Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr8
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: 19593398
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1222752 characters in sequence are not A, C, G, or T
File 5 of 50
Found at i:2637167 original size:23 final size:22
Alignment explanation
Indices: 2637135--2637224 Score: 92
Period size: 23 Copynumber: 4.0 Consensus size: 22
2637125 ACATTCTTTA
*
2637135 CTAACTAGTCACGCAATGCCTT
1 CTAACAAGTCACGCAATGCCTT
*
2637157 CCTAACAAGTCACACAATGCCTT
1 -CTAACAAGTCACGCAATGCCTT
* *
2637180 AATAACAAGTCACGCAATACCTAT
1 -CTAACAAGTCACGCAATGCCT-T
**
2637204 C-AATTAGTCACGCAATGCCTT
1 CTAACAAGTCACGCAATGCCTT
2637225 ATCAAAAACT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
21 1 0.02
22 16 0.29
23 38 0.68
24 1 0.02
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.24
Consensus pattern (22 bp):
CTAACAAGTCACGCAATGCCTT
Found at i:2637215 original size:22 final size:23
Alignment explanation
Indices: 2637187--2637229 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
2637177 CTTAATAACA
2637187 AGTCACGCAATACC-TATCAATT
1 AGTCACGCAATACCTTATCAATT
*
2637209 AGTCACGCAATGCCTTATCAA
1 AGTCACGCAATACCTTATCAA
2637230 AAACTAGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.26
Consensus pattern (23 bp):
AGTCACGCAATACCTTATCAATT
Found at i:2637239 original size:26 final size:26
Alignment explanation
Indices: 2637137--2637621 Score: 409
Period size: 26 Copynumber: 20.1 Consensus size: 26
2637127 ATTCTTTACT
**
2637137 AACTAGTCACGCAATGCC-T-TC-CT
1 AACTAGTCACGCAATGCCTTATCAAA
* * *
2637160 AACAAGTCACACAATGCC-T-T-AAT
1 AACTAGTCACGCAATGCCTTATCAAA
* *
2637183 AACAAGTCACGCAATACC-TATC---
1 AACTAGTCACGCAATGCCTTATCAAA
*
2637205 AATTAGTCACGCAATGCCTTATCAAA
1 AACTAGTCACGCAATGCCTTATCAAA
*
2637231 AACTAGTCACGCAA----TTCTC--A
1 AACTAGTCACGCAATGCCTTATCAAA
* *
2637251 AAGTAAGTCACGCAATGCCTTATCAGA
1 AACT-AGTCACGCAATGCCTTATCAAA
* *
2637278 AACTAGTCATGCAATTCCTTATCAAA
1 AACTAGTCACGCAATGCCTTATCAAA
2637304 AACTAGTCACGCAATGCC---T-AAA
1 AACTAGTCACGCAATGCCTTATCAAA
**
2637326 GTC-AGTCACGCAATGCC-TATC---
1 AACTAGTCACGCAATGCCTTATCAAA
* * * *
2637347 AACTAGTCATGTAATGCTTTATCAGA
1 AACTAGTCACGCAATGCCTTATCAAA
*
2637373 AACTAGTCACGCAATACCTTATCAAA
1 AACTAGTCACGCAATGCCTTATCAAA
2637399 AACTAGTCACGCAATGCC----CAAA
1 AACTAGTCACGCAATGCCTTATCAAA
**
2637421 GTC-AGTCACGCAATGCC----CAAA
1 AACTAGTCACGCAATGCCTTATCAAA
** *
2637442 GTC-AATCACGCAATGCC-TATC---
1 AACTAGTCACGCAATGCCTTATCAAA
*
2637463 AACTAGTCACGCAATGTCTTATCAAA
1 AACTAGTCACGCAATGCCTTATCAAA
*
2637489 AACTAGTCACGCAATGACTTATCAAA
1 AACTAGTCACGCAATGCCTTATCAAA
*
2637515 AACTAGTCACGCAATGCCTTCTCAAA
1 AACTAGTCACGCAATGCCTTATCAAA
2637541 AACTAGTCACGCAATGCCTTATCAAA
1 AACTAGTCACGCAATGCCTTATCAAA
* * *
2637567 AACTAATCACGCAATGACTTATTAAA
1 AACTAGTCACGCAATGCCTTATCAAA
2637593 AACTAGTCACGCAATGCCTTATCAAA
1 AACTAGTCACGCAATGCCTTATCAAA
2637619 AAC
1 AAC
2637622 CAAACACAAA
Statistics
Matches: 384, Mismatches: 48, Indels: 57
0.79 0.10 0.12
Matches are distributed among these distances:
20 4 0.01
21 60 0.16
22 51 0.13
23 50 0.13
24 2 0.01
25 4 0.01
26 209 0.54
27 4 0.01
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.24
Consensus pattern (26 bp):
AACTAGTCACGCAATGCCTTATCAAA
Found at i:2637298 original size:73 final size:69
Alignment explanation
Indices: 2637186--2637611 Score: 296
Period size: 73 Copynumber: 5.9 Consensus size: 69
2637176 CCTTAATAAC
* * * *
2637186 AAGTCACGCAATACCTATCAATTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAAT-TCTC
1 AAGTCACGCAATGCCTATCAACTAGTCATGCAATGCCTTATCAAAAACTAGTCACGCAATGCCT-
2637250 AAAGT
65 AAAGT
*
2637255 AAGTCACGCAATGCCTTATCAGAAACTAGTCATGCAATTCCTTATCAAAAACTAGTCACGCAATG
1 AAGTCACGCAATGCC-TATC---AACTAGTCATGCAATGCCTTATCAAAAACTAGTCACGCAATG
2637320 CCTAAAGT
62 CCTAAAGT
* * * * *
2637328 CAGTCACGCAATGCCTATCAACTAGTCATGTAATGCTTTATCAGAAACTAGTCACGCAATACCTT
1 AAGTCACGCAATGCCTATCAACTAGTCATGCAATGCCTTATCAAAAACTAGTCACGCAATGCC-T
**
2637393 ATCAAAA
65 A--AAGT
* * * ** *
2637400 ACTAGTCACGCAATGCCCA--AAGTCAGTCACGCAATGCC----CAAAGTC-AATCACGCAATGC
1 A--AGTCACGCAATGCCTATCAACT-AGTCATGCAATGCCTTATCAAAAACTAGTCACGCAATGC
*
2637458 CTATCAACT
63 CTA--AAGT
* * *
2637467 -AGTCACGCAATGTCTTATCAAAAACTAGTCACGCAATGACTTATCAAAAACTAGTCACGCAATG
1 AAGTCACGCAATG-CCTATC---AACTAGTCATGCAATGCCTTATCAAAAACTAGTCACGCAATG
*
2637531 CCTTCTCAAA-A
62 -C--CT-AAAGT
* * * *
2637542 ACTAGTCACGCAATGCCTTATCAAAAACTAATCACGCAATGACTTATTAAAAACTAGTCACGCAA
1 A--AGTCACGCAATGCC-TATC---AACTAGTCATGCAATGCCTTATCAAAAACTAGTCACGCAA
2637607 TGCCT
60 TGCCT
2637612 TATCAAAAAC
Statistics
Matches: 290, Mismatches: 37, Indels: 54
0.76 0.10 0.14
Matches are distributed among these distances:
64 12 0.04
65 2 0.01
67 6 0.02
68 12 0.04
69 70 0.24
70 9 0.03
72 9 0.03
73 73 0.25
74 28 0.10
75 3 0.01
76 2 0.01
77 4 0.01
78 60 0.21
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.24
Consensus pattern (69 bp):
AAGTCACGCAATGCCTATCAACTAGTCATGCAATGCCTTATCAAAAACTAGTCACGCAATGCCTA
AAGT
Found at i:2637345 original size:142 final size:142
Alignment explanation
Indices: 2637137--2637611 Score: 424
Period size: 142 Copynumber: 3.3 Consensus size: 142
2637127 ATTCTTTACT
** * * * * *
2637137 AACTAGTCACGCAATGCC-T-TC-CTAACAAGTCACACAATGCCTTAATAACAAGTCACGCAATA
1 AACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCC-T-ACAACTAGTCACGCAATG
* *
2637199 CCTATCAATTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAA-TTCTCAAAGTA-AGTCAC
64 CCTATCAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAACTTCTCAAA-AACAGTCAC
2637262 GCAATGCCTTATCAGA
128 GCAATGCCTTATCA-A
* * *
2637278 AACTAGTCATGCAATTCCTTATCAAAAACTAGTCACGCAATGCCTA-AAGTCAGTCACGCAATGC
1 AACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCCTACAACT-AGTCACGCAATGC
* * * * *
2637342 CTATCAACTAGTCATGTAATGCTTTATCAGAAACTAGTCACGCAATACCTTATCAAAAACTAGTC
65 CTATCAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGC-A-A-CTTCTCAAAAAC-AGTC
2637407 ACGCAATGCC----C-A
126 ACGCAATGCCTTATCAA
* ** *
2637419 AAGTCAGTCACGCAATGCC----CAAAGTC-AATCACGCAATGCCTATCAACTAGTCACGCAATG
1 AACT-AGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCCTA-CAACTAGTCACGCAATG
* *
2637479 TCTTATCAAAAACTAGTCACGCAATGACTTATCAAAAACTAGTCACGCAATGCCTTCTCAAAAAC
64 -CCTATC---AACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAA---CTTCTCAAAAAC
2637544 TAGTCACGCAATGCCTTATCAAA
122 -AGTCACGCAATGCCTTATC-AA
* * *
2637567 AACTAATCACGCAATGACTTATTAAAAACTAGTCACGCAATGCCT
1 AACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCCT
2637612 TATCAAAAAC
Statistics
Matches: 267, Mismatches: 37, Indels: 49
0.76 0.10 0.14
Matches are distributed among these distances:
137 15 0.06
138 17 0.06
139 8 0.03
140 1 0.00
141 23 0.09
142 124 0.46
143 5 0.02
144 17 0.06
145 1 0.00
146 8 0.03
147 26 0.10
148 4 0.01
151 4 0.01
152 14 0.05
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (142 bp):
AACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCCTACAACTAGTCACGCAATGCC
TATCAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAACTTCTCAAAAACAGTCACGCA
ATGCCTTATCAA
Found at i:2637427 original size:21 final size:21
Alignment explanation
Indices: 2637403--2637458 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
2637393 ATCAAAAACT
2637403 AGTCACGCAATGCCCAAAGTC
1 AGTCACGCAATGCCCAAAGTC
2637424 AGTCACGCAATGCCCAAAGTC
1 AGTCACGCAATGCCCAAAGTC
*
2637445 AATCACGCAATGCC
1 AGTCACGCAATGCC
2637459 TATCAACTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.34, C:0.34, G:0.18, T:0.14
Consensus pattern (21 bp):
AGTCACGCAATGCCCAAAGTC
Found at i:2637444 original size:116 final size:118
Alignment explanation
Indices: 2637256--2637621 Score: 407
Period size: 116 Copynumber: 3.0 Consensus size: 118
2637246 TCTCAAAGTA
* * * *
2637256 AGTCACGCAATGCCTTATCAGAAACTAGTCATGCAATTCCTTATCAAAAACTAGTCACGCAATGC
1 AGTCACGCAATACCTTATCAAAAACTAGTCACGCAATGCC---TCAAAAACTAGTCACGCAATGC
* * * * *
2637321 CTAAAGTCAGTCACGCAATGCCTATCAACTAGTCATGTAATG-CTTTATCAGAAACT
63 CCAAAGTCAATCACGCAATGCCTATCAACTAGTCACGCAATGTC-TTATCAAAAACT
**
2637377 AGTCACGCAATACCTTATCAAAAACTAGTCACGCAATGCC-CAAAGTC-AGTCACGCAATGCCCA
1 AGTCACGCAATACCTTATCAAAAACTAGTCACGCAATGCCTCAAAAACTAGTCACGCAATGCCCA
2637440 AAGTCAATCACGCAATGCCTATCAACTAGTCACGCAATGTCTTATCAAAAACT
66 AAGTCAATCACGCAATGCCTATCAACTAGTCACGCAATGTCTTATCAAAAACT
2637493 AGTCACGCAATGA-CTTATCAAAAACTAGTCACGCAATGCCTTCTCAAAAACTAGTCACGCAATG
1 AGTCACGCAAT-ACCTTATCAAAAACTAGTCACGCAATG-C--CTCAAAAACTAGTCACGCAATG
** * * *
2637557 CCTTATCAAAAACTAATCACGCAATGACTTATTAAAAACTAGTCACGCAATGCCTTATCAAAAAC
62 CC----CAAAGTC-AATCACGCAATG-CCTA-T--CAACTAGTCACGCAATGTCTTATCAAAAAC
2637622 CAAACACAAA
Statistics
Matches: 211, Mismatches: 18, Indels: 23
0.84 0.07 0.09
Matches are distributed among these distances:
116 98 0.46
117 8 0.04
119 1 0.00
120 5 0.02
121 50 0.24
125 5 0.02
126 12 0.06
127 3 0.01
128 1 0.00
130 28 0.13
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (118 bp):
AGTCACGCAATACCTTATCAAAAACTAGTCACGCAATGCCTCAAAAACTAGTCACGCAATGCCCA
AAGTCAATCACGCAATGCCTATCAACTAGTCACGCAATGTCTTATCAAAAACT
Found at i:2637521 original size:168 final size:163
Alignment explanation
Indices: 2637208--2637582 Score: 418
Period size: 168 Copynumber: 2.2 Consensus size: 163
2637198 ACCTATCAAT
* *
2637208 TAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATTCTCAAAGTAAGTCACGCAATGCCTTA
1 TAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCCCAAAGTAAGTCACGCAATGCC---
* * * * **
2637273 TCAGAAACTAGTCATGCAATTCCTTATCAAAAACTAGTCACGCAATGCCTAAAGTCAGTCACGCA
63 TCAGAAACTAATCACGCAATGCCTTATC--AAACTAGTCACGCAATGCATAAAAACAGTCACGCA
* * * *
2637338 ATGCCTATCAACTAGTCATGTAATGCTTTATCAGAAAC
126 ATGCCTATCAACTAGTCACGCAATGCCTTATCAAAAAC
* *
2637376 TAGTCACGCAATACCTTATCAAAAACTAGTCACGCAATGCCCAAAGTCAGTCACGCAATGCC-C-
1 TAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCCCAAAGTAAGTCACGCAATGCCTCA
*
2637439 -AAAGTCAATCACGCAATGCC-TATC-AACTAGTCACGCAATGTCTTATCAAAAACTAGTCACGC
66 GAAACT-AATCACGCAATGCCTTATCAAACTAGTCACGCAATG-C--AT-AAAAAC-AGTCACGC
* *
2637501 AATGACTTATCAAAAACTAGTCACGCAATGCCTTCTCAAAAAC
125 AATG-CCTATC---AACTAGTCACGCAATGCCTTATCAAAAAC
*
2637544 TAGTCACGCAATGCCTTATCAAAAACTAATCACGCAATG
1 TAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATG
2637583 ACTTATTAAA
Statistics
Matches: 178, Mismatches: 19, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
159 16 0.09
160 1 0.01
162 9 0.05
163 15 0.08
164 13 0.07
165 5 0.03
168 119 0.67
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (163 bp):
TAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCCCAAAGTAAGTCACGCAATGCCTCA
GAAACTAATCACGCAATGCCTTATCAAACTAGTCACGCAATGCATAAAAACAGTCACGCAATGCC
TATCAACTAGTCACGCAATGCCTTATCAAAAAC
Found at i:2637782 original size:15 final size:15
Alignment explanation
Indices: 2637762--2637791 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2637752 GGGAATAAAA
*
2637762 ACCAAAAATTGCAAC
1 ACCAAAAATTACAAC
2637777 ACCAAAAATTACAAC
1 ACCAAAAATTACAAC
2637792 CAAACACGCA
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:0.57, C:0.27, G:0.03, T:0.13
Consensus pattern (15 bp):
ACCAAAAATTACAAC
Found at i:2645050 original size:96 final size:96
Alignment explanation
Indices: 2644886--2645080 Score: 390
Period size: 96 Copynumber: 2.0 Consensus size: 96
2644876 GCCAAAAAGA
2644886 AAGTCGAATGCATTCAGGCAGGAGATTCACAATACCTTGGCATCTAGAAAGAGAAAATGAAGTCA
1 AAGTCGAATGCATTCAGGCAGGAGATTCACAATACCTTGGCATCTAGAAAGAGAAAATGAAGTCA
2644951 AGTTTGAACAGTAAAGTGGGCTAAAATATTT
66 AGTTTGAACAGTAAAGTGGGCTAAAATATTT
2644982 AAGTCGAATGCATTCAGGCAGGAGATTCACAATACCTTGGCATCTAGAAAGAGAAAATGAAGTCA
1 AAGTCGAATGCATTCAGGCAGGAGATTCACAATACCTTGGCATCTAGAAAGAGAAAATGAAGTCA
2645047 AGTTTGAACAGTAAAGTGGGCTAAAATATTT
66 AGTTTGAACAGTAAAGTGGGCTAAAATATTT
2645078 AAG
1 AAG
2645081 CAAATCCATT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 99 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (96 bp):
AAGTCGAATGCATTCAGGCAGGAGATTCACAATACCTTGGCATCTAGAAAGAGAAAATGAAGTCA
AGTTTGAACAGTAAAGTGGGCTAAAATATTT
Found at i:2648395 original size:45 final size:45
Alignment explanation
Indices: 2648331--2648444 Score: 192
Period size: 45 Copynumber: 2.5 Consensus size: 45
2648321 NCACGTCATG
2648331 TACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACACCATA
1 TACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACACCATA
* * *
2648376 TACAGAAACATGTGACACGTTATGGTTAGGTTGTTACACATCATG
1 TACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACACCATA
*
2648421 TATAGAAACATGTGACACGTCATG
1 TACAGAAACATGTGACACGTCATG
2648445 TATAAAAACA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 64 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (45 bp):
TACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACACCATA
Found at i:2648443 original size:24 final size:24
Alignment explanation
Indices: 2648411--2648742 Score: 169
Period size: 24 Copynumber: 14.4 Consensus size: 24
2648401 TTAGGTTGTT
* *
2648411 ACACATCATGTATAGAAACATGTG
1 ACACGTCATGTACAGAAACATGTG
* *
2648435 ACACGTCATGTATAAAAACATGTG
1 ACACGTCATGTACAGAAACATGTG
* ** *
2648459 ACACGTCATGGT-TAG---GTTGTT
1 ACACGTCAT-GTACAGAAACATGTG
** *
2648480 ACACACCATGTACAGGAACATGTG
1 ACACGTCATGTACAGAAACATGTG
2648504 ACACGTCATGTACAGAAACATGTG
1 ACACGTCATGTACAGAAACATGTG
*
2648528 TCACGTCATGTACAGAAACATGTG
1 ACACGTCATGTACAGAAACATGTG
* ** *
2648552 ACACGTCATGGT-TAG---GTTGTT
1 ACACGTCAT-GTACAGAAACATGTG
**
2648573 ACACACCATGTACAGAAACATGTG
1 ACACGTCATGTACAGAAACATGTG
* * ** *
2648597 ACACGCCATGGT-TAG---GTTGTT
1 ACACGTCAT-GTACAGAAACATGTG
**
2648618 ACACACCATGTACAGAAACATGTG
1 ACACGTCATGTACAGAAACATGTG
* *
2648642 ACACGACATGTACAGAAATATGTG
1 ACACGTCATGTACAGAAACATGTG
* * * ** *
2648666 ACATGCCATGGT-TAG-GTC--GTT
1 ACACGTCAT-GTACAGAAACATGTG
**
2648687 ACACACCATGTACAGAAACA--TG
1 ACACGTCATGTACAGAAACATGTG
*
2648709 ACACGTCATGTACAAAAACATGTG
1 ACACGTCATGTACAGAAACATGTG
*
2648733 ACATGTCATG
1 ACACGTCATG
2648743 GTTAGGTTGT
Statistics
Matches: 230, Mismatches: 57, Indels: 42
0.70 0.17 0.13
Matches are distributed among these distances:
20 8 0.03
21 48 0.21
22 19 0.08
24 147 0.64
25 8 0.03
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (24 bp):
ACACGTCATGTACAGAAACATGTG
Found at i:2648463 original size:69 final size:69
Alignment explanation
Indices: 2648376--2648754 Score: 421
Period size: 69 Copynumber: 5.5 Consensus size: 69
2648366 ACACACCATA
* * *
2648376 TACAGAAACATGTGACACGTTATGGTTAGGTTGTTACACATCATGTATAGAAACATGTGACACGT
1 TACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACACCATGTACAGAAACATGTGACACGT
2648441 CATG
66 CATG
* * *
2648445 TATAAAAACATGTGACACGTCATGGTTAGGTTGTTACACACCATGTACAGGAACATGTGACACGT
1 TACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACACCATGTACAGAAACATGTGACACGT
2648510 CATG
66 CATG
* * ** * ** * ** *
2648514 TACAGAAACATGTGTCACGTCAT-GTACAGAAACATGTGACACGTCATGGT-TAG---GTTGTTA
1 TACAGAAACATGTGACACGTCATGGT-TAG---GTTGTTACACACCAT-GTACAGAAACATGTGA
**
2648574 CACACCATG
61 CACGTCATG
* *
2648583 TACAGAAACATGTGACACGCCATGGTTAGGTTGTTACACACCATGTACAGAAACATGTGACACGA
1 TACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACACCATGTACAGAAACATGTGACACGT
2648648 CATG
66 CATG
* * * *
2648652 TACAGAAATATGTGACATGCCATGGTTAGGTCGTTACACACCATGTACAGAAACA--TGACACGT
1 TACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACACCATGTACAGAAACATGTGACACGT
2648715 CATG
66 CATG
* *
2648719 TACAAAAACATGTGACATGTCATGGTTAGGTTGTTA
1 TACAGAAACATGTGACACGTCATGGTTAGGTTGTTA
2648755 TACGTCATGT
Statistics
Matches: 257, Mismatches: 43, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
65 2 0.01
66 12 0.05
67 43 0.17
68 2 0.01
69 182 0.71
70 2 0.01
72 12 0.05
73 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (69 bp):
TACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACACCATGTACAGAAACATGTGACACGT
CATG
Found at i:2648500 original size:45 final size:45
Alignment explanation
Indices: 2648441--2648651 Score: 273
Period size: 45 Copynumber: 4.6 Consensus size: 45
2648431 TGTGACACGT
* *
2648441 CATGTATAAAAACATGTGACACGTCATGGTTAGGTTGTTACACAC
1 CATGTACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACAC
* * ** **
2648486 CATGTACAGGAACATGTGACACGTCAT-GTACAGAAACATGTGT-CACGT
1 CATGTACAGAAACATGTGACACGTCATGGT-TAG---GTTGT-TACACAC
2648534 CATGTACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACAC
1 CATGTACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACAC
*
2648579 CATGTACAGAAACATGTGACACGCCATGGTTAGGTTGTTACACAC
1 CATGTACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACAC
*
2648624 CATGTACAGAAACATGTGACACGACATG
1 CATGTACAGAAACATGTGACACGTCATG
2648652 TACAGAAATA
Statistics
Matches: 143, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
44 3 0.02
45 103 0.72
48 34 0.24
49 3 0.02
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (45 bp):
CATGTACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACAC
Found at i:2648533 original size:93 final size:93
Alignment explanation
Indices: 2648411--2648606 Score: 329
Period size: 93 Copynumber: 2.1 Consensus size: 93
2648401 TTAGGTTGTT
* * *
2648411 ACACATCATGTATAGAAACATGTGACACGTCATGTATAAAAACATGTGACACGTCATGGTTAGGT
1 ACACGTCATGTACAGAAACATGTGACACGTCATGTACAAAAACATGTGACACGTCATGGTTAGGT
*
2648476 TGTTACACACCATGTACAGGAACATGTG
66 TGTTACACACCATGTACAGAAACATGTG
* *
2648504 ACACGTCATGTACAGAAACATGTGTCACGTCATGTACAGAAACATGTGACACGTCATGGTTAGGT
1 ACACGTCATGTACAGAAACATGTGACACGTCATGTACAAAAACATGTGACACGTCATGGTTAGGT
2648569 TGTTACACACCATGTACAGAAACATGTG
66 TGTTACACACCATGTACAGAAACATGTG
*
2648597 ACACGCCATG
1 ACACGTCATG
2648607 GTTAGGTTGT
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 96 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (93 bp):
ACACGTCATGTACAGAAACATGTGACACGTCATGTACAAAAACATGTGACACGTCATGGTTAGGT
TGTTACACACCATGTACAGAAACATGTG
Found at i:2648678 original size:207 final size:205
Alignment explanation
Indices: 2648322--2648742 Score: 680
Period size: 207 Copynumber: 2.0 Consensus size: 205
2648312 TTTTCTGGTN
2648322 CACGTCATGTACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACACCATATACAGAAACAT
1 CACGTCATGTACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACACCATATACAGAAACAT
** * * * *
2648387 GTGACACGTTATGGTTAGGTTGTTACACATCATGTATAGAAACATGTGACACGTCATGTATAAAA
66 GTGACACGCCATGGTTAGGTTGTTACACACCATGTACAGAAACATGTGACACGACATGTACAAAA
* * *
2648452 ACATGTGACACGTCATGGTTAGGTTGTTACACACCATGTACAGGAACATGTGACACGTCATGTAC
131 ACATGTGACACGCCATGGTTAGGTCGTTACACACCATGTACAGAAACA--TGACACGTCATGTAC
* *
2648517 AGAAACATGTGT
194 AAAAACATGTGA
*
2648529 CACGTCATGTACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACACCATGTACAGAAACAT
1 CACGTCATGTACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACACCATATACAGAAACAT
*
2648594 GTGACACGCCATGGTTAGGTTGTTACACACCATGTACAGAAACATGTGACACGACATGTACAGAA
66 GTGACACGCCATGGTTAGGTTGTTACACACCATGTACAGAAACATGTGACACGACATGTACAAAA
* *
2648659 ATATGTGACATGCCATGGTTAGGTCGTTACACACCATGTACAGAAACATGACACGTCATGTACAA
131 ACATGTGACACGCCATGGTTAGGTCGTTACACACCATGTACAGAAACATGACACGTCATGTACAA
2648724 AAACATGTGA
196 AAACATGTGA
*
2648734 CATGTCATG
1 CACGTCATG
2648743 GTTAGGTTGT
Statistics
Matches: 198, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
205 33 0.17
207 165 0.83
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (205 bp):
CACGTCATGTACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACACCATATACAGAAACAT
GTGACACGCCATGGTTAGGTTGTTACACACCATGTACAGAAACATGTGACACGACATGTACAAAA
ACATGTGACACGCCATGGTTAGGTCGTTACACACCATGTACAGAAACATGACACGTCATGTACAA
AAACATGTGA
Found at i:2648833 original size:26 final size:25
Alignment explanation
Indices: 2648748--2648853 Score: 99
Period size: 26 Copynumber: 4.0 Consensus size: 25
2648738 TCATGGTTAG
*
2648748 GTTGTTATACGTCATGTTGAAAAAAATA
1 GTTGTTACACGTCATGTT--AAAAAA-A
*
2648776 TTGTTGTTACACGTCATG-TACAAAAA
1 --GTTGTTACACGTCATGTTAAAAAAA
*
2648802 -TATGTTACATGTCATGATTAAAAAAA
1 GT-TGTTACACGTCATG-TTAAAAAAA
2648828 GTTGTTACACGTCATGTTGAAAAAAA
1 GTTGTTACACGTCATGTT-AAAAAAA
2648854 AAGTTATTGT
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
23 1 0.02
24 13 0.20
25 2 0.03
26 28 0.42
27 6 0.09
29 1 0.02
30 15 0.23
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (25 bp):
GTTGTTACACGTCATGTTAAAAAAA
Found at i:2654520 original size:24 final size:25
Alignment explanation
Indices: 2654480--2654529 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
2654470 AAATCTTTTC
2654480 AGTTTGTATTTTTTTTTTGTTGTTT
1 AGTTTGTATTTTTTTTTTGTTGTTT
2654505 AGTTTGT-TTTTTTTTTTGTTGTTT
1 AGTTTGTATTTTTTTTTTGTTGTTT
2654529 A
1 A
2654530 AAGGTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.08, C:0.00, G:0.16, T:0.76
Consensus pattern (25 bp):
AGTTTGTATTTTTTTTTTGTTGTTT
Found at i:2659368 original size:18 final size:18
Alignment explanation
Indices: 2659345--2659387 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
2659335 ATTAATTCAA
2659345 GGTTTTAGCT-TACTTTT-G
1 GGTTTTA-CTCTA-TTTTAG
2659363 GGTTTTACTCTATTTTAG
1 GGTTTTACTCTATTTTAG
2659381 GGTTTTA
1 GGTTTTA
2659388 ATTGGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.14, C:0.09, G:0.21, T:0.56
Consensus pattern (18 bp):
GGTTTTACTCTATTTTAG
Found at i:2663242 original size:2 final size:2
Alignment explanation
Indices: 2663235--2663259 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2663225 CTAAGCTTAC
2663235 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2663260 TTCATGGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2681912 original size:25 final size:24
Alignment explanation
Indices: 2681884--2681985 Score: 75
Period size: 25 Copynumber: 4.1 Consensus size: 24
2681874 CATCTCTTAA
*
2681884 ATATATTTTTATTGTCATATATTTT
1 ATATATTTTTATT-TTATATATTTT
*
2681909 ATAT-TTATTTGTTATTATA-ATTTT
1 ATATATT-TTTATT-TTATATATTTT
* *
2681933 ATTATAATTTTATTTT-TATTTTTTT
1 A-TATATTTTTATTTTATA-TATTTT
*
2681958 AATATAATTTTTATATTATATATTTT
1 -ATAT-ATTTTTATTTTATATATTTT
2681984 AT
1 AT
2681986 TTTAATTTCT
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
23 2 0.03
24 10 0.17
25 30 0.50
26 16 0.27
27 2 0.03
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.67
Consensus pattern (24 bp):
ATATATTTTTATTTTATATATTTT
Found at i:2681934 original size:11 final size:11
Alignment explanation
Indices: 2681920--2681946 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2681910 TATTTATTTG
2681920 TTATTATAATT
1 TTATTATAATT
2681931 TTATTATAATT
1 TTATTATAATT
2681942 TTATT
1 TTATT
2681947 TTTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTATAATT
Found at i:2681953 original size:39 final size:40
Alignment explanation
Indices: 2681883--2681993 Score: 101
Period size: 36 Copynumber: 2.9 Consensus size: 40
2681873 TCATCTCTTA
* * *
2681883 AATATATTTTTAT-TGTCATATATTTTATATTTA--TTTGTT
1 AATATAATTTTATAT-T-ATATATTTTATTTTTATTTTTTTT
*
2681922 ATTATAA-TTT-TATTATA-ATTTTATTTTTA-TTTTTTT
1 AATATAATTTTATATTATATATTTTATTTTTATTTTTTTT
*
2681958 AATATAATTTTTATATTATATATTTTATTTTAATTT
1 AATATAA-TTTTATATTATATATTTTATTTTTATTT
2681994 CTTTAACCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
35 11 0.19
36 14 0.24
37 2 0.03
38 7 0.12
39 12 0.20
40 11 0.19
41 2 0.03
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.67
Consensus pattern (40 bp):
AATATAATTTTATATTATATATTTTATTTTTATTTTTTTT
Found at i:2687268 original size:17 final size:17
Alignment explanation
Indices: 2687228--2687268 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
2687218 TCATATTAAA
* *
2687228 AAATTTAATCAAAATTT
1 AAATTTAATAAAAAATT
2687245 AAA-TTAATAAAAAATT
1 AAATTTAATAAAAAATT
2687261 AAATTTAA
1 AAATTTAA
2687269 ATATAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTTAATAAAAAATT
Found at i:2701987 original size:153 final size:153
Alignment explanation
Indices: 2701709--2702006 Score: 431
Period size: 153 Copynumber: 1.9 Consensus size: 153
2701699 ATGTCAATCA
* *
2701709 TCTCAGGGCAACACAATTAAACTCTCACTGCAAGTTTCTCATCATCACTTGGACCGTTCTTCAGG
1 TCTCAGGGCAACACAATTAAACTCTCACTGCAAGTTTCTCATCATCACTTGGACAGGTCTTCAGG
* * ** * *
2701774 TAGCACTGGTCCTTTGTGATCTAAAGTTGTGATGCCAGTGGGTAGTATTCGTAGGAATGCTTTCT
66 AAGCACTGGTCCTTTATGATCTAAAGTTGTGATAACAGCGGGTAGTATTCATAGGAATGCTTTCT
* *
2701839 CTCATTGATTCAGATTTCAATAT
131 CCCATTGATACAGATTTCAATAT
*
2701862 TCTCA-GGCAACACAATTAAACTCTCATTGCAAGTTTCTCATCATCACTTGGGACAGGTCTTCAG
1 TCTCAGGGCAACACAATTAAACTCTCACTGCAAGTTTCTCATCATCACTT-GGACAGGTCTTCAG
* *
2701926 GAAGCACTGGT-CTTTCATGATCTAAAGTTGT-AGTAACAGCGGGTAGTATTCATATGTATGCTT
65 GAAGCACTGGTCCTTT-ATGATCTAAAGTTGTGA-TAACAGCGGGTAGTATTCATAGGAATGCTT
2701989 TCTCCCATTGATACAGAT
128 TCTCCCATTGATACAGAT
2702007 CATGGCTCAA
Statistics
Matches: 129, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
152 48 0.37
153 81 0.63
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (153 bp):
TCTCAGGGCAACACAATTAAACTCTCACTGCAAGTTTCTCATCATCACTTGGACAGGTCTTCAGG
AAGCACTGGTCCTTTATGATCTAAAGTTGTGATAACAGCGGGTAGTATTCATAGGAATGCTTTCT
CCCATTGATACAGATTTCAATAT
Found at i:2729141 original size:15 final size:15
Alignment explanation
Indices: 2729118--2729162 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2729108 ACANAACATG
*
2729118 TAAAGAAATAAAATA
1 TAAATAAATAAAATA
*
2729133 TAAATAAATATAATA
1 TAAATAAATAAAATA
2729148 TAATATAAATTAAAA
1 TAA-ATAAA-TAAAA
2729163 ATTTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 16 0.64
16 5 0.20
17 4 0.16
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
TAAATAAATAAAATA
Found at i:2729259 original size:28 final size:28
Alignment explanation
Indices: 2729207--2729285 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 28
2729197 TTTTTATTAT
2729207 TTATTTATATTAATTATT--AAA-TAAAAA
1 TTATTT-TA-TAATTATTAAAAATTAAAAA
2729234 TTATTTTATAATTATTAAAAATTAAAAA
1 TTATTTTATAATTATTAAAAATTAAAAA
* *
2729262 -AATTTTATATAATATGTAAAAATT
1 TTATTTTATA-ATTAT-TAAAAATT
2729286 TTGGTGGGAC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
25 8 0.18
26 2 0.04
27 17 0.38
28 10 0.22
29 8 0.18
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (28 bp):
TTATTTTATAATTATTAAAAATTAAAAA
Found at i:2729262 original size:29 final size:29
Alignment explanation
Indices: 2729229--2729285 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
2729219 ATTATTAAAT
*
2729229 AAAAATTATTTTATAATTAT-TAAAAATTAA
1 AAAAATT-TTATATAA-TATGTAAAAATTAA
2729259 AAAAATTTTATATAATATGTAAAAATT
1 AAAAATTTTATATAATATGTAAAAATT
2729286 TTGGTGGGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 3 0.12
29 15 0.60
30 7 0.28
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (29 bp):
AAAAATTTTATATAATATGTAAAAATTAA
Found at i:2741956 original size:13 final size:15
Alignment explanation
Indices: 2741938--2741972 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
2741928 TTGTGTTTAG
2741938 AAAAATA-TT-GAAA
1 AAAAATATTTAGAAA
2741951 AAAAATATTTAGAAA
1 AAAAATATTTAGAAA
2741966 AAAAATA
1 AAAAATA
2741973 AAAAAACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 2 0.10
15 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (15 bp):
AAAAATATTTAGAAA
Found at i:2743713 original size:2 final size:2
Alignment explanation
Indices: 2743706--2743737 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2743696 NNNNCCACAT
2743706 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
2743738 GAAAAATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2760969 original size:16 final size:16
Alignment explanation
Indices: 2760950--2760993 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
2760940 TCCCATTTGC
2760950 TTTTTCTCCTTTATTT
1 TTTTTCTCCTTTATTT
* * *
2760966 TTTTTCCCCATTGTTT
1 TTTTTCTCCTTTATTT
*
2760982 TTTTTCTTCTTT
1 TTTTTCTCCTTT
2760994 TTCTAAACAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTTCTCCTTTATTT
Found at i:2772205 original size:2 final size:2
Alignment explanation
Indices: 2772200--2772226 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2772190 ACATAATAAA
2772200 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 A
2772227 AGCATTACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2773609 original size:15 final size:15
Alignment explanation
Indices: 2773589--2773619 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2773579 GATTATTTGA
*
2773589 TGTTATTATTATTTT
1 TGTTATAATTATTTT
2773604 TGTTATAATTATTTT
1 TGTTATAATTATTTT
2773619 T
1 T
2773620 ATAATTATAG
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:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (15 bp):
TGTTATAATTATTTT
Found at i:2773826 original size:67 final size:71
Alignment explanation
Indices: 2773743--2773876 Score: 186
Period size: 73 Copynumber: 1.9 Consensus size: 71
2773733 TAATCGTGTT
2773743 GTGTTATGTTACACGTA-A-T-ATATATA-TATATATATTTTAAATTTAAGATACGAATATTAAA
1 GTGTTATGTTACACGTATATTAATATATACTATATATATTTTAAATTTAAGATACGAATATTAAA
2773804 TGTATC
66 TGTATC
* * * *
2773810 GTGTTGTGTTATACGTATATTAAATATATACGTGTATATATTTTAAATTTAAGATATGAATATTA
1 GTGTTATGTTACACGTATATT-AATATATAC-TATATATATTTTAAATTTAAGATACGAATATTA
2773875 AA
64 AA
2773877 CGTGTGTGTT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
67 15 0.26
68 1 0.02
69 1 0.02
71 7 0.12
73 33 0.58
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (71 bp):
GTGTTATGTTACACGTATATTAATATATACTATATATATTTTAAATTTAAGATACGAATATTAAA
TGTATC
Found at i:2779480 original size:3 final size:3
Alignment explanation
Indices: 2779474--2779500 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2779464 TCCCCTCACT
2779474 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
2779501 ATTGCTGCGA
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):
TTC
Found at i:2807994 original size:17 final size:18
Alignment explanation
Indices: 2807972--2808009 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2807962 TGTCGAAATT
2807972 TTTTAAT-TTTATTT-TAA
1 TTTTAATATTT-TTTCTAA
2807989 TTTTAATATTTTTTCTAA
1 TTTTAATATTTTTTCTAA
2808007 TTT
1 TTT
2808010 ATTTATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTAATATTTTTTCTAA
Found at i:2810080 original size:2 final size:2
Alignment explanation
Indices: 2810073--2810117 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
2810063 GAAATTTTGA
2810073 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2810114 AT AT
1 AT AT
2810118 CAATTTGGTN
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2823538 original size:69 final size:70
Alignment explanation
Indices: 2823427--2823572 Score: 208
Period size: 69 Copynumber: 2.1 Consensus size: 70
2823417 CATGCATGAA
* **
2823427 AGTGGATTTTCACAGCAACCTGATAGGCTCACAAGGTTTGACTCCATAAATAGTAGCGGAGACTT
1 AGTGGATTTTCACAGCAACCTGATAGGCTCACAAGGTTTGACTCCACAAATAGTAGCAAAGACTT
2823492 TGG-C
66 TGGCC
* * *
2823496 AGTGGATTTTCACATCAACCTGA-GGCGCTCACTAGGTTTGACTCCACAAATAGTAGCAAAGACT
1 AGTGGATTTTCACAGCAACCTGATAG-GCTCACAAGGTTTGACTCCACAAATAGTAGCAAAGACT
2823560 TTGGCC
65 TTGGCC
2823566 A-TGGATT
1 AGTGGATT
2823573 CTCTTTTGAT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
68 1 0.01
69 66 0.96
70 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (70 bp):
AGTGGATTTTCACAGCAACCTGATAGGCTCACAAGGTTTGACTCCACAAATAGTAGCAAAGACTT
TGGCC
Found at i:2826340 original size:31 final size:31
Alignment explanation
Indices: 2826304--2826368 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
2826294 TCAGTATTCT
2826304 CATACAAGTTCCCAAAACCCGTTGTATTCCA
1 CATACAAGTTCCCAAAACCCGTTGTATTCCA
2826335 CATACAAGTTCCCAAAACCCGTTGTATTCCA
1 CATACAAGTTCCCAAAACCCGTTGTATTCCA
2826366 CAT
1 CAT
2826369 CCAACTGCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.32, C:0.32, G:0.09, T:0.26
Consensus pattern (31 bp):
CATACAAGTTCCCAAAACCCGTTGTATTCCA
Found at i:2836010 original size:2 final size:2
Alignment explanation
Indices: 2836003--2836045 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
2835993 AAAGAAAAAC
* * *
2836003 AT AT AT AT AT AT AT AT AT AA AC AT AT CT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2836045 A
1 A
2836046 AATACAAAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2836027 original size:22 final size:22
Alignment explanation
Indices: 2835999--2836043 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2835989 CGCAAAAGAA
2835999 AAACATATATATATATATATAT
1 AAACATATATATATATATATAT
*
2836021 AAACATATCTATATATATATAT
1 AAACATATATATATATATATAT
2836043 A
1 A
2836044 TAAATACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (22 bp):
AAACATATATATATATATATAT
Found at i:2837650 original size:18 final size:18
Alignment explanation
Indices: 2837627--2837665 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2837617 TCTTTAAATT
2837627 TAATATTTAATAAA-AAAA
1 TAATATTT-ATAAATAAAA
2837645 TAATATTTATAAATAAAA
1 TAATATTTATAAATAAAA
2837663 TAA
1 TAA
2837666 GTTAATCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATATTTATAAATAAAA
Found at i:2837922 original size:20 final size:21
Alignment explanation
Indices: 2837884--2837930 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
2837874 TTTTTGACTA
*
2837884 ACTTTAATTATTAAATTGAAT
1 ACTTAAATTATTAAATTGAAT
* *
2837905 ATTTAAATTA-TAATTTGAAT
1 ACTTAAATTATTAAATTGAAT
2837925 ACTTAA
1 ACTTAA
2837931 TCTGTAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (21 bp):
ACTTAAATTATTAAATTGAAT
Found at i:2846396 original size:2 final size:2
Alignment explanation
Indices: 2846391--2846435 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
2846381 CCACCCAAAC
* * *
2846391 AG AG AG AG AG AG AT AT AG AG AG AG AG GG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2846433 AG A
1 AG A
2846436 AGCAAAAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.47, T:0.04
Consensus pattern (2 bp):
AG
Found at i:2876698 original size:18 final size:19
Alignment explanation
Indices: 2876656--2876698 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
2876646 CTAAATGTGG
* *
2876656 AAGCACCCAGGGGCGTTTC
1 AAGCGCCCAGGGGCGTTCC
*
2876675 ATGCGCCCA-GGGCGTTCC
1 AAGCGCCCAGGGGCGTTCC
2876693 AAGCGC
1 AAGCGC
2876699 AAAAGTGCCC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.19, C:0.35, G:0.33, T:0.14
Consensus pattern (19 bp):
AAGCGCCCAGGGGCGTTCC
Found at i:2876800 original size:14 final size:14
Alignment explanation
Indices: 2876781--2876810 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2876771 AGTGAAAGTA
2876781 ACTCAGAATAAGAG
1 ACTCAGAATAAGAG
2876795 ACTCAGAATAAGAG
1 ACTCAGAATAAGAG
2876809 AC
1 AC
2876811 AGGGTTCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (14 bp):
ACTCAGAATAAGAG
Found at i:2880127 original size:49 final size:49
Alignment explanation
Indices: 2880055--2880153 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
2880045 GAATGAAAGA
*
2880055 AAACCTTGTTTGCCGTGGGTTTTGCCTTAACCTTTTTACACAAATGTTT
1 AAACCTTGTTTGCCATGGGTTTTGCCTTAACCTTTTTACACAAATGTTT
2880104 AAACCTTGTTTGCCATGGGTTTTGCCTTAACCTTTTTACACAAATGTTT
1 AAACCTTGTTTGCCATGGGTTTTGCCTTAACCTTTTTACACAAATGTTT
2880153 A
1 A
2880154 CAGGCCCTCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.42
Consensus pattern (49 bp):
AAACCTTGTTTGCCATGGGTTTTGCCTTAACCTTTTTACACAAATGTTT
Found at i:2880813 original size:3 final size:3
Alignment explanation
Indices: 2880805--2880832 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2880795 ATTGTAGTTG
2880805 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2880833 AAAGGAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2881475 original size:15 final size:15
Alignment explanation
Indices: 2881454--2881496 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
2881444 AGTGAAGAGA
*
2881454 ATGAAAATGCTGCCC
1 ATGAAAATGCTGCAC
*
2881469 GTGAAAATGCTGCAC
1 ATGAAAATGCTGCAC
*
2881484 AAGAAAATGCTGC
1 ATGAAAATGCTGC
2881497 TGGATATCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (15 bp):
ATGAAAATGCTGCAC
Found at i:2882896 original size:14 final size:14
Alignment explanation
Indices: 2882873--2882902 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2882863 TAGTTGGTGG
2882873 GAAAGAGAGATTTT
1 GAAAGAGAGATTTT
*
2882887 GAAAGGGAGATTTT
1 GAAAGAGAGATTTT
2882901 GA
1 GA
2882903 TACGGTATTT
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:0.40, C:0.00, G:0.33, T:0.27
Consensus pattern (14 bp):
GAAAGAGAGATTTT
Found at i:2916185 original size:67 final size:67
Alignment explanation
Indices: 2916077--2916225 Score: 289
Period size: 67 Copynumber: 2.2 Consensus size: 67
2916067 CCAATATGCA
2916077 TGACAGGATTGATTTGTTAATCTGAAGCTAGGCTTTGATAATTTGTTGCCACCATATGCAACTGC
1 TGACAGGATTGATTTGTTAATCTGAAGCTAGGCTTTGATAATTTGTTGCCACCATATGCAACTGC
2916142 CT
66 CT
*
2916144 TGACAGGATTGATTTGTTAATCTGAAGCTAGGCTTTGATAATTTGTTGCCACCATATTCAACTGC
1 TGACAGGATTGATTTGTTAATCTGAAGCTAGGCTTTGATAATTTGTTGCCACCATATGCAACTGC
2916209 CT
66 CT
2916211 TGACAGGATTGATTT
1 TGACAGGATTGATTT
2916226 TCCATGACTC
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 81 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (67 bp):
TGACAGGATTGATTTGTTAATCTGAAGCTAGGCTTTGATAATTTGTTGCCACCATATGCAACTGC
CT
Found at i:2927860 original size:2 final size:2
Alignment explanation
Indices: 2927855--2927891 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2927845 TCTTTTTTTT
2927855 TA TA 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 TA TA T
2927892 NTGAGACAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2941310 original size:2 final size:2
Alignment explanation
Indices: 2941303--2941328 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2941293 AATAAAAATG
2941303 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2941329 TCTATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2942297 original size:2 final size:2
Alignment explanation
Indices: 2942290--2942337 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
2942280 NNNAACCATT
2942290 TA TA TA TA TA TA TA TA TA T- TA TA TA T- TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2942329 TA TA TA TA T
1 TA TA TA TA T
2942338 CCATGAGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2942347 original size:2 final size:2
Alignment explanation
Indices: 2942342--2942392 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
2942332 ATATATCCAT
*
2942342 GA GA GA GA GA G- GA GA GA GA GA GA GA GA GA G- GA GA GA GA CA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
2942382 GA GA GT GA GA G
1 GA GA GA GA GA G
2942393 TTAATTTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.45, C:0.02, G:0.51, T:0.02
Consensus pattern (2 bp):
GA
Found at i:2942366 original size:19 final size:19
Alignment explanation
Indices: 2942342--2942386 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
2942332 ATATATCCAT
2942342 GAGAGAGAGAGGAGAGAGA
1 GAGAGAGAGAGGAGAGAGA
2942361 GAGAGAGAGAGGAGAGAGA
1 GAGAGAGAGAGGAGAGAGA
*
2942380 CAGAGAG
1 GAGAGAG
2942387 TGAGAGTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.47, C:0.02, G:0.51, T:0.00
Consensus pattern (19 bp):
GAGAGAGAGAGGAGAGAGA
Found at i:2942368 original size:21 final size:20
Alignment explanation
Indices: 2942342--2942392 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
2942332 ATATATCCAT
*
2942342 GAGAGAGAGA-GGAGAGAGA
1 GAGAGAGAGAGGGAGAGACA
2942361 GAGAGAGAGAGGAGAGAGACA
1 GAGAGAGAGAGG-GAGAGACA
*
2942382 GAGAGTGAGAG
1 GAGAGAGAGAG
2942393 TTAATTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 10 0.36
20 1 0.04
21 17 0.61
ACGTcount: A:0.45, C:0.02, G:0.51, T:0.02
Consensus pattern (20 bp):
GAGAGAGAGAGGGAGAGACA
Found at i:2950912 original size:66 final size:66
Alignment explanation
Indices: 2950806--2950943 Score: 240
Period size: 66 Copynumber: 2.1 Consensus size: 66
2950796 AACCACCAAG
** *
2950806 AAGTGGAGGAATCAGGAATTAATTAGTGAGTAATGACATACCAGACAGACATGGCATCCACAGCC
1 AAGTGGAGGAATCAGGAATTAATTAACGAGTAATGACATACCAGACAGACAAGGCATCCACAGCC
2950871 A
66 A
2950872 AAGTGGAGGAATCAGGAATTAATTAACGAGTAATGACATACCAGACAGACAAGGCATCCACAGCC
1 AAGTGGAGGAATCAGGAATTAATTAACGAGTAATGACATACCAGACAGACAAGGCATCCACAGCC
2950937 A
66 A
*
2950938 AGGTGG
1 AAGTGG
2950944 CATTTTGCAG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (66 bp):
AAGTGGAGGAATCAGGAATTAATTAACGAGTAATGACATACCAGACAGACAAGGCATCCACAGCC
A
Found at i:2959631 original size:2 final size:2
Alignment explanation
Indices: 2959624--2959649 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2959614 ATCAAGCAGA
2959624 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2959650 CCAAATGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2961029 original size:5 final size:6
Alignment explanation
Indices: 2961014--2961039 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2961004 TCCACCCGCA
2961014 CCCCCG CCCCCG CCCCCG CCCCCG CC
1 CCCCCG CCCCCG CCCCCG CCCCCG CC
2961040 ACCACCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.85, G:0.15, T:0.00
Consensus pattern (6 bp):
CCCCCG
Found at i:2965270 original size:45 final size:45
Alignment explanation
Indices: 2965220--2965305 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
2965210 TATTATATAC
* * * * *
2965220 CATGTATAAAAATATGTTACACGTCATAGTTAGGTTGTTACGCGT
1 CATGTACAAAAACATGTGACACGCCATAATTAGGTTGTTACGCGT
*
2965265 CATGTACAAAAACATGTGACATGCCATAATTAGGTTGTTAC
1 CATGTACAAAAACATGTGACACGCCATAATTAGGTTGTTAC
2965306 ACTCCATGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (45 bp):
CATGTACAAAAACATGTGACACGCCATAATTAGGTTGTTACGCGT
Found at i:2965314 original size:45 final size:46
Alignment explanation
Indices: 2965219--2965314 Score: 115
Period size: 45 Copynumber: 2.1 Consensus size: 46
2965209 ATATTATATA
* * * * * *
2965219 CCATGTATAAAAATATGTTACACGTCATAGTTAGGTTGTTACGCGT
1 CCATGTACAAAAACATGTGACACGCCATAATTAGGTTGTTACACGT
*
2965265 -CATGTACAAAAACATGTGACATGCCATAATTAGGTTGTTACAC-T
1 CCATGTACAAAAACATGTGACACGCCATAATTAGGTTGTTACACGT
2965309 CCATGT
1 CCATGT
2965315 TGAAAAAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
44 1 0.02
45 41 0.98
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (46 bp):
CCATGTACAAAAACATGTGACACGCCATAATTAGGTTGTTACACGT
Found at i:2965433 original size:29 final size:29
Alignment explanation
Indices: 2965401--2965464 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
2965391 TATGTTGAAA
* *
2965401 AAAAAAATATCATTGTTACATGCCATGTT
1 AAAAAAATATCATTGTTACATACCATATT
*
2965430 AAAAAAATATTATTGTTACATACCATATT
1 AAAAAAATATCATTGTTACATACCATATT
*
2965459 CAAAAA
1 AAAAAA
2965465 TATTTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (29 bp):
AAAAAAATATCATTGTTACATACCATATT
Found at i:2965632 original size:19 final size:19
Alignment explanation
Indices: 2965608--2965664 Score: 87
Period size: 19 Copynumber: 3.0 Consensus size: 19
2965598 ATTTTCATAA
2965608 ATCAAAATACAAATTTTCT
1 ATCAAAATACAAATTTTCT
*
2965627 ATCAAAATACAAATCTTCT
1 ATCAAAATACAAATTTTCT
* *
2965646 ATCAAAACATAAATTTTCT
1 ATCAAAATACAAATTTTCT
2965665 TGTCTAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (19 bp):
ATCAAAATACAAATTTTCT
Found at i:2968336 original size:6 final size:6
Alignment explanation
Indices: 2968325--2968360 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
2968315 GGTTACAATT
* *
2968325 GGGTGG GGGTGG GGGTGG GGGTGG TGGTGG TGGTGG
1 GGGTGG GGGTGG GGGTGG GGGTGG GGGTGG GGGTGG
2968361 CGGCAGCATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.78, T:0.22
Consensus pattern (6 bp):
GGGTGG
Found at i:2968458 original size:3 final size:3
Alignment explanation
Indices: 2968452--2968480 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2968442 AGGAGGCGGC
2968452 GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
2968481 GGAGTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.69, T:0.31
Consensus pattern (3 bp):
GGT
Found at i:2968477 original size:57 final size:57
Alignment explanation
Indices: 2968338--2968477 Score: 201
Period size: 57 Copynumber: 2.5 Consensus size: 57
2968328 TGGGGGTGGG
* * *
2968338 GGTGGGGGTGGTGGTGGTGGTGGCGGCAGCATGGTATGGTTGCATTGAGGTGGAGGC
1 GGTGGTGGTGGTGGTGGTGGTGGTGGCAGCATGGTATGGTTGCATTGAGGAGGAGGC
* * * *
2968395 GGTGGTGGTGGTGGAGGTGGAGGTGGC-GTCATGGTATGGTTGCATTTAGGAGGCGGC
1 GGTGGTGGTGGTGGTGGTGGTGGTGGCAG-CATGGTATGGTTGCATTGAGGAGGAGGC
2968452 GGTGGTGGTGGTGGTGGTGGTGGTGG
1 GGTGGTGGTGGTGGTGGTGGTGGTGG
2968478 TGGGGAGTAA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
56 1 0.01
57 72 0.99
ACGTcount: A:0.09, C:0.07, G:0.57, T:0.26
Consensus pattern (57 bp):
GGTGGTGGTGGTGGTGGTGGTGGTGGCAGCATGGTATGGTTGCATTGAGGAGGAGGC
Found at i:2969826 original size:2 final size:2
Alignment explanation
Indices: 2969814--2969843 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2969804 TCTCAATTGC
*
2969814 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2969844 CAGAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2970814 original size:2 final size:2
Alignment explanation
Indices: 2970807--2970831 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2970797 AAGACCTTTG
2970807 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 T
2970832 GATTCATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2978088 original size:20 final size:20
Alignment explanation
Indices: 2978063--2978127 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
2978053 ACATATGAAC
*
2978063 AAATAAACTAAAAATGAAAA
1 AAATAAACTAAAAATAAAAA
*
2978083 AAATAAAC-AAATATAAATAA
1 AAATAAACTAAAAATAAA-AA
* * *
2978103 AAATAATAATATAAATTAAAA
1 AAATAA-ACTAAAAATAAAAA
2978124 AAAT
1 AAAT
2978128 TTAAAATTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
19 7 0.19
20 16 0.44
21 7 0.19
22 6 0.17
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.22
Consensus pattern (20 bp):
AAATAAACTAAAAATAAAAA
Found at i:2978116 original size:28 final size:28
Alignment explanation
Indices: 2978055--2978117 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
2978045 AACTTATAAC
* *
2978055 ATATGAACAAATAAACTAAAAATGAAAA
1 ATATAAACAAATAAAATAAAAATGAAAA
* *
2978083 AAATAAACAAATATAAATAAAAAT-AATA
1 ATATAAACAAATA-AAATAAAAATGAAAA
2978111 ATATAAA
1 ATATAAA
2978118 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (28 bp):
ATATAAACAAATAAAATAAAAATGAAAA
Found at i:2983957 original size:22 final size:22
Alignment explanation
Indices: 2983932--2983975 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2983922 TATAAATAGT
*
2983932 TAAAAATAATATATAAAATTAA
1 TAAAAAAAATATATAAAATTAA
* *
2983954 TAAAAAAAATTTATATAATTAA
1 TAAAAAAAATATATAAAATTAA
2983976 AATTATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAAAAAAATATATAAAATTAA
Found at i:2984389 original size:14 final size:15
Alignment explanation
Indices: 2984372--2984411 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
2984362 AAAAATAAAC
2984372 AAATATAAATGAAAAA
1 AAATATAAAT-AAAAA
2984388 ATAATATAAAT-AAAA
1 A-AATATAAATAAAAA
2984403 AAATATAAA
1 AAATATAAA
2984412 GTTGTGTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 8 0.35
15 5 0.22
16 1 0.04
17 9 0.39
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
AAATATAAATAAAAA
Found at i:2984393 original size:17 final size:17
Alignment explanation
Indices: 2984373--2984407 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2984363 AAAATAAACA
*
2984373 AATATAAATGAAAAAAT
1 AATATAAATAAAAAAAT
2984390 AATATAAATAAAAAAAT
1 AATATAAATAAAAAAAT
2984407 A
1 A
2984408 TAAAGTTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (17 bp):
AATATAAATAAAAAAAT
Found at i:2984398 original size:23 final size:23
Alignment explanation
Indices: 2984350--2984403 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
2984340 GAACAAATAG
2984350 AATAAAAATGAAAAAAATAAACA
1 AATAAAAATGAAAAAAATAAACA
* *
2984373 AATATAAATG-AAAAAATAATATA
1 AATAAAAATGAAAAAAATAA-ACA
2984396 AATAAAAA
1 AATAAAAA
2984404 AATATAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.19
Consensus pattern (23 bp):
AATAAAAATGAAAAAAATAAACA
Found at i:2988806 original size:11 final size:10
Alignment explanation
Indices: 2988778--2988811 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2988768 CAACCATTTT
2988778 AAACACACCA
1 AAACACACCA
*
2988788 GAACACACCA
1 AAACACACCA
2988798 AAGACACACCA
1 AA-ACACACCA
2988809 AAA
1 AAA
2988812 TCAGAAGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.59, C:0.35, G:0.06, T:0.00
Consensus pattern (10 bp):
AAACACACCA
Found at i:2991413 original size:16 final size:16
Alignment explanation
Indices: 2991388--2991431 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2991378 CGAAAACAGA
*
2991388 GATATTTATATGCAAT
1 GATATATATATGCAAT
*
2991404 GATATGTATAATGCAAT
1 GATATATAT-ATGCAAT
2991421 -ATATATATATG
1 GATATATATATG
2991432 TTATGCTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.12
16 15 0.60
17 7 0.28
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (16 bp):
GATATATATATGCAAT
Found at i:2991471 original size:3 final size:3
Alignment explanation
Indices: 2991463--2991547 Score: 50
Period size: 3 Copynumber: 27.7 Consensus size: 3
2991453 CATTTTTTAG
* *
2991463 TTA TTA TTAA TTAA TTA TTA TTT TTA TT- TTA TTA -TA TTT TTCA TTA
1 TTA TTA TT-A TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
* * * *
2991509 TCA -TA TTT TCTA TTC TTA TTTC TTA TTA TTA TTA TTA TT
1 TTA TTA TTA T-TA TTA TTA -TTA TTA TTA TTA TTA TTA TT
2991548 TTTTATACTT
Statistics
Matches: 63, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
2 5 0.08
3 45 0.71
4 13 0.21
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2991956 original size:14 final size:13
Alignment explanation
Indices: 2991931--2991965 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
2991921 NNTCATCATT
*
2991931 TTTTTATCTATTA
1 TTTTTATTTATTA
2991944 TTATTTATTTATTA
1 TT-TTTATTTATTA
2991958 TTTTTATT
1 TTTTTATT
2991966 GAGTAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTATTTATTA
Found at i:2992406 original size:49 final size:47
Alignment explanation
Indices: 2992318--2992412 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 47
2992308 TTTATATTAT
*
2992318 TATTTTATTATTGTTGTTTTTGTTATTTACCTATTTTTTTATGTTTTC
1 TATTTTATGATTGTTGTTTTTGTTATTTACCTATTTTTTTAT-TTTTC
* *
2992366 TATTTTAATGATT-TTGATTTTTTTTATTTA-TTATTTTTTTTATTTTT
1 TATTTT-ATGATTGTTG-TTTTTGTTATTTACCTA-TTTTTTTATTTTT
2992413 AATTTATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
48 15 0.37
49 26 0.63
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (47 bp):
TATTTTATGATTGTTGTTTTTGTTATTTACCTATTTTTTTATTTTTC
Found at i:2992417 original size:16 final size:15
Alignment explanation
Indices: 2992376--2992413 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
2992366 TATTTTAATG
*
2992376 ATTTTGATTTTTTTT
1 ATTTTTATTTTTTTT
2992391 ATTTATTATTTTTTTT
1 ATTT-TTATTTTTTTT
2992407 ATTTTTA
1 ATTTTTA
2992414 ATTTATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (15 bp):
ATTTTTATTTTTTTT
Found at i:2993093 original size:36 final size:37
Alignment explanation
Indices: 2993041--2993112 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 37
2993031 ATCGGCTCTC
* *
2993041 CAACTGGTGGCTGCTGCT-CCCTATCAGTCGACTTTT
1 CAACCGGTGGCTGCTGCTCCCCAATCAGTCGACTTTT
* *
2993077 CAACCGGTGGTTGCTGCTCCCCAATCGGTCGACTTT
1 CAACCGGTGGCTGCTGCTCCCCAATCAGTCGACTTT
2993113 CTCTCTAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 16 0.52
37 15 0.48
ACGTcount: A:0.14, C:0.32, G:0.24, T:0.31
Consensus pattern (37 bp):
CAACCGGTGGCTGCTGCTCCCCAATCAGTCGACTTTT
Found at i:2993163 original size:104 final size:104
Alignment explanation
Indices: 2993032--2993249 Score: 330
Period size: 104 Copynumber: 2.1 Consensus size: 104
2993022 CCTCCAATGA
* * * *
2993032 TCGGCTCTCCAACTGGTGGCTGCTGCTCCCTATCAGTCGACTTTTCAACCGGTGGTTGCTGCTCC
1 TCGGCTTTCCAACCGGTGGCTGCTGCTCCCTAACAGTCGACTTTTCAAACGGTGGTTGCTGCTCC
* * *
2993097 CCAATCGGTC-GACTTTCTCTCTAATCGGCGTCGCTCAAG
66 CCAATCGGTCAG-CTCTCTCTCCAATCGGCGACGCTCAAG
* *
2993136 TCGGCTTTCCAACCGGTGGCTGTTGCTCCCTAACAGTCGGCTTTTCAAACGGTGGTTGCTGCTCC
1 TCGGCTTTCCAACCGGTGGCTGCTGCTCCCTAACAGTCGACTTTTCAAACGGTGGTTGCTGCTCC
*
2993201 CCAATCGGTCAGCTCTCTTTCCAATCGGCGACGCTCAAG
66 CCAATCGGTCAGCTCTCTCTCCAATCGGCGACGCTCAAG
2993240 TCGGCTTTCC
1 TCGGCTTTCC
2993250 CCAACCGACG
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
104 102 0.99
105 1 0.01
ACGTcount: A:0.14, C:0.33, G:0.23, T:0.29
Consensus pattern (104 bp):
TCGGCTTTCCAACCGGTGGCTGCTGCTCCCTAACAGTCGACTTTTCAAACGGTGGTTGCTGCTCC
CCAATCGGTCAGCTCTCTCTCCAATCGGCGACGCTCAAG
Found at i:2993633 original size:35 final size:35
Alignment explanation
Indices: 2993549--2993637 Score: 133
Period size: 35 Copynumber: 2.5 Consensus size: 35
2993539 GAGCTCTGGA
2993549 GGGGGCACGCTCCACTACCTTGTCCCTGGGCACTG
1 GGGGGCACGCTCCACTACCTTGTCCCTGGGCACTG
* * *
2993584 GGGGCCACACTCCACTGCCTTGTCCCTGGGCACTG
1 GGGGGCACGCTCCACTACCTTGTCCCTGGGCACTG
* *
2993619 GGGGGCATGTTCCACTACC
1 GGGGGCACGCTCCACTACC
2993638 CTGCCAGACG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.12, C:0.37, G:0.30, T:0.20
Consensus pattern (35 bp):
GGGGGCACGCTCCACTACCTTGTCCCTGGGCACTG
Found at i:2997309 original size:11 final size:11
Alignment explanation
Indices: 2997281--2997313 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2997271 CAACCATTTT
*
2997281 AGACACACCAG
1 AGACACACCAA
2997292 A-ACACACCAA
1 AGACACACCAA
2997302 AGACACACCAA
1 AGACACACCAA
2997313 A
1 A
2997314 ATCAGAAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.55, C:0.36, G:0.09, T:0.00
Consensus pattern (11 bp):
AGACACACCAA
Found at i:2997900 original size:23 final size:22
Alignment explanation
Indices: 2997874--2997944 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 22
2997864 ACTGGTCAAA
*
2997874 CAATGTCTTATTAACTAGTCACG
1 CAATG-CTCATTAACTAGTCACG
*
2997897 CAATGC-CATTAACCAGTCACG
1 CAATGCTCATTAACTAGTCACG
* *
2997918 CAATGCCACATCAACTAGTCACG
1 CAATG-CTCATTAACTAGTCACG
2997941 CAAT
1 CAAT
2997945 ACTTAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.43
22 2 0.05
23 22 0.52
ACGTcount: A:0.34, C:0.30, G:0.13, T:0.24
Consensus pattern (22 bp):
CAATGCTCATTAACTAGTCACG
Found at i:2997909 original size:21 final size:23
Alignment explanation
Indices: 2997883--2997944 Score: 92
Period size: 21 Copynumber: 2.8 Consensus size: 23
2997873 ACAATGTCTT
2997883 ATTAACTAGTCACGCAATG-C-C
1 ATTAACTAGTCACGCAATGCCAC
*
2997904 ATTAACCAGTCACGCAATGCCAC
1 ATTAACTAGTCACGCAATGCCAC
*
2997927 ATCAACTAGTCACGCAAT
1 ATTAACTAGTCACGCAAT
2997945 ACTTAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 18 0.50
22 1 0.03
23 17 0.47
ACGTcount: A:0.35, C:0.31, G:0.13, T:0.21
Consensus pattern (23 bp):
ATTAACTAGTCACGCAATGCCAC
Found at i:2997964 original size:22 final size:22
Alignment explanation
Indices: 2997934--2998022 Score: 110
Period size: 22 Copynumber: 4.0 Consensus size: 22
2997924 CACATCAACT
2997934 AGTCACGCAATACTTAAAAATC
1 AGTCACGCAATACTTAAAAATC
*
2997956 AATCACGCAATACTTAAAAA-C
1 AGTCACGCAATACTTAAAAATC
*
2997977 TAGTCACGCAATACTCAAAAATC
1 -AGTCACGCAATACTTAAAAATC
* *
2998000 AGTTAC-CTAATGCTTAAAAATC
1 AGTCACGC-AATACTTAAAAATC
2998022 A
1 A
2998023 CCCAAACTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.03
22 55 0.95
23 1 0.02
ACGTcount: A:0.46, C:0.22, G:0.08, T:0.24
Consensus pattern (22 bp):
AGTCACGCAATACTTAAAAATC
Found at i:2998244 original size:60 final size:60
Alignment explanation
Indices: 2998122--2998245 Score: 151
Period size: 60 Copynumber: 2.1 Consensus size: 60
2998112 CTTGGCGAAG
* * * *
2998122 AATGATCAAAATGCTCAAAGGTTTTTCTTCATGTATCAAAAATCACTCAAAAATATTTAA
1 AATGATCAAAACGCTCAAAGATTTTTCTTCATGTATCAAAAATCACTCAAAAATACTCAA
* * * * *
2998182 AATGTTCAAAACGTTCAAAGATTTTTCTTCGTGTATCAAAAA-CTACTCTAAAATGCTCAA
1 AATGATCAAAACGCTCAAAGATTTTTCTTCATGTATCAAAAATC-ACTCAAAAATACTCAA
2998242 AATG
1 AATG
2998246 CTTAAAGATT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 53 0.98
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (60 bp):
AATGATCAAAACGCTCAAAGATTTTTCTTCATGTATCAAAAATCACTCAAAAATACTCAA
Found at i:3005221 original size:84 final size:84
Alignment explanation
Indices: 3005080--3005250 Score: 333
Period size: 84 Copynumber: 2.0 Consensus size: 84
3005070 ATACAGTATT
3005080 CCTGGATCATATGTATAAAACCTTGTTAACATGGCCTACAAGTAAAAAGAAAGATGGGGCTATTT
1 CCTGGATCATATGTATAAAACCTTGTTAACATGGCCTACAAGTAAAAAGAAAGATGGGGCTATTT
3005145 TGCCCAAATTCACATCAGA
66 TGCCCAAATTCACATCAGA
*
3005164 CCTGGATCATATGTATAAAACCTTGTTAACATGGCGTACAAGTAAAAAGAAAGATGGGGCTATTT
1 CCTGGATCATATGTATAAAACCTTGTTAACATGGCCTACAAGTAAAAAGAAAGATGGGGCTATTT
3005229 TGCCCAAATTCACATCAGA
66 TGCCCAAATTCACATCAGA
3005248 CCT
1 CCT
3005251 CGATTATTTG
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (84 bp):
CCTGGATCATATGTATAAAACCTTGTTAACATGGCCTACAAGTAAAAAGAAAGATGGGGCTATTT
TGCCCAAATTCACATCAGA
Found at i:3012058 original size:2 final size:2
Alignment explanation
Indices: 3012051--3012076 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3012041 ATGTGTATAT
3012051 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
3012077 ACGGGGAATC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3012934 original size:6 final size:6
Alignment explanation
Indices: 3012925--3012975 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
3012915 GGAGGTGGCA
3012925 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG
3012973 GAA
1 GAA
3012976 AACTTTGAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:3016907 original size:19 final size:19
Alignment explanation
Indices: 3016883--3016922 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3016873 TATCTGCGAC
3016883 CTGCTTTAAAGAATATGAG
1 CTGCTTTAAAGAATATGAG
3016902 CTGCTTTAAAGAATATGAG
1 CTGCTTTAAAGAATATGAG
3016921 CT
1 CT
3016923 TTACTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (19 bp):
CTGCTTTAAAGAATATGAG
Found at i:3023952 original size:17 final size:17
Alignment explanation
Indices: 3023920--3023952 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3023910 TATAACAAAA
3023920 CAAAATAACAAGAACAT
1 CAAAATAACAAGAACAT
3023937 CAAATATAACAA-AACA
1 CAAA-ATAACAAGAACA
3023953 AAATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.67, C:0.18, G:0.03, T:0.12
Consensus pattern (17 bp):
CAAAATAACAAGAACAT
Found at i:3024134 original size:18 final size:18
Alignment explanation
Indices: 3024113--3024170 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
3024103 GTATACACAT
3024113 TTAAACACGATAACACGA
1 TTAAACACGATAACACGA
* * * *
3024131 TTAAACACGTTTATACGT
1 TTAAACACGATAACACGA
*
3024149 TTAAACACAATAACACGA
1 TTAAACACGATAACACGA
3024167 TTAA
1 TTAA
3024171 TATGATTAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.26
Consensus pattern (18 bp):
TTAAACACGATAACACGA
Found at i:3025974 original size:25 final size:25
Alignment explanation
Indices: 3025928--3025975 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
3025918 AAAATTTATA
* * *
3025928 ATTAATAATTGATTAATTATTTTTT
1 ATTAATAAATAATTAATCATTTTTT
*
3025953 ATTAATAAATAATTTATCATTTT
1 ATTAATAAATAATTAATCATTTT
3025976 ATAACACGAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
ATTAATAAATAATTAATCATTTTTT
Found at i:3033730 original size:56 final size:56
Alignment explanation
Indices: 3033624--3033732 Score: 146
Period size: 56 Copynumber: 1.9 Consensus size: 56
3033614 ATTTTGAAAA
* * **
3033624 TAAAGTTTAAGTAAACTTATAAATTACAAGTCCACATTCTTAACCAAAAAACCATT
1 TAAAGTTTAAGTAAACCTATAAATCACAAGTCCACATTCCCAACCAAAAAACCATT
** *
3033680 TAAAGTTTAAGTAAACCTATAAATCACAAGTTTACATTCCCAACTTAAAAAAC
1 TAAAGTTTAAGTAAACCTATAAATCACAAGTCCACATTCCCAAC-CAAAAAAC
3033733 ATGTTTAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
56 38 0.84
57 7 0.16
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (56 bp):
TAAAGTTTAAGTAAACCTATAAATCACAAGTCCACATTCCCAACCAAAAAACCATT
Found at i:3036684 original size:2 final size:2
Alignment explanation
Indices: 3036677--3036708 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3036667 TTAAATGACA
3036677 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3036709 TTCTTGATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3040906 original size:77 final size:77
Alignment explanation
Indices: 3040814--3040978 Score: 208
Period size: 77 Copynumber: 2.1 Consensus size: 77
3040804 TGAATTTCTC
* * ***
3040814 AAATTAAAATACTATCCTTAATTTTA-AGAATTTCTTTTAAAGTAAGAAATAATTTTTTATTTTT
1 AAATTAAAATACTATCCTTAATTTTAGA-AATTGCTTTTAAAGTAAGAAACAATTACCTATTTTT
*
3040878 TATAAATCAC-CAA
65 TAGAAATCACTC-A
* * *
3040891 AAATTAAAATTCTATCCTTAATTTTTGAAATTGCTTTTAAAGTAGGAAACAATTACCTATTTTTT
1 AAATTAAAATACTATCCTTAATTTTAGAAATTGCTTTTAAAGTAAGAAACAATTACCTATTTTTT
*
3040956 AGGAATCACTCA
66 AGAAATCACTCA
3040968 AAATTAAAATA
1 AAATTAAAATA
3040979 TATGGTATTT
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
77 73 0.97
78 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.41
Consensus pattern (77 bp):
AAATTAAAATACTATCCTTAATTTTAGAAATTGCTTTTAAAGTAAGAAACAATTACCTATTTTTT
AGAAATCACTCA
Found at i:3043296 original size:22 final size:23
Alignment explanation
Indices: 3043260--3043315 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
3043250 AATTCAAAAA
*
3043260 ATTA-ATTAAATTAAATTTTT-T
1 ATTATATTTAATTAAATTTTTAT
3043281 ATTATATTTAATTAAATTTTTAT
1 ATTATATTTAATTAAATTTTTAT
*
3043304 ATTTTTATTTAA
1 A-TTATATTTAA
3043316 AAAATAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 4 0.13
22 15 0.50
23 2 0.07
24 9 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTATATTTAATTAAATTTTTAT
Found at i:3043320 original size:23 final size:22
Alignment explanation
Indices: 3043272--3043320 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
3043262 TAATTAAATT
*
3043272 AAATTTTTTATTATATTTAATT
1 AAATTTTTTATTATATTTAATA
*
3043294 AAATTTTTATATTTTTATTTAA-A
1 AAATTTTT-TA-TTATATTTAATA
3043317 AAAT
1 AAAT
3043321 AAAATTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 6 0.26
24 9 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
AAATTTTTTATTATATTTAATA
Found at i:3047853 original size:323 final size:321
Alignment explanation
Indices: 3047219--3047861 Score: 1252
Period size: 323 Copynumber: 2.0 Consensus size: 321
3047209 AATAATTCAA
3047219 AAAAATATATAAAAATTAAATTAAATTAAATTAAATAATAAAAAAATATTTAAATAATTCAATGA
1 AAAAATATATAAAAATTAAATTAAATTAAATTAAATAATAAAAAAATATTTAAATAATTCAATGA
3047284 CTTTTTAAAATATTATACCAAAAAAAATTTAGCAATCCACCCAAGTTATGCAATGGAGCTCTATT
66 CTTTTTAAAATATTATACCAAAAAAAATTTAGCAATCCACCCAAGTTATGCAATGGAGCTCTATT
3047349 TCTCCATACAATAAAAAATAATAAAATAATGTTTATAAATTTATTAAAAAAAGAGATAACTTATT
131 TCTCCATACAATAAAAAATAATAAAATAATGTTTATAAATTTATTAAAAAAAGAGATAACTTATT
3047414 GCAAAAAAAATAATATCCAAAGATTAGAAGACCGAATCATAAATTTATGATGCCAACAATTTCAT
196 GCAAAAAAAATAATATCCAAAGATTAGAAGACCGAATCATAAATTTATGATGCCAACAATTTCAT
3047479 TTTTGACAAATATTGAATTTTAGATTGATTAAAATTCTAAATATTGTTTTTGAATAACATNC
261 TTTTGACAAATATTGAATTTTAGATTGATTAAAATTCTAAATATTGTTTTTGAATAACAT-C
3047541 AAAAATATATAAAAA-TAAATTTAAATTAAATTAAATAATAAAAAAATATTTAAATAATTCAATG
1 AAAAATATATAAAAATTAAA-TTAAATTAAATTAAATAATAAAAAAATATTTAAATAATTCAATG
3047605 ACTTTTTAAAATATTATACCAAAAAAAATTTAGCAATCCACCCAAGTTATGCAATGGAGCTCTAT
65 ACTTTTTAAAATATTATACCAAAAAAAATTTAGCAATCCACCCAAGTTATGCAATGGAGCTCTAT
3047670 TTCTCCATACAATAAAAAATAATAAAATAAATGTTTATAAATTTATTAAAAAAAGAGATAACTTA
130 TTCTCCATACAATAAAAAATAATAAAAT-AATGTTTATAAATTTATTAAAAAAAGAGATAACTTA
3047735 TTGCAAAAAAAATAATATCCAAAGATTAGAAGACCGAATCATAAATTTATGATGCCAACAATTTC
194 TTGCAAAAAAAATAATATCCAAAGATTAGAAGACCGAATCATAAATTTATGATGCCAACAATTTC
3047800 ATTTTTGACAAATATTGAATTTTAGATTGATTAAAATTCTAAATATTGTTTTTGAATAACAT
259 ATTTTTGACAAATATTGAATTTTAGATTGATTAAAATTCTAAATATTGTTTTTGAATAACAT
3047862 TCGAATAGTT
Statistics
Matches: 319, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
321 4 0.01
322 152 0.48
323 163 0.51
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (321 bp):
AAAAATATATAAAAATTAAATTAAATTAAATTAAATAATAAAAAAATATTTAAATAATTCAATGA
CTTTTTAAAATATTATACCAAAAAAAATTTAGCAATCCACCCAAGTTATGCAATGGAGCTCTATT
TCTCCATACAATAAAAAATAATAAAATAATGTTTATAAATTTATTAAAAAAAGAGATAACTTATT
GCAAAAAAAATAATATCCAAAGATTAGAAGACCGAATCATAAATTTATGATGCCAACAATTTCAT
TTTTGACAAATATTGAATTTTAGATTGATTAAAATTCTAAATATTGTTTTTGAATAACATC
Found at i:3068735 original size:2 final size:2
Alignment explanation
Indices: 3068728--3068755 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3068718 CAAGGCCCAA
3068728 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3068756 TCTTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3073792 original size:20 final size:19
Alignment explanation
Indices: 3073767--3073805 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
3073757 GATTGCTTTC
3073767 TTGAACCAAAAAAAAAAAA
1 TTGAACCAAAAAAAAAAAA
3073786 NTTGAACCAAAAAAAAAAAA
1 -TTGAACCAAAAAAAAAAAA
3073806 AGAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.72, C:0.10, G:0.05, T:0.10
Consensus pattern (19 bp):
TTGAACCAAAAAAAAAAAA
Found at i:3073929 original size:8 final size:9
Alignment explanation
Indices: 3073895--3073931 Score: 53
Period size: 8 Copynumber: 4.4 Consensus size: 9
3073885 CTATCATTGC
3073895 TTCTTTC-T
1 TTCTTTCTT
3073903 TTCTTTCTT
1 TTCTTTCTT
3073912 TTCTTT-TT
1 TTCTTTCTT
3073920 TT-TTTCTT
1 TTCTTTCTT
3073928 TTCT
1 TTCT
3073932 GCATGTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 3 0.12
8 15 0.58
9 8 0.31
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTCTTTCTT
Found at i:3074099 original size:20 final size:20
Alignment explanation
Indices: 3074074--3074117 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
3074064 GTTAATCATC
*
3074074 TTAGGTACATATGAAAACTG
1 TTAGGTACATATCAAAACTG
*
3074094 TTAGGTACATATCAATACTG
1 TTAGGTACATATCAAAACTG
3074114 TTAG
1 TTAG
3074118 ACACATGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
TTAGGTACATATCAAAACTG
Found at i:3074123 original size:20 final size:20
Alignment explanation
Indices: 3074080--3074123 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
3074070 CATCTTAGGT
* **
3074080 ACATATGAAAACTGTTAGGT
1 ACATATCAAAACTGTTAGAC
*
3074100 ACATATCAATACTGTTAGAC
1 ACATATCAAAACTGTTAGAC
3074120 ACAT
1 ACAT
3074124 GATTGTATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
ACATATCAAAACTGTTAGAC
Found at i:3076943 original size:6 final size:6
Alignment explanation
Indices: 3076932--3076962 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3076922 TCCACCACTG
*
3076932 CCTCCA CCTCCA CCTCCA CCTCCA CCGCCA C
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA C
3076963 TGCTACTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.68, G:0.03, T:0.13
Consensus pattern (6 bp):
CCTCCA
Found at i:3086364 original size:41 final size:42
Alignment explanation
Indices: 3086298--3086382 Score: 145
Period size: 41 Copynumber: 2.0 Consensus size: 42
3086288 TTCCGGGAGA
3086298 AAAGTAGAAAACCGGCGTCGTTTAGTGGGAAAACAGAACGGC
1 AAAGTAGAAAACCGGCGTCGTTTAGTGGGAAAACAGAACGGC
* *
3086340 AAAGTAG-AAAGCGGCGTTGTTTAGTGGGAAAACAGAACGGC
1 AAAGTAGAAAACCGGCGTCGTTTAGTGGGAAAACAGAACGGC
3086381 AA
1 AA
3086383 TGGCAAAGGC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 34 0.83
42 7 0.17
ACGTcount: A:0.39, C:0.14, G:0.32, T:0.15
Consensus pattern (42 bp):
AAAGTAGAAAACCGGCGTCGTTTAGTGGGAAAACAGAACGGC
Found at i:3088591 original size:3 final size:3
Alignment explanation
Indices: 3088583--3088607 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3088573 TCCACCCGAA
3088583 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3088608 GGTGTAATTA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3100478 original size:3 final size:3
Alignment explanation
Indices: 3100470--3100503 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3100460 GTCATAAAAG
3100470 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3100504 CAACAACAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3106687 original size:69 final size:70
Alignment explanation
Indices: 3106575--3106781 Score: 242
Period size: 69 Copynumber: 3.0 Consensus size: 70
3106565 ATTTGCTAAC
*
3106575 AAATTTGACATCCACAA-GAGGCATCGCATATTTTCATAAAACCAATACGCCTCAAACACCATTG
1 AAATTTGACATCCACAATGA-GCATCGCATATGTTCATAAAACCAATACGCCTCAAACACCATTG
3106639 TTCAAT
65 TTCAAT
* * * *
3106645 -AATTTAACATCCACAATGAGCGTCGCATATGTTCATAAAACCAATATGCCTCAAACATCATTGT
1 AAATTTGACATCCACAATGAGCATCGCATATGTTCATAAAACCAATACGCCTCAAACACCATTGT
3106709 TCAAT
66 TCAAT
* * * * * * *
3106714 AAATCTGACATCCAAAATGAGCA-CTGCAAACT-TTCATAAACCCAAGACCCCTTAAACACCATT
1 AAATTTGACATCCACAATGAGCATC-GCATA-TGTTCATAAAACCAATACGCCTCAAACACCATT
*
3106777 CTTCA
64 GTTCA
3106782 CACACCTTTA
Statistics
Matches: 116, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
69 62 0.53
70 53 0.46
71 1 0.01
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.26
Consensus pattern (70 bp):
AAATTTGACATCCACAATGAGCATCGCATATGTTCATAAAACCAATACGCCTCAAACACCATTGT
TCAAT
Found at i:3106771 original size:70 final size:68
Alignment explanation
Indices: 3106606--3106781 Score: 201
Period size: 70 Copynumber: 2.5 Consensus size: 68
3106596 CATCGCATAT
* * *
3106606 TTTCATAAAACCAATACGCCTCAAACACCATTGTTCAATAATTTAACATCCACAATGAGCGTCGC
1 TTTCATAAAACCAATACGCCTCAAACACCATTGTTCAATAATCTAACATCCAAAATGAGCCTCGC
*
3106671 ATA
66 AAA
* * *
3106674 TGTTCATAAAACCAATATGCCTCAAACATCATTGTTCAATAAATCTGACATCCAAAATGAGCACT
1 T-TTCATAAAACCAATACGCCTCAAACACCATTGTTCAAT-AATCTAACATCCAAAATGAGC-CT
3106739 -GCAAA
63 CGCAAA
* * * * *
3106744 CTTTCATAAACCCAAGACCCCTTAAACACCATTCTTCA
1 -TTTCATAAAACCAATACGCCTCAAACACCATTGTTCA
3106782 CACACCTTTA
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
68 1 0.01
69 36 0.40
70 51 0.57
71 2 0.02
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.26
Consensus pattern (68 bp):
TTTCATAAAACCAATACGCCTCAAACACCATTGTTCAATAATCTAACATCCAAAATGAGCCTCGC
AAA
Found at i:3109792 original size:18 final size:17
Alignment explanation
Indices: 3109760--3109800 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
3109750 AAGTGTTTTT
*
3109760 ATTGCTTTTATTGACTC
1 ATTGCTTTCATTGACTC
3109777 ATTGCTTCTCATTGACTC
1 ATTGCTT-TCATTGACTC
3109795 ATTGCT
1 ATTGCT
3109801 ATTTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.17, C:0.22, G:0.12, T:0.49
Consensus pattern (17 bp):
ATTGCTTTCATTGACTC
Found at i:3114699 original size:21 final size:21
Alignment explanation
Indices: 3114658--3114705 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3114648 ATTTGGAAAC
* *
3114658 AAATAAAATAAAGACTCTTTT
1 AAATAAAAAAAAGAATCTTTT
3114679 AAATAAAAAAAAGTAAT-TTTT
1 AAATAAAAAAAAG-AATCTTTT
3114700 -AATAAA
1 AAATAAA
3114706 TTTTGTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 16 0.67
22 2 0.08
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (21 bp):
AAATAAAAAAAAGAATCTTTT
Found at i:3116318 original size:2 final size:2
Alignment explanation
Indices: 3116311--3116344 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3116301 TAGTATGGTT
* *
3116311 TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3116345 GTAGCAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3125344 original size:13 final size:14
Alignment explanation
Indices: 3125311--3125349 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3125301 ATAAGCTTTT
*
3125311 AAAAAAAACAAAAC
1 AAAAAAAAGAAAAC
3125325 AAAAAAAAGAAAA-
1 AAAAAAAAGAAAAC
*
3125338 AAGAAAAAGAAA
1 AAAAAAAAGAAA
3125350 TGAATGGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAAC
Found at i:3129348 original size:4 final size:4
Alignment explanation
Indices: 3129339--3129402 Score: 56
Period size: 4 Copynumber: 16.0 Consensus size: 4
3129329 GGTAAAAGCA
* * * * * *
3129339 AGAG AGAG AGAG AGAG AGAG AGAG GGAG GGAG TGCG ACAG TGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
* *
3129387 AGAG AAAG AGGG AGAG
1 AGAG AGAG AGAG AGAG
3129403 CATGTAGATA
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.42, C:0.03, G:0.52, T:0.03
Consensus pattern (4 bp):
AGAG
Found at i:3129350 original size:6 final size:6
Alignment explanation
Indices: 3129339--3129402 Score: 56
Period size: 6 Copynumber: 10.7 Consensus size: 6
3129329 GGTAAAAGCA
* * * * * *
3129339 AGAGAG AGAGAG AGAGAG AGAGAG GGAGGG AGTGCG ACAGTG AGAGAG
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG
* *
3129387 AGAGAA AGAGGG AGAG
1 AGAGAG AGAGAG AGAG
3129403 CATGTAGATA
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.42, C:0.03, G:0.52, T:0.03
Consensus pattern (6 bp):
AGAGAG
Found at i:3139729 original size:2 final size:2
Alignment explanation
Indices: 3139722--3139759 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3139712 ATGGTCTTCA
*
3139722 TG TG TG TG AG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3139760 AGAGAGAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.03, C:0.00, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Done.