Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 29
Found at i:2865162 original size:17 final size:17
Alignment explanation
Indices: 2865128--2865165 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2865118 CGGGTCAACG
*
2865128 GGTCGGTCAACGATTCA
1 GGTCGGTCAACGAGTCA
*
2865145 GGTCGGTCAACGGGTCA
1 GGTCGGTCAACGAGTCA
2865162 GGTC
1 GGTC
2865166 AGACCGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.24, G:0.37, T:0.21
Consensus pattern (17 bp):
GGTCGGTCAACGAGTCA
Found at i:2871070 original size:29 final size:29
Alignment explanation
Indices: 2871036--2871185 Score: 203
Period size: 29 Copynumber: 5.2 Consensus size: 29
2871026 AAAAATTTCA
* *
2871036 AAAATGTCACCTTTTTCAAAATAATTCTC
1 AAAATGTCACCATTTTCAAAATAATTCCC
*
2871065 AGAATGTCACC-TTTTCAAAATAATTCCC
1 AAAATGTCACCATTTTCAAAATAATTCCC
** *
2871093 AAAATGTCACTTTTTTCAAAATATTTCCC
1 AAAATGTCACCATTTTCAAAATAATTCCC
*
2871122 AAAATGTCACCATTTTCAAAATATTTCCC
1 AAAATGTCACCATTTTCAAAATAATTCCC
** *
2871151 AAAATGTCATGATTTTCAAAATAATTCCA
1 AAAATGTCACCATTTTCAAAATAATTCCC
2871180 AAAATG
1 AAAATG
2871186 GCATTGGGTC
Statistics
Matches: 109, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
28 25 0.23
29 84 0.77
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAATGTCACCATTTTCAAAATAATTCCC
Found at i:2871219 original size:17 final size:17
Alignment explanation
Indices: 2871191--2871251 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
2871181 AAATGGCATT
2871191 GGGTCGGGTCAACGGTTC
1 GGGTC-GGTCAACGGTTC
*
2871209 GGGTCGGTCAACGGGTC
1 GGGTCGGTCAACGGTTC
* *
2871226 GGGTCAG--ACCGGTTC
1 GGGTCGGTCAACGGTTC
*
2871241 GGATCGGTCAA
1 GGGTCGGTCAA
2871252 ACCGGTTCAG
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
15 11 0.32
17 18 0.53
18 5 0.15
ACGTcount: A:0.15, C:0.23, G:0.43, T:0.20
Consensus pattern (17 bp):
GGGTCGGTCAACGGTTC
Found at i:2871248 original size:32 final size:30
Alignment explanation
Indices: 2871191--2871251 Score: 95
Period size: 32 Copynumber: 2.0 Consensus size: 30
2871181 AAATGGCATT
*
2871191 GGGTCGGGTCAACGGTTCGGGTCGGTCAAC
1 GGGTCGGGTCAACGGTTCGGATCGGTCAAC
2871221 GGGTCGGGTCAGACCGGTTCGGATCGGTCAA
1 GGGTCGGGTCA-A-CGGTTCGGATCGGTCAA
2871252 ACCGGTTCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 11 0.39
31 1 0.04
32 16 0.57
ACGTcount: A:0.15, C:0.23, G:0.43, T:0.20
Consensus pattern (30 bp):
GGGTCGGGTCAACGGTTCGGATCGGTCAAC
Found at i:2871267 original size:19 final size:19
Alignment explanation
Indices: 2871227--2871267 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2871217 CAACGGGTCG
* * *
2871227 GGTCAGACCGGTTCGGATC
1 GGTCAAACCGGTTCAGACC
2871246 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
2871265 GGT
1 GGT
2871268 TTGGACCGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.20
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:2871277 original size:29 final size:29
Alignment explanation
Indices: 2871229--2871286 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
2871219 ACGGGTCGGG
*
2871229 TCAGACCGGTTCGGATCGGTCAAACCGGT
1 TCAGACCGGTTCGGACCGGTCAAACCGGT
* *
2871258 TCAGACCGGTTTGGACCGGTCAAGCCGGT
1 TCAGACCGGTTCGGACCGGTCAAACCGGT
2871287 CAACCAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.19, C:0.28, G:0.33, T:0.21
Consensus pattern (29 bp):
TCAGACCGGTTCGGACCGGTCAAACCGGT
Found at i:2879445 original size:7 final size:7
Alignment explanation
Indices: 2879428--2879464 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
2879418 AAGGTGAAAT
2879428 TATTATAA
1 TATT-TAA
2879436 TATTTAA
1 TATTTAA
2879443 TATTTAA
1 TATTTAA
*
2879450 TAATTAA
1 TATTTAA
2879457 TATTTAA
1 TATTTAA
2879464 T
1 T
2879465 TTGTTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 23 0.85
8 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TATTTAA
Found at i:2879479 original size:21 final size:20
Alignment explanation
Indices: 2879434--2879501 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
2879424 AAATTATTAT
* *
2879434 AATATTTAATATTTAATAATT
1 AATATTTAAT-TTTTATAATA
2879455 AATATTTAATTTGTTATAATA
1 AATATTTAATTT-TTATAATA
* *
2879476 AATAATATTAATTATTATAGTA
1 AAT-AT-TTAATTTTTATAATA
2879498 AATA
1 AATA
2879502 AATATAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 2 0.05
21 20 0.50
22 12 0.30
23 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
AATATTTAATTTTTATAATA
Found at i:2879509 original size:22 final size:22
Alignment explanation
Indices: 2879432--2879502 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
2879422 TGAAATTATT
2879432 ATAATATTTAA-TATT-TAATAA
1 ATAATA-TTAATTATTATAATAA
* *
2879453 TTAATATTTAATTTGTTATAATAA
1 ATAATA-TTAA-TTATTATAATAA
*
2879477 ATAATATTAATTATTATAGTAA
1 ATAATATTAATTATTATAATAA
2879499 ATAA
1 ATAA
2879503 ATATAATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
21 10 0.24
22 14 0.33
23 7 0.17
24 11 0.26
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (22 bp):
ATAATATTAATTATTATAATAA
Found at i:2882749 original size:44 final size:44
Alignment explanation
Indices: 2882683--2882768 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
2882673 ATCAGAGAAT
* *
2882683 ATGTTATTATTTCCCTAATATGTCACTCATGTCCCTCAGGGGTC
1 ATGTTATCATTACCCTAATATGTCACTCATGTCCCTCAGGGGTC
* * *
2882727 ATGTTATCATTACCTTATTATGTCACTCATGTCCCTCGGGGG
1 ATGTTATCATTACCCTAATATGTCACTCATGTCCCTCAGGGG
2882769 CATTATTCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.38
Consensus pattern (44 bp):
ATGTTATCATTACCCTAATATGTCACTCATGTCCCTCAGGGGTC
Found at i:2885466 original size:2 final size:2
Alignment explanation
Indices: 2885459--2885490 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2885449 TATTTTGATA
2885459 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
2885491 TAAATTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2885723 original size:22 final size:21
Alignment explanation
Indices: 2885645--2885751 Score: 83
Period size: 22 Copynumber: 5.5 Consensus size: 21
2885635 AAATATTCTA
2885645 ATTTTAATGAATAATTAATA-T
1 ATTTTAAT-AATAATTAATATT
*
2885666 A-ATTAATAAT-ATT--TATT
1 ATTTTAATAATAATTAATATT
*
2885683 ATTTTAATAATATAGTAATATT
1 ATTTTAATAATA-ATTAATATT
2885705 ATTTTAATAAATAATTAATA-T
1 ATTTTAAT-AATAATTAATATT
*
2885726 AATTTAA-AAT-ATT--T-TT
1 ATTTTAATAATAATTAATATT
2885742 ATTTTAATAA
1 ATTTTAATAA
2885752 AAGATAATAG
Statistics
Matches: 71, Mismatches: 6, Indels: 22
0.72 0.06 0.22
Matches are distributed among these distances:
16 10 0.14
17 4 0.06
18 14 0.20
19 6 0.08
20 7 0.10
21 8 0.11
22 18 0.25
23 4 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTTTAATAATAATTAATATT
Found at i:2885871 original size:25 final size:25
Alignment explanation
Indices: 2885841--2885903 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 25
2885831 TTAATAATAT
2885841 TAAATAAATTATTTAATAGTTAAAAA
1 TAAATAAATTATTTAAT-GTTAAAAA
* *
2885867 T-AAT--ATTA-TTAATTTTACAAA
1 TAAATAAATTATTTAATGTTAAAAA
2885888 TAAATAATATTATTTA
1 TAAATAA-ATTATTTA
2885904 TTATATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
21 7 0.23
22 8 0.27
23 4 0.13
25 7 0.23
26 4 0.13
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
TAAATAAATTATTTAATGTTAAAAA
Found at i:2887276 original size:141 final size:144
Alignment explanation
Indices: 2887096--2887388 Score: 412
Period size: 141 Copynumber: 2.0 Consensus size: 144
2887086 AAACTATTTA
* * * * *
2887096 AATTATAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
1 AATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* *
2887161 AATTCAATTCGATTTG-ATTTAAA-TTTATAAACTCAAAT-AAAAAAATTTCGAGTCAACTATTT
66 AATTCAATTCAATTTGTATTTAAATTTTATAAACTAAAATCAAAAAAATTTCGAGTCAACTATTT
* *
2887223 TATAAACTTAAATG
131 CATAAACTGAAATG
*
2887237 AATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACATAAACTCAAA
1 AATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* *
2887302 AATTCAATTCAATTTGACTTTATTTAAATTTTATAAACTAAAATCGAAAAAATTTCGAGTCATCT
66 AATTCAATTCAATTTG----TATTTAAATTTTATAAACTAAAATCAAAAAAATTTCGAGTCAACT
*
2887367 ATTTCATAAACTGAATTG
127 ATTTCATAAACTGAAATG
2887385 AATT
1 AATT
2887389 TTTAGGTCCA
Statistics
Matches: 132, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
141 74 0.56
146 7 0.05
147 14 0.11
148 37 0.28
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (144 bp):
AATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
AATTCAATTCAATTTGTATTTAAATTTTATAAACTAAAATCAAAAAAATTTCGAGTCAACTATTT
CATAAACTGAAATG
Found at i:2887996 original size:60 final size:59
Alignment explanation
Indices: 2887902--2888089 Score: 195
Period size: 59 Copynumber: 3.2 Consensus size: 59
2887892 TTACGTCATA
* * * *
2887902 TATCCTCAAACTATAATTTTGATTTCAAACTAGTCCTTAAACTTTTAAATATTTTAATTT
1 TATCCTCAAACTATGA-TTTCATTTTAAATTAGTCCTTAAACTTTTAAATATTTTAATTT
* * *
2887962 TATCCTCAAACTATGACTTTCATTTTAAATTAGT-CTTTAACTTTTTAACATTTTAATTT
1 TATCCTCAAACTATGA-TTTCATTTTAAATTAGTCCTTAAACTTTTAAATATTTTAATTT
* * * *
2888021 TATCC-CTAAACTATGA-TCCATTTTCTAAATTAGTCC-CAAACTTTTGAATATTTCAATTT
1 TATCCTC-AAACTATGATTTCA-TTT-TAAATTAGTCCTTAAACTTTTAAATATTTTAATTT
*
2888080 CATCCTCAAA
1 TATCCTCAAA
2888090 TTTATCCAAA
Statistics
Matches: 108, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
57 3 0.03
58 4 0.04
59 70 0.65
60 31 0.29
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.45
Consensus pattern (59 bp):
TATCCTCAAACTATGATTTCATTTTAAATTAGTCCTTAAACTTTTAAATATTTTAATTT
Found at i:2888284 original size:60 final size:59
Alignment explanation
Indices: 2888175--2888309 Score: 157
Period size: 60 Copynumber: 2.3 Consensus size: 59
2888165 ATATATACAT
* *
2888175 ATAGTTTGGGATGAAATTGTAATGTTAAAAAATTTGGGGAATAATTTAGAATGA-AGGTC
1 ATAGTTTGGGATGAAATTGTAATGTTAAAAAATTTGAGGAATAAGTTAGAATGATA-GTC
* * * *
2888234 ATAGTTTGGGGATGAAATTG-ATCTGTTCAAAAGTTTGAGGACTAAGTTAGAATGATAGTC
1 ATAGTTT-GGGATGAAATTGTA-ATGTTAAAAAATTTGAGGAATAAGTTAGAATGATAGTC
*
2888294 ATAATTTAGGGATGAA
1 ATAGTTT-GGGATGAA
2888310 TTAGAACATT
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
59 8 0.12
60 56 0.86
61 1 0.02
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (59 bp):
ATAGTTTGGGATGAAATTGTAATGTTAAAAAATTTGAGGAATAAGTTAGAATGATAGTC
Found at i:2892112 original size:21 final size:22
Alignment explanation
Indices: 2892066--2892116 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2892056 GATAAATTAT
2892066 TATAAATT-TTAAAAGATAAAA
1 TATAAATTATTAAAAGATAAAA
2892087 T-TAAATTATTAATAA-A-AAAA
1 TATAAATTATTAA-AAGATAAAA
2892107 TATAAATTAT
1 TATAAATTAT
2892117 ATGAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 11 0.41
21 14 0.52
22 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
TATAAATTATTAAAAGATAAAA
Found at i:2894041 original size:2 final size:2
Alignment explanation
Indices: 2894034--2894058 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2894024 ACATACATAC
2894034 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 A
2894059 ATTGTCATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2904938 original size:13 final size:13
Alignment explanation
Indices: 2904922--2904946 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2904912 ACCGTTAACT
2904922 TTGACTTTGACAG
1 TTGACTTTGACAG
2904935 TTGACTTTGACA
1 TTGACTTTGACA
2904947 AAAAAAAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGACTTTGACAG
Found at i:2905971 original size:185 final size:185
Alignment explanation
Indices: 2905642--2906018 Score: 630
Period size: 185 Copynumber: 2.0 Consensus size: 185
2905632 ATAAAATTTT
* * *
2905642 AAATTTTAAATATATTATATATAACATATGAGCTCAACTCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAAAATATTATATATAACATATGAGCTCAACCCAAACCATTTAAAACCCAATTAATAA
*
2905707 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
* * *
2905772 TTATTTTTTAATTATATATTTTTTAAATTAATTGTAAACTGTTTTTATGAATTA-A
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTT-TGAATTATA
* * * *
2905827 AAATATTAAAAATATTATATATAACATATGGGTTCAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAAAATATTATATATAACATATGAGCTCAACCCAAACCATTTAAAACCCAATTAATAA
2905892 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
*
2905957 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTAATTATA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTGAATTATA
2906012 AAATATT
1 AAATATT
2906019 TAATTTTTAT
Statistics
Matches: 179, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
184 6 0.03
185 173 0.97
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (185 bp):
AAATATTAAAAATATTATATATAACATATGAGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTGAATTATA
Found at i:2916427 original size:20 final size:20
Alignment explanation
Indices: 2916402--2916440 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2916392 TTTATTGTTG
2916402 AATGGAACCATTCAGCATTT
1 AATGGAACCATTCAGCATTT
**
2916422 AATGGAACTGTTCAGCATT
1 AATGGAACCATTCAGCATT
2916441 CAGTGTGTTT
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:0.18, G:0.18, T:0.31
Consensus pattern (20 bp):
AATGGAACCATTCAGCATTT
Found at i:2928202 original size:15 final size:16
Alignment explanation
Indices: 2928176--2928205 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2928166 GGGAATAAAA
2928176 GATTACCTGGGAATAG
1 GATTACCTGGGAATAG
2928192 GATTA-CTGGGAATA
1 GATTACCTGGGAATA
2928206 TTACATTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (16 bp):
GATTACCTGGGAATAG
Found at i:2928363 original size:15 final size:15
Alignment explanation
Indices: 2928345--2928375 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2928335 AAATTCTAAA
2928345 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
2928360 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
2928375 T
1 T
2928376 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:2932377 original size:2 final size:2
Alignment explanation
Indices: 2932370--2932395 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2932360 AAATTAAGTA
2932370 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
2932396 GTTTATAAGT
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:2944698 original size:23 final size:23
Alignment explanation
Indices: 2944627--2944710 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 23
2944617 TTGATTCGTA
**
2944627 TTCATTTAATGTTGGTAAACATG
1 TTCATTTAATGTTCATAAACATG
** * * * *
2944650 TTTGTTTATTTATTCATGAACGTG
1 TTCATTTA-ATGTTCATAAACATG
2944674 TTCATTTAATGTTCATAAACATG
1 TTCATTTAATGTTCATAAACATG
* *
2944697 TTCGTTTAACGTTC
1 TTCATTTAATGTTC
2944711 GTTTTGTGTT
Statistics
Matches: 44, Mismatches: 16, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
23 29 0.66
24 15 0.34
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (23 bp):
TTCATTTAATGTTCATAAACATG
Found at i:2944723 original size:22 final size:22
Alignment explanation
Indices: 2944695--2944736 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2944685 TTCATAAACA
2944695 TGTTCGTTTAACGTTCGTTTTG
1 TGTTCGTTTAACGTTCGTTTTG
* *
2944717 TGTTCGTTTATCGTTTGTTT
1 TGTTCGTTTAACGTTCGTTT
2944737 ATATGTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.07, C:0.12, G:0.21, T:0.60
Consensus pattern (22 bp):
TGTTCGTTTAACGTTCGTTTTG
Found at i:2950790 original size:53 final size:53
Alignment explanation
Indices: 2950727--2950833 Score: 169
Period size: 53 Copynumber: 2.0 Consensus size: 53
2950717 GGAGATAAAA
* *
2950727 TGATAAGGATATACAATTAAACTGAGAAAGTCAAAGGAGAAAATCAAGGGATT
1 TGATAAGGATATACAATCAAACTGAGAAAGTCAAAGGAGAAAATCAAGAGATT
** *
2950780 TGATAAGGATATACAATCAAGTTGAGAAAGTCAAATGAGAAAATCAAGAGATT
1 TGATAAGGATATACAATCAAACTGAGAAAGTCAAAGGAGAAAATCAAGAGATT
2950833 T
1 T
2950834 TCACGTTTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.22
Consensus pattern (53 bp):
TGATAAGGATATACAATCAAACTGAGAAAGTCAAAGGAGAAAATCAAGAGATT
Found at i:2952027 original size:20 final size:20
Alignment explanation
Indices: 2951881--2952017 Score: 256
Period size: 20 Copynumber: 6.8 Consensus size: 20
2951871 TTTTCTGACT
2951881 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
2951901 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
2951921 ATCGTAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
2951941 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
2951961 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
2951981 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
2952001 ATCGCAATGCGATTATG
1 ATCGCAATGCGAATATG
2952018 ACTATCGCAA
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 114 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:2952061 original size:20 final size:20
Alignment explanation
Indices: 2952002--2952064 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
2951992 AATATGTAAA
* *
2952002 TCGCAATGCGATTATGACTA
1 TCGCAACGCGATTATGACTG
*
2952022 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTATGACTG
2952042 TCGCAACGCGATTATGACTG
1 TCGCAACGCGATTATGACTG
2952062 TCG
1 TCG
2952065 TAACACTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTG
Found at i:2952921 original size:24 final size:24
Alignment explanation
Indices: 2952889--2952942 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2952879 GTATTCGAAA
2952889 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2952913 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2952937 TTTGAT
1 TTTGAT
2952943 GATGTTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2953125 original size:3 final size:3
Alignment explanation
Indices: 2953117--2953149 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2953107 ATATAACCCT
2953117 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2953150 TAAATCCCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2955229 original size:6 final size:6
Alignment explanation
Indices: 2955218--2955257 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
2955208 AGAAAAAGGC
**
2955218 AATCAA AATCAA AATCAA AATCAA AATCGT AATCAA AATC
1 AATCAA AATCAA AATCAA AATCAA AATCAA AATCAA AATC
2955258 CCAATCACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.60, C:0.17, G:0.03, T:0.20
Consensus pattern (6 bp):
AATCAA
Found at i:2955581 original size:140 final size:140
Alignment explanation
Indices: 2955324--2955593 Score: 504
Period size: 140 Copynumber: 1.9 Consensus size: 140
2955314 AAACGTTGTA
*
2955324 TTATATGTAAATTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATATGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
2955389 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCAAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCAAATTTGACTAT
2955454 TATGTGTATT
131 TATGTGTATT
*
2955464 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATATGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
2955529 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCAAATTTGACTAT
2955594 CGTAACTCAA
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 126 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATATGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCAAATTTGACTAT
TATGTGTATT
Found at i:2955638 original size:46 final size:46
Alignment explanation
Indices: 2955571--2955661 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
2955561 TTCATTTGAA
* * * *
2955571 TATCGCAACGCGAATTTGACTATCGTAACTCAAAAATCGCAACGCC
1 TATCGCAACACGAATATGACTATCGCAACGCAAAAATCGCAACGCC
2955617 TATCGCAACACGAATATGACTATCGCAACGCAAAAATCGCAACGC
1 TATCGCAACACGAATATGACTATCGCAACGCAAAAATCGCAACGC
2955662 GAATTTGACT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.37, C:0.29, G:0.15, T:0.19
Consensus pattern (46 bp):
TATCGCAACACGAATATGACTATCGCAACGCAAAAATCGCAACGCC
Found at i:2955665 original size:34 final size:34
Alignment explanation
Indices: 2955618--2955684 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
2955608 CGCAACGCCT
2955618 ATCGCAACACGAATATGACTATCGCAACGCAAAA
1 ATCGCAACACGAATATGACTATCGCAACGCAAAA
* *
2955652 ATCGCAACGCGAATTTGACTATCGCAACGCAAA
1 ATCGCAACACGAATATGACTATCGCAACGCAAA
2955685 TTTGATTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.40, C:0.27, G:0.16, T:0.16
Consensus pattern (34 bp):
ATCGCAACACGAATATGACTATCGCAACGCAAAA
Found at i:2955677 original size:20 final size:20
Alignment explanation
Indices: 2955616--2955814 Score: 136
Period size: 20 Copynumber: 10.6 Consensus size: 20
2955606 ATCGCAACGC
* *
2955616 CTATCGCAACACGAATATGA
1 CTATCGCAACGCGAATTTGA
2955636 CTATCGCAACGC-AA----A
1 CTATCGCAACGCGAATTTGA
*
2955651 -AATCGCAACGCGAATTTGA
1 CTATCGCAACGCGAATTTGA
*
2955670 CTATCGCAACGCAAATTTGA
1 CTATCGCAACGCGAATTTGA
* * * *
2955690 TTATCGCGATG-GCTATTTGA
1 CTATCGCAACGCG-AATTTGA
* *
2955710 CTAGCGCAACGAGAA----A
1 CTATCGCAACGCGAATTTGA
*
2955726 --ATCGCAACACGAATTTGA
1 CTATCGCAACGCGAATTTGA
*
2955744 CTATCGCAACGCAAATTTGA
1 CTATCGCAACGCGAATTTGA
*
2955764 GTATCGCAACGCGAATTTGA
1 CTATCGCAACGCGAATTTGA
* * * * *
2955784 TTATCGCAATGGGTATTTAA
1 CTATCGCAACGCGAATTTGA
2955804 CTATCGCAACG
1 CTATCGCAACG
2955815 AGAAAATCAC
Statistics
Matches: 137, Mismatches: 28, Indels: 28
0.71 0.15 0.15
Matches are distributed among these distances:
14 20 0.15
15 3 0.02
16 1 0.01
18 1 0.01
19 3 0.02
20 108 0.79
21 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (20 bp):
CTATCGCAACGCGAATTTGA
Found at i:2955769 original size:94 final size:94
Alignment explanation
Indices: 2955652--2955863 Score: 302
Period size: 94 Copynumber: 2.3 Consensus size: 94
2955642 CAACGCAAAA
* *
2955652 ATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGATTATCGCGATGGCTATTTGACTAGCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGATTATCGCAATGGCTATTTAACTAGCGC
* *
2955717 AACGAGAAAATCGCAACA-CGAATTTGACT
66 AACGAGAAAATCACAA-AGCGAATTAGACT
* * * * *
2955746 ATCGCAACGCAAATTTGAGTATCGCAACGCGAATTTGATTATCGCAATGGGTATTTAACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGATTATCGCAATGGCTATTTAACTAGCGC
*
2955811 AACGAGAAAATCACAAAGCGTATTAGACT
66 AACGAGAAAATCACAAAGCGAATTAGACT
*
2955840 ATCGCAACGCGAA-TTGACTTTCGC
1 ATCGCAACGCGAATTTGACTATCGC
2955864 GTTGTGATTT
Statistics
Matches: 104, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
93 10 0.10
94 94 0.90
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (94 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGATTATCGCAATGGCTATTTAACTAGCGC
AACGAGAAAATCACAAAGCGAATTAGACT
Found at i:2955782 original size:74 final size:74
Alignment explanation
Indices: 2955617--2955792 Score: 239
Period size: 74 Copynumber: 2.4 Consensus size: 74
2955607 TCGCAACGCC
* * *
2955617 TATCGCAACACGAATATGACTATCGCAACGCAAAAATCGCAACGCGAATTTGACTATCGCAACGC
1 TATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACACGAATTTGACTATCGCAACGC
*
2955682 AAATTTGAT
66 AAATTTGAG
* * * *
2955691 TATCGCGATG-GCTATTTGACTAGCGCAACG-AGAAAATCGCAACACGAATTTGACTATCGCAAC
1 TATCGCAACGCG-AATTTGACTATCGCAACGCA-AAAATCGCAACACGAATTTGACTATCGCAAC
2955754 GCAAATTTGAG
64 GCAAATTTGAG
*
2955765 TATCGCAACGCGAATTTGATTATCGCAA
1 TATCGCAACGCGAATTTGACTATCGCAA
2955793 TGGGTATTTA
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
73 2 0.02
74 83 0.97
75 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (74 bp):
TATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACACGAATTTGACTATCGCAACGC
AAATTTGAG
Found at i:2955809 original size:40 final size:40
Alignment explanation
Indices: 2955571--2955814 Score: 145
Period size: 40 Copynumber: 6.2 Consensus size: 40
2955561 TTCATTTGAA
* * **
2955571 TATCGCAACGCGAATTTGACTATCGTAACTCAAAAATCGCAACGCC
1 TATCGCAACGCGAATTTGACTATCGCAACGC--AAAT-TTAA---C
* *
2955617 TATCGCAACACGAATATGACTATCGCAACGC-AA---AA-
1 TATCGCAACGCGAATTTGACTATCGCAACGCAAATTTAAC
* *
2955652 -ATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGAT
1 TATCGCAACGCGAATTTGACTATCGCAACGCAAATTTAAC
* * * * *
2955691 TATCGCGATG-GCTATTTGACTAGCGCAACG-AGA---AA-
1 TATCGCAACGCG-AATTTGACTATCGCAACGCAAATTTAAC
* * *
2955726 -ATCGCAACACGAATTTGACTATCGCAACGCAAATTTGAG
1 TATCGCAACGCGAATTTGACTATCGCAACGCAAATTTAAC
* * ***
2955765 TATCGCAACGCGAATTTGATTATCGCAATGGGTATTTAAC
1 TATCGCAACGCGAATTTGACTATCGCAACGCAAATTTAAC
2955805 TATCGCAACG
1 TATCGCAACG
2955815 AGAAAATCAC
Statistics
Matches: 156, Mismatches: 28, Indels: 34
0.72 0.13 0.16
Matches are distributed among these distances:
34 50 0.32
35 5 0.03
36 1 0.01
38 2 0.01
39 5 0.03
40 64 0.41
43 2 0.01
46 27 0.17
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (40 bp):
TATCGCAACGCGAATTTGACTATCGCAACGCAAATTTAAC
Found at i:2955882 original size:20 final size:20
Alignment explanation
Indices: 2955857--2955895 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2955847 CGCGAATTGA
* *
2955857 CTTTCGCGTTGTGATTTTGT
1 CTTTCGCATTGCGATTTTGT
2955877 CTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
2955896 AGTTTAGTGT
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:0.08, C:0.18, G:0.23, T:0.51
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGT
Found at i:2956069 original size:14 final size:14
Alignment explanation
Indices: 2956009--2956070 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
2955999 CACAAATAAG
*
2956009 AATTATTTACACATC
1 AATT-TTTACAAATC
**
2956024 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
2956039 AACTTTTACAAATC
1 AATTTTTACAAATC
*
2956053 AATTTTTATAAATC
1 AATTTTTACAAATC
2956067 AATT
1 AATT
2956071 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:2957560 original size:42 final size:42
Alignment explanation
Indices: 2957481--2957571 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 42
2957471 CCTCTTCAAT
* * *
2957481 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
2957523 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAT
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
2957565 GATGACA
1 GATGACA
2957572 TGTGAGTCGG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 37 0.93
43 3 0.08
ACGTcount: A:0.23, C:0.16, G:0.38, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:2958082 original size:18 final size:19
Alignment explanation
Indices: 2958059--2958103 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
2958049 GAAACTTAAA
2958059 ATCGCAACACG-AATGACT
1 ATCGCAACACGAAATGACT
*
2958077 ATCGCAACGCGAAAATGACT
1 ATCGCAACACG-AAATGACT
2958097 ATCGCAA
1 ATCGCAA
2958104 TGAGAGAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 10 0.42
20 14 0.58
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.16
Consensus pattern (19 bp):
ATCGCAACACGAAATGACT
Found at i:2960108 original size:20 final size:20
Alignment explanation
Indices: 2960085--2960191 Score: 119
Period size: 20 Copynumber: 5.5 Consensus size: 20
2960075 TCTGAAACTT
*
2960085 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
*
2960105 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** **
2960125 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
**
2960145 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
*
2960164 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
2960183 AAAATCGCA
1 AAAATCGCA
2960192 TTGCGATTCT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
19 24 0.32
20 52 0.68
ACGTcount: A:0.46, C:0.23, G:0.17, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:2960595 original size:22 final size:22
Alignment explanation
Indices: 2960556--2960619 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
2960546 TCTGAGAGAT
2960556 GGAGATA--GACGGATTTCGCC
1 GGAGATAGGGACGGATTTCGCC
* *
2960576 GGAGATAGGGACTGATTTCGTC
1 GGAGATAGGGACGGATTTCGCC
* *
2960598 GGAGATGGGGACGGATGTCGCC
1 GGAGATAGGGACGGATTTCGCC
2960620 TTAGAGAGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
20 7 0.19
22 29 0.81
ACGTcount: A:0.22, C:0.17, G:0.41, T:0.20
Consensus pattern (22 bp):
GGAGATAGGGACGGATTTCGCC
Found at i:2960845 original size:20 final size:20
Alignment explanation
Indices: 2960785--2960862 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
2960775 AAGCTTTGAA
*
2960785 AATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAT
*
2960805 AATCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAT
*
2960825 AATCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAT
* *
2960845 ATTTGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
2960863 GGAAAATAGC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAT
Found at i:2970979 original size:27 final size:27
Alignment explanation
Indices: 2970930--2970988 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
2970920 AGAGGTGTAT
2970930 AAAAAATCCGAATATCCGATTTTGCGCA
1 AAAAAATCCGAATATCCGATTTTG-GCA
* *
2970958 AAAAATATCCGAA-A-CCGGTTTTGGGA
1 AAAAA-ATCCGAATATCCGATTTTGGCA
2970984 AAAAA
1 AAAAA
2970989 CGGTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 7 0.25
27 8 0.29
28 6 0.21
29 7 0.25
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (27 bp):
AAAAAATCCGAATATCCGATTTTGGCA
Found at i:2971329 original size:22 final size:21
Alignment explanation
Indices: 2971290--2971331 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2971280 AGTGAAAAAA
**
2971290 CCGGATCAATTTTTATCCGAT
1 CCGGATCAATTTAAATCCGAT
2971311 CCGGATCGAATTTAAATCCGA
1 CCGGATC-AATTTAAATCCGA
2971332 CTATTTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (21 bp):
CCGGATCAATTTAAATCCGAT
Found at i:2980780 original size:27 final size:27
Alignment explanation
Indices: 2980739--2980794 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
2980729 TTACGAAATC
* *
2980739 AATCTCTATTCTATTTTATT-TGAATTT
1 AATCCCTATTCTATTTCATTAT-AATTT
*
2980766 AATCCCTATTTTATTTCATTATAATTT
1 AATCCCTATTCTATTTCATTATAATTT
2980793 AA
1 AA
2980795 CCTCTTGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.30, C:0.12, G:0.02, T:0.55
Consensus pattern (27 bp):
AATCCCTATTCTATTTCATTATAATTT
Found at i:2983092 original size:34 final size:34
Alignment explanation
Indices: 2983027--2983092 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
2983017 TATAATTGAA
* * **
2983027 TTTCTAAAATTGATTTTTCAAATAAGTAATTAAT
1 TTTCTAAAATTAATTTTTCAAAAAACAAATTAAT
* *
2983061 TTTCTGAAATTAATTTTTTAAAAAACAAATTA
1 TTTCTAAAATTAATTTTTCAAAAAACAAATTA
2983093 CAACTAAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (34 bp):
TTTCTAAAATTAATTTTTCAAAAAACAAATTAAT
Found at i:2997689 original size:17 final size:16
Alignment explanation
Indices: 2997662--2997693 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2997652 TTAATTGTCT
2997662 GATTTAATTATAATTG
1 GATTTAATTATAATTG
2997678 GATTTAAATTATAATT
1 GATTT-AATTATAATT
2997694 TAATCCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
GATTTAATTATAATTG
Found at i:3005584 original size:16 final size:17
Alignment explanation
Indices: 3005557--3005591 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
3005547 TATCGCCGAC
3005557 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
3005574 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
3005590 CG
1 CG
3005592 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:3011839 original size:21 final size:20
Alignment explanation
Indices: 3011801--3011839 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3011791 TTTCCTAAAA
*
3011801 ATAATGAAGTATATATTTTT
1 ATAATCAAGTATATATTTTT
*
3011821 ATAATCAAGATATTTATTT
1 ATAATCAAG-TATATATTT
3011840 ATTTTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (20 bp):
ATAATCAAGTATATATTTTT
Found at i:3011962 original size:2 final size:2
Alignment explanation
Indices: 3011955--3011986 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3011945 AAATAAAACA
3011955 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
3011987 TGGTTTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3012131 original size:25 final size:25
Alignment explanation
Indices: 3012094--3012146 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
3012084 TTTCCTAAGA
*
3012094 AAATAATTTAAATAAAACA-AAATT
1 AAATAATATAAATAAAACATAAATT
* *
3012118 AAATATATATAAATATAACATATATT
1 AAATA-ATATAAATAAAACATAAATT
3012144 AAA
1 AAA
3012147 ATAAAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.21
25 12 0.50
26 7 0.29
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (25 bp):
AAATAATATAAATAAAACATAAATT
Found at i:3012499 original size:26 final size:27
Alignment explanation
Indices: 3012447--3012500 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
3012437 TATCTTATCC
3012447 TAATATATATATATATAAATAACTAAAAA
1 TAATATATATATATATAAAT-A-TAAAAA
3012476 TAAT-TATATATATACTAAAT-TAAAA
1 TAATATATATATATA-TAAATATAAAA
3012501 TAAACAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 5 0.21
28 10 0.42
29 9 0.38
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (27 bp):
TAATATATATATATATAAATATAAAAA
Found at i:3013816 original size:3 final size:3
Alignment explanation
Indices: 3013808--3013880 Score: 58
Period size: 3 Copynumber: 24.3 Consensus size: 3
3013798 TGTATTTATT
* * * *
3013808 TAA TAA TAA TAA TAAA TAA TTA TAA TAT TAA TAT TTA -AA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* ** *
3013853 TAA TAA TAG TAA TTT TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3013881 TTAAGTAATT
Statistics
Matches: 52, Mismatches: 16, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
2 1 0.02
3 48 0.92
4 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:3013883 original size:39 final size:36
Alignment explanation
Indices: 3013804--3013889 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 36
3013794 TATTTGTATT
* *
3013804 TATTT-AATAATAATAATAAATAATTATAATATTAA
1 TATTTAAATAATAATAATAAATAATTATAAAAATAA
*
3013839 TATTTAAATAATAATAATAATAGTAATTTTAAAAATAA
1 TATTTAAATAATAATAATAA-A-TAATTATAAAAATAA
*
3013877 TAATTTAAGTAAT
1 T-ATTTAAATAAT
3013890 TTAAGTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 5 0.12
36 14 0.33
37 1 0.02
38 13 0.30
39 10 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (36 bp):
TATTTAAATAATAATAATAAATAATTATAAAAATAA
Found at i:3013891 original size:24 final size:25
Alignment explanation
Indices: 3013822--3013880 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 25
3013812 AATAATAATA
* *
3013822 AATAATTATAATATTAATATTTAAAT
1 AATAATAATAATAGTAAT-TTTAAAT
3013848 AATAATAATAATAGTAATTTTAAA-
1 AATAATAATAATAGTAATTTTAAAT
3013872 AATAATAAT
1 AATAATAAT
3013881 TTAAGTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 9 0.29
25 6 0.19
26 16 0.52
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
AATAATAATAATAGTAATTTTAAAT
Found at i:3014182 original size:45 final size:45
Alignment explanation
Indices: 3014119--3014267 Score: 217
Period size: 45 Copynumber: 3.3 Consensus size: 45
3014109 CGAAGGCTTT
* * *
3014119 TTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACTCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGG
*
3014164 TTTTGAAAGCATCATGCACTGAAGGTCTTATGGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGG
* * **
3014209 TTTTGAAAACATCATGCACTTAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGG
*
3014254 TTTTGAAAATATCA
1 TTTTGAAAACATCA
3014268 AAAAACTCCC
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 94 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGG
Found at i:3014316 original size:121 final size:121
Alignment explanation
Indices: 3014164--3014388 Score: 360
Period size: 121 Copynumber: 1.9 Consensus size: 121
3014154 GACTCGAAGG
*
3014164 TTTTGAAAGCATCATGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACT
* *
3014229 TAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAACTCCCGAAGGCT
66 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAACTCCCGAAGGCT
* * * *
3014285 TTTTGAAAACATCCTGCACTGCATGTCTTATGGATGACTCGAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACT
* **
3014350 GAAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCA
66 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
3014389 TGCACTGAAG
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
121 94 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (121 bp):
TTTTGAAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACT
GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAACTCCCGAAGGCT
Found at i:3014335 original size:76 final size:74
Alignment explanation
Indices: 3014201--3014343 Score: 187
Period size: 76 Copynumber: 1.9 Consensus size: 74
3014191 TTATGGATGA
* *
3014201 CCCGAAGGTTTTGAAAACATCATGCACTTAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATAT
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACAT
3014266 CAAAAAACT
66 CAAAAAACT
* * * * ** *
3014275 CCCGAAGGCTTTTTGAAAACATCCTGCACTGCATGTCTTATGGATGACTCGAAGGTTTTGAAAAC
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
3014340 ATCA
64 ATCA
3014344 TGCACTGAAG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
74 8 0.14
76 50 0.86
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (74 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACAT
CAAAAAACT
Found at i:3014345 original size:166 final size:166
Alignment explanation
Indices: 3014050--3014554 Score: 836
Period size: 166 Copynumber: 3.0 Consensus size: 166
3014040 GAAGTCCTAT
* *
3014050 CATCTTGCAC-TATAGGTCTTACAGATGACTCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAG
1 CATCATGCACTTA-AGGGCTTACAGATGACTCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAG
*
3014114 GCTTTTTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACTCGAAGGTTTTGAAAGCATCAT
65 GC--TTTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACTCGAAGGTTTTGAAAACATCAT
3014179 GCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAA
128 GCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAA
* *
3014218 CATCATGCACTTAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAACTCCCGAAGG
1 CATCATGCACTTAAGGGCTTACAGATGACTCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGG
*
3014283 CTTTTTGAAAACATCCTGCACTGCATGTCTTATGGATGACTCGAAGGTTTTGAAAACATCATGCA
66 CTTTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACTCGAAGGTTTTGAAAACATCATGCA
3014348 CTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAA
131 CTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAA
*
3014384 CATCATGCACTGAAGGGCTTACAGATGACTCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGG
1 CATCATGCACTTAAGGGCTTACAGATGACTCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGG
* *
3014449 CTTTTTGAAAATATCCTGCACTGCAGGCCTTATGGATGAC-CTGAAGGTTTTGAAAACATCATGC
66 CTTTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACTC-GAAGGTTTTGAAAACATCATGC
* **
3014513 ACTGAAGGGCTTACAGATGACCCGAAGGTTTT-AAAA
130 ACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAA
3014549 CTATCA
1 C-ATCA
3014555 AAAAGCTCTC
Statistics
Matches: 319, Mismatches: 15, Indels: 8
0.93 0.04 0.02
Matches are distributed among these distances:
165 6 0.02
166 252 0.79
168 59 0.18
169 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (166 bp):
CATCATGCACTTAAGGGCTTACAGATGACTCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGG
CTTTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACTCGAAGGTTTTGAAAACATCATGCA
CTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAA
Found at i:3014348 original size:45 final size:45
Alignment explanation
Indices: 3014285--3014433 Score: 226
Period size: 45 Copynumber: 3.3 Consensus size: 45
3014275 CCCGAAGGCT
* * *
3014285 TTTTGAAAACATCCTGCACTGCATGTCTTATGGATGACTCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGTCTTATGGATGACTCGAAGG
*
3014330 TTTTGAAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGTCTTATGGATGACTCGAAGG
* **
3014375 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACTCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGTCTTATGGATGACTCGAAGG
*
3014420 TTTTGAAAATATCA
1 TTTTGAAAACATCA
3014434 AAAAGCTCCC
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 95 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGTCTTATGGATGACTCGAAGG
Found at i:3014455 original size:121 final size:121
Alignment explanation
Indices: 3014330--3014630 Score: 478
Period size: 121 Copynumber: 2.5 Consensus size: 121
3014320 GACTCGAAGG
*
3014330 TTTTGAAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACT
* *
3014395 GAAGGGCTTACAGATGACTCGAAGGTTTTGAAAA-TATCAAAAAGCTCCCGAAGGCT
66 GAAGGGCTTACAGATGACCCGAAGGTTTT-AAAACTATCAAAAAGCTCCCAAAGGCT
* * * *
3014451 TTTTGAAAATATCCTGCACTGCAGGCCTTATGGATGACCTGAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACT
* *
3014516 GAAGGGCTTACAGATGACCCGAAGGTTTTAAAACTATCAAAAAGCTCTCAAAGGTT
66 GAAGGGCTTACAGATGACCCGAAGGTTTTAAAACTATCAAAAAGCTCCCAAAGGCT
* * *
3014572 TTTTGAAAACATCCTGCACTGTAGATCTTATGGATGACCCGAAGGTTTTGAAAATATCA
1 TTTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCA
3014631 AAAAGCTCCC
Statistics
Matches: 164, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
120 4 0.02
121 160 0.98
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (121 bp):
TTTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACT
GAAGGGCTTACAGATGACCCGAAGGTTTTAAAACTATCAAAAAGCTCCCAAAGGCT
Found at i:3014501 original size:76 final size:74
Alignment explanation
Indices: 3014367--3014509 Score: 189
Period size: 76 Copynumber: 1.9 Consensus size: 74
3014357 TTATGGATGA
* *
3014367 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACTCGAAGGTTTTGAAAATAT
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGCCTTACAGATGACTCGAAGGTTTTGAAAACAT
3014432 CAAAAAGCT
66 CAAAAAGCT
* * * **
3014441 CCCGAAGGCTTTTTGAAAATATCCTGCACTGCAGGCCTTATGGATGAC-CTGAAGGTTTTGAAAA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGCCTTACAGATGACTC-GAAGGTTTTGAAAA
3014505 CATCA
63 CATCA
3014510 TGCACTGAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
74 8 0.14
75 1 0.02
76 50 0.85
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (74 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGCCTTACAGATGACTCGAAGGTTTTGAAAACAT
CAAAAAGCT
Found at i:3014514 original size:45 final size:45
Alignment explanation
Indices: 3014441--3014554 Score: 131
Period size: 45 Copynumber: 2.5 Consensus size: 45
3014431 TCAAAAAGCT
* * * **
3014441 CCCGAAGGCTTTTTGAAAATATCCTGCACTGCAGGCCTTATGGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGCCTTACAGATGA
* *
3014488 CCTGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGCCTTACAGATGA
3014533 CCCGAAGGTTTT-AAAACTATCA
1 CCCGAAGGTTTTGAAAAC-ATCA
3014555 AAAAGCTCTC
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 5 0.09
45 46 0.79
47 7 0.12
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGCCTTACAGATGA
Found at i:3014576 original size:76 final size:76
Alignment explanation
Indices: 3014496--3014858 Score: 557
Period size: 76 Copynumber: 4.8 Consensus size: 76
3014486 GACCTGAAGG
* * * **
3014496 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTT-AAAACTATCAAAAAG
1 TTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAA-TATCAAAAAG
* * *
3014560 CTCTCAAAGGTT
65 CTCCCGAAGGCT
* *
3014572 TTTTGAAAACATCCTGCACTGTAGATCTTATGGATGACCCGAAGGTTTTGAAAATATCAAAAAGC
1 TTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAATATCAAAAAGC
3014637 TCCCGAAGGCT
66 TCCCGAAGGCT
3014648 TTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAATATCAAAAAGC
1 TTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAATATCAAAAAGC
3014713 TCCCGAAGGCT
66 TCCCGAAGGCT
* * *
3014724 TTTTGAAAACATCCTGCACTGCGGGTCTTATGGATAACCCAAAGGTTTTGAAAATATCAAAAAGC
1 TTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAATATCAAAAAGC
*
3014789 TACCGAAGGCT
66 TCCCGAAGGCT
* * *
3014800 TTTTGAAAGCATCCTGCACTGCAGGTCTTATGGATGATCCGAAGGTTTTGAAAACATCA
1 TTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAATATCA
3014859 TGCACTGAAG
Statistics
Matches: 265, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
76 261 0.98
77 4 0.02
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (76 bp):
TTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAATATCAAAAAGC
TCCCGAAGGCT
Found at i:3014775 original size:197 final size:194
Alignment explanation
Indices: 3014330--3014782 Score: 459
Period size: 197 Copynumber: 2.3 Consensus size: 194
3014320 GACTCGAAGG
* * *
3014330 TTTTGAAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCCTGCACTGAAGGTCTTATGGATAACCCAAAGGTTTTGAAAACATCATGCACT
* *
3014395 GAAGGGCTTACAGATGACTCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
66 GAAGAGCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
* * * *
3014460 TATCCTGCACTGCAGGCCTTATGGATGACCTGAAGGTTTTGAAAACATCATGCACTGAAGGGCT
131 CATCCTGCACTGCAGGCCTTATGGATGACCCGAAGGTTTTGAAAACATCAAGCACCGAAGGGCT
*** ** * * * ** ** *
3014524 TACAGATGAC--CC-GAAGGTTTTAA-AAC-TATCAAAAAGCTCTCAAAGGTTTTTTGAAAACAT
1 TTTTGAAAACATCCTGCA---CTGAAGGTCTTATGGATAA-C-C-CAAAGG--TTTTGAAAACAT
* * * **
3014584 CCTGCACTGTAGATCTTATGGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCTT
58 CATGCACTGAAGAGCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCTT
* *
3014649 TTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAATATCAAAAAGCT
123 TTTGAAAACATCCTGCACTGCAGGCCTTATGGATGACCCGAAGGTTTTGAAAACATC---AAGC-
*
3014714 CCCGAA-GGCT
184 ACCGAAGGGCT
** *
3014724 TTTTGAAAACATCCTGCACTGCGGGTCTTATGGATAACCCAAAGGTTTTGAAAATATCA
1 TTTTGAAAACATCCTGCACTGAAGGTCTTATGGATAACCCAAAGGTTTTGAAAACATCA
3014783 AAAAGCTACC
Statistics
Matches: 195, Mismatches: 47, Indels: 31
0.71 0.17 0.11
Matches are distributed among these distances:
191 2 0.01
192 6 0.03
193 2 0.01
194 9 0.05
195 5 0.03
197 135 0.69
199 6 0.03
200 14 0.07
201 6 0.03
202 8 0.04
203 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (194 bp):
TTTTGAAAACATCCTGCACTGAAGGTCTTATGGATAACCCAAAGGTTTTGAAAACATCATGCACT
GAAGAGCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
CATCCTGCACTGCAGGCCTTATGGATGACCCGAAGGTTTTGAAAACATCAAGCACCGAAGGGCT
Found at i:3016978 original size:73 final size:74
Alignment explanation
Indices: 3016893--3017058 Score: 210
Period size: 75 Copynumber: 2.2 Consensus size: 74
3016883 ATATGGATCA
* * * *
3016893 TCAGCATTCCCCAACATTGGCTAATACAAACGTTCCGAAT-GTCAATATT-ATAATTTCTGATTG
1 TCAGCATGCCCCAACATTGGCTAATACAAACGTTCCAAATAATCAACATTCATAA-TTCTGATTG
3016956 AAATGGGCTT
65 AAATGGGCTT
* * * *
3016966 TCAGCATGCCCCAACATTGGTTAATACAATCGTTCCAAATACATCAACATTCCTGATTCTGATTG
1 TCAGCATGCCCCAACATTGGCTAATACAAACGTTCCAAATA-ATCAACATTCATAATTCTGATTG
3017031 AAATGGGCTT
65 AAATGGGCTT
* *
3017041 TCAGCATGCTCCATCATT
1 TCAGCATGCCCCAACATT
3017059 TGCTTCTTGT
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
73 36 0.45
75 42 0.52
76 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (74 bp):
TCAGCATGCCCCAACATTGGCTAATACAAACGTTCCAAATAATCAACATTCATAATTCTGATTGA
AATGGGCTT
Found at i:3023627 original size:13 final size:13
Alignment explanation
Indices: 3023611--3023676 Score: 105
Period size: 13 Copynumber: 5.1 Consensus size: 13
3023601 AACCTCGCAT
*
3023611 AAAAAGAACAAGA
1 AAAAAGAAAAAGA
*
3023624 AAAAAGAAGAAGA
1 AAAAAGAAAAAGA
*
3023637 AAAAAGAAGAAGA
1 AAAAAGAAAAAGA
3023650 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
3023663 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
3023676 A
1 A
3023677 GAAATAGAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:3023640 original size:26 final size:26
Alignment explanation
Indices: 3023611--3023686 Score: 107
Period size: 26 Copynumber: 2.8 Consensus size: 26
3023601 AACCTCGCAT
*
3023611 AAAAAGAACAAGAAAAAAGAAGAAGA
1 AAAAAGAAAAAGAAAAAAGAAGAAGA
* *
3023637 AAAAAGAAGAAGAAAAAAGAAAAAGA
1 AAAAAGAAAAAGAAAAAAGAAGAAGA
3023663 AAAAAGAAAAAGAAGAAATAGAAG
1 AAAAAGAAAAAGAA-AAA-AGAAG
3023687 TTATAAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 37 0.84
27 3 0.07
28 4 0.09
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.01
Consensus pattern (26 bp):
AAAAAGAAAAAGAAAAAAGAAGAAGA
Found at i:3027346 original size:18 final size:18
Alignment explanation
Indices: 3027323--3027381 Score: 104
Period size: 17 Copynumber: 3.4 Consensus size: 18
3027313 TCTTGATTCA
3027323 TTTTTTTCCTTTTTTTCC
1 TTTTTTTCCTTTTTTTCC
3027341 TTTTTTTCCTTTTTTTCC
1 TTTTTTTCCTTTTTTTCC
3027359 -TTTTTTCCTTTTTTT-C
1 TTTTTTTCCTTTTTTTCC
3027375 TTTTTTT
1 TTTTTTT
3027382 TTATGGATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
16 1 0.03
17 21 0.52
18 18 0.45
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTTTCCTTTTTTTCC
Found at i:3027382 original size:9 final size:9
Alignment explanation
Indices: 3027323--3027381 Score: 104
Period size: 9 Copynumber: 6.8 Consensus size: 9
3027313 TCTTGATTCA
3027323 TTTTTTTCC
1 TTTTTTTCC
3027332 TTTTTTTCC
1 TTTTTTTCC
3027341 TTTTTTTCC
1 TTTTTTTCC
3027350 TTTTTTTCC
1 TTTTTTTCC
3027359 -TTTTTTCC
1 TTTTTTTCC
3027367 TTTTTTT-C
1 TTTTTTTCC
3027375 TTTTTTT
1 TTTTTTT
3027382 TTATGGATGA
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
8 16 0.33
9 33 0.67
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTCC
Found at i:3027671 original size:2 final size:2
Alignment explanation
Indices: 3027664--3027700 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3027654 ACAACAAGGG
3027664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3027701 ATTTGAAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3028432 original size:61 final size:61
Alignment explanation
Indices: 3028355--3028477 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
3028345 CAAAAGACAA
3028355 GTTCAAACAAGATACTGAAAATAGAAAGTACTACAGTGGTAGATAACAGTTCCACTTGTTT
1 GTTCAAACAAGATACTGAAAATAGAAAGTACTACAGTGGTAGATAACAGTTCCACTTGTTT
3028416 GTTCAAACAAGATACTGAAAATAGAAAGTACTACAGTGGTAGATAACAGTTCCACTTGTTT
1 GTTCAAACAAGATACTGAAAATAGAAAGTACTACAGTGGTAGATAACAGTTCCACTTGTTT
3028477 G
1 G
3028478 CATCATTACT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (61 bp):
GTTCAAACAAGATACTGAAAATAGAAAGTACTACAGTGGTAGATAACAGTTCCACTTGTTT
Found at i:3030047 original size:60 final size:60
Alignment explanation
Indices: 3029954--3030070 Score: 234
Period size: 60 Copynumber: 1.9 Consensus size: 60
3029944 TATAACAGAT
3029954 TTCATTGAACACAAAAGTTTCTGTGCATCAAACAAAACTTTTACATGTAGGGGACATCAC
1 TTCATTGAACACAAAAGTTTCTGTGCATCAAACAAAACTTTTACATGTAGGGGACATCAC
3030014 TTCATTGAACACAAAAGTTTCTGTGCATCAAACAAAACTTTTACATGTAGGGGACAT
1 TTCATTGAACACAAAAGTTTCTGTGCATCAAACAAAACTTTTACATGTAGGGGACAT
3030071 TTTTCACTCC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (60 bp):
TTCATTGAACACAAAAGTTTCTGTGCATCAAACAAAACTTTTACATGTAGGGGACATCAC
Found at i:3032564 original size:16 final size:16
Alignment explanation
Indices: 3032545--3032577 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3032535 AAGTAATGTG
3032545 GATAAAAAATGATTTT
1 GATAAAAAATGATTTT
3032561 GATAAAAAATGATTTT
1 GATAAAAAATGATTTT
3032577 G
1 G
3032578 GAGTCGCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (16 bp):
GATAAAAAATGATTTT
Found at i:3035034 original size:3 final size:3
Alignment explanation
Indices: 3035026--3035110 Score: 64
Period size: 3 Copynumber: 28.3 Consensus size: 3
3035016 TGTATTTATT
* * * * *
3035026 TAA TAA TAA TAA TAAA TAA TTA TAA TAA TAT TAT TAA TAT TAA TAT
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * ** *
3035072 TTA -AA TAA TAA TAA TAA TAG TAA TTT TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3035111 TTAAGTAATT
Statistics
Matches: 62, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
2 1 0.02
3 58 0.94
4 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:3035121 original size:24 final size:25
Alignment explanation
Indices: 3035027--3035110 Score: 95
Period size: 26 Copynumber: 3.5 Consensus size: 25
3035017 GTATTTATTT
*
3035027 AATAATAATAATAA-A-TAATTAT-
1 AATAATAATAATAATAGTAATTTTA
* * *
3035049 AATAATATTATTAATATTAATATTTA
1 AATAATAATAATAATAGTAAT-TTTA
3035075 AATAATAATAATAATAGTAATTTTA
1 AATAATAATAATAATAGTAATTTTA
3035100 AA-AATAATAAT
1 AATAATAATAAT
3035111 TTAAGTAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
22 12 0.23
23 1 0.02
24 13 0.25
25 8 0.15
26 18 0.35
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (25 bp):
AATAATAATAATAATAGTAATTTTA
Found at i:3036457 original size:2 final size:2
Alignment explanation
Indices: 3036450--3036485 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3036440 TGCAACAATA
3036450 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
3036486 TAAATATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3043266 original size:7 final size:7
Alignment explanation
Indices: 3043256--3043317 Score: 70
Period size: 7 Copynumber: 8.9 Consensus size: 7
3043246 TGGATTTAGA
*
3043256 GTTTAGG
1 GTTTATG
*
3043263 GTTTAGG
1 GTTTATG
*
3043270 GTTTATA
1 GTTTATG
3043277 GTTTATG
1 GTTTATG
*
3043284 GTTTATA
1 GTTTATG
3043291 GTTTATG
1 GTTTATG
3043298 GTTTATG
1 GTTTATG
* *
3043305 ATTTAGG
1 GTTTATG
3043312 GTTTAT
1 GTTTAT
3043318 TGCAAAGATA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.19, C:0.00, G:0.27, T:0.53
Consensus pattern (7 bp):
GTTTATG
Found at i:3043279 original size:21 final size:21
Alignment explanation
Indices: 3043250--3043317 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
3043240 CATAATTGGA
* *
3043250 TTTAGAGTTTAGGGTTTAGGG
1 TTTATAGTTTATGGTTTAGGG
**
3043271 TTTATAGTTTATGGTTTATAG
1 TTTATAGTTTATGGTTTAGGG
* *
3043292 TTTATGGTTTATGATTTAGGG
1 TTTATAGTTTATGGTTTAGGG
3043313 TTTAT
1 TTTAT
3043318 TGCAAAGATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (21 bp):
TTTATAGTTTATGGTTTAGGG
Found at i:3043393 original size:21 final size:21
Alignment explanation
Indices: 3043364--3043426 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
3043354 ATAAGGTAAG
*
3043364 TATAATTTAGGATTTAGGGTT
1 TATAGTTTAGGATTTAGGGTT
*
3043385 TATAGTTTAAGG-TTTAGGATT
1 TATAGTTT-AGGATTTAGGGTT
3043406 TA-AGGTTTAGGATTTAGGGTT
1 TATA-GTTTAGGATTTAGGGTT
3043427 CATTACAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 4 0.11
21 29 0.81
22 3 0.08
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (21 bp):
TATAGTTTAGGATTTAGGGTT
Found at i:3043407 original size:14 final size:14
Alignment explanation
Indices: 3043369--3043426 Score: 73
Period size: 14 Copynumber: 4.1 Consensus size: 14
3043359 GTAAGTATAA
*
3043369 TTTAGGATTTAGGG
1 TTTAGGATTTAAGG
*
3043383 TTTA-TAGTTTAAGG
1 TTTAGGA-TTTAAGG
3043397 TTTAGGATTTAAGG
1 TTTAGGATTTAAGG
*
3043411 TTTAGGATTTAGGG
1 TTTAGGATTTAAGG
3043425 TT
1 TT
3043427 CATTACAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
13 1 0.03
14 36 0.95
15 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (14 bp):
TTTAGGATTTAAGG
Found at i:3043491 original size:11 final size:11
Alignment explanation
Indices: 3043475--3043536 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
3043465 ATTATACAAA
3043475 TTTTAATATAT
1 TTTTAATATAT
3043486 TTTTAA-AT-T
1 TTTTAATATAT
3043495 TTTT-ATA-AT
1 TTTTAATATAT
* *
3043504 TATCAATAGTGTAT
1 TTTTAATA---TAT
3043518 TTTTAATATAT
1 TTTTAATATAT
3043529 TTTTAATA
1 TTTTAATA
3043537 ATGTAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
8 1 0.03
9 9 0.22
10 5 0.12
11 17 0.43
14 8 0.20
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (11 bp):
TTTTAATATAT
Found at i:3057014 original size:40 final size:40
Alignment explanation
Indices: 3056865--3057140 Score: 176
Period size: 40 Copynumber: 6.8 Consensus size: 40
3056855 TAGAGGGATT
* * *
3056865 TTTAGTGGCGTTTTTTGAATAAACGCCGGTAAATACTCATAC
1 TTTAGCGGCG-TTTTTGTATAAACGCCGCTAAATACT-ATAC
* * * * *
3056907 TTTAGTGGCGTTTTTATATAAATGCCGCTCAATACTATAA
1 TTTAGCGGCGTTTTTGTATAAACGCCGCTAAATACTATAC
* ** * *
3056947 TTTAGTGGCGTTTTCATATAAATGCCGCTAATTACTATAC
1 TTTAGCGGCGTTTTTGTATAAACGCCGCTAAATACTATAC
* * * *
3056987 TTTAGCGGCATTTTTGTACAAACGCCGCTAAAAACTCGTAC
1 TTTAGCGGCGTTTTTGTATAAACGCCGCTAAATACT-ATAC
* * * * * ** **
3057028 TCTAGCGGCATTTTAAGAAAAAACGCCGCTAAAGGCCCCTAC
1 TTTAGCGGCGTTTT-TGTATAAACGCCGCTAAA-TACTATAC
* * ** **
3057070 -ATAGTGGCGTTTTCATATAAACGCCGCTAGTTACTATAC
1 TTTAGCGGCGTTTTTGTATAAACGCCGCTAAATACTATAC
* ** *
3057109 TTTAGCAGCGTTTTTGTGCAAACGCCACTAAA
1 TTTAGCGGCGTTTTTGTATAAACGCCGCTAAA
3057141 AGCTCTTATT
Statistics
Matches: 180, Mismatches: 50, Indels: 10
0.75 0.21 0.04
Matches are distributed among these distances:
39 4 0.02
40 100 0.56
41 47 0.26
42 28 0.16
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTGTATAAACGCCGCTAAATACTATAC
Found at i:3058746 original size:31 final size:31
Alignment explanation
Indices: 3058708--3058832 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
3058698 CCCGAAGGAC
* * *
3058708 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
3058739 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
3058770 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
3058801 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
3058832 C
1 C
3058833 CCTCGACCCT
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:3059443 original size:19 final size:19
Alignment explanation
Indices: 3059419--3059455 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3059409 TTTCATTTAG
3059419 GGGGAATCGATACCCCCTA
1 GGGGAATCGATACCCCCTA
3059438 GGGGAATCGATACCCCCT
1 GGGGAATCGATACCCCCT
3059456 GAACATACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.32, G:0.27, T:0.16
Consensus pattern (19 bp):
GGGGAATCGATACCCCCTA
Found at i:3063265 original size:31 final size:31
Alignment explanation
Indices: 3063229--3063353 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
3063219 CCCGAAGGAC
* * * *
3063229 CAGTCCATA-GATTCCGAAGAACCTAGATAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
3063260 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
3063291 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
3063322 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
3063353 C
1 C
3063354 CCTCGACCCT
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:3073631 original size:23 final size:23
Alignment explanation
Indices: 3073594--3073655 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
3073584 GACACTCAAA
* * *
3073594 CTCGATTGAAACTCGATTTTGAG
1 CTCGATTCAAGCTCGACTTTGAG
3073617 CTCGATTCAAGCTCGACTTTGAG
1 CTCGATTCAAGCTCGACTTTGAG
*
3073640 CTTGATTCAAGCTCGA
1 CTCGATTCAAGCTCGA
3073656 AGACGGGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (23 bp):
CTCGATTCAAGCTCGACTTTGAG
Found at i:3075468 original size:20 final size:22
Alignment explanation
Indices: 3075443--3075490 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
3075433 AAGTCATTGG
*
3075443 TTTAATTCTA-ATTT-TGTAAA
1 TTTAATTCTACATTTACGTAAA
*
3075463 TTTAATTTTACATTTACGTAAA
1 TTTAATTCTACATTTACGTAAA
3075485 TTTAAT
1 TTTAAT
3075491 CATCATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.38
21 4 0.17
22 11 0.46
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTAATTCTACATTTACGTAAA
Found at i:3082448 original size:24 final size:23
Alignment explanation
Indices: 3082405--3082459 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 23
3082395 TAAGTTTTTT
*
3082405 TGTTCGTTTATTGTGTTCGTTTA
1 TGTTCGTTCATTGTGTTCGTTTA
3082428 TGTTCGTTCATTCGTGTTCGTTTA
1 TGTTCGTTCATT-GTGTTCGTTTA
3082452 TGTTCGTT
1 TGTTCGTT
3082460 TATTATTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.07, C:0.13, G:0.22, T:0.58
Consensus pattern (23 bp):
TGTTCGTTCATTGTGTTCGTTTA
Found at i:3090719 original size:22 final size:22
Alignment explanation
Indices: 3090694--3090762 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
3090684 GGTCATACAT
3090694 GACATATATAGCAGTCATTCGG
1 GACATATATAGCAGTCATTCGG
*
3090716 GACATATATAGCAGTCCTTCGG
1 GACATATATAGCAGTCATTCGG
* *
3090738 GACATATATAACAGTCTTTCGG
1 GACATATATAGCAGTCATTCGG
3090760 GAC
1 GAC
3090763 GAATACTGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (22 bp):
GACATATATAGCAGTCATTCGG
Found at i:3093110 original size:32 final size:29
Alignment explanation
Indices: 3093027--3093118 Score: 76
Period size: 31 Copynumber: 2.9 Consensus size: 29
3093017 GTTTAGGAGG
** *
3093027 TTAATTTAATTTTTTTTAAAATTTAGAAGT
1 TTAATTTAA-TTTTTAAAAAATTTAAAAGT
*
3093057 TTAAATTAAGATTTTTAAAAAATTTAAAGAGT
1 TT-AATTTA-ATTTTTAAAAAATTTAAA-AGT
*
3093089 TTAATTTATATTTTTCCAAAAAAATTAAAA
1 TTAATTTA-ATTTTT--AAAAAATTTAAAA
3093119 TCTAACTATA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
30 2 0.04
31 30 0.60
32 7 0.14
33 11 0.22
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (29 bp):
TTAATTTAATTTTTAAAAAATTTAAAAGT
Found at i:3093251 original size:26 final size:25
Alignment explanation
Indices: 3093215--3093267 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
3093205 GAATGATTAA
*
3093215 AATATAAAATA-AGTAAATAATTGTTC
1 AATAAAAAATATA-TAAAT-ATTGTTC
*
3093241 AATAAAAAATATATAAATTTTGTTC
1 AATAAAAAATATATAAATATTGTTC
3093266 AA
1 AA
3093268 AAAGAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.33
26 15 0.62
27 1 0.04
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.36
Consensus pattern (25 bp):
AATAAAAAATATATAAATATTGTTC
Found at i:3096970 original size:12 final size:13
Alignment explanation
Indices: 3096953--3096985 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
3096943 TAAAACACAT
3096953 GGGCTGCTAA-GG
1 GGGCTGCTAAGGG
3096965 GGGCTGCTAAGGG
1 GGGCTGCTAAGGG
3096978 GGGCTGCT
1 GGGCTGCT
3096986 GTAATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.12, C:0.18, G:0.52, T:0.18
Consensus pattern (13 bp):
GGGCTGCTAAGGG
Found at i:3097379 original size:16 final size:16
Alignment explanation
Indices: 3097358--3097391 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3097348 TTACTATTCA
*
3097358 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
3097374 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
3097390 CG
1 CG
3097392 GTCGGCGATA
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:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:3098159 original size:15 final size:16
Alignment explanation
Indices: 3098139--3098170 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3098129 TGGCAGATCC
3098139 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
3098154 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
3098170 A
1 A
3098171 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:3101450 original size:13 final size:13
Alignment explanation
Indices: 3101432--3101460 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3101422 TAAAACACAT
3101432 GGGCTGCTAAGGG
1 GGGCTGCTAAGGG
3101445 GGGCTGCTAAGGG
1 GGGCTGCTAAGGG
3101458 GGG
1 GGG
3101461 GGGCTGCTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.59, T:0.14
Consensus pattern (13 bp):
GGGCTGCTAAGGG
Found at i:3107705 original size:19 final size:19
Alignment explanation
Indices: 3107681--3107717 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3107671 ATGACCAACA
*
3107681 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
3107700 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
3107718 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:3107757 original size:20 final size:20
Alignment explanation
Indices: 3107734--3107815 Score: 60
Period size: 21 Copynumber: 4.0 Consensus size: 20
3107724 CGCAATTCAG
3107734 TTTTCAGATTCGCAATGCGA
1 TTTTCAGATTCGCAATGCGA
* * *
3107754 TTTTGACCA-TCGCATTGCGA
1 TTTTCA-GATTCGCAATGCGA
* * *
3107774 TTTTCGAAATCCGCATTGCGA
1 TTTTC-AGATTCGCAATGCGA
3107795 TTTT-AGATAATCGCAATGCGA
1 TTTTCAGAT--TCGCAATGCGA
3107816 ATATGTAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
19 3 0.06
20 20 0.42
21 25 0.52
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (20 bp):
TTTTCAGATTCGCAATGCGA
Found at i:3107790 original size:21 final size:21
Alignment explanation
Indices: 3107743--3107815 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
3107733 GTTTTCAGAT
* **
3107743 TCGCAATGCGATTTT-GACCA
1 TCGCATTGCGATTTTAGATAA
*
3107763 TCGCATTGCGATTTTCGA-AA
1 TCGCATTGCGATTTTAGATAA
3107783 TCCGCATTGCGATTTTAGATAA
1 T-CGCATTGCGATTTTAGATAA
*
3107805 TCGCAATGCGA
1 TCGCATTGCGA
3107816 ATATGTAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
20 16 0.35
21 27 0.59
22 3 0.07
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATTTTAGATAA
Found at i:3107847 original size:20 final size:20
Alignment explanation
Indices: 3107824--3107950 Score: 166
Period size: 20 Copynumber: 6.3 Consensus size: 20
3107814 GAATATGTAA
3107824 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
3107844 ATCGCAACGCGATTCGGACT
1 ATCGCAACGCGATTCTGACT
* **
3107864 ATCGCATCGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
* *
3107884 GATCGCAACGTGATTTTGACT
1 -ATCGCAACGCGATTCTGACT
3107905 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
3107925 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
3107945 AACGCA
1 ATCGCA
3107951 TCACTGAATT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.02
20 75 0.82
21 13 0.14
22 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:3108793 original size:24 final size:24
Alignment explanation
Indices: 3108766--3108824 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
3108756 AGTCGGTATT
3108766 CGGAATTTGATCTTGGTCAATACC
1 CGGAATTTGATCTTGGTCAATACC
* *
3108790 CGGACTTTGATCTTGGTCAATACT
1 CGGAATTTGATCTTGGTCAATACC
*
3108814 CGGATTTTGAT
1 CGGAATTTGAT
3108825 GATGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (24 bp):
CGGAATTTGATCTTGGTCAATACC
Found at i:3109043 original size:14 final size:14
Alignment explanation
Indices: 3109014--3109050 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3109004 AGAAAAAGAA
3109014 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
3109029 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
3109043 GAAGAAAA
1 GAAGAAAA
3109051 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:3121839 original size:29 final size:28
Alignment explanation
Indices: 3121807--3121906 Score: 96
Period size: 29 Copynumber: 3.4 Consensus size: 28
3121797 TAAAAGAGAA
*
3121807 AAAAAAACGAAAAATGAAAAAATAATAAT
1 AAAAAAA-GAAAAATGAAAAAATAAAAAT
*
3121836 AAAAATGAGAAAAA-GAAAAAGA-AGAAAAT
1 AAAAA-AAGAAAAATGAAAAA-ATA-AAAAT
*
3121865 AAAAAAAGAAAAAATGAGAAAATAAAAAT
1 AAAAAAAG-AAAAATGAAAAAATAAAAAT
3121894 GAAAAAAAAGAAA
1 --AAAAAAAGAAA
3121907 GAAAAACAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
28 9 0.15
29 32 0.54
30 10 0.17
31 8 0.14
ACGTcount: A:0.78, C:0.01, G:0.12, T:0.09
Consensus pattern (28 bp):
AAAAAAAGAAAAATGAAAAAATAAAAAT
Found at i:3121863 original size:23 final size:20
Alignment explanation
Indices: 3121845--3121906 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 20
3121835 TAAAAATGAG
3121845 AAAAAGAAAAAGAAGAAAATAA
1 AAAAAGAAAAA-AAGAAAAT-A
3121867 AAAAAGAAAAAATGAGAAAATA
1 AAAAAGAAAAAA--AGAAAATA
*
3121889 AAAATGAAAAAAAAGAAA
1 AAAAAG-AAAAAAAGAAA
3121907 GAAAAACAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 6 0.17
22 17 0.47
23 13 0.36
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (20 bp):
AAAAAGAAAAAAAGAAAATA
Found at i:3121920 original size:47 final size:46
Alignment explanation
Indices: 3121846--3121950 Score: 124
Period size: 47 Copynumber: 2.2 Consensus size: 46
3121836 AAAAATGAGA
3121846 AAAAGAAAAAGAAGAAAATAAAAAAAGA-AAAAATGAGAAAATAAAAAT
1 AAAA-AAAAAGAAGAAAATAAAAAAAGAGAAAAATGA-AAAA-AAAAAT
* * *
3121894 GAAAAAAAAGAAAGAAAA-ACAAAAAGAGAAAAATGAAAAAAAAGAT
1 AAAAAAAAAG-AAGAAAATAAAAAAAGAGAAAAATGAAAAAAAAAAT
3121940 AAAAATAAAAG
1 AAAAA-AAAAG
3121951 GAGGGTTCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
46 9 0.18
47 23 0.46
48 18 0.36
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.07
Consensus pattern (46 bp):
AAAAAAAAAGAAGAAAATAAAAAAAGAGAAAAATGAAAAAAAAAAT
Found at i:3121933 original size:78 final size:78
Alignment explanation
Indices: 3121791--3121938 Score: 185
Period size: 78 Copynumber: 1.9 Consensus size: 78
3121781 TCGCTTGAAG
* * *
3121791 AAGAAATAAAAGAGAAAAAAAAACGAAAAATGAAAAAATAATAATAAAAATGAGAAAAAGAAAAA
1 AAGAAATAAAAGAGAAAAAAAAACGAAAAA-GAAAAAAGAAAAACAAAAATGAGAAAAAGAAAAA
*
3121856 GAAGAAAATAAAAA
65 AAAGAAAATAAAAA
* *
3121870 AAGAAA-AAATGAGAAAATAAAAATGAAAAA-AAAGAAAGAAAAACAAAAA-GAGAAAAATGAAA
1 AAGAAATAAAAGAGAAAA-AAAAACGAAAAAGAAA-AAAGAAAAACAAAAATGAGAAAAA-GAAA
3121932 AAAAAGA
63 AAAAAGA
3121939 TAAAAATAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
77 11 0.18
78 32 0.53
79 17 0.28
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.07
Consensus pattern (78 bp):
AAGAAATAAAAGAGAAAAAAAAACGAAAAAGAAAAAAGAAAAACAAAAATGAGAAAAAGAAAAAA
AAGAAAATAAAAA
Found at i:3121935 original size:18 final size:16
Alignment explanation
Indices: 3121851--3121949 Score: 80
Period size: 16 Copynumber: 6.1 Consensus size: 16
3121841 TGAGAAAAAG
3121851 AAAAAGAAGAAAAT-AA
1 AAAAAGAA-AAAATAAA
*
3121867 AAAAAGAAAAAAT-GA
1 AAAAAGAAAAAATAAA
* *
3121882 GAAAA-TAAAAATGAAA
1 AAAAAGAAAAAAT-AAA
*
3121898 AAAAAGAAAGAAA-AAC
1 AAAAAGAAA-AAATAAA
3121914 AAAAAGAGAAAAATGAAA
1 AAAAAGA-AAAAAT-AAA
3121932 AAAAAGATAAAAATAAA
1 AAAAAGA-AAAAATAAA
3121949 A
1 A
3121950 GGAGGGTTCA
Statistics
Matches: 67, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
14 6 0.09
15 10 0.15
16 25 0.37
17 8 0.12
18 18 0.27
ACGTcount: A:0.80, C:0.01, G:0.12, T:0.07
Consensus pattern (16 bp):
AAAAAGAAAAAATAAA
Found at i:3123560 original size:153 final size:152
Alignment explanation
Indices: 3123277--3123841 Score: 655
Period size: 153 Copynumber: 3.6 Consensus size: 152
3123267 AAGATTGTTC
* *
3123277 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGAGTCCTATACTCT
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTGT-TGAAGATTGAGTCCTATACTCT
* *
3123342 CTGAAGGAATAGGGAGCGGACAAGTTCGATGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGG
65 CTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGG
3123407 AGCGGACAAGTTCGTTGAAGATT
130 AGCGGACAAGTTCGTTGAAGATT
* * **
3123430 GAGTCCTATACTCTCTGAAGGAATAGGGAGTGGACAAGTTCGTTGAAGATTGAGTCCTATACTCT
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTT-GTTGAAGATTGAGTCCTATACTCT
3123495 CTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGG
65 CTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGG
3123560 AGCGGACAAGTTCGTTGAAGATT
130 AGCGGACAAGTTCGTTGAAGATT
*
3123583 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTCGAGTTCTAT
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCG--TTGTTGAAGA---TT-GAGTCCTAT
* ** * *
3123648 ACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTATTCGAGTTCTATACTCTCTGA
60 ACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAG---ATT-GAGTCCTATACTCTCTGA
* ** *
3123713 AGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTT
120 AGGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT
* * * * * * *
3123750 CGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACCCGTTTTATGAAAATTGTTCAAGTCTTA
1 -GAGTCCTATACTCTCTGAA-GGAATAGAGAGCGGACCCGTTGT-TGAAGATTG----AGTCCTA
* * *
3123814 TACTCTCTGAATGAATAGAGAGCAGACA
59 TACTCTCTGAAGGAATAGGGAGCGGACA
3123842 CATTTTATGA
Statistics
Matches: 356, Mismatches: 33, Indels: 32
0.85 0.08 0.08
Matches are distributed among these distances:
153 177 0.50
154 9 0.03
155 2 0.01
157 2 0.01
158 34 0.10
159 9 0.03
162 3 0.01
163 35 0.10
164 12 0.03
166 3 0.01
167 37 0.10
168 31 0.09
169 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (152 bp):
GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTGTTGAAGATTGAGTCCTATACTCTC
TGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGA
GCGGACAAGTTCGTTGAAGATT
Found at i:3123910 original size:55 final size:56
Alignment explanation
Indices: 3123260--3123885 Score: 595
Period size: 51 Copynumber: 11.8 Consensus size: 56
3123250 AGCAAACTCG
3123260 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGT
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGT
* * * **
3123316 TTT-ATGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGT
* * * * **
3123366 TTCGATGAAGA----TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGT
* * * * **
3123417 TTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGTGGACAAG-
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGT
* * * **
3123468 TTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGT
* * * **
3123519 TTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGT
* *
3123570 TTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGT
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGT
3123622 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGT
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGT
*
3123678 TTTGTTGAAGATTATTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGT
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGT
* * *
3123734 TTTGTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACCCGT
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAA-GGAATAGAGAGCGGACCCGT
* * * * * * *
3123790 TTT-ATGAAAATTGTTCAAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACACAT
1 TTTGTTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGT
*
3123845 TTT-ATGAAGATTGTTCGAG-TCTTATACT-TCCTGAAGGAATA
1 TTTGTTGAAGATTGTTCGAGTTC-TATACTCT-CTGAAGGAATA
3123886 CGGAGCAGAC
Statistics
Matches: 526, Mismatches: 32, Indels: 25
0.90 0.05 0.04
Matches are distributed among these distances:
50 3 0.01
51 275 0.52
52 13 0.02
54 4 0.01
55 81 0.15
56 148 0.28
57 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (56 bp):
TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGT
Found at i:3128334 original size:12 final size:12
Alignment explanation
Indices: 3128317--3128353 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
3128307 CAAGCAAAAG
3128317 GCAATCAAAATC
1 GCAATCAAAATC
3128329 GCAATCAAAATC
1 GCAATCAAAATC
* *
3128341 TCAATCACAATC
1 GCAATCAAAATC
3128353 G
1 G
3128354 GCTTCACCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.46, C:0.27, G:0.08, T:0.19
Consensus pattern (12 bp):
GCAATCAAAATC
Found at i:3128550 original size:20 final size:20
Alignment explanation
Indices: 3128522--3128805 Score: 279
Period size: 20 Copynumber: 14.8 Consensus size: 20
3128512 TTACACATTC
3128522 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
3128542 ATATGACTATCACAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
3128562 ATTTGAATATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
** * *
3128582 AAATGACTATCACAACGCTA
1 ATTTGACTATCGCAACGCGA
*
3128602 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
*
3128622 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* * *
3128642 A----A--ATCGCAAAGTGT
1 ATTTGACTATCGCAACGCGA
* * *
3128656 ATTAGACTATTGCAACGTGA
1 ATTTGACTATCGCAACGCGA
3128676 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
3128696 ATTTAACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
3128716 ATTTGACTATCGCAACGAG-
1 ATTTGACTATCGCAACGCGA
3128735 A--T-A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
3128750 A-ATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
3128769 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
3128789 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
3128806 AGAAAATCGC
Statistics
Matches: 215, Mismatches: 37, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
14 20 0.09
15 1 0.00
16 3 0.01
17 2 0.01
18 1 0.00
19 14 0.07
20 174 0.81
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:3128671 original size:54 final size:56
Alignment explanation
Indices: 3128530--3128838 Score: 228
Period size: 54 Copynumber: 5.5 Consensus size: 56
3128520 TCATTTGACT
* * *
3128530 ATCGCAACGCGAA-TATGACTATCACAACGTGAATTTGAATATCGCAATGCGA-AAATGAC
1 ATCGCAAAGCGAATTA-GACTATCGCAACGTGAATTTGACTATCGCAA--CGAGAAA--AC
* * * *
3128589 TATCACAACGCTAATTTGACTATCGCAACGTGAATTTGACTATCGCAACGAG-AAA-
1 -ATCGCAAAGCGAATTAGACTATCGCAACGTGAATTTGACTATCGCAACGAGAAAAC
* * * *
3128644 ATCGCAAAGTGTATTAGACTATTGCAACGTGAATTTGACTATCGCAACGCGAATTTAAC
1 ATCGCAAAGCGAATTAGACTATCGCAACGTGAATTTGACTATCGCAACGAGAA---AAC
* * * *
3128703 TATCGCAACGCGAATTTGACTATCGCAACGAG-A--T-A--ATCGCAACGCGAAATGAC
1 -ATCGCAAAGCGAATTAGACTATCGCAACGTGAATTTGACTATCGCAACGAGAAA--AC
* * * *
3128756 TATCGCAACGCGAATTTGATTATCGCAACGGGAATTTGACTATCGCAACGAG-AAA-
1 -ATCGCAAAGCGAATTAGACTATCGCAACGTGAATTTGACTATCGCAACGAGAAAAC
* *
3128811 ATCGCAAAGTGTATTAGACTATCGCAAC
1 ATCGCAAAGCGAATTAGACTATCGCAAC
3128839 ACGAATATGA
Statistics
Matches: 206, Mismatches: 27, Indels: 38
0.76 0.10 0.14
Matches are distributed among these distances:
51 1 0.00
53 32 0.16
54 80 0.39
55 1 0.00
56 4 0.02
57 2 0.01
58 9 0.04
59 11 0.05
60 65 0.32
61 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (56 bp):
ATCGCAAAGCGAATTAGACTATCGCAACGTGAATTTGACTATCGCAACGAGAAAAC
Found at i:3128699 original size:94 final size:93
Alignment explanation
Indices: 3128569--3128805 Score: 321
Period size: 94 Copynumber: 2.5 Consensus size: 93
3128559 TGAATTTGAA
* ** * * *
3128569 TATCGCAATGCGAAAATGACTATCACAACGCTAATTTGACTATCGCAACGTGAATTTGACTATCG
1 TATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCG
* * *
3128634 CAACGAGAAAATCGCAAAGTGTATTAGAC
66 CAACGAGAAAATCGCAAAGCGAAAT-GAC
* * *
3128663 TATTGCAACGTGAATTTGACTATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCG
1 TATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCG
* *
3128728 CAACGAGATAATCGCAACGCGAAATGAC
66 CAACGAGAAAATCGCAAAGCGAAATGAC
* *
3128756 TATCGCAACGCGAATTTGATTATCGCAACGGGAATTTGACTATCGCAACG
1 TATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACG
3128806 AGAAAATCGC
Statistics
Matches: 124, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
93 48 0.39
94 76 0.61
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (93 bp):
TATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCG
CAACGAGAAAATCGCAAAGCGAAATGAC
Found at i:3128766 original size:53 final size:54
Alignment explanation
Indices: 3128684--3128785 Score: 170
Period size: 53 Copynumber: 1.9 Consensus size: 54
3128674 GAATTTGACT
*
3128684 ATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCGCAACGAGATA
1 ATCGCAACGCGAATATAACTATCGCAACGCGAATTTGACTATCGCAACGAGATA
* *
3128738 ATCGCAACGCGAA-ATGACTATCGCAACGCGAATTTGATTATCGCAACG
1 ATCGCAACGCGAATATAACTATCGCAACGCGAATTTGACTATCGCAACG
3128786 GGAATTTGAC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 32 0.71
54 13 0.29
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (54 bp):
ATCGCAACGCGAATATAACTATCGCAACGCGAATTTGACTATCGCAACGAGATA
Found at i:3128780 original size:73 final size:73
Alignment explanation
Indices: 3128679--3128849 Score: 243
Period size: 73 Copynumber: 2.3 Consensus size: 73
3128669 AACGTGAATT
* * *
3128679 TGACTATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCA
1 TGACTATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCAACGAGAAAATCGCA
*
3128744 ACGCGAAA
66 AAGCGAAA
*
3128752 TGACTATCGCAACGCGAATTTGATTATCGCAACGGGAATTTGACTATCGCAACGAGAAAATCGCA
1 TGACTATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCAACGAGAAAATCGCA
* * *
3128817 AAGTGTAT
66 AAGCGAAA
* *
3128825 TAGACTATCGCAACACGAATATGAT
1 T-GACTATCGCAACGCGAATTTGAT
3128850 GCAGATTGAA
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
73 66 0.76
74 21 0.24
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (73 bp):
TGACTATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCAACGAGAAAATCGCA
AAGCGAAA
Found at i:3128810 original size:167 final size:172
Alignment explanation
Indices: 3128522--3128838 Score: 491
Period size: 167 Copynumber: 1.9 Consensus size: 172
3128512 TTACACATTC
* * *
3128522 ATTTGACTATCGCAACGCGAATATGACTATCACAACGTGAATTTGAATATCGCAATGCGAAAATG
1 ATTTAACTATCGCAACGCGAATATGACTATCACAACGAGAA-TT-AATATCGCAACGCGAAAATG
* *
3128587 ACTATCACAACGCTAATTTGACTATCGCAACGTGAATTTGACTATCGCAACGAGAAAATCGCAAA
64 ACTATCACAACGCGAATTTGACTATCGCAACGGGAATTTGACTATCGCAACGAGAAAATCGCAAA
*
3128652 GTGTATTAGACTATTGCAACGTGAATTTGACTATCGCAACGCGA
129 GTGTATTAGACTATCGCAACGTGAATTTGACTATCGCAACGCGA
* *
3128696 ATTTAACTATCGCAACGCGAATTTGACTATCGCAACGAG-A-T-A-ATCGCAACGCG-AAATGAC
1 ATTTAACTATCGCAACGCGAATATGACTATCACAACGAGAATTAATATCGCAACGCGAAAATGAC
* *
3128756 TATCGCAACGCGAATTTGATTATCGCAACGGGAATTTGACTATCGCAACGAGAAAATCGCAAAGT
66 TATCACAACGCGAATTTGACTATCGCAACGGGAATTTGACTATCGCAACGAGAAAATCGCAAAGT
3128821 GTATTAGACTATCGCAAC
131 GTATTAGACTATCGCAAC
3128839 ACGAATATGA
Statistics
Matches: 133, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
167 85 0.64
168 10 0.08
169 1 0.01
171 1 0.01
173 1 0.01
174 35 0.26
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (172 bp):
ATTTAACTATCGCAACGCGAATATGACTATCACAACGAGAATTAATATCGCAACGCGAAAATGAC
TATCACAACGCGAATTTGACTATCGCAACGGGAATTTGACTATCGCAACGAGAAAATCGCAAAGT
GTATTAGACTATCGCAACGTGAATTTGACTATCGCAACGCGA
Done.