Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 51 of 378
Found at i:12729316 original size:3 final size:3
Alignment explanation
Indices: 12729304--12729574 Score: 166
Period size: 3 Copynumber: 91.3 Consensus size: 3
12729294 GTTATTTTGC
* * * * *
12729304 TAT T-T TAT TAT TAA AAT TAA T-T TAT TTAT TAT TAC TAT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
* * * * * * *
12729348 TTT TAC TAT TAC TAT TAT TTT CTAT TAT TAC TGT TAT TGT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
* * *
12729393 TAT TAT TAT T-T ATAT TAT TGT TGT TAT TAT TAT TAT TCTT TAT T-T
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
* * * *
12729438 TAT TAT TAT TAT TTT CTAT TAT TAT TAC TAT TGT TAT TAT TGT CT-T
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * *
12729484 TAC TAT TAT TAT TAT TAT T-T TAT T-T TAT T-T TTT CTAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
* * * * *
12729527 TAT CAT TAT CAT TAT TAT TAT TAC TAT TAT T-T TTT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12729574 T
1 T
12729575 TCCTGTTTAT
Statistics
Matches: 205, Mismatches: 46, Indels: 34
0.72 0.16 0.12
Matches are distributed among these distances:
2 17 0.08
3 175 0.85
4 13 0.06
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:12736585 original size:18 final size:18
Alignment explanation
Indices: 12736562--12736617 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
12736552 AAAAAAGAGA
12736562 AATTGAAATTGTCCTAGT
1 AATTGAAATTGTCCTAGT
** *
12736580 AATTG--A--GTAATGGT
1 AATTGAAATTGTCCTAGT
12736594 AATTGAAATTGTCCTAGT
1 AATTGAAATTGTCCTAGT
12736612 AATTGA
1 AATTGA
12736618 GTAATGGTGT
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 10 0.36
16 2 0.07
18 16 0.57
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.38
Consensus pattern (18 bp):
AATTGAAATTGTCCTAGT
Found at i:12736603 original size:32 final size:32
Alignment explanation
Indices: 12736562--12736625 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
12736552 AAAAAAGAGA
12736562 AATTGAAATTGTCCTAGTAATTGAGTAATGGT
1 AATTGAAATTGTCCTAGTAATTGAGTAATGGT
12736594 AATTGAAATTGTCCTAGTAATTGAGTAATGGT
1 AATTGAAATTGTCCTAGTAATTGAGTAATGGT
12736626 GTATTTAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (32 bp):
AATTGAAATTGTCCTAGTAATTGAGTAATGGT
Found at i:12744969 original size:31 final size:31
Alignment explanation
Indices: 12744932--12745047 Score: 187
Period size: 31 Copynumber: 3.7 Consensus size: 31
12744922 TGTGTACAAT
12744932 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
*
12744963 GTGAAAAGTGGTAGCTTCGGCTACCTGATTA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
* *
12744994 GTGAAAAGTGGTAGCTCCAGCTACCTGATCA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
* *
12745025 GTGAATAGTGATAGCTTCGGCTA
1 GTGAAAAGTGGTAGCTTCGGCTA
12745048 TCGAATGTGA
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (31 bp):
GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
Found at i:12745066 original size:29 final size:31
Alignment explanation
Indices: 12744932--12745074 Score: 161
Period size: 31 Copynumber: 4.7 Consensus size: 31
12744922 TGTGTACAAT
12744932 GTGAAAAGTGGTAGCTTCGGCTACCTG-ATCA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGAAT-A
*
12744963 GTGAAAAGTGGTAGCTTCGGCTACCTGATTA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGAATA
* *
12744994 GTGAAAAGTGGTAGCTCCAGCTACCTG-ATCA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGAAT-A
* * *
12745025 GTGAATAGTGATAGCTTCGGCTATC-GAAT-
1 GTGAAAAGTGGTAGCTTCGGCTACCTGAATA
*
12745054 GTGAAAAG-GGATAGTTTCGGC
1 GTGAAAAGTGG-TAGCTTCGGC
12745075 CATCAAATGT
Statistics
Matches: 96, Mismatches: 12, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
28 1 0.01
29 16 0.17
30 2 0.02
31 76 0.79
32 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (31 bp):
GTGAAAAGTGGTAGCTTCGGCTACCTGAATA
Found at i:12745083 original size:29 final size:29
Alignment explanation
Indices: 12745025--12745120 Score: 120
Period size: 29 Copynumber: 3.3 Consensus size: 29
12745015 TACCTGATCA
* * *
12745025 GTGAATAGTGATAGCTTCGGCTATCGAAT
1 GTGAAAAGGGATAGCTTCGGCTATCAAAT
* *
12745054 GTGAAAAGGGATAGTTTCGGCCATCAAAT
1 GTGAAAAGGGATAGCTTCGGCTATCAAAT
*
12745083 GTAAAAAGGGATAGCTTCGGCTATCAAAT
1 GTGAAAAGGGATAGCTTCGGCTATCAAAT
* *
12745112 TTGGAAAGG
1 GTGAAAAGG
12745121 AAAGGTATAC
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.26
Consensus pattern (29 bp):
GTGAAAAGGGATAGCTTCGGCTATCAAAT
Found at i:12745147 original size:33 final size:33
Alignment explanation
Indices: 12745110--12745318 Score: 249
Period size: 33 Copynumber: 6.3 Consensus size: 33
12745100 CGGCTATCAA
* *
12745110 ATTTGGAAAGGAAAGGTATACTTTGTGTATACT
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
* **
12745143 ATTTGAAAATGTTAGGTATACTTTGTGTATACC
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
* *
12745176 ATTTGAAAAAGAAATGTATACTTTGTGTATACC
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
**
12745209 ATTTGAAAAGGTTAGGTATACTTTGTGTATACC
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
* * *
12745242 ATATGAAAAAGGGAAGGTATACTTTGTGTATATC
1 ATTTG-AAAAGGAAAGGTATACTTTGTGTATACC
* *
12745276 ATATGAAAAGGAAA-GTGATACTTTGTGTGTACC
1 ATTTGAAAAGGAAAGGT-ATACTTTGTGTATACC
* *
12745309 ACTTGGAAAG
1 ATTTGAAAAG
12745319 AAACGTACAC
Statistics
Matches: 151, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
32 2 0.01
33 119 0.79
34 30 0.20
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (33 bp):
ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
Found at i:12745309 original size:100 final size:99
Alignment explanation
Indices: 12745123--12745318 Score: 268
Period size: 100 Copynumber: 2.0 Consensus size: 99
12745113 TGGAAAGGAA
* * * ** *
12745123 AGGTATACTTTGTGTATACTATTTGAAAATGTTAGGTATACTTTGTGTATACCATTTGAAAAAGA
1 AGGTATACTTTGTGTATACCATATGAAAAGGGAAGGTATACTTTGTGTATACCATATGAAAAAGA
*
12745188 AATGTATACTTTGTGTATACCATTTGAAAAGGTT
66 AATGTATACTTTGTGTATACCACTTGAAAAGGTT
* *
12745222 AGGTATACTTTGTGTATACCATATGAAAAAGGGAAGGTATACTTTGTGTATATCATATGAAAAGG
1 AGGTATACTTTGTGTATACCATATG-AAAAGGGAAGGTATACTTTGTGTATACCATATGAAAAAG
* *
12745287 AAA-GTGATACTTTGTGTGTACCACTTGGAAAG
65 AAATGT-ATACTTTGTGTATACCACTTGAAAAG
12745319 AAACGTACAC
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
99 25 0.30
100 59 0.70
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (99 bp):
AGGTATACTTTGTGTATACCATATGAAAAGGGAAGGTATACTTTGTGTATACCATATGAAAAAGA
AATGTATACTTTGTGTATACCACTTGAAAAGGTT
Found at i:12748610 original size:17 final size:17
Alignment explanation
Indices: 12748588--12748622 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12748578 CTAGATAAGA
12748588 TGACAACCCAAGCACCT
1 TGACAACCCAAGCACCT
12748605 TGACAACCCAAGCACCT
1 TGACAACCCAAGCACCT
12748622 T
1 T
12748623 ACCCCGATTA
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:0.34, C:0.40, G:0.11, T:0.14
Consensus pattern (17 bp):
TGACAACCCAAGCACCT
Found at i:12749534 original size:26 final size:26
Alignment explanation
Indices: 12749505--12749586 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
12749495 TGATACAAAT
12749505 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
12749531 TGATAATGAGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12749557 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12749583 TGAT
1 TGAT
12749587 TAAAATTTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:12756003 original size:12 final size:11
Alignment explanation
Indices: 12755986--12756027 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
12755976 CTAATTTAAT
12755986 ATAAAATCAAAA
1 ATAAAAT-AAAA
12755998 ATAAAATAAAA
1 ATAAAATAAAA
*
12756009 ATAAAA-ATAA
1 ATAAAATAAAA
12756019 ATAAAATAA
1 ATAAAATAA
12756028 GATTTTCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 9 0.33
11 11 0.41
12 7 0.26
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:12756008 original size:17 final size:15
Alignment explanation
Indices: 12755986--12756027 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 15
12755976 CTAATTTAAT
12755986 ATAAAATCAAAAATAAA
1 ATAAAAT-AAAAAT-AA
12756003 ATAAAAATAAAAATAA
1 AT-AAAATAAAAATAA
12756019 ATAAAATAA
1 ATAAAATAA
12756028 GATTTTCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.29
16 4 0.17
17 8 0.33
18 5 0.21
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAAAATAAAAATAA
Found at i:12756411 original size:28 final size:29
Alignment explanation
Indices: 12756378--12756438 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
12756368 GTAACAAATA
*
12756378 TATATTTAAAT-AATATTAAAA-ATATTAT
1 TATATTTAAATAAAAATTAAAAGA-ATTAT
*
12756406 TATATTTTAATAAAAATTAAAAGAATTAT
1 TATATTTAAATAAAAATTAAAAGAATTAT
12756435 TATA
1 TATA
12756439 ACTTGCCGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 10 0.34
29 18 0.62
30 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (29 bp):
TATATTTAAATAAAAATTAAAAGAATTAT
Found at i:12756731 original size:48 final size:48
Alignment explanation
Indices: 12756675--12756793 Score: 202
Period size: 48 Copynumber: 2.5 Consensus size: 48
12756665 AAAAACATAC
*
12756675 TTTATTCTATTTGCTTTTAGAAAACTAATTCAGCCAAAATCAATTTAT
1 TTTATTCTATTTGCTTTTAAAAAACTAATTCAGCCAAAATCAATTTAT
12756723 TTTATTCTATTTGCTTTTAAAAAACTAATTCAGCCAAAATCAATTTAT
1 TTTATTCTATTTGCTTTTAAAAAACTAATTCAGCCAAAATCAATTTAT
* **
12756771 TATATTCTATTTATTTTTAAAAA
1 TTTATTCTATTTGCTTTTAAAAA
12756794 TACTTTTAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 67 1.00
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (48 bp):
TTTATTCTATTTGCTTTTAAAAAACTAATTCAGCCAAAATCAATTTAT
Found at i:12757097 original size:2 final size:2
Alignment explanation
Indices: 12757090--12757115 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12757080 TAGAAGGTTG
12757090 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
12757116 TGTTTTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12758000 original size:31 final size:31
Alignment explanation
Indices: 12757957--12758048 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 31
12757947 AATAAAGAAG
* *
12757957 ATAAAAGAGATAGCTAACAG-TAATTCAAAAC
1 ATAATAGAGATAGCTAA-AGCCAATTCAAAAC
*
12757988 ATAATAGAGATAGCT-AAGCCAATTCAAAAT
1 ATAATAGAGATAGCTAAAGCCAATTCAAAAC
* *
12758018 ACTAATAGAGATGGCT-AAGTCCAGTTCAAAA
1 A-TAATAGAGATAGCTAAAG-CCAATTCAAAA
12758049 TACCTAATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
29 2 0.04
30 11 0.21
31 30 0.57
32 10 0.19
ACGTcount: A:0.49, C:0.14, G:0.15, T:0.22
Consensus pattern (31 bp):
ATAATAGAGATAGCTAAAGCCAATTCAAAAC
Found at i:12758051 original size:32 final size:31
Alignment explanation
Indices: 12757978--12758057 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 31
12757968 AGCTAACAGT
*
12757978 AATTCAAAACA-TAATAGAGATAGCTAAGCC
1 AATTCAAAATACTAATAGAGATAGCTAAGCC
*
12758008 AATTCAAAATACTAATAGAGATGGCTAAGTCC
1 AATTCAAAATACTAATAGAGATAGCTAAG-CC
*
12758040 AGTTCAAAATACCTAATA
1 AATTCAAAATA-CTAATA
12758058 AAATAACAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 10 0.23
31 16 0.36
32 12 0.27
33 6 0.14
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.24
Consensus pattern (31 bp):
AATTCAAAATACTAATAGAGATAGCTAAGCC
Found at i:12765289 original size:23 final size:23
Alignment explanation
Indices: 12765263--12765309 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
12765253 TGATTATGTG
12765263 AATTATTTTACAAA-TTCTTAATT
1 AATTATTTTA-AAATTTCTTAATT
*
12765286 AATTTTTTTAAAATTTCTTAATT
1 AATTATTTTAAAATTTCTTAATT
12765309 A
1 A
12765310 TGAGGAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (23 bp):
AATTATTTTAAAATTTCTTAATT
Found at i:12765881 original size:22 final size:21
Alignment explanation
Indices: 12765833--12765883 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
12765823 GAGTAGTAAA
* *
12765833 TTTTTTTATTTTTTTTATAAC
1 TTTTTTTATATTTCTTATAAC
* *
12765854 TATTTTCTATATTTCTTATAAT
1 T-TTTTTTATATTTCTTATAAC
12765876 TTTTTTTA
1 TTTTTTTA
12765884 CAATTTTCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTTTATATTTCTTATAAC
Found at i:12765962 original size:20 final size:21
Alignment explanation
Indices: 12765939--12765991 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
12765929 TTTTTTCTAT
12765939 TTTTATAAT-ATTT-TAATAAG
1 TTTT-TAATCATTTCTAATAAG
12765959 -TTTTAATCATTTCTAATAAG
1 TTTTTAATCATTTCTAATAAG
*
12765979 TTTTCAATCATTT
1 TTTTTAATCATTT
12765992 TTAAAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.14
19 7 0.24
20 7 0.24
21 11 0.38
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.55
Consensus pattern (21 bp):
TTTTTAATCATTTCTAATAAG
Found at i:12765989 original size:21 final size:19
Alignment explanation
Indices: 12765944--12765992 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 19
12765934 TCTATTTTTA
12765944 TAAT-ATTTTAATAAGTTT
1 TAATCATTTTAATAAGTTT
12765962 TAATCATTTCTAATAAGTTT
1 TAATCATTT-TAATAAGTTT
12765982 TCAATCATTTT
1 T-AATCATTTT
12765993 TAAAATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.14
19 4 0.14
20 12 0.43
21 8 0.29
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.53
Consensus pattern (19 bp):
TAATCATTTTAATAAGTTT
Found at i:12768224 original size:11 final size:11
Alignment explanation
Indices: 12768208--12768240 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
12768198 GTTTAGTGTT
*
12768208 ATTTAGGATCA
1 ATTTAGTATCA
12768219 ATTTAGTATCA
1 ATTTAGTATCA
12768230 ATTTAGTATCA
1 ATTTAGTATCA
12768241 TTTTTAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (11 bp):
ATTTAGTATCA
Found at i:12769126 original size:3 final size:3
Alignment explanation
Indices: 12769118--12769144 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12769108 TCGATCATGG
12769118 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
12769145 TCTTTGTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:12769179 original size:3 final size:3
Alignment explanation
Indices: 12769171--12769195 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12769161 CCCTTTACTT
12769171 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
12769196 CACATGTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:12772880 original size:19 final size:19
Alignment explanation
Indices: 12772834--12772881 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
12772824 GTATATATTT
12772834 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
12772852 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
12772871 TAAGTTTTATT
1 TAAATTTTATT
12772882 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:12776666 original size:15 final size:15
Alignment explanation
Indices: 12776646--12776676 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12776636 TTTATTTAGG
12776646 TAGGTAAATCTTATT
1 TAGGTAAATCTTATT
*
12776661 TAGGTAAATTTTATT
1 TAGGTAAATCTTATT
12776676 T
1 T
12776677 TATCTTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.52
Consensus pattern (15 bp):
TAGGTAAATCTTATT
Found at i:12781596 original size:23 final size:22
Alignment explanation
Indices: 12781561--12781603 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
12781551 ATTTAACCCC
* *
12781561 TTAAAAATGATAAAATTATAAA
1 TTAAAAATAATAAAACTATAAA
12781583 TTAATAAATAATAAAACTATA
1 TTAA-AAATAATAAAACTATA
12781604 TTTTGACTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
TTAAAAATAATAAAACTATAAA
Found at i:12788969 original size:21 final size:20
Alignment explanation
Indices: 12788945--12788986 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
12788935 TACGATGTTG
12788945 AAAGACATTAAA-TGATATGTA
1 AAAGACA-TAAATTGA-ATGTA
*
12788966 AAAGATATAAATTGAATGTA
1 AAAGACATAAATTGAATGTA
12788986 A
1 A
12788987 GAGATGAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.55, C:0.02, G:0.14, T:0.29
Consensus pattern (20 bp):
AAAGACATAAATTGAATGTA
Found at i:12789617 original size:20 final size:20
Alignment explanation
Indices: 12789592--12789632 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
12789582 GCCCCATGGC
12789592 CATGTCCCAAGCCACACGGG
1 CATGTCCCAAGCCACACGGG
*
12789612 CATGTCCCAGGCCACACGGG
1 CATGTCCCAAGCCACACGGG
12789632 C
1 C
12789633 GTGTGCCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.41, G:0.27, T:0.10
Consensus pattern (20 bp):
CATGTCCCAAGCCACACGGG
Found at i:12795446 original size:48 final size:48
Alignment explanation
Indices: 12795394--12795506 Score: 154
Period size: 48 Copynumber: 2.4 Consensus size: 48
12795384 CCATGTTAAC
* ** * * *
12795394 CCGCACACATAGTGCCTTAGTAATTCACATACATATTGACATTCCAAT
1 CCGCACACATAGTGCCATACAAATTCACACACATAGTGACATTCAAAT
*
12795442 CCGCACACATAGTGCCATACAAATTCACACACATAGTGCCATTCAAAT
1 CCGCACACATAGTGCCATACAAATTCACACACATAGTGACATTCAAAT
*
12795490 TCGCACACATAGTGCCA
1 CCGCACACATAGTGCCA
12795507 AAATCATTTC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.35, C:0.30, G:0.12, T:0.24
Consensus pattern (48 bp):
CCGCACACATAGTGCCATACAAATTCACACACATAGTGACATTCAAAT
Found at i:12795451 original size:24 final size:24
Alignment explanation
Indices: 12795415--12795506 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
12795405 GTGCCTTAGT
* * * * *
12795415 AATTCACATACATATTGACATTCC
1 AATTCGCACACATAGTGCCATTCA
* *
12795439 AATCCGCACACATAGTGCCATACA
1 AATTCGCACACATAGTGCCATTCA
*
12795463 AATTCACACACATAGTGCCATTCA
1 AATTCGCACACATAGTGCCATTCA
12795487 AATTCGCACACATAGTGCCA
1 AATTCGCACACATAGTGCCA
12795507 AAATCATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.37, C:0.29, G:0.10, T:0.24
Consensus pattern (24 bp):
AATTCGCACACATAGTGCCATTCA
Found at i:12796703 original size:17 final size:17
Alignment explanation
Indices: 12796681--12796714 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12796671 CCCCACTTAA
*
12796681 TATATTATAACTTATTT
1 TATATTATAACATATTT
12796698 TATATTATAACATATTT
1 TATATTATAACATATTT
12796715 CAATCATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTATAACATATTT
Found at i:12797858 original size:21 final size:21
Alignment explanation
Indices: 12797832--12797889 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
12797822 GGCGCGACCC
12797832 ATTTTTTTAATAATAATATAT
1 ATTTTTTTAATAATAATATAT
* * * *
12797853 ATTTTTTAAATATTATTATTT
1 ATTTTTTTAATAATAATATAT
12797874 ATTATATTTTAATAAT
1 ATT-T-TTTTAATAAT
12797890 TTTTAAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 20 0.69
22 1 0.03
23 8 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTTTAATAATAATATAT
Found at i:12798106 original size:25 final size:25
Alignment explanation
Indices: 12798064--12798125 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
12798054 AAAGAAATTT
*
12798064 TTTATTAAGTTTAATAA--TTATTTAA
1 TTTATT-ATTTTAATAATGTTA-TTAA
12798089 TATTATTATTTTAATAATGTTATTAA
1 T-TTATTATTTTAATAATGTTATTAA
12798115 TTTATTATTTT
1 TTTATTATTTT
12798126 TTATACTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 20 0.61
26 10 0.30
27 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (25 bp):
TTTATTATTTTAATAATGTTATTAA
Found at i:12798188 original size:17 final size:17
Alignment explanation
Indices: 12798174--12798206 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12798164 AATAATTTTT
12798174 TAATATTATTAATTTAA
1 TAATATTATTAATTTAA
*
12798191 TAATGTTATTAATTTA
1 TAATATTATTAATTTA
12798207 TTATTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TAATATTATTAATTTAA
Found at i:12798194 original size:25 final size:25
Alignment explanation
Indices: 12798161--12798209 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
12798151 TGAAATTATG
*
12798161 TTTAATAAT-TTTTTAATATTATTAA
1 TTTAATAATGTTATTAAT-TTATTAA
12798186 TTTAATAATGTTATTAATTTATTA
1 TTTAATAATGTTATTAATTTATTA
12798210 TTTTTTATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
TTTAATAATGTTATTAATTTATTAA
Found at i:12798279 original size:87 final size:88
Alignment explanation
Indices: 12798067--12798367 Score: 457
Period size: 88 Copynumber: 3.4 Consensus size: 88
12798057 GAAATTTTTT
* * *
12798067 ATTAAGTTTAATAATTATTTAATATTATTATTTTAATAATGTTATTAATTTATTATTTTTTATAC
1 ATTAAGTTTAATAATTTTTTAATATTATTAATTTAATAATGTTATTAATTTATTATTTTTTATGC
12798132 TTAAATTTTTTAATAATTTTGAA
66 TTAAATTTTTTAATAATTTTGAA
*
12798155 ATTATGTTTAATAATTTTTTAATATTATTAATTTAATAATGTTATTAATTTATTATTTTTTATGC
1 ATTAAGTTTAATAATTTTTTAATATTATTAATTTAATAATGTTATTAATTTATTATTTTTTATGC
12798220 TTAAATTTTTTAATAATTTTGAA
66 TTAAATTTTTTAATAATTTTGAA
*
12798243 ATTAAGTTTAATAA-TTTTTAATATTATTATTTTAATAAT-TCTGA-TAATTTATTATTTTTTAT
1 ATTAAGTTTAATAATTTTTTAATATTATTAATTTAATAATGT-T-ATTAATTTATTATTTTTTAT
* * * *
12798305 GCTCAGA-TTTTTAATATTTTTAAA
64 GCTTAAATTTTTTAATAATTTTGAA
* *
12798329 ATTAAGTCTAATAATTTTTTAGTATTATTAATTTAATAA
1 ATTAAGTTTAATAATTTTTTAATATTATTAATTTAATAA
12798368 ATTTTTATTG
Statistics
Matches: 197, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
86 29 0.15
87 70 0.36
88 98 0.50
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (88 bp):
ATTAAGTTTAATAATTTTTTAATATTATTAATTTAATAATGTTATTAATTTATTATTTTTTATGC
TTAAATTTTTTAATAATTTTGAA
Found at i:12798761 original size:33 final size:33
Alignment explanation
Indices: 12798698--12798761 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
12798688 ATGAACTCGA
* *
12798698 GCCGGGTGGAGTAGAGAACGGCGCTGGATATGG
1 GCCGGGAGGAGTAGAGAACGGCGCTAGATATGG
* * *
12798731 GCCGGGAGGAGTAGAGTACGGTGGTAGATAT
1 GCCGGGAGGAGTAGAGAACGGCGCTAGATAT
12798762 AAGCCAAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.47, T:0.17
Consensus pattern (33 bp):
GCCGGGAGGAGTAGAGAACGGCGCTAGATATGG
Found at i:12800587 original size:11 final size:11
Alignment explanation
Indices: 12800573--12800600 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
12800563 ACATTATATC
12800573 AAAATTACATT
1 AAAATTACATT
12800584 AAAATTACATT
1 AAAATTACATT
12800595 AAAATT
1 AAAATT
12800601 TCTTACTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAATTACATT
Found at i:12801667 original size:3 final size:3
Alignment explanation
Indices: 12801661--12801761 Score: 116
Period size: 3 Copynumber: 33.7 Consensus size: 3
12801651 TAACATTTTT
* * * *
12801661 TTC TTC TTCC TCC TTC TCC TTC TCC TTC TCC TTC TTC TTC TTC TTC
1 TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* *
12801707 TTT TTC TTC TTC TTC TT- TTC TTC TTC TTC ATC TTC TTC TTC TTC TT-
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
12801753 TTC TCTC TT
1 TTC T-TC TT
12801762 TGCTGCTGCC
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.05
3 73 0.89
4 5 0.06
ACGTcount: A:0.01, C:0.36, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:12802277 original size:24 final size:24
Alignment explanation
Indices: 12802228--12802286 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
12802218 TAAAGTAAGT
* *
12802228 TATA-TATTATTTTTATAATATTA
1 TATATTATAATTTTTATAATATCA
12802251 TATATTATAATTTTTATGAAT-TCA
1 TATATTATAATTTTTAT-AATATCA
*
12802275 TATTTTAATAAT
1 TATATT-ATAAT
12802287 AATTATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.13
24 18 0.60
25 8 0.27
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
TATATTATAATTTTTATAATATCA
Found at i:12802306 original size:28 final size:28
Alignment explanation
Indices: 12802275--12802355 Score: 67
Period size: 28 Copynumber: 2.8 Consensus size: 28
12802265 TATGAATTCA
12802275 TATTTTAATAATAATTATATTAAGAATT
1 TATTTTAATAATAATTATATTAAGAATT
* * **
12802303 TA-TTAAATTACAT-ATTCTATTATTAATT
1 TATTTTAA-TA-ATAATTATATTAAGAATT
*
12802331 TGTATTTAATAATAATTATGATTAA
1 TAT-TTTAATAATAATTAT-ATTAA
12802356 ATATGATTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
27 4 0.10
28 19 0.49
29 8 0.21
30 8 0.21
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (28 bp):
TATTTTAATAATAATTATATTAAGAATT
Found at i:12802317 original size:40 final size:39
Alignment explanation
Indices: 12802235--12802318 Score: 91
Period size: 40 Copynumber: 2.1 Consensus size: 39
12802225 AGTTATATAT
* * *
12802235 TATTTTTATAATATTATATATTATAATTTTTATGAATTCA
1 TATTTTAATAATATTATATATAAGAATTTTTA-GAATTCA
12802275 TATTTTAATAATAATTATAT-TAAGAATTTATTA-AATTACA
1 TATTTTAATAAT-ATTATATATAAGAATTT-TTAGAATT-CA
12802315 TATT
1 TATT
12802319 CTATTATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
39 4 0.11
40 24 0.63
41 10 0.26
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (39 bp):
TATTTTAATAATATTATATATAAGAATTTTTAGAATTCA
Found at i:12802603 original size:16 final size:16
Alignment explanation
Indices: 12802582--12802635 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
12802572 TGAATTGCTG
*
12802582 ATTACAAGTTTATTCC
1 ATTACAACTTTATTCC
* *
12802598 ATTACATCTTTATTCA
1 ATTACAACTTTATTCC
*
12802614 ATTACAACTCTATTCC
1 ATTACAACTTTATTCC
12802630 ATTACA
1 ATTACA
12802636 GTTAACCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.33, C:0.22, G:0.02, T:0.43
Consensus pattern (16 bp):
ATTACAACTTTATTCC
Found at i:12811777 original size:17 final size:18
Alignment explanation
Indices: 12811755--12811793 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
12811745 ACTATTTTTC
*
12811755 TATTAT-ATATAAAATAT
1 TATTATAATATAAAACAT
12811772 TATTATACATATAAAACAT
1 TATTATA-ATATAAAACAT
12811791 TAT
1 TAT
12811794 CAAGTCTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
TATTATAATATAAAACAT
Found at i:12811943 original size:11 final size:11
Alignment explanation
Indices: 12811927--12811951 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12811917 TCTTTCTCCA
12811927 TAGTTCTTCAT
1 TAGTTCTTCAT
12811938 TAGTTCTTCAT
1 TAGTTCTTCAT
12811949 TAG
1 TAG
12811952 AGAGCTCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.16, G:0.12, T:0.52
Consensus pattern (11 bp):
TAGTTCTTCAT
Found at i:12814914 original size:93 final size:93
Alignment explanation
Indices: 12814799--12814983 Score: 352
Period size: 93 Copynumber: 2.0 Consensus size: 93
12814789 TTCCAACCCT
*
12814799 TACAATTTCCTTTTTCAAAATTTGAAATAGATCTCTACAATAATTTAAACTTGAATCTGATCATC
1 TACAATTTCCTTTTTCAAAATTTGAAATAGATCTCTACAATAATTTAAACTTGAATCTCATCATC
12814864 CAAACAACTAGTAATTTCATTGAGTGTC
66 CAAACAACTAGTAATTTCATTGAGTGTC
*
12814892 TACAATTTCCTTTTTGAAAATTTGAAATAGATCTCTACAATAATTTAAACTTGAATCTCATCATC
1 TACAATTTCCTTTTTCAAAATTTGAAATAGATCTCTACAATAATTTAAACTTGAATCTCATCATC
12814957 CAAACAACTAGTAATTTCATTGAGTGT
66 CAAACAACTAGTAATTTCATTGAGTGT
12814984 TGTAACTTAA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.38
Consensus pattern (93 bp):
TACAATTTCCTTTTTCAAAATTTGAAATAGATCTCTACAATAATTTAAACTTGAATCTCATCATC
CAAACAACTAGTAATTTCATTGAGTGTC
Found at i:12827162 original size:2 final size:2
Alignment explanation
Indices: 12827157--12827197 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
12827147 TTTTTTTATC
12827157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12827198 AACCTTATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12828485 original size:2 final size:2
Alignment explanation
Indices: 12828478--12828503 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12828468 ATTTAAAATT
12828478 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
12828504 ATGGATGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12829895 original size:26 final size:28
Alignment explanation
Indices: 12829858--12829909 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
12829848 GTGCAAAACA
12829858 ATAAAAATCTTAAACA-TTAAAAATATT
1 ATAAAAATCTTAAACATTTAAAAATATT
*
12829885 ATAAAAA-CTTAAATATTTAAAAATA
1 ATAAAAATCTTAAACATTTAAAAATA
12829910 ATAGAAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAAAAATCTTAAACATTTAAAAATATT
Found at i:12829917 original size:26 final size:25
Alignment explanation
Indices: 12829852--12829917 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 25
12829842 GAATGAGTGC
*
12829852 AAAACAATAAAAATCTTAAACATTA
1 AAAATAATAAAAATCTTAAACATTA
*
12829877 AAAATATTATAAAAA-CTTAAATATTTA
1 AAAATA--ATAAAAATCTTAAACA-TTA
12829904 AAAATAATAGAAAA
1 AAAATAATA-AAAA
12829918 GGAACATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
25 8 0.23
26 11 0.31
27 16 0.46
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (25 bp):
AAAATAATAAAAATCTTAAACATTA
Found at i:12830446 original size:14 final size:15
Alignment explanation
Indices: 12830422--12830455 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
12830412 AACTATCAGA
12830422 GTTTATAAAACAGTT
1 GTTTATAAAACAGTT
*
12830437 GTTT-TAAAACATTT
1 GTTTATAAAACAGTT
12830451 GTTTA
1 GTTTA
12830456 GTTTAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (15 bp):
GTTTATAAAACAGTT
Found at i:12843322 original size:2 final size:2
Alignment explanation
Indices: 12843315--12843377 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
12843305 TAGGATTGGA
12843315 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
12843357 AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC A
12843378 TATCTATATC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12844100 original size:10 final size:10
Alignment explanation
Indices: 12844085--12844113 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
12844075 AACAGTTCCC
12844085 GAACCAACTG
1 GAACCAACTG
12844095 GAACCAACTG
1 GAACCAACTG
12844105 GAACCAACT
1 GAACCAACT
12844114 CCATTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.31, G:0.17, T:0.10
Consensus pattern (10 bp):
GAACCAACTG
Found at i:12846092 original size:55 final size:55
Alignment explanation
Indices: 12846014--12846121 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 55
12846004 CATAACCGTT
12846014 CTATCCACAGATCAATGTCTTAAAATGCTAGAATTCG-CAAGTTAACATAAACTAC
1 CTATCCACAGATCAATGTCTTAAAATGCTAGAATT-GACAAGTTAACATAAACTAC
*
12846069 CTATCCACAGATCAATGTGTTAAAATGCTAGAATTGACAAGTTAACATAAACT
1 CTATCCACAGATCAATGTCTTAAAATGCTAGAATTGACAAGTTAACATAAACT
12846122 GCATACGAAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
54 1 0.02
55 50 0.98
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (55 bp):
CTATCCACAGATCAATGTCTTAAAATGCTAGAATTGACAAGTTAACATAAACTAC
Found at i:12849160 original size:18 final size:18
Alignment explanation
Indices: 12849137--12849173 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
12849127 CATTAGCCCC
12849137 TAATTTCCACAATGTCGT
1 TAATTTCCACAATGTCGT
12849155 TAATTTCCACAATGTCGT
1 TAATTTCCACAATGTCGT
12849173 T
1 T
12849174 TATCATTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (18 bp):
TAATTTCCACAATGTCGT
Found at i:12849790 original size:25 final size:25
Alignment explanation
Indices: 12849757--12849805 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
12849747 GGCCAAAATC
*
12849757 GAAGCTCTCTTTCATTTCTCTCGTT
1 GAAGCTCTCTCTCATTTCTCTCGTT
12849782 GAAGCTCTCTCTCATTTCTCTCGT
1 GAAGCTCTCTCTCATTTCTCTCGT
12849806 CTCTAGCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.31, G:0.12, T:0.45
Consensus pattern (25 bp):
GAAGCTCTCTCTCATTTCTCTCGTT
Found at i:12850035 original size:15 final size:15
Alignment explanation
Indices: 12850003--12850055 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
12849993 ATAGTTTTTG
* * *
12850003 TGGTATTTCTTATTT
1 TGGTTTTTCTTCTAT
12850018 TGGTTTTTCTTCTAT
1 TGGTTTTTCTTCTAT
*
12850033 TGGGTTTTTCTGCTAT
1 T-GGTTTTTCTTCTAT
12850049 TGTGTTT
1 TG-GTTT
12850056 ATAGTTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 14 0.44
16 18 0.56
ACGTcount: A:0.08, C:0.09, G:0.19, T:0.64
Consensus pattern (15 bp):
TGGTTTTTCTTCTAT
Found at i:12850040 original size:16 final size:16
Alignment explanation
Indices: 12850019--12850055 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
12850009 TTCTTATTTT
*
12850019 GGTTTTTCTTCTATTG
1 GGTTTTTCTGCTATTG
12850035 GGTTTTTCTGCTATTG
1 GGTTTTTCTGCTATTG
*
12850051 TGTTT
1 GGTTT
12850056 ATAGTTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.05, C:0.11, G:0.22, T:0.62
Consensus pattern (16 bp):
GGTTTTTCTGCTATTG
Found at i:12850047 original size:63 final size:63
Alignment explanation
Indices: 12849972--12850097 Score: 184
Period size: 63 Copynumber: 2.0 Consensus size: 63
12849962 TTCTACTTTT
* * *
12849972 GGTTTTTTTGCTATTGTGCTTATAGTTTTTGTG-GTATTTCTTATTTTGGTTTTTCTT-CTATTG
1 GGTTTTTCTGCTATTGTGCTTATAGTTTTTGTGAGT-TTTCTTATTCTAGTTTTT-TTGCTATTG
*
12850035 GGTTTTTCTGCTATTGTGTTTATAGTTTTTGTGAGTTTTCTTATTCTAGTTTTTTTGCTATTG
1 GGTTTTTCTGCTATTGTGCTTATAGTTTTTGTGAGTTTTCTTATTCTAGTTTTTTTGCTATTG
12850098 CGATTTCTAG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
62 2 0.04
63 53 0.93
64 2 0.04
ACGTcount: A:0.10, C:0.08, G:0.19, T:0.63
Consensus pattern (63 bp):
GGTTTTTCTGCTATTGTGCTTATAGTTTTTGTGAGTTTTCTTATTCTAGTTTTTTTGCTATTG
Found at i:12852805 original size:40 final size:37
Alignment explanation
Indices: 12852718--12852827 Score: 127
Period size: 35 Copynumber: 2.9 Consensus size: 37
12852708 GTTTTCCTCA
*
12852718 TTGAAATACCATACCTACATTT-TACAACTCGGTATAG
1 TTGAAATACCATACCTACATTTCT-CAACTCAGTATAG
* *
12852755 --GAAATGCCATACCTACATTTCTTAACTCAGTATAG
1 TTGAAATACCATACCTACATTTCTCAACTCAGTATAG
*
12852790 ATTTGATAATACCATACCTACATTTCACAACTCAGTAT
1 --TTGA-AATACCATACCTACATTTCTCAACTCAGTAT
12852828 GGATGATACA
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
35 30 0.49
36 1 0.02
39 2 0.03
40 28 0.46
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (37 bp):
TTGAAATACCATACCTACATTTCTCAACTCAGTATAG
Found at i:12853760 original size:9 final size:9
Alignment explanation
Indices: 12853746--12853772 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
12853736 TCCAATTTTG
12853746 CCCTTATTT
1 CCCTTATTT
12853755 CCCTTATTT
1 CCCTTATTT
12853764 CCCTTATTT
1 CCCTTATTT
12853773 TTCTGCTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.33, G:0.00, T:0.56
Consensus pattern (9 bp):
CCCTTATTT
Found at i:12855018 original size:31 final size:29
Alignment explanation
Indices: 12854971--12855030 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
12854961 AATAAAGAAA
* *
12854971 ATAATAATAAAAAATATTTTTCTAATAAT
1 ATAATAAAAAAAAATATATTTCTAATAAT
*
12855000 ATAATAAAAGAAATAATATATTTGTAATAAT
1 ATAATAAAA-AAA-AATATATTTCTAATAAT
12855031 TGTAGAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 8 0.31
30 3 0.12
31 15 0.58
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (29 bp):
ATAATAAAAAAAAATATATTTCTAATAAT
Found at i:12855237 original size:3 final size:3
Alignment explanation
Indices: 12855223--12855305 Score: 114
Period size: 3 Copynumber: 27.7 Consensus size: 3
12855213 AAATATACAC
* *
12855223 TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
12855271 TAA TAA TAT TAA TAA TAT TAGA -AA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA
12855306 TTTAATAAAG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.01
3 69 0.99
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:12857213 original size:77 final size:76
Alignment explanation
Indices: 12857053--12857263 Score: 271
Period size: 77 Copynumber: 2.7 Consensus size: 76
12857043 AGAAACTAAA
* * * * *
12857053 AGGCTCAACTCACTTCTCGCAATATGAGTCAATTTTTTTGGAAAAACATAAATTGAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTT-GAAAAATA-AAACTAAAAATACCTC
*
12857118 AGCATGTGTCCCG
64 AGCATGTGACCCG
* *
12857131 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAATAGAAACTAAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTGAAAAATA-AAACTAAAAATACCTCA
**
12857196 GTGTGTGACCCG
65 GCATGTGACCCG
* *
12857208 AGGCTCAACTCACCTATCGCAATATGAGTTAATTTTTTTTGAAACAT-AAACTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTAA-TTTTTTTGAAAAATAAAACTAAAA
12857264 GGCTCAACTC
Statistics
Matches: 117, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
76 9 0.08
77 60 0.51
78 48 0.41
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (76 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTGAAAAATAAAACTAAAAATACCTCAG
CATGTGACCCG
Found at i:12857308 original size:55 final size:55
Alignment explanation
Indices: 12857208--12857312 Score: 147
Period size: 55 Copynumber: 1.9 Consensus size: 55
12857198 GTGTGACCCG
* ***
12857208 AGGCTCAACTCACCTATCGCAATATGAGTTAATTTTTTTTGAAACATAAACTAAA
1 AGGCTCAACTCACCTATCGCAATATGAGTCAATTTTTTGAAAAACATAAACTAAA
* * *
12857263 AGGCTCAACTCACTTCTCGCAATATGAGTCGATTTTTTGAAAAACATAAA
1 AGGCTCAACTCACCTATCGCAATATGAGTCAATTTTTTGAAAAACATAAA
12857313 TTGAAAATAC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 43 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.31
Consensus pattern (55 bp):
AGGCTCAACTCACCTATCGCAATATGAGTCAATTTTTTGAAAAACATAAACTAAA
Found at i:12857366 original size:131 final size:132
Alignment explanation
Indices: 12857131--12857376 Score: 368
Period size: 131 Copynumber: 1.9 Consensus size: 132
12857121 ATGTGTCCCG
* * *
12857131 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAATAGAAACTAAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTGAAAAACAGAAACTAAAAATACCTCA
**
12857196 GTGTGTGACCCGAGGCTCAACTCACCTATCGCAATATGAGTTAATTTTTTTTGAAACATAAACTA
66 GCATGTGACCCGAGGCTCAACTCACCTATCGCAATATGAGTTAATTTTTTTTGAAACATAAACTA
12857261 AA
131 AA
* * * *
12857263 AGGCTCAACTCACTTCTCGCAATATGAGTCGA-TTTTTTGAAAAACATAAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTGAAAAACAGAAACTAAAAATACCTCA
* * * *
12857327 GCATGTGTCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTT
66 GCATGTGACCCGAGGCTCAACTCACCTATCGCAATATGAGTTAATTTTTT
12857377 AAAAAAAATA
Statistics
Matches: 101, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
131 72 0.71
132 29 0.29
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (132 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTGAAAAACAGAAACTAAAAATACCTCA
GCATGTGACCCGAGGCTCAACTCACCTATCGCAATATGAGTTAATTTTTTTTGAAACATAAACTA
AA
Found at i:12857368 original size:208 final size:211
Alignment explanation
Indices: 12856923--12857465 Score: 839
Period size: 212 Copynumber: 2.6 Consensus size: 211
12856913 AAACTGACGT
* * * * * * *
12856923 TCAACTCATCTCTCGGATTATGAGTT-A-ATTTTTGAAAAAAGTAAAAATTAAAAATACCTTAGT
1 TCAACTCACCTCTCGTAATATGAGTTGATTTTTTTG-AAAAA-TAGAAACTAAAAATACCTCAGT
* *
12856986 GTGTGACCTGAGGCTCAACTGACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAACTA
64 GTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTG-AAAACAGAAACTA
12857051 AAAGGCTCAACTCACTTCTCGCAATATGAGTCAATTTTTTTGGAAAAACATAAATTGAAAATACC
128 AAAGGCTCAACTCACTTCTCGCAATATGAGTCAATTTTTTTGGAAAAACATAAATTGAAAATACC
12857116 TCAGCATGTGTCCCGAGGC
193 TCAGCATGTGTCCCGAGGC
12857135 TCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAATAGAAACTAAAAATACCTCAGTGT
1 TCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAATAGAAACTAAAAATACCTCAGTGT
* * *
12857200 GTGACCCGAGGCTCAACTCACCTATCGCAATATGAGTTAATTTTTTTTG-AAACATAAACTAAAA
66 GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAACAGAAACTAAAA
*
12857264 GGCTCAACTCACTTCTCGCAATATGAGTCGA-TTTTTT-GAAAAACATAAATTGAAAATACCTCA
131 GGCTCAACTCACTTCTCGCAATATGAGTCAATTTTTTTGGAAAAACATAAATTGAAAATACCTCA
12857327 GCATGTGTCCCGAGGC
196 GCATGTGTCCCGAGGC
** *
12857343 TCAACTCACCTCTCGTAATATGAGTTGATTTTTTAAAAAAAATAGAAACTAAAAATACCTCAGCG
1 TCAACTCACCTCTCGTAATATGAGTTGATTTTTT-TGAAAAATAGAAACTAAAAATACCTCAGTG
* *
12857408 TGTGACCCGAGGCTCAACTCACCTCTTGTAATATGAGTTGATTTTTTTT-AAAA-AGAAA
65 TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAACAGAAA
12857466 GAAACTAAAA
Statistics
Matches: 306, Mismatches: 21, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
208 80 0.26
209 81 0.26
210 44 0.14
212 89 0.29
213 6 0.02
214 6 0.02
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (211 bp):
TCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAATAGAAACTAAAAATACCTCAGTGT
GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAACAGAAACTAAAA
GGCTCAACTCACTTCTCGCAATATGAGTCAATTTTTTTGGAAAAACATAAATTGAAAATACCTCA
GCATGTGTCCCGAGGC
Found at i:12857427 original size:78 final size:78
Alignment explanation
Indices: 12857263--12857539 Score: 380
Period size: 79 Copynumber: 3.6 Consensus size: 78
12857253 ATAAACTAAA
* * * * * *
12857263 AGGCTCAACTCACTTCTCGCAATATGAGTCGATTTTTTGAAAAACAT--AAATTGAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAAAATAGAAACTAAAAATACCTC
* *
12857326 AGCATGTGTCCCG
66 AGCGTGTGACCCG
*
12857339 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTAAAAAAAATAGAAACTAAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAAAATAGAAACTAAAAATACCTC
12857404 AGCGTGTGACCCG
66 AGCGTGTGACCCG
* * *
12857417 AGGCTCAACTCACCTCTTGTAATATGAGTTGATTTTTTTTAAAAAGAA-AGAAACTAAAAATACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTAAAAAAAATAGAAACTAAAAATACC
*
12857481 TTAGCGTGTGACCCG
64 TCAGCGTGTGACCCG
* *
12857496 AGACTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAA
12857540 CAGAAATAAA
Statistics
Matches: 180, Mismatches: 17, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
76 42 0.23
77 10 0.06
78 56 0.31
79 59 0.33
80 13 0.07
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (78 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAAAATAGAAACTAAAAATACCTC
AGCGTGTGACCCG
Found at i:12871801 original size:3 final size:3
Alignment explanation
Indices: 12871788--12871931 Score: 72
Period size: 3 Copynumber: 47.0 Consensus size: 3
12871778 AAAAGCAAAT
*
12871788 ATA AT- ATA ATA ATA AT- ATCA A-A ATA A-A ATA ATTA AAA ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA A-TA ATA ATA ATA
*
12871831 CT- ATA TATA A-A CATA TATA TATA CATA TATA ATA ATA AT- ATA CACTA
1 ATA ATA -ATA ATA -ATA -ATA -ATA -ATA -ATA ATA ATA ATA ATA -A-TA
* *
12871878 ATA ATA ATA ATA GTA ATA AT- ATAA ATA ATA TTA GA-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA ATA ATA ATA
*
12871923 ATA TTA ATA
1 ATA ATA ATA
12871932 TTTAATAAAG
Statistics
Matches: 111, Mismatches: 13, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
2 15 0.14
3 69 0.62
4 25 0.23
5 2 0.02
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:12872518 original size:12 final size:13
Alignment explanation
Indices: 12872501--12872531 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
12872491 AAAAAGGTAC
12872501 TTTTTTAGTTT-T
1 TTTTTTAGTTTCT
12872513 TTTTTTAGTTTCT
1 TTTTTTAGTTTCT
12872526 TTTTTT
1 TTTTTT
12872532 TGCTTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (13 bp):
TTTTTTAGTTTCT
Found at i:12875754 original size:21 final size:21
Alignment explanation
Indices: 12875730--12875800 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 21
12875720 TACTTATCGG
12875730 TTTACATGGATTTAGTTTCTT
1 TTTACATGGATTTAGTTTCTT
* * **
12875751 TTTAATAATGG-TTATACTTATCGG
1 TTT-A-CATGGATT-TAGTT-TCTT
12875775 TTTACATGGATTTAGTTTCTT
1 TTTACATGGATTTAGTTTCTT
12875796 TTTAC
1 TTTAC
12875801 TTTTATTTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
21 10 0.27
22 11 0.30
23 11 0.30
24 5 0.14
ACGTcount: A:0.23, C:0.10, G:0.14, T:0.54
Consensus pattern (21 bp):
TTTACATGGATTTAGTTTCTT
Found at i:12875774 original size:45 final size:45
Alignment explanation
Indices: 12875710--12875799 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
12875700 AATTGTCAGG
12875710 ATAATGGTTATACTTATCGGTTTACATGGATTTAGTTTCTTTTTA
1 ATAATGGTTATACTTATCGGTTTACATGGATTTAGTTTCTTTTTA
12875755 ATAATGGTTATACTTATCGGTTTACATGGATTTAGTTTCTTTTTA
1 ATAATGGTTATACTTATCGGTTTACATGGATTTAGTTTCTTTTTA
12875800 CTTTTATTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.24, C:0.09, G:0.16, T:0.51
Consensus pattern (45 bp):
ATAATGGTTATACTTATCGGTTTACATGGATTTAGTTTCTTTTTA
Found at i:12875783 original size:22 final size:22
Alignment explanation
Indices: 12875713--12875783 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
12875703 TGTCAGGATA
12875713 ATGGTTATACTTATCGGTTTAC
1 ATGGTTATACTTATCGGTTTAC
* ** *
12875735 ATGGATT-TAGTT-TCTTTTTAATA
1 ATGG-TTATACTTATCGGTTT-A-C
12875758 ATGGTTATACTTATCGGTTTAC
1 ATGGTTATACTTATCGGTTTAC
12875780 ATGG
1 ATGG
12875784 ATTTAGTTTC
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
21 5 0.14
22 15 0.42
23 11 0.31
24 5 0.14
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.48
Consensus pattern (22 bp):
ATGGTTATACTTATCGGTTTAC
Found at i:12883803 original size:26 final size:24
Alignment explanation
Indices: 12883774--12883822 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
12883764 TAAATAAAAA
* *
12883774 ATTTTAAAATATAATAAATCAAATAC
1 ATTTAAAAACATAA-AAA-CAAATAC
12883800 ATTTAAAAACATAAAAACAAATA
1 ATTTAAAAACATAAAAACAAATA
12883823 TTAAAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAC
Found at i:12886168 original size:2 final size:2
Alignment explanation
Indices: 12886161--12886196 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12886151 TCATTTAACC
12886161 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12886197 CATGACTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12886746 original size:29 final size:27
Alignment explanation
Indices: 12886667--12886761 Score: 88
Period size: 27 Copynumber: 3.4 Consensus size: 27
12886657 GAATATCCAA
* *
12886667 CCCAAACACACCCGGAATATATAAATCCT
1 CCCAAACACA-CCGGTATATATATA-CCT
* *
12886696 -CCATAACATACCAGTATA-ATATAGCCT
1 CCCA-AACACACCGGTATATATATA-CCT
12886723 CCCAAACACACCGGTATATCATAT-CCT
1 CCCAAACACACCGGTATAT-ATATACCT
12886750 CCCAAACACACC
1 CCCAAACACACC
12886762 AAAAAGCATT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
27 34 0.62
28 12 0.22
29 9 0.16
ACGTcount: A:0.39, C:0.36, G:0.06, T:0.19
Consensus pattern (27 bp):
CCCAAACACACCGGTATATATATACCT
Found at i:12887706 original size:3 final size:3
Alignment explanation
Indices: 12887698--12887751 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
12887688 TTTTAAATCA
* * *
12887698 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT ATT AAC AAT AAT AATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
12887747 AAT AA
1 AAT AA
12887752 AATCTAAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:12890357 original size:51 final size:49
Alignment explanation
Indices: 12890195--12890359 Score: 224
Period size: 49 Copynumber: 3.3 Consensus size: 49
12890185 GCTATTGTGA
*
12890195 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
12890244 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * *
12890294 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
*
12890344 GGTCACATATGT-GTAC
1 GGTCACATGTGTAGTAC
12890360 CAGATAGCTT
Statistics
Matches: 101, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
48 4 0.04
49 52 0.51
50 4 0.04
51 41 0.41
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:12893262 original size:18 final size:18
Alignment explanation
Indices: 12893231--12893281 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
12893221 TGTATTATAA
12893231 TATTAATTAATAAAATAT
1 TATTAATTAATAAAATAT
* *
12893249 TATTACTTATTAAAATAT
1 TATTAATTAATAAAATAT
*
12893267 TATTATTTAATAAAA
1 TATTAATTAATAAAA
12893282 ATATCATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAATTAATAAAATAT
Found at i:12895771 original size:2 final size:2
Alignment explanation
Indices: 12895766--12895798 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12895756 TTATTAAAAT
12895766 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12895799 GATAAAGTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12898367 original size:2 final size:2
Alignment explanation
Indices: 12898360--12898398 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
12898350 TAGTGAATTA
* *
12898360 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12898399 ACTATTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:12901406 original size:25 final size:25
Alignment explanation
Indices: 12901372--12901423 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
12901362 GTTTCATTTA
12901372 AGCAAGAGGCATAGCTGCTGTTTGT
1 AGCAAGAGGCATAGCTGCTGTTTGT
12901397 AGCAAGAGGCATAGCTGCTGTTTGT
1 AGCAAGAGGCATAGCTGCTGTTTGT
12901422 AG
1 AG
12901424 TTTTTTTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (25 bp):
AGCAAGAGGCATAGCTGCTGTTTGT
Found at i:12905453 original size:22 final size:21
Alignment explanation
Indices: 12905405--12905454 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
12905395 TAAAAAAAAT
* *
12905405 TATTTTTTGTTGTTTTCTTAT
1 TATTTTTTGTTATTTTCTTAC
* *
12905426 TGTTTTGTTGTTATTTTTTTAC
1 TATTTT-TTGTTATTTTCTTAC
12905448 TATTTTT
1 TATTTTT
12905455 AACTATTTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.10, C:0.04, G:0.10, T:0.76
Consensus pattern (21 bp):
TATTTTTTGTTATTTTCTTAC
Found at i:12905657 original size:18 final size:18
Alignment explanation
Indices: 12905636--12905672 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12905626 AGTATTTTTG
*
12905636 ATATATTATATTTAAAAA
1 ATATATTATATATAAAAA
*
12905654 ATATATTTTATATAAAAA
1 ATATATTATATATAAAAA
12905672 A
1 A
12905673 ATTTAATACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATATTATATATAAAAA
Found at i:12910557 original size:30 final size:30
Alignment explanation
Indices: 12910521--12910582 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
12910511 TATTCATCTC
**
12910521 TAATTTTTCAATAAATC-TGAACTTTTAATT
1 TAATTTTTCAATAAA-CAAAAACTTTTAATT
12910551 TAATTTTTCAATAAACAAAAACTTTTAATT
1 TAATTTTTCAATAAACAAAAACTTTTAATT
12910581 TA
1 TA
12910583 TTTCATTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.47
Consensus pattern (30 bp):
TAATTTTTCAATAAACAAAAACTTTTAATT
Found at i:12915726 original size:120 final size:120
Alignment explanation
Indices: 12915511--12916461 Score: 1006
Period size: 120 Copynumber: 7.9 Consensus size: 120
12915501 CAGATTCCTC
* * * * * * *
12915511 AACATTGGCTCCAGAGACAGTGGCCTTAGCACTATCATTAGGTAAACCATCTCCGTCGTAATCAC
1 AACATTAGCTTCAGAGACAGTGGCCTCAGCACTATCATTAGCTAAACCATCTCCATTGCAATCAC
* * * *
12915576 CATCAGCAGCTACAGTCATTTCAGAGCCCTCTTTCTCTTCTGACCTGGAATCAAT
66 CATCATCAGCTACAGCCATTTCAGAGCCCTCATTCTCTTTTGACCTGGAATCAAT
* * * **
12915631 AACATTAGTTTCAGAGACAATGGCGTTTGCACTATCATTAGCTAAACCATCTCCATTGCAATCAC
1 AACATTAGCTTCAGAGACAGTGGCCTCAGCACTATCATTAGCTAAACCATCTCCATTGCAATCAC
* * * * * * *
12915696 CATCAGCAGCTACGGCCACTCCAGAACCCTCTTTCTCTTCTGACCTGGAATCAAT
66 CATCATCAGCTACAGCCATTTCAGAGCCCTCATTCTCTTTTGACCTGGAATCAAT
* * * *
12915751 AACATTGGCTTCGGAGACAGTGGCCTCAGCACTATCATTAGATAAACCAT-TGGCATTGCAATCA
1 AACATTAGCTTCAGAGACAGTGGCCTCAGCACTATCATTAGCTAAACCATCT-CCATTGCAATCA
* * *
12915815 CCACCATCAGCTACAGCCATTTCAGAGCCCGCATTCTCTTTTGACCAGGAATCAAT
65 CCATCATCAGCTACAGCCATTTCAGAGCCCTCATTCTCTTTTGACCTGGAATCAAT
** * * * * *** *
12915871 AACGCTGGCTTCAGAGACTGTGGTCTTAGCACTATCATTAGCTAAATTGTCTCCATTGCTATCAC
1 AACATTAGCTTCAGAGACAGTGGCCTCAGCACTATCATTAGCTAAACCATCTCCATTGCAATCAC
** ** **
12915936 CATCATCAGCTACAGTTATTTTGGAGCCCTCATTCTCTTTTGACCTGGAATTGAT
66 CATCATCAGCTACAGCCATTTCAGAGCCCTCATTCTCTTTTGACCTGGAATCAAT
* * *
12915991 AACGTTGGCTTCAGAGACAGTGGCCTCAGCATTATCATTAGCTAAACCATCTCCATTGCAATCAC
1 AACATTAGCTTCAGAGACAGTGGCCTCAGCACTATCATTAGCTAAACCATCTCCATTGCAATCAC
* * * *
12916056 CATCATCGGCTACAGCCATTTCAGAGCCCTCATTATCTTTTGACCTGAAATCAAG
66 CATCATCAGCTACAGCCATTTCAGAGCCCTCATTCTCTTTTGACCTGGAATCAAT
* * * * * * * * *
12916111 AACAGTATCTTCAGAAACAGTTGCCTCAACACTGTCATT-GACAAAACCATCTCCATTGAAATCT
1 AACATTAGCTTCAGAGACAGTGGCCTCAGCACTATCATTAG-CTAAACCATCTCCATTGCAATCA
* ** * * ** *
12916175 CCATCACCAGCTACAGCCATTTCATTGCCCCCATTCTCTTTTGACCTGAAATTGAG
65 CCATCATCAGCTACAGCCATTTCAGAGCCCTCATTCTCTTTTGACCTGGAATCAAT
* * * * ** *
12916231 CACATTAGCTTCAGAAACAGGGGCCTCAACACTATCATTAATTAAACCATCTCCACTGCAATCAC
1 AACATTAGCTTCAGAGACAGTGGCCTCAGCACTATCATTAGCTAAACCATCTCCATTGCAATCAC
* * * * * * *
12916296 CATCATCAGCTACTGTCATTTCGGAGCACTCACTCTCTTTTGACCTGAAATCAAG
66 CATCATCAGCTACAGCCATTTCAGAGCCCTCATTCTCTTTTGACCTGGAATCAAT
* * * * * * * * * *
12916351 AACATCACCTTCAGAAACAGGGGCTTCAACACTATAATAAACTAAACCATCTCCACTGCAATCAC
1 AACATTAGCTTCAGAGACAGTGGCCTCAGCACTATCATTAGCTAAACCATCTCCATTGCAATCAC
* *
12916416 CATCATCAGCTACAGCTATTTCGGAGCCCTCATTCTCTTTTGACCT
66 CATCATCAGCTACAGCCATTTCAGAGCCCTCATTCTCTTTTGACCT
12916462 AAAATCAAGG
Statistics
Matches: 698, Mismatches: 129, Indels: 8
0.84 0.15 0.01
Matches are distributed among these distances:
119 2 0.00
120 695 1.00
121 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (120 bp):
AACATTAGCTTCAGAGACAGTGGCCTCAGCACTATCATTAGCTAAACCATCTCCATTGCAATCAC
CATCATCAGCTACAGCCATTTCAGAGCCCTCATTCTCTTTTGACCTGGAATCAAT
Found at i:12920930 original size:19 final size:19
Alignment explanation
Indices: 12920886--12920930 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
12920876 AGAAGATAAA
12920886 TAAATTA-ATAATAAAAAC
1 TAAATTACATAATAAAAAC
*
12920904 TAAA-TACATTAA-AAAAAG
1 TAAATTACA-TAATAAAAAC
12920922 TAAATTACA
1 TAAATTACA
12920931 AAAATAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 2 0.09
18 14 0.61
19 7 0.30
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAATTACATAATAAAAAC
Found at i:12921159 original size:18 final size:18
Alignment explanation
Indices: 12921136--12921178 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
12921126 GAATAGGTAT
12921136 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
12921154 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
12921172 TTAATTA
1 TTAATTA
12921179 TACTTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:12927639 original size:24 final size:23
Alignment explanation
Indices: 12927596--12927650 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
12927586 ATCTTCCATT
12927596 TTATTT-TTTTAATATCTATTTC
1 TTATTTATTTTAATATCTATTTC
* * *
12927618 TTATTTATTTATAATTTTTATTTG
1 TTATTTATTT-TAATATCTATTTC
*
12927642 TTCTTTATT
1 TTATTTATT
12927651 CTCAAATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 6 0.22
23 3 0.11
24 18 0.67
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (23 bp):
TTATTTATTTTAATATCTATTTC
Found at i:12929496 original size:8 final size:8
Alignment explanation
Indices: 12929459--12929499 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
12929449 TAATTTTTTA
12929459 AAAATTAT
1 AAAATTAT
12929467 AAAGA-TAT
1 AAA-ATTAT
12929475 AAAA-TATT
1 AAAATTA-T
12929483 AAAATTAT
1 AAAATTAT
12929491 AAAATTAT
1 AAAATTAT
12929499 A
1 A
12929500 TTTTTACTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 3 0.10
8 24 0.80
9 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (8 bp):
AAAATTAT
Found at i:12930149 original size:20 final size:20
Alignment explanation
Indices: 12930126--12930188 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
12930116 ATATTTTATT
12930126 ATATTAAAAAATAGAAATAA
1 ATATTAAAAAATAGAAATAA
* *** *
12930146 ATA-TAATAAATA-TTTTATT
1 ATATTAAAAAATAGAAATA-A
12930165 ATATTAAAAAATAGAAATAA
1 ATATTAAAAAATAGAAATAA
12930185 ATAT
1 ATAT
12930189 AATAAATATT
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
18 2 0.07
19 11 0.37
20 15 0.50
21 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
ATATTAAAAAATAGAAATAA
Found at i:12930149 original size:39 final size:39
Alignment explanation
Indices: 12930103--12930208 Score: 203
Period size: 39 Copynumber: 2.7 Consensus size: 39
12930093 AAACCCTACC
12930103 ATAAATATAATAAATATTTTATTATATTAAAAAATAGAA
1 ATAAATATAATAAATATTTTATTATATTAAAAAATAGAA
12930142 ATAAATATAATAAATATTTTATTATATTAAAAAATAGAA
1 ATAAATATAATAAATATTTTATTATATTAAAAAATAGAA
*
12930181 ATAAATATAATAAATATTTTATTGTATT
1 ATAAATATAATAAATATTTTATTATATT
12930209 TAATATAAAT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 66 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (39 bp):
ATAAATATAATAAATATTTTATTATATTAAAAAATAGAA
Found at i:12930168 original size:19 final size:19
Alignment explanation
Indices: 12930107--12930168 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
12930097 CCTACCATAA
12930107 ATATAATAAATATTTTATT
1 ATATAATAAATATTTTATT
* *** *
12930126 ATATTAAAAAATA-GAAATAA
1 ATA-TAATAAATATTTTAT-T
12930146 ATATAATAAATATTTTATT
1 ATATAATAAATATTTTATT
12930165 ATAT
1 ATAT
12930169 TAAAAAATAG
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
ATATAATAAATATTTTATT
Found at i:12930343 original size:10 final size:11
Alignment explanation
Indices: 12930312--12930348 Score: 58
Period size: 12 Copynumber: 3.4 Consensus size: 11
12930302 ATTAATGATT
12930312 TAATATAAATA
1 TAATATAAATA
12930323 TAAATATAAATA
1 T-AATATAAATA
12930335 TAA-ATAAATA
1 TAATATAAATA
12930345 TAAT
1 TAAT
12930349 TATTATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.42
11 3 0.12
12 11 0.46
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATATAAATA
Found at i:12930347 original size:6 final size:6
Alignment explanation
Indices: 12930313--12930340 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12930303 TTAATGATTT
12930313 AATATA AATATA AATATA AATATA AATA
1 AATATA AATATA AATATA AATATA AATA
12930341 AATATAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:12936468 original size:20 final size:21
Alignment explanation
Indices: 12936430--12936471 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
12936420 TTTAATATTC
12936430 GATAAAAAAAGGTAATATTGTA
1 GATAAAAAAA-GTAATATTGTA
*
12936452 GATAAAAAAA-TAGTATTGTA
1 GATAAAAAAAGTAATATTGTA
12936472 AAAATTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
22 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.29
Consensus pattern (21 bp):
GATAAAAAAAGTAATATTGTA
Found at i:12942572 original size:36 final size:36
Alignment explanation
Indices: 12942481--12942575 Score: 145
Period size: 36 Copynumber: 2.6 Consensus size: 36
12942471 ATCCCAACTA
* * *
12942481 CTGTATACGTGAACAGTACCGTATTCGTAAATAGTG
1 CTGTATACGTGAATAGTACTGTATACGTAAATAGTG
* *
12942517 CCGTATATGTGAATAGTACTGTATACGTAAATAGTG
1 CTGTATACGTGAATAGTACTGTATACGTAAATAGTG
12942553 CTGTATACGTGAATAGTACTGTA
1 CTGTATACGTGAATAGTACTGTA
12942576 AACGGTCGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.33
Consensus pattern (36 bp):
CTGTATACGTGAATAGTACTGTATACGTAAATAGTG
Found at i:12942574 original size:18 final size:18
Alignment explanation
Indices: 12942479--12942575 Score: 113
Period size: 18 Copynumber: 5.4 Consensus size: 18
12942469 CAATCCCAAC
*
12942479 TACTGTATACGTGAACAG
1 TACTGTATACGTGAATAG
* * *
12942497 TACCGTATTCGTAAATAG
1 TACTGTATACGTGAATAG
* * *
12942515 TGCCGTATATGTGAATAG
1 TACTGTATACGTGAATAG
*
12942533 TACTGTATACGTAAATAG
1 TACTGTATACGTGAATAG
*
12942551 TGCTGTATACGTGAATAG
1 TACTGTATACGTGAATAG
12942569 TACTGTA
1 TACTGTA
12942576 AACGGTCGTA
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (18 bp):
TACTGTATACGTGAATAG
Found at i:12944412 original size:13 final size:13
Alignment explanation
Indices: 12944394--12944420 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12944384 GAAAACGTGC
12944394 TGAAATTTAAATA
1 TGAAATTTAAATA
12944407 TGAAATTTAAATA
1 TGAAATTTAAATA
12944420 T
1 T
12944421 AATAGTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (13 bp):
TGAAATTTAAATA
Found at i:12945407 original size:18 final size:18
Alignment explanation
Indices: 12945386--12945420 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12945376 CATGAGATTT
*
12945386 AAATAATAATAATTATTA
1 AAATAATAATAAATATTA
*
12945404 AAATATTAATAAATATT
1 AAATAATAATAAATATT
12945421 CAATTCAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATAATAATAAATATTA
Found at i:12948462 original size:34 final size:34
Alignment explanation
Indices: 12948419--12948486 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
12948409 TTATGTAAAA
12948419 AACAAAACTTCTTCAAAATAAGTGAATTTTTTTT
1 AACAAAACTTCTTCAAAATAAGTGAATTTTTTTT
*
12948453 AACAAAACTTCTTCAAAATAAGTGATTTTTTTTT
1 AACAAAACTTCTTCAAAATAAGTGAATTTTTTTT
12948487 CTTTCTCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.43
Consensus pattern (34 bp):
AACAAAACTTCTTCAAAATAAGTGAATTTTTTTT
Found at i:12950264 original size:28 final size:25
Alignment explanation
Indices: 12950233--12950303 Score: 67
Period size: 28 Copynumber: 2.8 Consensus size: 25
12950223 TTTAATTGAG
12950233 ATAATTTTCATTTAATAAATGATAATT
1 ATAATTTT-ATTTAATAAAT-ATAATT
*
12950260 AATAAGTTTTGTTCT-ATAAA-ATAATT
1 -ATAA-TTTTATT-TAATAAATATAATT
12950286 ATAATTTTATTTAA-AAAT
1 ATAATTTTATTTAATAAAT
12950304 TTAGACCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
23 4 0.11
24 7 0.19
25 4 0.11
26 6 0.16
28 11 0.30
29 5 0.14
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (25 bp):
ATAATTTTATTTAATAAATATAATT
Found at i:12950302 original size:22 final size:26
Alignment explanation
Indices: 12950254--12950303 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 26
12950244 TTAATAAATG
*
12950254 ATAATTAATAAGTTTTGTTCTATAAA
1 ATAATTAATAAGTTTTATTCTATAAA
12950280 ATAATT-ATAA-TTTTATT-TA-AAA
1 ATAATTAATAAGTTTTATTCTATAAA
12950302 AT
1 AT
12950304 TTAGACCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 5 0.22
23 2 0.09
24 6 0.26
25 4 0.17
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (26 bp):
ATAATTAATAAGTTTTATTCTATAAA
Found at i:12950419 original size:16 final size:16
Alignment explanation
Indices: 12950377--12950419 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
12950367 ATGAATATTA
*
12950377 TTGTTATAAGTGAAATG
1 TTGTTATAA-CGAAATG
12950394 TTGTCT-TAACGAAATG
1 TTGT-TATAACGAAATG
12950410 TTGTTATAAC
1 TTGTTATAAC
12950420 TAGTAAGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 1 0.04
16 14 0.61
17 7 0.30
18 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.42
Consensus pattern (16 bp):
TTGTTATAACGAAATG
Found at i:12953559 original size:13 final size:14
Alignment explanation
Indices: 12953538--12953566 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12953528 TGAAAAATGG
12953538 ATTAGAAAATATTT
1 ATTAGAAAATATTT
12953552 ATTA-AAAATATTT
1 ATTAGAAAATATTT
12953565 AT
1 AT
12953567 GAAGTTAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTAGAAAATATTT
Found at i:12954129 original size:31 final size:32
Alignment explanation
Indices: 12954080--12954143 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
12954070 ATATTAAATA
*
12954080 AGATGTTTATTAATTAAATA-ATTATATTATG
1 AGATGTTTATTAATTAAATATATTAAATTATG
*
12954111 AGATTTTTATGTAA-TAAATATATTAAATTATG
1 AGATGTTTAT-TAATTAAATATATTAAATTATG
12954143 A
1 A
12954144 CAAATGTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (32 bp):
AGATGTTTATTAATTAAATATATTAAATTATG
Found at i:12954279 original size:19 final size:19
Alignment explanation
Indices: 12954233--12954279 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
12954223 AGATTTTTAA
* * *
12954233 ATATAGATATTTTATTTTT
1 ATATATATATTTTATATAT
12954252 AT-TATTATATTTTATATAT
1 ATATA-TATATTTTATATAT
12954271 ATATATATA
1 ATATATATA
12954280 GTAAATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.09
19 19 0.83
20 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATATATATATTTTATATAT
Found at i:12955089 original size:15 final size:15
Alignment explanation
Indices: 12955066--12955109 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
12955056 TATCAAATTT
12955066 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
12955081 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
12955096 ATATTGATTGAAAT
1 ATATTGATTGAAAT
12955110 ATAATATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:12958011 original size:22 final size:23
Alignment explanation
Indices: 12957961--12958009 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
12957951 AAATTAAATA
*
12957961 AAAATTAAAATGACTTTTTTTAT
1 AAAATTAAAATGACATTTTTTAT
*
12957984 AAAATTGAAATGACATTTTTTAT
1 AAAATTAAAATGACATTTTTTAT
12958007 AAA
1 AAA
12958010 TTTTAAGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (23 bp):
AAAATTAAAATGACATTTTTTAT
Found at i:12962301 original size:7 final size:7
Alignment explanation
Indices: 12962286--12962317 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
12962276 AGAGATAACG
*
12962286 AGAATAA
1 AGAACAA
12962293 AGAACAA
1 AGAACAA
12962300 AGAACAA
1 AGAACAA
12962307 AGAACAA
1 AGAACAA
12962314 AGAA
1 AGAA
12962318 AATATGAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.72, C:0.09, G:0.16, T:0.03
Consensus pattern (7 bp):
AGAACAA
Found at i:12962455 original size:16 final size:16
Alignment explanation
Indices: 12962430--12962462 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12962420 TCTAATTCTA
12962430 ATAACAATTAGAATTT
1 ATAACAATTAGAATTT
*
12962446 ATAACTATTAGAATTT
1 ATAACAATTAGAATTT
12962462 A
1 A
12962463 AAGTACATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
ATAACAATTAGAATTT
Found at i:12962546 original size:8 final size:9
Alignment explanation
Indices: 12962533--12962569 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
12962523 ACTTTTTATC
*
12962533 ATTTTTTAA
1 ATTTTTAAA
12962542 ATTTTTAAA
1 ATTTTTAAA
12962551 ATTTTTAAA
1 ATTTTTAAA
12962560 ATTTTTAAA
1 ATTTTTAAA
12962569 A
1 A
12962570 ATTAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:12963307 original size:33 final size:33
Alignment explanation
Indices: 12963265--12963334 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
12963255 CACTTCCGCC
12963265 TAATATCGCGCCACACGCGGCCGCGCAACCGTG
1 TAATATCGCGCCACACGCGGCCGCGCAACCGTG
12963298 TAATATCGCGCCACACGCGGCCGCGCAACCGTG
1 TAATATCGCGCCACACGCGGCCGCGCAACCGTG
12963331 TAAT
1 TAAT
12963335 GTGCCTTCGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.23, C:0.37, G:0.26, T:0.14
Consensus pattern (33 bp):
TAATATCGCGCCACACGCGGCCGCGCAACCGTG
Found at i:12965298 original size:3 final size:3
Alignment explanation
Indices: 12965284--12965322 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
12965274 TTGTGTTGAC
* * *
12965284 ATT ATA ATT ATT ATT ATT ATT ATT GTT ATT ATA ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12965323 GATCAGTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:12966931 original size:3 final size:3
Alignment explanation
Indices: 12966923--12966966 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
12966913 AAGAATTTAC
* * * *
12966923 TAA TAA TAA CAA CAA CAA CAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
12966967 GGATTTATGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (3 bp):
TAA
Found at i:12974711 original size:120 final size:121
Alignment explanation
Indices: 12974576--12974799 Score: 314
Period size: 121 Copynumber: 1.9 Consensus size: 121
12974566 CTTATTTCTG
*
12974576 TTTTTGGTTTGCATG-TGCTTATTTCATTAAGCACAAAAAAGATTTAAAAT-AAAA-TT-ATTTT
1 TTTTTGGTATGCATGTTG-TTATTT-ATTAAGCAC-AAAAAGATTTAAAATAAAAACTTGATTTT
* * *
12974637 TTTTCTTCTGAAAATTAGAAACCAGAATT-GAAAAATTGTATCTTTTACTTTTCGTTTTT
63 TTTT-TTCTGAAAATCAGAAACCAAAATTAAAAAAATTGTATCTTTTACTTTTCGTTTTT
*
12974696 TTTTTTGTATGCATGTTGTTATTTATTAAGCACAAAAAGATTTAAAATAAAAATCTTGATTTTTT
1 TTTTTGGTATGCATGTTGTTATTTATTAAGCACAAAAAGATTTAAAATAAAAA-CTTGATTTTTT
*
12974761 TTTTTTGAAAATCAGAAACCAAAATTAAAAAAATTGTAT
65 TTTTCTGAAAATCAGAAACCAAAATTAAAAAAATTGTAT
12974800 TTTCAGAAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
118 15 0.16
119 13 0.14
120 19 0.21
121 25 0.27
122 20 0.22
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.44
Consensus pattern (121 bp):
TTTTTGGTATGCATGTTGTTATTTATTAAGCACAAAAAGATTTAAAATAAAAACTTGATTTTTTT
TTTCTGAAAATCAGAAACCAAAATTAAAAAAATTGTATCTTTTACTTTTCGTTTTT
Found at i:12975845 original size:17 final size:18
Alignment explanation
Indices: 12975813--12975846 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12975803 TTACAATTAA
12975813 AATAAACATAAATATATG
1 AATAAACATAAATATATG
*
12975831 AATAATCAT-AATATAT
1 AATAAACATAAATATAT
12975847 TAAAACAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (18 bp):
AATAAACATAAATATATG
Found at i:12978944 original size:25 final size:25
Alignment explanation
Indices: 12978911--12978960 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
12978901 AATCCCTCAT
12978911 TTTTTTTTAAAGAAGAAAATAAATA
1 TTTTTTTTAAAGAAGAAAATAAATA
12978936 TTTTTTTTAAAGAAGAAAATAAATA
1 TTTTTTTTAAAGAAGAAAATAAATA
12978961 AAAATTCACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (25 bp):
TTTTTTTTAAAGAAGAAAATAAATA
Found at i:12979815 original size:6 final size:6
Alignment explanation
Indices: 12979798--12979843 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
12979788 CCTAGACCTC
*
12979798 AAAAAT -AAAAT AAGAAT AAAAAT -AAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
12979844 TACTTTTCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
5 10 0.28
6 26 0.72
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (6 bp):
AAAAAT
Done.