTAA
Found at i:3132051 original size:6 final size:6
Alignment explanation
Indices: 3132042--3132074 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
3132032 CTCTTTTCTT
3132042 TTTTTC TTTTTC TTTTT- TTTTTC TTTTTTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTT
3132075 ATACAAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTTC
Found at i:3132062 original size:17 final size:18
Alignment explanation
Indices: 3132040--3132074 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3132030 ATCTCTTTTC
3132040 TTTTTTTC-TTTTTCTTT
1 TTTTTTTCTTTTTTCTTT
3132057 TTTTTTTCTTTTTTCTTT
1 TTTTTTTCTTTTTTCTTT
3132075 ATACAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (18 bp):
TTTTTTTCTTTTTTCTTT
Found at i:3146613 original size:25 final size:25
Alignment explanation
Indices: 3146564--3146622 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
3146554 GAGCAGAATT
* *
3146564 GAACAAAACATAGTAGAATAGAACA
1 GAACAGAACATAGTAGAAGAGAACA
*
3146589 TAACAGAACATAGTAGAACGA-AACA
1 GAACAGAACATAGTAGAA-GAGAACA
*
3146614 GAGCAGAAC
1 GAACAGAAC
3146623 TGAACAGAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.56, C:0.15, G:0.19, T:0.10
Consensus pattern (25 bp):
GAACAGAACATAGTAGAAGAGAACA
Found at i:3150152 original size:15 final size:15
Alignment explanation
Indices: 3150132--3150161 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3150122 TTCCAATTCT
*
3150132 TTCTTTTTCTATTGA
1 TTCTTTTTCGATTGA
3150147 TTCTTTTTCGATTGA
1 TTCTTTTTCGATTGA
3150162 GATGTATGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.13, G:0.10, T:0.63
Consensus pattern (15 bp):
TTCTTTTTCGATTGA
Found at i:3159696 original size:3 final size:3
Alignment explanation
Indices: 3159688--3159802 Score: 65
Period size: 3 Copynumber: 38.7 Consensus size: 3
3159678 AATATGATAG
* * * * * * * *
3159688 TAA TAA TAA CAA T-A TAG TAA TAG TAG TAG TAA TAG TGA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * **
3159735 AAA TAA TAG TAA TAA -AGA TAG TTC TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3159780 TAA TAA TTAA -AA TAA TCA TAA TA
1 TAA TAA -TAA TAA TAA TAA TAA TA
3159803 TAAAATTTGA
Statistics
Matches: 84, Mismatches: 23, Indels: 10
0.72 0.20 0.09
Matches are distributed among these distances:
2 5 0.06
3 75 0.89
4 4 0.05
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:3159704 original size:17 final size:16
Alignment explanation
Indices: 3159666--3159709 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
3159656 ATAAAAATAG
* *
3159666 TATAGTAATGATAATA
1 TATAGTAATAATAAAA
3159682 TGATAGTAATAATAACAA
1 T-ATAGTAATAATAA-AA
3159700 TATAGTAATA
1 TATAGTAATA
3159710 GTAGTAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.04
17 21 0.88
18 2 0.08
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.34
Consensus pattern (16 bp):
TATAGTAATAATAAAA
Found at i:3159748 original size:6 final size:6
Alignment explanation
Indices: 3159661--3159733 Score: 55
Period size: 6 Copynumber: 12.7 Consensus size: 6
3159651 AATAGATAAA
* * * *
3159661 AATAGT -ATAGT AAT-GAT AATA-T GATAGT AATAAT AACAAT -ATAGT
1 AATAGT AATAGT AATAG-T AATAGT AATAGT AATAGT AATAGT AATAGT
* *
3159706 AATAGT AGTAGT AATAGT GATAGT AATA
1 AATAGT AATAGT AATAGT AATAGT AATA
3159734 AAAATAATAG
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
5 13 0.25
6 39 0.75
ACGTcount: A:0.49, C:0.01, G:0.16, T:0.33
Consensus pattern (6 bp):
AATAGT
Found at i:3159872 original size:12 final size:12
Alignment explanation
Indices: 3159759--3159879 Score: 57
Period size: 12 Copynumber: 9.2 Consensus size: 12
3159749 AAGATAGTTC
*
3159759 TAATAATAATAA
1 TAATAATAAAAA
*
3159771 TAATAATAATAA
1 TAATAATAAAAA
*
3159783 TAATTAA-AATAA
1 TAA-TAATAAAAA
*
3159795 TCATAATATAAAA
1 TAATAATA-AAAA
* *
3159808 T-TTGAAAAAAAA
1 TAAT-AATAAAAA
3159820 TATATATATAAAATA
1 TA-ATA-ATAAAA-A
3159835 TACATAAGTAAATAAA
1 TA-ATAA-T-AA-AAA
*
3159851 TAATGAAATACAAA
1 TAAT--AATAAAAA
3159865 TAATAATAAAAA
1 TAATAATAAAAA
3159877 TAA
1 TAA
3159880 ACAAACCAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 26
0.71 0.07 0.21
Matches are distributed among these distances:
11 3 0.03
12 39 0.45
13 11 0.13
14 14 0.16
15 10 0.11
16 6 0.07
17 4 0.05
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (12 bp):
TAATAATAAAAA
Found at i:3160003 original size:3 final size:3
Alignment explanation
Indices: 3159997--3160100 Score: 61
Period size: 3 Copynumber: 34.0 Consensus size: 3
3159987 ATGGTAAAAC
** **
3159997 ATA ATA ATA ATA AT- ATGA ATA ATA ATA ACG ATA ATAA ATA ATA GCA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA AT-A ATA ATA ATA
* * * * *
3160043 AGA ATA ATA ATA GTA ATG ATA ATA GA-A GATA ATA ATA GTA CT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA -ATA ATA ATA ATA ATA ATA
3160088 ATAA ATA ATA ATA
1 AT-A ATA ATA ATA
3160101 GATTAAATTA
Statistics
Matches: 78, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
2 3 0.04
3 65 0.83
4 10 0.13
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:3160048 original size:31 final size:30
Alignment explanation
Indices: 3159997--3160097 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 30
3159987 ATGGTAAAAC
3159997 ATAAT-AATAATA-ATATGAATAATAATAACG
1 ATAATAAATAATAGA-A-GAATAATAATAACG
3160027 ATAATAAATAATAGCAAGAATAATAAT-A-G
1 ATAATAAATAATAG-AAGAATAATAATAACG
* *
3160056 -TAAT-GATAATAGAAG-ATAATAATAGTACT
1 ATAATAAATAATAGAAGAATAATAATA--ACG
3160085 ATAATAAATAATA
1 ATAATAAATAATA
3160098 ATAGATTAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 17
0.75 0.04 0.22
Matches are distributed among these distances:
25 8 0.14
26 3 0.05
27 7 0.12
28 5 0.08
29 1 0.02
30 10 0.17
31 23 0.39
32 1 0.02
33 1 0.02
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.29
Consensus pattern (30 bp):
ATAATAAATAATAGAAGAATAATAATAACG
Found at i:3167282 original size:32 final size:33
Alignment explanation
Indices: 3167241--3167316 Score: 109
Period size: 32 Copynumber: 2.3 Consensus size: 33
3167231 GAGTGGGGTT
*
3167241 TATAATATATATATGCGTGTATGGGTGTTATA-
1 TATAATATATATATGCGTGCATGGGTGTTATAG
* *
3167273 TATAATATATATTTGGGTGCATGGGTGTTATATG
1 TATAATATATATATGCGTGCATGGGTGTTATA-G
3167307 TATAATATAT
1 TATAATATAT
3167317 CTGCGTGGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
32 29 0.74
34 10 0.26
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.45
Consensus pattern (33 bp):
TATAATATATATATGCGTGCATGGGTGTTATAG
Found at i:3168378 original size:17 final size:17
Alignment explanation
Indices: 3168358--3168438 Score: 58
Period size: 17 Copynumber: 4.8 Consensus size: 17
3168348 ATGATGAAGC
3168358 ATGAACTGTTATTCGGT
1 ATGAACTGTTATTCGGT
* *
3168375 ATGAACTGATATTTC-AT
1 ATGAACTGTTA-TTCGGT
* * *
3168392 ATGAACTATTATTCTGC
1 ATGAACTGTTATTCGGT
* * *
3168409 ATGAGCTGTCATTTGGT
1 ATGAACTGTTATTCGGT
3168426 -TAGAACTGTTATT
1 AT-GAACTGTTATT
3168439 TCATATGAAC
Statistics
Matches: 47, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
16 4 0.09
17 40 0.85
18 3 0.06
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (17 bp):
ATGAACTGTTATTCGGT
Found at i:3168448 original size:17 final size:17
Alignment explanation
Indices: 3168358--3168448 Score: 55
Period size: 17 Copynumber: 5.4 Consensus size: 17
3168348 ATGATGAAGC
*
3168358 ATGAACTGTTA-TTCGGT
1 ATGAACTGTTATTTC-AT
*
3168375 ATGAACTGATATTTCAT
1 ATGAACTGTTATTTCAT
*
3168392 ATGAACTATTA-TTC-T
1 ATGAACTGTTATTTCAT
* * **
3168407 GCATGAGCTGTCATTTGGT
1 --ATGAACTGTTATTTCAT
3168426 -TAGAACTGTTATTTCAT
1 AT-GAACTGTTATTTCAT
3168443 ATGAAC
1 ATGAAC
3168449 AGATGTTTGG
Statistics
Matches: 55, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
15 1 0.02
16 4 0.07
17 43 0.78
18 6 0.11
19 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.41
Consensus pattern (17 bp):
ATGAACTGTTATTTCAT
Found at i:3169868 original size:68 final size:69
Alignment explanation
Indices: 3169796--3169927 Score: 176
Period size: 68 Copynumber: 1.9 Consensus size: 69
3169786 TTTAATAGTT
* * * * * *
3169796 TTAATATTAAATTTAATTTACTACCTATCTTAAT-AGTGTTTTATTAATTTAATATTATAGTGAT
1 TTAATATTAAATATAATCTAATACCTATCTTAATAAGTATTATATTAATTTAATATTAAAGTGAT
3169860 TATC
66 TATC
** *
3169864 TTAATATTAAATATAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAAGTGA
1 TTAATATTAAATATAATCTAATACCTATCTTAATAAGTATTATATTAATTTAATATTAAAGTGA
3169928 GTAAGTTTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
68 28 0.52
69 26 0.48
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.49
Consensus pattern (69 bp):
TTAATATTAAATATAATCTAATACCTATCTTAATAAGTATTATATTAATTTAATATTAAAGTGAT
TATC
Found at i:3172039 original size:51 final size:51
Alignment explanation
Indices: 3171963--3172082 Score: 186
Period size: 51 Copynumber: 2.4 Consensus size: 51
3171953 CTCAAACTTA
* *
3171963 CTTCATACTTCATCCGGAATTATTACCTTGTTGCTCTAACTTCAACAAGAG
1 CTTCATATTTCATCCGGAATAATTACCTTGTTGCTCTAACTTCAACAAGAG
* * *
3172014 CTTCATATTTCATCCGGAATAATTACTTTGTTGCTCTAGCTTTAACAAGAG
1 CTTCATATTTCATCCGGAATAATTACCTTGTTGCTCTAACTTCAACAAGAG
*
3172065 CTTCATATTTTATCCGGA
1 CTTCATATTTCATCCGGA
3172083 TAACTTAGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (51 bp):
CTTCATATTTCATCCGGAATAATTACCTTGTTGCTCTAACTTCAACAAGAG
Found at i:3177778 original size:17 final size:16
Alignment explanation
Indices: 3177758--3177798 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
3177748 TTTTCAAAGG
3177758 CCCAAATTAACCCTAAA
1 CCCAAATTAACCCT-AA
**
3177775 CCCAAACAAACCCTAA
1 CCCAAATTAACCCTAA
3177791 CCCAAATT
1 CCCAAATT
3177799 GGCCCAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.46, C:0.39, G:0.00, T:0.15
Consensus pattern (16 bp):
CCCAAATTAACCCTAA
Found at i:3179664 original size:17 final size:18
Alignment explanation
Indices: 3179624--3179664 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
3179614 TTGTAATTTA
3179624 TTTGTATAATATTTCATC
1 TTTGTATAATATTTCATC
* *
3179642 TATGTATAA-ATTTCATG
1 TTTGTATAATATTTCATC
3179659 TTTGTA
1 TTTGTA
3179665 ACTTTGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (18 bp):
TTTGTATAATATTTCATC
Found at i:3182355 original size:23 final size:23
Alignment explanation
Indices: 3182321--3182402 Score: 101
Period size: 23 Copynumber: 3.6 Consensus size: 23
3182311 TGGCTATCCA
* *
3182321 GAGCTTCCCGATAGGCTCTTTGC
1 GAGCTTCTCGATAGGCTCTTTGT
* *
3182344 GAGCTTTTCGATAGGCTTTTTGT
1 GAGCTTCTCGATAGGCTCTTTGT
* * *
3182367 AAGCTTCCCGATAGGCTCTTCGT
1 GAGCTTCTCGATAGGCTCTTTGT
3182390 GAGCTTCTCGATA
1 GAGCTTCTCGATA
3182403 TGATTCCTTG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.35
Consensus pattern (23 bp):
GAGCTTCTCGATAGGCTCTTTGT
Found at i:3184950 original size:21 final size:22
Alignment explanation
Indices: 3184926--3184966 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
3184916 TCCCTTCAGT
3184926 GGTATCGCGATATCC-CCTCTA
1 GGTATCGCGATATCCACCTCTA
3184947 GGTATCGCGATATCCACCTC
1 GGTATCGCGATATCCACCTC
3184967 CCAAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.20, C:0.34, G:0.20, T:0.27
Consensus pattern (22 bp):
GGTATCGCGATATCCACCTCTA
Found at i:3185228 original size:11 final size:11
Alignment explanation
Indices: 3185214--3185276 Score: 58
Period size: 11 Copynumber: 5.9 Consensus size: 11
3185204 TTTTAGGTTA
3185214 GTTTTCTTTAG
1 GTTTTCTTTAG
3185225 GTTTTCTTTAG
1 GTTTTCTTTAG
* * *
3185236 TTTTTCTGTAC
1 GTTTTCTTTAG
* *
3185247 ATTTT-TCTAG
1 GTTTTCTTTAG
*
3185257 G-GTTCTTTAG
1 GTTTTCTTTAG
3185267 GTTTTCTTTA
1 GTTTTCTTTA
3185277 CTTATTGTTC
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
9 2 0.05
10 8 0.20
11 30 0.75
ACGTcount: A:0.11, C:0.11, G:0.16, T:0.62
Consensus pattern (11 bp):
GTTTTCTTTAG
Found at i:3187116 original size:16 final size:19
Alignment explanation
Indices: 3187084--3187121 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
3187074 GCAATTATAA
3187084 TTAAGTTGAGAAAATT-AT
1 TTAAGTTGAGAAAATTAAT
3187102 TTAA-TTGAG-AAATTAAT
1 TTAAGTTGAGAAAATTAAT
3187119 TTA
1 TTA
3187122 GTTAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 10 0.53
18 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (19 bp):
TTAAGTTGAGAAAATTAAT
Found at i:3187128 original size:9 final size:9
Alignment explanation
Indices: 3187112--3187152 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
3187102 TTAATTGAGA
3187112 AATTAATTT
1 AATTAATTT
*
3187121 AGTTAATTT
1 AATTAATTT
3187130 AATTAATTT
1 AATTAATTT
3187139 AATTAATTT
1 AATTAATTT
3187148 -ATTAA
1 AATTAA
3187153 ATGATATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 5 0.17
9 25 0.83
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
AATTAATTT
Found at i:3187757 original size:44 final size:44
Alignment explanation
Indices: 3187707--3187792 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
3187697 CGTTTATTTG
*
3187707 AAAAAACGCCACTAAAAGT-TGGGACCATTAGCGGCGCTTTTCTC
1 AAAAAACGCCACTAAAAGTCT-GGACCATTAGCGACGCTTTTCTC
* *
3187751 AAAAAACGCCGCTAAAGGTCTGGACCATTAGCGACGCTTTTC
1 AAAAAACGCCACTAAAAGTCTGGACCATTAGCGACGCTTTTC
3187793 CCGCAAACGC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 37 0.97
45 1 0.03
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (44 bp):
AAAAAACGCCACTAAAAGTCTGGACCATTAGCGACGCTTTTCTC
Found at i:3187841 original size:10 final size:10
Alignment explanation
Indices: 3187828--3187897 Score: 52
Period size: 10 Copynumber: 6.8 Consensus size: 10
3187818 AAATTTAAAA
3187828 AAAATATTAT
1 AAAATATTAT
3187838 AAAATATTAT
1 AAAATATTAT
* *
3187848 AAAAGTCTTAA
1 AAAA-TATTAT
* *
3187859 AAAATATAAA
1 AAAATATTAT
*
3187869 AAAAAATTA-
1 AAAATATTAT
*
3187878 AAATTCATTAT
1 AAAAT-ATTAT
3187889 CAAAATATT
1 -AAAATATT
3187898 GAAAAGAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
9 3 0.06
10 29 0.62
11 11 0.23
12 4 0.09
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.33
Consensus pattern (10 bp):
AAAATATTAT
Found at i:3187994 original size:16 final size:16
Alignment explanation
Indices: 3187969--3187999 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3187959 ACTACACCAG
*
3187969 AAATATAACAAAATAC
1 AAATAGAACAAAATAC
3187985 AAATAGAACAAAATA
1 AAATAGAACAAAATA
3188000 ATGATAGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.03, T:0.16
Consensus pattern (16 bp):
AAATAGAACAAAATAC
Found at i:3188489 original size:12 final size:12
Alignment explanation
Indices: 3188472--3188504 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
3188462 TTGAAGAACC
3188472 ATTAATCATGTT
1 ATTAATCATGTT
3188484 ATTAATCATGTT
1 ATTAATCATGTT
3188496 ATTAATCAT
1 ATTAATCAT
3188505 ATATGCAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (12 bp):
ATTAATCATGTT
Found at i:3194397 original size:15 final size:15
Alignment explanation
Indices: 3194350--3194398 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
3194340 CCCCTATCAC
*
3194350 CACCTCTTCCACCAC
1 CACCTCTTCCACCAT
* *
3194365 CTCCTCTTCC-TC-T
1 CACCTCTTCCACCAT
3194378 C-CCTCTTCCACCAT
1 CACCTCTTCCACCAT
3194392 CACCTCT
1 CACCTCT
3194399 GCCCCTAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 8 0.30
13 2 0.07
14 3 0.11
15 14 0.52
ACGTcount: A:0.12, C:0.57, G:0.00, T:0.31
Consensus pattern (15 bp):
CACCTCTTCCACCAT
Found at i:3195575 original size:21 final size:21
Alignment explanation
Indices: 3195521--3195588 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
3195511 CCATAAACAC
*
3195521 TAAACTCTAAACCCTTAACGCT
1 TAAACTC-CAACCCTTAACGCT
*
3195543 T-AACCCCAAACCCTTATAC-CT
1 TAAACTCC-AACCCTTA-ACGCT
* *
3195564 TAAACTCCAA-CCATAACCCT
1 TAAACTCCAACCCTTAACGCT
3195584 TAAAC
1 TAAAC
3195589 CCTAAATCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
19 2 0.05
20 11 0.29
21 17 0.45
22 8 0.21
ACGTcount: A:0.38, C:0.37, G:0.01, T:0.24
Consensus pattern (21 bp):
TAAACTCCAACCCTTAACGCT
Found at i:3195608 original size:21 final size:22
Alignment explanation
Indices: 3195575--3195620 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
3195565 AAACTCCAAC
3195575 CATAACCCTTAAACCC-TAAAT
1 CATAACCCTTAAACCCATAAAT
*
3195596 CATAATCCC-TAAACCCATAATT
1 CATAA-CCCTTAAACCCATAAAT
3195618 CAT
1 CAT
3195621 CATAAACCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (22 bp):
CATAACCCTTAAACCCATAAAT
Found at i:3195680 original size:21 final size:21
Alignment explanation
Indices: 3195654--3195738 Score: 98
Period size: 21 Copynumber: 3.9 Consensus size: 21
3195644 ACTCTTAAAC
*
3195654 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
* *
3195675 CTTAAACCATAGTTAACTCATAAAC
1 CTTAAACCATA---AAC-CATATAT
*
3195700 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
3195721 CTTAAACCATAAACCATA
1 CTTAAACCATAAACCATA
3195739 AACTATAATG
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
21 32 0.60
22 3 0.06
24 3 0.06
25 15 0.28
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (21 bp):
CTTAAACCATAAACCATATAT
Found at i:3195681 original size:46 final size:46
Alignment explanation
Indices: 3195630--3195731 Score: 179
Period size: 46 Copynumber: 2.2 Consensus size: 46
3195620 TCATAAACCT
*
3195630 TTAAA-CACTAGTTAACTCTTAAACCTTAAACCCTAAACCATATATC
1 TTAAACCA-TAGTTAACTCATAAACCTTAAACCCTAAACCATATATC
3195676 TTAAACCATAGTTAACTCATAAACCTTAAACCCTAAACCATATATC
1 TTAAACCATAGTTAACTCATAAACCTTAAACCCTAAACCATATATC
3195722 TTAAACCATA
1 TTAAACCATA
3195732 AACCATAAAC
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
46 52 0.96
47 2 0.04
ACGTcount: A:0.43, C:0.25, G:0.02, T:0.29
Consensus pattern (46 bp):
TTAAACCATAGTTAACTCATAAACCTTAAACCCTAAACCATATATC
Found at i:3195703 original size:25 final size:25
Alignment explanation
Indices: 3195620--3195707 Score: 87
Period size: 25 Copynumber: 3.6 Consensus size: 25
3195610 CCATAATTCA
3195620 TCATAAACCTTTAAA-CACTAGTTAAC
1 TCATAAACC-TTAAACCA-TAGTTAAC
* *
3195646 TCTTAAACCTTAAACCCTA---AAC
1 TCATAAACCTTAAACCATAGTTAAC
* *
3195668 -CATATATCTTAAACCATAGTTAAC
1 TCATAAACCTTAAACCATAGTTAAC
3195692 TCATAAACCTTAAACC
1 TCATAAACCTTAAACC
3195708 CTAAACCATA
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
21 14 0.29
22 3 0.06
24 3 0.06
25 20 0.41
26 9 0.18
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (25 bp):
TCATAAACCTTAAACCATAGTTAAC
Found at i:3195746 original size:7 final size:7
Alignment explanation
Indices: 3195649--3195746 Score: 61
Period size: 7 Copynumber: 13.4 Consensus size: 7
3195639 AGTTAACTCT
*
3195649 TAAACCT
1 TAAACCA
*
3195656 TAAACCC
1 TAAACCA
3195663 TAAACCA
1 TAAACCA
* * *
3195670 TATATCT
1 TAAACCA
3195677 TAAACCA
1 TAAACCA
3195684 TAGTTAACTCA
1 TA---AAC-CA
*
3195695 TAAACCT
1 TAAACCA
*
3195702 TAAACCC
1 TAAACCA
3195709 TAAACCA
1 TAAACCA
* * *
3195716 TATATCT
1 TAAACCA
3195723 TAAACCA
1 TAAACCA
3195730 TAAACCA
1 TAAACCA
*
3195737 TAAACTA
1 TAAACCA
3195744 TAA
1 TAA
3195747 TGATAATTAA
Statistics
Matches: 69, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
7 59 0.86
8 3 0.04
10 3 0.04
11 4 0.06
ACGTcount: A:0.47, C:0.26, G:0.01, T:0.27
Consensus pattern (7 bp):
TAAACCA
Found at i:3196039 original size:82 final size:81
Alignment explanation
Indices: 3195880--3196088 Score: 226
Period size: 82 Copynumber: 2.6 Consensus size: 81
3195870 GTTATATGAC
* * *
3195880 TTTTAGTGGCGTTTTGCGAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTGCCAAAAGC
1 TTTTAGTGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGATTTTTAGCGGCGTTTTACCAAAAGC
**
3195945 GTTGCTAATGCTCTGTT
66 GCCGCTAATGCTCTG-T
* * * *
3195962 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCT-ATTTTTCGCGGCATTTTTTACTAAAA
1 TTTTAGTGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGATTTTTAGCGGC--GTTTTACCAAAA
*
3196026 -CGCCGCTATTGCTCTGT
64 GCGCCGCTAATGCTCTGT
** * * *
3196043 TTTTAGTGGCGTTTTTGGTAAAA-CGCCGCTATTGCTATGAGTTTTA
1 TTTTAGTGGCG-TTTTGCCAAAAGCGCCGCTAATGCTCTGATTTTTA
3196089 CAATTTTTAC
Statistics
Matches: 106, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
81 34 0.32
82 63 0.59
83 9 0.08
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.38
Consensus pattern (81 bp):
TTTTAGTGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGATTTTTAGCGGCGTTTTACCAAAAGC
GCCGCTAATGCTCTGT
Found at i:3196078 original size:40 final size:40
Alignment explanation
Indices: 3195880--3196057 Score: 214
Period size: 41 Copynumber: 4.4 Consensus size: 40
3195870 GTTATATGAC
* *
3195880 TTTTAGTGGCGTTTTGCGAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCT-GT
**
3195921 TTTTAGCGGCGTTTTGCCAAAAGCGTTGCTAATGCTCTGTT
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTG-T
*
3195962 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTAT
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGT
* * * * *
3196002 TTTTCGCGGCATTTTTTACTAAAA-CGCCGCTATTGCTCTGT
1 TTTTAGCGGC--GTTTTGCCAAAAGCGCCGCTAATGCTCTGT
*
3196043 TTTTAGTGGCGTTTT
1 TTTTAGCGGCGTTTT
3196058 TGGTAAAACG
Statistics
Matches: 118, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
39 4 0.03
40 11 0.09
41 94 0.80
42 9 0.08
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.39
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGT
Found at i:3198828 original size:36 final size:33
Alignment explanation
Indices: 3198772--3198837 Score: 80
Period size: 36 Copynumber: 1.9 Consensus size: 33
3198762 CATATTTCAA
3198772 TTATTATTATTAATTAATTTT-AAACTATACATT
1 TTATTATTATTAATTAATTTTCAAA-TATACATT
*
3198805 TTATTATTTATTATATGTCATTTTCAAATATAC
1 TTATTA-TTATTA-AT-TAATTTTCAAATATAC
3198838 TTTAACATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
33 6 0.21
34 6 0.21
35 2 0.07
36 11 0.39
37 3 0.11
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.55
Consensus pattern (33 bp):
TTATTATTATTAATTAATTTTCAAATATACATT
Found at i:3199812 original size:12 final size:12
Alignment explanation
Indices: 3199795--3199820 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3199785 AAAACTCTCT
3199795 CTCGCTCGTTCG
1 CTCGCTCGTTCG
3199807 CTCGCTCGTTCG
1 CTCGCTCGTTCG
3199819 CT
1 CT
3199821 TGTTCCTCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.42, G:0.23, T:0.35
Consensus pattern (12 bp):
CTCGCTCGTTCG
Found at i:3201751 original size:40 final size:40
Alignment explanation
Indices: 3201706--3201783 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
3201696 GTAGGTCTCA
3201706 AAAATAAGTATTAATATACTTATGTTCATCTAATCTTTTC
1 AAAATAAGTATTAATATACTTATGTTCATCTAATCTTTTC
3201746 AAAATAAGTATTAATATACTTATGTTCATCTAATCTTT
1 AAAATAAGTATTAATATACTTATGTTCATCTAATCTTT
3201784 ACTTTGTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (40 bp):
AAAATAAGTATTAATATACTTATGTTCATCTAATCTTTTC
Found at i:3202788 original size:32 final size:33
Alignment explanation
Indices: 3202745--3202824 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 33
3202735 TTGTCTTGAT
*
3202745 GGAACTGTTGCTTACTGT-TGAGT-TTCTTCCAG
1 GGAACTGTTGCTTACTGTCTGA-TCATCTTCCAG
* * *
3202777 GTAACTGTTGCTTA-TTTCTTATCATCTTCCAG
1 GGAACTGTTGCTTACTGTCTGATCATCTTCCAG
3202809 GGAACTGTTGCTTACT
1 GGAACTGTTGCTTACT
3202825 ACTTACTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
31 3 0.08
32 36 0.90
33 1 0.03
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.42
Consensus pattern (33 bp):
GGAACTGTTGCTTACTGTCTGATCATCTTCCAG
Found at i:3205412 original size:17 final size:17
Alignment explanation
Indices: 3205372--3205406 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3205362 GTATTTGATG
3205372 TATTATATTTTAAAAAA
1 TATTATATTTTAAAAAA
3205389 TATTATATTTTAAAAAA
1 TATTATATTTTAAAAAA
3205406 T
1 T
3205407 TATATAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTATATTTTAAAAAA
Found at i:3231191 original size:26 final size:26
Alignment explanation
Indices: 3231155--3231223 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
3231145 CTCAATAGAA
*
3231155 CTTACTATCCATCAGCTCAGGAGGAG
1 CTTACTGTCCATCAGCTCAGGAGGAG
*
3231181 CTTACTGTCCATCAGCTCGGGAGGAG
1 CTTACTGTCCATCAGCTCAGGAGGAG
*
3231207 CTTACTGTTCAT-AGCTC
1 CTTACTGTCCATCAGCTC
3231224 GAAAGAGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 5 0.12
26 35 0.88
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.28
Consensus pattern (26 bp):
CTTACTGTCCATCAGCTCAGGAGGAG
Found at i:3233952 original size:43 final size:43
Alignment explanation
Indices: 3233896--3234015 Score: 127
Period size: 43 Copynumber: 2.8 Consensus size: 43
3233886 ACTGAGATGT
* * *
3233896 GATTACATGTAAGACCATGTCTGGGACATTGGCATTG-T-ATT
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAATC
* * * *
3233937 GTAATTACGTTTAAGACCATGTTTGGGGCATTAGCATCGTTAATC
1 G--ATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAATC
* *
3233982 GATTACGTGTAAGACCTTGTCTGGGACAGTGGCA
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCA
3234016 CTGATATGTG
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
41 1 0.02
43 57 0.92
44 1 0.02
45 3 0.05
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAATC
Found at i:3272983 original size:19 final size:18
Alignment explanation
Indices: 3272961--3273023 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
3272951 ACAATGTGTT
3272961 AAAATCATTAATTAAATAAA
1 AAAAT-ATTAATTAAAT-AA
**
3272981 AAAATATTTTTTAAATAA
1 AAAATATTAATTAAATAA
*
3272999 TAAAATGTTAATATAAA-AA
1 -AAAATATTAAT-TAAATAA
3273018 AAAATA
1 AAAATA
3273024 AAATAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 7 0.20
19 19 0.54
20 9 0.26
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAATATTAATTAAATAA
Found at i:3273099 original size:44 final size:44
Alignment explanation
Indices: 3273051--3273189 Score: 127
Period size: 51 Copynumber: 3.0 Consensus size: 44
3273041 TAATTTTTTT
3273051 AAAAATATTAAAATATAAAAAAAAAAAAAAAAAAAAATAAATAAA
1 AAAAATATTAAAATATAAAAAAAAAAAAAAAAAAAAATAAA-AAA
* * * *
3273096 AAAAAAAATAAATAAATAAAAAAAATAAAAAGAAAATGTAAAAAATAAAAA
1 AAAAATATTAAA-ATATAAAAAAAA-AAAAA-AAAA---AAAATA-AAAAA
* *
3273147 AAAAATA-TCAAATATTACAAAAAAAAAAAATAAAAAAATAAAA
1 AAAAATATTAAAATA-TA-AAAAAAAAAAAAAAAAAAAATAAAA
3273190 TTATTTCTGT
Statistics
Matches: 76, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
45 13 0.17
46 16 0.21
47 5 0.07
48 4 0.05
49 5 0.07
50 10 0.13
51 21 0.28
52 2 0.03
ACGTcount: A:0.82, C:0.01, G:0.01, T:0.15
Consensus pattern (44 bp):
AAAAATATTAAAATATAAAAAAAAAAAAAAAAAAAAATAAAAAA
Found at i:3273171 original size:1 final size:1
Alignment explanation
Indices: 3273067--3273151 Score: 71
Period size: 1 Copynumber: 85.0 Consensus size: 1
3273057 ATTAAAATAT
* * * * * * *
3273067 AAAAAAAAAAAAAAAAAAAAATAAATAAAAAAAAAAATAAATAAATAAAAAAAATAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*** *
3273132 TGTAAAAAATAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAA
3273152 TATCAAATAT
Statistics
Matches: 64, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.87, C:0.00, G:0.02, T:0.11
Consensus pattern (1 bp):
A
Found at i:3279361 original size:21 final size:22
Alignment explanation
Indices: 3279337--3279381 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
3279327 TATTTAACCC
*
3279337 AAAATAAATTGGATTA-AAATT
1 AAAATAAATTAGATTATAAATT
* *
3279358 AAAATTAATTATATTATAAATT
1 AAAATAAATTAGATTATAAATT
3279380 AA
1 AA
3279382 TATTCATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
AAAATAAATTAGATTATAAATT
Found at i:3280482 original size:324 final size:328
Alignment explanation
Indices: 3279877--3280527 Score: 1044
Period size: 324 Copynumber: 2.0 Consensus size: 328
3279867 TCTTGATGAA
* * * *
3279877 GGTTTGAAGATTATTGATGCAAGATTCAACAATTCGATGGAAGAATGATTTAGTTGAGACTTGAT
1 GGTTTGAAGATTATTGATGAAAGATTCAACAATTCGAGGGAAGAATGATTTAATCGAGACTTGAT
* *
3279942 TTCAATTTAGGATTTAAAAGATTAATTTTCCAGCAATGAAGGTAAAATATTTTATAAAAAGAAAA
66 TTCAATTTAGGATTCAAAAGATTAATTTTCCAGCAATGAAGGCAAAATATTTTATAAAAAGAAAA
* *
3280007 GAGGGAAAATAAAAGAAAGAAAGGATTTTAAAGAGAAGAGAAAAGAATTCAATTTAGGGATGGAA
131 GAGAGAAAAT--AAGAAAGAAAGGATTTTAAAGAGAAGAGAAAAGAATTCAATTTAGGGATGAAA
* *
3280072 AGGATTCAAAATCATAGTATAAGTAGGGGAAGTTAATAAATTCCTAGGTTTTCAAAATTGGAGGG
194 AGGATTCAAAATCATAGTATAACTAGGGGAAGTTAATAAATTCCTAAGTTTTCAAAATTGGAGGG
* * *
3280137 TTGATTGGGAAAATAACCCATCTACTAAAAATTAAGAAAATGAGAGGGGGAATGGCACGCTTTGA
259 ATGATTAGGAAAATAACCCATCTACCAAAAATTAAGAAAATGAGAGGGGGAATGGCACGCTTTGA
3280202 ACATG
324 ACATG
*
3280207 GGTTTGAAGA-TATTGATGAAAGATTCAACAATTC-AGGGGAAGAATGATTTAATCGGGACTTGA
1 GGTTTGAAGATTATTGATGAAAGATTCAACAATTCGA-GGGAAGAATGATTTAATCGAGACTTGA
3280270 TTTCAATTTAGGATTCAAAAGATTAAGTTTT-CAGCAATGAAGGCAAAATATTTTAT-AAAAGAA
65 TTTCAATTTAGGATTCAAAAGATTAA-TTTTCCAGCAATGAAGGCAAAATATTTTATAAAAAGAA
* *
3280333 GAGAGAGAAAAT-A-AAAGAAAGGATTTTAAAGAGAAGAGAAAAGAATTCAATTTAGGGTTGAAA
129 AAGAGAGAAAATAAGAAAGAAAGGATTTTAAAGAGAAGAGAAAAGAATTCAATTTAGGGATGAAA
3280396 AGGATTCAAAATCATAGTATAACTAGGGGAAGTTAATAAATTCCTAAGTTTTCAAAATTGGAGGG
194 AGGATTCAAAATCATAGTATAACTAGGGGAAGTTAATAAATTCCTAAGTTTTCAAAATTGGAGGG
* * * *
3280461 ATGATTAGGCAAATAACCCATCTACCGAAAATTAAGAAAATGGGAGGGGGAATGGCATGCTTTGA
259 ATGATTAGGAAAATAACCCATCTACCAAAAATTAAGAAAATGAGAGGGGGAATGGCACGCTTTGA
3280526 AC
324 AC
3280528 CTAGAAGCAA
Statistics
Matches: 299, Mismatches: 20, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
324 171 0.57
325 1 0.00
328 18 0.06
329 95 0.32
330 14 0.05
ACGTcount: A:0.43, C:0.08, G:0.23, T:0.27
Consensus pattern (328 bp):
GGTTTGAAGATTATTGATGAAAGATTCAACAATTCGAGGGAAGAATGATTTAATCGAGACTTGAT
TTCAATTTAGGATTCAAAAGATTAATTTTCCAGCAATGAAGGCAAAATATTTTATAAAAAGAAAA
GAGAGAAAATAAGAAAGAAAGGATTTTAAAGAGAAGAGAAAAGAATTCAATTTAGGGATGAAAAG
GATTCAAAATCATAGTATAACTAGGGGAAGTTAATAAATTCCTAAGTTTTCAAAATTGGAGGGAT
GATTAGGAAAATAACCCATCTACCAAAAATTAAGAAAATGAGAGGGGGAATGGCACGCTTTGAAC
ATG
Found at i:3280768 original size:15 final size:16
Alignment explanation
Indices: 3280743--3280775 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3280733 TTAATGTAAC
3280743 AAATATTTTAATATGT
1 AAATATTTTAATATGT
3280759 AAAT-TTTTAATATGT
1 AAATATTTTAATATGT
3280774 AA
1 AA
3280776 TATAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
AAATATTTTAATATGT
Found at i:3282756 original size:87 final size:86
Alignment explanation
Indices: 3282639--3282810 Score: 247
Period size: 87 Copynumber: 2.0 Consensus size: 86
3282629 GCCCCTCCTT
* * *
3282639 TTTTTTTTGCACTCAATTGAGAACTTGAACTTTCAAAATACATCAAAAAGGCCCTCAAACTTCTT
1 TTTTTTTTGCACTCAATTGAGAACTTGAACTTTCAAAATACATAAAAAAGACCCTCAAAATTCTT
3282704 CAAAAAAAAGCAATTAAACCCCA
66 C--AAAAAAGCAATTAAACCCCA
* * * *
3282727 TTTTTTTT-CACTCAATTGGGTACTTGAACTTTCAAAATATATAAAAAAGACCCTCAAAATTTTT
1 TTTTTTTTGCACTCAATTGAGAACTTGAACTTTCAAAATACATAAAAAAGACCCTCAAAATTCTT
*
3282791 CAAAAAAGCAATTAAGCCCC
66 CAAAAAAGCAATTAAACCCC
3282811 TGCTCTTAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
85 18 0.24
87 50 0.66
88 8 0.11
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (86 bp):
TTTTTTTTGCACTCAATTGAGAACTTGAACTTTCAAAATACATAAAAAAGACCCTCAAAATTCTT
CAAAAAAGCAATTAAACCCCA
Found at i:3283299 original size:23 final size:21
Alignment explanation
Indices: 3283248--3283303 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 21
3283238 TATAAAAAAA
3283248 TTACAATTTTT-TATATATTT
1 TTACAATTTTTATATATATTT
*
3283268 TTACGATTTTTATATATATATT
1 TTACAATTTTTATATATAT-TT
*
3283290 TTTCTAATTTTTAT
1 TTAC-AATTTTTAT
3283304 TATTTGAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.33
21 7 0.23
22 5 0.17
23 8 0.27
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (21 bp):
TTACAATTTTTATATATATTT
Found at i:3283376 original size:47 final size:47
Alignment explanation
Indices: 3283273--3283379 Score: 110
Period size: 47 Copynumber: 2.2 Consensus size: 47
3283263 TATTTTTACG
* *
3283273 ATTTTTATATATATATTTTTCTAATTTTTATTATTTGAATTTTTTATTA
1 ATTTTTA-ATA-ATATTTATCTAATTTTAATTATTTGAATTTTTTATTA
** * *
3283322 AAATTTAATAATATTTAT-TGATTTTAATTTTTTGTAATTTTTT-TCTA
1 ATTTTTAATAATATTTATCTAATTTTAATTATTTG-AATTTTTTAT-TA
3283369 ATTTTTAATAA
1 ATTTTTAATAA
3283380 GAGTAGGGGC
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
46 14 0.29
47 26 0.54
48 3 0.06
49 5 0.10
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (47 bp):
ATTTTTAATAATATTTATCTAATTTTAATTATTTGAATTTTTTATTA
Found at i:3290895 original size:13 final size:13
Alignment explanation
Indices: 3290877--3290901 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3290867 GTCCTGGTGA
3290877 TCTAGTAAAACAC
1 TCTAGTAAAACAC
3290890 TCTAGTAAAACA
1 TCTAGTAAAACA
3290902 AAAGTTTCCA
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:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (13 bp):
TCTAGTAAAACAC
Found at i:3293421 original size:18 final size:20
Alignment explanation
Indices: 3293398--3293435 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
3293388 ATCTCCACCT
3293398 TTAGATTT-TT-TTGCCTAA
1 TTAGATTTATTCTTGCCTAA
3293416 TTAGATTTATTCTTGCCTAA
1 TTAGATTTATTCTTGCCTAA
3293436 ACTTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 2 0.11
20 8 0.44
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.53
Consensus pattern (20 bp):
TTAGATTTATTCTTGCCTAA
Found at i:3293785 original size:111 final size:112
Alignment explanation
Indices: 3293591--3293801 Score: 361
Period size: 111 Copynumber: 1.9 Consensus size: 112
3293581 CCTAACCTTC
*
3293591 TTTTTTGGCCTAATAACAAATTCAACCTTCCAATATTTCTAATTTTATTAATTTGATCCTAAATC
1 TTTTTTGGCCTAATAACAAATTCAACCTTCAAATATTTCTAATTTTATTAATTTGATCCTAAATC
* *
3293656 TAAAGAAATCAACGAATTTAG-CCTTAATGTTTTATATAGTTCACTT
66 TAAAGAAACCAAAGAATTTAGCCCTTAATGTTTTATATAGTTCACTT
* *
3293702 TTTTTTGGCCTAATAACAAATTTAACCTTCAAATATTTCTAATTTTATTAATTTGATCCTACATC
1 TTTTTTGGCCTAATAACAAATTCAACCTTCAAATATTTCTAATTTTATTAATTTGATCCTAAATC
*
3293767 TAAAGCAACCAAAGAATTTAGCCCTTAATGTTTTA
66 TAAAGAAACCAAAGAATTTAGCCCTTAATGTTTTA
3293802 ATTCTAATTC
Statistics
Matches: 93, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
111 80 0.86
112 13 0.14
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.42
Consensus pattern (112 bp):
TTTTTTGGCCTAATAACAAATTCAACCTTCAAATATTTCTAATTTTATTAATTTGATCCTAAATC
TAAAGAAACCAAAGAATTTAGCCCTTAATGTTTTATATAGTTCACTT
Found at i:3293984 original size:15 final size:15
Alignment explanation
Indices: 3293964--3294016 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
3293954 CATTAAAGAA
3293964 TATTTTTTAAAAATG
1 TATTTTTTAAAAATG
*
3293979 TATTTTTCT-TAAATG
1 TATTTTT-TAAAAATG
*
3293994 TATATTTTTAAAATATC
1 TAT-TTTTTAAAA-ATG
3294011 TATTTT
1 TATTTT
3294017 AGAATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 16 0.52
16 10 0.32
17 5 0.16
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (15 bp):
TATTTTTTAAAAATG
Found at i:3294124 original size:61 final size:62
Alignment explanation
Indices: 3294028--3294193 Score: 176
Period size: 61 Copynumber: 2.7 Consensus size: 62
3294018 GAATTAAAAT
* * ** * * *
3294028 TAAATTGACAAATTTTGTAATTGTTGAGTGATAAATTTATT-GAGTTTTTTAACATTTAA-AC
1 TAAATTGACAAATTTTGTAAATATTGAAAGTTAAATTTATTAAACTTTTTT-ACATTTAAGAC
* * *
3294089 TACAA-TGACAAATTTTGTAAATATTGAAAGTTAAATTTGTTAAACTTTTTTATATTTAAGAT
1 TA-AATTGACAAATTTTGTAAATATTGAAAGTTAAATTTATTAAACTTTTTTACATTTAAGAC
* *
3294151 TAAATTGATAAATTGTGTAAATATTGAAAAGTTAAATTTATTA
1 TAAATTGACAAATTTTGTAAATATTG-AAAGTTAAATTTATTA
3294194 TTAGATCAAT
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
61 41 0.47
62 31 0.36
63 15 0.17
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (62 bp):
TAAATTGACAAATTTTGTAAATATTGAAAGTTAAATTTATTAAACTTTTTTACATTTAAGAC
Found at i:3294667 original size:13 final size:13
Alignment explanation
Indices: 3294649--3294673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3294639 CTAAAAAAAA
3294649 ATCATCTAATTTC
1 ATCATCTAATTTC
3294662 ATCATCTAATTT
1 ATCATCTAATTT
3294674 AAATATAGTC
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:0.00, T:0.48
Consensus pattern (13 bp):
ATCATCTAATTTC
Found at i:3312011 original size:15 final size:16
Alignment explanation
Indices: 3311986--3312018 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3311976 TTAATGTAAC
3311986 AAATATTTTAATATGT
1 AAATATTTTAATATGT
3312002 AAAT-TTTTAATATGT
1 AAATATTTTAATATGT
3312017 AA
1 AA
3312019 TATAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
AAATATTTTAATATGT
Found at i:3313775 original size:74 final size:78
Alignment explanation
Indices: 3313647--3313795 Score: 191
Period size: 74 Copynumber: 1.9 Consensus size: 78
3313637 GCCCCTCCTT
* *
3313647 TTTTTTGCACTCAATTGAGAACTTGAACTTTCAAATACATCAAAAAGGCCTC-AAACTTTCAAAA
1 TTTTTTGCACTCAATTGAGAACTTGAAC-TTCAAATACATAAAAAAGACCTCAAAACTTTC-AAA
3313711 AAAGCAATTAACCCA
64 AAAGCAATTAACCCA
* * * *
3313726 TTTTTT-CACTCAA-TGGGTACTTGAAC-TCAAA-ATATAAAAAAGACCTCAAAATTTTCAAAAA
1 TTTTTTGCACTCAATTGAGAACTTGAACTTCAAATACATAAAAAAGACCTCAAAACTTTCAAAAA
3313787 AGCAATTAA
66 AGCAATTAA
3313796 GCCCTGCTCT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
74 27 0.43
75 12 0.19
77 11 0.17
78 7 0.11
79 6 0.10
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.29
Consensus pattern (78 bp):
TTTTTTGCACTCAATTGAGAACTTGAACTTCAAATACATAAAAAAGACCTCAAAACTTTCAAAAA
AGCAATTAACCCA
Found at i:3313876 original size:17 final size:17
Alignment explanation
Indices: 3313819--3313876 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
3313809 AAAATTAGAA
*
3313819 AAAAATTATAAAAATA-
1 AAAATTTATAAAAATAT
3313835 AAAATTT-TAGAAACATAT
1 AAAATTTATA-AAA-ATAT
* *
3313853 TAGATTTATAAAAATAT
1 AAAATTTATAAAAATAT
3313870 AAAATTT
1 AAAATTT
3313877 TGAAATATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
15 2 0.06
16 9 0.27
17 12 0.36
18 8 0.24
19 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAATTTATAAAAATAT
Found at i:3313922 original size:33 final size:34
Alignment explanation
Indices: 3313885--3313952 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
3313875 TTTGAAATAT
* **
3313885 TAAAAATTATAATTTTTATAAAAATC-GAAAAAA
1 TAAAAAATATAAAATTTATAAAAATCAGAAAAAA
* *
3313918 TAAAAAATCTAAAATTTATAAAAATCATAAAAAA
1 TAAAAAATATAAAATTTATAAAAATCAGAAAAAA
3313952 T
1 T
3313953 TAATGGCCCC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 22 0.76
34 7 0.24
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (34 bp):
TAAAAAATATAAAATTTATAAAAATCAGAAAAAA
Found at i:3314236 original size:18 final size:18
Alignment explanation
Indices: 3314173--3314238 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
3314163 TATTCTATTT
3314173 ATTTTATA-ATTTTTTACG
1 ATTTTATATA-TTTTTACG
* *** *
3314191 ATTTTATAAAAAATTACA
1 ATTTTATATATTTTTACG
3314209 ATTTTTATATATTTTTACG
1 A-TTTTATATATTTTTACG
3314228 ATTTTATATAT
1 ATTTTATATAT
3314239 ATATTTTTCT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
18 23 0.62
19 14 0.38
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (18 bp):
ATTTTATATATTTTTACG
Found at i:3314253 original size:22 final size:22
Alignment explanation
Indices: 3314214--3314256 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3314204 TTACAATTTT
*
3314214 TATATATTTTTACGATTTTATA
1 TATATATTTTTACAATTTTATA
3314236 TATATATTTTT-CTAATTTTAT
1 TATATATTTTTAC-AATTTTAT
3314257 TATTTGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (22 bp):
TATATATTTTTACAATTTTATA
Found at i:3321799 original size:13 final size:13
Alignment explanation
Indices: 3321781--3321805 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3321771 GTCCTGGTGA
3321781 TCTAGTAAAACAC
1 TCTAGTAAAACAC
3321794 TCTAGTAAAACA
1 TCTAGTAAAACA
3321806 AAAGTTTCCA
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:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (13 bp):
TCTAGTAAAACAC
Found at i:3324690 original size:112 final size:112
Alignment explanation
Indices: 3324493--3324705 Score: 372
Period size: 112 Copynumber: 1.9 Consensus size: 112
3324483 CCTAACCTTC
*
3324493 TTTTTTTGGCCTAATAACAAATTCAACCTTCCAATATTTCTAATTTTATTAATTTGATCCTAAAT
1 TTTTTTTGGCCTAATAACAAATTCAACCTTCAAATATTTCTAATTTTATTAATTTGATCCTAAAT
* *
3324558 CTAAAGAAATCAACGAATTTAGCCCTTAATGTTTTATATAGTTCACT
66 CTAAAGAAACCAAAGAATTTAGCCCTTAATGTTTTATATAGTTCACT
* *
3324605 TTTTTTTGGCCTAATAACAAATTTAACCTTCAAATATTTCTAATTTTATTAATTTGATCCTACAT
1 TTTTTTTGGCCTAATAACAAATTCAACCTTCAAATATTTCTAATTTTATTAATTTGATCCTAAAT
*
3324670 CTAAAGCAACCAAAGAATTTAGCCCTTAATGTTTTA
66 CTAAAGAAACCAAAGAATTTAGCCCTTAATGTTTTA
3324706 ATTCTAATTC
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 95 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (112 bp):
TTTTTTTGGCCTAATAACAAATTCAACCTTCAAATATTTCTAATTTTATTAATTTGATCCTAAAT
CTAAAGAAACCAAAGAATTTAGCCCTTAATGTTTTATATAGTTCACT
Found at i:3324888 original size:15 final size:15
Alignment explanation
Indices: 3324868--3324919 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 15
3324858 CATTAAAGAA
3324868 TATTTTTTAAAAATG
1 TATTTTTTAAAAATG
3324883 TATTTTCTT--AAATG
1 TATTTT-TTAAAAATG
*
3324897 TATATTTTTAAAATATC
1 TAT-TTTTTAAAA-ATG
3324914 TATTTT
1 TATTTT
3324920 AGAATTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
14 10 0.32
15 9 0.29
16 7 0.23
17 5 0.16
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (15 bp):
TATTTTTTAAAAATG
Found at i:3325027 original size:61 final size:62
Alignment explanation
Indices: 3324931--3325096 Score: 176
Period size: 61 Copynumber: 2.7 Consensus size: 62
3324921 GAATTAAAAT
* * ** * * *
3324931 TAAATTGACAAATTTTGTAATTGTTGAGTGATAAATTTATT-GAGTTTTTTAACATTTAA-AC
1 TAAATTGACAAATTTTGTAAATATTGAAAGTTAAATTTATTAAACTTTTTT-ACATTTAAGAC
* * *
3324992 TACAA-TGACAAATTTTGTAAATATTGAAAGTTAAATTTGTTAAACTTTTTTATATTTAAGAT
1 TA-AATTGACAAATTTTGTAAATATTGAAAGTTAAATTTATTAAACTTTTTTACATTTAAGAC
* *
3325054 TAAATTGATAAATTGTGTAAATATTGAAAAGTTAAATTTATTA
1 TAAATTGACAAATTTTGTAAATATTG-AAAGTTAAATTTATTA
3325097 TTAGATCAAT
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
61 41 0.47
62 31 0.36
63 15 0.17
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (62 bp):
TAAATTGACAAATTTTGTAAATATTGAAAGTTAAATTTATTAAACTTTTTTACATTTAAGAC
Found at i:3325572 original size:13 final size:13
Alignment explanation
Indices: 3325554--3325578 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3325544 TAAAAAAAAA
3325554 ATCATCTAATTTC
1 ATCATCTAATTTC
3325567 ATCATCTAATTT
1 ATCATCTAATTT
3325579 AAATATAGTC
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:0.00, T:0.48
Consensus pattern (13 bp):
ATCATCTAATTTC
Found at i:3331895 original size:12 final size:13
Alignment explanation
Indices: 3331880--3331908 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3331870 ATATATTTTT
3331880 ATATAAAAAA-TA
1 ATATAAAAAATTA
3331892 ATATAAAAAATTA
1 ATATAAAAAATTA
3331905 ATAT
1 ATAT
3331909 GGACGGACCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATAAAAAATTA
Found at i:3333136 original size:99 final size:99
Alignment explanation
Indices: 3332956--3333139 Score: 257
Period size: 99 Copynumber: 1.9 Consensus size: 99
3332946 AAGCAAAGCC
* *
3332956 ATGGAAGTGGGAGGAAATCGGATGATGAAGATGAAGGGTATAAGAAATCTAGTTATAGGAAATCG
1 ATGGAAGTGGAAGGAAATCGGATGATGAAGATGAAGGGTATAAGAAATCGAGTTATAGGAAATCG
* **
3333021 AGTTATGATAGATCAGATGAAAGAGAAGAAGGAT
66 AGTGACAATAGATCAGATGAAAGAGAAGAAGGAT
* *
3333055 ATGGAGGTGGAAGGAAATCGGATGATGAAGATGAAGGGTATAAGAAGTCGAGTTATAGAAGAAAT
1 ATGGAAGTGGAAGGAAATCGGATGATGAAGATGAAGGGTATAAGAAATCGAGTTATAG--GAAAT
3333120 -G-GTGACAAT-GATTCAGATGA
64 CGAGTGACAATAGA-TCAGATGA
3333140 TGAAAGGAGG
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
98 2 0.03
99 67 0.89
100 1 0.01
101 5 0.07
ACGTcount: A:0.41, C:0.04, G:0.33, T:0.21
Consensus pattern (99 bp):
ATGGAAGTGGAAGGAAATCGGATGATGAAGATGAAGGGTATAAGAAATCGAGTTATAGGAAATCG
AGTGACAATAGATCAGATGAAAGAGAAGAAGGAT
Found at i:3336520 original size:18 final size:18
Alignment explanation
Indices: 3336497--3336532 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3336487 TCTTTTACAA
3336497 ATATATATATATAATCAT
1 ATATATATATATAATCAT
*
3336515 ATATATATATATAGTCAT
1 ATATATATATATAATCAT
3336533 TATCAGTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (18 bp):
ATATATATATATAATCAT
Found at i:3338216 original size:81 final size:82
Alignment explanation
Indices: 3338124--3338327 Score: 193
Period size: 82 Copynumber: 2.5 Consensus size: 82
3338114 AATATTATAC
* * * *
3338124 ATTAGCGGCGTTTGAACCA-AAACGCCACTATAAGTC-GAGAAAT-AGCAACA-TTTTCGGAAAA
1 ATTAGCGGCGTTT-AACAAGAAACGCCACCAAAAGTCTGAGAAATCA-CAACATTTTTC-CAAAA
3338185 ACGCCGCCAAAAGTCTGAGA
63 ACGCCGCCAAAAGTCTGAGA
** ** * *
3338205 ATTAGCGGCGTTTTTCAAGAAACGCTGCCAAAAGTCTGAGAATTCACGACATTTTTCCAAAAACG
1 ATTAGCGGCGTTTAACAAGAAACGCCACCAAAAGTCTGAGAAATCACAACATTTTTCCAAAAACG
*
3338270 CCGCCAAAAGTCTGAGC
66 CCGCCAAAAGTCTGAGA
* * * *
3338287 ATTAGCGGCATTTTTTAGAA-AAACGCCGCCAAAAGTCTGAG
1 ATTAGCGGC--GTTTAACAAGAAACGCCACCAAAAGTCTGAG
3338328 CATCTAAAAA
Statistics
Matches: 102, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
80 2 0.02
81 26 0.25
82 42 0.41
83 26 0.25
84 6 0.06
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (82 bp):
ATTAGCGGCGTTTAACAAGAAACGCCACCAAAAGTCTGAGAAATCACAACATTTTTCCAAAAACG
CCGCCAAAAGTCTGAGA
Found at i:3338228 original size:41 final size:40
Alignment explanation
Indices: 3338181--3338664 Score: 355
Period size: 41 Copynumber: 12.1 Consensus size: 40
3338171 ACATTTTCGG
*
3338181 AAAAACGCCGCCAAAAGTCTGAGAATTAGCGGCGTTTTTC
1 AAAAACGCCGCCAAAAGTCTGAGAATTAGCGGCATTTTTC
* *
3338221 AAGAAACGCTGCCAAAAGTCTGAGAATTCA-CGACATTTTTCC
1 AA-AAACGCCGCCAAAAGTCTGAGAATT-AGCGGCATTTTT-C
* *
3338263 AAAAACGCCGCCAAAAGTCTGAGCATTAGCGGCATTTTTTAG
1 AAAAACGCCGCCAAAAGTCTGAGAATTAGCGGCA-TTTTT-C
*
3338305 AAAAACGCCGCCAAAAGTCT--G----A---GCA--TCT-
1 AAAAACGCCGCCAAAAGTCTGAGAATTAGCGGCATTTTTC
* * ** * *
3338333 AAAAATGCCGCCAAAGGTCTGAGCGTTAACGGCGTTTTTTAC
1 AAAAACGCCGCCAAAAGTCTGAGAATTAGCGGC-ATTTTT-C
* * * * *
3338375 CAAAACGCCGCCAAAGGTCTGAGCATTAGCGGCGTTTTTGG
1 AAAAACGCCGCCAAAAGTCTGAGAATTAGCGGCATTTTT-C
* * * * * **
3338416 AAAAGCGACGCTAAAAGTCTGAGCATTAGCGGCGTTGTTGG
1 AAAAACGCCGCCAAAAGTCTGAGAATTAGCGGCATT-TTTC
* * * * **
3338457 AAAAATGCCGCTAAAAGTCTGAGCATTAGCGGCGTTGTTGG
1 AAAAACGCCGCCAAAAGTCTGAGAATTAGCGGCATT-TTTC
* * * *
3338498 AAAAACGCCGCCAAAAGTCTGAGCATTTGCGGCGTTTTTGG
1 AAAAACGCCGCCAAAAGTCTGAGAATTAGCGGCATTTTT-C
* * * *
3338539 AAAAAAGCCGCTAAAAGTCTGAGAATTAGCGGCGTTTTTGG
1 AAAAACGCCGCCAAAAGTCTGAGAATTAGCGGCATTTTT-C
* * * *
3338580 GAAAACGCCGCCAAAAGTCTGAGTATTAGCGGCGTTTTTGG
1 AAAAACGCCGCCAAAAGTCTGAGAATTAGCGGCATTTTT-C
* * *
3338621 GAAAACGCCGCCAAAAGTCTGAGTATTAGCGGCGTTTTTC
1 AAAAACGCCGCCAAAAGTCTGAGAATTAGCGGCATTTTTC
3338661 AAAA
1 AAAA
3338665 GTCTGAGTAT
Statistics
Matches: 380, Mismatches: 43, Indels: 42
0.82 0.09 0.09
Matches are distributed among these distances:
28 18 0.05
30 3 0.01
33 3 0.01
34 1 0.00
36 1 0.00
37 2 0.01
40 11 0.03
41 281 0.74
42 60 0.16
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (40 bp):
AAAAACGCCGCCAAAAGTCTGAGAATTAGCGGCATTTTTC
Found at i:3338380 original size:70 final size:70
Alignment explanation
Indices: 3338263--3338400 Score: 204
Period size: 70 Copynumber: 2.0 Consensus size: 70
3338253 ACATTTTTCC
* *
3338263 AAAAACGCCGCCAAAAGTCTGAGCATTAGCGGCATTTTTTAGAAAAACGCCGCCAAAAGTCTGAG
1 AAAAACGCCGCCAAAAGTCTGAGCATTAACGGCATTTTTTACAAAAACGCCGCCAAAAGTCTGAG
3338328 CATCT
66 CATCT
* * * * * *
3338333 AAAAATGCCGCCAAAGGTCTGAGCGTTAACGGCGTTTTTTACCAAAACGCCGCCAAAGGTCTGAG
1 AAAAACGCCGCCAAAAGTCTGAGCATTAACGGCATTTTTTACAAAAACGCCGCCAAAAGTCTGAG
3338398 CAT
66 CAT
3338401 TAGCGGCGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (70 bp):
AAAAACGCCGCCAAAAGTCTGAGCATTAACGGCATTTTTTACAAAAACGCCGCCAAAAGTCTGAG
CATCT
Found at i:3338487 original size:82 final size:81
Alignment explanation
Indices: 3338334--3338750 Score: 464
Period size: 82 Copynumber: 5.2 Consensus size: 81
3338324 TGAGCATCTA
* * * * * *
3338334 AAAATGCCGCCAAAGGTCTGAGCGTTAACGGCGTTTTT-TACCAAAACGCCGCCAAAGGTCTGAG
1 AAAACGCCGCCAAAAGTCTGAGCATTAGCGGCGTTTTTGGA--AAAACGCCGCCAAAAGTCTGAG
3338398 CATTAGCGGCGTTTTTGG
64 CATTAGCGGCGTTTTTGG
* * * * *
3338416 AAAAGCGACGCTAAAAGTCTGAGCATTAGCGGCGTTGTTGGAAAAATGCCGCTAAAAGTCTGAGC
1 AAAA-CGCCGCCAAAAGTCTGAGCATTAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGC
*
3338481 ATTAGCGGCGTTGTTGG
65 ATTAGCGGCGTTTTTGG
* * * *
3338498 AAAAACGCCGCCAAAAGTCTGAGCATTTGCGGCGTTTTTGGAAAAAAGCCGCTAAAAGTCTGAGA
1 -AAAACGCCGCCAAAAGTCTGAGCATTAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGC
3338563 ATTAGCGGCGTTTTTGGG
65 ATTAGCGGCGTTTTT-GG
* * *
3338581 AAAACGCCGCCAAAAGTCTGAGTATTAGCGGCGTTTTTGGGAAAACGCCGCCAAAAGTCTGAGTA
1 AAAACGCCGCCAAAAGTCTGAGCATTAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGCA
3338646 TTAGCGGCGTTTTT--
66 TTAGCGGCGTTTTTGG
* * * *
3338660 ----------CAAAAGTCTGAGTATTTGCAGCGTTTTTGGAAAAACGCCGCCAAAAGTCGGAGCA
1 AAAACGCCGCCAAAAGTCTGAGCATTAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGCA
3338715 TTAGCGGCGTTTTTGG
66 TTAGCGGCGTTTTTGG
* *
3338731 AGAAACGCCGCTAAACGTCT
1 A-AAACGCCGCCAAAAGTCT
3338751 TTTTTGAATT
Statistics
Matches: 286, Mismatches: 32, Indels: 34
0.81 0.09 0.10
Matches are distributed among these distances:
69 64 0.22
82 188 0.66
83 33 0.12
84 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (81 bp):
AAAACGCCGCCAAAAGTCTGAGCATTAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGCA
TTAGCGGCGTTTTTGG
Found at i:3338553 original size:123 final size:122
Alignment explanation
Indices: 3338333--3338750 Score: 457
Period size: 123 Copynumber: 3.5 Consensus size: 122
3338323 CTGAGCATCT
* * * ** *
3338333 AAAAATGCCGCCAAAGGTCTGAGCGTTAACGGCGTTTTTTACCAAAACGCCGCCAAAGGTCTGAG
1 AAAAATGCCGCCAAAAGTCTGAGCATTAGCGGCGTTTTGGA--AAAACGCCGCCAAAAGTCTGAG
** *
3338398 CATTAGCGGCGTTTTTGGAAAAGCGACGCTAAAAGTCTGAGCATTAGCGGCGTTGTTGG
64 CATTAGCGGCGTTTTTGGAAAAAAGACGCTAAAAGTCTGAGAATTAGCGGCGTTGTTGG
*
3338457 AAAAATGCCGCTAAAAGTCTGAGCATTAGCGGCGTTGTTGGAAAAACGCCGCCAAAAGTCTGAGC
1 AAAAATGCCGCCAAAAGTCTGAGCATTAGCGGCGTT-TTGGAAAAACGCCGCCAAAAGTCTGAGC
* * *
3338522 ATTTGCGGCGTTTTTGGAAAAAAGCCGCTAAAAGTCTGAGAATTAGCGGCGTTTTTGG
65 ATTAGCGGCGTTTTTGGAAAAAAGACGCTAAAAGTCTGAGAATTAGCGGCGTTGTTGG
* * * * *
3338580 GAAAACGCCGCCAAAAGTCTGAGTATTAGCGGCGTTTTTGGGAAAACGCCGCCAAAAGTCTGAGT
1 AAAAATGCCGCCAAAAGTCTGAGCATTAGCGGCG-TTTTGGAAAAACGCCGCCAAAAGTCTGAGC
* * * *
3338645 ATTAGCGGCGTTTTT------------C-AAAAGTCTGAGTATTTGCAGCGTTTTTGG
65 ATTAGCGGCGTTTTTGGAAAAAAGACGCTAAAAGTCTGAGAATTAGCGGCGTTGTTGG
* * * * *
3338690 AAAAACGCCGCCAAAAGTCGGAGCATTAGCGGCGTTTTTGGAGAAACGCCGCTAAACGTCT
1 AAAAATGCCGCCAAAAGTCTGAGCATTAGCGGCG-TTTTGGAAAAACGCCGCCAAAAGTCT
3338751 TTTTTGAATT
Statistics
Matches: 262, Mismatches: 30, Indels: 18
0.85 0.10 0.06
Matches are distributed among these distances:
110 80 0.31
111 1 0.00
123 144 0.55
124 34 0.13
125 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (122 bp):
AAAAATGCCGCCAAAAGTCTGAGCATTAGCGGCGTTTTGGAAAAACGCCGCCAAAAGTCTGAGCA
TTAGCGGCGTTTTTGGAAAAAAGACGCTAAAAGTCTGAGAATTAGCGGCGTTGTTGG
Found at i:3338672 original size:28 final size:28
Alignment explanation
Indices: 3338632--3338687 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
3338622 AAAACGCCGC
*
3338632 CAAAAGTCTGAGTATTAGCGGCGTTTTT
1 CAAAAGTCTGAGTATTAGCAGCGTTTTT
*
3338660 CAAAAGTCTGAGTATTTGCAGCGTTTTT
1 CAAAAGTCTGAGTATTAGCAGCGTTTTT
3338688 GGAAAAACGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (28 bp):
CAAAAGTCTGAGTATTAGCAGCGTTTTT
Found at i:3338702 original size:69 final size:69
Alignment explanation
Indices: 3338591--3338728 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
3338581 AAAACGCCGC
* * * *
3338591 CAAAAGTCTGAGTATTAGCGGCGTTTTTGGGAAAACGCCGCCAAAAGTCTGAGTATTAGCGGCGT
1 CAAAAGTCTGAGTATTAGCAGCGTTTTTGGAAAAACGCCGCCAAAAGTCGGAGCATTAGCGGCGT
3338656 TTTT
66 TTTT
*
3338660 CAAAAGTCTGAGTATTTGCAGCGTTTTTGGAAAAACGCCGCCAAAAGTCGGAGCATTAGCGGCGT
1 CAAAAGTCTGAGTATTAGCAGCGTTTTTGGAAAAACGCCGCCAAAAGTCGGAGCATTAGCGGCGT
3338725 TTTT
66 TTTT
3338729 GGAGAAACGC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (69 bp):
CAAAAGTCTGAGTATTAGCAGCGTTTTTGGAAAAACGCCGCCAAAAGTCGGAGCATTAGCGGCGT
TTTT
Found at i:3338725 original size:41 final size:41
Alignment explanation
Indices: 3338660--3338741 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
3338650 CGGCGTTTTT
* * *
3338660 CAAAAGTCTGAGTATTTGCAGCGTTTTTGGAAAAACGCCGC
1 CAAAAGTCGGAGCATTAGCAGCGTTTTTGGAAAAACGCCGC
* *
3338701 CAAAAGTCGGAGCATTAGCGGCGTTTTTGGAGAAACGCCGC
1 CAAAAGTCGGAGCATTAGCAGCGTTTTTGGAAAAACGCCGC
3338742 TAAACGTCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (41 bp):
CAAAAGTCGGAGCATTAGCAGCGTTTTTGGAAAAACGCCGC
Found at i:3338917 original size:7 final size:7
Alignment explanation
Indices: 3338905--3338929 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3338895 GGGTTTGAGA
3338905 TTTAGTG
1 TTTAGTG
3338912 TTTAGTG
1 TTTAGTG
3338919 TTTAGTG
1 TTTAGTG
3338926 TTTA
1 TTTA
3338930 TGATCTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (7 bp):
TTTAGTG
Found at i:3338978 original size:22 final size:22
Alignment explanation
Indices: 3338951--3339026 Score: 75
Period size: 22 Copynumber: 3.4 Consensus size: 22
3338941 TTTAGCGATA
3338951 TTAAGGGTTTATGGGTTTAGGT
1 TTAAGGGTTTATGGGTTTAGGT
* *
3338973 TTAAGGGTTCAT-GGTTTATGT
1 TTAAGGGTTTATGGGTTTAGGT
**
3338994 TTTTGTGGTTTA-GGGTTTAGGGGT
1 TTAAG-GGTTTATGGGTTTA--GGT
3339018 TTAAGGGTT
1 TTAAGGGTT
3339027 GGTGGTTAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
21 11 0.26
22 22 0.52
23 4 0.10
24 5 0.12
ACGTcount: A:0.16, C:0.01, G:0.36, T:0.47
Consensus pattern (22 bp):
TTAAGGGTTTATGGGTTTAGGT
Found at i:3340327 original size:7 final size:7
Alignment explanation
Indices: 3340316--3340361 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
3340306 ATAAGGTTAG
3340316 GGGTTTA
1 GGGTTTA
*
3340323 TGGTTTA
1 GGGTTTA
*
3340330 GAGTTTA
1 GGGTTTA
3340337 GGGTTTA
1 GGGTTTA
* *
3340344 AGATTTA
1 GGGTTTA
3340351 GGGTTTA
1 GGGTTTA
3340358 GGGT
1 GGGT
3340362 CTGATTTTGT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (7 bp):
GGGTTTA
Found at i:3340342 original size:21 final size:21
Alignment explanation
Indices: 3340284--3340361 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
3340274 ATTCAGTATC
*
3340284 TAGAATTTAGGGTTTAAT-GTT
1 TAGAGTTTAGGGTTT-ATGGTT
* *
3340305 TATAAGGTTAGGGGTTTATGGTT
1 TA-GAGTTTA-GGGTTTATGGTT
* *
3340328 TAGAGTTTAGGGTTTAAGATT
1 TAGAGTTTAGGGTTTATGGTT
*
3340349 TAGGGTTTAGGGT
1 TAGAGTTTAGGGT
3340362 CTGATTTTGT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
21 24 0.52
22 11 0.24
23 11 0.24
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (21 bp):
TAGAGTTTAGGGTTTATGGTT
Found at i:3341788 original size:25 final size:26
Alignment explanation
Indices: 3341760--3341815 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
3341750 CAATTTTTTA
* *
3341760 ATTAAT-CGAAATTTTTTTATCTAAT
1 ATTAATCCGAAATTTTTATATATAAT
* *
3341785 ATT-ATCCTAAATTTTTATATATTAT
1 ATTAATCCGAAATTTTTATATATAAT
3341810 ATTAAT
1 ATTAAT
3341816 TTAATTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 2 0.08
25 21 0.84
26 2 0.08
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTAATCCGAAATTTTTATATATAAT
Found at i:3343772 original size:21 final size:21
Alignment explanation
Indices: 3343746--3343805 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
3343736 AACTCACGTA
3343746 ACCTACATAATTTACATAACT
1 ACCTACATAATTTACATAACT
*
3343767 ACCTACATAACTTACATAACT
1 ACCTACATAATTTACATAACT
*
3343788 ---TACATAATTTATATAACT
1 ACCTACATAATTTACATAACT
3343806 CACATAACGT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 16 0.44
21 20 0.56
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (21 bp):
ACCTACATAATTTACATAACT
Found at i:3343792 original size:39 final size:39
Alignment explanation
Indices: 3343731--3343805 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
3343721 TTAAATAAGT
*
3343731 TACATAACTCACGTAACCTACATAATTTACATAACTACC
1 TACATAACTCACATAACCTACATAATTTACATAACTACC
* * *
3343770 TACATAACTTACATAACTTACATAATTTATATAACT
1 TACATAACTCACATAACCTACATAATTTACATAACT
3343806 CACATAACGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.43, C:0.23, G:0.01, T:0.33
Consensus pattern (39 bp):
TACATAACTCACATAACCTACATAATTTACATAACTACC
Found at i:3343793 original size:57 final size:57
Alignment explanation
Indices: 3343719--3343853 Score: 146
Period size: 57 Copynumber: 2.4 Consensus size: 57
3343709 ATTGATCATT
* * * ** *
3343719 ACTTAAATAAGTTACATAACTCACGTAAC-CTACATAATTTACATAACTACCTACATA
1 ACTTACATAACTTACATAACTCACATAACTC-ACATAACGTACATAACAACCTACATA
* * * * *
3343776 ACTTACATAACTTACATAATTTATATAACTCACATAACGTATATAACAACTTACATA
1 ACTTACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACCTACATA
*
3343833 ACTCACATAACTTACATAACT
1 ACTTACATAACTTACATAACT
3343854 TAATTAATAC
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
57 63 0.98
58 1 0.02
ACGTcount: A:0.44, C:0.22, G:0.02, T:0.31
Consensus pattern (57 bp):
ACTTACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACCTACATA
Found at i:3343811 original size:48 final size:48
Alignment explanation
Indices: 3343730--3343853 Score: 142
Period size: 48 Copynumber: 2.6 Consensus size: 48
3343720 CTTAAATAAG
* * * * * *
3343730 TTACATAACTCACGTAACCTACATAATTTACATAAC-TACCTACATAAC
1 TTACATAACTCACATAACTTACATAACTCACATAACGTACATA-ACAAC
* * * *
3343778 TTACATAACTTACATAATTTATATAACTCACATAACGTATATAACAAC
1 TTACATAACTCACATAACTTACATAACTCACATAACGTACATAACAAC
3343826 TTACATAACTCACATAACTTACATAACT
1 TTACATAACTCACATAACTTACATAACT
3343854 TAATTAATAC
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
48 58 0.94
49 4 0.06
ACGTcount: A:0.44, C:0.23, G:0.02, T:0.31
Consensus pattern (48 bp):
TTACATAACTCACATAACTTACATAACTCACATAACGTACATAACAAC
Found at i:3343812 original size:9 final size:9
Alignment explanation
Indices: 3343719--3343855 Score: 112
Period size: 9 Copynumber: 14.6 Consensus size: 9
3343709 ATTGATCATT
*
3343719 ACTTAAATA
1 ACTTACATA
*
3343728 AGTTACATA
1 ACTTACATA
* *
3343737 ACTCACGTA
1 ACTTACATA
*
3343746 ACCTACATA
1 ACTTACATA
*
3343755 ATTTACATA
1 ACTTACATA
3343764 ACTACCTACATA
1 ACT---TACATA
3343776 ACTTACATA
1 ACTTACATA
3343785 ACTTACATA
1 ACTTACATA
* *
3343794 ATTTATATA
1 ACTTACATA
*
3343803 ACTCACATA
1 ACTTACATA
* *
3343812 ACGTATATAACA
1 AC-T-TA-CATA
3343824 ACTTACATA
1 ACTTACATA
*
3343833 ACTCACATA
1 ACTTACATA
3343842 ACTTACATA
1 ACTTACATA
3343851 ACTTA
1 ACTTA
3343856 ATTAATACAT
Statistics
Matches: 99, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
9 81 0.82
10 3 0.03
11 2 0.02
12 13 0.13
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:3349525 original size:45 final size:46
Alignment explanation
Indices: 3349458--3349581 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
3349448 CATATGACCT
*
3349458 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
3349501 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
3349547 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
3349582 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:3349564 original size:46 final size:45
Alignment explanation
Indices: 3349458--3349655 Score: 198
Period size: 37 Copynumber: 4.8 Consensus size: 45
3349448 CATATGACCT
*
3349458 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
3349501 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
3349547 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
3349584 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
3349621 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
3349656 CACTTATCAC
Statistics
Matches: 140, Mismatches: 7, Indels: 18
0.85 0.04 0.11
Matches are distributed among these distances:
37 64 0.46
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.06
44 6 0.04
45 21 0.15
46 34 0.24
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:3349585 original size:37 final size:37
Alignment explanation
Indices: 3349544--3349682 Score: 242
Period size: 37 Copynumber: 3.8 Consensus size: 37
3349534 GCTGAAGCTA
* **
3349544 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
*
3349581 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
3349618 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
3349655 CCACTTATCACTTTGTTTCTTGATCAGA
1 CCACTTATCACTTTGTTTCTTGATCAGA
3349683 AGTACTCAAA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
Found at i:3352276 original size:21 final size:21
Alignment explanation
Indices: 3352252--3352309 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
3352242 CTAGCCGATG
*
3352252 CAGCAGAGAGGGAGGCAGCGA
1 CAGCAGCGAGGGAGGCAGCGA
*
3352273 CAGCAGCGAGGGAGGCAGCGG
1 CAGCAGCGAGGGAGGCAGCGA
*
3352294 CAGCAGCGAGAGAGGC
1 CAGCAGCGAGGGAGGC
3352310 GGAGCAGAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.22, G:0.48, T:0.00
Consensus pattern (21 bp):
CAGCAGCGAGGGAGGCAGCGA
Found at i:3352300 original size:24 final size:22
Alignment explanation
Indices: 3352251--3352316 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 22
3352241 TCTAGCCGAT
3352251 GCAGCAGAGAGGGAGGCAGCGA
1 GCAGCAGAGAGGGAGGCAGCGA
*
3352273 -CAGCAGCGAGGGAGGCAGCG-
1 GCAGCAGAGAGGGAGGCAGCGA
* *
3352293 GCAGCAGCGAGAGAGGC-G-GA
1 GCAGCAGAGAGGGAGGCAGCGA
3352313 GCAG
1 GCAG
3352317 AGCAGAAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.03
20 5 0.12
21 34 0.85
ACGTcount: A:0.29, C:0.21, G:0.50, T:0.00
Consensus pattern (22 bp):
GCAGCAGAGAGGGAGGCAGCGA
Found at i:3352730 original size:44 final size:43
Alignment explanation
Indices: 3352641--3352813 Score: 159
Period size: 44 Copynumber: 4.0 Consensus size: 43
3352631 TATAAATTTA
* * *
3352641 GCGGCGTTTGTGGGGAAAGCGCCGA-TAAAGGACTCTACTTTTG
1 GCGGCGTTTGTGGAGAAAGCGCC-ACTAAAGGTCTGTACTTTTG
*
3352684 GCGGCATTTGTGGAGAAAGCGCCACTAAAAGGTCTGTACTTTTG
1 GCGGCGTTTGTGGAGAAAGCGCCACT-AAAGGTCTGTACTTTTG
* * * * * ** *
3352728 GCGGCGTTTTTGGTGTAAGCGCCGCTATAGGTCTGTAAATTTA
1 GCGGCGTTTGTGGAGAAAGCGCCACTAAAGGTCTGTACTTTTG
* * * * *
3352771 GCGGCTTTTTTGGGAAAAAGCTCCGCTAAAGGTCTGTACTTTT
1 GCGGCGTTTGT-GGAGAAAGCGCCACTAAAGGTCTGTACTTTT
3352814 AACGGTGCTT
Statistics
Matches: 106, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
42 1 0.01
43 45 0.42
44 60 0.57
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (43 bp):
GCGGCGTTTGTGGAGAAAGCGCCACTAAAGGTCTGTACTTTTG
Found at i:3352775 original size:43 final size:43
Alignment explanation
Indices: 3352633--3352974 Score: 156
Period size: 43 Copynumber: 7.9 Consensus size: 43
3352623 TTTCAATCTA
* * * *
3352633 TAAATTTAGCGGCGTTTGTGGGGAAAGCGCCGATAAAGGACTC
1 TAAATTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCTG
** * * *
3352676 TACTTTTGGCGGCATTTGTGGAGAAAGCGCCACTAAAAGGTCTG
1 TAAATTTAGCGGCGTTTGTGGAGAAAGCGCCGCT-AAAGGTCTG
** * * * * *
3352720 TACTTTTGGCGGCGTTTTTGGTGTAAGCGCCGCTATAGGTCTG
1 TAAATTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCTG
* * * *
3352763 TAAATTTAGCGGCTTTTTTGGGAAAAAGCTCCGCTAAAGGTCTG
1 TAAATTTAGCGGCGTTTGT-GGAGAAAGCGCCGCTAAAGGTCTG
** * * * * * **
3352807 TACTTTTAACGGTGCTT-TGCAAACAAAAGCCGCTAAAGGTCTG
1 TAAATTTAGCGGCGTTTGTGGAGA-AAGCGCCGCTAAAGGTCTG
* ** * * * *
3352850 CACTTTTAGCGGCGCTTTCCTCGA-AAA-TGCCGCTAAAGGTCTA
1 TAAATTTAGCGGCG-TTT-GTGGAGAAAGCGCCGCTAAAGGTCTG
* ** * ** *
3352893 CACCTTTAGCGGCGTTTGTTTGCTAAA-CGCCGCTAAAGGTCTA
1 TAAATTTAGCGGCGTTTG-TGGAGAAAGCGCCGCTAAAGGTCTG
* * * *
3352936 T-ACTATGAGCGGCGTTTATGG-TAAAGCGCCGCTAAAGGT
1 TAAAT-TTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGT
3352975 ATCTACTTTT
Statistics
Matches: 237, Mismatches: 52, Indels: 21
0.76 0.17 0.07
Matches are distributed among these distances:
41 4 0.02
42 26 0.11
43 134 0.57
44 70 0.30
45 1 0.00
46 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (43 bp):
TAAATTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCTG
Found at i:3358889 original size:17 final size:16
Alignment explanation
Indices: 3358864--3358902 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
3358854 AATTTTTAAG
* *
3358864 TTTTAAAAATTATATA
1 TTTTTAAAATGATATA
3358880 TATTTTAAAATGATATA
1 T-TTTTAAAATGATATA
3358897 TTTTTA
1 TTTTTA
3358903 TTTTTTATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTTTTAAAATGATATA
Found at i:3366335 original size:45 final size:44
Alignment explanation
Indices: 3366272--3366364 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 44
3366262 ACTTTAATTG
*
3366272 ACTTAGTGCAATCCAATGGCTCTGTTTTAGGTGACTTATTATCA
1 ACTTAGTACAATCCAATGGCTCTGTTTTAGGTGACTTATTATCA
3366316 ACTTAAGTACAATCCAATGGCTCTGTTTTAGGTGACTTATTATCA
1 ACTT-AGTACAATCCAATGGCTCTGTTTTAGGTGACTTATTATCA
3366361 ACTT
1 ACTT
3366365 CGACCCAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 4 0.09
45 43 0.91
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (44 bp):
ACTTAGTACAATCCAATGGCTCTGTTTTAGGTGACTTATTATCA
Found at i:3366634 original size:69 final size:69
Alignment explanation
Indices: 3366516--3366750 Score: 290
Period size: 69 Copynumber: 3.4 Consensus size: 69
3366506 ACTTATAATG
* * *
3366516 TCAGCTGGGAGCATAGGTCCGCTAGCTGCTTTGAAGGTTGTGATCTTAAATCGTCAAACCTTTAT
1 TCAGTTGGGAGCGTAGGTCCGCTAGCTGCTTTGGAGGTTGTGATCTTAAATCGTCAAACCTTTAT
3366581 GACA
66 GACA
* * * *
3366585 TCAGTTGGGAACGTAGGTCCGTTAGCTGCTTTGGAGGTTGTGATATTAAATCATCAAACCTTTAT
1 TCAGTTGGGAGCGTAGGTCCGCTAGCTGCTTTGGAGGTTGTGATCTTAAATCGTCAAACCTTTAT
3366650 GACA
66 GACA
* ** * ** ** *
3366654 TCAGTTAGGAGCGTAGGTTTGCTACCTATTTTGGAGGTTACGATCTTAAATTGTCAAACCTTTAT
1 TCAGTTGGGAGCGTAGGTCCGCTAGCTGCTTTGGAGGTTGTGATCTTAAATCGTCAAACCTTTAT
3366719 GACA
66 GACA
* * * *
3366723 TAAATTGGGAGCGTAGATTCGCTAGCTG
1 TCAGTTGGGAGCGTAGGTCCGCTAGCTG
3366751 TGTCAGAGTT
Statistics
Matches: 139, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
69 139 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (69 bp):
TCAGTTGGGAGCGTAGGTCCGCTAGCTGCTTTGGAGGTTGTGATCTTAAATCGTCAAACCTTTAT
GACA
Found at i:3372869 original size:47 final size:49
Alignment explanation
Indices: 3372811--3372918 Score: 123
Period size: 47 Copynumber: 2.3 Consensus size: 49
3372801 ACATAACAAT
* *
3372811 ATTTTATATTTTATAT-TTTAAATATTATGATTTAAATAAGATTTTTAG
1 ATTTTAGATTTTATATCTTTAAATATTAGGATTTAAATAAGATTTTTAG
* * * * * *
3372859 ATTTTA-ATTTT-TGTCTTTATATATTAGGTTTTGAATTAGCTTTTTAG
1 ATTTTAGATTTTATATCTTTAAATATTAGGATTTAAATAAGATTTTTAG
3372906 ATTTTAGATTTTA
1 ATTTTAGATTTTA
3372919 AATATTAAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
46 2 0.04
47 37 0.74
48 11 0.22
ACGTcount: A:0.31, C:0.02, G:0.09, T:0.58
Consensus pattern (49 bp):
ATTTTAGATTTTATATCTTTAAATATTAGGATTTAAATAAGATTTTTAG
Found at i:3372924 original size:41 final size:40
Alignment explanation
Indices: 3372874--3372973 Score: 119
Period size: 41 Copynumber: 2.5 Consensus size: 40
3372864 AATTTTTGTC
* *
3372874 TTTATATATTAGGTTTTGAATTAGCTTTTTAGATTTTAGA
1 TTTAAATATTAGGTTTTGAATTAGATTTTTAGATTTTAGA
* * * *
3372914 TTTTAAATATTAAGTTTTAAATTAGATTTTTGGTTTTTAGA
1 -TTTAAATATTAGGTTTTGAATTAGATTTTTAGATTTTAGA
*
3372955 TTTAAATAATAAGGTTTTG
1 TTTAAAT-ATTAGGTTTTG
3372974 TTTTCAAAAG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 7 0.14
41 42 0.86
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (40 bp):
TTTAAATATTAGGTTTTGAATTAGATTTTTAGATTTTAGA
Found at i:3374443 original size:44 final size:44
Alignment explanation
Indices: 3374382--3374468 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
3374372 GCTGACGATC
*
3374382 CCCGAGCTCGTAACTTGATTCCAAAATTTATAAAACAAAGACAT
1 CCCGAGCTCGTAACTTGATCCCAAAATTTATAAAACAAAGACAT
3374426 CCCGAGCTCGTAACTTGATCCCAAAATTTATAAAACAAAGACA
1 CCCGAGCTCGTAACTTGATCCCAAAATTTATAAAACAAAGACA
3374469 AACATATACA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.23
Consensus pattern (44 bp):
CCCGAGCTCGTAACTTGATCCCAAAATTTATAAAACAAAGACAT
Found at i:3375152 original size:45 final size:40
Alignment explanation
Indices: 3375037--3375157 Score: 100
Period size: 41 Copynumber: 2.8 Consensus size: 40
3375027 ATGCTATCTC
* *
3375037 ATATCAATGCCACTGTCCCAGACAGGGTCTTACACGAATCAA
1 ATATCGATGCCAC-GTCCCAGAC-GGGTCTTACACGAACCAA
* * * *
3375079 ATA-CGATGTCGATGTCTCAGACACGGTCTTACACGTAACCACA
1 ATATCGATG-CCACGTCCCAGAC-GGGTCTTACACG-AACCA-A
3375122 TATATCGATGCCAACGTCCCAGACGTGGTCTTACAC
1 -ATATCGATGCC-ACGTCCCAGACG-GGTCTTACAC
3375158 AAAAACACAT
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
41 24 0.39
42 9 0.15
43 1 0.02
44 4 0.06
45 24 0.39
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (40 bp):
ATATCGATGCCACGTCCCAGACGGGTCTTACACGAACCAA
Found at i:3379098 original size:29 final size:29
Alignment explanation
Indices: 3379056--3379115 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
3379046 GTGACGTGAC
3379056 CCCTGTCTTACAACAAAGACCAATTTGTA
1 CCCTGTCTTACAACAAAGACCAATTTGTA
3379085 CCCTGTCTTACAACAAAGACCAATTTGTA
1 CCCTGTCTTACAACAAAGACCAATTTGTA
3379114 CC
1 CC
3379116 TATTTAACCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.30, G:0.10, T:0.27
Consensus pattern (29 bp):
CCCTGTCTTACAACAAAGACCAATTTGTA
Found at i:3380083 original size:25 final size:23
Alignment explanation
Indices: 3380031--3380088 Score: 84
Period size: 21 Copynumber: 2.5 Consensus size: 23
3380021 AACAATCATT
3380031 TTGTTAAAAATTTCATTCATTTC
1 TTGTTAAAAATTTCATTCATTTC
3380054 -T-TTAAAAATTTCATTCATTTC
1 TTGTTAAAAATTTCATTCATTTC
3380075 TATTGTTAAAAATT
1 --TTGTTAAAAATT
3380089 AATCCATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 20 0.65
22 1 0.03
24 1 0.03
25 9 0.29
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.52
Consensus pattern (23 bp):
TTGTTAAAAATTTCATTCATTTC
Found at i:3389489 original size:37 final size:37
Alignment explanation
Indices: 3389440--3389514 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
3389430 TGACCATATG
3389440 TATGTAACTCATGTGCTTTGATATAAGTCGAGGCTTA
1 TATGTAACTCATGTGCTTTGATATAAGTCGAGGCTTA
*
3389477 TATGTAACTCATGTGCTTTGATATAAGTCGAGGTTTA
1 TATGTAACTCATGTGCTTTGATATAAGTCGAGGCTTA
3389514 T
1 T
3389515 GCTTTACAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (37 bp):
TATGTAACTCATGTGCTTTGATATAAGTCGAGGCTTA
Found at i:3390733 original size:68 final size:69
Alignment explanation
Indices: 3390661--3390788 Score: 213
Period size: 69 Copynumber: 1.9 Consensus size: 69
3390651 TTATTTTTAA
* *
3390661 TAAATTTAATTTAATATTTATATTG-ATAGTATTTTATTAATTTAATATTAAAATAATTATCTTA
1 TAAATTTAAATTAATATTTATATTGAAAAGTATTTTATTAATTTAATATTAAAATAATTATCTTA
3390725 ATAT
66 ATAT
* *
3390729 TAAATTTAAATTAATATTTATCTTGAAAAGTATTTTATTAATTTAATATTAAAGTAATTA
1 TAAATTTAAATTAATATTTATATTGAAAAGTATTTTATTAATTTAATATTAAAATAATTA
3390789 AGTTTAATTA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
68 23 0.42
69 32 0.58
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (69 bp):
TAAATTTAAATTAATATTTATATTGAAAAGTATTTTATTAATTTAATATTAAAATAATTATCTTA
ATAT
Found at i:3400033 original size:45 final size:45
Alignment explanation
Indices: 3399955--3400045 Score: 107
Period size: 44 Copynumber: 2.0 Consensus size: 45
3399945 AATTTTCATT
*
3399955 TCCATTTTGAGGAAACCACATAATTTTCCAAATG-ATTCCATTTC
1 TCCATTTTGAGGAAAACACATAATTTTCCAAATGTATTCCATTTC
* *
3399999 TCCATTTCTGA-GAAAAC-CATAATCATTTCTAAATGTTTTCCATTTC
1 TCCATTT-TGAGGAAAACACATAAT--TTTCCAAATGTATTCCATTTC
3400045 T
1 T
3400046 TTATTTATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
43 6 0.15
44 12 0.30
45 12 0.30
46 10 0.25
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
TCCATTTTGAGGAAAACACATAATTTTCCAAATGTATTCCATTTC
Found at i:3406207 original size:14 final size:14
Alignment explanation
Indices: 3406184--3406213 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3406174 TTGAAATTAT
3406184 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
3406198 GTTGATTTGGATTG
1 GTTGAATTGGATTG
3406212 GT
1 GT
3406214 CTCGATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:3409106 original size:43 final size:41
Alignment explanation
Indices: 3409029--3409113 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 41
3409019 TTTATCTTAG
* * *
3409029 AAAAAAAATTTAAAAATGAGAAGATAATCTTGGGTTGTTGA
1 AAAAAAAATTAAAAAAGGAGAAGATAATCATGGGTTGTTGA
3409070 AAAAAGAAATTAAAAAGAGGAGAAGATACA-CATGGGTTGTTGA
1 AAAAA-AAATTAAAAA-AGGAGAAGATA-ATCATGGGTTGTTGA
3409113 A
1 A
3409114 TTTACCCTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 5 0.13
42 9 0.24
43 23 0.61
44 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.24
Consensus pattern (41 bp):
AAAAAAAATTAAAAAAGGAGAAGATAATCATGGGTTGTTGA
Found at i:3415695 original size:57 final size:58
Alignment explanation
Indices: 3415624--3415763 Score: 142
Period size: 57 Copynumber: 2.4 Consensus size: 58
3415614 GTTATGGATT
* * * *
3415624 GGATTTAACTTAGACGGGTAATCCAGA-TCAAGCTCT-TTAGAGCAT-ATGTCATAAAAA
1 GGATTTAGCCTAGACTGGTAATCCAGACT-AAGCTCTATT-GAGCATAATATCATAAAAA
* * * * * *
3415681 GGATTTAGCCTAGACTGATAATCCTGACTAAGCTCTATTGAGTATAAATATTATAGACA
1 GGATTTAGCCTAGACTGGTAATCCAGACTAAGCTCTATTGAGCAT-AATATCATAAAAA
3415740 GGATTTAGCCTAGACTGGTAATCC
1 GGATTTAGCCTAGACTGGTAATCC
3415764 TATTGCATAC
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
57 34 0.50
58 3 0.04
59 31 0.46
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (58 bp):
GGATTTAGCCTAGACTGGTAATCCAGACTAAGCTCTATTGAGCATAATATCATAAAAA
Found at i:3417649 original size:48 final size:48
Alignment explanation
Indices: 3417594--3417689 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
3417584 CCACTTATCA
3417594 AAATCCACTATAAGAGATTGGGAGTATATATATGGTGAAGGGGTTTTT
1 AAATCCACTATAAGAGATTGGGAGTATATATATGGTGAAGGGGTTTTT
3417642 AAATCCACTATAAGAGATTGGGAGTATATATATGGTGAAGGGGTTTTT
1 AAATCCACTATAAGAGATTGGGAGTATATATATGGTGAAGGGGTTTTT
3417690 CTCTTCCGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (48 bp):
AAATCCACTATAAGAGATTGGGAGTATATATATGGTGAAGGGGTTTTT
Found at i:3418599 original size:25 final size:25
Alignment explanation
Indices: 3418542--3418608 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
3418532 AAATGGATTA
* * * *
3418542 TCTGTAAAGTCTTTATGGCAATCTC
1 TCTGGAAAGCCTTTGTGACAATCTC
**
3418567 TCAAGAAAGCCTTTGTGACAATCTC
1 TCTGGAAAGCCTTTGTGACAATCTC
3418592 TCTGGAAAGCCTTTGTG
1 TCTGGAAAGCCTTTGTG
3418609 GTATATTATC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (25 bp):
TCTGGAAAGCCTTTGTGACAATCTC
Found at i:3425674 original size:50 final size:49
Alignment explanation
Indices: 3425536--3425675 Score: 147
Period size: 50 Copynumber: 2.8 Consensus size: 49
3425526 CTTTGTGGCA
* * * * *
3425536 ATCTCTCTGGAAAGCCTTTGTGGCAAATTCCCTATAAAACCTTATGGTG
1 ATCTCTCTGGAAAGCCTTTGTGGCGATTTCTCTATAAAGCCTTATGATG
* * * * *
3425585 ATCTCTCTGAAAAGCCTTTGCGGCGATATCTTTGA-AAAGCTTTTATGATG
1 ATCTCTCTGGAAAGCCTTTGTGGCGATTTCTCT-ATAAAGC-CTTATGATG
* *
3425635 ATCTCTCTGGAAAGGCTTTTTGGCGATTTCTCTATAAAGCC
1 ATCTCTCTGGAAAGCCTTTGTGGCGATTTCTCTATAAAGCC
3425676 ATTGTGGGAT
Statistics
Matches: 71, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
49 31 0.44
50 40 0.56
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (49 bp):
ATCTCTCTGGAAAGCCTTTGTGGCGATTTCTCTATAAAGCCTTATGATG
Found at i:3435595 original size:102 final size:102
Alignment explanation
Indices: 3435416--3435609 Score: 334
Period size: 102 Copynumber: 1.9 Consensus size: 102
3435406 TCTACGATCT
* *
3435416 CAAAAATATAAAAATTAAAATAAAATGATTAAATTGCACTAAATAATATTGTAGAATAAAAACTT
1 CAAAAATATAAAAATTAAAATAAAATGACTAAATTGCACTAAACAATATTGTAGAATAAAAACTT
* *
3435481 GGTATTCGGCTATGGCGTTTTCTCCTTTATTTTTTCC
66 GATATTCCGCTATGGCGTTTTCTCCTTTATTTTTTCC
* *
3435518 CAAAAATATAAAAATTACAATAAAATGACTAAGTTGCACTAAACAATATTGTAGAATAAAAACTT
1 CAAAAATATAAAAATTAAAATAAAATGACTAAATTGCACTAAACAATATTGTAGAATAAAAACTT
3435583 GATATTCCGCTATGGCGTTTTCTCCTT
66 GATATTCCGCTATGGCGTTTTCTCCTT
3435610 CAATTTCTCT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 86 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (102 bp):
CAAAAATATAAAAATTAAAATAAAATGACTAAATTGCACTAAACAATATTGTAGAATAAAAACTT
GATATTCCGCTATGGCGTTTTCTCCTTTATTTTTTCC
Found at i:3436072 original size:25 final size:26
Alignment explanation
Indices: 3436038--3436093 Score: 105
Period size: 25 Copynumber: 2.2 Consensus size: 26
3436028 ACTTTCGGGT
3436038 TGTTACATTTCTAACATGAAAGGGC-
1 TGTTACATTTCTAACATGAAAGGGCA
3436063 TGTTACATTTCTAACATGAAAGGGCA
1 TGTTACATTTCTAACATGAAAGGGCA
3436089 TGTTA
1 TGTTA
3436094 AAAAATTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 25 0.83
26 5 0.17
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (26 bp):
TGTTACATTTCTAACATGAAAGGGCA
Found at i:3437194 original size:17 final size:18
Alignment explanation
Indices: 3437164--3437197 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3437154 ATTTAAATTG
3437164 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
3437182 CGGTCGC-GTCGCGTTT
1 CGGTCGCGGTCGCGTTT
3437198 GTCGTGGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.00, C:0.29, G:0.38, T:0.32
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:3441541 original size:21 final size:21
Alignment explanation
Indices: 3441499--3441541 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3441489 TTCAGGTGGA
*
3441499 TCAGCTCTTATGAGATTTTGT
1 TCAGCTCTTATGAGATTCTGT
* *
3441520 TCAGTTCTTATGAGCTTCTGT
1 TCAGCTCTTATGAGATTCTGT
3441541 T
1 T
3441542 GGCGTGTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49
Consensus pattern (21 bp):
TCAGCTCTTATGAGATTCTGT
Done.