Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 3 of 193
Found at i:944761 original size:23 final size:23
Alignment explanation
Indices: 944692--944761 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
944682 CCATTAATAT
* *
944692 TGTTCGTGACCATGTTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* *
944716 TGTTCGTGAACATGTTTGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
* *
944739 TGTTCATGAACATATTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
944762 ATTTGAACAC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:950236 original size:26 final size:26
Alignment explanation
Indices: 950187--950255 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
950177 AACAAATAAT
* * *
950187 TTAAAACTTATAAAATATTCAAAAAG
1 TTAAAAATTAAAAAATATTCAAAAAC
950213 TTAAAAATTAAAAAATATAT-AAAAAC
1 TTAAAAATTAAAAAATAT-TCAAAAAC
*
950239 TTCATGAAATTAAAAAA
1 TT-A-AAAATTAAAAAA
950256 AAAAAAACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 23 0.64
27 2 0.06
28 11 0.31
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (26 bp):
TTAAAAATTAAAAAATATTCAAAAAC
Found at i:951508 original size:22 final size:22
Alignment explanation
Indices: 951480--951523 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
951470 TACTATGTAT
951480 AAAGTTATAGATTTAGCCTATG
1 AAAGTTATAGATTTAGCCTATG
*
951502 AAAGTTATATATTTAGCCTATG
1 AAAGTTATAGATTTAGCCTATG
951524 TTCTCCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
AAAGTTATAGATTTAGCCTATG
Found at i:956348 original size:301 final size:296
Alignment explanation
Indices: 955803--956402 Score: 850
Period size: 301 Copynumber: 2.0 Consensus size: 296
955793 GGATGTCTTA
* *
955803 ATCTTTAAGATATCAGTATCAACTTGGGTCCCTGCCTTTGTCTTTTCTTATTTTCCCCCCTTGTG
1 ATCTTTAAGATATCAATATCAACTTGGGTCCCTGCCTTTGTCTTTTCTTATTTTCCCCCCTTGTA
* * * *
955868 ATTAGAGGGTTATGAGTAAAAGTAATTACAGCTCGATATAGATGAATGAGAACGAGAACAATATT
66 ATTAGAGGGTTAGGAGTAAAAGTAATCAAAGCTCGATATA-A-GAAT-AGAACGAGAACAATAGT
* * * *
955933 TCCGAATAAAACTGAAGCATCCAATGAGCTCGATACAAAATAAGGACCCTAACAGTTCGAGCAAT
128 TCCGAATAAAACTAAAGCATCCAATGAGCTCAATACAAAACAAAGACCCTAACAGTTCGAGCAAT
*
955998 ACAAGAAGATCCAACACTTGAATTCGATCTTCAGTATTGAGCGTCGATAAAAGAGTAAATAAGGT
193 ACAAGAAGATCCAACACTTGAATTCGATCTTCAGTATTGAGCATCGATAAAAGAGTAAATAAGGT
* *
956063 ATAAATATCATGAAGATTTTTGCATTAAGAGTTGAATTG
258 AAAAATATCATGAAGACTTTTGCATTAAGAGTTGAATTG
* **
956102 ATCTTTAAGATATCAATATCAACTTGGAG-CCTTGCCTTTGTCTTTTCTTATTTTTTCCCCTTTT
1 ATCTTTAAGATATCAATATCAACTTGG-GTCCCTGCCTTTGTCTTTTCTTA--TTTTCCCCCCTT
956166 GATAAAAAATTTTAGAGGGTTAGGAGTAAAAGTAATCAAAGCTCGATAT-A-AAT-GAACGAGAA
63 G-T----AA--TTAGAGGGTTAGGAGTAAAAGTAATCAAAGCTCGATATAAGAATAGAACGAGAA
* *
956228 CAATAGTTCCGAATAAAAC-AAAGCATCTAATGAGCTCAATACAAAACAAAGACCCTAATAGTTC
121 CAATAGTTCCGAATAAAACTAAAGCATCCAATGAGCTCAATACAAAACAAAGACCCTAACAGTTC
* * *
956292 GAGCAATACAAGAAGATCCAACACTTGAATTCGATCTTTATTATTGAGCATCGATAAAGGAGTAA
186 GAGCAATACAAGAAGATCCAACACTTGAATTCGATCTTCAGTATTGAGCATCGATAAAAGAGTAA
*
956357 ATAAGGTAAAAATATCATGAAGGCTTTTGCATTAAGAGTTGAATTG
251 ATAAGGTAAAAATATCATGAAGACTTTTGCATTAAGAGTTGAATTG
956403 CATTTTATCC
Statistics
Matches: 269, Mismatches: 22, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
299 46 0.17
300 1 0.00
301 154 0.57
302 28 0.10
304 3 0.01
306 2 0.01
308 35 0.13
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (296 bp):
ATCTTTAAGATATCAATATCAACTTGGGTCCCTGCCTTTGTCTTTTCTTATTTTCCCCCCTTGTA
ATTAGAGGGTTAGGAGTAAAAGTAATCAAAGCTCGATATAAGAATAGAACGAGAACAATAGTTCC
GAATAAAACTAAAGCATCCAATGAGCTCAATACAAAACAAAGACCCTAACAGTTCGAGCAATACA
AGAAGATCCAACACTTGAATTCGATCTTCAGTATTGAGCATCGATAAAAGAGTAAATAAGGTAAA
AATATCATGAAGACTTTTGCATTAAGAGTTGAATTG
Found at i:960957 original size:30 final size:31
Alignment explanation
Indices: 960891--960959 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 31
960881 CTTAACAGCC
960891 CAATGACTTAAATAAAAAAGTTTCAAATAATT
1 CAATGACTTAAATAAAAAAG-TTCAAATAATT
* * *
960923 CAATGATTTAAATAAAAAA-TTCATATAGTT
1 CAATGACTTAAATAAAAAAGTTCAAATAATT
960953 CAATGAC
1 CAATGAC
960960 CATTTTGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 15 0.45
32 18 0.55
ACGTcount: A:0.51, C:0.10, G:0.07, T:0.32
Consensus pattern (31 bp):
CAATGACTTAAATAAAAAAGTTCAAATAATT
Found at i:969498 original size:3 final size:3
Alignment explanation
Indices: 969490--969515 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
969480 ATATCATTGA
969490 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
969516 CAATTAAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:984181 original size:4 final size:4
Alignment explanation
Indices: 984172--984203 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
984162 GGGGTCAACG
984172 TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA
984204 GTATTTACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:984202 original size:132 final size:130
Alignment explanation
Indices: 983910--984204 Score: 330
Period size: 132 Copynumber: 2.2 Consensus size: 130
983900 CATAACTGCA
* ** * *
983910 ACATACATACATACATGCATGCATGCATGTACACATACATATATATAGTATTTACAGCATATAGG
1 ACATACATACATACATACATGCATGCATACAGACATACATATATATAGTATTTACAGCATATAGA
* * * *
983975 TGCCAAGCAATCTCATATTCTATCAATTTAAAGGCAAATCATACATAAGCAACTATGGGTCAACT
66 TGCCAAGAAACCTCATATTCTATCAATTTAAAGGCAAATCATAAATAAGCAACTAGGGGTCAACT
* * *
984040 A-AT-CATTCATTGACATA-ACTGCAGTGCATACAGATATACATATACATGTAGTATTTACAGCA
1 ACATACATACA-T-ACATACA-TGCA-TGCATACAGACATACATAT--ATATAGTATTTACAGCA
* * *
984102 TGTAGATG-CAAGAAACCTCATATTTTATCAATTCT-AAGGCAAATCATAAATCAGCAACTAGGG
60 TATAGATGCCAAGAAACCTCATATTCTATCAATT-TAAAGGCAAATCATAAATAAGCAACTAGGG
984165 GTCAACGT
124 GTCAAC-T
* *
984173 ACATACATACATACATACATACATACATACAG
1 ACATACATACATACATACATGCATGCATACAG
984205 TATTTACAGC
Statistics
Matches: 136, Mismatches: 18, Indels: 20
0.78 0.10 0.11
Matches are distributed among these distances:
128 5 0.04
129 4 0.03
130 9 0.07
131 15 0.11
132 61 0.45
133 33 0.24
134 4 0.03
135 5 0.04
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.28
Consensus pattern (130 bp):
ACATACATACATACATACATGCATGCATACAGACATACATATATATAGTATTTACAGCATATAGA
TGCCAAGAAACCTCATATTCTATCAATTTAAAGGCAAATCATAAATAAGCAACTAGGGGTCAACT
Found at i:984341 original size:134 final size:134
Alignment explanation
Indices: 984183--984466 Score: 374
Period size: 134 Copynumber: 2.1 Consensus size: 134
984173 ACATACATAC
* * * * *
984183 ATACATACATACATACATACAGTATTTACAGCATTTAGATGCAATAAAAGTCATATTCTATCATT
1 ATACATACATACATATAAACAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAAT
* * * * *
984248 TCTGAGGAAAATAAT-AAATAAGCATCTATGGGTCAA-TAAATCATTCAGTGACATAACTGCACT
66 TCTAAGGAAAATAATAAAAT-ACCAACAATGGGTCAACT-AATCATTCAGTGACATAACTGCAAT
984311 ATACAT
129 ATACAT
* * *
984317 ATATATACATACATATAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCGTATTCTATCAAT
1 ATACATACATACATATAAACAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAAT
* * * *
984382 TCTAAGGCAAATTATAAAATACCAACAATGGGTCAACTAATCATTCATTGACATAGCTGCAATAT
66 TCTAAGGAAAATAATAAAATACCAACAATGGGTCAACTAATCATTCAGTGACATAACTGCAATAT
984447 ACAT
131 ACAT
*
984451 ATACATGCATACATAT
1 ATACATACATACATAT
984467 CTACATATCT
Statistics
Matches: 129, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
134 124 0.96
135 5 0.04
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.31
Consensus pattern (134 bp):
ATACATACATACATATAAACAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAAT
TCTAAGGAAAATAATAAAATACCAACAATGGGTCAACTAATCATTCAGTGACATAACTGCAATAT
ACAT
Found at i:984602 original size:154 final size:154
Alignment explanation
Indices: 984317--984696 Score: 437
Period size: 154 Copynumber: 2.5 Consensus size: 154
984307 CACTATACAT
* *
984317 ATATATACATACATATAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCGTATTCTATCAAT
1 ATATATACATACATACAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAAT
* * *
984382 TCTAAGGCAAATTATAAAATACCAACAATGGGTCAACTAATCATTCATTGACATAGCTGCAATAT
66 TCTAAGGCAAATCATAAAATACCAACAATGGGTCAACTAATCATTCATTAACATAACTGCAATAT
984447 ACATATACATGCATACATATCTAC
131 ACATATACATGCATACATATCTAC
* * * * * * *
984471 ATATCTACATCCATACATATAGTATTTACAGCATTTATATGCAAGAGAACTCATGTTCTGA-CAG
1 ATATATACATACATACAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCT-ATCAA
* * * *
984535 TTCTAAGGCAAATCAT-AAATAAGCAACTATGGGTCAACTAGTCATTCATTAACATAATTGCAAT
65 TTCTAAGGCAAATCATAAAAT-ACCAACAATGGGTCAACTAATCATTCATTAACATAACTGCAAT
* *
984599 ATACATATAC-T--ACACAT-GCATA-
129 ATACATATACATGCATACATATC-TAC
* *
984621 A-A-A-AC--ACAT--ATATAGTATTTACAGCATTTAGATGCAAGAAATCTCATATTCTATCAAT
1 ATATATACATACATACAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAAT
* *
984679 TCTAAGGCATATTATAAA
66 TCTAAGGCAAATCATAAA
984697 GAAACCAAAC
Statistics
Matches: 194, Mismatches: 27, Indels: 20
0.80 0.11 0.08
Matches are distributed among these distances:
142 1 0.01
143 55 0.28
144 2 0.01
145 3 0.02
147 2 0.01
149 1 0.01
150 2 0.01
151 7 0.04
153 5 0.03
154 115 0.59
155 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (154 bp):
ATATATACATACATACAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAAT
TCTAAGGCAAATCATAAAATACCAACAATGGGTCAACTAATCATTCATTAACATAACTGCAATAT
ACATATACATGCATACATATCTAC
Found at i:993127 original size:91 final size:90
Alignment explanation
Indices: 992946--993167 Score: 318
Period size: 91 Copynumber: 2.5 Consensus size: 90
992936 GATAATGTCA
* * * * *
992946 TATTTGGTACCTGTATTTTTATAAAATATTTAATGTGGTACTTATGTTTGAAAATGTCCAATGTG
1 TATTCGGTACCTATACTTTCATAAAATATTTAATGTGGTACCTATGTTTGAAAATGTCCAATGTG
993011 GTATTTAAACTATCAATGTGCGGAT
66 GTATTTAAACTATCAATGTGCGGAT
* * *
993036 TATTCGGTATCTATACTTTCATAAAATATTTAATGTGGTACCTATGGTTTGAAAATGTTCAATTT
1 TATTCGGTACCTATACTTTCATAAAATATTTAATGTGGTACCTAT-GTTTGAAAATGTCCAATGT
* * *
993101 GGTATTTAAATTATCAATTTGTGGAT
65 GGTATTTAAACTATCAATGTGCGGAT
* *
993127 TATTTGGTACCTATACTTTCATAAAATGTTTAATGTGGTAC
1 TATTCGGTACCTATACTTTCATAAAATATTTAATGTGGTAC
993168 TTAAACAATC
Statistics
Matches: 117, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
90 39 0.33
91 78 0.67
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.44
Consensus pattern (90 bp):
TATTCGGTACCTATACTTTCATAAAATATTTAATGTGGTACCTATGTTTGAAAATGTCCAATGTG
GTATTTAAACTATCAATGTGCGGAT
Found at i:1011072 original size:32 final size:31
Alignment explanation
Indices: 1011009--1011074 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
1010999 TTTGCCTAGC
*** *
1011009 AAACTTAAATGATTTGGACCCCAAATAACTT
1 AAACTTAAATGATTCAAACCCAAAATAACTT
*
1011040 AAACTTCAAATGATTCAAACCCAAAATGACTT
1 AAACTT-AAATGATTCAAACCCAAAATAACTT
1011072 AAA
1 AAA
1011075 TATGAAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 6 0.21
32 23 0.79
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.26
Consensus pattern (31 bp):
AAACTTAAATGATTCAAACCCAAAATAACTT
Found at i:1015520 original size:83 final size:84
Alignment explanation
Indices: 1015346--1015551 Score: 236
Period size: 83 Copynumber: 2.5 Consensus size: 84
1015336 GTGAACAGTT
* * * * * **
1015346 AAATTAGCTGTCTTTAAGATGTTTGATAAAATGTTTGTGTTGGGCCAAATGGAGTTGTAGAAGAA
1 AAATTAGTTGTCTTTCAGATGTTTGATAATATGTTTGTGTTAGACCAAATCAAGTTGTAGAAGAA
* *
1015411 ATATTACTGACCCAAAGTC
66 ATATTAATGACCCAAAGAC
* ** *
1015430 AAATTAGTTGCCTTTCAGATGTTTGATAATATGTTTGTGTTAGACTTATTCAAGTT-TAGAAGAA
1 AAATTAGTTGTCTTTCAGATGTTTGATAATATGTTTGTGTTAGACCAAATCAAGTTGTAGAAGAA
1015494 A-ATTCAATGACCCAAAGAC
66 ATATT-AATGACCCAAAGAC
* * * *
1015513 AAATTAGTTGTCTTTCAGAAGTTAGATTATATATTTGTG
1 AAATTAGTTGTCTTTCAGATGTTTGATAATATGTTTGTG
1015552 CCTTGGTGTA
Statistics
Matches: 103, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
82 3 0.03
83 55 0.53
84 45 0.44
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.37
Consensus pattern (84 bp):
AAATTAGTTGTCTTTCAGATGTTTGATAATATGTTTGTGTTAGACCAAATCAAGTTGTAGAAGAA
ATATTAATGACCCAAAGAC
Found at i:1054783 original size:181 final size:180
Alignment explanation
Indices: 1054479--1054820 Score: 488
Period size: 181 Copynumber: 1.9 Consensus size: 180
1054469 AGCTAATAGC
*
1054479 AATGGCATGTTTTGCATTAACCCCCTTTTTCTCTAATAATTATAGGCAAAAACATCCACGGAAGA
1 AATGGCATGTTTTGCATTAACCCCCTTTTTCTCTAATAATTATAGGCAAAAACATCCACAGAAGA
** ** * *
1054544 TACTACTTTTATTGCATAAAACAACAAGGAGAACAGAGGGTTGAAACTTGAAATCAAGCAATGTA
66 TACTACTACTACCGCATAAAACAAAAAGGAGAACAAAGGGTTGAAACTTGAAATCAAGCAATG-A
* *
1054609 AAATACATCCATGAAACACAGTATCGATCCAAATAACAATCCCGTGACAGA
130 AAATACATCAATGAAACACAGTATCAATCCAAATAACAATCCCGTGACAGA
* ** * * * *
1054660 AATGGCATGTTTTGTATTAGTCCCCTTTTTCTCTAATACTTATAGGCCAAAACGTCTACAGAAGA
1 AATGGCATGTTTTGCATTAACCCCCTTTTTCTCTAATAATTATAGGCAAAAACATCCACAGAAGA
*
1054725 TACTACTACTACCGCATAAAACAAGAAAGG-GAACAAAGGGTTGAAACTTGAAATCAAGCAATGC
66 TACTACTACTACCGCATAAAACAA-AAAGGAGAACAAAGGGTTGAAACTTGAAATCAAGCAATGA
* *
1054789 AATTACATCAATGAAACACCGTATCAATCCAA
130 AAATACATCAATGAAACACAGTATCAATCCAA
1054821 GTAAAGATCC
Statistics
Matches: 141, Mismatches: 19, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
180 28 0.20
181 109 0.77
182 4 0.03
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (180 bp):
AATGGCATGTTTTGCATTAACCCCCTTTTTCTCTAATAATTATAGGCAAAAACATCCACAGAAGA
TACTACTACTACCGCATAAAACAAAAAGGAGAACAAAGGGTTGAAACTTGAAATCAAGCAATGAA
AATACATCAATGAAACACAGTATCAATCCAAATAACAATCCCGTGACAGA
Found at i:1064391 original size:13 final size:13
Alignment explanation
Indices: 1064373--1064406 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
1064363 AAGCTAAAAA
1064373 CTAAATTTATCAG
1 CTAAATTTATCAG
1064386 CTAAATTTATCAG
1 CTAAATTTATCAG
1064399 CTAAATTT
1 CTAAATTT
1064407 GATTAAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (13 bp):
CTAAATTTATCAG
Found at i:1067632 original size:29 final size:27
Alignment explanation
Indices: 1067600--1067666 Score: 64
Period size: 31 Copynumber: 2.3 Consensus size: 27
1067590 ATAATTTCAA
1067600 AATTATACATGAAA-TTTGATTCAATGTAC
1 AATTATACAT-AAATTTTGATT-AA-GTAC
* *
1067629 AATTTGATATATAAATTTTGATTTAGTAC
1 AA-TT-ATACATAAATTTTGATTAAGTAC
1067658 AATTATACA
1 AATTATACA
1067667 CATGAAACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
27 4 0.12
28 2 0.06
29 8 0.25
30 6 0.19
31 12 0.38
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (27 bp):
AATTATACATAAATTTTGATTAAGTAC
Found at i:1067933 original size:16 final size:17
Alignment explanation
Indices: 1067904--1067939 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1067894 TCTTTATTAA
*
1067904 TTTAAAATTTAAAAAAT
1 TTTAAAATTCAAAAAAT
1067921 TTTAAAA-TCAAAAAAT
1 TTTAAAATTCAAAAAAT
1067937 TTT
1 TTT
1067940 CATTTTAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAAATTCAAAAAAT
Found at i:1077689 original size:14 final size:15
Alignment explanation
Indices: 1077662--1077692 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1077652 AAATTTAATG
1077662 AATTTAATAAATAAA
1 AATTTAATAAATAAA
1077677 AATTTAA-AAATAAA
1 AATTTAATAAATAAA
1077691 AA
1 AA
1077693 ATTATAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATTTAATAAATAAA
Found at i:1090286 original size:39 final size:39
Alignment explanation
Indices: 1090221--1090299 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
1090211 TGCAATTATA
* * * *
1090221 AAGTGTAGAATTAAACTATTATAACATAAATGGATTAAG
1 AAGTGTAAAATTAAACTATTACAACATAAATAGACTAAG
1090260 AAGTGTAAAATTAAA-TAATTACAACATAAATAGACTAAG
1 AAGTGTAAAATTAAACT-ATTACAACATAAATAGACTAAG
1090299 A
1 A
1090300 TTCACAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.03
39 34 0.97
ACGTcount: A:0.53, C:0.06, G:0.13, T:0.28
Consensus pattern (39 bp):
AAGTGTAAAATTAAACTATTACAACATAAATAGACTAAG
Found at i:1103446 original size:24 final size:24
Alignment explanation
Indices: 1103419--1103470 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
1103409 TTCAAACCAA
*
1103419 TGCAACACATTGGCTAATGT-AAG
1 TGCAACACATTAGCTAATGTGAAG
*
1103442 TTGC-ATACATTAGCTAATGTGAAG
1 -TGCAACACATTAGCTAATGTGAAG
1103466 TGCAA
1 TGCAA
1103471 ATGAAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (24 bp):
TGCAACACATTAGCTAATGTGAAG
Found at i:1103947 original size:21 final size:20
Alignment explanation
Indices: 1103921--1103961 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1103911 ATTCATGTAC
1103921 CATAGATAT-TCAATAACTTAT
1 CATAGAT-TGTCAATAA-TTAT
1103942 CATAGATTGTCAATAATTAT
1 CATAGATTGTCAATAATTAT
1103962 AAAAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.39
Consensus pattern (20 bp):
CATAGATTGTCAATAATTAT
Found at i:1105933 original size:18 final size:18
Alignment explanation
Indices: 1105875--1105933 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
1105865 TCTTTTCCTT
1105875 TATATTATTATATAA-TAA
1 TATATTATTAT-TAATTAA
* *
1105893 AATATTATTATTTATT-A
1 TATATTATTATTAATTAA
*
1105910 TAATATTATAATTAATTAA
1 T-ATATTATTATTAATTAA
1105929 TATAT
1 TATAT
1105934 CTTTTGATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
17 3 0.09
18 28 0.85
19 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATATTATTATTAATTAA
Found at i:1116870 original size:11 final size:11
Alignment explanation
Indices: 1116838--1116880 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
1116828 GTCCAACTTG
1116838 AATTTTAAATT
1 AATTTTAAATT
* *
1116849 AAGTTTGAATT
1 AATTTTAAATT
1116860 AATTTTAAATT
1 AATTTTAAATT
*
1116871 TA-TTTAAATT
1 AATTTTAAATT
1116881 TAAATACATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (11 bp):
AATTTTAAATT
Found at i:1116883 original size:22 final size:22
Alignment explanation
Indices: 1116838--1116880 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1116828 GTCCAACTTG
*
1116838 AATTTTAAATTAAGTTTGAATT
1 AATTTTAAATTAAGTTTAAATT
*
1116860 AATTTTAAATTTA-TTTAAATT
1 AATTTTAAATTAAGTTTAAATT
1116881 TAAATACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
AATTTTAAATTAAGTTTAAATT
Found at i:1118554 original size:32 final size:32
Alignment explanation
Indices: 1118503--1118565 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
1118493 TGCGCGTTTG
1118503 GTCCTTTCGCATTTTTAATT-GTTTTAATTTT
1 GTCCTTTCGCATTTTTAATTAGTTTTAATTTT
*
1118534 GTCCTTTC-CATACTTTTAATTATTTTTAATTT
1 GTCCTTTCGCAT--TTTTAATTAGTTTTAATTT
1118566 GGCCCAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 3 0.11
31 8 0.29
32 8 0.29
33 9 0.32
ACGTcount: A:0.19, C:0.14, G:0.06, T:0.60
Consensus pattern (32 bp):
GTCCTTTCGCATTTTTAATTAGTTTTAATTTT
Found at i:1118926 original size:59 final size:59
Alignment explanation
Indices: 1118834--1119239 Score: 467
Period size: 58 Copynumber: 7.0 Consensus size: 59
1118824 TCTAGTCCCT
* * *
1118834 AAACTTTCTAAAATTCCATTTTTAACCTCGATTTTATCC-AAAATTACCATTTGACCCCC
1 AAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA-CCAAAAATTACCATTTTACCCCC
* * * **
1118893 AAACTTTCCAAAATTCCTTTTTTAGCCTTGATTTCACC-AAAATTACCATTTTACCCGT
1 AAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCC
*
1118951 AAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCC
1 AAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCC
* *
1119010 AAACTTTCCAAAATCCCA-TTTTAACC-CTGATTTTACCAAAAATTACCATTTTACCCCC
1 AAACTTTCCAAAATTCCATTTTTAACCTC-GATTTCACCAAAAATTACCATTTTACCCCC
* * *
1119068 TAAACATTCCAAAA-TCTCA-TCTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCC
1 -AAACTTTCCAAAATTC-CATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCC
* * * * * *
1119127 TAACTTTCCAAAA---CACTATTTAGCCTCAATTTCACCAAAAATTACCGTTTTACCCTC
1 AAACTTTCCAAAATTCCA-TTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCC
* *
1119184 GAACTTTCCAAAATTCCA-TTTTAACC-CTAATTTCACCAAAAATTA-CATTTTTACCC
1 AAACTTTCCAAAATTCCATTTTTAACCTC-GATTTCACCAAAAATTACCA-TTTTACCC
1119240 TCGAAAGTCA
Statistics
Matches: 301, Mismatches: 34, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
55 2 0.01
57 48 0.16
58 133 0.44
59 115 0.38
60 3 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (59 bp):
AAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCC
Found at i:1118944 original size:29 final size:29
Alignment explanation
Indices: 1118843--1119062 Score: 84
Period size: 29 Copynumber: 7.5 Consensus size: 29
1118833 TAAACTTTCT
* *
1118843 AAAATT-CCATTTTTAACCTCGATTTTATCC
1 AAAATTACCA-TTTTAACCTAGATTTCA-CC
* * * *
1118873 AAAATTACCATTTGACCCCCAAACTTT--CC
1 AAAATTACCATTTTA-ACCTAGA-TTTCACC
* * *
1118902 AAAATT-CCTTTTTTAGCCTTGATTTCACC
1 AAAATTACC-ATTTTAACCTAGATTTCACC
* * *
1118931 AAAATTACCATTTTACCCGTAAACTTT--CT
1 AAAATTACCATTTTAACC-TAGA-TTTCACC
*
1118960 AAAATT-CCATTTTTAACCTCGATTTCACC
1 AAAATTACCA-TTTTAACCTAGATTTCACC
* * *
1118989 AAAAATTACCATTTTACCCCCAAACTTT--CC
1 -AAAATTACCATTTTA-ACCTAGA-TTTCACC
* *
1119019 AAAA-TCCCATTTTAACCCT-GATTTTACC
1 AAAATTACCATTTTAA-CCTAGATTTCACC
1119047 AAAAATTACCATTTTA
1 -AAAATTACCATTTTA
1119063 CCCCCTAAAC
Statistics
Matches: 140, Mismatches: 29, Indels: 42
0.66 0.14 0.20
Matches are distributed among these distances:
26 3 0.02
27 7 0.05
28 23 0.16
29 50 0.36
30 36 0.26
31 15 0.11
32 6 0.04
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAATTACCATTTTAACCTAGATTTCACC
Found at i:1119052 original size:117 final size:114
Alignment explanation
Indices: 1118830--1119239 Score: 474
Period size: 117 Copynumber: 3.5 Consensus size: 114
1118820 GCTCTCTAGT
* * *
1118830 CCCTAAACTTTCTAAAATTCCATTTTTAACCTCGATTTTATCC-AAAATTACCATTTGACCCCCA
1 CCCTAAACTTTCCAAAATTCCA-TTTTAACCTCGATTTCA-CCAAAAATTACCATTTTACCCCCA
* * *
1118894 AACTTTCCAAAATTCCTTTTTTAGCCTTGATTTCACC-AAAATTACCATTTTA
64 AACTTTCCAAAA-TCC-CTTTTAACCCTGATTTCACCAAAAATTACCATTTTA
*
1118946 CCCGTAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCA
1 CCC-TAAACTTTCCAAAATTCCA-TTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCA
*
1119011 AACTTTCCAAAATCCCATTTTAACCCTGATTTTACCAAAAATTACCATTTTA
64 AACTTTCCAAAATCCC-TTTTAACCCTGATTTCACCAAAAATTACCATTTTA
* * *
1119063 CCCCCTAAACATTCCAAAA-TCTCATCTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCC
1 --CCCTAAACTTTCCAAAATTC-CATTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCC
* * * * *
1119127 TAACTTTCCAAAA-CACTATTT-AGCCTCAATTTCACCAAAAATTACCGTTTTA
63 AAACTTTCCAAAATCCCT-TTTAACCCT-GATTTCACCAAAAATTACCATTTTA
* *
1119179 CCCTCGAACTTTCCAAAATTCCATTTTAACC-CTAATTTCACCAAAAATTA-CATTTTTACCC
1 CCCT-AAACTTTCCAAAATTCCATTTTAACCTC-GATTTCACCAAAAATTACCA-TTTTACCC
1119240 TCGAAAGTCA
Statistics
Matches: 261, Mismatches: 20, Indels: 27
0.85 0.06 0.09
Matches are distributed among these distances:
114 7 0.03
115 49 0.19
116 53 0.20
117 135 0.52
118 14 0.05
119 3 0.01
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.35
Consensus pattern (114 bp):
CCCTAAACTTTCCAAAATTCCATTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCAAA
CTTTCCAAAATCCCTTTTAACCCTGATTTCACCAAAAATTACCATTTTA
Found at i:1121791 original size:8 final size:8
Alignment explanation
Indices: 1121778--1121806 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1121768 CTATGTTGCC
1121778 TATTAGAT
1 TATTAGAT
1121786 TATTAGAT
1 TATTAGAT
1121794 TATTAGAT
1 TATTAGAT
1121802 TATTA
1 TATTA
1121807 TTTTATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (8 bp):
TATTAGAT
Found at i:1125920 original size:23 final size:25
Alignment explanation
Indices: 1125894--1125939 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1125884 CCAATTAAGG
1125894 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
1125917 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
1125940 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:1127053 original size:20 final size:22
Alignment explanation
Indices: 1127009--1127059 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 22
1126999 TATTATTATT
*
1127009 TATTTTT-ATTTTATTATTTGC
1 TATTTTTAATTTAATTATTTGC
1127030 -ATTTTTAATTTAATT-TTT-C
1 TATTTTTAATTTAATTATTTGC
1127049 TA-TTTTAATTT
1 TATTTTTAATTT
1127060 TTTTCTCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 10 0.37
20 10 0.37
21 7 0.26
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (22 bp):
TATTTTTAATTTAATTATTTGC
Found at i:1127074 original size:15 final size:16
Alignment explanation
Indices: 1127043--1127080 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1127033 TTTAATTTAA
1127043 TTTTTCTATTTTAATT
1 TTTTTCTATTTTAATT
*
1127059 TTTTTCTCTTTT-ATT
1 TTTTTCTATTTTAATT
*
1127074 TGTTTCT
1 TTTTTCT
1127081 GGCAGGTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTTCTATTTTAATT
Found at i:1133779 original size:29 final size:29
Alignment explanation
Indices: 1133707--1133994 Score: 221
Period size: 30 Copynumber: 9.8 Consensus size: 29
1133697 ATTTGGGGTC
* *
1133707 AAAATATAATTTTGGAAAAG-TTAAGGGGTA
1 AAAATGTAATTTTGGAAAAGTTTAA--GGTT
*
1133737 AAAATGTAATTTTGGGAAAGTTTAAGGTT
1 AAAATGTAATTTTGGAAAAGTTTAAGGTT
* * *
1133766 AAAACGTAATTTTGGAAAAGTTTAGGGGTA
1 AAAATGTAATTTTGGAAAAGTTTA-AGGTT
* *
1133796 AAAATGTGATTTTAGG-AAAGTTTAAGGCT
1 AAAATGTAATTTT-GGAAAAGTTTAAGGTT
* * *
1133825 GAAATGTGATTTTTGG--AAGTTTAGGGTT
1 AAAATGT-AATTTTGGAAAAGTTTAAGGTT
* *
1133853 CAAAATGTAATTTTGG-AAAGTTCAAGGGT
1 -AAAATGTAATTTTGGAAAAGTTTAAGGTT
* * *
1133882 CAAA-GTATGATTTTGAAAAAGTTTAAGGTC
1 AAAATGTA--ATTTTGGAAAAGTTTAAGGTT
* * *
1133912 AAAATATAATTTTGGAAAAGTTTAGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTA-AGGTT
* **
1133942 AAAATGTAATTTTGAAAAAGTTTAAGGAAC
1 AAAATGTAATTTTGGAAAAGTTTAAGG-TT
* *
1133972 AAAATATAATTTTAG-AAAGTTTA
1 AAAATGTAATTTTGGAAAAGTTTA
1133995 GGGATCTACT
Statistics
Matches: 208, Mismatches: 38, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
27 3 0.01
28 20 0.10
29 81 0.39
30 96 0.46
31 8 0.04
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTTAAGGTT
Found at i:1133991 original size:59 final size:59
Alignment explanation
Indices: 1133688--1133997 Score: 244
Period size: 59 Copynumber: 5.3 Consensus size: 59
1133678 AAAAAGAAAG
* *
1133688 TTTTAGAGAA-TTT-GGGGTCAAAATATAATTTTGGAAAAG-TTAAGGGGTA-AAAATGTAA
1 TTTTAGA-AAGTTTAGGGGTCAAAATGTAATTTTGAAAAAGTTTAA--GGTACAAAATGTAA
* * * * * * *
1133746 TTTTGGGAAAGTTTA-AGGTTAAAACGTAATTTTGGAAAAGTTTAGGGGTA-AAAATGTGA
1 TTTT-AGAAAGTTTAGGGGTCAAAATGTAATTTTGAAAAAGTTTA-AGGTACAAAATGTAA
* * * * * * *
1133805 TTTTAGGAAAGTTTAAGGCT-GAAATGTGATTTTTG--GAAGTTTAGGGTTCAAAATGTAA
1 TTTTA-GAAAGTTTAGGGGTCAAAATGT-AATTTTGAAAAAGTTTAAGGTACAAAATGTAA
* * * * * * *
1133863 TTTTGGAAAGTTCAAGGGTCAAAGTATGATTTTGAAAAAGTTTAAGGT-CAAAATATAA
1 TTTTAGAAAGTTTAGGGGTCAAAATGTAATTTTGAAAAAGTTTAAGGTACAAAATGTAA
* * *
1133921 TTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTGAAAAAGTTTAAGGAACAAAATATAA
1 TTTTAG-AAAGTTTAGGGGTCAAAATGTAATTTTGAAAAAGTTTAAGGTACAAAATGTAA
1133981 TTTTAGAAAGTTTAGGG
1 TTTTAGAAAGTTTAGGG
1133998 ATCTACTGGG
Statistics
Matches: 204, Mismatches: 34, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
57 21 0.10
58 44 0.22
59 113 0.55
60 26 0.13
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (59 bp):
TTTTAGAAAGTTTAGGGGTCAAAATGTAATTTTGAAAAAGTTTAAGGTACAAAATGTAA
Found at i:1136209 original size:173 final size:174
Alignment explanation
Indices: 1135901--1136266 Score: 477
Period size: 173 Copynumber: 2.1 Consensus size: 174
1135891 CTCTTGGTAT
* * * * *
1135901 ACTTCTCTATATCTCATCAAGAAGATGACCGTTTTATTGTTTCGACCCACTTCTCTGTATCTCAT
1 ACTTCTCTGTATCTCATCAAAAAGATGACCGCTTTATTGCTTCAACCCACTTCTCTGTATCTCAT
* * * * *
1135966 CAGGAATATAAGGGTTTGAAGTTTCACTCACATTGAACTTTGCTTCATTTGATTTGGTCTACTTC
66 CAGGAATATAAGGGTTTGAAGCTTCACTCACATTGAACTTTGCTTCATTTAAATTAGTCTACTCC
* * * *
1136031 TCTGTATCTCATCAGGAAGATGACCGCTTCA-TTATCGTGATCC
131 TCTGTAGCTCATCAAGAAGATGACCGCATCACTTATCGTAATCC
* *
1136074 ACTTCTCTGTTTCTCATCAAAAAGGTGACCGCTTTATTGCTTCAACCCACTTCAT-TGTATCTCA
1 ACTTCTCTGTATCTCATCAAAAAGATGACCGCTTTATTGCTTCAACCCACTTC-TCTGTATCTCA
* ** *
1136138 TCAGGAATATAGGGGTTTGGAAGCTTCACTCACATTGAGTTTTGCTTCA-TTAAATTAGTCTTCT
65 TCAGGAATATAAGGGTTT-GAAGCTTCACTCACATTGAACTTTGCTTCATTTAAATTAGTCTACT
**
1136202 CCTCTGTAGCTCATCAAGAAGATGACCGCATCACTTATTTTAATCC
129 CCTCTGTAGCTCATCAAGAAGATGACCGCATCACTTATCGTAATCC
**
1136248 GTTTCTCTGTATCTCATCA
1 ACTTCTCTGTATCTCATCA
1136267 GGAAGATGGA
Statistics
Matches: 165, Mismatches: 25, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
173 112 0.68
174 53 0.32
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (174 bp):
ACTTCTCTGTATCTCATCAAAAAGATGACCGCTTTATTGCTTCAACCCACTTCTCTGTATCTCAT
CAGGAATATAAGGGTTTGAAGCTTCACTCACATTGAACTTTGCTTCATTTAAATTAGTCTACTCC
TCTGTAGCTCATCAAGAAGATGACCGCATCACTTATCGTAATCC
Found at i:1136532 original size:209 final size:206
Alignment explanation
Indices: 1136073--1136690 Score: 806
Period size: 209 Copynumber: 2.9 Consensus size: 206
1136063 TATCGTGATC
* *
1136073 CACTTCTCTGTTTCTCATCAA-AAAGGTGACCGCTTTATTGCTTCAACCCACTTCATTGTATCTC
1 CACTTCTCTGTATCTCATCAAGAAA-GTGACCGCTTTATTGCTTCGACCCACTTC-TTGTATCTC
* ** * *
1136137 ATCAGGAATATAGGGGTTTGGAAGCTTCACTCACATTGAGTTTTGCTTCATTAAATTAGTCTTCT
64 ATCAGGAAGAT-GGGGTTTGGAAATTTCACTCACATTGAGTTTTGCTTCATTGAATTGGTCTTCT
* * * * * **
1136202 CCTCTGTAGCTCATCAAGAAGATGACCGCATCACTTATTTTAATCCGTTTCTCTGTATCTCATCA
128 TCTCTGTATCTCATCAGGAAGATAACCGCTTCA-TTA-TTTAATCCACTTCTCTGTATCTCATCA
* **
1136267 GGAAGATGGATTTGGT
191 GAAAGACAGATTTGGT
* * *
1136283 CTACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTATTGCTTCGACCCATTTCTCTGTATCTC
1 C-ACTTCTCTGTATCTCATCAAGAAAGTGACCGCTTTATTGCTTCGACCCACTTCT-TGTATCTC
* *
1136348 ATTAGGAAGATGGGGTTTGGAAATTTCACTCACATTGAGTTTTGCTTTATTGAATTGGTCTTCTT
64 ATCAGGAAGATGGGGTTTGGAAATTTCACTCACATTGAGTTTTGCTTCATTGAATTGGTCTTCTT
* * * * * *
1136413 CACTATATCTCATCAGGAAGATAATCGGTTCATTATCGTGATCCACTTCTCTGTATCTCATCAGA
129 CTCTGTATCTCATCAGGAAGATAACCGCTTCATTAT-TTAATCCACTTCTCTGTATCTCATCAGA
1136478 AAGACAGATTTGGCT
193 AAGACAGATTTGG-T
* * *
1136493 CACTTCTTTGTATCTCATCAAGAAAGTGACCGTTTTATTGGTTCGACCCACTTCTTCGTATCTCA
1 CACTTCTCTGTATCTCATCAAGAAAGTGACCGCTTTATTGCTTCGACCCACTTCTT-GTATCTCA
* *
1136558 TCAGAAAGATGGGGTTTGGAAATTTCACTCACATTGAGTTTTCCTTCATTGAATTGGTCTTCTTC
65 TCAGGAAGATGGGGTTTGGAAATTTCACTCACATTGAGTTTTGCTTCATTGAATTGGTCTTCTTC
* *
1136623 TCTGTATCTCATTAGGAAGATAACCGCTTCATTGATTTAATCCACTTCTTTGTATCTCATCAGGA
130 TCTGTATCTCATCAGGAAGATAACCGCTTCATT-ATTTAATCCACTTCTCTGTATCTCATCA-GA
1136688 AAG
193 AAG
1136691 TGACCGCTTT
Statistics
Matches: 354, Mismatches: 46, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
208 2 0.01
209 205 0.58
210 83 0.23
211 62 0.18
212 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (206 bp):
CACTTCTCTGTATCTCATCAAGAAAGTGACCGCTTTATTGCTTCGACCCACTTCTTGTATCTCAT
CAGGAAGATGGGGTTTGGAAATTTCACTCACATTGAGTTTTGCTTCATTGAATTGGTCTTCTTCT
CTGTATCTCATCAGGAAGATAACCGCTTCATTATTTAATCCACTTCTCTGTATCTCATCAGAAAG
ACAGATTTGGT
Found at i:1136677 original size:48 final size:48
Alignment explanation
Indices: 1136619--1136739 Score: 156
Period size: 48 Copynumber: 2.5 Consensus size: 48
1136609 AATTGGTCTT
* *
1136619 CTTCTCTGTATCTCATTAGGAAGATAACCGCTTCATTGA-TTTAATCCA
1 CTTCTCTGTATCTCATCAGGAAGATAACCGCTTCATT-ACTTTAACCCA
* * *
1136667 CTTCTTTGTATCTCATCAGGAA-AGTGACCGCTTTATTACTTTAACCCA
1 CTTCTCTGTATCTCATCAGGAAGA-TAACCGCTTCATTACTTTAACCCA
*
1136715 CTTCTCTATATCTCATCAGGAAGAT
1 CTTCTCTGTATCTCATCAGGAAGAT
1136740 GGGGTTGGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
47 2 0.03
48 60 0.95
49 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.37
Consensus pattern (48 bp):
CTTCTCTGTATCTCATCAGGAAGATAACCGCTTCATTACTTTAACCCA
Found at i:1136838 original size:171 final size:172
Alignment explanation
Indices: 1136493--1136859 Score: 540
Period size: 171 Copynumber: 2.1 Consensus size: 172
1136483 AGATTTGGCT
* ** * *
1136493 CACTTCTTTGTATCTCATCAAGAAAGTGACCGTTTTATTGGTTCGACCCACTTCTTCGTATCTCA
1 CACTTCTTTGTATCTCATCAAGAAAGTGACCGCTTTATTACTTCAACCCACTTCTTCATATCTCA
* * *
1136558 TCAGAAAGATGGGGTTTGGAAATTTCACTCACATTGAGTTTTCCTTCATTGAATTGGTCTTCTTC
66 TCAGAAAGATGGGGTTTGGAAATTTCACTCACATTGAGCTTTCCTTCATTAAATTGGTCTTCTCC
* * *
1136623 TCTGTATCTCATTAGGAAGATAACCGCTTCATTGATTTAATC
131 TCTGTATCTCATCAAGAAGATAACCACTTCATTGATTTAATC
* *
1136665 CACTTCTTTGTATCTCATCAGGAAAGTGACCGCTTTATTACTTTAACCCACTTC-TCTATATCTC
1 CACTTCTTTGTATCTCATCAAGAAAGTGACCGCTTTATTACTTCAACCCACTTCTTC-ATATCTC
* * * *
1136729 ATCAGGAAGATGGGG-TTGGAAGTTTTACTCACATTGAGCTTTGCTTCATTAAATTGGTCTTCTC
65 ATCAGAAAGATGGGGTTTGGAAATTTCACTCACATTGAGCTTTCCTTCATTAAATTGGTCTTCTC
*
1136793 CTCTGTATCTCATCAAGAAGATGACCACTTCATTGATTTAATC
130 CTCTGTATCTCATCAAGAAGATAACCACTTCATTGATTTAATC
*
1136836 CACTTCTCTGTATCTCATCAAGAA
1 CACTTCTTTGTATCTCATCAAGAA
1136860 GACGGATTTG
Statistics
Matches: 174, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
171 106 0.61
172 68 0.39
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (172 bp):
CACTTCTTTGTATCTCATCAAGAAAGTGACCGCTTTATTACTTCAACCCACTTCTTCATATCTCA
TCAGAAAGATGGGGTTTGGAAATTTCACTCACATTGAGCTTTCCTTCATTAAATTGGTCTTCTCC
TCTGTATCTCATCAAGAAGATAACCACTTCATTGATTTAATC
Found at i:1136843 original size:380 final size:381
Alignment explanation
Indices: 1136285--1137068 Score: 1119
Period size: 380 Copynumber: 2.1 Consensus size: 381
1136275 GATTTGGTCT
* * * * * *
1136285 ACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTATTGCTTCGACCCATTTCTCTGTATCTCAT
1 ACTTCTTTGTATCTCATCAGGAAAGTGACCGCTTTATTACTTCAACCCACTTCTCTATATCTCAT
* * * * *
1136350 TAGGAAGATGGGGTTTGGAAATTTCACTCACATTGAGTTTTGCTTTATTGAATTGGTCTTCTTCA
66 CAGGAAGATGGGGTTTGGAAATTTCACTCACATTGAGCTTTGCTTCATTAAATTGGTCTTCTCCA
* * ** *
1136415 CTATATCTCATCAGGAAGATAATCGGTTCATTATCGTGATCCACTTCTCTGTATCTCATC-AGAA
131 CTATATCTCATCAAGAAGATAACCACTTCATTATCGTAATCCACTTCTCTGTATCTCATCAAG-A
* * * * *
1136479 AGACAGATTTGG-CTCACTTCTTTGTATCTCATCAAGAAAGTGACCGTTTTATTGGTTCGACCCA
195 AGACAGATTTGGTCT-ACTTCTCTATATCTCATCAAGAAAGTGACCGCTTTATTGCTTCAACCCA
* *
1136543 CTTCT-TCGTATCTCATCAGAAAGATGGGGTTTGGAAATTTCACTCACATTGAGTTTTCCTTCAT
259 CTTCTCT-GTATCTCATCAGAAAGATGGGGTTTGGAAATGTCACTCACATTGAGTTTTCATTCAT
*
1136607 TGAATTGGTCTTCTTCTCTGTATCTCATTAGGAAGATAACCGCTTCATTGATTTAATCC
323 TGAATTGGTCTTCTTCTCTGTATCTCATCAGGAAGATAACCGCTTCATTGATTTAATCC
*
1136666 ACTTCTTTGTATCTCATCAGGAAAGTGACCGCTTTATTACTTTAACCCACTTCTCTATATCTCAT
1 ACTTCTTTGTATCTCATCAGGAAAGTGACCGCTTTATTACTTCAACCCACTTCTCTATATCTCAT
* * *
1136731 CAGGAAGATGGGG-TTGGAAGTTTTACTCACATTGAGCTTTGCTTCATTAAATTGGTCTTCTCCT
66 CAGGAAGATGGGGTTTGGAAATTTCACTCACATTGAGCTTTGCTTCATTAAATTGGTCTTCTCCA
* * *
1136795 CTGTATCTCATCAAGAAGATGACCACTTCATTGAT-TTAATCCACTTCTCTGTATCTCATCAAGA
131 CTATATCTCATCAAGAAGATAACCACTTCATT-ATCGTAATCCACTTCTCTGTATCTCATCAAGA
* * * *
1136859 AGACGGATTTGGTCTACTTCTCTATATCTCATCAGGAAGGTGACTGCTTTATTGCTTCAACCCAC
195 AGACAGATTTGGTCTACTTCTCTATATCTCATCAAGAAAGTGACCGCTTTATTGCTTCAACCCAC
* * *
1136924 TTCTCTGTATCTCATCAGGAAGATGGGGTTTGGAAATGTCACTTACATTGAGTTTTGATTCATTG
260 TTCTCTGTATCTCATCAGAAAGATGGGGTTTGGAAATGTCACTCACATTGAGTTTTCATTCATTG
* * *
1136989 AATTGGTCTTCTTCTCTGTATTTTATCAGGAAGATGACCGCTTCATTGATTTAATCC
325 AATTGGTCTTCTTCTCTGTATCTCATCAGGAAGATAACCGCTTCATTGATTTAATCC
*
1137046 ACTTCTTTATATCTCATCAGGAA
1 ACTTCTTTGTATCTCATCAGGAA
1137069 GAAGGATTTG
Statistics
Matches: 357, Mismatches: 42, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
380 280 0.78
381 77 0.22
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (381 bp):
ACTTCTTTGTATCTCATCAGGAAAGTGACCGCTTTATTACTTCAACCCACTTCTCTATATCTCAT
CAGGAAGATGGGGTTTGGAAATTTCACTCACATTGAGCTTTGCTTCATTAAATTGGTCTTCTCCA
CTATATCTCATCAAGAAGATAACCACTTCATTATCGTAATCCACTTCTCTGTATCTCATCAAGAA
GACAGATTTGGTCTACTTCTCTATATCTCATCAAGAAAGTGACCGCTTTATTGCTTCAACCCACT
TCTCTGTATCTCATCAGAAAGATGGGGTTTGGAAATGTCACTCACATTGAGTTTTCATTCATTGA
ATTGGTCTTCTTCTCTGTATCTCATCAGGAAGATAACCGCTTCATTGATTTAATCC
Found at i:1136927 original size:85 final size:85
Alignment explanation
Indices: 1136782--1136946 Score: 222
Period size: 85 Copynumber: 1.9 Consensus size: 85
1136772 CTTCATTAAA
* * * *
1136782 TTGGTCTTCTCCTCTGTATCTCATCAAGAAGATGACCACTTCATTGATTTAATCCACTTCTCTGT
1 TTGGTCTACTCCTCTATATCTCATCAAGAAGATGACCACTTCATTGATTCAACCCACTTCTCTGT
1136847 ATCTCATCAAGAAGACGGAT
66 ATCTCATCAAGAAGACGGAT
* * * ** * *
1136867 TTGGTCTACTTCTCTATATCTCATCAGGAAGGTGACTGCTTTATTGCTTCAACCCACTTCTCTGT
1 TTGGTCTACTCCTCTATATCTCATCAAGAAGATGACCACTTCATTGATTCAACCCACTTCTCTGT
*
1136932 ATCTCATCAGGAAGA
66 ATCTCATCAAGAAGA
1136947 TGGGGTTTGG
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 68 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (85 bp):
TTGGTCTACTCCTCTATATCTCATCAAGAAGATGACCACTTCATTGATTCAACCCACTTCTCTGT
ATCTCATCAAGAAGACGGAT
Found at i:1137048 original size:589 final size:593
Alignment explanation
Indices: 1135901--1137275 Score: 1940
Period size: 589 Copynumber: 2.3 Consensus size: 593
1135891 CTCTTGGTAT
* * *
1135901 ACTTCTCTATATCTCATCAAG-AAGATGACCGTTTTATTGTTTCGACCCACTTCTCTGTATCTCA
1 ACTTCTTTGTATCTCATCAAGAAAG-TGACCGTTTTATTGCTTCGACCCACTTCTCTGTATCTCA
* * * * *
1135965 TCAGGAATATAAGGGTTT-GAAGTTTCACTCACATTGAACTTTGCTTCATTTGATTTGGTCTACT
65 TCAGGAAGAT-GGGGTTTGGAAGTTTCACTCACATTGAGCTTTGCTTCA-TTGAATTGGTCTTCT
* * * *
1136029 TCTCTGTATCTCATCAGGAAGATGACCGCTTCATT-ATCGTGATCCACTTCTCTGTTTCTCATCA
128 TCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGAT-TTAATCCACTTCTTTGTATCTCATCA
* * * *
1136093 -AAAAGGTGACCGCTTTATTGCTTCAACCCACTTCATTGTATCTCATCAGGAATATAGGGGTTTG
192 GGAAAGGTGACCGCTTTATTACTTCAACCCACTTCATTATATCTCATCAGGAAGATAGGGGTTTG
*
1136157 GAAGCTTCACTCACATTGAGTTTTGCTTCATTAAATTAGTCTTCTCCTCTGTAGCTCATCAAGAA
257 GAAGCTTCACTCACATTGAGCTTTGCTTCATTAAATTAGTCTTCTCCTCTGTAGCTCATCAAGAA
* ** * *
1136222 GATGACCGCATCACTTATTTTAATCCGTTTCTCTGTATCTCATCAGGAAGATGGATTTGGTCTAC
322 GATGACCACATCACTTATTTTAATCCACTTCTCTGTATCTCATCAAGAAGACGGATTTGGTCTAC
* * * *
1136287 TTCTCTGTATCTCATCAGGAAGGTGACCGCTTTATTGCTTCGACCCATTTCTCTGTATCTCATTA
387 TTCTCTATATCTCATCAGGAAGGTGACCGCTTTATTGCTTCAACCCACTTCTCTGTATCTCATCA
* * *
1136352 GGAAGATGGGGTTTGGAAATTTCACTCACATTGAGTTTTGCTTTATTGAATTGGTCTTCTTCACT
452 GGAAGATGGGGTTTGGAAATGTCACTCACATTGAGTTTTGATTCATTGAATTGGTCTTCTTCACT
* * * *
1136417 ATATCTCATCAGGAAGATAATCGGTTCATTATCGTGATCCACTTCTCTGTATCTCATCAGAAAGA
517 ATATCTCATCAGGAAGATAACCGCTTCATTATCGTAATCCACTTCTCTATATCTCATCAGAAAGA
1136482 CA-GATTTGG-CTC
582 -AGGATTTGGTC-C
*
1136494 ACTTCTTTGTATCTCATCAAGAAAGTGACCGTTTTATTGGTTCGACCCACTTCT-TCGTATCTCA
1 ACTTCTTTGTATCTCATCAAGAAAGTGACCGTTTTATTGCTTCGACCCACTTCTCT-GTATCTCA
* * * *
1136558 TCAGAAAGATGGGGTTTGGAAATTTCACTCACATTGAGTTTTCCTTCATTGAATTGGTCTTCTTC
65 TCAGGAAGATGGGGTTTGGAAGTTTCACTCACATTGAGCTTTGCTTCATTGAATTGGTCTTCTTC
* *
1136623 TCTGTATCTCATTAGGAAGATAACCGCTTCATTGATTTAATCCACTTCTTTGTATCTCATCAGGA
130 TCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTTTGTATCTCATCAGGA
*
1136688 AA-GTGACCGCTTTATTACTTTAACCCACTTC-TCTATATCTCATCAGGAAGAT-GGGG-TTGGA
195 AAGGTGACCGCTTTATTACTTCAACCCACTTCAT-TATATCTCATCAGGAAGATAGGGGTTTGGA
* * * *
1136749 AGTTTTACTCACATTGAGCTTTGCTTCATTAAATTGGTCTTCTCCTCTGTATCTCATCAAGAAGA
259 AGCTTCACTCACATTGAGCTTTGCTTCATTAAATTAGTCTTCTCCTCTGTAGCTCATCAAGAAGA
*
1136814 TGACCACTTCA-TTGA-TTTAATCCACTTCTCTGTATCTCATCAAGAAGACGGATTTGGTCTACT
324 TGACCACATCACTT-ATTTTAATCCACTTCTCTGTATCTCATCAAGAAGACGGATTTGGTCTACT
*
1136877 TCTCTATATCTCATCAGGAAGGTGACTGCTTTATTGCTTCAACCCACTTCTCTGTATCTCATCAG
388 TCTCTATATCTCATCAGGAAGGTGACCGCTTTATTGCTTCAACCCACTTCTCTGTATCTCATCAG
* * *
1136942 GAAGATGGGGTTTGGAAATGTCACTTACATTGAGTTTTGATTCATTGAATTGGTCTTCTTCTCTG
453 GAAGATGGGGTTTGGAAATGTCACTCACATTGAGTTTTGATTCATTGAATTGGTCTTCTTCACTA
* * * * * *
1137007 TATTTTATCAGGAAGATGACCGCTTCATTGAT-TTAATCCACTTCTTTATATCTCATCAGGAAGA
518 TATCTCATCAGGAAGATAACCGCTTCATT-ATCGTAATCCACTTCTCTATATCTCATCAGAAAGA
1137071 AGGATTTGGTCC
582 AGGATTTGGTCC
* * * * *
1137083 ACTT-TTCTGTTTCTCATCAAGAAGGTGACCGCTTTATTACTTTGACCCACTTCTCTGTATCTCA
1 ACTTCTT-TGTATCTCATCAAGAAAGTGACCGTTTTATTGCTTCGACCCACTTCTCTGTATCTCA
* *
1137147 TCAGGAAGATGGGG-TTGGAAGTTTTACTCACATTGAGCTTTGCTTCATTGAATTGGTCTTCTCC
65 TCAGGAAGATGGGGTTTGGAAGTTTCACTCACATTGAGCTTTGCTTCATTGAATTGGTCTTCTTC
*
1137211 TCTGTATCTCATCAGGAAGATGACCGCCTCATTGATTTAATCCA-TT-TTATGTATCTCATCAGG
130 TCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTT-TGTATCTCATCAGG
1137274 AA
194 AA
1137276 GACGAATTTG
Statistics
Matches: 699, Mismatches: 70, Indels: 32
0.87 0.09 0.04
Matches are distributed among these distances:
586 2 0.00
587 18 0.03
588 89 0.13
589 290 0.41
590 79 0.11
591 5 0.01
592 119 0.17
593 94 0.13
594 3 0.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (593 bp):
ACTTCTTTGTATCTCATCAAGAAAGTGACCGTTTTATTGCTTCGACCCACTTCTCTGTATCTCAT
CAGGAAGATGGGGTTTGGAAGTTTCACTCACATTGAGCTTTGCTTCATTGAATTGGTCTTCTTCT
CTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTTTGTATCTCATCAGGAA
AGGTGACCGCTTTATTACTTCAACCCACTTCATTATATCTCATCAGGAAGATAGGGGTTTGGAAG
CTTCACTCACATTGAGCTTTGCTTCATTAAATTAGTCTTCTCCTCTGTAGCTCATCAAGAAGATG
ACCACATCACTTATTTTAATCCACTTCTCTGTATCTCATCAAGAAGACGGATTTGGTCTACTTCT
CTATATCTCATCAGGAAGGTGACCGCTTTATTGCTTCAACCCACTTCTCTGTATCTCATCAGGAA
GATGGGGTTTGGAAATGTCACTCACATTGAGTTTTGATTCATTGAATTGGTCTTCTTCACTATAT
CTCATCAGGAAGATAACCGCTTCATTATCGTAATCCACTTCTCTATATCTCATCAGAAAGAAGGA
TTTGGTCC
Found at i:1137359 original size:207 final size:208
Alignment explanation
Indices: 1136663--1137577 Score: 1282
Period size: 208 Copynumber: 4.4 Consensus size: 208
1136653 ATTGATTTAA
* * * *
1136663 TCCACTTCTTTGTATCTCATCAGGAAA-GTGACCGCTTTATTACTTTAACCCACTTCTCTATATC
1 TCCACTTCTCTGTATCTCATCA-GAAAGGTGACCGCTTTATTGCTTCAACCCACTTCTCTGTATC
*
1136727 TCATCAGGAAGATGGGGTTGGAAGTTTTACTCACATTGAGCTTTGCTTCATTAAATTGGTCTTCT
65 TCATCAGGAAGATGGGGTTGGAAGTTTTACTCACATTGAGCTTTGCTTCATTGAATTGGTCTTCT
* * * *
1136792 CCTCTGTATCTCATCAAGAAGATGACCACTTCATTGATTTAATCCACTTCTCTGTATCTCATCAA
130 CCTCTGTATCTCATCAAGAAGATGACCGCCTCATTGATTTAATCCACTTCTTTGTATCTCATCAG
1136857 GAAGACGGATTTGG
195 GAAGACGGATTTGG
* * * *
1136871 TCTACTTCTCTATATCTCATCAGGAAGGTGACTGCTTTATTGCTTCAACCCACTTCTCTGTATCT
1 TCCACTTCTCTGTATCTCATCAGAAAGGTGACCGCTTTATTGCTTCAACCCACTTCTCTGTATCT
* * * * * *
1136936 CATCAGGAAGATGGGGTTTGGAAATGTCACTTACATTGAGTTTTGATTCATTGAATTGGTCTTCT
66 CATCAGGAAGATGGGG-TTGGAAGTTTTACTCACATTGAGCTTTGCTTCATTGAATTGGTCTTCT
* * * * * *
1137001 TCTCTGTATTTTATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTTTATATCTCATCAG
130 CCTCTGTATCTCATCAAGAAGATGACCGCCTCATTGATTTAATCCACTTCTTTGTATCTCATCAG
*
1137066 GAAGAAGGATTTGG
195 GAAGACGGATTTGG
* * * **
1137080 TCCACTTTTCTGTTTCTCATCA-AGAAGGTGACCGCTTTATTACTTTGACCCACTTCTCTGTATC
1 TCCACTTCTCTGTATCTCATCAGA-AAGGTGACCGCTTTATTGCTTCAACCCACTTCTCTGTATC
1137144 TCATCAGGAAGATGGGGTTGGAAGTTTTACTCACATTGAGCTTTGCTTCATTGAATTGGTCTTCT
65 TCATCAGGAAGATGGGGTTGGAAGTTTTACTCACATTGAGCTTTGCTTCATTGAATTGGTCTTCT
*
1137209 CCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGATTTAATCCA-TT-TTATGTATCTCATCA
130 CCTCTGTATCTCATCAAGAAGATGACCGCCTCATTGATTTAATCCACTTCTT-TGTATCTCATCA
*
1137272 GGAAGACGAATTTGG
194 GGAAGACGGATTTGG
* * * *
1137287 TCCACTTCTCTGTATCTCATCAGAAAGGTGACCGCTTTATTGCTTCGACCCACTTTTTTGTATAT
1 TCCACTTCTCTGTATCTCATCAGAAAGGTGACCGCTTTATTGCTTCAACCCACTTCTCTGTATCT
* * * *
1137352 AATCAGGAAGATAGGGTTGAAAGTTTTACTCACATTTAGCTTTGCTTCATTGAATTGGTCTTCTC
66 CATCAGGAAGATGGGGTTGGAAGTTTTACTCACATTGAGCTTTGCTTCATTGAATTGGTCTTCTC
* * * *
1137417 CTCTGTATCTCATCAAGAAGATGACCGCCTCATTGATTTAATCGACTTCTTTTTATCTAATTAGG
131 CTCTGTATCTCATCAAGAAGATGACCGCCTCATTGATTTAATCCACTTCTTTGTATCTCATCAGG
1137482 AAGACGGATTTGG
196 AAGACGGATTTGG
* * * * **
1137495 TTCACTTCTCTGTATCTCATCAGGAAA-GTGACCACTTTATTGATTTAATTCACTTCTCTGTATC
1 TCCACTTCTCTGTATCTCATCA-GAAAGGTGACCGCTTTATTGCTTCAACCCACTTCTCTGTATC
*
1137559 TCATTAGGAAGATGGGGTT
65 TCATCAGGAAGATGGGGTT
1137578 TGAAAATTTC
Statistics
Matches: 623, Mismatches: 76, Indels: 16
0.87 0.11 0.02
Matches are distributed among these distances:
206 2 0.00
207 189 0.30
208 244 0.39
209 188 0.30
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (208 bp):
TCCACTTCTCTGTATCTCATCAGAAAGGTGACCGCTTTATTGCTTCAACCCACTTCTCTGTATCT
CATCAGGAAGATGGGGTTGGAAGTTTTACTCACATTGAGCTTTGCTTCATTGAATTGGTCTTCTC
CTCTGTATCTCATCAAGAAGATGACCGCCTCATTGATTTAATCCACTTCTTTGTATCTCATCAGG
AAGACGGATTTGG
Found at i:1149450 original size:30 final size:30
Alignment explanation
Indices: 1149398--1149669 Score: 292
Period size: 30 Copynumber: 9.2 Consensus size: 30
1149388 TTTTGGAGAA
* *
1149398 TTTAAGGTTAAAAA-GTAATTTTGGAAAAG
1 TTTAAGGGTAAAAATGTAATTTTAGAAAAG
* * *
1149427 TTTAAGGGTAAAAATGCAATTTTGGGAAAG
1 TTTAAGGGTAAAAATGTAATTTTAGAAAAG
*
1149457 TTTAA-GGT-TAAATGTAATTTTAGAAAAG
1 TTTAAGGGTAAAAATGTAATTTTAGAAAAG
* *
1149485 TTTAGGGGTAAAAATGCAATTTT-GAGAAAG
1 TTTAAGGGTAAAAATGTAATTTTAGA-AAAG
* * *
1149515 ATTGA-GGTCAAAATGTAATTTTAGAAAAG
1 TTTAAGGGTAAAAATGTAATTTTAGAAAAG
* *
1149544 TTTAAGGGTTAAAATATAATTTTAGAAAAG
1 TTTAAGGGTAAAAATGTAATTTTAGAAAAG
* *
1149574 TTTAAGGGTTAAAATATAATTTTAGAAAAG
1 TTTAAGGGTAAAAATGTAATTTTAGAAAAG
1149604 TTTAAGGGTAAAAATGT-ATTGTT-GAAAAG
1 TTTAAGGGTAAAAATGTAATT-TTAGAAAAG
* *
1149633 TTT-AGAGATTAAAATGTAATTTCTA-AAAAG
1 TTTAAG-GGTAAAAATGTAATTT-TAGAAAAG
1149663 TTTAAGG
1 TTTAAGG
1149670 ACCTACTAGA
Statistics
Matches: 208, Mismatches: 23, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
28 22 0.11
29 65 0.31
30 119 0.57
31 2 0.01
ACGTcount: A:0.43, C:0.01, G:0.21, T:0.35
Consensus pattern (30 bp):
TTTAAGGGTAAAAATGTAATTTTAGAAAAG
Found at i:1149450 original size:58 final size:60
Alignment explanation
Indices: 1149378--1149669 Score: 320
Period size: 59 Copynumber: 5.0 Consensus size: 60
1149368 AATGGGGTCA
*
1149378 AAAAATG-AATTTTTGGAG-AA-TTTAAGGTTAAAAAGTAATTTTGGAAAAGTTTAAGGGT
1 AAAAATGCAA-TTTTGGAGAAAGTTTAAGGTTAAAAAGTAATTTTAGAAAAGTTTAAGGGT
* *
1149436 AAAAATGCAATTTTGG-GAAAGTTTAAGGTT-AAATGTAATTTTAGAAAAGTTTAGGGGT
1 AAAAATGCAATTTTGGAGAAAGTTTAAGGTTAAAAAGTAATTTTAGAAAAGTTTAAGGGT
* * * *
1149494 AAAAATGCAATTTT-GAGAAAGATTGAGGTCAAAATGTAATTTTAGAAAAGTTTAAGGGT
1 AAAAATGCAATTTTGGAGAAAGTTTAAGGTTAAAAAGTAATTTTAGAAAAGTTTAAGGGT
* ** *
1149553 TAAAATATAATTTTAGA-AAAGTTTAAGGGTTAAAATA-TAATTTTAGAAAAGTTTAAGGGT
1 AAAAATGCAATTTTGGAGAAAGTTTAA-GGTTAAAA-AGTAATTTTAGAAAAGTTTAAGGGT
* * *
1149613 AAAAATG-TATTGTT-GA-AAAGTTTAGAGATTAAAATGTAATTTCTA-AAAAGTTTAAGG
1 AAAAATGCAATT-TTGGAGAAAGTTTA-AGGTTAAAAAGTAATTT-TAGAAAAGTTTAAGG
1149670 ACCTACTAGA
Statistics
Matches: 203, Mismatches: 19, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
57 2 0.01
58 65 0.32
59 94 0.46
60 42 0.21
ACGTcount: A:0.44, C:0.01, G:0.21, T:0.34
Consensus pattern (60 bp):
AAAAATGCAATTTTGGAGAAAGTTTAAGGTTAAAAAGTAATTTTAGAAAAGTTTAAGGGT
Found at i:1149588 original size:89 final size:90
Alignment explanation
Indices: 1149398--1149669 Score: 321
Period size: 89 Copynumber: 3.1 Consensus size: 90
1149388 TTTTGGAGAA
* * *
1149398 TTTAA-GGTTAAAAAGTAATTTTG-GAAAAGTTTAAGGGTAAAAATGCAATTTTGGGAAAGTTTA
1 TTTAAGGGTTAAAATGTAATTTTGAGAAAAGTTTAAGGGTAAAAATGTAATTTT-GAAAAGTTTA
1149461 A-GGTT-AAATGTAATTTTAGAAAAG
65 AGGGTTAAAATGTAATTTTAGAAAAG
* * * * * *
1149485 TTTAGGGGTAAAAATGCAATTTTGAG-AAAGATTGA-GGTCAAAATGTAATTTTAGAAAAGTTTA
1 TTTAAGGGTTAAAATGTAATTTTGAGAAAAGTTTAAGGGTAAAAATGTAATTTT-GAAAAGTTTA
*
1149548 AGGGTTAAAATATAATTTTAGAAAAG
65 AGGGTTAAAATGTAATTTTAGAAAAG
*
1149574 TTTAAGGGTTAAAATATAATTTT-AGAAAAGTTTAAGGGTAAAAATGT-ATTGTTGAAAAGTTT-
1 TTTAAGGGTTAAAATGTAATTTTGAGAAAAGTTTAAGGGTAAAAATGTAATT-TTGAAAAGTTTA
*
1149636 AGAGATTAAAATGTAATTTCTA-AAAAG
65 AG-GGTTAAAATGTAATTT-TAGAAAAG
1149663 TTTAAGG
1 TTTAAGG
1149670 ACCTACTAGA
Statistics
Matches: 156, Mismatches: 20, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
87 29 0.19
88 30 0.19
89 83 0.53
90 14 0.09
ACGTcount: A:0.43, C:0.01, G:0.21, T:0.35
Consensus pattern (90 bp):
TTTAAGGGTTAAAATGTAATTTTGAGAAAAGTTTAAGGGTAAAAATGTAATTTTGAAAAGTTTAA
GGGTTAAAATGTAATTTTAGAAAAG
Found at i:1151192 original size:6 final size:6
Alignment explanation
Indices: 1151181--1151213 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1151171 ATTTGAACAT
*
1151181 TTTAAA TTTAAA -ATAAA TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
1151214 TTTTTTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:1153000 original size:11 final size:11
Alignment explanation
Indices: 1152984--1153025 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
1152974 TAACCATTTA
1152984 TAATAAAATAT
1 TAATAAAATAT
1152995 TAATAAAATATCT
1 TAATAAAATA--T
*
1153008 TATTAAAATAT
1 TAATAAAATAT
1153019 TAATAAA
1 TAATAAA
1153026 GTAATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 17 0.63
13 10 0.37
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:1153041 original size:24 final size:24
Alignment explanation
Indices: 1152987--1153053 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
1152977 CCATTTATAA
*
1152987 TAAAATATTAATAAAATATCTTAT
1 TAAAATATTAATAAAATATATTAT
*
1153011 TAAAATATTAATAAAGTAATATTAT
1 TAAAATATTAATAAAAT-ATATTAT
*
1153036 T-TAATAATT-ATAAAATAT
1 TAAAAT-ATTAATAAAATAT
1153054 TATTGAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 2 0.05
24 25 0.68
25 10 0.27
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (24 bp):
TAAAATATTAATAAAATATATTAT
Found at i:1166611 original size:179 final size:179
Alignment explanation
Indices: 1166311--1166671 Score: 713
Period size: 179 Copynumber: 2.0 Consensus size: 179
1166301 TGTTAGCAAT
*
1166311 TGGTTAGCAGAAGTTAGTTAGGGTTTACTTCTATAAATAGAAGTCTGGTCAAGGTTCAATGTATG
1 TGGTTAGCAGAAGTTAGTCAGGGTTTACTTCTATAAATAGAAGTCTGGTCAAGGTTCAATGTATG
1166376 TAGCTTTGATAATATTCAAATTCAGAAAATCAATTCTAAGAATTCTTCATTTCTTTCCTCTTGTT
66 TAGCTTTGATAATATTCAAATTCAGAAAATCAATTCTAAGAATTCTTCATTTCTTTCCTCTTGTT
1166441 TTACGATAAAACTTAGGGTGTTTACATGGTATCAGTCGCTTGAAGTTCC
131 TTACGATAAAACTTAGGGTGTTTACATGGTATCAGTCGCTTGAAGTTCC
1166490 TGGTTAGCAGAAGTTAGTCAGGGTTTACTTCTATAAATAGAAGTCTGGTCAAGGTTCAATGTATG
1 TGGTTAGCAGAAGTTAGTCAGGGTTTACTTCTATAAATAGAAGTCTGGTCAAGGTTCAATGTATG
1166555 TAGCTTTGATAATATTCAAATTCAGAAAATCAATTCTAAGAATTCTTCATTTCTTTCCTCTTGTT
66 TAGCTTTGATAATATTCAAATTCAGAAAATCAATTCTAAGAATTCTTCATTTCTTTCCTCTTGTT
1166620 TTACGATAAAACTTAGGGTGTTTACATGGTATCAGTCGCTTGAAGTTCC
131 TTACGATAAAACTTAGGGTGTTTACATGGTATCAGTCGCTTGAAGTTCC
1166669 TGG
1 TGG
1166672 GCGTTGTTGT
Statistics
Matches: 181, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
179 181 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (179 bp):
TGGTTAGCAGAAGTTAGTCAGGGTTTACTTCTATAAATAGAAGTCTGGTCAAGGTTCAATGTATG
TAGCTTTGATAATATTCAAATTCAGAAAATCAATTCTAAGAATTCTTCATTTCTTTCCTCTTGTT
TTACGATAAAACTTAGGGTGTTTACATGGTATCAGTCGCTTGAAGTTCC
Found at i:1179449 original size:58 final size:58
Alignment explanation
Indices: 1179385--1179504 Score: 188
Period size: 58 Copynumber: 2.1 Consensus size: 58
1179375 AAAATGAGTT
*
1179385 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGATTTAAAAATATTT-GAGTTTA
1 GTTTATGAGTATTATTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGA-TTTA
* * *
1179443 GTTTATGAGTATTTTTTAAGAATGAAATTATATTTGGGTTTAAAAATATTTGGATTTA
1 GTTTATGAGTATTATTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGATTTA
1179501 GTTT
1 GTTT
1179505 GTTGATGGAT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
58 55 0.96
59 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (58 bp):
GTTTATGAGTATTATTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGATTTA
Found at i:1179668 original size:9 final size:9
Alignment explanation
Indices: 1179642--1179680 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
1179632 TAATATAATT
*
1179642 TTATTCGAT
1 TTATTCGAA
1179651 TTATTCGAA
1 TTATTCGAA
1179660 TTATTCGAA
1 TTATTCGAA
* *
1179669 TAATTCAAA
1 TTATTCGAA
1179678 TTA
1 TTA
1179681 GAAAATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (9 bp):
TTATTCGAA
Found at i:1179754 original size:14 final size:14
Alignment explanation
Indices: 1179735--1179764 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1179725 ACTTGATTCG
1179735 TTTAATTCGAATAA
1 TTTAATTCGAATAA
1179749 TTTAATTCGAATAA
1 TTTAATTCGAATAA
1179763 TT
1 TT
1179765 CAAAATCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (14 bp):
TTTAATTCGAATAA
Found at i:1191569 original size:42 final size:42
Alignment explanation
Indices: 1191507--1191636 Score: 133
Period size: 42 Copynumber: 3.1 Consensus size: 42
1191497 GGGGTTGAAT
*
1191507 ATCCTATTCTATTACTTTAAATTACTTTAAATCACTTTTTTTA
1 ATCCTATTC-ACTACTTTAAATTACTTTAAATCACTTTTTTTA
*
1191550 ATCCTATTCACTACTTTAAATTACTTTAAATCCCACCTTTTTT-
1 ATCCTATTCACTACTTTAAATTACTTTAAAT--CACTTTTTTTA
* * * *
1191593 AT-TTAAATC-CTATTTTAAATTACTTTAATTC-CTATTTTTTA
1 ATCCT-ATTCACTACTTTAAATTACTTTAAATCACT-TTTTTTA
1191634 ATC
1 ATC
1191637 TGTAAATTAT
Statistics
Matches: 74, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
39 1 0.01
40 7 0.09
41 2 0.03
42 41 0.55
43 14 0.19
44 9 0.12
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (42 bp):
ATCCTATTCACTACTTTAAATTACTTTAAATCACTTTTTTTA
Found at i:1198039 original size:59 final size:59
Alignment explanation
Indices: 1197938--1198294 Score: 450
Period size: 59 Copynumber: 6.1 Consensus size: 59
1197928 TTTGACTTTC
* * * *
1197938 GGGGGTAAAAAT-GTAAATTTTGGTGGAATC-AGGGTTAAAAATGGAATTTTGGAAAGTTC
1 GGGGGT-AAAATGGTAATTTTTGGTGAAATCGA-GGTCAAAAATGGAATTTTGGAAAGTTT
** * * * * * * * *
1197997 AAGGGTGAAACGGTAATTTTTTGTGAAATCGGGGTTAAAAATGGGATTTTAGAAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTT
* *
1198056 GGGGGTAAAATGGTAATTTTTGGTGAAACCAAGGTCAAAAATGGAATTTTGGAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTT
*
1198115 GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGAAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTT
* * * *
1198174 GGGGGTAAAATTGTAATTTTTGGTGAAACCGAGGTCAAAAATAGAAGTTTGG-AAGTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTT
* * * *
1198232 GGGGGTTAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTT
1198291 GGGG
1 GGGG
1198295 TCAAAATATA
Statistics
Matches: 257, Mismatches: 38, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
58 53 0.21
59 204 0.79
ACGTcount: A:0.34, C:0.04, G:0.31, T:0.32
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTT
Found at i:1198163 original size:30 final size:31
Alignment explanation
Indices: 1198062--1198164 Score: 94
Period size: 30 Copynumber: 3.5 Consensus size: 31
1198052 GTTCGGGGGT
* *
1198062 AAAATGGTAATTTTTGGTGAAACCAAGGTCA
1 AAAATGGTAATTTTTGGTGAAATCGAGGTCA
* *
1198093 AAAATGG-AA-TTTT-G-GAAAGTTTGGGGGT--
1 AAAATGGTAATTTTTGGTGAAA---TCGAGGTCA
1198121 AAAATGGTAATTTTTGGTGAAATCGAGGTCA
1 AAAATGGTAATTTTTGGTGAAATCGAGGTCA
1198152 AAAATGG-AATTTT
1 AAAATGGTAATTTT
1198165 GAAAAGTTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
27 4 0.07
28 8 0.14
29 11 0.19
30 15 0.26
31 15 0.26
32 4 0.07
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGTGAAATCGAGGTCA
Found at i:1200110 original size:17 final size:17
Alignment explanation
Indices: 1200090--1200140 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
1200080 GTTTCAAATT
*
1200090 ATTTTAAATATATTTAA
1 ATTTTAAATAAATTTAA
* *
1200107 ATTTAAAATAAATATAA
1 ATTTTAAATAAATTTAA
*
1200124 A-TTTGAATAAATTTAA
1 ATTTTAAATAAATTTAA
1200140 A
1 A
1200141 ATTAATTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
ATTTTAAATAAATTTAA
Found at i:1200112 original size:6 final size:6
Alignment explanation
Indices: 1200101--1200162 Score: 53
Period size: 6 Copynumber: 11.2 Consensus size: 6
1200091 TTTTAAATAT
* * * *
1200101 ATTTAA ATTTAA A-ATAA ATATAA ATTTGA A--TAA ATTTAA AATT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
1200145 ATTTAA ATTT-A ATTTAA A
1 ATTTAA ATTTAA ATTTAA A
1200163 ATTCAAGTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
4 3 0.07
5 13 0.29
6 29 0.64
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:1200124 original size:27 final size:28
Alignment explanation
Indices: 1200101--1200162 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
1200091 TTTTAAATAT
1200101 ATTTAAATTTAAAATAAATATAAATTTGA
1 ATTTAAATTTAAAATAAATATAAATTT-A
* *
1200130 A--TAAATTTAAAATTAATTTAAATTTA
1 ATTTAAATTTAAAATAAATATAAATTTA
1200156 ATTTAAA
1 ATTTAAA
1200163 ATTCAAGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 2 0.07
27 22 0.76
28 4 0.14
29 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
ATTTAAATTTAAAATAAATATAAATTTA
Found at i:1211910 original size:77 final size:73
Alignment explanation
Indices: 1211640--1211997 Score: 637
Period size: 73 Copynumber: 4.9 Consensus size: 73
1211630 AAGTAACGGT
1211640 TTTTTTTTTTAATATCATTATTGAGAGAGGAAGATGACAAAATTTAAATGTACTATTTAAGTGCC
1 TTTTTTTTTTAATATCATTATTGAGAGAGGAAGATGACAAAATTTAAATGTACTATTTAAGTGCC
1211705 ATATACTC
66 ATATACTC
* * *
1211713 TCTCTTTTTTAATATCATTATTGAGAGAGGAAGATGACAAAATTTAAATGTATTATTTAAGTGCC
1 TTTTTTTTTTAATATCATTATTGAGAGAGGAAGATGACAAAATTTAAATGTACTATTTAAGTGCC
1211778 ATATACTC
66 ATATACTC
1211786 TTTTTTTTTTAATATCATTATTGAGAGAGGAAGATGACAAAATTTAAATGTACTATTTAAGTGCC
1 TTTTTTTTTTAATATCATTATTGAGAGAGGAAGATGACAAAATTTAAATGTACTATTTAAGTGCC
1211851 ATATACTCTC
66 ATATA--CTC
1211861 TTTTTTTTTTTTAATATCATTATTGAGAGAGGAAGATGACAAAATTTAAATGTACTATTTAAGTG
1 --TTTTTTTTTTAATATCATTATTGAGAGAGGAAGATGACAAAATTTAAATGTACTATTTAAGTG
1211926 CCATATACTC
64 CCATATACTC
*
1211936 -TTTTTTTTTAATATCATTATTGAGAGAGGAAGGTGACAAAATTTAAATGTACTATTTAAGTG
1 TTTTTTTTTTAATATCATTATTGAGAGAGGAAGATGACAAAATTTAAATGTACTATTTAAGTG
1211998 TCATCTAGAC
Statistics
Matches: 274, Mismatches: 7, Indels: 9
0.94 0.02 0.03
Matches are distributed among these distances:
72 61 0.22
73 137 0.50
75 6 0.02
77 70 0.26
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.41
Consensus pattern (73 bp):
TTTTTTTTTTAATATCATTATTGAGAGAGGAAGATGACAAAATTTAAATGTACTATTTAAGTGCC
ATATACTC
Found at i:1217137 original size:84 final size:84
Alignment explanation
Indices: 1216963--1217137 Score: 253
Period size: 84 Copynumber: 2.1 Consensus size: 84
1216953 GAATCATATC
* * *
1216963 ATTATTTATTAAATATCGATTTAAAATCTAACAAACAATAGTAATTGATTGATGGATGGTAAACA
1 ATTATTTATTAAATATAGATTTAAAATCCAACAAACAATAGTAATTAATTGATGGATGGTAAACA
* *
1217028 AAAGTAGGAAGACGAGGAG
66 AAACTAAGAAGACGAGGAG
* * *
1217047 ATTATTTATTAAATATAGGTTTAAAATCCAACAAACAATAGTAATTAATTGTTGGATTGGTAAAT
1 ATTATTTATTAAATATAGATTTAAAATCCAACAAACAATAGTAATTAATTGATGGA-TGGTAAAC
*
1217112 AGAACTAAGAAGACGAGGAG
65 AAAACTAAGAAGACGAGGAG
1217132 A-TATTT
1 ATTATTT
1217138 GAACTTTCAA
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
84 56 0.69
85 25 0.31
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.31
Consensus pattern (84 bp):
ATTATTTATTAAATATAGATTTAAAATCCAACAAACAATAGTAATTAATTGATGGATGGTAAACA
AAACTAAGAAGACGAGGAG
Found at i:1220990 original size:96 final size:96
Alignment explanation
Indices: 1220812--1220993 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 96
1220802 AAAGATGTTT
* ** * * *
1220812 GATTATCTTGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCATAACCTAAGA
1 GATTATCTTGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAAATTTCAAAACCTAAAA
* *
1220877 TAAGGAAACATTGCCTCGATTAAGGGTATTC
66 TAAAGAAACATTACCTCGATTAAGGGTATTC
1220908 GATTAT-TTCGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAAATTTCAAAA-CTCAA
1 GATTATCTT-GATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAAATTTCAAAACCT-AA
*
1220971 AATAAA-AGAATATTACCTCGATT
64 AATAAAGA-AACATTACCTCGATT
1220994 TTAAAGTTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
95 5 0.07
96 69 0.93
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (96 bp):
GATTATCTTGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAAATTTCAAAACCTAAAA
TAAAGAAACATTACCTCGATTAAGGGTATTC
Found at i:1221287 original size:58 final size:59
Alignment explanation
Indices: 1221225--1221360 Score: 150
Period size: 59 Copynumber: 2.3 Consensus size: 59
1221215 GGATACCGGG
* *** * *
1221225 GGGTAAAATGGTAATTTTGGGACATTTTTGGG-TTAAAAATA-AAATTTTGGACGTTCGA
1 GGGTAAAATGGTAATTTTGGCA-AAAATTGGGATCAAAAATAGAAATTTTGGACATTCGA
* * **
1221283 GGGTAAAATAGTAATTTTTGCAAAAATTGGGATCAAAAATAGAGTTTTTGGACATTCGA
1 GGGTAAAATGGTAATTTTGGCAAAAATTGGGATCAAAAATAGAAATTTTGGACATTCGA
*
1221342 GGGTAGAATGGTAATTTTG
1 GGGTAAAATGGTAATTTTG
1221361 AGAGTTTCGG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
57 6 0.10
58 27 0.43
59 30 0.48
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.35
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTGGCAAAAATTGGGATCAAAAATAGAAATTTTGGACATTCGA
Found at i:1221378 original size:58 final size:59
Alignment explanation
Indices: 1221259--1221392 Score: 157
Period size: 58 Copynumber: 2.3 Consensus size: 59
1221249 TTTTTGGGTT
* * *
1221259 AAAAATA-AAATTTTGGACGTTCGAGGGTAAAATAGTAATTTTTGCAAAAATTGGGATC
1 AAAAATAGAATTTTTGGACATTCGAGGGTAAAATAGTAATTTTTGCAAAAATTCGGATC
* * * * **
1221317 AAAAATAGAGTTTTTGGACATTCGAGGGTAGAATGGTAA-TTTTG-AGAGTTTCGGAGTC
1 AAAAATAGAATTTTTGGACATTCGAGGGTAAAATAGTAATTTTTGCAAAAATTCGGA-TC
1221375 AAAAATAGAATTTTTGGA
1 AAAAATAGAATTTTTGGA
1221393 AGTTTCGAGG
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
57 7 0.11
58 31 0.48
59 26 0.41
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (59 bp):
AAAAATAGAATTTTTGGACATTCGAGGGTAAAATAGTAATTTTTGCAAAAATTCGGATC
Found at i:1221397 original size:30 final size:30
Alignment explanation
Indices: 1221363--1221572 Score: 141
Period size: 29 Copynumber: 7.2 Consensus size: 30
1221353 TAATTTTGAG
*
1221363 AGTTTCGGAGTCAAAAATAGAATTTTTGGA
1 AGTTTCGGAGTCAAAAATGGAATTTTTGGA
*
1221393 AGTTTC-GAGGTCAAAAATGGAATTATTGGA
1 AGTTTCGGA-GTCAAAAATGGAATTTTTGGA
* * *
1221423 AG-CTCGGGGGCAAAAATGGAATTTTTGGA
1 AGTTTCGGAGTCAAAAATGGAATTTTTGGA
* * * *
1221452 AATTTGGGGGT-AAAAATGGAATTTTTAGA
1 AGTTTCGGAGTCAAAAATGGAATTTTTGGA
** * **
1221481 AGTTT-GG-GGGAAAAATGTAATTTTTTAA
1 AGTTTCGGAGTCAAAAATGGAATTTTTGGA
* * *
1221509 AG-TTCAGG-GGCAAAAATGTATTTTTTGGA
1 AGTTTC-GGAGTCAAAAATGGAATTTTTGGA
* * *
1221538 AGTTTTATGG-G-CAAAAATGTAATTTTTGAA
1 AG-TTT-CGGAGTCAAAAATGGAATTTTTGGA
1221568 AGTTT
1 AGTTT
1221573 TGGGGTTAAA
Statistics
Matches: 148, Mismatches: 23, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
27 3 0.02
28 19 0.13
29 69 0.47
30 52 0.35
31 5 0.03
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (30 bp):
AGTTTCGGAGTCAAAAATGGAATTTTTGGA
Found at i:1221400 original size:59 final size:59
Alignment explanation
Indices: 1221259--1221402 Score: 152
Period size: 59 Copynumber: 2.5 Consensus size: 59
1221249 TTTTTGGGTT
* * *
1221259 AAAAATA-AAATTTTGGACGTTCGAGGGTAAAATAGTAATTTTTGCAAAAATTGGGATC
1 AAAAATAGAATTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTTGCAAAAATTCGGATC
* * * * **
1221317 AAAAATAGAGTTTTTGGACA-TTCGAGGGTAGAATGGTAA-TTTTG-AGAGTTTCGGAGTC
1 AAAAATAGAATTTTTGGA-AGTTCGAGGGTAAAATAGTAATTTTTGCAAAAATTCGGA-TC
1221375 AAAAATAGAATTTTTGGAAGTTTCGAGG
1 AAAAATAGAATTTTTGGAAG-TTCGAGG
1221403 TCAAAAATGG
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
57 8 0.11
58 31 0.44
59 32 0.45
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (59 bp):
AAAAATAGAATTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTTGCAAAAATTCGGATC
Found at i:1221573 original size:30 final size:29
Alignment explanation
Indices: 1221352--1221613 Score: 167
Period size: 30 Copynumber: 8.9 Consensus size: 29
1221342 GGGTAGAATG
* * *
1221352 GTAA-TTTTGAGAGTTTCGGAGTCAAAAAT
1 GTAATTTTTGAAAGTTTAGG-GGCAAAAAT
* * *
1221381 AG-AATTTTTGGAAGTTTCGAGGTCAAAAAT
1 -GTAATTTTTGAAAGTTTAG-GGGCAAAAAT
* * * * **
1221411 GGAATTATTGGAAGCTCGGGGGCAAAAAT
1 GTAATTTTTGAAAGTTTAGGGGCAAAAAT
* * *
1221440 GGAATTTTTGGAAA-TTTGGGGGTAAAAAT
1 GTAATTTTT-GAAAGTTTAGGGGCAAAAAT
* *
1221469 GGAATTTTT-AGAAGTTT-GGGGGAAAAAT
1 GTAATTTTTGA-AAGTTTAGGGGCAAAAAT
* *
1221497 GTAATTTTTTAAAGTTCAGGGGCAAAAAT
1 GTAATTTTTGAAAGTTTAGGGGCAAAAAT
* * *
1221526 GTATTTTTTGGAAGTTTTATGGGCAAAAAT
1 GTAATTTTTGAAAG-TTTAGGGGCAAAAAT
* *
1221556 GTAATTTTTGAAAGTTTTGGGGTTAAAAAT
1 GTAATTTTTGAAAGTTTAGGGG-CAAAAAT
* *
1221586 ATAATTTTGGAGAAGTTT-GGGGACAAAA
1 GTAATTTTTGA-AAGTTTAGGGG-CAAAA
1221614 TATGATTTTT
Statistics
Matches: 191, Mismatches: 30, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
27 1 0.01
28 25 0.13
29 72 0.38
30 86 0.45
31 7 0.04
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (29 bp):
GTAATTTTTGAAAGTTTAGGGGCAAAAAT
Found at i:1221614 original size:59 final size:58
Alignment explanation
Indices: 1221352--1221624 Score: 168
Period size: 59 Copynumber: 4.7 Consensus size: 58
1221342 GGGTAGAATG
* * * * * *
1221352 GTAATTTTGAG-AGTTTCGGAGTCAAAAATAG-AATTTTTGGAAGTTTCGAGGTCAAAAAT
1 GTAATTTTGAGAAGTTTAGGGGAC-AAAAT-GTAATTTTTGAAAGTTTTGGGGT-AAAAAT
* * * * * *
1221411 GGAATTATTG-GAAG-CTCGGGGGCAAAAATGGAATTTTTGGAAA-TTTGGGGGTAAAAAT
1 GTAATT-TTGAGAAGTTTAGGGGAC-AAAATGTAATTTTT-GAAAGTTTTGGGGTAAAAAT
* * * * ** *
1221469 GGAATTTTTAGAAGTTTGGGGGA-AAAATGTAATTTTTTAAAGTTCAGGGGCAAAAAT
1 GTAATTTTGAGAAGTTTAGGGGACAAAATGTAATTTTTGAAAGTTTTGGGGTAAAAAT
* *
1221526 GTATTTTTTG-GAAGTTTTATGGG-CAAAAATGTAATTTTTGAAAGTTTTGGGGTTAAAAAT
1 GTA-ATTTTGAGAAG-TTTAGGGGAC-AAAATGTAATTTTTGAAAGTTTTGGGG-TAAAAAT
* * *
1221586 ATAATTTTGGAGAAGTTT-GGGGACAAAATATGATTTTTG
1 GTAATTTT-GAGAAGTTTAGGGGACAAAATGTAATTTTTG
1221625 GACAATTTAG
Statistics
Matches: 169, Mismatches: 30, Indels: 30
0.74 0.13 0.13
Matches are distributed among these distances:
56 3 0.02
57 33 0.20
58 27 0.16
59 81 0.48
60 21 0.12
61 4 0.02
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.35
Consensus pattern (58 bp):
GTAATTTTGAGAAGTTTAGGGGACAAAATGTAATTTTTGAAAGTTTTGGGGTAAAAAT
Found at i:1221637 original size:29 final size:29
Alignment explanation
Indices: 1221581--1221638 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1221571 TTTGGGGTTA
* *
1221581 AAAATATAATTTTGGAGAAGTTTGGGGAC
1 AAAATATAATTTTGGACAAGTTTAGGGAC
*
1221610 AAAATATGATTTTTGGACAA-TTTAGGGAC
1 AAAATAT-AATTTTGGACAAGTTTAGGGAC
1221639 CTCCAAGGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (29 bp):
AAAATATAATTTTGGACAAGTTTAGGGAC
Found at i:1222860 original size:2 final size:2
Alignment explanation
Indices: 1222853--1222882 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1222843 TAATAATTTA
1222853 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
1222883 TTATGTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1223498 original size:52 final size:52
Alignment explanation
Indices: 1223428--1223541 Score: 174
Period size: 52 Copynumber: 2.2 Consensus size: 52
1223418 AAATATGTTG
* *
1223428 AAATCTATTTGACAATCATAATGATAAAGTAGAGGCAAGTTTATATGGATATA
1 AAATC-ATATGACAATCATAATGATAAAGTAGAGACAAGTTTATATGGATATA
* *
1223481 AAATCATATGACAATCATAATGATAAAGTAGAGACATGTTTATATGGATGTA
1 AAATCATATGACAATCATAATGATAAAGTAGAGACAAGTTTATATGGATATA
*
1223533 TAATCATAT
1 AAATCATAT
1223542 CATGATGTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 51 0.91
53 5 0.09
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (52 bp):
AAATCATATGACAATCATAATGATAAAGTAGAGACAAGTTTATATGGATATA
Found at i:1226212 original size:52 final size:52
Alignment explanation
Indices: 1226139--1226240 Score: 204
Period size: 52 Copynumber: 2.0 Consensus size: 52
1226129 CTAAATTGGC
1226139 TTTATAGTATTAGGTTTCGATTTTTCAAAAGAATTACATATGAATCATTTAT
1 TTTATAGTATTAGGTTTCGATTTTTCAAAAGAATTACATATGAATCATTTAT
1226191 TTTATAGTATTAGGTTTCGATTTTTCAAAAGAATTACATATGAATCATTT
1 TTTATAGTATTAGGTTTCGATTTTTCAAAAGAATTACATATGAATCATTT
1226241 TCTATGATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.46
Consensus pattern (52 bp):
TTTATAGTATTAGGTTTCGATTTTTCAAAAGAATTACATATGAATCATTTAT
Found at i:1228310 original size:24 final size:24
Alignment explanation
Indices: 1228249--1228311 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
1228239 TAGAGTAATA
* *
1228249 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
1228273 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
1228297 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
1228312 AATTATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:1230294 original size:24 final size:24
Alignment explanation
Indices: 1230233--1230295 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
1230223 TAGAGTAATA
* * *
1230233 AGAGTTTGACTCAAATAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
1230257 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
1230281 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
1230296 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:1230548 original size:20 final size:20
Alignment explanation
Indices: 1230525--1230562 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1230515 ATTTAGTCAT
*
1230525 TTTTATTTTTATTTTAATAC
1 TTTTATTTTTAATTTAATAC
1230545 TTTTATTTTTAATTTAAT
1 TTTTATTTTTAATTTAAT
1230563 TTTTAAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTATTTTTAATTTAATAC
Found at i:1245179 original size:15 final size:15
Alignment explanation
Indices: 1245159--1245187 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1245149 AAATGTCATT
1245159 AAGAGCTAGATTGAG
1 AAGAGCTAGATTGAG
1245174 AAGAGCTAGATTGA
1 AAGAGCTAGATTGA
1245188 AAAAGGATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.31, T:0.21
Consensus pattern (15 bp):
AAGAGCTAGATTGAG
Found at i:1246026 original size:17 final size:17
Alignment explanation
Indices: 1246006--1246074 Score: 86
Period size: 17 Copynumber: 4.1 Consensus size: 17
1245996 TCAATTTTAA
1246006 ATTTTAAATGTT-AATTT
1 ATTTTAAAT-TTAAATTT
*
1246023 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
1246040 ATTTTTAATTTAAATTT
1 ATTTTAAATTTAAATTT
* *
1246057 ACTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
1246074 A
1 A
1246075 AAATTTAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
16 2 0.04
17 44 0.96
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:1246040 original size:6 final size:6
Alignment explanation
Indices: 1246001--1246082 Score: 55
Period size: 6 Copynumber: 13.8 Consensus size: 6
1245991 TAAACTCAAT
* * * *
1246001 TTTAAA TTTTAAA TGTT-AA TTT-AT TTTAAG TTTAAA TTT-AT TTTTAA
1 TTTAAA -TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
1246048 TTTAAA TTT-AC TTTGAA TTTAAA TTTAAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA
1246083 TTAAAAGTCC
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
5 14 0.23
6 33 0.54
7 14 0.23
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:1246113 original size:14 final size:15
Alignment explanation
Indices: 1246081--1246116 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1246071 TTTAAAATTT
*
1246081 AATTAAAAGTCCAAA
1 AATTACAAGTCCAAA
1246096 AATTACAAGTCC-AA
1 AATTACAAGTCCAAA
1246110 AATTACA
1 AATTACA
1246117 TTACTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.56, C:0.17, G:0.06, T:0.22
Consensus pattern (15 bp):
AATTACAAGTCCAAA
Found at i:1246400 original size:17 final size:17
Alignment explanation
Indices: 1246380--1246448 Score: 86
Period size: 17 Copynumber: 4.1 Consensus size: 17
1246370 TCAATTTTAA
1246380 ATTTTAAATGTT-AATTT
1 ATTTTAAAT-TTAAATTT
*
1246397 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
1246414 ATTTTCAATTTAAATTT
1 ATTTTAAATTTAAATTT
* *
1246431 ACTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
1246448 A
1 A
1246449 AAATTTAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
16 2 0.04
17 44 0.96
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:1246414 original size:6 final size:6
Alignment explanation
Indices: 1246375--1246456 Score: 55
Period size: 6 Copynumber: 13.8 Consensus size: 6
1246365 TAAACTCAAT
* * * *
1246375 TTTAAA TTTTAAA TGTT-AA TTT-AT TTTAAG TTTAAA TTT-AT TTTCAA
1 TTTAAA -TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
1246422 TTTAAA TTT-AC TTTGAA TTTAAA TTTAAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA
1246457 TTAAAAGTCC
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
5 14 0.23
6 33 0.54
7 14 0.23
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:1246425 original size:23 final size:23
Alignment explanation
Indices: 1246375--1246456 Score: 62
Period size: 23 Copynumber: 3.5 Consensus size: 23
1246365 TAAACTCAAT
*
1246375 TTTAAATTTTAAATGTTAATTTAT
1 TTTAAA-TTTAAATGTTAATTTAA
* *
1246399 TTTAAGTTTAAAT-TTATTTTCAA
1 TTTAAATTTAAATGTTAATTT-AA
*
1246422 TTTAAATTT-ACT-TTGAATTTAAA
1 TTTAAATTTAAATGTT-AATTT-AA
1246445 TTTAAAATTTAA
1 TTT-AAATTTAA
1246457 TTAAAAGTCC
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
22 10 0.21
23 25 0.53
24 11 0.23
25 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTAAATTTAAATGTTAATTTAA
Found at i:1246487 original size:14 final size:15
Alignment explanation
Indices: 1246455--1246491 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1246445 TTTAAAATTT
*
1246455 AATTAAAAGTCCAAA
1 AATTACAAGTCCAAA
1246470 AATTACAAGTCC-AA
1 AATTACAAGTCCAAA
1246484 AATTACAA
1 AATTACAA
1246492 ACCCAAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.57, C:0.16, G:0.05, T:0.22
Consensus pattern (15 bp):
AATTACAAGTCCAAA
Found at i:1247076 original size:10 final size:10
Alignment explanation
Indices: 1247061--1247088 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1247051 ATACGCATTC
1247061 AATAAATAAT
1 AATAAATAAT
1247071 AATAAATAAT
1 AATAAATAAT
1247081 AATAAATA
1 AATAAATA
1247089 TAGCGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AATAAATAAT
Found at i:1248308 original size:29 final size:29
Alignment explanation
Indices: 1248256--1248575 Score: 256
Period size: 29 Copynumber: 10.9 Consensus size: 29
1248246 CCTAAAAGGT
*
1248256 CCCTAAACTTTCCATAAATCACATTTTTAC
1 CCCTAAAC-TTCCAAAAATCACATTTTTAC
* * * *
1248286 TCTTGAACCTCCAAAAATCACATTTTTAC
1 CCCTAAACTTCCAAAAATCACATTTTTAC
* *
1248315 CCCTAAACTTTTCAAAAATTACATTTTTAC
1 CCCTAAAC-TTCCAAAAATCACATTTTTAC
* *
1248345 CCCTAAACTTCTCAAAAATCATATTTTT-G
1 CCCTAAACTTC-CAAAAATCACATTTTTAC
*
1248374 CCCTCGAACTTCCAAAAATCACATTTTTAC
1 CCCT-AAACTTCCAAAAATCACATTTTTAC
* * *
1248404 CCCTATATTTCCAAAAATCACATTTTTTC
1 CCCTAAACTTCCAAAAATCACATTTTTAC
* * *
1248433 CCCTATATTTCCAAAAAGT-GCATTTTTA-
1 CCCTAAACTTCCAAAAA-TCACATTTTTAC
* * *
1248461 CCCTCGAACTTCTCAAAAATTACATTTTTGC
1 CCCT-AAACTTC-CAAAAATCACATTTTTAC
* *
1248492 CCCCAAACTTCCAAAAATCACCA-TTTTGC
1 CCCTAAACTTCCAAAAATCA-CATTTTTAC
** * * *
1248521 CCCCGAGCATCCAAAAATTACCA-TTTTA-
1 CCCTAAACTTCCAAAAATCA-CATTTTTAC
* *
1248549 CCCTCAAATTTCCAAAAGTCACATTTT
1 CCCT-AAACTTCCAAAAATCACATTTT
1248576 CGACCCCCAA
Statistics
Matches: 234, Mismatches: 44, Indels: 25
0.77 0.15 0.08
Matches are distributed among these distances:
28 9 0.04
29 145 0.62
30 77 0.33
31 3 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.34
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATCACATTTTTAC
Found at i:1248339 original size:59 final size:59
Alignment explanation
Indices: 1248256--1248575 Score: 268
Period size: 59 Copynumber: 5.5 Consensus size: 59
1248246 CCTAAAAGGT
* * * *
1248256 CCCTAAACTTTCCATAAATCACATTTTTACTCTTGAACCTC-CAAAAATCACATTTTTAC
1 CCCTAAACTTTCCAAAAATCACATTTTTACCCCTGAACTTCTCAAAAATCACATTTTT-C
* * * * *
1248315 CCCTAAACTTTTCAAAAATTACATTTTTACCCCTAAACTTCTCAAAAATCATATTTTTG
1 CCCTAAACTTTCCAAAAATCACATTTTTACCCCTGAACTTCTCAAAAATCACATTTTTC
* *
1248374 CCCTCGAAC-TTCCAAAAATCACATTTTTACCCCT-ATATTTC-CAAAAATCACATTTTTTC
1 CCCT-AAACTTTCCAAAAATCACATTTTTACCCCTGA-ACTTCTCAAAAATCACA-TTTTTC
* * *
1248433 CCCTATA-TTTCCAAAAAGT-GCATTTTTA-CCCTCGAACTTCTCAAAAATTACATTTTTGC
1 CCCTAAACTTTCCAAAAA-TCACATTTTTACCCCT-GAACTTCTCAAAAATCACATTTTT-C
* * * * * * *
1248492 CCCCAAAC-TTCCAAAAATCACCA-TTTTGCCCCCGAGCATC-CAAAAATTACCA-TTTTA
1 CCCTAAACTTTCCAAAAATCA-CATTTTTACCCCTGAACTTCTCAAAAATCA-CATTTTTC
*
1248549 CCCTCAAA-TTTCCAAAAGTCACATTTT
1 CCCT-AAACTTTCCAAAAATCACATTTT
1248576 CGACCCCCAA
Statistics
Matches: 213, Mismatches: 30, Indels: 37
0.76 0.11 0.13
Matches are distributed among these distances:
57 9 0.04
58 69 0.32
59 112 0.53
60 23 0.11
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.34
Consensus pattern (59 bp):
CCCTAAACTTTCCAAAAATCACATTTTTACCCCTGAACTTCTCAAAAATCACATTTTTC
Found at i:1248459 original size:28 final size:28
Alignment explanation
Indices: 1248295--1248523 Score: 167
Period size: 30 Copynumber: 7.8 Consensus size: 28
1248285 CTCTTGAACC
*
1248295 TCCAAAAATCACATTTTTACCCCTAAACTT
1 TCCAAAAATCACATTTTT-CCCCTATA-TT
* * * *
1248325 TTCAAAAATTACATTTTTACCCCTAAACT
1 TCCAAAAATCACATTTTT-CCCCTATATT
* * *
1248354 TCTCAAAAATCATATTTTTGCCCTCGA-ACT
1 TC-CAAAAATCACATTTTT-CCC-CTATATT
1248384 TCCAAAAATCACATTTTTACCCCTATATT
1 TCCAAAAATCACATTTTT-CCCCTATATT
1248413 TCCAAAAATCACATTTTTTCCCCTATATT
1 TCCAAAAATCACA-TTTTTCCCCTATATT
* * *
1248442 TCCAAAAAGT-GCATTTTTACCCTCGA-ACT
1 TCCAAAAA-TCACATTTTT-CCC-CTATATT
* * * *
1248471 TCTCAAAAATTACATTTTTGCCCCCAAACT
1 TC-CAAAAATCACATTTTT-CCCCTATATT
*
1248501 TCCAAAAATCACCATTTTGCCCC
1 TCCAAAAATCA-CATTTTTCCCC
1248524 CGAGCATCCA
Statistics
Matches: 168, Mismatches: 20, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
28 7 0.04
29 77 0.46
30 82 0.49
31 2 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (28 bp):
TCCAAAAATCACATTTTTCCCCTATATT
Found at i:1248534 original size:88 final size:87
Alignment explanation
Indices: 1248277--1248597 Score: 265
Period size: 88 Copynumber: 3.6 Consensus size: 87
1248267 CCATAAATCA
* * * * * * *
1248277 CATTTTTACTCTTGAACCTCCAAAAATCACATTTTTACCCCTAAACTTTTCAAAAATTACATTTT
1 CATTTTTACCCTCGAACTTCCAAAAATCACATTTTTGCCCCCAAA-TTTCCAAAAATCACATTTT
** * *
1248342 TACCCCTAAACTTCTCAAAAA-T-C
65 GCCCCCGACA-TTC-CAAAAAGTAC
* * * * *
1248365 ATATTTTTGCCCTCGAACTTCCAAAAATCACATTTTTACCCCTATATTTCCAAAAATCACATTTT
1 -CATTTTTACCCTCGAACTTCCAAAAATCACATTTTTGCCCCCAAATTTCCAAAAATCACATTTT
** * * *
1248430 TTCCCCTATATTTCCAAAAAGT-G
65 GCCCCCGACA-TTCCAAAAAGTAC
* *
1248453 CATTTTTACCCTCGAACTTCTCAAAAATTACATTTTTGCCCCCAAACTTCCAAAAATCACCATTT
1 CATTTTTACCCTCGAACTTC-CAAAAATCACATTTTTGCCCCCAAATTTCCAAAAATCA-CATTT
*
1248518 TGCCCCCGAGCA-TCCAAAAATTAC
64 TGCCCCCGA-CATTCCAAAAAGTAC
* * * * *
1248542 CA-TTTTACCCTCAAATTTCCAAAAGTCACATTTTCGACCCCCAATTTTCCAAAAAT
1 CATTTTTACCCTCGAACTTCCAAAAATCACATTTTTG-CCCCCAAATTTCCAAAAAT
1248598 TTGGTTTTAA
Statistics
Matches: 194, Mismatches: 32, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
87 38 0.20
88 103 0.53
89 52 0.27
90 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (87 bp):
CATTTTTACCCTCGAACTTCCAAAAATCACATTTTTGCCCCCAAATTTCCAAAAATCACATTTTG
CCCCCGACATTCCAAAAAGTAC
Found at i:1248560 original size:117 final size:116
Alignment explanation
Indices: 1248295--1248575 Score: 320
Period size: 117 Copynumber: 2.4 Consensus size: 116
1248285 CTCTTGAACC
* *
1248295 TCCAAAAATCACATTTTTACCCCTAAACTTTTCAAAAATTACATTTTTACCCCTAAACTTCTCAA
1 TCCAAAAATCACATTTTTACCCCTAAA-TTTCCAAAAAGTACATTTTTACCCCTAAACTTCTCAA
* * * * * *
1248360 AAATCATATTTTTGCCCTCGAACTTCCAAAAATCACATTTTTACCCCTATATT
65 AAATCACATTTTTGCCCCCAAACTTCCAAAAATCACATTTTGACCCCGACA-T
* * * *
1248413 TCCAAAAATCACATTTTTTCCCCTATATTTCCAAAAAGTGCATTTTTA-CCCTCGAACTTCTCAA
1 TCCAAAAATCACATTTTTACCCCTAAATTTCCAAAAAGTACATTTTTACCCCT-AAACTTCTCAA
* *
1248477 AAATTACATTTTTGCCCCCAAACTTCCAAAAATCACCATTTTGCCCCCGAGCA-
65 AAATCACATTTTTGCCCCCAAACTTCCAAAAATCA-CATTTTGACCCCGA-CAT
*
1248530 TCCAAAAATTACCA-TTTTA-CCCTCAAATTTCC-AAAAGTCACATTTT
1 TCCAAAAATCA-CATTTTTACCCCT-AAATTTCCAAAAAGT-ACATTTT
1248576 CGACCCCCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
116 14 0.10
117 86 0.62
118 38 0.27
119 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (116 bp):
TCCAAAAATCACATTTTTACCCCTAAATTTCCAAAAAGTACATTTTTACCCCTAAACTTCTCAAA
AATCACATTTTTGCCCCCAAACTTCCAAAAATCACATTTTGACCCCGACAT
Found at i:1250337 original size:23 final size:23
Alignment explanation
Indices: 1250310--1250356 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1250300 ATGTTTCTGT
1250310 AGTAAAGAATATGAGAAGAGAGA
1 AGTAAAGAATATGAGAAGAGAGA
1250333 AGTAAAGAATATGAGAAGAGAGA
1 AGTAAAGAATATGAGAAGAGAGA
1250356 A
1 A
1250357 ACTAAGGCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.30, T:0.13
Consensus pattern (23 bp):
AGTAAAGAATATGAGAAGAGAGA
Found at i:1251778 original size:29 final size:30
Alignment explanation
Indices: 1251746--1251804 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
1251736 TATGGTTTAA
1251746 TGTGTAATTGTATACAT-AAAGTTTGATTT
1 TGTGTAATTGTATACATGAAAGTTTGATTT
* *
1251775 TGTGTAATTTTATACATGAAATTTTGATTT
1 TGTGTAATTGTATACATGAAAGTTTGATTT
1251805 GATCCAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (30 bp):
TGTGTAATTGTATACATGAAAGTTTGATTT
Found at i:1255535 original size:31 final size:29
Alignment explanation
Indices: 1255466--1255536 Score: 72
Period size: 31 Copynumber: 2.4 Consensus size: 29
1255456 AGTTGTGGAT
* *
1255466 TTAATTTTTATACTTTAATTCGATCAATT
1 TTAATTTTTGTACTTTAATTCGATCAATA
* *
1255495 TTAGTTTTTGTACTTTTCGAATT-GATCGATA
1 TTAATTTTTGTAC-TTT--AATTCGATCAATA
1255526 TTAATTTTTGT
1 TTAATTTTTGT
1255537 GTTTTTCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
29 11 0.32
30 3 0.09
31 16 0.47
32 4 0.12
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.56
Consensus pattern (29 bp):
TTAATTTTTGTACTTTAATTCGATCAATA
Found at i:1256066 original size:19 final size:16
Alignment explanation
Indices: 1256030--1256061 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1256020 ACTATGATTT
1256030 AAGTTCAACTCCATCA
1 AAGTTCAACTCCATCA
1256046 AAGTTCAACTCCATCA
1 AAGTTCAACTCCATCA
1256062 TCAAATGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.06, T:0.25
Consensus pattern (16 bp):
AAGTTCAACTCCATCA
Found at i:1262396 original size:2 final size:2
Alignment explanation
Indices: 1262391--1262423 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1262381 TATACACAAA
1262391 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 A
1262424 ATAATGGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1265091 original size:20 final size:21
Alignment explanation
Indices: 1265066--1265104 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1265056 TATTTTTTAA
1265066 AAATTC-G-AAAATTAAATTTT
1 AAATTCAGTAAAA-TAAATTTT
1265086 AAATTCAGTAAAATAAATT
1 AAATTCAGTAAAATAAATT
1265105 GGGGATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (21 bp):
AAATTCAGTAAAATAAATTTT
Found at i:1281916 original size:16 final size:16
Alignment explanation
Indices: 1281891--1281932 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1281881 CTTAAGTGTC
* *
1281891 AAACTCAAAATTATCT
1 AAACTCAAAATAACCT
*
1281907 AAATTCAAAATAACCT
1 AAACTCAAAATAACCT
1281923 AAACTCAAAA
1 AAACTCAAAA
1281933 ACCAAACTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.57, C:0.19, G:0.00, T:0.24
Consensus pattern (16 bp):
AAACTCAAAATAACCT
Found at i:1282039 original size:19 final size:18
Alignment explanation
Indices: 1282006--1282041 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1281996 TGAATATTAG
*
1282006 TTTTTTTTTTCTTTTTTC
1 TTTTTTTTTTATTTTTTC
1282024 TTTTTTTTTTAATTTTTT
1 TTTTTTTTTT-ATTTTTT
1282042 TATAATCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.89
Consensus pattern (18 bp):
TTTTTTTTTTATTTTTTC
Found at i:1293231 original size:16 final size:17
Alignment explanation
Indices: 1293210--1293247 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1293200 TCTACGTATA
1293210 TTTTATAT-TTTTTTAG
1 TTTTATATATTTTTTAG
*
1293226 TTTTATATATTTTTTAT
1 TTTTATATATTTTTTAG
1293243 TTTTA
1 TTTTA
1293248 AAGTTTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTATATATTTTTTAG
Found at i:1293252 original size:25 final size:25
Alignment explanation
Indices: 1293206--1293254 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1293196 ACAATCTACG
**
1293206 TATATTTTATATTTTTTTAGTTTTA
1 TATATTTTATATTTTTAAAGTTTTA
*
1293231 TATATTTTTTATTTTTAAAGTTTT
1 TATATTTTATATTTTTAAAGTTTT
1293255 CATCACTCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (25 bp):
TATATTTTATATTTTTAAAGTTTTA
Found at i:1309639 original size:5 final size:6
Alignment explanation
Indices: 1309624--1309648 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1309614 TTAAAGGGAG
1309624 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
1309649 GAAGTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:1313694 original size:40 final size:41
Alignment explanation
Indices: 1313626--1313704 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 41
1313616 ACACTTAAAA
*
1313626 ATATTAAAACAAATATTAAAATAACAAACAAATTAAAAACG
1 ATATTAAAACAAATATTAAAACAACAAACAAATTAAAAACG
1313667 ATATTAAAAC-AAT-TCTAAAACAACAAACAAATTAAAAA
1 ATATTAAAACAAATAT-TAAAACAACAAACAAATTAAAAA
1313705 TATAATAAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
39 1 0.03
40 25 0.69
41 10 0.28
ACGTcount: A:0.66, C:0.11, G:0.01, T:0.22
Consensus pattern (41 bp):
ATATTAAAACAAATATTAAAACAACAAACAAATTAAAAACG
Found at i:1320619 original size:83 final size:86
Alignment explanation
Indices: 1320440--1320620 Score: 269
Period size: 83 Copynumber: 2.1 Consensus size: 86
1320430 TTTTTTCATT
* * *
1320440 TTTAGGGGGGTTAAAGTGCAATTTTACTATATATTAGTTTATAATTAGTTTATTTATTTATAAGA
1 TTTAGGGGGGTTAAAGTGCAATTTCACTATATATTAG-ATATAATTAGTTTATCTATTTATAAGA
*
1320505 GGACTGAATTGAAAATTTTTCA
65 GGACTGAATTGAAAAATTTTCA
* *
1320527 TTTGGGGGGGTTGAAGTGCAATTTCACTATATATTA-ATAT-A-TAGTTTATCTATTTATAAGAG
1 TTTAGGGGGGTTAAAGTGCAATTTCACTATATATTAGATATAATTAGTTTATCTATTTATAAGAG
1320589 GACTGAATTGAAAAATTTTCA
66 GACTGAATTGAAAAATTTTCA
1320610 TTTATGGGGGG
1 TTTA-GGGGGG
1320621 CAAAGGCCCC
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
83 43 0.50
84 7 0.08
85 3 0.03
87 33 0.38
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42
Consensus pattern (86 bp):
TTTAGGGGGGTTAAAGTGCAATTTCACTATATATTAGATATAATTAGTTTATCTATTTATAAGAG
GACTGAATTGAAAAATTTTCA
Found at i:1326305 original size:16 final size:16
Alignment explanation
Indices: 1326284--1326319 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1326274 AAACTTTTTG
*
1326284 ATAACCCAAAATTAAA
1 ATAACCCAAAACTAAA
*
1326300 ATAACCCAAACCTAAA
1 ATAACCCAAAACTAAA
1326316 ATAA
1 ATAA
1326320 TTTAAATCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.61, C:0.22, G:0.00, T:0.17
Consensus pattern (16 bp):
ATAACCCAAAACTAAA
Found at i:1326342 original size:32 final size:31
Alignment explanation
Indices: 1326292--1326357 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
1326282 TGATAACCCA
*
1326292 AAATTAAAATAACCCAAAC-CTAAAATAATTT
1 AAATTAAAATAACACAAACTC-AAAATAATTT
*
1326323 AAATCTAAAATAACACAAACTCGAAATAATTT
1 AAAT-TAAAATAACACAAACTCAAAATAATTT
1326355 AAA
1 AAA
1326358 AATTGAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 4 0.13
32 26 0.84
33 1 0.03
ACGTcount: A:0.59, C:0.15, G:0.02, T:0.24
Consensus pattern (31 bp):
AAATTAAAATAACACAAACTCAAAATAATTT
Found at i:1327275 original size:9 final size:9
Alignment explanation
Indices: 1327246--1327297 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
1327236 ATCAATTAAA
*
1327246 TTAATTATT
1 TTAATTTTT
*
1327255 TAAATTTATT
1 TTAATTT-TT
1327265 TTAATTTTT
1 TTAATTTTT
*
1327274 TTAATTTTA
1 TTAATTTTT
* *
1327283 ATAATTTAT
1 TTAATTTTT
1327292 TTAATT
1 TTAATT
1327298 AAATTTTTTA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
9 26 0.76
10 8 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTAATTTTT
Found at i:1339881 original size:31 final size:31
Alignment explanation
Indices: 1339846--1339913 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
1339836 TAATAAAATG
* *
1339846 GTCACTGAATTATTTAAAAAGTTTCATTCAA
1 GTCACTGAACTATTCAAAAAGTTTCATTCAA
*
1339877 GTCACTGAACTATTCAAAAATTTTCATTCAA
1 GTCACTGAACTATTCAAAAAGTTTCATTCAA
*
1339908 GGCACT
1 GTCACT
1339914 AGGCTGTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (31 bp):
GTCACTGAACTATTCAAAAAGTTTCATTCAA
Found at i:1342055 original size:23 final size:23
Alignment explanation
Indices: 1341990--1342061 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 23
1341980 CCATATATGT
*
1341990 TTTTAATTGTTTAAATATTT-ATA
1 TTTT-ATTGTTTTAATATTTAATA
*
1342013 TTTTATTTTTTTGAA-A---AATA
1 TTTTATTGTTTT-AATATTTAATA
1342033 TTTTATTGTTTTAATATTTAATA
1 TTTTATTGTTTTAATATTTAATA
*
1342056 ATTTAT
1 TTTTAT
1342062 ACATTTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
19 2 0.05
20 15 0.38
22 7 0.18
23 15 0.38
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
TTTTATTGTTTTAATATTTAATA
Found at i:1350763 original size:2 final size:2
Alignment explanation
Indices: 1350756--1350785 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1350746 CAAAACTTGA
*
1350756 AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1350786 GTGCAGGCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1357978 original size:16 final size:17
Alignment explanation
Indices: 1357952--1357984 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1357942 GAAGTTTTTG
1357952 AGTCAATTTTAAATTTA
1 AGTCAATTTTAAATTTA
*
1357969 AGTC-ATTTTAGATTTA
1 AGTCAATTTTAAATTTA
1357985 TTTCATTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (17 bp):
AGTCAATTTTAAATTTA
Found at i:1364857 original size:12 final size:12
Alignment explanation
Indices: 1364840--1364886 Score: 94
Period size: 12 Copynumber: 3.9 Consensus size: 12
1364830 CTGTAACAAA
1364840 CTAACTACTCTG
1 CTAACTACTCTG
1364852 CTAACTACTCTG
1 CTAACTACTCTG
1364864 CTAACTACTCTG
1 CTAACTACTCTG
1364876 CTAACTACTCT
1 CTAACTACTCT
1364887 AACTGAAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.26, C:0.34, G:0.06, T:0.34
Consensus pattern (12 bp):
CTAACTACTCTG
Found at i:1366240 original size:15 final size:15
Alignment explanation
Indices: 1366215--1366258 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1366205 TTAAATTGGT
1366215 TCAATTATAATTTAAA
1 TCAATT-TAATTTAAA
* *
1366231 TGAATTTAATTTAAT
1 TCAATTTAATTTAAA
*
1366246 TCAATTTTATTTA
1 TCAATTTAATTTA
1366259 CAAGTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (15 bp):
TCAATTTAATTTAAA
Found at i:1367619 original size:21 final size:21
Alignment explanation
Indices: 1367595--1367635 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1367585 AAAATGTAAT
* *
1367595 AAAATTAACATTTACTGTTTC
1 AAAAATAAAATTTACTGTTTC
*
1367616 AAAAATAAAATTTATTGTTT
1 AAAAATAAAATTTACTGTTT
1367636 AACGGAGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (21 bp):
AAAAATAAAATTTACTGTTTC
Found at i:1372604 original size:26 final size:26
Alignment explanation
Indices: 1372575--1372646 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 26
1372565 TATACATGCC
*
1372575 AACATTTAATAATTTTTATTTAATAA
1 AACATTTAATAATTTTTATTAAATAA
* * **
1372601 AACATTTAATATTTTTTA-AAAATCC
1 AACATTTAATAATTTTTATTAAATAA
*
1372626 AACATTTAATAATTATTATTA
1 AACATTTAATAATTTTTATTA
1372647 TGTTATTGAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
25 19 0.51
26 18 0.49
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (26 bp):
AACATTTAATAATTTTTATTAAATAA
Found at i:1375728 original size:10 final size:10
Alignment explanation
Indices: 1375707--1375744 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1375697 TAGCAATTTG
1375707 AAACATAAAAA
1 AAACA-AAAAA
1375718 AAA-AAAAAA
1 AAACAAAAAA
*
1375727 AAACAAAACA
1 AAACAAAAAA
1375737 AAACAAAA
1 AAACAAAA
1375745 CAAGTATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 8 0.32
10 14 0.56
11 3 0.12
ACGTcount: A:0.87, C:0.11, G:0.00, T:0.03
Consensus pattern (10 bp):
AAACAAAAAA
Found at i:1378502 original size:23 final size:23
Alignment explanation
Indices: 1378469--1378530 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
1378459 CTTATTTAAG
* *
1378469 TTAAATGAATATGTTCGTGAACA
1 TTAAATAAATATGTTCGTAAACA
1378492 TTAAATAAATATGTTCGTAAACA
1 TTAAATAAATATGTTCGTAAACA
* *
1378515 TATAATTAAACATGTT
1 T-TAAATAAATATGTT
1378531 TACGAACAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 22 0.65
24 12 0.35
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (23 bp):
TTAAATAAATATGTTCGTAAACA
Found at i:1380497 original size:105 final size:105
Alignment explanation
Indices: 1380309--1380553 Score: 278
Period size: 105 Copynumber: 2.3 Consensus size: 105
1380299 TATAACCTTT
* * * * * ** *
1380309 CTTCAATCCTTAAATTAAAAGAAATAA-ACACTTACGTGTGGTCAAACCCATGCCCACCTCGTTA
1 CTTCAATCCTTAAA-TCAAAGAAAAAACACACTTACATGCGCTCAAACCCACACCCACCTCATTA
* * * * *
1380373 TTGCAATAGCAATGGTGCCAACAAAGCTAAATCTCAATCGA
65 CTGCAATAGCAACGATGCCAACAAAACTAAATCCCAATCGA
*
1380414 CTTCAA-CCTTTAAATCAAAGAAAAAACACACTTACATGCGCTCAAACCCACATCCACCTCATTA
1 CTTCAATCC-TTAAATCAAAGAAAAAACACACTTACATGCGCTCAAACCCACACCCACCTCATTA
* *
1380478 CTGCAATAGCAACGATGCCAACAAAACTGAATCCCAATCGG
65 CTGCAATAGCAACGATGCCAACAAAACTAAATCCCAATCGA
* * *
1380519 CCTCAATCCTTAAATCAGAGGGAAAAACACACTTA
1 CTTCAATCCTTAAATCA-AAGAAAAAACACACTTA
1380554 ACTGCGCCTG
Statistics
Matches: 117, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
104 12 0.10
105 88 0.75
106 17 0.15
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (105 bp):
CTTCAATCCTTAAATCAAAGAAAAAACACACTTACATGCGCTCAAACCCACACCCACCTCATTAC
TGCAATAGCAACGATGCCAACAAAACTAAATCCCAATCGA
Found at i:1382518 original size:6 final size:6
Alignment explanation
Indices: 1382507--1382537 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1382497 AAAGAGAATA
1382507 TGCCAT TGCCAT TGCCAT TGCCAT TGCCAT T
1 TGCCAT TGCCAT TGCCAT TGCCAT TGCCAT T
1382538 ATCAACTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.35
Consensus pattern (6 bp):
TGCCAT
Found at i:1392103 original size:25 final size:25
Alignment explanation
Indices: 1392069--1392120 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1392059 AAAAAATTGG
1392069 TAAGATTTTAGCCTAATTATGTGGA
1 TAAGATTTTAGCCTAATTATGTGGA
1392094 TAAGATTTTAGCCTAATTATGTGGA
1 TAAGATTTTAGCCTAATTATGTGGA
1392119 TA
1 TA
1392121 TAATAATGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (25 bp):
TAAGATTTTAGCCTAATTATGTGGA
Found at i:1395973 original size:66 final size:66
Alignment explanation
Indices: 1395867--1396053 Score: 329
Period size: 66 Copynumber: 2.8 Consensus size: 66
1395857 AAAAGGAAAA
1395867 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAG
1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAG
1395932 G
66 G
* * *
1395933 AAAGAGAAAATAACCTCGTTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCGTCGACATAGAG
1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAG
1395998 G
66 G
* *
1395999 AAAGAGAATATAACCTCATTGATGGTGGTGTGGCTGCAAATAATCCAGTATGCAT
1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCAT
1396054 TCTCAAAATG
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 114 1.00
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.22
Consensus pattern (66 bp):
AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAG
G
Found at i:1411783 original size:10 final size:10
Alignment explanation
Indices: 1411754--1411809 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
1411744 TGTTCTGGTT
*
1411754 TTTTTTACTG
1 TTTTTTGCTG
1411764 TTTTAGTTGCTG
1 TTTT--TTGCTG
1411776 TTTTTTGCT-
1 TTTTTTGCTG
*
1411785 TTTTTGTGTTG
1 TTTTT-TGCTG
*
1411796 TTTTTTACTG
1 TTTTTTGCTG
1411806 TTTT
1 TTTT
1411810 AATGCTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 5 0.13
10 19 0.50
11 5 0.13
12 9 0.24
ACGTcount: A:0.05, C:0.07, G:0.16, T:0.71
Consensus pattern (10 bp):
TTTTTTGCTG
Found at i:1411809 original size:20 final size:22
Alignment explanation
Indices: 1411754--1411842 Score: 87
Period size: 20 Copynumber: 4.2 Consensus size: 22
1411744 TGTTCTGGTT
1411754 TTTTTTACTGTTTTAGTTGCTG
1 TTTTTTACTGTTTTAGTTGCTG
* * *
1411776 TTTTTTGCT-TTTTTG-TGTTG
1 TTTTTTACTGTTTTAGTTGCTG
*
1411796 TTTTTTACTGTTTTA-ATGCT-
1 TTTTTTACTGTTTTAGTTGCTG
* * *
1411816 TTTTTTACTGCTTTGGTTACTG
1 TTTTTTACTGTTTTAGTTGCTG
1411838 TTTTT
1 TTTTT
1411843 ATGTTGTTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
20 25 0.47
21 15 0.28
22 13 0.25
ACGTcount: A:0.08, C:0.09, G:0.16, T:0.67
Consensus pattern (22 bp):
TTTTTTACTGTTTTAGTTGCTG
Done.