Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008397.1 Hibiscus syriacus cultivar Beakdansim tig00111166_pilon, whole genome shotgun sequence
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: 2560905
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:1207912 original size:19 final size:20
Alignment explanation
Indices: 1207877--1207917 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1207867 ATTTATTAAA
1207877 TTTAGCAATTTATATTATTT
1 TTTAGCAATTTATATTATTT
*
1207897 TTTATCAATTTA-ATTATTT
1 TTTAGCAATTTATATTATTT
1207916 TT
1 TT
1207918 AATGATATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTAGCAATTTATATTATTT
Found at i:1209043 original size:31 final size:31
Alignment explanation
Indices: 1208998--1209109 Score: 109
Period size: 31 Copynumber: 3.5 Consensus size: 31
1208988 CTACCTAAGA
* *
1208998 GAATACCTTGGGGCCTTAGAGCCTACCCAGG
1 GAATATCTTGGGGCCTCAGAGCCTACCCAGG
* * * *
1209029 GAATATCTTAGGGCCTCAGAACTTACCAAAGG
1 GAATATCTTGGGGCCTCAGAGCCTACC-CAGG
*
1209061 GAA-ATACTTTGGGGCCTGAGAGCCTACCCAAGG
1 GAATAT-C-TTGGGGCCTCAGAGCCTACCC-AGG
*
1209094 GAATATCTCGGGGCCT
1 GAATATCTTGGGGCCT
1209110 AAAAGCCCCT
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
31 24 0.38
32 15 0.23
33 23 0.36
34 2 0.03
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.21
Consensus pattern (31 bp):
GAATATCTTGGGGCCTCAGAGCCTACCCAGG
Found at i:1211882 original size:23 final size:23
Alignment explanation
Indices: 1211839--1211882 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1211829 AATTTTTTCA
* *
1211839 AATTAATTAATTTTATTTAAAGC
1 AATTAATTAATTTCATATAAAGC
1211862 AATTAATTAATATTCA-ATAAA
1 AATTAATTAAT-TTCATATAAA
1211883 TGGATCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (23 bp):
AATTAATTAATTTCATATAAAGC
Found at i:1214160 original size:20 final size:19
Alignment explanation
Indices: 1214137--1214178 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
1214127 TCTTGTAAAG
* *
1214137 ATGAAAGTTCTTTTGTAAGA
1 ATGAAAGCTC-TTTCTAAGA
1214157 ATG-AAGCTCTTTCTAAGA
1 ATGAAAGCTCTTTCTAAGA
1214175 ATGA
1 ATGA
1214179 TTACTTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
18 11 0.58
19 5 0.26
20 3 0.16
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (19 bp):
ATGAAAGCTCTTTCTAAGA
Found at i:1217923 original size:39 final size:39
Alignment explanation
Indices: 1217880--1218618 Score: 955
Period size: 39 Copynumber: 19.2 Consensus size: 39
1217870 TTCTTAAAAC
* *
1217880 AAGATTTTATCTCGCTTGAGATAGTTTCTCTTGAAACAT
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
*
1217919 AAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAT
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
* *
1217958 AATATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAT
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
* * *
1217997 AATATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
*
1218036 AAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAT
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
* *
1218075 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTTAAACAA
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
* *
1218114 AATATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAG
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
* * *
1218153 AAGATTTTGTCTCTCTTAAGATAGTTTCCCTTGAAATAT
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
* *
1218192 AAGATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAG
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
* * *
1218231 AATATTTTATCTTGCTTGAGATAGTTTCCCTTGAAACAT
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
* *
1218270 AATATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAG
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
* *
1218309 AATATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAG
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
* *
1218348 AAGATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAG
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
* * * *
1218387 AAGATTTCGTCTCTCTTGAGATAGTTTCACTTGAAACAG
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
* * * * * *
1218426 AAGATTTTATCTCACTCGAGATTGTTTTTCCTTTAAAC--
1 AAGATTTTGTCTCGCTTGAGATAG-TTTCCCTTGAAACAT
* * *
1218464 AA-ATTTTGTCTCACTTGAGACAATTTCCCTTGAAAC--
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
*
1218500 AA-ATTTTGTCTCACTTGAGATAGTTTCCCTTGAAAC--
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
* *
1218536 AA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC--
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
* * *
1218572 -AGATTTTATCTCTCTTGAAATAGTTTCCCTTGAAACAAT
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC-AT
1218611 AA-ATTTTG
1 AAGATTTTG
1218619 AGAACATTTC
Statistics
Matches: 640, Mismatches: 54, Indels: 12
0.91 0.08 0.02
Matches are distributed among these distances:
35 1 0.00
36 110 0.17
37 16 0.03
38 2 0.00
39 500 0.78
40 11 0.02
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (39 bp):
AAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT
Found at i:1218486 original size:21 final size:21
Alignment explanation
Indices: 1218462--1218519 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1218452 TTTCCTTTAA
1218462 ACAAATTTTGTCTCACTTGAG
1 ACAAATTTTGTCTCACTTGAG
*
1218483 AC-AA--TT-TC-C-CTTGAA
1 ACAAATTTTGTCTCACTTGAG
1218498 ACAAATTTTGTCTCACTTGAG
1 ACAAATTTTGTCTCACTTGAG
1218519 A
1 A
1218520 TAGTTTCCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
15 7 0.24
16 3 0.10
17 2 0.07
18 4 0.14
19 2 0.07
20 3 0.10
21 8 0.28
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (21 bp):
ACAAATTTTGTCTCACTTGAG
Found at i:1218590 original size:21 final size:20
Alignment explanation
Indices: 1218528--1218591 Score: 57
Period size: 21 Copynumber: 3.4 Consensus size: 20
1218518 GATAGTTTCC
*
1218528 CTTGAAACAAATTTTGTCTCT
1 CTTGAAACAGATTTT-TCTCT
*
1218549 CTTGAGACAG---TTTC-C-
1 CTTGAAACAGATTTTTCTCT
1218564 CTTGAAACAGATTTTATCTCT
1 CTTGAAACAGATTTT-TCTCT
1218585 CTTGAAA
1 CTTGAAA
1218592 TAGTTTCCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
15 9 0.26
16 1 0.03
17 2 0.06
18 4 0.12
19 2 0.06
20 1 0.03
21 15 0.44
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.39
Consensus pattern (20 bp):
CTTGAAACAGATTTTTCTCT
Found at i:1218814 original size:73 final size:73
Alignment explanation
Indices: 1218695--1218900 Score: 288
Period size: 73 Copynumber: 2.8 Consensus size: 73
1218685 AAACAAGTCT
* * * *
1218695 TTGAGACAAATTTCCCTTGAAATAAAATGTGTCTCCCTTGAGATGGTTTTTCTTAAAATCAACTT
1 TTGAGACAAATTTCCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAACCAACTT
1218760 -TGTCTCGC
66 CT-TCTCGC
* *
1218768 TTGAGACAACTTTCCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAACCTACTT
1 TTGAGACAAATTTCCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAACCAACTT
*
1218833 CTTCTTGC
66 CTTCTCGC
* ** * *
1218841 TTAAGACAGTTTTCCCTTGAAACAAAATTTATCTCACTTGAGATGCTTTTTCTTAAAACC
1 TTGAGACAAATTTCCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAACC
1218901 CTTGAGACAA
Statistics
Matches: 120, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
73 119 0.99
74 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (73 bp):
TTGAGACAAATTTCCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAACCAACTT
CTTCTCGC
Found at i:1219579 original size:135 final size:131
Alignment explanation
Indices: 1219220--1219674 Score: 591
Period size: 131 Copynumber: 3.5 Consensus size: 131
1219210 TTCAGTACAT
* *
1219220 AGTTCATAATGAGAAGAACTCATCCAGGAAGCATAAGTTCATAATGAGAAGAGCTTGTTCGACCT
1 AGTTCATAATGAGAAGAACTCATCCAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCT
* * * *
1219285 ATCACTCGATTCACGGCATTTCGAATCAGTGATGCCTCGCATGA-GGATTTGAAATTTCCAATGG
66 ATCACTCGATTCACTGCATTTCGAATCAGTGACGCCTCGCTTGAGGGA-TTGACATTTCCAATGG
1219349 AG
130 AG
* *
1219351 AGTTCATAATGAGAAGAACTCATCCAGGAAGAATAAGTTCATAATGAGAAGAACTTGTTCGACCT
1 AGTTCATAATGAGAAGAACTCATCCAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCT
*
1219416 ATCACTCGATTCA-TGACATTTCGGATCAGTGACGCCTCGCTTGAGGGATTGACATTTCCAATGG
66 ATCACTCGATTCACTG-CATTTCGAATCAGTGACGCCTCGCTTGAGGGATTGACATTTCCAATGG
1219480 AG
130 AG
* * *
1219482 AGTTCATAATGAGAA-AACTCATCCGACAGATGGAGAAGAAGTTAATAACGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCAT-C--CAG--GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* * *
1219546 GACCTATCACTTGATTCACTGCATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTTTC-
61 GACCTATCACTCGATTCACTGCATTTCGAATCAGTGACGCCTCGCTTGAGGGATTGACATTTCCA
*
1219610 A-GAAG
126 ATGGAG
* * * * *
1219615 AGTTCATAATGAGAATAACTCGTTCTA--AAGGAGAAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTC-ATCCAGGAAGAAG-AAGTTCATAATGAGAAGAGCTTGTTC
1219675 CTTTCGATTC
Statistics
Matches: 289, Mismatches: 24, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
128 4 0.01
129 23 0.08
130 8 0.03
131 134 0.46
132 4 0.01
133 21 0.07
134 7 0.02
135 86 0.30
136 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (131 bp):
AGTTCATAATGAGAAGAACTCATCCAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCT
ATCACTCGATTCACTGCATTTCGAATCAGTGACGCCTCGCTTGAGGGATTGACATTTCCAATGGA
G
Found at i:1220008 original size:241 final size:240
Alignment explanation
Indices: 1219467--1220032 Score: 832
Period size: 241 Copynumber: 2.4 Consensus size: 240
1219457 TGAGGGATTG
* *
1219467 ACATTTCCAATGGAGAGTTCATAATGAGAA-AACTCATCCGACAGATGGAGAAGAAGTTAATAAC
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGA-GGAGAAGAAGTTCATAAT
* * *
1219531 GAGAAGAGCTTGTTCGACCTATCACTTGATTCACTGCATTTCGAATCAGTGACACCTCGCTTGAG
65 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAATGACACCTCGCTTGAG
*** * * * *
1219596 GGATTGACATTTTCAGAAGAGTTCATAATGAGAATAACTCGTTCTAAAGGAGAAAGTTCATAATG
130 GGACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATTCAAAAGGAGAAAGTTCATAATG
1219661 AGAAGAACTTGTTCCTTTCGATTCCATAACAGAAAAAGGTGGATCA
195 AGAAGAACTTGTTCCTTTCGATTCCATAACAGAAAAAGGTGGATCA
*
1219707 ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGA-GGAGAAGAAGTTCATAAT
* ** *
1219772 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGTATTTCGAATCAATGATGCCTTGCTTGAG
65 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAATGACACCTCGCTTGAG
1219837 GGACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATTCAACAAGGAGAAAGTTCATAAT
130 GGACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATTCAA-AAGGAGAAAGTTCATAAT
* * **
1219902 GAGAAGAGCTTGTTCCTTTTGATTCCATCAA-AGAAGGAGGTGGATCA
194 GAGAAGAACTTGTTCCTTTCGATTCCAT-AACAGAAAAAGGTGGATCA
* * *
1219949 ACGTTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AAAGAGGAAGAAAAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGG-AGAAGAAGTTCATAAT
* *
1220013 GAGAAGAACTTGTTCAACCT
65 GAGAAGAGCTTGTTCGACCT
1220033 TGCATCATTG
Statistics
Matches: 294, Mismatches: 28, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
240 31 0.11
241 165 0.56
242 96 0.33
243 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.26
Consensus pattern (240 bp):
ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGAGAAGAAGTTCATAATG
AGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAATGACACCTCGCTTGAGG
GACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATTCAAAAGGAGAAAGTTCATAATGA
GAAGAACTTGTTCCTTTCGATTCCATAACAGAAAAAGGTGGATCA
Found at i:1220027 original size:20 final size:20
Alignment explanation
Indices: 1219964--1220028 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
1219954 TCCAATGGAG
1219964 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* **
1219984 CA-TCCA-AA-GAGGAAGAAAA
1 -AGTTCATAATGA-GAAGAACT
1220003 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
1220023 TGTTCA
1 AGTTCA
1220029 ACCTTGCATC
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 16 0.48
21 3 0.09
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:1220061 original size:91 final size:90
Alignment explanation
Indices: 1219951--1220119 Score: 304
Period size: 91 Copynumber: 1.9 Consensus size: 90
1219941 GTGGATCAAC
*
1219951 GTTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCA-AAGAGGAAGAAAAAGTTCATAATGA
1 GTTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCACAAGA-G-AGAAAAAGTTCATAATGA
1220015 GAAGAACTTGTTCAACCTTGCATCATT
64 GAAGAACTTGTTCAACCTTGCATCATT
1220042 GTTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCACAAGAGAGAAAAAGTTCATAATGAGA
1 GTTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCACAAGAGAGAAAAAGTTCATAATGAGA
1220107 AGAACTTGTTCAA
66 AGAACTTGTTCAA
1220120 ACCAACAACG
Statistics
Matches: 76, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
90 33 0.43
91 39 0.51
92 4 0.05
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (90 bp):
GTTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCACAAGAGAGAAAAAGTTCATAATGAGA
AGAACTTGTTCAACCTTGCATCATT
Found at i:1220260 original size:3 final size:3
Alignment explanation
Indices: 1220245--1220298 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
1220235 GCTTAAAAAA
* *
1220245 TAT TAT TAA TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1220293 TAT TAT
1 TAT TAT
1220299 ATTTATTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1221850 original size:23 final size:23
Alignment explanation
Indices: 1221807--1221850 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1221797 AATTTTTTCT
* *
1221807 AATTAATTAATTTTATTTAAAGC
1 AATTAATTAATTTCATATAAAGC
1221830 AATTAATTAATATTCA-ATAAA
1 AATTAATTAAT-TTCATATAAA
1221851 TGGATCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (23 bp):
AATTAATTAATTTCATATAAAGC
Found at i:1222888 original size:36 final size:36
Alignment explanation
Indices: 1222841--1222912 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1222831 CAATGGCCAG
*
1222841 GTCAAAGTCAACGGGTTAGACCGATTCGGGTTGACT
1 GTCAAAGTCAACGGGTCAGACCGATTCGGGTTGACT
1222877 GTCAAAGTCAACGGGTCAGACCGATTCGGGTTGACT
1 GTCAAAGTCAACGGGTCAGACCGATTCGGGTTGACT
1222913 TATGCCAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.24
Consensus pattern (36 bp):
GTCAAAGTCAACGGGTCAGACCGATTCGGGTTGACT
Found at i:1224262 original size:16 final size:18
Alignment explanation
Indices: 1224219--1224254 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1224209 AACATAGACT
1224219 TAGATTTTCCTAAACTAA
1 TAGATTTTCCTAAACTAA
1224237 TAGATTTTCCTAAACTAA
1 TAGATTTTCCTAAACTAA
1224255 GGTTTTCCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (18 bp):
TAGATTTTCCTAAACTAA
Found at i:1233830 original size:55 final size:55
Alignment explanation
Indices: 1233769--1233964 Score: 286
Period size: 55 Copynumber: 3.6 Consensus size: 55
1233759 ATCCTACGTG
* *
1233769 GATGAATAACCGTACATGTACTATGTGTGCAAAACCACAGAATTCATCATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAAACCACGGAATTCATCATGAGTT
*
1233824 GATGAATAACCATACATGCACTATGTGTGCAAAACCACGGAATTCATCATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAAACCACGGAATTCATCATGAGTT
* * * *
1233879 GATGAATAACCGTACATGCACGATGTGTGTAAAATCACGGAATTCATCATGAGTG
1 GATGAATAACCGTACATGCACTATGTGTGCAAAACCACGGAATTCATCATGAGTT
* * *
1233934 GATGAACT-ACCGTATAGGCACTACGTGTGCA
1 GATGAA-TAACCGTACATGCACTATGTGTGCA
1233965 TCTTAATAAA
Statistics
Matches: 127, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
55 126 0.99
56 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (55 bp):
GATGAATAACCGTACATGCACTATGTGTGCAAAACCACGGAATTCATCATGAGTT
Found at i:1235937 original size:17 final size:18
Alignment explanation
Indices: 1235902--1235938 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1235892 GGATTAATAA
1235902 ATCTGAAAAGACATATTG
1 ATCTGAAAAGACATATTG
1235920 ATCTGATAAA-AC-TATTG
1 ATCTGA-AAAGACATATTG
1235937 AT
1 AT
1235939 GTGCATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (18 bp):
ATCTGAAAAGACATATTG
Found at i:1237591 original size:12 final size:13
Alignment explanation
Indices: 1237572--1237613 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
1237562 TCTGATATGG
1237572 ATTCTGTTTTGAT
1 ATTCTGTTTTGAT
*
1237585 ATT-TGTTCTGA-
1 ATTCTGTTTTGAT
1237596 ATTCTGTTTTGAT
1 ATTCTGTTTTGAT
1237609 -TTCTG
1 ATTCTG
1237614 ATATTTCCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 3 0.12
12 19 0.76
13 3 0.12
ACGTcount: A:0.14, C:0.10, G:0.17, T:0.60
Consensus pattern (13 bp):
ATTCTGTTTTGAT
Found at i:1237776 original size:2 final size:2
Alignment explanation
Indices: 1237769--1237809 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1237759 GAGATGAGGG
1237769 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1237810 GTTTTAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1239853 original size:28 final size:29
Alignment explanation
Indices: 1239799--1239854 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
1239789 AGTGAGCATC
*
1239799 GTTTGGGTGTTAATTTTGTAATTAATTTCT
1 GTTTGGGTGCTAATTTTGTAA-TAATTTCT
1239829 GTTTGGGTGCT-ATTTGTGTAA-AATTT
1 GTTTGGGTGCTAATTT-TGTAATAATTT
1239855 GGGTGTTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 5 0.21
29 4 0.17
30 15 0.62
ACGTcount: A:0.20, C:0.04, G:0.23, T:0.54
Consensus pattern (29 bp):
GTTTGGGTGCTAATTTTGTAATAATTTCT
Found at i:1239863 original size:156 final size:157
Alignment explanation
Indices: 1239625--1239933 Score: 593
Period size: 156 Copynumber: 2.0 Consensus size: 157
1239615 CATGCGCCAC
1239625 CCCCGAGAGTGAGCATCGTTTGGGGTGTTAATTTTGTAATTAATTTCTGTTTGGGTGATATTTGT
1 CCCCGAGAGTGAGCATCGTTTGGGGTGTTAATTTTGTAATTAATTTCTGTTTGGGTGATATTTGT
1239690 GTAAAATTTGGGTGTTAGTTTCGTAAATATTTACAGAAGGTGGCTAATTTTGTAATTAATTTATG
66 GTAAAATTTGGGTGTTAGTTTCGTAAATATTTACAGAAGGTGGCTAATTTTGTAATTAATTTATG
1239755 TTAGGGTGATATTTGTATAAAATATCA
131 TTAGGGTGATATTTGTATAAAATATCA
*
1239782 CCCCGAGAGTGAGCATCGTTT-GGGTGTTAATTTTGTAATTAATTTCTGTTTGGGTGCTATTTGT
1 CCCCGAGAGTGAGCATCGTTTGGGGTGTTAATTTTGTAATTAATTTCTGTTTGGGTGATATTTGT
1239846 GTAAAATTTGGGTGTTAGTTTCGTAAATATTTACAGAAGGTGGCTAATTTTGTAATTAATTTATG
66 GTAAAATTTGGGTGTTAGTTTCGTAAATATTTACAGAAGGTGGCTAATTTTGTAATTAATTTATG
*
1239911 TTAGGGTGATATTTGTGTAAAAT
131 TTAGGGTGATATTTGTATAAAAT
1239934 GGTCGACTGT
Statistics
Matches: 150, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
156 129 0.86
157 21 0.14
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (157 bp):
CCCCGAGAGTGAGCATCGTTTGGGGTGTTAATTTTGTAATTAATTTCTGTTTGGGTGATATTTGT
GTAAAATTTGGGTGTTAGTTTCGTAAATATTTACAGAAGGTGGCTAATTTTGTAATTAATTTATG
TTAGGGTGATATTTGTATAAAATATCA
Found at i:1239907 original size:81 final size:81
Alignment explanation
Indices: 1239653--1239933 Score: 317
Period size: 81 Copynumber: 3.5 Consensus size: 81
1239643 TTTGGGGTGT
* *
1239653 TAATTTTGTAATTAATTTCTGTTTGGGTGATATTTGTGTAAAATTTGGGTGTTAGTTTCGTAAAT
1 TAATTTTGTAATTAATTTATGTTAGGGTGATATTTGTGTAAAATTTGGGTGTTAGTTTCGTAAAT
1239718 ATTTACAGAAGGTGGC
66 ATTTACAGAAGGTGGC
* * ******* ** *
1239734 TAATTTTGTAATTAATTTATGTTAGGGTGATATTTGTATAAAATATCACCCCGAGAGT-G-AGCA
1 TAATTTTGTAATTAATTTATGTTAGGGTGATATTTGTGTAAAATTTGGGTGTTAGTTTCGTA-AA
* *
1239797 TCGTTT---G--GGT-GT
65 T-ATTTACAGAAGGTGGC
* * *
1239809 TAATTTTGTAATTAATTTCTGTTTGGGTGCTATTTGTGTAAAATTTGGGTGTTAGTTTCGTAAAT
1 TAATTTTGTAATTAATTTATGTTAGGGTGATATTTGTGTAAAATTTGGGTGTTAGTTTCGTAAAT
1239874 ATTTACAGAAGGTGGC
66 ATTTACAGAAGGTGGC
1239890 TAATTTTGTAATTAATTTATGTTAGGGTGATATTTGTGTAAAAT
1 TAATTTTGTAATTAATTTATGTTAGGGTGATATTTGTGTAAAAT
1239934 GGTCGACTGT
Statistics
Matches: 154, Mismatches: 36, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
75 48 0.31
76 6 0.04
77 1 0.01
78 2 0.01
79 1 0.01
80 6 0.04
81 90 0.58
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.45
Consensus pattern (81 bp):
TAATTTTGTAATTAATTTATGTTAGGGTGATATTTGTGTAAAATTTGGGTGTTAGTTTCGTAAAT
ATTTACAGAAGGTGGC
Found at i:1240779 original size:17 final size:18
Alignment explanation
Indices: 1240744--1240780 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1240734 GGATTAATAA
1240744 ATCTGAAAAGACATATTG
1 ATCTGAAAAGACATATTG
1240762 ATCTGATAAA-AC-TATTG
1 ATCTGA-AAAGACATATTG
1240779 AT
1 AT
1240781 GTGCATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (18 bp):
ATCTGAAAAGACATATTG
Found at i:1242406 original size:12 final size:12
Alignment explanation
Indices: 1242391--1242455 Score: 62
Period size: 12 Copynumber: 5.4 Consensus size: 12
1242381 ATGACCTGAA
*
1242391 TTCTGTTCTGAT
1 TTCTGTTTTGAT
* *
1242403 TTCTGATATGGA-
1 TTCTG-TTTTGAT
1242415 TTCTGTTTTGAT
1 TTCTGTTTTGAT
*
1242427 ATCTGTTTTGAAT
1 TTCTGTTTTG-AT
1242440 TT-TGTTTTGAT
1 TTCTGTTTTGAT
1242451 TTCTG
1 TTCTG
1242456 ATATTTTCGT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 8 0.19
12 28 0.67
13 6 0.14
ACGTcount: A:0.14, C:0.09, G:0.18, T:0.58
Consensus pattern (12 bp):
TTCTGTTTTGAT
Found at i:1242417 original size:24 final size:24
Alignment explanation
Indices: 1242387--1242459 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
1242377 ATACATGACC
*
1242387 TGAATTCTGTTCTGATTTCTGATA
1 TGAATTCTGTTTTGATTTCTGATA
* * * *
1242411 TGGATTCTGTTTTGATATCTGTTT
1 TGAATTCTGTTTTGATTTCTGATA
*
1242435 TGAATTTTGTTTTGATTTCTGATA
1 TGAATTCTGTTTTGATTTCTGATA
1242459 T
1 T
1242460 TTTCGTTTAC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.56
Consensus pattern (24 bp):
TGAATTCTGTTTTGATTTCTGATA
Found at i:1255642 original size:3 final size:3
Alignment explanation
Indices: 1255631--1255667 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
1255621 TTTTTTATCG
1255631 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T
1255668 GTTTATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1255679 original size:13 final size:13
Alignment explanation
Indices: 1255632--1255675 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
1255622 TTTTTATCGT
1255632 TATT-TTATTAT-
1 TATTATTATTATG
*
1255643 TATTATTATTATT
1 TATTATTATTATG
1255656 TATTATTATTATG
1 TATTATTATTATG
1255669 T-TTATTA
1 TATTATTA
1255676 ATTACATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 4 0.13
12 13 0.43
13 13 0.43
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TATTATTATTATG
Found at i:1255679 original size:19 final size:19
Alignment explanation
Indices: 1255638--1255679 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1255628 TCGTTATTTT
*
1255638 ATTATTATTATTATTATTT
1 ATTATTATTATTATTATTA
1255657 ATTATTATTATGT-TTATTA
1 ATTATTATTAT-TATTATTA
1255676 ATTA
1 ATTA
1255680 CATATTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTATTATTATTATTATTA
Found at i:1259670 original size:31 final size:32
Alignment explanation
Indices: 1259634--1259697 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1259624 TTATTTTACA
1259634 TATACTAACTTATTT-TTCTCTTTTGTTTGTG
1 TATACTAACTTATTTCTTCTCTTTTGTTTGTG
1259665 TATACTAACTTATTTCTTCTCTTTTGTTTGTG
1 TATACTAACTTATTTCTTCTCTTTTGTTTGTG
1259697 T
1 T
1259698 CATTTTGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 15 0.47
32 17 0.53
ACGTcount: A:0.16, C:0.14, G:0.09, T:0.61
Consensus pattern (32 bp):
TATACTAACTTATTTCTTCTCTTTTGTTTGTG
Found at i:1262150 original size:26 final size:25
Alignment explanation
Indices: 1262121--1262197 Score: 74
Period size: 26 Copynumber: 3.2 Consensus size: 25
1262111 AATTTTTGAC
1262121 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
1262147 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
*
1262167 ATTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
1262193 ATTCT
1 ATTCT
1262198 CTCCACCTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 13
0.67 0.10 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 4 0.10
26 14 0.36
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:1262834 original size:18 final size:17
Alignment explanation
Indices: 1262790--1262836 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
1262780 GAGTGCAAAG
*
1262790 ATCAAACCAAAGAAAAA
1 ATCAAAGCAAAGAAAAA
1262807 A-CAAAGAGCAAAGAGAAAA
1 ATC-AA-AGCAAAGA-AAAA
1262826 ATCAAAGCAAA
1 ATCAAAGCAAA
1262837 AATCAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 1 0.04
17 3 0.12
18 13 0.52
19 7 0.28
20 1 0.04
ACGTcount: A:0.68, C:0.15, G:0.13, T:0.04
Consensus pattern (17 bp):
ATCAAAGCAAAGAAAAA
Found at i:1262839 original size:12 final size:11
Alignment explanation
Indices: 1262820--1262857 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
1262810 AAGAGCAAAG
1262820 AGAAAAATCAA
1 AGAAAAATCAA
1262831 AGCAAAAATCAA
1 AG-AAAAATCAA
*
1262843 AGAAAAAGCAA
1 AGAAAAATCAA
1262854 AGAA
1 AGAA
1262858 CAAAAGAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:1264043 original size:4 final size:4
Alignment explanation
Indices: 1264034--1264067 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1264024 AAAAGTATAC
1264034 ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1264068 GATACATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
4 26 0.93
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1264058 original size:22 final size:21
Alignment explanation
Indices: 1264030--1264075 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
1264020 CGAGAAAAGT
1264030 ATACACATACATACATACATAC
1 ATACACATACATACAT-CATAC
*
1264052 ATACACATACATACATGATAC
1 ATACACATACATACATCATAC
1264073 ATA
1 ATA
1264076 AAATTTAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (21 bp):
ATACACATACATACATCATAC
Found at i:1265084 original size:29 final size:29
Alignment explanation
Indices: 1265051--1265122 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
1265041 TTTCTCTTGA
1265051 AAAAATCTTTGAGTTTGTTCCCTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCCTTTGAAT
* *
1265080 AAAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCCTTTGAAT
*
1265109 AAATATCTTTGAGT
1 AAAAATCTTTGAGT
1265123 CGTTTCTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.44
Consensus pattern (29 bp):
AAAAATCTTTGAGTTTGTTCCCTTTGAAT
Found at i:1265145 original size:25 final size:25
Alignment explanation
Indices: 1265080--1265162 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 25
1265070 CCCTTTGAAT
* * *
1265080 AAAAATCTTGGAGTTTGTTCCTTTTG
1 AAAAATCTTTGAG-TCGTTTCTTTTG
1265106 AATAAATATCTTTGAGTCGTTTCTTTTG
1 -A-AAA-ATCTTTGAGTCGTTTCTTTTG
* *
1265134 AAAAATCTTTGAGTCTATTTATTTTG
1 AAAAATCTTTGAGTC-GTTTCTTTTG
1265160 AAA
1 AAA
1265163 CAAAGTTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
25 11 0.23
26 14 0.29
27 2 0.04
28 13 0.27
29 8 0.17
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (25 bp):
AAAAATCTTTGAGTCGTTTCTTTTG
Found at i:1265236 original size:52 final size:53
Alignment explanation
Indices: 1265158--1265261 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 53
1265148 CTATTTATTT
*
1265158 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTGGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
1265210 TGAAACAAAGTTTGGTCTCTCTTGAGACAATTTTGTGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTGGTCTCTCTTGAGACAATTTCGTG-AAAAAATCTTTGAG
1265262 ATTGTTTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 35 0.73
54 13 0.27
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (53 bp):
TGAAACAAAGTTTGGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:1265261 original size:26 final size:28
Alignment explanation
Indices: 1265231--1265289 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
1265221 TTGGTCTCTC
1265231 TTGAGA-CAATT-TTGTGAAAAAAATCT
1 TTGAGATCAATTCTTGTGAAAAAAATCT
*** *
1265257 TTGAGATTGTTTCTTTTGAAAAAAATCT
1 TTGAGATCAATTCTTGTGAAAAAAATCT
1265285 TTGAG
1 TTGAG
1265290 TTTGTTTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.22
27 2 0.07
28 19 0.70
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.41
Consensus pattern (28 bp):
TTGAGATCAATTCTTGTGAAAAAAATCT
Found at i:1265283 original size:28 final size:29
Alignment explanation
Indices: 1265245--1265382 Score: 129
Period size: 28 Copynumber: 4.6 Consensus size: 29
1265235 GACAATTTTG
1265245 TGAAA-AAAATCTTTGAGATTGTTTCTTT
1 TGAAACAAAATCTTTGAGATTGTTTCTTT
*
1265273 TGAAA-AAAATCTTTGAGTTTGTTTCTTT
1 TGAAACAAAATCTTTGAGATTGTTTCTTT
* * *
1265301 GGAAACAAAATTTTTTCTCTCTTAAGATAGTTTCTTT
1 TGAAACAAAA-------TCT-TTGAGATTGTTTCTTT
*
1265338 TGAAACCAAAATCTTTGAGTTTGTTTCTTT
1 TGAAA-CAAAATCTTTGAGATTGTTTCTTT
1265368 TGAAACAAAAT-TTTG
1 TGAAACAAAATCTTTG
1265383 TCTCTCTTAA
Statistics
Matches: 91, Mismatches: 9, Indels: 20
0.76 0.08 0.17
Matches are distributed among these distances:
28 35 0.38
29 10 0.11
30 18 0.20
31 3 0.03
36 3 0.03
37 17 0.19
38 5 0.05
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (29 bp):
TGAAACAAAATCTTTGAGATTGTTTCTTT
Found at i:1265343 original size:37 final size:36
Alignment explanation
Indices: 1265293--1265414 Score: 123
Period size: 37 Copynumber: 3.5 Consensus size: 36
1265283 CTTTGAGTTT
*
1265293 GTTTCTTTGGAAACAAAATTTTTTCTCTCTTAAGATA
1 GTTTCTTTTGAAACAAAA-TTTTTCTCTCTTAAGATA
* * *
1265330 GTTTCTTTTGAAACCAAAA------TCT-TTGAGTTT
1 GTTTCTTTTGAAA-CAAAATTTTTCTCTCTTAAGATA
1265360 GTTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTTGAAACAAAATTTT-TCTCTCTTAAGATA
*
1265397 ATTTCTTTTGAAACAAAA
1 GTTTCTTTTGAAACAAAA
1265415 ATCTTTGAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
29 5 0.07
30 18 0.26
31 3 0.04
36 3 0.04
37 34 0.50
38 5 0.07
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (36 bp):
GTTTCTTTTGAAACAAAATTTTTCTCTCTTAAGATA
Found at i:1265468 original size:66 final size:66
Alignment explanation
Indices: 1265260--1265474 Score: 276
Period size: 67 Copynumber: 3.3 Consensus size: 66
1265250 AAAATCTTTG
* *
1265260 AGATTGTTTCTTTTG-AA-AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTTTCTCTCT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTT-GAAACAAAATTTTGTCTCTCT
1265323 TA
65 TA
*
1265325 AGATAGTTTCTTTTGAAACCAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCTCT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTC-TTTGAAACAAAATTTTGTCTCTCT
1265390 TA
65 TA
* * * *
1265392 AGATAATTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCTCTT-AAA-ATAAATTTTGTATCTC
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT-TTGAAACA-AAATTTTGTCTCTC
*
1265455 TTG
64 TTA
**
1265458 AGACCGTTTCTTTTGAA
1 AGATAGTTTCTTTTGAA
1265475 GTAAATCTTT
Statistics
Matches: 133, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
65 15 0.11
66 35 0.26
67 80 0.60
68 3 0.02
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.47
Consensus pattern (66 bp):
AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGAAACAAAATTTTGTCTCTCTT
A
Found at i:1265756 original size:64 final size:63
Alignment explanation
Indices: 1265664--1265784 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 63
1265654 ATGAGATCCC
* * *
1265664 TCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAATGACAATTTCTTTTGAGAAAAA
1 TCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTCAA-GACAACTTCTTTTGAGAAAAA
* * *
1265728 TCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGA
1 TCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTCAAGACAACTTCTTTTGA
1265785 AAATACCCAC
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
63 14 0.27
64 37 0.73
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (63 bp):
TCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTCAAGACAACTTCTTTTGAGAAAAA
Found at i:1265832 original size:40 final size:40
Alignment explanation
Indices: 1265769--1265848 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
1265759 TTGTCTCTCG
1265769 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
* * *
1265809 AGACAATTTCTTTT-AAAACTACCCACCTTTGAGATTGTTT
1 AGACAACTTCTTTTGAAAA-TACCCACATTTGAGATCGTTT
1265849 TTATTAAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
Found at i:1266280 original size:1 final size:1
Alignment explanation
Indices: 1266274--1266303 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
1266264 CGTTTCCCTT
1266274 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1266304 TTTTGTCTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1266555 original size:28 final size:28
Alignment explanation
Indices: 1266505--1266558 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1266495 TCAAAATCCA
* *
1266505 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTTCCTATTGAAACAC
1266533 ATCTTTGAGTTGGTCTCCT-TTGAAAC
1 ATCTTTGAGTTGGT-TCCTATTGAAAC
1266559 CATTATCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
ATCTTTGAGTTGGTTCCTATTGAAACAC
Found at i:1266721 original size:43 final size:43
Alignment explanation
Indices: 1266570--1267041 Score: 279
Period size: 40 Copynumber: 10.9 Consensus size: 43
1266560 ATTATCCTAG
* * * *
1266570 AGATAACCAG-CCGTCCTCATCACGTAGGAACCATGTTATCACCTTT
1 AGATAACCAGACC-TCCTCATCACGTAGGAGCCGTGTCA--ACC-AT
** * * * * **
1266616 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCC
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCAT
*
1266659 AG---ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCAT
* * *
1266699 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATAACCAGACC-TCCTCATCACGTAGGAGCCGTGTCA--ACC-AT
** * * * * *
1266745 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCC-C
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCA-ACCAT
* * *
1266788 CG---ACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCAT
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCAT
* * *
1266828 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATAACCAGACC-TCCTCATCACGTAGGAGCCGTGTCA--ACC-AT
** * * * * **
1266874 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCC
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCAT
*
1266917 AG---ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCAT
* * *
1266957 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATAACCAGACC-TCCTCATCACGTAGGAGCCGTGTCA--ACC-AT
* * * *
1267003 AAATAGCCAAGAACTCTTCATCACGTAGGAGCCGTGTCA
1 AGATAACC-AGACCTCCTCATCACGTAGGAGCCGTGTCA
1267042 CCTTTAGACG
Statistics
Matches: 328, Mismatches: 71, Indels: 53
0.73 0.16 0.12
Matches are distributed among these distances:
39 2 0.01
40 97 0.30
42 3 0.01
43 88 0.27
44 4 0.01
45 11 0.03
46 95 0.29
47 27 0.08
48 1 0.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (43 bp):
AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCAT
Found at i:1266805 original size:129 final size:129
Alignment explanation
Indices: 1266570--1267041 Score: 874
Period size: 129 Copynumber: 3.7 Consensus size: 129
1266560 ATTATCCTAG
*
1266570 AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1266635 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
1266699 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
*
1266764 TCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCA-TCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
1266828 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1266893 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
* *
1266957 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAAATAGCCAAGAACTCTTC
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCC-AGAACTCTTC
*
1267022 ATCACGTAGGAGCCGTGTCA
65 ATCACGTATGAGCCGTGTCA
1267042 CCTTTAGACG
Statistics
Matches: 334, Mismatches: 6, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
128 5 0.01
129 295 0.88
130 34 0.10
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (129 bp):
AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
Found at i:1267254 original size:3 final size:3
Alignment explanation
Indices: 1267243--1267279 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
1267233 TTTTTTATCG
1267243 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T
1267280 GTTTATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1267291 original size:13 final size:13
Alignment explanation
Indices: 1267244--1267287 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
1267234 TTTTTATCGT
1267244 TATT-TTATTAT-
1 TATTATTATTATG
*
1267255 TATTATTATTATT
1 TATTATTATTATG
1267268 TATTATTATTATG
1 TATTATTATTATG
1267281 T-TTATTA
1 TATTATTA
1267288 ATTACATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 4 0.13
12 13 0.43
13 13 0.43
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TATTATTATTATG
Found at i:1267291 original size:19 final size:19
Alignment explanation
Indices: 1267250--1267291 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1267240 TCGTTATTTT
*
1267250 ATTATTATTATTATTATTT
1 ATTATTATTATTATTATTA
1267269 ATTATTATTATGT-TTATTA
1 ATTATTATTAT-TATTATTA
1267288 ATTA
1 ATTA
1267292 CATATTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTATTATTATTATTATTA
Found at i:1275613 original size:16 final size:16
Alignment explanation
Indices: 1275592--1275625 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1275582 ATGATAAGCT
1275592 ATATGAAATGGTATAA
1 ATATGAAATGGTATAA
1275608 ATATGAAATGGTATAA
1 ATATGAAATGGTATAA
1275624 AT
1 AT
1275626 GGTAAAACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (16 bp):
ATATGAAATGGTATAA
Found at i:1275757 original size:46 final size:46
Alignment explanation
Indices: 1275690--1275786 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 46
1275680 GAGTCGAGGA
* * *
1275690 TTCTACGCAGTCTTTCGGGACAATTCTATATGGTCCTTCGAGACAT
1 TTCTACGCAGTCCTTCAGGACAATACTATATGGTCCTTCGAGACAT
* * * *
1275736 TTCTACGCTGTCCTTCAGGACAATACTATGTGGTCTTTCGTGACAT
1 TTCTACGCAGTCCTTCAGGACAATACTATATGGTCCTTCGAGACAT
1275782 TTCTA
1 TTCTA
1275787 TGTGGCACTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.37
Consensus pattern (46 bp):
TTCTACGCAGTCCTTCAGGACAATACTATATGGTCCTTCGAGACAT
Found at i:1275788 original size:23 final size:22
Alignment explanation
Indices: 1275707--1275799 Score: 73
Period size: 23 Copynumber: 4.1 Consensus size: 22
1275697 CAGTCTTTCG
*
1275707 GGACAATTCTATATGGTCCTTC
1 GGACAATTCTATGTGGTCCTTC
* *
1275729 GAGACATTTCTACGCT-GTCCTTC
1 G-GACAATTCTATG-TGGTCCTTC
* *
1275752 AGGACAATACTATGTGGTCTTTC
1 -GGACAATTCTATGTGGTCCTTC
*
1275775 GTGACATTTCTATGTGG-CACTTC
1 G-GACAATTCTATGTGGTC-CTTC
1275798 GG
1 GG
1275800 TGCAATTTAT
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
22 5 0.09
23 48 0.87
24 2 0.04
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (22 bp):
GGACAATTCTATGTGGTCCTTC
Found at i:1275929 original size:6 final size:6
Alignment explanation
Indices: 1275918--1275954 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
1275908 ATGAATAGTG
* *
1275918 AATGAT AATGAT AATGAT AGTGAT AATGAT GATGAT A
1 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT A
1275955 TGTATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (6 bp):
AATGAT
Found at i:1275964 original size:2 final size:2
Alignment explanation
Indices: 1275952--1275986 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1275942 AATGATGATG
*
1275952 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1275987 AAAGTGCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1277678 original size:21 final size:21
Alignment explanation
Indices: 1277652--1277730 Score: 131
Period size: 21 Copynumber: 3.8 Consensus size: 21
1277642 ACTAGTGGCA
1277652 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
* *
1277673 GGTGCATGGATACACTGTAGG
1 GGTGCATGGATGCACTGCAGG
*
1277694 GGTGCATGGATGCACTGCATG
1 GGTGCATGGATGCACTGCAGG
1277715 GGTGCATGGATGCACT
1 GGTGCATGGATGCACT
1277731 TTGACACCCT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.20, C:0.18, G:0.39, T:0.23
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAGG
Found at i:1277976 original size:21 final size:21
Alignment explanation
Indices: 1277952--1277991 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1277942 ATGTTTAATG
1277952 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
1277973 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
1277992 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:1279129 original size:19 final size:21
Alignment explanation
Indices: 1279093--1279140 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1279083 TCTAAATCCT
*
1279093 TTTTCAAAATTTCA-TTTTGC
1 TTTTCAAAATTCCATTTTTGC
1279113 TTTTCAAAA-TCCATTTTTGC
1 TTTTCAAAATTCCATTTTTGC
1279133 -TTTCAAAA
1 TTTTCAAAA
1279141 GAAAATTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.29, C:0.17, G:0.04, T:0.50
Consensus pattern (21 bp):
TTTTCAAAATTCCATTTTTGC
Found at i:1280480 original size:20 final size:20
Alignment explanation
Indices: 1280454--1280592 Score: 147
Period size: 21 Copynumber: 6.8 Consensus size: 20
1280444 TCAAAATGGA
1280454 GTGCATGGATGCACTGCAAG
1 GTGCATGGATGCACTGCAAG
*
1280474 CTGCATGGATGCACTGCAAG
1 GTGCATGGATGCACTGCAAG
* * *
1280494 CTGCATCGATGCAGTAGTGGC-AG
1 GTGCATGGATGC---ACT-GCAAG
* *
1280517 GTGCATAGATGCACTGCAGGG
1 GTGCATGGATGCACTGCA-AG
*
1280538 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCA-AG
1280559 GTGCATGGATGCACTGC-AG
1 GTGCATGGATGCACTGCAAG
1280578 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1280593 TTGACACCCT
Statistics
Matches: 104, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
19 18 0.17
20 32 0.31
21 38 0.37
23 14 0.13
24 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.36, T:0.21
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAAG
Found at i:1280969 original size:19 final size:20
Alignment explanation
Indices: 1280945--1280983 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1280935 ATTGAAGTTC
*
1280945 TACTTTTCTTTCA-TATTTT
1 TACTTTTCTCTCATTATTTT
1280964 TACTTTTCTCTCATTATTTT
1 TACTTTTCTCTCATTATTTT
1280984 CTTTTCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (20 bp):
TACTTTTCTCTCATTATTTT
Found at i:1281504 original size:20 final size:20
Alignment explanation
Indices: 1281475--1281513 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1281465 AAAGCCCATA
*
1281475 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1281495 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1281514 GTGGTGGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1294757 original size:3 final size:3
Alignment explanation
Indices: 1294751--1294828 Score: 65
Period size: 3 Copynumber: 26.7 Consensus size: 3
1294741 TTTATTATCG
* * * *
1294751 TTA TTA TTA TT- TTA TTTG TTA CTA TTA TTA TT- TTA TAA TCA -TA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1294794 TTA TTA TTA TT- TATA TTA TTA ATA TTA TTA TTA TT
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT
1294829 TACATTACAG
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
2 6 0.10
3 51 0.85
4 3 0.05
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1294776 original size:18 final size:20
Alignment explanation
Indices: 1294740--1294779 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
1294730 CATCCATTTG
*
1294740 TTTTATTATCGTTATTATTA
1 TTTTATTATCGTTACTATTA
1294760 TTTTATT-T-GTTACTATTA
1 TTTTATTATCGTTACTATTA
1294778 TT
1 TT
1294780 ATTTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 1 0.05
20 7 0.37
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTATTATCGTTACTATTA
Found at i:1295532 original size:16 final size:18
Alignment explanation
Indices: 1295499--1295533 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1295489 TCTCCGTTTT
1295499 AGAGAGAGAGAGAGAATG
1 AGAGAGAGAGAGAGAATG
1295517 AGAGAGA-AGAGA-AATG
1 AGAGAGAGAGAGAGAATG
1295533 A
1 A
1295534 AAATTTGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 5 0.29
18 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.40, T:0.06
Consensus pattern (18 bp):
AGAGAGAGAGAGAGAATG
Found at i:1297399 original size:16 final size:17
Alignment explanation
Indices: 1297356--1297399 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1297346 AATTTCTATT
1297356 TTATTTTATTTTAGTCA
1 TTATTTTATTTTAGTCA
* * *
1297373 TTAGTTAATTTT-GTTA
1 TTATTTTATTTTAGTCA
1297389 TTATTTTATTT
1 TTATTTTATTT
1297400 ATGAATATGA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (17 bp):
TTATTTTATTTTAGTCA
Found at i:1297566 original size:8 final size:8
Alignment explanation
Indices: 1297553--1297590 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
1297543 TATATGGGAT
1297553 ATAATATA
1 ATAATATA
1297561 ATAATATA
1 ATAATATA
1297569 ATAAT-TA
1 ATAATATA
1297576 ATTAA-ATA
1 A-TAATATA
1297584 ATAATAT
1 ATAATAT
1297591 TTATTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATAATATA
Found at i:1298127 original size:122 final size:123
Alignment explanation
Indices: 1297852--1298149 Score: 325
Period size: 122 Copynumber: 2.4 Consensus size: 123
1297842 AGGAAGTTCA
* *
1297852 TAATAAGAAGAACTCA-TCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
1 TAATAAGAAGAACTCACT-TGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTT
* * * * * *
1297916 TTGCTCGACTCTATCACAGAAGGAGATAGATCAACACCAACACTTCCAGAAAAAGTTCG
65 TTGCTCGACTCTATCACACAAGGAGATACAACAACACAAACACTTACAGAAAAAGATCG
* * **
1297975 TAATAAGAAGAACTTATCTT-AAGAGAAAGAAGAAGTTCATAATTTGAAGAACTTATTCAACCTT
1 TAATAAGAAGAACTCA-CTTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTT
* ** * ** * * **
1298039 TTGCTC-A-TTTCATTGCACATGGAGATACAACAGTATAAACATTTACAGAATGAGATCG
65 TTGCTCGACTCT-ATCACACAAGGAGATACAACAACACAAACACTTACAGAAAAAGATCG
* *
1298097 TAATAAAAAGAACTCACTTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACT
1 TAATAAGAAGAACTCACTTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACT
1298150 CATCCGAAGG
Statistics
Matches: 143, Mismatches: 28, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
121 5 0.03
122 76 0.53
123 60 0.42
124 1 0.01
125 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (123 bp):
TAATAAGAAGAACTCACTTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTT
TGCTCGACTCTATCACACAAGGAGATACAACAACACAAACACTTACAGAAAAAGATCG
Found at i:1299601 original size:4 final size:4
Alignment explanation
Indices: 1299592--1299616 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1299582 AATATAGTAC
1299592 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
1299617 GTTTTATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1299658 original size:8 final size:8
Alignment explanation
Indices: 1299645--1299683 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
1299635 TATATGGGAT
1299645 ATAATATA
1 ATAATATA
1299653 ATAATATA
1 ATAATATA
*
1299661 ATAATTTA
1 ATAATATA
1299669 ATTAA-ATA
1 A-TAATATA
1299677 ATAATAT
1 ATAATAT
1299684 TTATTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 3 0.11
8 21 0.78
9 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATAATATA
Found at i:1300225 original size:122 final size:123
Alignment explanation
Indices: 1299943--1300247 Score: 364
Period size: 122 Copynumber: 2.5 Consensus size: 123
1299933 TTTCCAGAGG
* * *
1299943 AAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTATTC
* * * * *
1300008 AACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAACACCAACACTTCCAGAAA
66 AACCTTTTGCTCGACTCTATCACACAAGGAGATACAACAACACAAACACTTACAGAAA
* * **
1300066 AAGTTCGTAATAAGAAGAACTTATCTGAAGAGAAAGAAGAAGTTCATAATTTGAAGAACTTATTC
1 AAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTATTC
* ** * ** * * *
1300131 AACCTTTTGCTC-A-TTTCATTGCACATGGAGATACAACAGTATAAACATTTACAGAAT
66 AACCTTTTGCTCGACTCT-ATCACACAAGGAGATACAACAACACAAACACTTACAGAAA
* *
1300188 GAGTTCGTAATAAGAAGAACTCA-CTTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACT
1 AAGTTCGTAATAAGAAGAACTCATC-TGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACT
1300248 CATCCGAAGG
Statistics
Matches: 153, Mismatches: 27, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
121 3 0.02
122 80 0.52
123 70 0.46
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (123 bp):
AAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTATTC
AACCTTTTGCTCGACTCTATCACACAAGGAGATACAACAACACAAACACTTACAGAAA
Found at i:1302325 original size:122 final size:123
Alignment explanation
Indices: 1302043--1302347 Score: 391
Period size: 122 Copynumber: 2.5 Consensus size: 123
1302033 TTTCCTGAGG
* * *
1302043 AAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTATTC
* * * *
1302108 AACCTTTTGCTCGATTCTATCACAGAAGGAGATAAATCAGCACCAATATTTCCAGAAA
66 AACCTTTTGCTCGATTCTATCACACAAGGAGATAAATCAGCACAAACATTTACAGAAA
* * **
1302166 AAGTTCGTAATAAGAAGAACTTATCTGAAGAGAAAGAAGAAGTTCATAATTTGAAGAACTTATTC
1 AAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTATTC
** * * * *
1302231 AACCTTTTGCTC-ATT-TCATTGCACATGGAGATACAA-CAGTATAAACATTTACAGAAT
66 AACCTTTTGCTCGATTCT-ATCACACAAGGAGATA-AATCAGCACAAACATTTACAGAAA
* * *
1302288 GAGTTCGTAATAAGAAGAACTCACCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACT
1 AAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACT
1302348 CATCTGAAGG
Statistics
Matches: 156, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
121 1 0.01
122 83 0.53
123 72 0.46
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (123 bp):
AAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTATTC
AACCTTTTGCTCGATTCTATCACACAAGGAGATAAATCAGCACAAACATTTACAGAAA
Found at i:1304020 original size:30 final size:31
Alignment explanation
Indices: 1303976--1304078 Score: 79
Period size: 31 Copynumber: 3.4 Consensus size: 31
1303966 AGACCCCTGT
* * *
1303976 AACTATCCAGAGGT-CATAAAGAACCTCGG-C
1 AACTGTCCATAGGTCCAT-AAGAACCTAGGTC
* *
1304006 AACTGTCCATAGGTCCCTAAGAACCTAGGTG
1 AACTGTCCATAGGTCCATAAGAACCTAGGTC
* * *
1304037 AACTGTCCATATGTTCC-TTAGAACATAGGT-
1 AACTGTCCATA-GGTCCATAAGAACCTAGGTC
1304067 ATACTGTCCATA
1 A-ACTGTCCATA
1304079 TGTCTCAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
30 23 0.38
31 34 0.56
32 4 0.07
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (31 bp):
AACTGTCCATAGGTCCATAAGAACCTAGGTC
Found at i:1304126 original size:32 final size:32
Alignment explanation
Indices: 1304006--1304132 Score: 118
Period size: 31 Copynumber: 4.0 Consensus size: 32
1303996 GAACCTCGGC
* * * *
1304006 AACTGTCCATA-GGTCCCTAAGAACCTAGGT-G
1 AACTGTCCATATGTTCCAT-AGAACATAGGTAA
*
1304037 AACTGTCCATATGTTCCTTAGAACATAGGT-A
1 AACTGTCCATATGTTCCATAGAACATAGGTAA
* * *
1304068 TACTGTCCATATGTCTCAAAAG-ACATAGGTAA
1 AACTGTCCATATGT-TCCATAGAACATAGGTAA
* *
1304100 AATTGTCCATATGTTCCGTAGAACATAGGTAA
1 AACTGTCCATATGTTCCATAGAACATAGGTAA
1304132 A
1 A
1304133 CCATCGACTC
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
31 46 0.58
32 33 0.42
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (32 bp):
AACTGTCCATATGTTCCATAGAACATAGGTAA
Found at i:1304854 original size:20 final size:20
Alignment explanation
Indices: 1304826--1304883 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
1304816 TTCCCATTGA
* *
1304826 AGTGTATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
1304846 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
1304869 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
1304884 CTACCATGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.47
22 1 0.03
23 3 0.09
24 13 0.41
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1305100 original size:20 final size:20
Alignment explanation
Indices: 1305072--1305114 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1305062 AATGTATTGT
*
1305072 TTAACCCCAAATTCTACTTA
1 TTAACCCCAAATTATACTTA
* **
1305092 TTAATCCCACCTTATACTTA
1 TTAACCCCAAATTATACTTA
1305112 TTA
1 TTA
1305115 TCATATTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAACCCCAAATTATACTTA
Found at i:1307732 original size:31 final size:31
Alignment explanation
Indices: 1307694--1307787 Score: 125
Period size: 31 Copynumber: 3.0 Consensus size: 31
1307684 ACCTCGACAG
* * * *
1307694 CTGTCCATAGGTCCCAAAGAACCTAGGTAAA
1 CTGTCCATATGTTCCATAGAACATAGGTAAA
* *
1307725 CTGTCCATATGTTCCTTAGAACATAGGTATA
1 CTGTCCATATGTTCCATAGAACATAGGTAAA
*
1307756 CTGTCTATATGTTCCATAGAACATAGGTAAA
1 CTGTCCATATGTTCCATAGAACATAGGTAAA
1307787 C
1 C
1307788 CCTCGACTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (31 bp):
CTGTCCATATGTTCCATAGAACATAGGTAAA
Found at i:1309945 original size:16 final size:17
Alignment explanation
Indices: 1309902--1309945 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1309892 AATTTCTATT
1309902 TTATTTTATTTTAGTCA
1 TTATTTTATTTTAGTCA
* * *
1309919 TTAGTTAATTTT-GTTA
1 TTATTTTATTTTAGTCA
1309935 TTATTTTATTT
1 TTATTTTATTT
1309946 ATGATTATGA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (17 bp):
TTATTTTATTTTAGTCA
Found at i:1311898 original size:35 final size:35
Alignment explanation
Indices: 1311854--1311928 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
1311844 AACAATCCTT
*
1311854 AATTTCATTCTAAACCCCAAATTCCAAAATAATTC
1 AATTTCATTCTAAACCCAAAATTCCAAAATAATTC
* *
1311889 AATTTCATTCTAAACCCAAAATTCTAAAATATTTC
1 AATTTCATTCTAAACCCAAAATTCCAAAATAATTC
1311924 AATTT
1 AATTT
1311929 AAGGTTTAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (35 bp):
AATTTCATTCTAAACCCAAAATTCCAAAATAATTC
Found at i:1312576 original size:40 final size:40
Alignment explanation
Indices: 1312521--1312600 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
1312511 TATAAAGAAG
1312521 AAATTGGGGGAAAGAGGGTTCCAACCAATACTATTTTGCA
1 AAATTGGGGGAAAGAGGGTTCCAACCAATACTATTTTGCA
1312561 AAATTGGGGGAAAGAGGGTTCCAACCAATACTATTTTGCA
1 AAATTGGGGGAAAGAGGGTTCCAACCAATACTATTTTGCA
1312601 GGCAGCCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (40 bp):
AAATTGGGGGAAAGAGGGTTCCAACCAATACTATTTTGCA
Found at i:1319273 original size:23 final size:23
Alignment explanation
Indices: 1319247--1319298 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
1319237 CAAATTTGGG
1319247 GGCACCGAAAGTGCACAATTAAT
1 GGCACCGAAAGTGCACAATTAAT
1319270 GGCACCGAAAGTGCACAATTAAT
1 GGCACCGAAAGTGCACAATTAAT
1319293 GGCACC
1 GGCACC
1319299 AAAAAGTAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (23 bp):
GGCACCGAAAGTGCACAATTAAT
Found at i:1322333 original size:24 final size:24
Alignment explanation
Indices: 1322303--1322358 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
1322293 TAGAAGTTCG
1322303 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
*
1322327 ATTGAAGCCTAAAATTTGAGCTTA
1 ATTGAAGCCTAAAATTTGAGCTCA
1322351 ATTGAAGC
1 ATTGAAGC
1322359 GAAAGAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:1328132 original size:24 final size:26
Alignment explanation
Indices: 1328105--1328153 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1328095 AGTTATTTTG
*
1328105 TTAAAATT-TTA-TTTAGAAAAATAT
1 TTAAAATTATTATTTTAAAAAAATAT
1328129 TTAAAATTATTATTTTAAAAAAATA
1 TTAAAATTATTATTTTAAAAAAATA
1328154 ATATTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.36
25 3 0.14
26 11 0.50
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
TTAAAATTATTATTTTAAAAAAATAT
Found at i:1328572 original size:19 final size:19
Alignment explanation
Indices: 1328551--1328594 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1328541 AAATATTAGT
1328551 TTTTTAAA-TAAATTTTAA
1 TTTTTAAATTAAATTTTAA
*
1328569 TTTTAAAATTAAATTTTAAA
1 TTTTTAAATTAAATTTT-AA
1328589 TTTTTA
1 TTTTTA
1328595 TATGCATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 8 0.36
20 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTTAAATTAAATTTTAA
Found at i:1328575 original size:13 final size:13
Alignment explanation
Indices: 1328559--1328592 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1328549 GTTTTTTAAA
1328559 TAAATTTTAATTT
1 TAAATTTTAATTT
* *
1328572 TAAAATTAAATTT
1 TAAATTTTAATTT
1328585 TAAATTTT
1 TAAATTTT
1328593 TATATGCATG
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATTTTAATTT
Found at i:1329395 original size:2 final size:2
Alignment explanation
Indices: 1329388--1329439 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1329378 GCTAATGGGC
1329388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1329430 AT AT AT AT AT
1 AT AT AT AT AT
1329440 GGTTGAAGTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1330927 original size:23 final size:23
Alignment explanation
Indices: 1330901--1330948 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1330891 ATAAAGTACA
*
1330901 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1330924 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1330947 AT
1 AT
1330949 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1331696 original size:18 final size:18
Alignment explanation
Indices: 1331673--1331709 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1331663 CGAAATATAT
1331673 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1331691 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1331709 A
1 A
1331710 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1331938 original size:23 final size:23
Alignment explanation
Indices: 1331912--1331975 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
1331902 ATGCGAGATA
1331912 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
* **
1331935 GATACATATTACA-TATATAAGG
1 GATACCTATTACATTATATAAAC
* *
1331957 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
1331976 GTTTACCTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 18 0.53
23 16 0.47
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:1332371 original size:22 final size:23
Alignment explanation
Indices: 1332340--1332401 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
1332330 ATATAACCAC
1332340 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1332363 TA-CTATTACATTATATAAAGGC
1 TACCTATTACATTATATAAACGA
*
1332385 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1332402 GTTTACCTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1332395 original size:23 final size:23
Alignment explanation
Indices: 1332330--1332401 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
1332320 ACACTTTACA
* *
1332330 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
1332353 ATATAAACGATA-CTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
1332375 ATATAAAGGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
1332398 ATAT
1 ATAT
1332402 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 20 0.48
23 22 0.52
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.35
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:1332799 original size:23 final size:23
Alignment explanation
Indices: 1332769--1332824 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
1332759 AACCACTACC
1332769 TACATTATATAAACGATACCTAT
1 TACATTATATAAACGATACCTAT
** *
1332792 TACATTATATAAGGGCTACCTAT
1 TACATTATATAAACGATACCTAT
*
1332815 TACATCATAT
1 TACATTATAT
1332825 GTTACCTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (23 bp):
TACATTATATAAACGATACCTAT
Found at i:1333170 original size:18 final size:19
Alignment explanation
Indices: 1333133--1333169 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1333123 TCCACAGTGA
* *
1333133 AAAAAGTATGGACACTTTT
1 AAAAAGGATAGACACTTTT
1333152 AAAAAGGATAGACACTTT
1 AAAAAGGATAGACACTTT
1333170 ACAATATAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (19 bp):
AAAAAGGATAGACACTTTT
Found at i:1333198 original size:21 final size:22
Alignment explanation
Indices: 1333173--1333224 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1333163 ACACTTTACA
*
1333173 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1333196 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1333219 ATATAA
1 ATATAA
1333225 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1333209 original size:23 final size:23
Alignment explanation
Indices: 1333183--1333245 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1333173 ATATAACCAC
1333183 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1333206 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1333229 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1333246 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1333628 original size:23 final size:23
Alignment explanation
Indices: 1333591--1333662 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
1333581 ACACTTTACA
*
1333591 ATAAACCACTACCTATTACATTAT
1 ATAAACGA-TACCTATTACATTAT
1333615 ATAAACGATACCTATTACATTAT
1 ATAAACGATACCTATTACATTAT
** * *
1333638 ATAAGGGCTACCTATTACATCAT
1 ATAAACGATACCTATTACATTAT
1333661 AT
1 AT
1333663 GTTTACCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 36 0.84
24 7 0.16
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (23 bp):
ATAAACGATACCTATTACATTAT
Found at i:1333695 original size:419 final size:427
Alignment explanation
Indices: 1331914--1334174 Score: 4001
Period size: 421 Copynumber: 5.4 Consensus size: 427
1331904 GCGAGATAGA
*
1331914 TACCTATTACATTATATAAACGATACATATTACA-TATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1331978 TTACCTATTATA-TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
1332042 TGTAATTTATGTTTCAATTTTTTTAACAGTG-TTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
1332106 ATTTCATTTGCAC-AAAAATTATTTGATTGTTTTTATA-TTTATATAAATATTATTTAGAATTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATA-AAATATTATTTAGAATTTT
1332169 TAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
260 TAATTTAATAAT-ATATATACCGT-A--TAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
1332234 TAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAGTATG
321 TAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATG
1332298 GACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
386 GACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
*
1332340 TACCTATTACATTATATAAACGATA-CTATTACATTATATAAAGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1332404 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAACTT
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTT-AAAACTT
1332469 ATGTAATTTATGTTTCAA-TTTTTTAACAGTG-TTCATGTTTTCCACCTACAATATTGATTTAAT
130 ATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAAT
1332532 AATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTT
195 AATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTT
1332597 TAATTTAATAATA-ATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
260 TAATTTAATAATATATATACCGT-A--TAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
1332661 AATATCTTAAAACTCACTC-AAAGATAACCTTAAATTAATG-TTTCCACAGTGAAAAAAGTATGG
322 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
1332724 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
387 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
1332765 TACC---TACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATG-
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1332826 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA-CGATAC-TTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
1332889 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
1332954 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATT-TTTAGAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
1333018 AATTTAATAATATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAA-T--TAAATTA
261 AATTTAATAATATATATACCGT-A--TAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
1333080 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGA
323 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGA
1333145 CAC-TTT-TAAAAAGGATAGACACTTTACAATATAACCAC
388 CACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
1333183 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1333248 TTACCTA-T-TATTGAAAGTGTCCATAC-TTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
1333310 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTT-ATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
1333374 ATTTCATTTGCAC-AAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAA-TTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
1333437 AATTTAATAATATATATA-CGT-TAAAAAATAAATCATTAGACGCCTATAATTACTAAATT-ATA
261 AATTTAATAATATATATACCGTATAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATA
1333499 TCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACAC
326 TCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACAC
1333564 TTTTATAAAAAGGATAGACACTTTACAATA-AACCAC
391 TTTTATAAAAAGGATAGACACTTTACAATATAACCAC
1333600 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
*
1333665 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCAATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
1333730 TGTAATTTA--TTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
1333793 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATA-TTTATAAAATATTATTTAGAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
**
1333857 AA-TTAAT-A-ATATATACCGTA-ACGTAAA-AAATCATTAGACGCCTATAATTACTAAATTAAT
261 AATTTAATAATATATATACCGTATA-AAAAATAAATCATTAGACGCCTATAATTACTAAATTAAT
1333917 ATCTTAAAACTCACTCAAAAGATAACCTTAAA-TAATGTTTT-CACAGTGAAAAAAGTATGGACA
325 ATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACA
1333980 CTTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
390 C-TTTTATAAAAAGGATAGACACTTTACAATATAACCAC
1334019 TACCTATTACATTATAT-AACGATACCTATTACA--ATATAAGGG-TACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1334080 TTACCTA-TATA-TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
1334143 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
1334175 ACTGCGAATT
Statistics
Matches: 1790, Mismatches: 7, Indels: 87
0.95 0.00 0.05
Matches are distributed among these distances:
413 60 0.03
414 32 0.02
415 48 0.03
416 77 0.04
417 117 0.07
418 230 0.13
419 243 0.14
420 192 0.11
421 265 0.15
422 68 0.04
423 37 0.02
424 11 0.01
425 84 0.05
426 136 0.08
427 104 0.06
428 80 0.04
429 6 0.00
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (427 bp):
TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
AATTTAATAATATATATACCGTATAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATA
TCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACAC
TTTTATAAAAAGGATAGACACTTTACAATATAACCAC
Found at i:1334057 original size:20 final size:20
Alignment explanation
Indices: 1334004--1334071 Score: 82
Period size: 20 Copynumber: 3.2 Consensus size: 20
1333994 GATAGACACT
*
1334004 TTACAATATAACCACTACCTA
1 TTACAATATAACGA-TACCTA
1334025 TTACATTATATAACGATACCTA
1 TTACA--ATATAACGATACCTA
* *
1334047 TTACAATATAAGGGTACCTA
1 TTACAATATAACGATACCTA
1334067 TTACA
1 TTACA
1334072 TCATATGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
20 18 0.43
21 5 0.12
22 11 0.26
23 8 0.19
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.32
Consensus pattern (20 bp):
TTACAATATAACGATACCTA
Found at i:1335183 original size:33 final size:33
Alignment explanation
Indices: 1335145--1335211 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1335135 ATAGACGCCT
1335145 ATAATTACTAAATTAATATCTTAAAACTCACTC
1 ATAATTACTAAATTAATATCTTAAAACTCACTC
1335178 ATAATTACTAAATTAATATCTTAAAACTCACTC
1 ATAATTACTAAATTAATATCTTAAAACTCACTC
1335211 A
1 A
1335212 AAAGATAACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (33 bp):
ATAATTACTAAATTAATATCTTAAAACTCACTC
Found at i:1336621 original size:33 final size:33
Alignment explanation
Indices: 1336575--1336640 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1336565 CCATCTTATA
*
1336575 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
1336608 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
1336641 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:1338470 original size:232 final size:230
Alignment explanation
Indices: 1338042--1338503 Score: 849
Period size: 232 Copynumber: 2.0 Consensus size: 230
1338032 AAGTACATAT
1338042 CCACCCTTTGGTTGCTTTCGAGTCTCGGCCTCAATTTCAAAGTCATCTGCTCCACCACAATTTCC
1 CCACCCTTTGGTTGCTTTCGAGTCTCGGCCTCAATTTCAAAGTCATCTGCTCCACCACAATTTCC
1338107 AACCCATTGACTCCATTTTTCCTTCATATATCAGTTTACGCAAATCAAATTATTGTGTTACATAC
66 AACCCATTGACTCCATTTTTCCTTCATATATCAGTTTACGCAAATCAAATTATTGTGTTACATAC
1338172 CTTTTCAATATAAAATATAGATAACTACTCTTGTGGTAAAACAGTTTTTCTTCAAAAGAATTTGA
131 CTTTTCAATATAAAATATAGATAACTACTCTTGTGGTAAAACAGTTTTTCTTCAAAAGAATTTGA
1338237 ATGGCCACACCAAAATGGTCGGCACATTTATACAACC
196 ATGGCCACACCAAAAT-GTCGGCACA-TTATACAACC
1338274 CCACCCTTTGGTTGCTTTCGAGTCTCGGCCTCAATTTCAAAGTCATCTGCTCCACCAACAATTTT
1 CCACCCTTTGGTTGCTTTCGAGTCTCGGCCTCAATTTCAAAGTCATCTGCTCCACC-ACAA-TTT
*
1338339 CCAACCCATTGACTCCATTTTTCCTTCATATATCAGTTTACGCAAATCAAATTATTTTGTTACAT
64 CCAACCCATTGACTCCATTTTTCCTTCATATATCAGTTTACGCAAATCAAATTATTGTGTTACAT
1338404 ACCTTTTCAATATACAAATATAGATAACTACTCTTGTGGTAAAAC-G-TTTTCTTC-AAAGAATT
129 ACCTTTTCAATATA-AAATATAGATAACTACTCTTGTGGTAAAACAGTTTTTCTTCAAAAGAATT
1338466 TGAATGGCCACACCAAAATGTCGGCACATTATACAACC
193 TGAATGGCCACACCAAAATGTCGGCACATTATACAACC
1338504 TAATATCATT
Statistics
Matches: 226, Mismatches: 1, Indels: 8
0.96 0.00 0.03
Matches are distributed among these distances:
230 10 0.04
231 9 0.04
232 83 0.37
233 12 0.05
234 82 0.36
235 30 0.13
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (230 bp):
CCACCCTTTGGTTGCTTTCGAGTCTCGGCCTCAATTTCAAAGTCATCTGCTCCACCACAATTTCC
AACCCATTGACTCCATTTTTCCTTCATATATCAGTTTACGCAAATCAAATTATTGTGTTACATAC
CTTTTCAATATAAAATATAGATAACTACTCTTGTGGTAAAACAGTTTTTCTTCAAAAGAATTTGA
ATGGCCACACCAAAATGTCGGCACATTATACAACC
Found at i:1338819 original size:24 final size:24
Alignment explanation
Indices: 1338782--1338834 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1338772 CCGTTCTATC
1338782 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
1338806 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
1338830 TATTT
1 TATTT
1338835 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:1339011 original size:19 final size:19
Alignment explanation
Indices: 1338987--1339031 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
1338977 TTTTACGTTT
1338987 TTTATCAT-TTTGATACCTG
1 TTTATCATATTT-ATACCTG
*
1339006 TTTATCATATTTTTACCTG
1 TTTATCATATTTATACCTG
1339025 TTATATC
1 TT-TATC
1339032 GTGTGGATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.16, G:0.07, T:0.56
Consensus pattern (19 bp):
TTTATCATATTTATACCTG
Found at i:1339184 original size:19 final size:20
Alignment explanation
Indices: 1339140--1339185 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 20
1339130 CACTTTTAAA
1339140 TTTACCGGTTTTAATCATTT
1 TTTACCGGTTTTAATCATTT
1339160 TGTTACC-GTTTT-ATCATATT
1 T-TTACCGGTTTTAATCAT-TT
1339180 TTTACC
1 TTTACC
1339186 TGGTATATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 10 0.42
20 9 0.38
21 5 0.21
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTAATCATTT
Found at i:1347954 original size:16 final size:16
Alignment explanation
Indices: 1347930--1347963 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1347920 TATCGCCGAC
*
1347930 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
1347946 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
1347962 CG
1 CG
1347964 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:1351323 original size:17 final size:17
Alignment explanation
Indices: 1351301--1351341 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
1351291 TTAGCTTTAA
1351301 GAACCCATCCAGGGGAG
1 GAACCCATCCAGGGGAG
1351318 GAACCCATCCAGGGGAG
1 GAACCCATCCAGGGGAG
1351335 GAACCCA
1 GAACCCA
1351342 GCAAGAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.32, C:0.32, G:0.32, T:0.05
Consensus pattern (17 bp):
GAACCCATCCAGGGGAG
Found at i:1352379 original size:28 final size:28
Alignment explanation
Indices: 1352322--1352379 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
1352312 AAGCATGGGA
*
1352322 CAAAGAAAAAGAAATTGAAATACTTAGT
1 CAAAGAAAAAGAAATTGAAATACCTAGT
*
1352350 CAAAGAAAAAGAAATTGAAATACCTGGT
1 CAAAGAAAAAGAAATTGAAATACCTAGT
1352378 CA
1 CA
1352380 GGGTCGGAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.55, C:0.10, G:0.16, T:0.19
Consensus pattern (28 bp):
CAAAGAAAAAGAAATTGAAATACCTAGT
Found at i:1354084 original size:27 final size:27
Alignment explanation
Indices: 1354054--1354114 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
1354044 AGGTTCCAGA
1354054 GAACTATTCACGATAGTGAAATAGTGG
1 GAACTATTCACGATAGTGAAATAGTGG
1354081 GAACTATTCACGATAGTGAAATAGTGG
1 GAACTATTCACGATAGTGAAATAGTGG
*
1354108 GAGCTAT
1 GAACTAT
1354115 CCGTAAACGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.26
Consensus pattern (27 bp):
GAACTATTCACGATAGTGAAATAGTGG
Found at i:1366804 original size:20 final size:21
Alignment explanation
Indices: 1366781--1366821 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1366771 TGAGAAATTG
1366781 TTTTT-AAAATAT-AAAAATGA
1 TTTTTCAAAAT-TGAAAAATGA
1366801 TTTTTCAAAATTGAAAAATGA
1 TTTTTCAAAATTGAAAAATGA
1366822 AAACAAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (21 bp):
TTTTTCAAAATTGAAAAATGA
Found at i:1370627 original size:20 final size:21
Alignment explanation
Indices: 1370602--1370683 Score: 71
Period size: 20 Copynumber: 3.9 Consensus size: 21
1370592 TTTTGGAGCA
*
1370602 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
**
1370622 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCAT
1370643 GAAGGGGAACCGATTCCCCCACA-
1 G-A-GGGAACCGATTCCCCC-CAT
* *
1370666 G-GGGAATCGATACCCCCC
1 GAGGGAACCGATTCCCCCC
1370684 TGGGGTTCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
19 1 0.02
20 24 0.47
21 8 0.16
22 1 0.02
23 17 0.33
ACGTcount: A:0.24, C:0.35, G:0.26, T:0.15
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:1378750 original size:2 final size:2
Alignment explanation
Indices: 1378745--1378771 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1378735 AAAATGATAG
1378745 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1378772 TACTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1386462 original size:20 final size:20
Alignment explanation
Indices: 1386437--1386486 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1386427 ACAACACTAA
1386437 AAATTCGCAACACATAAGTC
1 AAATTCGCAACACATAAGTC
*
1386457 AAATTCGAAACACATAAGTC
1 AAATTCGCAACACATAAGTC
1386477 AAATTCGCAA
1 AAATTCGCAA
1386487 AGCGCATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.48, C:0.22, G:0.10, T:0.20
Consensus pattern (20 bp):
AAATTCGCAACACATAAGTC
Found at i:1387053 original size:19 final size:19
Alignment explanation
Indices: 1387031--1387095 Score: 96
Period size: 19 Copynumber: 3.4 Consensus size: 19
1387021 AAATCGCAAC
1387031 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
*
1387050 GCGATTTTCATTTCACGTT
1 GCGATTTTCATTTCGCGTT
1387069 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
*
1387088 GCAATTTT
1 GCGATTTT
1387096 AAGTTTCAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
19 41 0.98
20 1 0.02
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:1388518 original size:21 final size:21
Alignment explanation
Indices: 1388492--1388536 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1388482 GATTTCTGGG
* *
1388492 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1388513 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1388534 CAA
1 CAA
1388537 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1390208 original size:13 final size:13
Alignment explanation
Indices: 1390190--1390230 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
1390180 TCTACGGGCA
1390190 CTACGGTGCAATT
1 CTACGGTGCAATT
1390203 CTACGG-GC-A--
1 CTACGGTGCAATT
1390212 CTACGGTGCAATT
1 CTACGGTGCAATT
1390225 CTACGG
1 CTACGG
1390231 GCACTTCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.25
10 2 0.08
11 2 0.08
12 2 0.08
13 12 0.50
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:1390251 original size:22 final size:22
Alignment explanation
Indices: 1390178--1390243 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
1390168 TATGGACATC
1390178 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
1390200 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
*
1390222 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTACGGTGCA
1390244 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.24
Consensus pattern (22 bp):
ATTCTACGGGCACTACGGTGCA
Found at i:1392359 original size:21 final size:21
Alignment explanation
Indices: 1392309--1392370 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
1392299 GATTCACCTG
* *
1392309 TCATCATTCAAGAGGCCTC-T
1 TCATCGTTCAAGAGGCCCCTT
* *
1392329 CCTATTGTTCAAGAGGCCCCTT
1 TC-ATCGTTCAAGAGGCCCCTT
*
1392351 TCATCGTTCAAGAGGTCCCT
1 TCATCGTTCAAGAGGCCCCT
1392371 CCCACCGTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 1 0.03
21 30 0.91
22 2 0.06
ACGTcount: A:0.21, C:0.31, G:0.18, T:0.31
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTT
Found at i:1392379 original size:21 final size:21
Alignment explanation
Indices: 1392315--1392385 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
1392305 CCTGTCATCA
* * **
1392315 TTCAAGAGGCCTCTCCTATTG
1 TTCAAGAGGCCCCTCCCACCG
** *
1392336 TTCAAGAGGCCCCTTTCATCG
1 TTCAAGAGGCCCCTCCCACCG
*
1392357 TTCAAGAGGTCCCTCCCACCG
1 TTCAAGAGGCCCCTCCCACCG
*
1392378 TTCGAGAG
1 TTCAAGAG
1392386 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.20, C:0.32, G:0.21, T:0.27
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCCACCG
Found at i:1393948 original size:21 final size:21
Alignment explanation
Indices: 1393906--1393948 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1393896 TTTCTAGGCT
* * *
1393906 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1393927 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1393948 A
1 A
1393949 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1394021 original size:23 final size:22
Alignment explanation
Indices: 1393977--1394021 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1393967 AATGTCATGG
*
1393977 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1393999 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1394022 AGAAAAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Done.