Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 6 of 325
Found at i:1372533 original size:3 final size:3
Alignment explanation
Indices: 1372525--1372582 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
1372515 GTATACATGA
1372525 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1372573 AAT AAT AAT A
1 AAT AAT AAT A
1372583 GTAAAATCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1374397 original size:135 final size:137
Alignment explanation
Indices: 1374154--1374438 Score: 529
Period size: 135 Copynumber: 2.1 Consensus size: 137
1374144 CATTGGGCCT
**
1374154 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1374219 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
1374283 CATATGC
131 CATATGC
1374290 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCA-ATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
1374354 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
1374419 CATATGC
131 CATATGC
1374426 AAGCCCATTTGGG
1 AAGCCCATTTGGG
1374439 GAGACTACTC
Statistics
Matches: 145, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
135 81 0.56
136 64 0.44
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
CATATGC
Found at i:1376255 original size:25 final size:25
Alignment explanation
Indices: 1376221--1376353 Score: 205
Period size: 26 Copynumber: 5.2 Consensus size: 25
1376211 CATGAAATTC
1376221 TTATCATGAAACATTTACCTAACC-A
1 TTATCATG-AACATTTACCTAACCTA
1376246 TTATCATGAACATTTACCTAACCTA
1 TTATCATGAACATTTACCTAACCTA
*
1376271 TTATCATGGAACACTTACCTAACCTA
1 TTATCAT-GAACATTTACCTAACCTA
*
1376297 TTATTATGAAACATTTACCTAACCTA
1 TTATCATG-AACATTTACCTAACCTA
*
1376323 TTATTATGAACATTTACCTAACCTA
1 TTATCATGAACATTTACCTAACCTA
1376348 TTATCA
1 TTATCA
1376354 ATTTGTATCA
Statistics
Matches: 101, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
24 15 0.15
25 39 0.39
26 47 0.47
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.36
Consensus pattern (25 bp):
TTATCATGAACATTTACCTAACCTA
Found at i:1381624 original size:135 final size:137
Alignment explanation
Indices: 1381381--1381665 Score: 529
Period size: 135 Copynumber: 2.1 Consensus size: 137
1381371 CATTGGGCCT
**
1381381 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1381446 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
1381510 CATATGC
131 CATATGC
1381517 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCA-ATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
1381581 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
1381646 CATATGC
131 CATATGC
1381653 AAGCCCATTTGGG
1 AAGCCCATTTGGG
1381666 GAGACTACTC
Statistics
Matches: 145, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
135 81 0.56
136 64 0.44
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
CATATGC
Found at i:1383477 original size:26 final size:26
Alignment explanation
Indices: 1383439--1383574 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
1383429 CATGAAATTC
1383439 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
1383465 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
* *
1383491 TTATCATGGAACACTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
1383517 TTATTATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
1383543 TTATTATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
1383569 TTATCA
1 TTATCA
1383575 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.36
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:1384006 original size:27 final size:27
Alignment explanation
Indices: 1383967--1384035 Score: 95
Period size: 26 Copynumber: 2.6 Consensus size: 27
1383957 AAAAAAAAAA
* *
1383967 AACTTTACTTTTTTTTATTCCATTACC
1 AACTTTCCCTTTTTTTATTCCATTACC
1383994 AACTTTCCC-TTTTTTATTCCATTACC
1 AACTTTCCCTTTTTTTATTCCATTACC
*
1384020 AATTTTTCCCTTTTTT
1 AA-CTTTCCCTTTTTT
1384036 ATTTTTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 19 0.51
27 13 0.35
28 5 0.14
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.57
Consensus pattern (27 bp):
AACTTTCCCTTTTTTTATTCCATTACC
Found at i:1384013 original size:26 final size:27
Alignment explanation
Indices: 1383977--1384038 Score: 108
Period size: 26 Copynumber: 2.3 Consensus size: 27
1383967 AACTTTACTT
1383977 TTTTTTATTCCATTACCAA-CTTTCCC
1 TTTTTTATTCCATTACCAATCTTTCCC
*
1384003 TTTTTTATTCCATTACCAATTTTTCCC
1 TTTTTTATTCCATTACCAATCTTTCCC
1384030 TTTTTTATT
1 TTTTTTATT
1384039 TTTTATTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 19 0.56
27 15 0.44
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTTTTATTCCATTACCAATCTTTCCC
Found at i:1399539 original size:42 final size:41
Alignment explanation
Indices: 1399489--1399632 Score: 128
Period size: 42 Copynumber: 3.3 Consensus size: 41
1399479 GAGTCTTAAA
1399489 CCCCTAAGCAGTAGGGAAACAGACCAAATTGCAGATCTTAT
1 CCCCTAAGCAGTAGGGAAACAGACCAAATTGCAGATCTTAT
* * * *
1399530 CTCCCTAAGCAGTAGTGGAAACAGATCGAAGA-TGAAGAAGCCTTAAA
1 C-CCCTAAGCAGTAG-GGAAACAGA-CCAA-ATTGCAG-A-TCTT-AT
* ****
1399577 CCCCTAAGCAGTAGGGTAACAGGTTGAATTGCAGATCTTAT
1 CCCCTAAGCAGTAGGGAAACAGACCAAATTGCAGATCTTAT
1399618 CCCCCTAAGCAGTAG
1 -CCCCTAAGCAGTAG
1399633 TGGAGCAAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
41 2 0.02
42 30 0.37
43 11 0.13
44 12 0.15
45 9 0.11
46 16 0.20
47 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (41 bp):
CCCCTAAGCAGTAGGGAAACAGACCAAATTGCAGATCTTAT
Found at i:1399701 original size:87 final size:87
Alignment explanation
Indices: 1399483--1399943 Score: 641
Period size: 86 Copynumber: 5.3 Consensus size: 87
1399473 TTCATAGAGT
****
1399483 CTTAAACCCCTAAGCAGTAGGG-AAACAGACCAAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
1 CTTAAACCCCTAAGCAGTAGGGTAAACAGGTTGAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
* *
1399547 GAAACAGATCGAAGATGAAGAAGC
66 G-AGCAGATCGAAGACGAAGAA-C
*
1399571 CTTAAACCCCTAAGCAGTAGGGT-AACAGGTTGAATTGCAGATCTTATCCCCCTAAGCAGTAGTG
1 CTTAAACCCCTAAGCAGTAGGGTAAACAGGTTGAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
*
1399635 GAGCAAATCGAAGACGAAGAAC
66 GAGCAGATCGAAGACGAAGAAC
*
1399657 CTTAAACCCCTAAGCAGTAGGGTAAATAGGTTGAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
1 CTTAAACCCCTAAGCAGTAGGGTAAACAGGTTGAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
1399722 GAGCAGATCGAAGACGAAGAAC
66 GAGCAGATCGAAGACGAAGAAC
*
1399744 CTTAAACCCCTAAGCAGTAGGGT-AACAAGTTGAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
1 CTTAAACCCCTAAGCAGTAGGGTAAACAGGTTGAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
1399808 GAGCAGATCGAAGACGAAGAAC
66 GAGCAGATCGAAGACGAAGAAC
* ***
1399830 CTTAAACCCCTAAGCAGTAGGGT-AACAGGTTGAATTACAGATC-TAAAGCCCTAAGCAGTAG-G
1 CTTAAACCCCTAAGCAGTAGGGTAAACAGGTTGAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
* * * *
1399892 GAAACAGATCAAAGATGACA-AGC
66 G-AGCAGATCGAAGACGA-AGAAC
* * *
1399915 CTGAATCCCCTAAACAGTAGGGT-AACAGG
1 CTTAAACCCCTAAGCAGTAGGGTAAACAGG
1399944 CTGGAAATTA
Statistics
Matches: 344, Mismatches: 25, Indels: 11
0.91 0.07 0.03
Matches are distributed among these distances:
84 2 0.01
85 56 0.16
86 127 0.37
87 100 0.29
88 59 0.17
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (87 bp):
CTTAAACCCCTAAGCAGTAGGGTAAACAGGTTGAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
GAGCAGATCGAAGACGAAGAAC
Found at i:1399788 original size:173 final size:174
Alignment explanation
Indices: 1399483--1399941 Score: 687
Period size: 173 Copynumber: 2.7 Consensus size: 174
1399473 TTCATAGAGT
****
1399483 CTTAAACCCCTAAGCAGTAGGG-AAACAGACCAAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
1 CTTAAACCCCTAAGCAGTAGGGTAAACAGGTTGAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
*
1399547 GAAACAGATCGAAGATGAAGAAGCCTTAAACCCCTAAGCAGTAGGGTAACAGGTTGAATTGCAGA
66 GAAACAGATCGAAGATGAAGAA-CCTTAAACCCCTAAGCAGTAGGGTAACAAGTTGAATTGCAGA
1399612 TCTTATCCCCCTAAGCAGTAGTGGAGCAAATCGAAGACGAAGAAC
130 TCTTATCCCCCTAAGCAGTAGTGGAGCAAATCGAAGACGAAGAAC
*
1399657 CTTAAACCCCTAAGCAGTAGGGTAAATAGGTTGAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
1 CTTAAACCCCTAAGCAGTAGGGTAAACAGGTTGAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
* *
1399722 G-AGCAGATCGAAGACGAAGAACCTTAAACCCCTAAGCAGTAGGGTAACAAGTTGAATTGCAGAT
66 GAAACAGATCGAAGATGAAGAACCTTAAACCCCTAAGCAGTAGGGTAACAAGTTGAATTGCAGAT
* *
1399786 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGAAGAAC
131 CTTATCCCCCTAAGCAGTAGTGGAGCAAATCGAAGACGAAGAAC
* ***
1399830 CTTAAACCCCTAAGCAGTAGGGT-AACAGGTTGAATTACAGATC-TAAAGCCCTAAGCAGTAG-G
1 CTTAAACCCCTAAGCAGTAGGGTAAACAGGTTGAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
* * * * *
1399892 GAAACAGATCAAAGATGACA-AGCCTGAATCCCCTAAACAGTAGGGTAACA
66 GAAACAGATCGAAGATGA-AGAACCTTAAACCCCTAAGCAGTAGGGTAACA
1399942 GGCTGGAAAT
Statistics
Matches: 260, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
170 2 0.01
171 54 0.21
172 19 0.07
173 107 0.41
174 40 0.15
175 38 0.15
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.20
Consensus pattern (174 bp):
CTTAAACCCCTAAGCAGTAGGGTAAACAGGTTGAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
GAAACAGATCGAAGATGAAGAACCTTAAACCCCTAAGCAGTAGGGTAACAAGTTGAATTGCAGAT
CTTATCCCCCTAAGCAGTAGTGGAGCAAATCGAAGACGAAGAAC
Found at i:1406310 original size:18 final size:18
Alignment explanation
Indices: 1406273--1406365 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
1406263 CCCAACTACT
*
1406273 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* * *
1406291 GTATTCGTAAATAGTGCC
1 GTATACGTGAATAGTACC
*
1406309 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
* *
1406327 GTATACGTGAATAGTGCT
1 GTATACGTGAATAGTACC
1406345 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
1406363 GTA
1 GTA
1406366 AACGGTCGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:1406325 original size:36 final size:36
Alignment explanation
Indices: 1406273--1406365 Score: 141
Period size: 36 Copynumber: 2.6 Consensus size: 36
1406263 CCCAACTACT
* *
1406273 GTATACGTGAACAGTACCGTATTCGTAAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
* * *
1406309 GTATACGTGAATAGTACTGTATACGTGAATAGTGCT
1 GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
1406345 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
1406366 AACGGTCGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
Found at i:1413139 original size:21 final size:22
Alignment explanation
Indices: 1413115--1413155 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1413105 CAATTGATAA
1413115 ATAAGATATTT-CAATATGTGT
1 ATAAGATATTTACAATATGTGT
* *
1413136 ATAATATGTTTACAATATGT
1 ATAAGATATTTACAATATGT
1413156 CAATATCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (22 bp):
ATAAGATATTTACAATATGTGT
Found at i:1417900 original size:26 final size:26
Alignment explanation
Indices: 1417863--1417946 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
1417853 TGATACAAAT
*
1417863 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
1417889 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
1417915 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
1417941 TGATAA
1 TGATAA
1417947 GAATTTCATA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:1419480 original size:26 final size:26
Alignment explanation
Indices: 1419428--1419480 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1419418 TTTACAGTTT
*
1419428 TACCCCTAGGAGATAAATTATCGAAA
1 TACCCCTAGGAGATAAATTACCGAAA
* *
1419454 TACCCCTAGG-GTTAAATTGACCTAAA
1 TACCCCTAGGAGATAAATT-ACCGAAA
1419480 T
1 T
1419481 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (26 bp):
TACCCCTAGGAGATAAATTACCGAAA
Found at i:1419970 original size:137 final size:137
Alignment explanation
Indices: 1419724--1420010 Score: 538
Period size: 137 Copynumber: 2.1 Consensus size: 137
1419714 GAGTAGTCTC
1419724 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
1419789 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTTTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
1419854 ACTGTTA
131 ACTGTTA
*
1419861 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAGTGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1419926 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
1419991 ACTGTTA
131 ACTGTTA
**
1419998 CCTGAATGGGCTT
1 CCCAAATGGGCTT
1420011 AGGCCCAATG
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 146 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:1421070 original size:3 final size:3
Alignment explanation
Indices: 1421062--1421115 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
1421052 AACCTTCACA
* * * *
1421062 TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TTT TAC TAT CTAA TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
1421107 TAT TAT TAT
1 TAT TAT TAT
1421116 ACTTATTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1421218 original size:18 final size:17
Alignment explanation
Indices: 1421172--1421224 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
1421162 GTTATTGTAC
*
1421172 ATATA-TATACTTTTAT
1 ATATAGTATATTTTTAT
1421188 ATATAGTATTATTTTTAT
1 ATATAGTA-TATTTTTAT
*
1421206 ATATCATTATATTTATTAT
1 ATAT-AGTATATTT-TTAT
1421225 TATGCTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 5 0.16
17 2 0.06
18 17 0.55
19 7 0.23
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (17 bp):
ATATAGTATATTTTTAT
Found at i:1421840 original size:18 final size:18
Alignment explanation
Indices: 1421819--1421873 Score: 78
Period size: 17 Copynumber: 3.2 Consensus size: 18
1421809 ATTCGGATCC
1421819 CAAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTGTTTT
1421837 C-AAAATTTTCGTGTTTT
1 CAAAAATTTTCGTGTTTT
* *
1421854 AAAAAATTCTCGT-TTTT
1 CAAAAATTTTCGTGTTTT
1421871 CAA
1 CAA
1421874 TCGGATCACG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 22 0.67
18 11 0.33
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (18 bp):
CAAAAATTTTCGTGTTTT
Found at i:1424156 original size:136 final size:136
Alignment explanation
Indices: 1423912--1424185 Score: 521
Period size: 136 Copynumber: 2.0 Consensus size: 136
1423902 TTGGGCTTCA
*
1423912 GGTAACAGTGGTACTGGACCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATT
1 GGTAACAGTGGTACTGGACCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATT
*
1423977 CAGATAACAGTATGGCCCATAGGCCTATTTCAAAATACATGCAACATCAATAACATATGCAAGCC
66 CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAACATATGCAAGCC
1424042 CATTTG
131 CATTTG
*
1424048 GGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATT
1 GGTAACAGTGGTACTGGACCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATT
1424113 CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAACATATGCAAGCC
66 CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAACATATGCAAGCC
1424178 CATTTG
131 CATTTG
1424184 GG
1 GG
1424186 GAGACTACTC
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 135 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (136 bp):
GGTAACAGTGGTACTGGACCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATT
CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAACATATGCAAGCC
CATTTG
Found at i:1424470 original size:25 final size:27
Alignment explanation
Indices: 1424433--1424486 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
1424423 TCAAACATGC
1424433 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
* **
1424459 ATTTCGGT-AATTTTGCACCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
1424485 AT
1 AT
1424487 AACAGTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACACCTAGGGGT
Found at i:1424494 original size:26 final size:27
Alignment explanation
Indices: 1424450--1424525 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 27
1424440 TCAATTTAAC
* * *
1424450 CCTAGGGGTATTTCGGTAATTTTGC-A
1 CCTAGGGGTATTACAGTAATTTTCCAA
*
1424476 CCTAGGGGTATAACAGTAATTTTCCATA
1 CCTAGGGGTATTACAGTAATTTTCCA-A
* *
1424504 CATAGGGGTATTATAGTAATTT
1 CCTAGGGGTATTACAGTAATTT
1424526 AGCTGCTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 21 0.51
28 20 0.49
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (27 bp):
CCTAGGGGTATTACAGTAATTTTCCAA
Found at i:1426009 original size:26 final size:26
Alignment explanation
Indices: 1425971--1426106 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
1425961 CATGAAATTC
*
1425971 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
1425997 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
*
1426023 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
*
1426049 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
*
1426075 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
1426101 TTATCA
1 TTATCA
1426107 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCCA
Found at i:1426858 original size:2 final size:2
Alignment explanation
Indices: 1426851--1426892 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1426841 ATGTACATAA
* *
1426851 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT 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
1426893 GTTAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1426858 original size:16 final size:16
Alignment explanation
Indices: 1426839--1426894 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1426829 GAAAATACCA
*
1426839 ATATGTACATAAATAT
1 ATATGTATATAAATAT
*
1426855 ATATATATATATATATAT
1 ATATGTATATA-A-ATAT
**
1426873 ATATGTATATGTATAT
1 ATATGTATATAAATAT
1426889 ATATGT
1 ATATGT
1426895 TAATAATGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 19 0.58
17 1 0.03
18 13 0.39
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (16 bp):
ATATGTATATAAATAT
Found at i:1427097 original size:2 final size:2
Alignment explanation
Indices: 1427049--1427085 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1427039 AATAAAAGAA
*
1427049 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1427086 CCAAAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1427152 original size:23 final size:23
Alignment explanation
Indices: 1427121--1427164 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1427111 ATTGAGTATT
* *
1427121 AAAAGTATATATATAATATAGAC
1 AAAAATATATACATAATATAGAC
*
1427144 AAAAATATATGCATAATATAG
1 AAAAATATATACATAATATAG
1427165 TATTGAAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.30
Consensus pattern (23 bp):
AAAAATATATACATAATATAGAC
Found at i:1427255 original size:26 final size:25
Alignment explanation
Indices: 1427189--1427251 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 25
1427179 ATATGGGATA
1427189 ATATAAAAAATATATGAATAATGTG
1 ATATAAAAAATATATGAATAATGTG
*
1427214 ATATTAAAAAATATAT-ACATAAT-TT
1 ATA-TAAAAAATATATGA-ATAATGTG
1427239 ATAT-AAAAATATA
1 ATATAAAAAATATA
1427252 ATATTATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
23 9 0.26
24 1 0.03
25 8 0.23
26 17 0.49
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (25 bp):
ATATAAAAAATATATGAATAATGTG
Found at i:1427263 original size:37 final size:39
Alignment explanation
Indices: 1427222--1427298 Score: 104
Period size: 37 Copynumber: 2.0 Consensus size: 39
1427212 TGATATTAAA
* * *
1427222 AAATATATACATAATTTATATAAAA-ATATA-ATATTAT
1 AAATATACACATAATATATATAAAATATATACATAATAT
*
1427259 AAATATACATATAATATATATAAAATATATACATAATAT
1 AAATATACACATAATATATATAAAATATATACATAATAT
1427298 A
1 A
1427299 GTATTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 22 0.65
38 5 0.15
39 7 0.21
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (39 bp):
AAATATACACATAATATATATAAAATATATACATAATAT
Found at i:1427264 original size:22 final size:22
Alignment explanation
Indices: 1427239--1427311 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 22
1427229 TACATAATTT
1427239 ATATAAAAATATAATATTATAA
1 ATATAAAAATATAATATTATAA
*
1427261 ATAT--ACATATAATATATATAAA
1 ATATAAAAATATAATAT-TAT-AA
*
1427283 ATATATACATAATATAGTATTA-AA
1 ATATA-A-A-AATATAATATTATAA
1427307 ATATA
1 ATATA
1427312 TACATGATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
20 10 0.24
21 3 0.07
22 10 0.24
24 7 0.17
26 3 0.07
27 8 0.20
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (22 bp):
ATATAAAAATATAATATTATAA
Found at i:1427265 original size:24 final size:24
Alignment explanation
Indices: 1427238--1427345 Score: 100
Period size: 24 Copynumber: 4.5 Consensus size: 24
1427228 ATACATAATT
*
1427238 TATATA-AAAATATAATATTATAAA
1 TATATACATAATATAATATTA-AAA
* *
1427262 TATACATATAATAT-ATA-TAAAA
1 TATATACATAATATAATATTAAAA
*
1427284 TATATACATAATATAGTATTAAAA
1 TATATACATAATATAATATTAAAA
1427308 TATATACATGATATATACATATTAGAAA
1 TATATACAT-A-ATATA-ATATTA-AAA
1427336 TA-ATA-ATAAT
1 TATATACATAAT
1427346 GTTACAAAAC
Statistics
Matches: 71, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
22 15 0.21
23 4 0.06
24 24 0.34
25 8 0.11
26 7 0.10
27 8 0.11
28 5 0.07
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (24 bp):
TATATACATAATATAATATTAAAA
Found at i:1427276 original size:11 final size:11
Alignment explanation
Indices: 1427223--1427324 Score: 74
Period size: 11 Copynumber: 9.7 Consensus size: 11
1427213 GATATTAAAA
*
1427223 AATATATACAT
1 AATATATATAT
1427234 AAT-T-TATAT
1 AATATATATAT
1427243 AA-A-A-ATAT
1 AATATATATAT
1427251 AATAT-TATA-
1 AATATATATAT
*
1427260 AATATACATAT
1 AATATATATAT
*
1427271 AATATATATAA
1 AATATATATAT
*
1427282 AATATATACAT
1 AATATATATAT
*
1427293 AATATAGTATTAA
1 AATATA-TA-TAT
*
1427306 AATATATACAT
1 AATATATATAT
*
1427317 GATATATA
1 AATATATA
1427325 CATATTAGAA
Statistics
Matches: 71, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
8 6 0.08
9 12 0.17
10 7 0.10
11 35 0.49
12 4 0.06
13 7 0.10
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (11 bp):
AATATATATAT
Found at i:1427279 original size:15 final size:16
Alignment explanation
Indices: 1427238--1427329 Score: 50
Period size: 15 Copynumber: 5.8 Consensus size: 16
1427228 ATACATAATT
*
1427238 TATATAAAAATATA-A
1 TATATATAAATATACA
1427253 TAT-TATAAATATACA
1 TATATATAAATATACA
*
1427268 TATA-ATATATATA-A
1 TATATATAAATATACA
* * *
1427282 AATATATACATA-ATA
1 TATATATAAATATACA
*
1427297 TAGTATTAAAATATATACA
1 TA-TA-TATAA-ATATACA
*
1427316 TGATATATACATAT
1 T-ATATATAAATAT
1427330 TAGAAATAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
14 14 0.24
15 23 0.40
16 2 0.03
17 7 0.12
18 6 0.10
19 5 0.09
20 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (16 bp):
TATATATAAATATACA
Found at i:1428676 original size:3 final size:3
Alignment explanation
Indices: 1428661--1428691 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1428651 TCCATGTTTT
*
1428661 TTA TTA TTC TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1428692 AGGGTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1428734 original size:2 final size:2
Alignment explanation
Indices: 1428724--1428758 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1428714 TTTTAGTGCG
* *
1428724 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1428759 TTTACTCACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1430995 original size:131 final size:129
Alignment explanation
Indices: 1430804--1431321 Score: 441
Period size: 131 Copynumber: 4.0 Consensus size: 129
1430794 ATTTTTAGAA
* * * *
1430804 TTTTAAAAAACATGAGTGAAATTCTAGAGGAATATTCAATTATTTTGAACAAAC-AGGAAATTGC
1 TTTTTAAAAACATGAGTGAAATTCTAAAGGAATCTTCGATTATTTTGAACAAACGA-GAAATTGC
* * *
1430868 AACCTAGCACGATAGGGCACGATTCCCCAAGTTGCCAAACATCGAGTATTACCTTCGGTTTGAAG
65 AACCCAGCACGATAGGGCACGATTCCCCAA-TTGCCAAACATCGAGTATTGCCTTCGATTT-AAG
1430933 AG
128 AG
* * * * * **
1430935 TTTTTAAAGATATGAGTGAAATTCCAAAGGAATCTTCGATTGTTTCGAACAAACGAGAAATCACA
1 TTTTTAAAAACATGAGTGAAATTCTAAAGGAATCTTCGATTATTTTGAACAAACGAGAAATTGCA
* * * * * * *
1431000 ACCCAGCACGATAGGGCACAATTCTCAAATTGCCAAGCACCGAGTATTGGCTTCGTTTTAAAGAG
66 ACCCAGCACGATAGGGCACGATTCCCCAATTGCCAAACATCGAGTATTGCCTTCGATTT-AAGAG
* * * * * * * *
1431065 ATTTTAGAAAACGTAAGTGAAATTCAAAAGGGACCTTCGATTATTTTGAACAAACAAGAGATTGC
1 TTTTTA-AAAACATGAGTGAAATTCTAAAGGAATCTTCGATTATTTTGAACAAACGAGAAATTGC
*** * * * ** * * *
1431130 AACCCAGCACGATAAAACACGATTCCGCGAATTGCCAAATATCAAACATCGCCTT-TATTTAGGA
65 AACCCAGCACGATAGGGCACGATTCC-CCAATTGCCAAACATCGAGTATTGCCTTCGATTTAAGA
1431194 -
129 G
** * * * *
1431194 TTTAGAAAAACACGAGTGAGATTCTAAAGGAA-CATTCGATTGTTTTGAACAAACGAGAAATTGA
1 TTTTTAAAAACATGAGTGAAATTCTAAAGGAATC-TTCGATTATTTTGAACAAACGAGAAATTGC
* * * ** * * * *
1431258 AACCCAGCACGATATGGCATGATTCCCGAATTTTCAAGCAATCAAATATTGCCTTCGTTTTAAG
65 AACCCAGCACGATAGGGCACGATTCCCCAATTGCCAAAC-ATCGAGTATTGCCTTCGATTTAAG
1431322 GAATTTTCAA
Statistics
Matches: 303, Mismatches: 78, Indels: 14
0.77 0.20 0.04
Matches are distributed among these distances:
127 10 0.03
128 81 0.27
129 8 0.03
130 38 0.13
131 146 0.48
132 20 0.07
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (129 bp):
TTTTTAAAAACATGAGTGAAATTCTAAAGGAATCTTCGATTATTTTGAACAAACGAGAAATTGCA
ACCCAGCACGATAGGGCACGATTCCCCAATTGCCAAACATCGAGTATTGCCTTCGATTTAAGAG
Found at i:1435971 original size:130 final size:131
Alignment explanation
Indices: 1435735--1435981 Score: 363
Period size: 130 Copynumber: 1.9 Consensus size: 131
1435725 GGCGAGATTT
*
1435735 GATATTTGGCAATTCGATGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCGCGTTTGCTCAAAA
1 GATATTTGGCAATTCGATGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCGCGATTGCTCAAAA
* * * * *
1435800 TAATCGAATATCACTTCAAAATTTCACTTATGTCTT-TTAAAATCCCTTAAACGAAGGTGATGTG
66 TAATCAAATATCACTTCAAAATTTCACTCAGGACTTCTAAAAATCCCTTAAACGAAGGTGATGTG
1435864 C
131 C
* * * *
1435865 GATATTTGGCAATTCG-TGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGATTGCTTAAG
1 GATATTTGGCAATTCGAT-GAATCGTGCCCTAACGTGCTGGGTTGCAATTTCGCGATTGCTCAAA
* *
1435929 ATAATCAAATATCCCTTCAAAATTTCACTCAGGACTTCTAAAAATCCTTTAAA
65 ATAATCAAATATCACTTCAAAATTTCACTCAGGACTTCTAAAAATCCCTTAAA
1435982 ACAAAGGTAA
Statistics
Matches: 103, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
129 1 0.01
130 89 0.86
131 13 0.13
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (131 bp):
GATATTTGGCAATTCGATGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCGCGATTGCTCAAAA
TAATCAAATATCACTTCAAAATTTCACTCAGGACTTCTAAAAATCCCTTAAACGAAGGTGATGTG
C
Found at i:1437179 original size:26 final size:26
Alignment explanation
Indices: 1437143--1437252 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
1437133 TGATACAAAT
1437143 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
1437169 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
1437195 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
1437221 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
1437247 TGATAA
1 TGATAA
1437253 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:1438910 original size:27 final size:27
Alignment explanation
Indices: 1438869--1439008 Score: 183
Period size: 27 Copynumber: 5.2 Consensus size: 27
1438859 GAGGAAGCGT
*
1438869 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
1438896 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
1438923 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
1438950 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
1438978 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
1439004 TCTGG
1 TCTGG
1439009 CAGCCATGCT
Statistics
Matches: 102, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
26 5 0.05
27 82 0.80
28 15 0.15
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:1438954 original size:54 final size:55
Alignment explanation
Indices: 1438869--1439008 Score: 203
Period size: 54 Copynumber: 2.6 Consensus size: 55
1438859 GAGGAAGCGT
* * *
1438869 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
* *
1438923 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
* *
1438978 TCTGGTGACTCTGTCACAT-TATCTGTTCTGG
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG
1439009 CAGCCATGCT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 60 0.77
55 18 0.23
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
Found at i:1443008 original size:26 final size:26
Alignment explanation
Indices: 1442946--1443054 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
1442936 TGATACAAAT
1442946 TGATAATAGGTTAGGTAAATG-TTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
1442971 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
1442997 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
1443023 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
1443049 TGATAA
1 TGATAA
1443055 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
25 21 0.26
26 59 0.74
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:1444709 original size:27 final size:27
Alignment explanation
Indices: 1444668--1444780 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
1444658 GAGGAAGCGT
*
1444668 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
1444695 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
1444722 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
1444750 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
1444776 TCTGG
1 TCTGG
1444781 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 5 0.07
27 55 0.73
28 15 0.20
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:1444773 original size:54 final size:54
Alignment explanation
Indices: 1444666--1444780 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
1444656 TGGAGGAAGC
*
1444666 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * *
1444720 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
1444774 GTTCTGG
1 GTTCTGG
1444781 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:1446084 original size:2 final size:2
Alignment explanation
Indices: 1446077--1446120 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
1446067 TACAATAGAC
* *
1446077 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AG AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1446118 AT A
1 AT A
1446121 ATAAAACATA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1446140 original size:3 final size:3
Alignment explanation
Indices: 1446134--1446172 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1446124 AAACATATAC
1446134 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1446173 AGATGTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1447557 original size:2 final size:2
Alignment explanation
Indices: 1447550--1447580 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1447540 CTTTTAAATT
1447550 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 T
1447581 GTATGTATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1448439 original size:131 final size:130
Alignment explanation
Indices: 1448218--1448461 Score: 346
Period size: 131 Copynumber: 1.9 Consensus size: 130
1448208 TAATTATTCA
* * **
1448218 TTTAAAAACTCTTTAAAACGAAGGCAATACTCGATGTTTGACAATTCGGGAATCGTGCCCTATTG
1 TTTAAAAACTCTTCAAAACGAAGGCAATACTCGATGTTTGACAATTCGGGAATAGTGCCCTATCA
*
1448283 TGCTGGGTTGCGATTTCTCGCTTGTTCAAAATAATCGAATATTCCTTTTGTTTTTCACCCATGTC
66 TGCTGGGTTGCGATTTCTCGCTTGTTCAAAATAATCGAATATCCCTTTTGTTTTTCACCCATGTC
* * ** * *
1448348 TTTAAAAATTCTTCAAAACGAAGGTAATGTTTGATGTTTGGCAATTCGGGGAATAGTGCCCTATC
1 TTTAAAAACTCTTCAAAACGAAGGCAATACTCGATGTTTGACAATTC-GGGAATAGTGCCCTATC
* *
1448413 ATGTTGGGTTGCGATTTC-CTGTTTGTTCAAAATAATCGAATATCCCTTT
65 ATGCTGGGTTGCGATTTCTC-GCTTGTTCAAAATAATCGAATATCCCTTT
1448462 AGAATTTCAC
Statistics
Matches: 99, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
130 41 0.41
131 58 0.59
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (130 bp):
TTTAAAAACTCTTCAAAACGAAGGCAATACTCGATGTTTGACAATTCGGGAATAGTGCCCTATCA
TGCTGGGTTGCGATTTCTCGCTTGTTCAAAATAATCGAATATCCCTTTTGTTTTTCACCCATGTC
Found at i:1450560 original size:21 final size:22
Alignment explanation
Indices: 1450536--1450576 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1450526 CAATTGATAA
1450536 ATAAGATATTT-CAATATGTGT
1 ATAAGATATTTACAATATGTGT
* *
1450557 ATAATATGTTTACAATATGT
1 ATAAGATATTTACAATATGT
1450577 CAATATCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (22 bp):
ATAAGATATTTACAATATGTGT
Found at i:1453920 original size:18 final size:17
Alignment explanation
Indices: 1453895--1453945 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
1453885 TCAGTTTTTT
1453895 ATTAAATTATTTATTTA
1 ATTAAATTATTTATTTA
*
1453912 ATATAAATTAATTT-TATA
1 AT-TAAATT-ATTTATTTA
*
1453930 ATTAAATTAATTATTT
1 ATTAAATTATTTATTT
1453946 GGATTGGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 3 0.11
17 10 0.36
18 11 0.39
19 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTAAATTATTTATTTA
Found at i:1455259 original size:44 final size:44
Alignment explanation
Indices: 1455196--1455290 Score: 181
Period size: 44 Copynumber: 2.1 Consensus size: 44
1455186 CAGTAGTGCT
1455196 AATATAATTCAAATTCAAACATATTGCATTAAAAATAAATAAGC
1 AATATAATTCAAATTCAAACATATTGCATTAAAAATAAATAAGC
1455240 AATATAATTCAAATTCAAACATATTGCATTAAAAATAAATAAGC
1 AATATAATTCAAATTCAAACATATTGCATTAAAAATAAATAAGC
1455284 AAGTATA
1 AA-TATA
1455291 TATAACACCT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 46 0.92
45 4 0.08
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (44 bp):
AATATAATTCAAATTCAAACATATTGCATTAAAAATAAATAAGC
Found at i:1457297 original size:64 final size:64
Alignment explanation
Indices: 1457224--1457434 Score: 146
Period size: 64 Copynumber: 3.2 Consensus size: 64
1457214 CTGGGCTAGA
*
1457224 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* ** * ** *
1457288 GCCCATTTCAAAATACATGCAACATCAATAAACATATG-C-AAG-CCC--ATTTGGGTAACAGTG
1 GCCCATTTC-AGAT---T-----A-CAATAAAC-TGGGCCTTAGCCCCTTATTCAGATAACA---
* *
1457348 GTACTGGGCCAGA-
52 GTA-TGGCCCATAG
*
1457361 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1457425 GCCCATTTCA
1 GCCCATTTCA
1457435 AAATACATGC
Statistics
Matches: 105, Mismatches: 21, Indels: 42
0.62 0.12 0.25
Matches are distributed among these distances:
62 2 0.02
63 16 0.15
64 23 0.22
65 6 0.06
67 9 0.09
68 1 0.01
69 1 0.01
70 9 0.09
72 6 0.06
73 14 0.13
74 16 0.15
75 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:1457436 original size:137 final size:137
Alignment explanation
Indices: 1457190--1457476 Score: 529
Period size: 137 Copynumber: 2.1 Consensus size: 137
1457180 TATTGGGCCT
** * *
1457190 AAGCCCATTCAGGTAATAGTGGTACTGGGCTAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1457255 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
1457320 CATATGC
131 CATATGC
1457327 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
1457392 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
1457457 CATATGC
131 CATATGC
1457464 AAGCCCATTTGGG
1 AAGCCCATTTGGG
1457477 GAGACTACTC
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 145 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
CATATGC
Found at i:1457761 original size:25 final size:27
Alignment explanation
Indices: 1457724--1457776 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
1457714 TCAAACATGC
1457724 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
1457750 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
1457776 A
1 A
1457777 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:1459298 original size:26 final size:26
Alignment explanation
Indices: 1459262--1459345 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
1459252 CATGAAATTC
1459262 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
1459288 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
1459314 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
1459340 TTATCA
1 TTATCA
1459346 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:1460630 original size:41 final size:42
Alignment explanation
Indices: 1460563--1460688 Score: 161
Period size: 41 Copynumber: 3.0 Consensus size: 42
1460553 CTTCGTTTTC
** * *
1460563 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
1460606 T-GATGCCATAG-CCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
1460646 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
1460687 TC
1 TC
1460689 TCACTGATGC
Statistics
Matches: 75, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
40 2 0.03
41 42 0.56
42 29 0.39
43 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:1460750 original size:47 final size:46
Alignment explanation
Indices: 1460648--1460770 Score: 156
Period size: 47 Copynumber: 2.7 Consensus size: 46
1460638 TTCATATATC
* * * * * *
1460648 GATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCACT
1 GATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACACA
* *
1460694 GATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACACA
1 GATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACACA
*
1460741 GATGCCATATCCCAAATATGGTCTTATACG
1 GATGCCATATCCCAGATATGGTCTTATACG
1460771 GAAATCACTT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
46 27 0.40
47 40 0.60
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (46 bp):
GATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACACA
Found at i:1460787 original size:7 final size:7
Alignment explanation
Indices: 1460775--1460803 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1460765 TATACGGAAA
1460775 TCACTTG
1 TCACTTG
1460782 TCACTTG
1 TCACTTG
1460789 TCACTTG
1 TCACTTG
1460796 TCACTTG
1 TCACTTG
1460803 T
1 T
1460804 AGCCGGAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (7 bp):
TCACTTG
Found at i:1460837 original size:31 final size:31
Alignment explanation
Indices: 1460802--1460981 Score: 297
Period size: 31 Copynumber: 5.8 Consensus size: 31
1460792 CTTGTCACTT
*
1460802 GTAGCCGGAGCTACCACTATTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
*
1460833 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1460864 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
*
1460895 GTAGTCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
* *
1460926 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
* *
1460957 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGGAGCTACCACTTTTCACT
1460982 TGTCATTTGT
Statistics
Matches: 141, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 141 1.00
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (31 bp):
GTAGCCGGAGCTACCACTTTTCACTGATCAG
Found at i:1461047 original size:49 final size:51
Alignment explanation
Indices: 1460963--1461084 Score: 185
Period size: 50 Copynumber: 2.4 Consensus size: 51
1460953 TCAGGTAGCT
* *
1460963 GAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT-TAACC
1 GAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGTGTAACC
* * *
1461013 GAAGCTATTACTTATCACTT-TCATTTGTCCTTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGTGTAACC
1461063 GAAGCTATCACTTATCACTTGT
1 GAAGCTATCACTTATCACTTGT
1461085 TGCCATGGTC
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
49 23 0.36
50 40 0.62
51 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (51 bp):
GAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGTGTAACC
Found at i:1464643 original size:32 final size:32
Alignment explanation
Indices: 1464602--1464665 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1464592 CCTACGCCTT
1464602 CGCCTCCGTACTCCTCACGCCAAGCGCCAGCA
1 CGCCTCCGTACTCCTCACGCCAAGCGCCAGCA
1464634 CGCCTCCGTACTCCTCACGCCAAGCGCCAGCA
1 CGCCTCCGTACTCCTCACGCCAAGCGCCAGCA
1464666 TGACTCCCGT
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:0.19, C:0.50, G:0.19, T:0.12
Consensus pattern (32 bp):
CGCCTCCGTACTCCTCACGCCAAGCGCCAGCA
Found at i:1465571 original size:24 final size:25
Alignment explanation
Indices: 1465525--1465571 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1465515 AATTGAGTCC
* *
1465525 TTTTAATTTGTGTAGCTCATTATCT
1 TTTTAATTCGTGTAGCACATTATCT
*
1465550 TTTTAATTCGTTTAGCAC-TTAT
1 TTTTAATTCGTGTAGCACATTAT
1465572 TTTATTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.21, C:0.13, G:0.11, T:0.55
Consensus pattern (25 bp):
TTTTAATTCGTGTAGCACATTATCT
Found at i:1466394 original size:2 final size:2
Alignment explanation
Indices: 1466387--1466412 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1466377 TTTTAAATCA
1466387 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
1466413 TAAGAAAATT
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:1467098 original size:5 final size:5
Alignment explanation
Indices: 1467088--1467119 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1467078 TTGTGTGTTC
1467088 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1467120 TCACAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:1467102 original size:9 final size:9
Alignment explanation
Indices: 1467088--1467118 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1467078 TTGTGTGTTC
1467088 TTTATTTTA
1 TTTATTTTA
1467097 TTTATTTTA
1 TTTATTTTA
1467106 TTTTATTTTA
1 -TTTATTTTA
1467116 TTT
1 TTT
1467119 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1471549 original size:5 final size:5
Alignment explanation
Indices: 1471539--1471570 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1471529 TTGTGTGTTC
1471539 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1471571 TCACAGCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:1471553 original size:9 final size:9
Alignment explanation
Indices: 1471539--1471569 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1471529 TTGTGTGTTC
1471539 TTTATTTTA
1 TTTATTTTA
1471548 TTTATTTTA
1 TTTATTTTA
1471557 TTTTATTTTA
1 -TTTATTTTA
1471567 TTT
1 TTT
1471570 TTCACAGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1472174 original size:131 final size:131
Alignment explanation
Indices: 1471936--1472311 Score: 368
Period size: 131 Copynumber: 2.9 Consensus size: 131
1471926 AAAATTCTTT
* *
1471936 AAAACGAAGGCAATACTCGGTGTTTGATAATTCGAGAATCGTGCTCTATCGTGCTGGGTTGTGAT
1 AAAACGAAGACAATACTCGGTGTTTGATAATTCGAGAATCGTGCCCTATCGTGCTGGGTTGTGAT
** * **
1472001 TTCTTGTTTGTTCAAAACAATCGAATATTCCTTTAGGTTTTCACTCGTGTTTATTAAAAACCTTC
66 TTCTCATTTGTTCAAAACAATCGAAGATTCCTTTAGAATTTCACTCGTGTTTATTAAAAACCTTC
1472066 C
131 C
* * *
1472067 AAAACGAATACAATACTCGGTGTTTGATAATTCGGGAATCGTGCCCTAAT-GTGTTGGGTTGTGA
1 AAAACGAAGACAATACTCGGTGTTTGATAATTCGAGAATCGTGCCCT-ATCGTGCTGGGTTGTGA
* * **
1472131 TTTCTCATTTTTTCAAAACAATCGAAGATT-CTTTCGAAATTTCACTCACGTTT-TCTAAAAACC
65 TTTCTCATTTGTTCAAAACAATCGAAGATTCCTTTAG-AATTTCACTCGTGTTTAT-TAAAAA-C
*
1472194 CTT-T
127 CTTCC
* * * * * ** * * * * **
1472198 AAAACGAAGGCGATATTCGATGCTTGGCAATTTGGGGAATAGTACCCTATCGTGCTGGGTTGCAA
1 AAAACGAAGACAATACTCGGTGTTTGATAA-TTCGAGAATCGTGCCCTATCGTGCTGGGTTGTGA
* * *
1472263 TTT-TCCATTTGTTCAAAATAATCGAATA-TCTCTTCAGAATTTCACTCGT
65 TTTCT-CATTTGTTCAAAACAATCGAAGATTC-CTTTAGAATTTCACTCGT
1472312 ATTTTCTAAG
Statistics
Matches: 200, Mismatches: 36, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
130 6 0.03
131 126 0.63
132 64 0.32
133 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (131 bp):
AAAACGAAGACAATACTCGGTGTTTGATAATTCGAGAATCGTGCCCTATCGTGCTGGGTTGTGAT
TTCTCATTTGTTCAAAACAATCGAAGATTCCTTTAGAATTTCACTCGTGTTTATTAAAAACCTTC
C
Found at i:1475621 original size:64 final size:64
Alignment explanation
Indices: 1475434--1475614 Score: 310
Period size: 64 Copynumber: 2.8 Consensus size: 64
1475424 TCATTCATAA
*
1475434 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATTCTAATTATTTGACATAAACAT
1 CACATCTAGTTAGGAACATTTGATTCATTTCGATCATAGCATTCTAATTATTTGACATAAACAT
*
1475498 CACATCTAGTTAGGAACATTTGATTCATTTCGATCGTAGCATTCTAATTATTTGACATAAACAT
1 CACATCTAGTTAGGAACATTTGATTCATTTCGATCATAGCATTCTAATTATTTGACATAAACAT
* *
1475562 CACATCTAGTTAGGAACAATTGATTCATGTT-GATCATAGCATCCTAATTATTT
1 CACATCTAGTTAGGAACATTTGATTCAT-TTCGATCATAGCATTCTAATTATTT
1475615 TGCATAAGCA
Statistics
Matches: 111, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
64 109 0.98
65 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.38
Consensus pattern (64 bp):
CACATCTAGTTAGGAACATTTGATTCATTTCGATCATAGCATTCTAATTATTTGACATAAACAT
Found at i:1475817 original size:45 final size:44
Alignment explanation
Indices: 1475740--1475984 Score: 126
Period size: 45 Copynumber: 5.5 Consensus size: 44
1475730 GCAAGTCCTA
* * * *
1475740 GCTCCCTAAAGTTGTAGTGGAG-TAAGCTGAAGATTGTAGATCTTG
1 GCTCCCTGAAGTTGCAGTGGAGCAAATC-GAAGA-TGTAGATCTTG
* * *
1475785 TCTCCCTGAAGTTGCAGTGGGGCAAATCGAAGACG-ACGAATCTTG
1 GCTCCCTGAAGTTGCAGTGGAGCAAATCGAAGATGTA-G-ATCTTG
* * * ** * * *
1475830 GCTTCCTGAAGTTGCAGTGAAGCATATTTAAG--CTAG-TCCTA
1 GCTCCCTGAAGTTGCAGTGGAGCAAATCGAAGATGTAGATCTTG
* * * * ** *
1475871 GCTCCCTAAAATTGTAGTGGAG-TAGGCTGAATATTGTAGATCTTG
1 GCTCCCTGAAGTTGCAGTGGAGCAAATC-GAAGA-TGTAGATCTTG
* * *
1475916 TCTCCCTGAAGTTGCAGTGGGGAAAATCGAAGATG-ACGAATCTTG
1 GCTCCCTGAAGTTGCAGTGGAGCAAATCGAAGATGTA-G-ATCTTG
* *
1475961 GCTTCCTGAAGTTGCAGTGAAGCA
1 GCTCCCTGAAGTTGCAGTGGAGCA
1475985 GACTTAAGCT
Statistics
Matches: 142, Mismatches: 46, Indels: 24
0.67 0.22 0.11
Matches are distributed among these distances:
41 22 0.15
43 3 0.02
44 9 0.06
45 103 0.73
46 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (44 bp):
GCTCCCTGAAGTTGCAGTGGAGCAAATCGAAGATGTAGATCTTG
Found at i:1475877 original size:131 final size:131
Alignment explanation
Indices: 1475643--1476431 Score: 1218
Period size: 131 Copynumber: 6.0 Consensus size: 131
1475633 TGAAACAGAA
** * * *
1475643 TGTAGATCTTGTCTCTTTGAAGTTGCAGTAGGGCAAATCGAAGACGACAAATCTTGGCTTCCTGA
1 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGAAAATCGAAGACGACGAATCTTGGCTTCCTGA
* * *
1475708 AGATGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCCCTAAAGTTGTAGTGGAGTAAGCTGAAGA
66 AGATGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAAGA
1475773 T
131 T
*
1475774 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCGAAGACGACGAATCTTGGCTTCCTGA
1 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGAAAATCGAAGACGACGAATCTTGGCTTCCTGA
* * *
1475839 AGTTGCAGTGAAGCATATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAATA
66 AGATGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAAGA
1475904 T
131 T
*
1475905 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGAAAATCGAAGATGACGAATCTTGGCTTCCTGA
1 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGAAAATCGAAGACGACGAATCTTGGCTTCCTGA
* * *
1475970 AGTTGCAGTGAAGCAGACTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAATA
66 AGATGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAAGA
1476035 T
131 T
* * * * *
1476036 TGTAGATCTTGTCTCCCTGAAGTTACAGTGGGGCAAATAGAAGATGACGAATCTTGGCTTCTTGA
1 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGAAAATCGAAGACGACGAATCTTGGCTTCCTGA
*
1476101 AGATGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAATA
66 AGATGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAAGA
1476166 T
131 T
* * * * * * *
1476167 TGTAGATCTTGTCTACCTCAAGTTGTAGTGGGGAAAATTGAAAATGACAAATCTTGGCTTCCTGA
1 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGAAAATCGAAGACGACGAATCTTGGCTTCCTGA
* *
1476232 AGATGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAGA
66 AGATGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAAGA
1476297 T
131 T
1476298 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGAAAATCGAAGACGACGAATCTTGGCTTCCTGA
1 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGAAAATCGAAGACGACGAATCTTGGCTTCCTGA
* * * * ** *
1476363 AGTTGCAGTGAAGTAGATTTAAGCCACCATCCTAGCTCCCTAATGTTGTAGTGGAGTAGGCTAAA
66 AGATGCAGTGAAGCAGATTTAAGCTA--GTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAA
1476428 GAT
129 GAT
1476431 T
1 T
1476432 ACAGACCTTG
Statistics
Matches: 611, Mismatches: 45, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
131 573 0.94
133 38 0.06
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (131 bp):
TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGAAAATCGAAGACGACGAATCTTGGCTTCCTGA
AGATGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAAGA
T
Found at i:1478763 original size:2 final size:2
Alignment explanation
Indices: 1478756--1478788 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1478746 TCAATATTTC
1478756 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
1478789 TTAAGAAAAT
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:1479863 original size:132 final size:130
Alignment explanation
Indices: 1479509--1479896 Score: 431
Period size: 131 Copynumber: 3.0 Consensus size: 130
1479499 TTAAAAATTA
* * *
1479509 TTTAAAACGAAGGCAATACTCGATGTTTGATAATTCGAGAATCGTGCCCTATCGTGTAGGGTTGT
1 TTTAAAACGAAGGCAATACTCGATGTTTGATAATTCGGGAATCGTGCCCTATTGTGTTGGGTTGT
** *
1479574 GATTTCTCGTTTGTTCAAAACAATCGAACATTCCTTT-AGGTTTTCACTCGTGTTTAT-TAAAAA
66 GATTTCTCGTTTGTTCAAAACAATCGAACATTCCTTTGA-AATTTCACTCATGTTT-TCTAAAAA
1479637 CC
129 CC
* ** * *
1479639 TTCCAAAACGAATACAATACTCGGTGTTTGATAATTCGGGAATCGTGCCCTAATGTGTTGGGTTG
1 TT-TAAAACGAAGGCAATACTCGATGTTTGATAATTCGGGAATCGTGCCCTATTGTGTTGGGTTG
* * *
1479704 TGATTTCTCGTTTTTTCAAAACAATCGAAGATTCCTTTGAAATTTCACTCACGTTTTCTAAAAAC
65 TGATTTCTCGTTTGTTCAAAACAATCGAACATTCCTTTGAAATTTCACTCATGTTTTCTAAAAA-
1479769 CC
129 CC
* * * ** * * *
1479771 TTTAAAACGAAGGCGATATTCGATGCTTGGCAATTTGGGGAATAGTACCCTATTGTGTTGGGTTG
1 TTTAAAACGAAGGCAATACTCGATGTTTGATAA-TTCGGGAATCGTGCCCTATTGTGTTGGGTTG
** * * * * * *
1479836 CAATTTCCCGTTTGTTCAAAATAATCGAATA-TCTCTTCGGAATTTCACTCATATTTTCTAA
65 TGATTTCTCGTTTGTTCAAAACAATCGAACATTC-CTTTGAAATTTCACTCATGTTTTCTAA
1479897 GGTGAGGCAA
Statistics
Matches: 215, Mismatches: 37, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
130 3 0.01
131 132 0.61
132 80 0.37
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (130 bp):
TTTAAAACGAAGGCAATACTCGATGTTTGATAATTCGGGAATCGTGCCCTATTGTGTTGGGTTGT
GATTTCTCGTTTGTTCAAAACAATCGAACATTCCTTTGAAATTTCACTCATGTTTTCTAAAAACC
Found at i:1482617 original size:26 final size:26
Alignment explanation
Indices: 1482588--1482697 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
1482578 TGATACAAAT
1482588 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
1482614 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
1482640 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
1482666 TGATAATGGTTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1482692 TGATAA
1 TGATAA
1482698 GAAATTCATG
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:1484720 original size:136 final size:137
Alignment explanation
Indices: 1484475--1484760 Score: 529
Period size: 136 Copynumber: 2.1 Consensus size: 137
1484465 GAGTAGTCTC
1484475 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
1484540 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTACC
1484605 ACTGTTA
131 ACTGTTA
*
1484612 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1484676 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTACC
1484741 ACTGTTA
131 ACTGTTA
**
1484748 CCTGAATGGGCTT
1 CCCAAATGGGCTT
1484761 AGGCCCAATA
Statistics
Matches: 145, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
136 125 0.86
137 20 0.14
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTACC
ACTGTTA
Found at i:1488991 original size:18 final size:19
Alignment explanation
Indices: 1488954--1488994 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1488944 ATTTAGAATC
1488954 AAAACTAAAATAAATAATA
1 AAAACTAAAATAAATAATA
* *
1488973 AAAACTAGATTAAAT-ATA
1 AAAACTAAAATAAATAATA
1488991 AAAA
1 AAAA
1488995 TATCAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAACTAAAATAAATAATA
Found at i:1488996 original size:31 final size:31
Alignment explanation
Indices: 1488920--1488993 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
1488910 TCAAGTTATC
*
1488920 TTAAATATTAAAATAAAAATAAAAATTTAGAA
1 TTAAATA-TAAAATAAAAATAAAAATCTAGAA
*
1488952 TCAAA-ACTAAAATAAATAATAAAAA-CTAG-A
1 TTAAATA-TAAAATAAA-AATAAAAATCTAGAA
1488982 TTAAATATAAAA
1 TTAAATATAAAA
1488994 ATATCAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 10 0.28
31 14 0.39
32 12 0.33
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (31 bp):
TTAAATATAAAATAAAAATAAAAATCTAGAA
Found at i:1493850 original size:18 final size:16
Alignment explanation
Indices: 1493819--1493856 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
1493809 TATTGATTAA
1493819 TTTTAAATTTTTTTAT
1 TTTTAAATTTTTTTAT
1493835 TTTTAACATATTTTTTAT
1 TTTTAA-AT-TTTTTTAT
1493853 TTTT
1 TTTT
1493857 CTCTTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 2 0.10
18 12 0.60
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTAAATTTTTTTAT
Found at i:1493863 original size:26 final size:25
Alignment explanation
Indices: 1493825--1493881 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
1493815 TTAATTTTAA
* *
1493825 ATTTTTTTATTTTTAACATATTTTTT
1 ATTTTTCTATTTTGAA-ATATTTTTT
* *
1493851 ATTTTTCTCTTTTGAAATTTTTTTT
1 ATTTTTCTATTTTGAAATATTTTTT
*
1493876 AATTTT
1 ATTTTT
1493882 GAATATTGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (25 bp):
ATTTTTCTATTTTGAAATATTTTTT
Found at i:1493938 original size:8 final size:8
Alignment explanation
Indices: 1493927--1493996 Score: 51
Period size: 8 Copynumber: 9.4 Consensus size: 8
1493917 ATATTAAATA
1493927 TTAAATTT
1 TTAAATTT
*
1493935 TTAAGTTT
1 TTAAATTT
1493943 TT--ATTT
1 TTAAATTT
*
1493949 TTTAATTT
1 TTAAATTT
*
1493957 TT-TATTT
1 TTAAATTT
1493964 TTAAA-TT
1 TTAAATTT
1493971 TT-AATTT
1 TTAAATTT
**
1493978 TTTTATTT
1 TTAAATTT
*
1493986 TTTAATTT
1 TTAAATTT
1493994 TTA
1 TTA
1493997 TTTTTTGAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
6 7 0.14
7 14 0.28
8 29 0.58
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.73
Consensus pattern (8 bp):
TTAAATTT
Found at i:1493948 original size:14 final size:14
Alignment explanation
Indices: 1493931--1493979 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
1493921 TAAATATTAA
*
1493931 ATTTTTAAGTTTTT
1 ATTTTTAAATTTTT
*
1493945 ATTTTTTAATTTTTT
1 A-TTTTTAAATTTTT
*
1493960 ATTTTTAAATTTTA
1 ATTTTTAAATTTTT
1493974 ATTTTT
1 ATTTTT
1493980 TTATTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (14 bp):
ATTTTTAAATTTTT
Found at i:1493950 original size:7 final size:7
Alignment explanation
Indices: 1493940--1494019 Score: 74
Period size: 7 Copynumber: 11.3 Consensus size: 7
1493930 AATTTTTAAG
1493940 TTTTTAT
1 TTTTTAT
1493947 TTTTTAAT
1 TTTTT-AT
1493955 TTTTTAT
1 TTTTTAT
* *
1493962 TTTTAAA
1 TTTTTAT
*
1493969 TTTTAATT
1 TTTTTA-T
1493977 TTTTTAT
1 TTTTTAT
*
1493984 TTTTTAA
1 TTTTTAT
1493991 TTTTTAT
1 TTTTTAT
1493998 TTTTTGA-
1 TTTTT-AT
*
1494005 -GTTTAT
1 TTTTTAT
1494011 TTTTTAT
1 TTTTTAT
1494018 TT
1 TT
1494020 CGATTTAATG
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
5 1 0.02
6 3 0.05
7 43 0.72
8 13 0.22
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (7 bp):
TTTTTAT
Found at i:1493950 original size:15 final size:15
Alignment explanation
Indices: 1493932--1494002 Score: 83
Period size: 15 Copynumber: 4.9 Consensus size: 15
1493922 AAATATTAAA
*
1493932 TTTTTAAGTTTTTAT
1 TTTTTAATTTTTTAT
1493947 TTTTTAATTTTTTA-
1 TTTTTAATTTTTTAT
* *
1493961 TTTTTAAATTTTAAT
1 TTTTTAATTTTTTAT
* *
1493976 TTTTTTATTTTTTAA
1 TTTTTAATTTTTTAT
1493991 TTTTT-ATTTTTT
1 TTTTTAATTTTTT
1494003 GAGTTTATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
14 19 0.40
15 29 0.60
ACGTcount: A:0.21, C:0.00, G:0.01, T:0.77
Consensus pattern (15 bp):
TTTTTAATTTTTTAT
Found at i:1494002 original size:37 final size:37
Alignment explanation
Indices: 1493927--1494001 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
1493917 ATATTAAATA
1493927 TTAAATTTTTAAGTTTTTATTTTTTAATTTTTTATTT
1 TTAAATTTTTAAGTTTTTATTTTTTAATTTTTTATTT
*
1493964 TTAAA-TTTTAATTTTTTTATTTTTTAA-TTTTTATTT
1 TTAAATTTTTAA-GTTTTTATTTTTTAATTTTTTATTT
1494000 TT
1 TT
1494002 TGAGTTTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
36 17 0.47
37 19 0.53
ACGTcount: A:0.24, C:0.00, G:0.01, T:0.75
Consensus pattern (37 bp):
TTAAATTTTTAAGTTTTTATTTTTTAATTTTTTATTT
Found at i:1494822 original size:16 final size:17
Alignment explanation
Indices: 1494801--1494834 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1494791 GAAGTTATAG
1494801 TTTAGGGTTT-AGGGTT
1 TTTAGGGTTTAAGGGTT
1494817 TTTAGGGTTTAAGGGTT
1 TTTAGGGTTTAAGGGTT
1494834 T
1 T
1494835 AGTATTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (17 bp):
TTTAGGGTTTAAGGGTT
Found at i:1494946 original size:41 final size:41
Alignment explanation
Indices: 1494901--1495229 Score: 410
Period size: 41 Copynumber: 8.0 Consensus size: 41
1494891 AGGGGTTATA
* **
1494901 TGACTTTTAGTGGCGTTTTATTAAAAGCGCCGCTATTGCTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
* *
1494942 TGACTTTTAGTGGCGTTTTACCAAAAACGCCGCTATTGCTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
1494983 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
* * *
1495024 CGACTTTTAGTGGCATTTTACCAAAAGCGCCGCTATTGCTCC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCT-C
* ** *
1495066 T-ACTTTTAGCGGCGTTTTATCTGAAGTGCCGCTATTGCTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
*
1495106 CGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
* * * * *
1495147 CGACTTTTAGCGACGTTTTAACAAAAAACGCCGCTATTACTC
1 TGACTTTTAGCGGCGTTTT-ACCAAAAGCGCCGCTATTGCTC
* * * * **
1495189 T-ATTTTTAGCGGCGTGTTAACAAAAACGCAACTATTGCTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
1495229 T
1 T
1495230 ATGTTTTACA
Statistics
Matches: 252, Mismatches: 33, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
40 19 0.08
41 213 0.85
42 20 0.08
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (41 bp):
TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
Found at i:1503835 original size:19 final size:19
Alignment explanation
Indices: 1503813--1503852 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1503803 ATAACAAAAT
*
1503813 AATAGCAACATAATAGTGA
1 AATAGCAACAAAATAGTGA
* *
1503832 AATAGTAGCAAAATAGTGA
1 AATAGCAACAAAATAGTGA
1503851 AA
1 AA
1503853 AAAATAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.20
Consensus pattern (19 bp):
AATAGCAACAAAATAGTGA
Found at i:1503848 original size:11 final size:11
Alignment explanation
Indices: 1503799--1503846 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
1503789 AGAATTATAC
*
1503799 AATAATAACAA
1 AATAATAGCAA
1503810 AATAATAGCAA
1 AATAATAGCAA
* **
1503821 CATAATAGTGA
1 AATAATAGCAA
*
1503832 AATAGTAGCAA
1 AATAATAGCAA
1503843 AATA
1 AATA
1503847 GTGAAAAAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.21
Consensus pattern (11 bp):
AATAATAGCAA
Found at i:1504462 original size:25 final size:23
Alignment explanation
Indices: 1504433--1504497 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 23
1504423 AAATAAAAAC
*
1504433 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
1504458 TTTAAAACATAAAAACAAAT--A
1 TTTAAAACATAAAAACAAATACA
1504479 -TTAAAACA-AAAAACAAATA
1 TTTAAAACATAAAAACAAATA
1504498 AAAAAATAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
19 10 0.26
20 8 0.21
21 1 0.03
23 5 0.13
24 3 0.08
25 11 0.29
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:1504492 original size:19 final size:20
Alignment explanation
Indices: 1504459--1504497 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
1504449 TCAAATACAT
1504459 TTAAAACATAAAAACAAATA
1 TTAAAACATAAAAACAAATA
1504479 TTAAAACA-AAAAACAAATA
1 TTAAAACATAAAAACAAATA
1504498 AAAAAATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (20 bp):
TTAAAACATAAAAACAAATA
Found at i:1504503 original size:19 final size:20
Alignment explanation
Indices: 1504461--1504503 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1504451 AAATACATTT
**
1504461 AAAACATAAAAACAAATATT
1 AAAACATAAAAACAAATAAA
1504481 AAAACA-AAAAACAAATAAA
1 AAAACATAAAAACAAATAAA
1504500 AAAA
1 AAAA
1504504 TAAGACTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (20 bp):
AAAACATAAAAACAAATAAA
Found at i:1506114 original size:26 final size:26
Alignment explanation
Indices: 1506085--1506137 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1506075 AATTCTATTT
1506085 TTAAGTGAAATAAAAATAATAAACTA
1 TTAAGTGAAATAAAAATAATAAACTA
*
1506111 TTAATTGAAATAAAAATAATAAACTA
1 TTAAGTGAAATAAAAATAATAAACTA
1506137 T
1 T
1506138 CTCTTCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (26 bp):
TTAAGTGAAATAAAAATAATAAACTA
Found at i:1513148 original size:15 final size:15
Alignment explanation
Indices: 1513128--1513178 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1513118 ACAAATTTAT
1513128 AAATAAATTTTAATA
1 AAATAAATTTTAATA
1513143 AAATAAAATTTT-A-A
1 AAAT-AAATTTTAATA
* * *
1513157 AAATATATTATAATT
1 AAATAAATTTTAATA
1513172 AAATAAA
1 AAATAAA
1513179 ATAAGTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 5 0.17
14 6 0.21
15 11 0.38
16 7 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATAAATTTTAATA
Found at i:1513161 original size:29 final size:29
Alignment explanation
Indices: 1513123--1513180 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1513113 TTTGTACAAA
* *
1513123 TTTATAAATAAATTTTAATAAAATAAAAT
1 TTTAAAAATAAATTATAATAAAATAAAAT
* *
1513152 TTTAAAAATATATTATAATTAAATAAAAT
1 TTTAAAAATAAATTATAATAAAATAAAAT
1513181 AAGTTTTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
TTTAAAAATAAATTATAATAAAATAAAAT
Found at i:1514318 original size:15 final size:16
Alignment explanation
Indices: 1514293--1514334 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1514283 CACAAACAAA
1514293 TAATCAATATAACT-GT
1 TAAT-AATATAACTAGT
1514309 TAATAATAT-ACTAGT
1 TAATAATATAACTAGT
*
1514324 TAATATTATAA
1 TAATAATATAA
1514335 TGTACTGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 15 0.65
16 5 0.22
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (16 bp):
TAATAATATAACTAGT
Found at i:1515323 original size:42 final size:42
Alignment explanation
Indices: 1515260--1515386 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
1515250 CTTCGTTTTC
** * *
1515260 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCGCAGCTATGGTCTTACACATATTCACAT-A
*
1515303 T-GATGCCATAGCGCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCGCAGCTATGGTCTTACACATATTCACATA
1515344 TCGATGCCATAGCGCAGCTATGGTCTTACACGA-ATT-ACATA
1 TCGATGCCATAGCGCAGCTATGGTCTTACAC-ATATTCACATA
1515385 TC
1 TC
1515387 TCATTGATGC
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
41 8 0.11
42 66 0.87
43 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGCGCAGCTATGGTCTTACACATATTCACATA
Found at i:1515413 original size:46 final size:47
Alignment explanation
Indices: 1515345--1515464 Score: 143
Period size: 47 Copynumber: 2.6 Consensus size: 47
1515335 ATTCATATAT
* * * * * *
1515345 CGATGCCATAGCGCAGCTATGGTCTTACAC-GAATTACATATCTCAT
1 CGATGCCATATCCCAGATATGGTCTTACACAGAAGTACATATCACAC
* * * *
1515391 TGATGCCATATCCCAGATATGGTCTTATACAGTAGTATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTACACAGAAGTACATATCACAC
1515438 CGATGCCATATCCCAGATATGGTCTTA
1 CGATGCCATATCCCAGATATGGTCTTA
1515465 TACGGAAATC
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
46 25 0.40
47 37 0.60
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (47 bp):
CGATGCCATATCCCAGATATGGTCTTACACAGAAGTACATATCACAC
Found at i:1515528 original size:31 final size:31
Alignment explanation
Indices: 1515493--1515672 Score: 213
Period size: 31 Copynumber: 5.8 Consensus size: 31
1515483 CTTGTCACTT
* *
1515493 GTAGCCAAATCTACCACTATTCA-TCGATCAG
1 GTAGCCAAAGCTACCACTTTTCACT-GATCAG
** *
1515524 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCAAAGCTACCACTTTTCACTGATCAG
* *
1515555 GTAGCCAGAGCTACCACTTTTCACTGATCAA
1 GTAGCCAAAGCTACCACTTTTCACTGATCAG
*
1515586 GTAGCCGGAA-CTACCACTTTTCACTGATCAG
1 GTAGCC-AAAGCTACCACTTTTCACTGATCAG
1515617 GTAG-CAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCA-AAGCTACCACTTTTCACTGATCAG
***
1515648 GTAGATGAAGCTACCACTTTTCACT
1 GTAGCCAAAGCTACCACTTTTCACT
1515673 TGTCATTTGT
Statistics
Matches: 130, Mismatches: 14, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
30 3 0.02
31 125 0.96
32 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (31 bp):
GTAGCCAAAGCTACCACTTTTCACTGATCAG
Found at i:1515590 original size:62 final size:62
Alignment explanation
Indices: 1515493--1515672 Score: 247
Period size: 62 Copynumber: 2.9 Consensus size: 62
1515483 CTTGTCACTT
* * * *
1515493 GTAGCCAAATCTACCACTATTCA-TCGATCAGGTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCAGAGCTACCACTTTTCACT-GATCAGGTAGCCGGAGCTACCACTTTTCACTGATCAG
* *
1515555 GTAGCCAGAGCTACCACTTTTCACTGATCAAGTAGCCGGAACTACCACTTTTCACTGATCAG
1 GTAGCCAGAGCTACCACTTTTCACTGATCAGGTAGCCGGAGCTACCACTTTTCACTGATCAG
** *
1515617 GTAG-CAGAAGCTACCACTTTTCACTGATCAGGTAGATGAAGCTACCACTTTTCACT
1 GTAGCCAG-AGCTACCACTTTTCACTGATCAGGTAGCCGGAGCTACCACTTTTCACT
1515673 TGTCATTTGT
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
61 3 0.03
62 101 0.96
63 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (62 bp):
GTAGCCAGAGCTACCACTTTTCACTGATCAGGTAGCCGGAGCTACCACTTTTCACTGATCAG
Found at i:1515660 original size:93 final size:92
Alignment explanation
Indices: 1515503--1515672 Score: 254
Period size: 93 Copynumber: 1.8 Consensus size: 92
1515493 GTAGCCAAAT
* * *
1515503 CTACCACTATTCATCGATCAGGTAGCCGGAGCTACCATTTTTCACTGATCAGGTAGCCAGAGCTA
1 CTACCACTATTCATCGATCAGGTAGCAGAAGCTACCACTTTTCACTGATCAGGTAG-CAGAGCTA
1515568 CCACTTTTCACTGATCAAGTAGCCGGAA
65 CCACTTTTCACTGATCAAGTAGCCGGAA
*
1515596 CTACCACTTTTCA-CTGATCAGGTAGCAGAAGCTACCACTTTTCACTGATCAGGTAG-ATGAAGC
1 CTACCACTATTCATC-GATCAGGTAGCAGAAGCTACCACTTTTCACTGATCAGGTAGCA-G-AGC
1515659 TACCACTTTTCACT
63 TACCACTTTTCACT
1515673 TGTCATTTGT
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
91 1 0.01
92 2 0.03
93 67 0.96
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.28
Consensus pattern (92 bp):
CTACCACTATTCATCGATCAGGTAGCAGAAGCTACCACTTTTCACTGATCAGGTAGCAGAGCTAC
CACTTTTCACTGATCAAGTAGCCGGAA
Found at i:1515753 original size:50 final size:51
Alignment explanation
Indices: 1515654--1515776 Score: 187
Period size: 50 Copynumber: 2.4 Consensus size: 51
1515644 TCAGGTAGAT
* *
1515654 GAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCC
* *
1515705 GAAGCTATCACTTATCACTT-TCACTTTTTC-TTGATCAGATATGTGTAGCC
1 GAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGTGTAGCC
1515755 GAAGCTATCACTTATCACTTGT
1 GAAGCTATCACTTATCACTTGT
1515777 TGCCATGGTC
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
50 42 0.64
51 24 0.36
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (51 bp):
GAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCC
Found at i:1518965 original size:22 final size:22
Alignment explanation
Indices: 1518940--1518983 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1518930 ACTAAAATAT
*
1518940 AATTTTAT-CATTACTAATTTAA
1 AATTTTATAAATTA-TAATTTAA
1518962 AATTTTATAAATTATAATTTAA
1 AATTTTATAAATTATAATTTAA
1518984 CTTAAATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTTTATAAATTATAATTTAA
Found at i:1520414 original size:20 final size:21
Alignment explanation
Indices: 1520375--1520414 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1520365 ATAACAAGTT
1520375 TTGAACATAGATAAACAAAAA
1 TTGAACATAGATAAACAAAAA
1520396 TTGAA-ATA-ATAATACAAAA
1 TTGAACATAGATAA-ACAAAA
1520415 GACAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 9 0.50
21 5 0.28
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.23
Consensus pattern (21 bp):
TTGAACATAGATAAACAAAAA
Found at i:1520940 original size:4 final size:4
Alignment explanation
Indices: 1520931--1520963 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1520921 AGCAAACGTG
1520931 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1520964 TAGAAAAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1524781 original size:26 final size:26
Alignment explanation
Indices: 1524745--1524879 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
1524735 ACATGAATTC
*
1524745 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
1524771 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
1524797 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
1524823 TTATCATG-AACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
1524848 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
1524874 TTATCA
1 TTATCA
1524880 ATTTGTATCA
Statistics
Matches: 106, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
25 25 0.24
26 81 0.76
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:1524856 original size:51 final size:52
Alignment explanation
Indices: 1524745--1524879 Score: 236
Period size: 51 Copynumber: 2.6 Consensus size: 52
1524735 ACATGAATTC
* *
1524745 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCCA
*
1524797 TTATCATGGAACATTTACCTAACCTATTATCATG-AACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCCA
1524848 TTATCATGGAACATTTACCTAACCTATTATCA
1 TTATCATGGAACATTTACCTAACCTATTATCA
1524880 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 48 0.60
52 32 0.40
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (52 bp):
TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCCA
Found at i:1528798 original size:135 final size:137
Alignment explanation
Indices: 1528603--1528876 Score: 516
Period size: 135 Copynumber: 2.0 Consensus size: 137
1528593 TAAGCCATTA
*
1528603 GGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATT
1 GGTAACAGTGATACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATT
1528668 CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AACATATGCAAGC
66 CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGC
1528732 CCATTTG
131 CCATTTG
1528739 GGTAACAGTGATACTGGGCCA-AGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATT
1 GGTAACAGTGATACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATT
*
1528803 CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGC
66 CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGC
1528868 CCATTTG
131 CCATTTG
1528875 GG
1 GG
1528877 GAGACTACTC
Statistics
Matches: 135, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
135 93 0.69
136 42 0.31
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (137 bp):
GGTAACAGTGATACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATT
CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGC
CCATTTG
Found at i:1530696 original size:26 final size:26
Alignment explanation
Indices: 1530660--1530795 Score: 218
Period size: 26 Copynumber: 5.2 Consensus size: 26
1530650 CATGATATTC
1530660 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
1530686 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
1530712 TTATCATGGAATATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
1530738 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
1530764 TTATCATGGAACATTTACCTAGCCTA
1 TTATCATGAAACATTTACCTAACCCA
1530790 TTATCA
1 TTATCA
1530796 ATTTGTATCA
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 101 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:1532415 original size:26 final size:26
Alignment explanation
Indices: 1532367--1532419 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
1532357 AAGAATAAAC
* *
1532367 TATATACATAATAGATTTGAAAGGAAA
1 TATATACATAATAAATTT-AAAAGAAA
*
1532394 TATATATA-AATAAATTTAAAAGAAA
1 TATATACATAATAAATTTAAAAGAAA
1532419 T
1 T
1532420 TGCATATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 8 0.35
26 8 0.35
27 7 0.30
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (26 bp):
TATATACATAATAAATTTAAAAGAAA
Found at i:1539174 original size:2 final size:2
Alignment explanation
Indices: 1539167--1539215 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
1539157 TATGTGCAAA
*
1539167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1539209 GT AT AT A
1 AT AT AT A
1539216 AAATATACAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1539317 original size:2 final size:2
Alignment explanation
Indices: 1539304--1539441 Score: 69
Period size: 2 Copynumber: 72.0 Consensus size: 2
1539294 GGAATTTAAA
* * *
1539304 AT AT AC AT AT AT AT AT AT AT AT AT AT GT AT AT A- AT AGT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * * * **
1539346 A- AG A- AT AT AT AC AT A- AG AA AT AT AT A- ACT A- AT GGC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT AT AT
* * *
1539385 AT AC AT A- AT AT AT AT AT AT A- AT AC AC AT A- 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
*
1539424 AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT
1539442 TAGAAATGAT
Statistics
Matches: 104, Mismatches: 20, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
1 9 0.09
2 92 0.88
3 3 0.03
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (2 bp):
AT
Found at i:1539973 original size:11 final size:12
Alignment explanation
Indices: 1539957--1539993 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
1539947 AGAAAAAAAA
1539957 GGAAGAGAG-AG
1 GGAAGAGAGAAG
1539968 GGAAGAGAGAAG
1 GGAAGAGAGAAG
1539980 GG-AGAGAGAAG
1 GGAAGAGAGAAG
1539991 GGA
1 GGA
1539994 GGGGAAGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (12 bp):
GGAAGAGAGAAG
Found at i:1539994 original size:11 final size:11
Alignment explanation
Indices: 1539955--1540003 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
1539945 AAAGAAAAAA
*
1539955 AAGGAAGAGAG
1 AAGGGAGAGAG
1539966 -AGGGAAGAGAG
1 AAGGG-AGAGAG
1539977 AAGGGAGAGAG
1 AAGGGAGAGAG
*
1539988 AAGGGAG-GGG
1 AAGGGAGAGAG
1539998 AAGGGA
1 AAGGGA
1540004 AATCCGGTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 11 0.32
11 19 0.56
12 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (11 bp):
AAGGGAGAGAG
Found at i:1540282 original size:17 final size:17
Alignment explanation
Indices: 1540262--1540320 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
1540252 TTTTTTGGTT
1540262 TTTTTTTTTGCTGGAAA
1 TTTTTTTTTGCTGGAAA
1540279 ---TTTTTT--TGGAAA
1 TTTTTTTTTGCTGGAAA
**
1540291 TTTTTTTTTTGCTGGATT
1 -TTTTTTTTTGCTGGAAA
1540309 TTTTTTTTTGCT
1 TTTTTTTTTGCT
1540321 TCCCCTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
12 6 0.18
14 6 0.18
16 6 0.18
17 12 0.35
18 4 0.12
ACGTcount: A:0.12, C:0.05, G:0.15, T:0.68
Consensus pattern (17 bp):
TTTTTTTTTGCTGGAAA
Found at i:1540298 original size:13 final size:12
Alignment explanation
Indices: 1540273--1540297 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1540263 TTTTTTTTGC
1540273 TGGAAATTTTTT
1 TGGAAATTTTTT
1540285 TGGAAATTTTTT
1 TGGAAATTTTTT
1540297 T
1 T
1540298 TTTGCTGGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (12 bp):
TGGAAATTTTTT
Found at i:1540756 original size:35 final size:35
Alignment explanation
Indices: 1540716--1540821 Score: 194
Period size: 35 Copynumber: 3.0 Consensus size: 35
1540706 GGGGTGTGTG
*
1540716 ATGGTGCTGGCGGCAGACAGCATGGGAGAGTGGGA
1 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
*
1540751 GTGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1540786 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1540821 A
1 A
1540822 GAGGCAAGTG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.23, C:0.12, G:0.49, T:0.16
Consensus pattern (35 bp):
ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
Found at i:1541606 original size:48 final size:50
Alignment explanation
Indices: 1541530--1541676 Score: 183
Period size: 54 Copynumber: 2.9 Consensus size: 50
1541520 ATATGACCTA
**
1541530 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAAACAA-AA-
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAATAAC
* *
1541578 AGG-TACAACTCACCTCTCGCAATATGAGTTGCTTTTTGAAAGACAGAAATTAAC
1 AGGCT-CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA-A-A-CAA-TAAC
*
1541632 AGGCTCAACTCACCTCTCGCAATGTGAGTTGATTTTTGAAAAACA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
1541677 GGAATTGGAA
Statistics
Matches: 84, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
47 1 0.01
48 36 0.43
49 1 0.01
50 1 0.01
51 3 0.04
52 1 0.01
53 3 0.04
54 37 0.44
55 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (50 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAATAAC
Found at i:1541854 original size:77 final size:70
Alignment explanation
Indices: 1541733--1542256 Score: 789
Period size: 70 Copynumber: 7.2 Consensus size: 70
1541723 TCAACTCACC
1541733 TATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTC
1 TATGAGTTGA-TTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTC
*
1541798 TCGCCA
65 TCGCAA
*
1541804 TATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGCTCAACT
1 TATGAGTTGATTTTGAAAC----A-T--AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACT
1541869 CACCTCTCGCAA
59 CACCTCTCGCAA
1541881 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
1541946 CGC-A
66 CGCAA
*
1541950 TATGAGTTGATTTTGAAACATAAATTGAAATTGAAATTACCTCAACGTGTTTTGAGGCTCAACTC
1 TATGAGTTGATTTTGAAAC----A-T-AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTC
1542015 ACCTCTCGCAA
60 ACCTCTCGCAA
*
1542026 TATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGCTCAACT
1 TATGAGTTGATTTTGAAAC----A-T--AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACT
1542091 CACCTCTCGCAA
59 CACCTCTCGCAA
*
1542103 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTTAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
1542168 CGCAA
66 CGCAA
*
1542173 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
1542238 CGCAA
66 CGCAA
*
1542243 TGTGAGTTGATTTT
1 TATGAGTTGATTTT
1542257 CTGTCACTTG
Statistics
Matches: 428, Mismatches: 10, Indels: 31
0.91 0.02 0.07
Matches are distributed among these distances:
69 20 0.05
70 183 0.43
71 10 0.02
72 2 0.00
73 3 0.01
74 2 0.00
75 47 0.11
76 27 0.06
77 134 0.31
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (70 bp):
TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
CGCAA
Found at i:1542023 original size:222 final size:217
Alignment explanation
Indices: 1541733--1542256 Score: 933
Period size: 222 Copynumber: 2.4 Consensus size: 217
1541723 TCAACTCACC
1541733 TATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTC
1 TATGAGTTGA-TTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTC
*
1541798 TCGCCATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGC
65 TCGCAATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGC
1541863 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTT
130 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTT
1541928 GAGGCTCAACTCACCTCTCGC-A
195 GAGGCTCAACTCACCTCTCGCAA
*
1541950 TATGAGTTGATTTTGAAACATAAATTGAAATTGAAATTACCTCAACGTGTTTTGAGGCTCAACTC
1 TATGAGTTGATTTTGAAAC----A-T-AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTC
1542015 ACCTCTCGCAATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTT
60 ACCTCTCGCAATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTT
1542080 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGT
125 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGT
*
1542145 GTCTTGAGGCTTAACTCACCTCTCGCAA
190 GTCTTGAGGCTCAACTCACCTCTCGCAA
*
1542173 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
*
1542238 CGCAATGTGAGTTGATTTT
66 CGCAATATGAGTTGATTTT
1542257 CTGTCACTTG
Statistics
Matches: 294, Mismatches: 6, Indels: 14
0.94 0.02 0.04
Matches are distributed among these distances:
216 9 0.03
217 70 0.24
218 1 0.00
219 1 0.00
220 1 0.00
221 1 0.00
222 191 0.65
223 20 0.07
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (217 bp):
TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
CGCAATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGCT
CAACTCACCTCTCGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTG
AGGCTCAACTCACCTCTCGCAA
Found at i:1548951 original size:13 final size:14
Alignment explanation
Indices: 1548927--1548957 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1548917 ATCATTATCA
1548927 ATATTAATATATGT
1 ATATTAATATATGT
1548941 ATATT-ATATATGT
1 ATATTAATATATGT
1548954 ATAT
1 ATAT
1548958 ATTCATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
ATATTAATATATGT
Found at i:1561604 original size:74 final size:74
Alignment explanation
Indices: 1561503--1561781 Score: 384
Period size: 74 Copynumber: 3.8 Consensus size: 74
1561493 TTTTCCAAAA
* * * *
1561503 ATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGCT
1 ATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGCT
1561568 TTTTAGTTC
66 TTTTAGTTC
* * * *
1561577 ATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATG--
1 ATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGCT
* ***
1561640 TTTCA-AAA
66 TTTTAGTTC
* * *
1561648 ATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGCT
1 ATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGCT
1561713 TTTTAGTTC
66 TTTTAGTTC
* *
1561722 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTT
1 ATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
1561782 ATGTTTCAAA
Statistics
Matches: 174, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
71 56 0.32
72 4 0.02
73 4 0.02
74 110 0.63
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.33
Consensus pattern (74 bp):
ATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGCT
TTTTAGTTC
Done.