Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 134 of 172
Found at i:44256959 original size:177 final size:177
Alignment explanation
Indices: 44256550--44256932 Score: 423
Period size: 177 Copynumber: 2.2 Consensus size: 177
44256540 TTAAGCCACC
* ** * *
44256550 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAAATTA-CAGATCTTATCTCCCTAAGCA
1 AGTCTTATCTCCCTGAAGTAGCAGTAAAGCAGACTGAAAA-CAGCAGATCTTATCTCCCTAAGCA
* * * * *
44256614 ATAGTGAAGTAGATCGAATACGGCAAATCTTATCTCCATGTAGCGAAAATGGAGCAGATTTAAGC
65 ATAGTGAAGCAGACCGAAGACGACAAATCTTATCTCCATATAGCGAAAATGGAGCAGATTTAAGC
* * ** * *
44256679 CATCAGTCTTATCTTCCTAAAGTTGCAGTGAAGCAGGTTTAAGATACA
130 CACCAGTCTTATCTCCCTAAAGTTGCAGTGAAGCAGACTGAAAATACA
* ** ** * * *
44256727 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAATTGCAGATCTTATCTCCTTAAGTAG
1 AGTCTTATCTCCCTGAAGTAGCAGTAAAGCAGACTGAAAACAGCAGATCTTATCTCCCTAAGCAA
* * * *
44256792 TAGTGGAGCAGACCGAAGACGACAAATCTTATCTCTATATAGC-AGCAATGGAGTAGATTTAAGC
66 TAGTGAAGCAGACCGAAGACGACAAATCTTATCTCCATATAGCGA-AAATGGAGCAGATTTAAGC
*
44256856 CACCGGTCTTATCTCCCTAAAGTTGCAGTGAAGCAGACTGAAAATTAC-
130 CACCAGTCTTATCTCCCTAAAGTTGCAGTGAAGCAGACTGAAAA-TACA
* *
44256904 AGATCTTATCTCTCT-AAGTAGTAGTAAAG
1 AG-TCTTATCTCCCTGAAGTAGCAGTAAAG
44256933 TAGATCGAGG
Statistics
Matches: 176, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
176 2 0.01
177 160 0.91
178 14 0.08
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (177 bp):
AGTCTTATCTCCCTGAAGTAGCAGTAAAGCAGACTGAAAACAGCAGATCTTATCTCCCTAAGCAA
TAGTGAAGCAGACCGAAGACGACAAATCTTATCTCCATATAGCGAAAATGGAGCAGATTTAAGCC
ACCAGTCTTATCTCCCTAAAGTTGCAGTGAAGCAGACTGAAAATACA
Found at i:44257002 original size:177 final size:177
Alignment explanation
Indices: 44256819--44257164 Score: 390
Period size: 177 Copynumber: 2.0 Consensus size: 177
44256809 GACGACAAAT
* * * * **
44256819 CTTATCTCTATATAGCAGCAATGGAGTAGATTTAAGCCACCGGTCTTATCTCCCTAAAGTTGCAG
1 CTTATCTCTATAAAGCAGCAATGGAGCAGATTCAAGACACAAGTCTTATCTCCCTAAAGTTGCAG
* * * * * * *
44256884 TGAAGCAGACTGAAAATTAC-AGATCTTATCTCTCTAAGTAGTAGTAAAGTAGATCGAGGGCAGC
66 TGAAGCAAACTGAAAATAACGA-ATCTTATCTCCCTAAGCAGTAGTAAAGCAGATCGAAGACAGC
*
44256948 GAATCTTATCTCTATGTAGCGGCAATAGAGCT-GATTTAAGCTACCAGC
130 AAATCTTATCTCTATGTAGCGGCAATAGAG-TAGATTTAAGCTACCAGC
* ** * * * * * *
44256996 CTTATCTCTTTAAAGTTGCAGTGGAGCAGGTTCAATATACAAGTCTTATCTCCTTGAAGTTGCAG
1 CTTATCTCTATAAAGCAGCAATGGAGCAGATTCAAGACACAAGTCTTATCTCCCTAAAGTTGCAG
* * * * **
44257061 TGGAGCAAACTGAAGATAACGAATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAATATGGCA
66 TGAAGCAAACTGAAAATAACGAATCTTATCTCCCTAAGCAGTAGTAAAGCAGATCGAAGACAGCA
*
44257126 AATCTTATCTCTATGTAGCGGCAATGGAGTAGATTTAAG
131 AATCTTATCTCTATGTAGCGGCAATAGAGTAGATTTAAG
44257165 TCACCAGATC
Statistics
Matches: 137, Mismatches: 30, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
176 1 0.01
177 135 0.99
178 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (177 bp):
CTTATCTCTATAAAGCAGCAATGGAGCAGATTCAAGACACAAGTCTTATCTCCCTAAAGTTGCAG
TGAAGCAAACTGAAAATAACGAATCTTATCTCCCTAAGCAGTAGTAAAGCAGATCGAAGACAGCA
AATCTTATCTCTATGTAGCGGCAATAGAGTAGATTTAAGCTACCAGC
Found at i:44257330 original size:133 final size:134
Alignment explanation
Indices: 44257169--44257461 Score: 392
Period size: 134 Copynumber: 2.2 Consensus size: 134
44257159 TTTAAGTCAC
* * * *
44257169 CAGATCTTATTTCCTTGAAGTTACAGCGGAATAGATCTAGGATAACAAACCTTATCTCTCTGAAG
1 CAGATCTTATCTCCTTGAAGTTGCAGCGGAATAGATCAAAGATAACAAACCTTATCTCTCTGAAG
* * * * * *
44257234 TTGCAG-AGAGCAGGTTGAAGTTACAGGTCTCATCTCTCTGAAGTTGCAGTGGAACATATCGAAG
66 TTGCAGTAGAACAGGTTGAAGTAACAAGTCTCATCTCCCTAAAGTTGCAGTGGAACAGATCGAAG
44257298 A-TA
131 ACTA
* * * **
44257301 GCAGATCTTATCTCCCTGAAGTTGTAGCGGAGTAGATCAAAGATAGTAAACCTTATCTCTCTGAA
1 -CAGATCTTATCTCCTTGAAGTTGCAGCGGAATAGATCAAAGATAACAAACCTTATCTCTCTGAA
* *
44257366 GTTGCAGTAGAACAGGTTGAAGTAACAAGTCTTATCTCCCTAAAGTTGCAGTGGAACAGATTGAA
65 GTTGCAGTAGAACAGGTTGAAGTAACAAGTCTCATCTCCCTAAAGTTGCAGTGGAACAGATCGAA
44257431 GACTA
130 GACTA
* *
44257436 CAAACCTTATCTCCTTGAAGTTGCAG
1 CAGATCTTATCTCCTTGAAGTTGCAG
44257462 TGGAGCAGGT
Statistics
Matches: 137, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
133 62 0.45
134 73 0.53
135 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (134 bp):
CAGATCTTATCTCCTTGAAGTTGCAGCGGAATAGATCAAAGATAACAAACCTTATCTCTCTGAAG
TTGCAGTAGAACAGGTTGAAGTAACAAGTCTCATCTCCCTAAAGTTGCAGTGGAACAGATCGAAG
ACTA
Found at i:44257442 original size:89 final size:90
Alignment explanation
Indices: 44257265--44257638 Score: 343
Period size: 89 Copynumber: 4.2 Consensus size: 90
44257255 TACAGGTCTC
* * * * *
44257265 ATCTCTCTGAAGTTGCAGTGGAACATATCGAAGATAGC-AGATCTTATCTCCCTGAAGTTGTAGC
1 ATCTCCCTGAAGTTGCAGTGGAACAGATTGAAG-TAACAAG-TCTTATCTCCCTGAAGTTGCAGC
* *
44257329 GGAGTAGATCAAAGA-TAGTAAACCTT
64 GGAGTAGATCGAAGACTAGCAAACCTT
* * * * *
44257355 ATCTCTCTGAAGTTGCAGTAGAACAGGTTGAAGTAACAAGTCTTATCTCCCTAAAGTTGCAGTGG
1 ATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGTAACAAGTCTTATCTCCCTGAAGTTGCAGCGG
** *
44257420 AACAGATTGAAGACTA-CAAACCTT
66 AGTAGATCGAAGACTAGCAAACCTT
* * * * * * * * *
44257444 ATCTCCTTGAAGTTGCAGTGGAGCAGGTTGAAATTACAAACTCTTACCTCCTTGAAGTTCCAGCG
1 ATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGTAAC-AAGTCTTATCTCCCTGAAGTTGCAGCG
* *
44257509 GAGTAGATCGAAG-TTA-CAAATCTCT
65 GAGTAGATCGAAGACTAGCAAACCT-T
* * * * *
44257534 -TCTCCCTGAAATTACATTGGAATAGATTGAAGCAACAAGTCTTATCTCCCTGAAGTTGCAGCGG
1 ATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGTAACAAGTCTTATCTCCCTGAAGTTGCAGCGG
*
44257598 AGTAGA-CTGAAGAC-AGCTAATCC-T
66 AGTAGATC-GAAGACTAGC-AAACCTT
44257622 ATCTCCCTGAAGTTGCA
1 ATCTCCCTGAAGTTGCA
44257639 ATAGAGTGGA
Statistics
Matches: 226, Mismatches: 49, Indels: 19
0.77 0.17 0.06
Matches are distributed among these distances:
87 1 0.00
88 36 0.16
89 121 0.54
90 68 0.30
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (90 bp):
ATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGTAACAAGTCTTATCTCCCTGAAGTTGCAGCGG
AGTAGATCGAAGACTAGCAAACCTT
Found at i:44257460 original size:45 final size:44
Alignment explanation
Indices: 44256995--44257638 Score: 227
Period size: 45 Copynumber: 14.5 Consensus size: 44
44256985 AAGCTACCAG
* * * * * * *
44256995 CCTTATCTCTTTAAAGTTGCAGTGGAGCAGGTTCAATATACAAG
1 CCTTATCTCCTTGAAGTTGCAGTGGAACAGATTGAAGATACAAA
* * * * *
44257039 TCTTATCTCCTTGAAGTTGCAGTGGAGCAAACTGAAGATAACGAA
1 CCTTATCTCCTTGAAGTTGCAGTGGAACAGATTGAAGAT-ACAAA
* * ** * * * *
44257084 TCTTATCTCCCT-AAGCAGTAGT-GAAGCAGATCGAATATGGCAAA
1 CCTTATCTCCTTGAAGTTGCAGTGGAA-CAGATTGAAGAT-ACAAA
* * ** * ** * *
44257128 TCTTATCT-CTATGTAGCGGCAATGGAGTAGATTTAAG-TCACCAGA
1 CCTTATCTCCT-TGAAGTTGCAGTGGAACAGATTGAAGAT-A-CAAA
* * * * * *
44257173 TCTTATTTCCTTGAAGTTACAGCGGAATAGATCT-AGGATAACAAA
1 CCTTATCTCCTTGAAGTTGCAGTGGAACAGAT-TGAAGAT-ACAAA
* * * * **
44257218 CCTTATCT-CTCTGAAGTTGCAG-AGAGCAGGTTGAAGTTACAGG
1 CCTTATCTCCT-TGAAGTTGCAGTGGAACAGATTGAAGATACAAA
* * * * *
44257261 TCTCATCT-CTCTGAAGTTGCAGTGGAACATATCGAAGATAGCAGA
1 CCTTATCTCCT-TGAAGTTGCAGTGGAACAGATTGAAGATA-CAAA
* * * * ** ** *
44257306 TCTTATCTCCCTGAAGTTGTAGCGGAGTAGATCAAAGATAGTAAA
1 CCTTATCTCCTTGAAGTTGCAGTGGAACAGATTGAAGATA-CAAA
* * *
44257351 CCTTATCT-CTCTGAAGTTGCAGTAGAACAGGTTGAAG-TAACAAG
1 CCTTATCTCCT-TGAAGTTGCAGTGGAACAGATTGAAGAT-ACAAA
* * *
44257395 TCTTATCTCCCTAAAGTTGCAGTGGAACAGATTGAAGACTACAAA
1 CCTTATCTCCTTGAAGTTGCAGTGGAACAGATTGAAGA-TACAAA
* *
44257440 CCTTATCTCCTTGAAGTTGCAGTGGAGCAGGTTGAA-ATTACAAA
1 CCTTATCTCCTTGAAGTTGCAGTGGAACAGATTGAAGA-TACAAA
* * * ** * *
44257484 CTCTTACCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGTTACAAA
1 C-CTTATCTCCTTGAAGTTGCAGTGGAACAGATTGAAGATACAAA
* * * * * * *
44257529 TCTCT-TCTCCCTGAAATTACATTGGAATAGATTGAAGCA-ACAAG
1 CCT-TATCTCCTTGAAGTTGCAGTGGAACAGATTGAAG-ATACAAA
* * * ** * * *
44257573 TCTTATCTCCCTGAAGTTGCAGCGGAGTAGACTGAAGACAGCTAAT
1 CCTTATCTCCTTGAAGTTGCAGTGGAACAGATTGAAGATA-C-AAA
*
44257619 CC-TATCTCCCTGAAGTTGCA
1 CCTTATCTCCTTGAAGTTGCA
44257639 ATAGAGTGGA
Statistics
Matches: 447, Mismatches: 126, Indels: 53
0.71 0.20 0.08
Matches are distributed among these distances:
43 29 0.06
44 182 0.41
45 224 0.50
46 12 0.03
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
CCTTATCTCCTTGAAGTTGCAGTGGAACAGATTGAAGATACAAA
Found at i:44257500 original size:134 final size:132
Alignment explanation
Indices: 44257172--44257599 Score: 391
Period size: 134 Copynumber: 3.2 Consensus size: 132
44257162 AAGTCACCAG
* * * ** * *
44257172 ATCTTATTTCCTTGAAGTTACAGCGGAATAGATCTAGGATAACAAACCTTATCTCTCTGAAGTTG
1 ATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCAAAGAT-ACAAACCTTATCTCTCTGAAGTTG
* * * * * *
44257237 CAGAGAGCAGGTTGAAGTTACAGGTCTCATCTCTCTGAAGTTGCAGTGGAACATATCGAAGA-TA
65 CAGAGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAACAGATTGAAGACTA
*
44257301 GCAG
130 -CAA
* * *
44257305 ATCTTATCTCCCTGAAGTTGTAGCGGAGTAGATCAAAGATAGTAAACCTTATCTCTCTGAAGTTG
1 ATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCAAAGATA-CAAACCTTATCTCTCTGAAGTTG
* *
44257370 CAGTAGAACAGGTTGAAGTAACAAGTCTTATCTCCCTAAAGTTGCAGTGGAACAGATTGAAGACT
65 CAG-AGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAACAGATTGAAGACT
44257435 ACAA
129 ACAA
* * * * * * *
44257439 ACCTTATCTCCTTGAAGTTGCAGTGGAGCAGGTTGAAA-TTACAAACTCTTACCTC-CTTGAAGT
1 ATCTTATCTCCCTGAAGTTGCAGCGGAGCA-GATCAAAGATACAAAC-CTTATCTCTC-TGAAGT
* * * * * * * * *
44257502 TCCAGCGGAGTAGATCGAAGTTACAAATCTCT-TCTCCCTGAAA-TTACATTGGAATAGATTGAA
63 TGCAG-AGAGCAGGTTGAAGTTACAAGTCT-TATCTCCCT-AAAGTTGCAGTGGAACAGATTGAA
*
44257565 G-CAACAA
125 GACTACAA
*
44257572 GTCTTATCTCCCTGAAGTTGCAGCGGAG
1 ATCTTATCTCCCTGAAGTTGCAGCGGAG
44257600 TAGACTGAAG
Statistics
Matches: 243, Mismatches: 44, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
132 1 0.00
133 92 0.38
134 139 0.57
135 11 0.05
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (132 bp):
ATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCAAAGATACAAACCTTATCTCTCTGAAGTTGC
AGAGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAACAGATTGAAGACTAC
AA
Found at i:44258394 original size:3 final size:3
Alignment explanation
Indices: 44258386--44258714 Score: 53
Period size: 3 Copynumber: 109.0 Consensus size: 3
44258376 AAGGGGAGAG
* * * *
44258386 TAT TAT TAT TAT TAT TAT TAACC TAC TAT TAT TAT TTT TAT TAA TA-
1 TAT TAT TAT TAT TAT TAT T-A-T TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
44258432 TAA TAT TGT T-T TCT T-T T-T TTT TA- TAT TGT TAT TAT TAT TAG CACG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* * *
44258477 TA- TAT TAT TAT TAT TAAT GTAT CAT TGT TAT TTT CTAT T-T TAT TAT
1 TAT TAT TAT TAT TAT T-AT -TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* * *
44258523 TACT T-T TAT TAC TAC TGT T-T CTAT TAT TAT TAT T-T TCAT TACT TCCAT
1 TA-T TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT T-AT TA-T T--AT
* * * *
44258571 TAT TAT T-T TCAT TAT TTT CTAT TAT CAT TAA TAT GTCGT T-T GT-T
1 TAT TAT TAT T-AT TAT TAT -TAT TAT TAT TAT TAT -T-AT TAT -TAT
* * * * * *
44258615 TAT TAT TAT TAT TAT TTT TAA CAC TAT TAT CAT CAT TA- TATT TACT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA-T
* * * * * *
44258661 T-T TTT TAA TAT TAT TAC CAT TA- TAT T-T TTT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
44258706 TTT TAT TAT
1 TAT TAT TAT
44258715 CCGTTCTATT
Statistics
Matches: 242, Mismatches: 51, Indels: 66
0.67 0.14 0.18
Matches are distributed among these distances:
2 31 0.13
3 178 0.74
4 27 0.11
5 5 0.02
6 1 0.00
ACGTcount: A:0.27, C:0.09, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:44258438 original size:23 final size:23
Alignment explanation
Indices: 44258389--44258438 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
44258379 GGGAGAGTAT
* *
44258389 TATTATTATTATTATTAACCTAC
1 TATTATTATTATTATTAACATAA
* *
44258412 TATTATTATTTTTATTAATATAA
1 TATTATTATTATTATTAACATAA
44258435 TATT
1 TATT
44258439 GTTTTCTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (23 bp):
TATTATTATTATTATTAACATAA
Found at i:44258694 original size:22 final size:21
Alignment explanation
Indices: 44258662--44258714 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
44258652 ATATTTACTT
*
44258662 TTTTTAATATTATTACCATTA
1 TTTTTATTATTATTACCATTA
* *
44258683 TATTTTTTTATTATTACTATTA
1 T-TTTTATTATTATTACCATTA
44258705 TTTTTATTAT
1 TTTTTATTAT
44258715 CCGTTCTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTTATTATTATTACCATTA
Found at i:44259012 original size:126 final size:128
Alignment explanation
Indices: 44258876--44259137 Score: 329
Period size: 126 Copynumber: 2.1 Consensus size: 128
44258866 TTTTTCAAGT
* * *
44258876 AAAGGCAATATTC-GATATTTAGAAATTC-AATAAATCGTGTCCTAACATACTGGG-TTCTGGTT
1 AAAGGCAATATTCTG-TATTTAGAAATTCGAAT-AATCGTGCCCCAACATACTGGGTTTC-GATT
* * *
44258938 TTTCGTTTGATCTAAGTAAT-CGATTATCC-TTTT-AAATTAAAATACATGAGTTTTAAATAAAA
63 TTCCGTTTGATCTAAAT-ATCCGAATATCCTTTTTAAAATTAAAATACATGAGTTTTAAATAAAA
44259000 TA
127 TA
* * * *
44259002 AAAGGCAATATTCTGTATTTAGAAATTCGAGTAGTCGTGCCCCAACGTATTGGGTTTCGATTTTC
1 AAAGGCAATATTCTGTATTTAGAAATTCGAATAATCGTGCCCCAACATACTGGGTTTCGATTTTC
* *
44259067 CGTTTGATCTAAATATCCGAATATCCTTTTTAAAATTTAAATACATGAGTTTTAAATGAAATA
66 CGTTTGATCTAAATATCCGAATATCCTTTTTAAAATTAAAATACATGAGTTTTAAATAAAATA
*
44259130 GAAGGCAA
1 AAAGGCAA
44259138 GCTCATACTC
Statistics
Matches: 117, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
125 2 0.02
126 69 0.59
127 10 0.09
128 36 0.31
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (128 bp):
AAAGGCAATATTCTGTATTTAGAAATTCGAATAATCGTGCCCCAACATACTGGGTTTCGATTTTC
CGTTTGATCTAAATATCCGAATATCCTTTTTAAAATTAAAATACATGAGTTTTAAATAAAATA
Found at i:44284232 original size:18 final size:18
Alignment explanation
Indices: 44284185--44284235 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 18
44284175 AATAGGATAA
44284185 TATATTTAA-TAAGTCCT
1 TATATTTAATTAAGTCCT
*
44284202 T-TA---AATTTA-TCCT
1 TATATTTAATTAAGTCCT
44284215 TATATTTAATTAAGTCCT
1 TATATTTAATTAAGTCCT
44284233 TAT
1 TAT
44284236 GCTTACAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 11
0.67 0.05 0.28
Matches are distributed among these distances:
13 7 0.27
14 4 0.15
16 2 0.08
17 6 0.23
18 7 0.27
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (18 bp):
TATATTTAATTAAGTCCT
Found at i:44290971 original size:16 final size:17
Alignment explanation
Indices: 44290952--44290984 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
44290942 GTATGAAATA
44290952 TTTA-ATGAAATTTATT
1 TTTACATGAAATTTATT
44290968 TTTACATGAAATTTATT
1 TTTACATGAAATTTATT
44290985 ATTATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (17 bp):
TTTACATGAAATTTATT
Found at i:44293314 original size:55 final size:55
Alignment explanation
Indices: 44293230--44293338 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 55
44293220 TATTCATTGA
* * * *
44293230 ATGATAAATTATCACTTTTAATTTGAATAGTGCTTATGAATAACTAATTTGCAAG
1 ATGATAAATCATCACTTTAAATTTGAATAGTGCTCATAAATAACTAATTTGCAAG
*
44293285 ATGATAAATCATCACTTTAAATTTGAATAGTGCTCATAAATAATTAATTTGCAA
1 ATGATAAATCATCACTTTAAATTTGAATAGTGCTCATAAATAACTAATTTGCAA
44293339 TCTATAATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (55 bp):
ATGATAAATCATCACTTTAAATTTGAATAGTGCTCATAAATAACTAATTTGCAAG
Found at i:44294155 original size:50 final size:51
Alignment explanation
Indices: 44294100--44294200 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
44294090 ACTAGTTTTA
44294100 TTTTATTGTA-TTTTTTTATCAAATTCTTGTCTTTTCACCAAAAAAATATT
1 TTTTATTGTATTTTTTTTATCAAATTCTTGTCTTTTCACCAAAAAAATATT
44294150 TTTTATTGTATTTTTTTTATCAAATTCTTGTCTTTTCACCAAAAAAATATT
1 TTTTATTGTATTTTTTTTATCAAATTCTTGTCTTTTCACCAAAAAAATATT
44294201 GTAAAGAAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 10 0.20
51 40 0.80
ACGTcount: A:0.30, C:0.12, G:0.04, T:0.54
Consensus pattern (51 bp):
TTTTATTGTATTTTTTTTATCAAATTCTTGTCTTTTCACCAAAAAAATATT
Found at i:44294668 original size:41 final size:41
Alignment explanation
Indices: 44294611--44294694 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
44294601 GGAAAAAATT
44294611 TAAGGAATATTTTGTATGAATATGACATGGATATGAATCAA
1 TAAGGAATATTTTGTATGAATATGACATGGATATGAATCAA
44294652 TAAGGAATATTTTGTATGAATATGACATGGATATGAATCAA
1 TAAGGAATATTTTGTATGAATATGACATGGATATGAATCAA
44294693 TA
1 TA
44294695 GATGGAGTCG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.35
Consensus pattern (41 bp):
TAAGGAATATTTTGTATGAATATGACATGGATATGAATCAA
Found at i:44298020 original size:154 final size:154
Alignment explanation
Indices: 44297749--44298083 Score: 562
Period size: 154 Copynumber: 2.2 Consensus size: 154
44297739 TTGGTTATGG
*
44297749 TCCTGCATATGTTGCGGACACACTACAACTCGAAAGAGCGTCCCGTTATTAGCTCTCATGAGCAT
1 TCCTGCATATGTTGCGGACACACCACAACTCGAAAGAGCGTCCCGTTATTAGCTCTCATGAGCAT
* ** ** * *
44297814 TCTGATATTTTTCTCTCACGAGCTTCCTGTTATATGGTTCTTGTGAGCTTCCCATTAATAGCTCT
66 CCCAATATTTGGCTCTCACGAGCTTCCTATTATATGGTTCTTGCGAGCTTCCCATTAATAGCTCT
*
44297879 TCGGAGCATCCCGATTGGTTGTAA
131 TCGGAGCATCCCAATTGGTTGTAA
44297903 TCCTGCATATGTTGCGGACACACCACAACTCGAAAGAGCGTCCCGTTATTAGCTCTCATGAGCAT
1 TCCTGCATATGTTGCGGACACACCACAACTCGAAAGAGCGTCCCGTTATTAGCTCTCATGAGCAT
* *
44297968 CCCAATATTTGGCTCTCACGAGCTTCCTATTATATGGTTCTTGCGAGTTTCCCTTTAATAGCTCT
66 CCCAATATTTGGCTCTCACGAGCTTCCTATTATATGGTTCTTGCGAGCTTCCCATTAATAGCTCT
44298033 TCGGAGCATCCCAATTGGTTGTAA
131 TCGGAGCATCCCAATTGGTTGTAA
*
44298057 TCCTGCATGTGTTGCGGACACACCACA
1 TCCTGCATATGTTGCGGACACACCACA
44298084 GCTCTTATAA
Statistics
Matches: 169, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
154 169 1.00
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.32
Consensus pattern (154 bp):
TCCTGCATATGTTGCGGACACACCACAACTCGAAAGAGCGTCCCGTTATTAGCTCTCATGAGCAT
CCCAATATTTGGCTCTCACGAGCTTCCTATTATATGGTTCTTGCGAGCTTCCCATTAATAGCTCT
TCGGAGCATCCCAATTGGTTGTAA
Found at i:44298130 original size:154 final size:154
Alignment explanation
Indices: 44297749--44298135 Score: 512
Period size: 154 Copynumber: 2.5 Consensus size: 154
44297739 TTGGTTATGG
* * * *
44297749 TCCTGCATATGTTGCGGACACACTACAACTCGAAAGAGCGTCCCGTTATTAGCTCTCATGAGCAT
1 TCCTGCATATGTTGCGGACACACCACAACTCGAAAGAGCATCCCGATATTAGCTCTCAGGAGCAT
* * ** * *
44297814 TCTGATATTTTTCTCTCACGAGCTTCCTGTTATATGGTTCTTGTGAGCTTCCCATTAATAGCTCT
66 CCCGATATTTGGCTCTCACGAGCTTCCTATTATATGGTTCTTGCGAGCTTCCCATTAATAGCTCT
*
44297879 TCGGAGCATCCCGATTGGTTGTAA
131 TCGGAGCATCCCAATTGGTTGTAA
* * *
44297903 TCCTGCATATGTTGCGGACACACCACAACTCGAAAGAGCGTCCCGTTATTAGCTCTCATGAGCAT
1 TCCTGCATATGTTGCGGACACACCACAACTCGAAAGAGCATCCCGATATTAGCTCTCAGGAGCAT
* * *
44297968 CCCAATATTTGGCTCTCACGAGCTTCCTATTATATGGTTCTTGCGAGTTTCCCTTTAATAGCTCT
66 CCCGATATTTGGCTCTCACGAGCTTCCTATTATATGGTTCTTGCGAGCTTCCCATTAATAGCTCT
44298033 TCGGAGCATCCCAATTGGTTGTAA
131 TCGGAGCATCCCAATTGGTTGTAA
* * * * *
44298057 TCCTGCATGTGTTGCGGACACACCACAGCTCTTATA-AGCAT-CCGATATATGGCTCTTC-GGAG
1 TCCTGCATATGTTGCGGACACACCACAACTC-GAAAGAGCATCCCGATAT-TAGCTC-TCAGGAG
*
44298119 CTTCCCGATA-TTGGCTC
63 CATCCCGATATTTGGCTC
44298136 GCTTGAACTT
Statistics
Matches: 209, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
153 13 0.06
154 192 0.92
155 4 0.02
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (154 bp):
TCCTGCATATGTTGCGGACACACCACAACTCGAAAGAGCATCCCGATATTAGCTCTCAGGAGCAT
CCCGATATTTGGCTCTCACGAGCTTCCTATTATATGGTTCTTGCGAGCTTCCCATTAATAGCTCT
TCGGAGCATCCCAATTGGTTGTAA
Found at i:44299944 original size:43 final size:43
Alignment explanation
Indices: 44299896--44299995 Score: 148
Period size: 43 Copynumber: 2.3 Consensus size: 43
44299886 GATTAACGAG
*
44299896 ATGTGATTATGTGTAAGACCATGTCTG-GGACATTGGCATCATT
1 ATGTGATTACGTGTAAGACCATGTC-GAGGACATTGGCATCATT
*
44299939 ATGTGATTACGTGTAAGACCATGTCGAGGACATTGGCATCGTT
1 ATGTGATTACGTGTAAGACCATGTCGAGGACATTGGCATCATT
* *
44299982 ATTTGATTTCGTGT
1 ATGTGATTACGTGT
44299996 GAGATTATAG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 1 0.02
43 51 0.98
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (43 bp):
ATGTGATTACGTGTAAGACCATGTCGAGGACATTGGCATCATT
Found at i:44300927 original size:22 final size:22
Alignment explanation
Indices: 44300894--44300947 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
44300884 AACATATTGT
44300894 TTTG-GTATGTTTATGGTTATGA
1 TTTGAGTA-GTTTATGGTTATGA
44300916 TTTGAGTAGTTTATGGTTATGA
1 TTTGAGTAGTTTATGGTTATGA
44300938 TTTGAGTAGT
1 TTTGAGTAGT
44300948 GAAATAGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (22 bp):
TTTGAGTAGTTTATGGTTATGA
Found at i:44300934 original size:76 final size:77
Alignment explanation
Indices: 44300840--44300999 Score: 279
Period size: 76 Copynumber: 2.1 Consensus size: 77
44300830 GACATATTGT
* *
44300840 TTTG-GTATGTTTGTGGTTATGATTTGAGTAGTGAAATGGTTGAAAACATATTGTTTTGGTATGT
1 TTTGAGTATGTTTATGGTTATGATTTGAGTAGTGAAATAGTTGAAAACATATTGTTTTGGTATGT
44300904 TTATGGTTATGA
66 TTATGGTTATGA
*
44300916 TTTGAGTA-GTTTATGGTTATGATTTGAGTAGTGAAATAGTTGAAGACATATTGTTTTGGTATGT
1 TTTGAGTATGTTTATGGTTATGATTTGAGTAGTGAAATAGTTGAAAACATATTGTTTTGGTATGT
44300980 TTATGGTTATGA
66 TTATGGTTATGA
44300992 TTTGAGTA
1 TTTGAGTA
44301000 ATGAAATGGT
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
76 77 0.96
77 3 0.04
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.47
Consensus pattern (77 bp):
TTTGAGTATGTTTATGGTTATGATTTGAGTAGTGAAATAGTTGAAAACATATTGTTTTGGTATGT
TTATGGTTATGA
Found at i:44303583 original size:20 final size:20
Alignment explanation
Indices: 44303542--44303584 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
44303532 ATCTTCTACT
**
44303542 TTTATTTTATTTTTTGTTTA
1 TTTATTTTATTTTTTGAATA
44303562 TTTA-TTTATTATTTTGAATA
1 TTTATTTTATT-TTTTGAATA
44303582 TTT
1 TTT
44303585 CTTAAATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTATTTTATTTTTTGAATA
Found at i:44305638 original size:22 final size:22
Alignment explanation
Indices: 44305605--44305658 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
44305595 AACATATTGT
44305605 TTTG-GTATGTTTATGGTTATGA
1 TTTGAGTA-GTTTATGGTTATGA
44305627 TTTGAGTAGTTTATGGTTATGA
1 TTTGAGTAGTTTATGGTTATGA
44305649 TTTGAGTAGT
1 TTTGAGTAGT
44305659 GAAATAGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (22 bp):
TTTGAGTAGTTTATGGTTATGA
Found at i:44305645 original size:76 final size:77
Alignment explanation
Indices: 44305551--44305710 Score: 279
Period size: 76 Copynumber: 2.1 Consensus size: 77
44305541 GACATATTGT
* *
44305551 TTTG-GTATGTTTGTGGTTATGATTTGAGTAGTGAAATGGTTGAAAACATATTGTTTTGGTATGT
1 TTTGAGTATGTTTATGGTTATGATTTGAGTAGTGAAATAGTTGAAAACATATTGTTTTGGTATGT
44305615 TTATGGTTATGA
66 TTATGGTTATGA
*
44305627 TTTGAGTA-GTTTATGGTTATGATTTGAGTAGTGAAATAGTTGAAGACATATTGTTTTGGTATGT
1 TTTGAGTATGTTTATGGTTATGATTTGAGTAGTGAAATAGTTGAAAACATATTGTTTTGGTATGT
44305691 TTATGGTTATGA
66 TTATGGTTATGA
44305703 TTTGAGTA
1 TTTGAGTA
44305711 ATGAAATGGT
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
76 77 0.96
77 3 0.04
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.47
Consensus pattern (77 bp):
TTTGAGTATGTTTATGGTTATGATTTGAGTAGTGAAATAGTTGAAAACATATTGTTTTGGTATGT
TTATGGTTATGA
Found at i:44308294 original size:20 final size:20
Alignment explanation
Indices: 44308253--44308295 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
44308243 ATCTTCTACT
**
44308253 TTTATTTTATTTTTTGTTTA
1 TTTATTTTATTTTTTGAATA
44308273 TTTA-TTTATTATTTTGAATA
1 TTTATTTTATT-TTTTGAATA
44308293 TTT
1 TTT
44308296 CTTAAATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTATTTTATTTTTTGAATA
Found at i:44311824 original size:22 final size:22
Alignment explanation
Indices: 44311791--44311844 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
44311781 AACATATTGT
44311791 TTTG-GTATGTTTATGGTTATGA
1 TTTGAGTA-GTTTATGGTTATGA
44311813 TTTGAGTAGTTTATGGTTATGA
1 TTTGAGTAGTTTATGGTTATGA
44311835 TTTGAGTAGT
1 TTTGAGTAGT
44311845 GAAATAGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (22 bp):
TTTGAGTAGTTTATGGTTATGA
Found at i:44311831 original size:76 final size:77
Alignment explanation
Indices: 44311737--44311896 Score: 279
Period size: 76 Copynumber: 2.1 Consensus size: 77
44311727 GACATATTGT
* *
44311737 TTTG-GTATGTTTGTGGTTATGATTTGAGTAGTGAAATGGTTGAAAACATATTGTTTTGGTATGT
1 TTTGAGTATGTTTATGGTTATGATTTGAGTAGTGAAATAGTTGAAAACATATTGTTTTGGTATGT
44311801 TTATGGTTATGA
66 TTATGGTTATGA
*
44311813 TTTGAGTA-GTTTATGGTTATGATTTGAGTAGTGAAATAGTTGAAGACATATTGTTTTGGTATGT
1 TTTGAGTATGTTTATGGTTATGATTTGAGTAGTGAAATAGTTGAAAACATATTGTTTTGGTATGT
44311877 TTATGGTTATGA
66 TTATGGTTATGA
44311889 TTTGAGTA
1 TTTGAGTA
44311897 ATGAAATGGT
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
76 77 0.96
77 3 0.04
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.47
Consensus pattern (77 bp):
TTTGAGTATGTTTATGGTTATGATTTGAGTAGTGAAATAGTTGAAAACATATTGTTTTGGTATGT
TTATGGTTATGA
Found at i:44314480 original size:20 final size:20
Alignment explanation
Indices: 44314439--44314481 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
44314429 ATCTTCTACT
**
44314439 TTTATTTTATTTTTTGTTTA
1 TTTATTTTATTTTTTGAATA
44314459 TTTA-TTTATTATTTTGAATA
1 TTTATTTTATT-TTTTGAATA
44314479 TTT
1 TTT
44314482 CTTAAATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTATTTTATTTTTTGAATA
Found at i:44323105 original size:21 final size:21
Alignment explanation
Indices: 44323079--44323131 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
44323069 TGCATATTCA
44323079 TTTTTATCAATATATATCCTT
1 TTTTTATCAATATATATCCTT
44323100 TTTTTATCAATATATATCCTT
1 TTTTTATCAATATATATCCTT
*
44323121 TTTCT-TCAATA
1 TTTTTATCAATA
44323132 ATTGGTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 6 0.19
21 25 0.81
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTATCAATATATATCCTT
Found at i:44323846 original size:18 final size:18
Alignment explanation
Indices: 44323825--44323870 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
44323815 AATAAAATAA
44323825 AATTTATAAATTCAAAAT
1 AATTTATAAATTCAAAAT
* *
44323843 AATTTTTAAAATTTAAAAT
1 AATTTAT-AAATTCAAAAT
44323862 -ATTTATAAA
1 AATTTATAAA
44323871 AATTTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 3 0.12
18 11 0.46
19 10 0.42
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTTATAAATTCAAAAT
Found at i:44323860 original size:19 final size:19
Alignment explanation
Indices: 44323817--44323881 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
44323807 AAAAATAAAA
**
44323817 TAAAATAAAATTTATAAATT
1 TAAAATAATTTTTA-AAATT
*
44323837 CAAAATAATTTTTAAAATT
1 TAAAATAATTTTTAAAATT
*
44323856 TAAAAT-ATTTATAAAAATT
1 TAAAATAATTT-TTAAAATT
44323875 TCAAAAT
1 T-AAAAT
44323882 TTATATTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
18 4 0.11
19 18 0.47
20 16 0.42
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAATAATTTTTAAAATT
Found at i:44323871 original size:18 final size:18
Alignment explanation
Indices: 44323826--44323886 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
44323816 ATAAAATAAA
*
44323826 ATTTAT-AAATTCAAAAT
1 ATTTATAAAATTTAAAAT
*
44323843 AATTTTTAAAATTTAAAAT
1 -ATTTATAAAATTTAAAAT
*
44323862 ATTTATAAAAATTTCAAA-
1 ATTTAT-AAAATTTAAAAT
44323880 ATTTATA
1 ATTTATA
44323887 TTTTTAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 1 0.03
18 16 0.43
19 20 0.54
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTATAAAATTTAAAAT
Found at i:44323880 original size:27 final size:28
Alignment explanation
Indices: 44323849--44323943 Score: 81
Period size: 26 Copynumber: 3.4 Consensus size: 28
44323839 AAATAATTTT
*
44323849 TAAAATTTAAAATATTTATAAAAATTTC
1 TAAAATTTAAAATATTTATAAAAAATTC
* *
44323877 -AAAATTT-ATATTTTTA-AGAAAAATTC
1 TAAAATTTAAAATATTTATA-AAAAATTC
* * *
44323903 TAAAATTCTAAAAAATATATAAAAAAAGT-
1 TAAAATT-TAAAATATTTAT-AAAAAATTC
44323932 TAAAATTTAAAA
1 TAAAATTTAAAA
44323944 AAATAATTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
25 1 0.02
26 14 0.26
27 13 0.25
28 6 0.11
29 12 0.23
30 6 0.11
31 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (28 bp):
TAAAATTTAAAATATTTATAAAAAATTC
Found at i:44334094 original size:220 final size:220
Alignment explanation
Indices: 44333712--44334156 Score: 890
Period size: 220 Copynumber: 2.0 Consensus size: 220
44333702 GCGAAAGTGC
44333712 GGACAGAGGTCTGGGGTTTGAGTTTCACCTCGAGCACAGAAGGCTTGGGTTTTTGCTGCTCACGT
1 GGACAGAGGTCTGGGGTTTGAGTTTCACCTCGAGCACAGAAGGCTTGGGTTTTTGCTGCTCACGT
44333777 GGGGAAGAAGTTGGAGTCTGATCCGGACTCTCCTGGCAGCATGCTGAAACGGTGCAAGGGGTGGA
66 GGGGAAGAAGTTGGAGTCTGATCCGGACTCTCCTGGCAGCATGCTGAAACGGTGCAAGGGGTGGA
44333842 TAAGGATGCTGCTAATCGGTGGGGGAGTTTGAGCTGATCAGGGGATTAGGTAAGGATGAGATAAG
131 TAAGGATGCTGCTAATCGGTGGGGGAGTTTGAGCTGATCAGGGGATTAGGTAAGGATGAGATAAG
44333907 GGAGGAAATTTAGGAGCCTGATCAA
196 GGAGGAAATTTAGGAGCCTGATCAA
44333932 GGACAGAGGTCTGGGGTTTGAGTTTCACCTCGAGCACAGAAGGCTTGGGTTTTTGCTGCTCACGT
1 GGACAGAGGTCTGGGGTTTGAGTTTCACCTCGAGCACAGAAGGCTTGGGTTTTTGCTGCTCACGT
44333997 GGGGAAGAAGTTGGAGTCTGATCCGGACTCTCCTGGCAGCATGCTGAAACGGTGCAAGGGGTGGA
66 GGGGAAGAAGTTGGAGTCTGATCCGGACTCTCCTGGCAGCATGCTGAAACGGTGCAAGGGGTGGA
44334062 TAAGGATGCTGCTAATCGGTGGGGGAGTTTGAGCTGATCAGGGGATTAGGTAAGGATGAGATAAG
131 TAAGGATGCTGCTAATCGGTGGGGGAGTTTGAGCTGATCAGGGGATTAGGTAAGGATGAGATAAG
44334127 GGAGGAAATTTAGGAGCCTGATCAA
196 GGAGGAAATTTAGGAGCCTGATCAA
44334152 GGACA
1 GGACA
44334157 TGGTGTTGGC
Statistics
Matches: 225, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
220 225 1.00
ACGTcount: A:0.24, C:0.15, G:0.37, T:0.23
Consensus pattern (220 bp):
GGACAGAGGTCTGGGGTTTGAGTTTCACCTCGAGCACAGAAGGCTTGGGTTTTTGCTGCTCACGT
GGGGAAGAAGTTGGAGTCTGATCCGGACTCTCCTGGCAGCATGCTGAAACGGTGCAAGGGGTGGA
TAAGGATGCTGCTAATCGGTGGGGGAGTTTGAGCTGATCAGGGGATTAGGTAAGGATGAGATAAG
GGAGGAAATTTAGGAGCCTGATCAA
Found at i:44334319 original size:22 final size:22
Alignment explanation
Indices: 44334294--44334335 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
44334284 CTCCCCTCTC
44334294 TTTCATTCATATTTTCTTTTAT
1 TTTCATTCATATTTTCTTTTAT
* *
44334316 TTTCTTTCATCTTTTCTTTT
1 TTTCATTCATATTTTCTTTT
44334336 TCCATCATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTCATTCATATTTTCTTTTAT
Found at i:44334332 original size:12 final size:12
Alignment explanation
Indices: 44334294--44334334 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
44334284 CTCCCCTCTC
*
44334294 TTTCATTCATAT
1 TTTCTTTCATAT
44334306 TTTCTTT--TAT
1 TTTCTTTCATAT
*
44334316 TTTCTTTCATCT
1 TTTCTTTCATAT
44334328 TTTCTTT
1 TTTCTTT
44334335 TTCCATCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 10 0.40
12 15 0.60
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTCTTTCATAT
Found at i:44337688 original size:20 final size:20
Alignment explanation
Indices: 44337646--44337685 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
44337636 TTGTATGAGA
*
44337646 AAAAATTGAAAATTACATGG
1 AAAAATTGAAAATTAAATGG
*
44337666 AAAAATTGATAATTTAAATG
1 AAAAATTGA-AAATTAAATG
44337686 AAATGAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (20 bp):
AAAAATTGAAAATTAAATGG
Found at i:44337781 original size:27 final size:27
Alignment explanation
Indices: 44337751--44337802 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
44337741 AAAAAAGATA
* *
44337751 AATTTAAAAGAAATGAGGAAAAAATTT
1 AATTGAAAAGAAATGAGAAAAAAATTT
* *
44337778 AATTGAAATGAAATGATAAAAAAAT
1 AATTGAAAAGAAATGAGAAAAAAAT
44337803 GAAATTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.25
Consensus pattern (27 bp):
AATTGAAAAGAAATGAGAAAAAAATTT
Found at i:44337808 original size:27 final size:26
Alignment explanation
Indices: 44337676--44337812 Score: 81
Period size: 26 Copynumber: 5.3 Consensus size: 26
44337666 AAAAATTGAT
*
44337676 AATTTAAATGAAATGAGAAAAAAATA
1 AATTGAAATGAAATGAGAAAAAAATA
** * * *
44337702 AATTGGTATGAAACGA-TACAAAAT-
1 AATTGAAATGAAATGAGAAAAAAATA
44337726 --TT-AAATGAAAATTGA-AAAAAAGATA
1 AATTGAAATG-AAA-TGAGAAAAAA-ATA
* * * *
44337751 AATTTAAAAGAAATGAGGAAAAAATTT
1 AATTGAAATGAAATGA-GAAAAAAATA
*
44337778 AATTGAAATGAAATGATAAAAAAATGA
1 AATTGAAATGAAATGAGAAAAAAAT-A
44337805 AATT-AAAT
1 AATTGAAAT
44337813 TTGAAAGAAA
Statistics
Matches: 82, Mismatches: 19, Indels: 20
0.68 0.16 0.17
Matches are distributed among these distances:
21 3 0.04
22 5 0.06
23 6 0.07
24 2 0.02
25 6 0.07
26 26 0.32
27 24 0.29
28 10 0.12
ACGTcount: A:0.61, C:0.01, G:0.13, T:0.25
Consensus pattern (26 bp):
AATTGAAATGAAATGAGAAAAAAATA
Found at i:44337817 original size:76 final size:73
Alignment explanation
Indices: 44337676--44337924 Score: 222
Period size: 76 Copynumber: 3.4 Consensus size: 73
44337666 AAAAATTGAT
* * * ** ** *
44337676 AATTTAAATGAAATGA-GAAAAAAATAAATTGGTATGAAACGATACAAAATTTAAATGAAAATTG
1 AATTTAAAAGAAATGAGGAAAAAATTTAATTGAAATGAAA-GATA-AAAAAATAAAT-TAAATTG
*
44337740 AAAAAAAGATA
63 AAAGAAAGATA
44337751 AATTTAAAAGAAATGAGGAAAAAATTTAATTGAAATGAAATGATAAAAAAATGAAATTAAATTTG
1 AATTTAAAAGAAATGAGGAAAAAATTTAATTGAAATGAAA-GATAAAAAAAT-AAATTAAA-TTG
44337816 AAAGAAAGATA
63 AAAGAAAGATA
* ** * * * *
44337827 AATTTAAATGAAATG-GGAGAAACTTTTAATTTAAAT--AAGATGAGAAAA-AAATTAAATGGAA
1 AATTTAAAAGAAATGAGGA-AAAAATTTAATTGAAATGAAAGATAAAAAAATAAATTAAATTGAA
*
44337888 AGATAGAT-
65 AGAAAGATA
**
44337896 AATTTAAAAGAAATGACAAAAAAATTTAA
1 AATTTAAAAGAAATGAGGAAAAAATTTAA
44337925 ATTTGCATTG
Statistics
Matches: 146, Mismatches: 23, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
69 22 0.15
70 12 0.08
71 8 0.05
73 8 0.05
74 2 0.01
75 26 0.18
76 68 0.47
ACGTcount: A:0.59, C:0.02, G:0.14, T:0.25
Consensus pattern (73 bp):
AATTTAAAAGAAATGAGGAAAAAATTTAATTGAAATGAAAGATAAAAAAATAAATTAAATTGAAA
GAAAGATA
Found at i:44338048 original size:5 final size:5
Alignment explanation
Indices: 44338038--44338082 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
44338028 AAAATAATTT
* *
44338038 AAATG AAATG AAATT AGAATG AAATA AAATG AAGATG AAATG AAA
1 AAATG AAATG AAATG A-AATG AAATG AAATG AA-ATG AAATG AAA
44338083 AAAAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
5 25 0.74
6 9 0.26
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.20
Consensus pattern (5 bp):
AAATG
Found at i:44338051 original size:19 final size:21
Alignment explanation
Indices: 44337998--44338045 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
44337988 AGTATAAATG
44337998 AATTGAAAAAAAATAAATTTA
1 AATTGAAAAAAAATAAATTTA
44338019 AATTGAAAAAAAAT-AATTTA
1 AATTGAAAAAAAATAAATTTA
44338039 AA-TGAAA
1 AATTGAAA
44338046 TGAAATTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 5 0.19
20 8 0.30
21 14 0.52
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (21 bp):
AATTGAAAAAAAATAAATTTA
Found at i:44338058 original size:16 final size:15
Alignment explanation
Indices: 44338038--44338082 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
44338028 AAAATAATTT
*
44338038 AAATGAAATGAAATT
1 AAATGAAATGAAATG
*
44338053 AGAATGAAATAAAATG
1 A-AATGAAATGAAATG
44338069 AAGATGAAATGAAA
1 AA-ATGAAATGAAA
44338083 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.20
Consensus pattern (15 bp):
AAATGAAATGAAATG
Found at i:44338078 original size:11 final size:10
Alignment explanation
Indices: 44338038--44338082 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
44338028 AAAATAATTT
44338038 AAATGAAATG
1 AAATGAAATG
*
44338048 AAATTAGAATG
1 AAATGA-AATG
*
44338059 AAATAAAATG
1 AAATGAAATG
44338069 AAGATGAAATG
1 AA-ATGAAATG
44338080 AAA
1 AAA
44338083 AAAAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 12 0.40
11 18 0.60
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.20
Consensus pattern (10 bp):
AAATGAAATG
Found at i:44338422 original size:14 final size:14
Alignment explanation
Indices: 44338395--44338509 Score: 61
Period size: 14 Copynumber: 8.3 Consensus size: 14
44338385 TAATTAATTA
44338395 GAAAAAATATTAATAT
1 GAAAAAA-A-TAATAT
44338411 GAAAAAAATAATAT
1 GAAAAAAATAATAT
44338425 ----AAAATGAAT-T
1 GAAAAAAAT-AATAT
44338435 GAAAAAAATAATAT
1 GAAAAAAATAATAT
44338449 GAAAAGAAAATAATAATAT
1 G---A-AAAA-AATAATAT
*
44338468 GAAATAAATAATAT
1 GAAAAAAATAATAT
*
44338482 --AAAATA-AAT-T
1 GAAAAAAATAATAT
44338492 GAAAAAAAATAAT-T
1 G-AAAAAAATAATAT
44338506 GAAA
1 GAAA
44338510 TGAAATAAAA
Statistics
Matches: 80, Mismatches: 4, Indels: 33
0.68 0.03 0.28
Matches are distributed among these distances:
10 7 0.09
11 6 0.08
12 4 0.05
13 11 0.14
14 26 0.32
15 4 0.05
16 8 0.10
17 1 0.01
18 4 0.05
19 9 0.11
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (14 bp):
GAAAAAAATAATAT
Found at i:44338431 original size:19 final size:19
Alignment explanation
Indices: 44338396--44338537 Score: 80
Period size: 19 Copynumber: 7.3 Consensus size: 19
44338386 AATTAATTAG
*
44338396 AAAAAAT-AT-TAATATGA
1 AAAAAATAATATAAAATGA
44338413 AAAAAATAATATAAAATGAATTGA
1 AAAAAATAATAT--AA--AA-TGA
44338437 AAAAAATAATATGAAAA-GA
1 AAAAAATAATAT-AAAATGA
* *
44338456 AAATAATAATATGAAAT-A
1 AAAAAATAATATAAAATGA
* * *
44338474 AATAATATAAAATAAATTGAA
1 AA-AAAATAATATAAAATG-A
*
44338495 AAAAAATAAT-TGAAATGA
1 AAAAAATAATATAAAATGA
*
44338513 AATAAAATAAAATTAAAAT-A
1 AA-AAAATAATA-TAAAATGA
44338533 AAAAA
1 AAAAA
44338538 TAAAAGGGTT
Statistics
Matches: 96, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
17 7 0.07
18 11 0.11
19 39 0.41
20 9 0.09
21 12 0.12
23 3 0.03
24 15 0.16
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (19 bp):
AAAAAATAATATAAAATGA
Found at i:44338466 original size:57 final size:57
Alignment explanation
Indices: 44338398--44338521 Score: 182
Period size: 57 Copynumber: 2.2 Consensus size: 57
44338388 TTAATTAGAA
* *
44338398 AAAATATTAATATGAAAAAAATAATATAAAATGAATTG-AAAAAAATAATATGAAAAG
1 AAAATAATAATATGAAAAAAATAATATAAAATAAATTGAAAAAAAATAAT-TGAAAAG
* *
44338455 AAAATAATAATATGAAATAAATAATATAAAATAAATTGAAAAAAAATAATTGAAATG
1 AAAATAATAATATGAAAAAAATAATATAAAATAAATTGAAAAAAAATAATTGAAAAG
44338512 -AAATAA-AATA
1 AAAATAATAATA
44338522 AAATTAAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
55 4 0.06
56 6 0.10
57 41 0.66
58 11 0.18
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (57 bp):
AAAATAATAATATGAAAAAAATAATATAAAATAAATTGAAAAAAAATAATTGAAAAG
Found at i:44338515 original size:14 final size:14
Alignment explanation
Indices: 44338423--44338517 Score: 63
Period size: 14 Copynumber: 6.6 Consensus size: 14
44338413 AAAAAATAAT
44338423 ATAAAATGAATTGAA
1 ATAAAAT-AATTGAA
44338438 A-AAAATAATATGAAA
1 ATAAAATAAT-TG-AA
*
44338453 AGAAAATAA-T-AA
1 ATAAAATAATTGAA
* *
44338465 TATGAAATAAAT-AA
1 -ATAAAATAATTGAA
44338479 TATAAAATAAATTGAA
1 -ATAAAAT-AATTGAA
*
44338495 AAAAAATAATTGAA
1 ATAAAATAATTGAA
*
44338509 ATGAAATAA
1 ATAAAATAA
44338518 AATAAAATTA
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
12 2 0.03
13 10 0.15
14 32 0.48
15 13 0.20
16 9 0.14
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (14 bp):
ATAAAATAATTGAA
Found at i:44338542 original size:5 final size:5
Alignment explanation
Indices: 44338415--44338535 Score: 61
Period size: 5 Copynumber: 23.8 Consensus size: 5
44338405 TAATATGAAA
* * * * * *
44338415 AAAAT AATAT AAAAT GAATT GAAA- AAAAT AATAT GAAAAG AAAAT AATAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AA-AAT
* * * *
44338466 ATGAAAT -AAAT AATAT AAAAT AAATT GAAAA- AAAAT -AATT GAAAT
1 A--AAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT
*
44338511 GAAAT AAAAT AAAATT AAAAT AAAA
1 AAAAT AAAAT AAAA-T AAAAT AAAA
44338536 AATAAAAGGG
Statistics
Matches: 89, Mismatches: 17, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
4 14 0.16
5 56 0.63
6 15 0.17
7 3 0.03
8 1 0.01
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:44339053 original size:107 final size:111
Alignment explanation
Indices: 44338919--44339214 Score: 429
Period size: 107 Copynumber: 2.7 Consensus size: 111
44338909 TAGGATCTGT
** *
44338919 ATTGACAGGCCAGCACCAAATTTTTTTTAAAAAAACTCGTATTCTGGTGCCGGCCTTTCAAAGGC
1 ATTGACAGGCCAGCACCAAATTTTTTTTTTAAAAACTCGTATTCTGGTGCCGGCCTTTAAAAGGC
44338984 CAGCACCAAAAAAA-TT-AA-TTTTTTT-AATTACTGGTGCCGGCC
66 CAGCACCAAAAAAATTTGAATTTTTTTTAAATTACTGGTGCCGGCC
* * * *
44339026 ATTGATAGGCCAGCACCAAATTTTTTTTTTGAAAACTCGTATTCTGGTGCCAGCCATTAAAAGGC
1 ATTGACAGGCCAGCACCAAATTTTTTTTTTAAAAACTCGTATTCTGGTGCCGGCCTTTAAAAGGC
*
44339091 CAGCACCAAAAAAATTTGAATTTTTTTTTAAATTATTGGTGCCGGCC
66 CAGCACCAAAAAAATTTGAA-TTTTTTTTAAATTACTGGTGCCGGCC
* * * *
44339138 ATTGACAGGCCAGCACCCAAAATTTTTTTTTTAAAAACTCATATTCTTGTGCCGGCCTTTGACAG
1 ATTGACAGGCCAGCA-CC-AAATTTTTTTTTTAAAAACTCGTATTCTGGTGCCGGCCTTTAAAAG
44339203 GCCAGCACCAAA
64 GCCAGCACCAAA
44339215 TTACTGGTGC
Statistics
Matches: 166, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
107 72 0.43
108 2 0.01
109 2 0.01
111 7 0.04
112 30 0.18
113 2 0.01
114 51 0.31
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (111 bp):
ATTGACAGGCCAGCACCAAATTTTTTTTTTAAAAACTCGTATTCTGGTGCCGGCCTTTAAAAGGC
CAGCACCAAAAAAATTTGAATTTTTTTTAAATTACTGGTGCCGGCC
Found at i:44339083 original size:55 final size:55
Alignment explanation
Indices: 44338919--44339214 Score: 240
Period size: 55 Copynumber: 5.4 Consensus size: 55
44338909 TAGGATCTGT
**
44338919 ATTGACAGGCCAGCACC-AAATTTTTTTTAAAAAAACTCGTATTCTGGTGCCGGCC
1 ATTGACAGGCCAGCACCAAAATTTTTTTTTTAAAAACTC-TATTCTGGTGCCGGCC
* * * *
44338974 TTTCAAAGGCCAGCACCAAAAAAATTAATTTTTTT---AA-T-TA--CTGGTGCCGGCC
1 ATTGACAGGCCAGCACC---AAAATT-TTTTTTTTAAAAACTCTATTCTGGTGCCGGCC
* * *
44339026 ATTGATAGGCCAGCACC-AAATTTTTTTTTTGAAAACTCGTATTCTGGTGCCAGCC
1 ATTGACAGGCCAGCACCAAAATTTTTTTTTTAAAAACTC-TATTCTGGTGCCGGCC
* * **
44339081 ATTAAAAGGCCAGCACCAAAAAAATTTGAATTTTTTTTTAAA-T-TA-T-TGGTGCCGGCC
1 ATTGACAGGCCAGCACC---AAAATTT---TTTTTTTAAAAACTCTATTCTGGTGCCGGCC
*
44339138 ATTGACAGGCCAGCACCCAAAATTTTTTTTTTAAAAACTCATATTCTTGTGCCGGCC
1 ATTGACAGGCCAGCA-CCAAAATTTTTTTTTTAAAAACTC-TATTCTGGTGCCGGCC
*
44339195 TTTGACAGGCCAGCACCAAA
1 ATTGACAGGCCAGCACCAAA
44339215 TTACTGGTGC
Statistics
Matches: 193, Mismatches: 22, Indels: 51
0.73 0.08 0.19
Matches are distributed among these distances:
47 7 0.04
48 5 0.03
50 2 0.01
51 1 0.01
52 36 0.19
53 3 0.02
54 2 0.01
55 49 0.25
56 7 0.04
57 49 0.25
58 3 0.02
59 13 0.07
60 5 0.03
61 1 0.01
62 10 0.05
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (55 bp):
ATTGACAGGCCAGCACCAAAATTTTTTTTTTAAAAACTCTATTCTGGTGCCGGCC
Found at i:44339190 original size:57 final size:56
Alignment explanation
Indices: 44338919--44339211 Score: 229
Period size: 57 Copynumber: 5.3 Consensus size: 56
44338909 TAGGATCTGT
**
44338919 ATTGACAGGCCAGCA-CC-AAATTTTTTTTAAAAAAACTCGTATTCTGGTGCCGGCC
1 ATTGACAGGCCAGCACCCAAAATTTTTTTTTTAAAAACTC-TATTCTGGTGCCGGCC
* * * * *
44338974 TTTCAAAGGCCAGCACCAAAAAAATTAATTTTTTT---AA-T-TA--CTGGTGCCGGCC
1 ATTGACAGGCCAGCACC--CAAAATT-TTTTTTTTAAAAACTCTATTCTGGTGCCGGCC
* * *
44339026 ATTGATAGGCCAGCA-CC-AAATTTTTTTTTTGAAAACTCGTATTCTGGTGCCAGCC
1 ATTGACAGGCCAGCACCCAAAATTTTTTTTTTAAAAACTC-TATTCTGGTGCCGGCC
* * * **
44339081 ATTAAAAGGCCAGCACCAAAAAAATTTGAATTTTTTTTTAAA-T-TA-T-TGGTGCCGGCC
1 ATTGACAGGCCAGCACC--CAAAATTT---TTTTTTTAAAAACTCTATTCTGGTGCCGGCC
*
44339138 ATTGACAGGCCAGCACCCAAAATTTTTTTTTTAAAAACTCATATTCTTGTGCCGGCC
1 ATTGACAGGCCAGCACCCAAAATTTTTTTTTTAAAAACTC-TATTCTGGTGCCGGCC
*
44339195 TTTGACAGGCCAGCACC
1 ATTGACAGGCCAGCACC
44339212 AAATTACTGG
Statistics
Matches: 187, Mismatches: 26, Indels: 48
0.72 0.10 0.18
Matches are distributed among these distances:
47 7 0.04
48 5 0.03
50 2 0.01
51 2 0.01
52 34 0.18
53 3 0.02
54 2 0.01
55 45 0.24
56 4 0.02
57 53 0.28
58 1 0.01
59 13 0.07
60 5 0.03
61 1 0.01
62 10 0.05
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (56 bp):
ATTGACAGGCCAGCACCCAAAATTTTTTTTTTAAAAACTCTATTCTGGTGCCGGCC
Found at i:44345002 original size:50 final size:50
Alignment explanation
Indices: 44344927--44345022 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 50
44344917 GATATGAGAG
* *
44344927 TTATTGCCAAATTTAGGCAACTAATAGTGATTTAACCTTCCAACTTAGAA
1 TTATTGCCAAATTTAGGCAACTAATAGTAATTTAACCTTCAAACTTAGAA
*
44344977 TTATTGCCAAATTT-GGACACCTAATAGTAATTTAACCTTCAAACTT
1 TTATTGCCAAATTTAGG-CAACTAATAGTAATTTAACCTTCAAACTT
44345023 TAAAGTGAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
49 2 0.05
50 40 0.95
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (50 bp):
TTATTGCCAAATTTAGGCAACTAATAGTAATTTAACCTTCAAACTTAGAA
Found at i:44346466 original size:138 final size:132
Alignment explanation
Indices: 44345907--44346595 Score: 482
Period size: 128 Copynumber: 5.2 Consensus size: 132
44345897 GATGTTTTCT
* * * * *
44345907 TTAAAAGATCAATGCTT-ACTCATATTTGCTAATACT-GCGTTTTTGCAATGT-AAACACCAGAT
1 TTAAAAGATCAATG-TTCATTCATATTTGCTAATA-TAGCG-TTGTGCAGTGTAAAAAACCA-AC
* * * ** *
44345969 CACCATGTATTAATCTCAATA--TTTGTTTGGATTCTATGTTAATGTTTCGTCACTTATGTCTAA
62 CACCATGTATTAATCTCAATATGTTTGTTTCGATTTTATGTTGATGTTTTATCAATTATGTCTAA
*
44346032 GATTCA
127 CATTCA
* * * *
44346038 TTAAAAGATCAATGTCCATTCATGTATTGCTAATATAAGTGTCTGTGCAGTAT-AAAAACCAATC
1 TTAAAAGATCAATGTTCATTCATAT-TTGCTAATAT-AGCGT-TGTGCAGTGTAAAAAACCAA-C
* * * * * * * * *
44346102 AACCA--TCTCAA-C-C--TA--TTTGTTTGGATTTTATGTTGGTTTTTTTGTCACTTATGTCTG
62 CACCATGTATTAATCTCAATATGTTTGTTTCGATTTTATGTT-GATGTTTTATCAATTATGTCTA
**
44346159 TGATTCA
126 ACATTCA
* * * *
44346166 TTACAAGATCAATGTTTATTCATACATTGCTAATGTAAGCGTCCT-TGCAGTGT-AAAAACCAAA
1 TTAAAAGATCAATGTTCATTCATA-TTTGCTAATAT-AGCGT--TGTGCAGTGTAAAAAACC-AA
* * * * *
44346229 CCACCTTGCATTAATCTCAATATATTTGTTTTGATTTTATGTTGATGTTTTATTAATTATGTCTA
61 CCACCATGTATTAATCTCAATATGTTTGTTTCGATTTTATGTTGATGTTTTATCAATTATGTCTA
*
44346294 AGATTCA
126 ACATTCA
* * ** * * *
44346301 CTAAAAGATCAATTTTTGTTCATATATTTCTAGTATAAGTGTCTGTGCAGTGTAAAAAACCAAGC
1 TTAAAAGATCAATGTTCATTCATAT-TTGCTAATAT-AGCGT-TGTGCAGTGTAAAAAACCAA-C
* * * *
44346366 CATCATGTATTTATCTCAATATGTTTGTTTCGATTTTTATGTTGATAGTTTTGTCAGTTATGTCT
62 CACCATGTATTAATCTCAATATGTTTGTTTCGA-TTTTATGTTGAT-GTTTTATCAATTATGTCT
44346431 AACATTCA
125 AACATTCA
* * * * * * *
44346439 TTAAAAGAGATCAATGCTCATTCATATTTGCTAATATTGCGTTTTCGTAATGTAAAAACCCGACC
1 TT-AAA-AGATCAATGTTCATTCATATTTGCTAATATAGCGTTGT-GCAGTGTAAAAAACCAACC
* * * *
44346504 ACCATGTAATAATCTC-A-ATG--TGTTTGGATTTTATGTTGATGTTTTTCTCATTTATGTCTAA
63 ACCATGTATTAATCTCAATATGTTTGTTTCGATTTTATGTTGATG-TTTTATCAATTATGTCTAA
44346565 CATTCA
127 CATTCA
*
44346571 TTCAAAGATCAATGTTCATTCATAT
1 TTAAAAGATCAATGTTCATTCATAT
44346596 GTGTTTTGTC
Statistics
Matches: 449, Mismatches: 81, Indels: 57
0.76 0.14 0.10
Matches are distributed among these distances:
127 20 0.04
128 75 0.17
129 5 0.01
130 24 0.05
131 29 0.06
132 49 0.11
133 27 0.06
134 4 0.01
135 67 0.15
136 54 0.12
137 29 0.06
138 39 0.09
139 11 0.02
140 16 0.04
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (132 bp):
TTAAAAGATCAATGTTCATTCATATTTGCTAATATAGCGTTGTGCAGTGTAAAAAACCAACCACC
ATGTATTAATCTCAATATGTTTGTTTCGATTTTATGTTGATGTTTTATCAATTATGTCTAACATT
CA
Found at i:44365008 original size:27 final size:26
Alignment explanation
Indices: 44364971--44365053 Score: 130
Period size: 27 Copynumber: 3.1 Consensus size: 26
44364961 GTATGGCTGT
* *
44364971 CAGAACAGATATTGTGACAGAGTCAC
1 CAGAACAGATATTGTGGCAGAGCCAC
44364997 CAGATACAGATATTGTGGCAGAGCCAC
1 CAGA-ACAGATATTGTGGCAGAGCCAC
44365024 CAGAACAGATATTTGTGGCAGAGCCAC
1 CAGAACAGATA-TTGTGGCAGAGCCAC
44365051 CAG
1 CAG
44365054 TATACTCTCT
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
26 11 0.21
27 42 0.79
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (26 bp):
CAGAACAGATATTGTGGCAGAGCCAC
Found at i:44375063 original size:16 final size:17
Alignment explanation
Indices: 44375042--44375092 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 17
44375032 TTTCTTTTCC
44375042 TTTTGTTTCTCTATTT-
1 TTTTGTTTCTCTATTTA
44375058 TTTTGTTTCTCT-TTTA
1 TTTTGTTTCTCTATTTA
44375074 CTTTTCGTTCTCTCTATTT
1 -TTTT-GTT-TCTCTATTT
44375093 GTTGCGTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.10
16 12 0.40
17 4 0.13
18 3 0.10
19 5 0.17
20 3 0.10
ACGTcount: A:0.06, C:0.18, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTTGTTTCTCTATTTA
Found at i:44375071 original size:33 final size:35
Alignment explanation
Indices: 44375022--44375092 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 35
44375012 AGTTATCCGT
* *
44375022 TTTTTTTCTTTTTCTTTTCCTTTT-GTT-TCTCTA
1 TTTTTTTCTTTCTCTTTTACTTTTCGTTCTCTCTA
*
44375055 TTTTTTTGTTTCTCTTTTACTTTTCGTTCTCTCTA
1 TTTTTTTCTTTCTCTTTTACTTTTCGTTCTCTCTA
44375090 TTT
1 TTT
44375093 GTTGCGTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 21 0.64
34 3 0.09
35 9 0.27
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.73
Consensus pattern (35 bp):
TTTTTTTCTTTCTCTTTTACTTTTCGTTCTCTCTA
Found at i:44378350 original size:17 final size:19
Alignment explanation
Indices: 44378344--44378378 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
44378334 ATAAAATAGA
44378344 ACAATAAATCAAAGATTAG
1 ACAATAAATCAAAGATTAG
44378363 ACAATAAA--AAAGATTA
1 ACAATAAATCAAAGATTA
44378379 TAAAGAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.20
Consensus pattern (19 bp):
ACAATAAATCAAAGATTAG
Found at i:44381296 original size:44 final size:44
Alignment explanation
Indices: 44381233--44381319 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
44381223 GTAGGTCAAA
* *
44381233 TAATATTAAAGTAACCTACACTAATCAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAGAGCTTAAGTGGGAAAC
*
44381277 TAATATTAAAATAATCTACACTAATCAGAGCTTAAGTGGGAAA
1 TAATATTAAAATAACCTACACTAATCAGAGCTTAAGTGGGAAA
44381320 TTAAAAACAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.28
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAGAGCTTAAGTGGGAAAC
Found at i:44384557 original size:132 final size:133
Alignment explanation
Indices: 44384351--44384636 Score: 355
Period size: 132 Copynumber: 2.2 Consensus size: 133
44384341 TATTTTTAGA
* * * * *
44384351 ATTTTTA-AGAAACATGAGTGAAATTCTAAAGGGGATATTCGATTATTTTAAACCAACAGGAAAT
1 ATTTTTAGA-AAACATGAATGAAATTCCAAAGGGGACATTCGATTATTTCAAACAAACAGGAAAT
* * ** * *
44384415 CGCAACCCAGCATGATAGGGCACGATTCCCCGAATTGCCAAACATCGAGTATTACCTTCGTTTTA
65 CGCAACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACACCGAACATCACCTTCGTTTCA
44384480 AA-G
130 AAGG
* *
44384483 AGTTTTTAGAAAACATGAATGAAATTCCAAA-GGGACATTCGATTATTTCGAGCAAAC-GAGAAA
1 A-TTTTTAGAAAACATGAATGAAATTCCAAAGGGGACATTCGATTATTTCAAACAAACAG-GAAA
* * * * *
44384546 TTGCAACCCAGCACGTTAGGGCACGATTCCGCGAATTGCCAAATACCGAACATCGCCTTCGTTTC
64 TCGCAACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACACCGAACATCACCTTCGTTTC
44384611 AAAGG
129 AAAGG
44384616 ATTTTTAGAAAACATGAATGA
1 ATTTTTAGAAAACATGAATGA
44384637 TTATAAAACT
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
131 1 0.01
132 103 0.78
133 27 0.20
134 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (133 bp):
ATTTTTAGAAAACATGAATGAAATTCCAAAGGGGACATTCGATTATTTCAAACAAACAGGAAATC
GCAACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACACCGAACATCACCTTCGTTTCAA
AGG
Found at i:44394213 original size:15 final size:15
Alignment explanation
Indices: 44394190--44394219 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44394180 TCTCATCACC
*
44394190 AAAACTAAACAAAAG
1 AAAAATAAACAAAAG
44394205 AAAAATAAACAAAAG
1 AAAAATAAACAAAAG
44394220 CTTTGTAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.10, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAAATAAACAAAAG
Found at i:44395874 original size:52 final size:52
Alignment explanation
Indices: 44395796--44395899 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
44395786 CTGTTTTATA
44395796 AATTTTGGATTCAAGTTACAAGCTCGGGGATCGTCAGCAAAGCCTATCACTC
1 AATTTTGGATTCAAGTTACAAGCTCGGGGATCGTCAGCAAAGCCTATCACTC
44395848 AATTTTGGATTCAAGTTACAAGCTCGGGGATCGTCAGCAAAGCCTATCACTC
1 AATTTTGGATTCAAGTTACAAGCTCGGGGATCGTCAGCAAAGCCTATCACTC
44395900 TATCAACCAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (52 bp):
AATTTTGGATTCAAGTTACAAGCTCGGGGATCGTCAGCAAAGCCTATCACTC
Found at i:44400488 original size:25 final size:25
Alignment explanation
Indices: 44400460--44400508 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
44400450 TCAAGCCTAT
*
44400460 TTTGATTTGGATCGTAGAGAGCAAC
1 TTTGATTTGGATCATAGAGAGCAAC
44400485 TTTGATTTGGATCATAGAGAGCAA
1 TTTGATTTGGATCATAGAGAGCAA
44400509 TCTAACCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.33
Consensus pattern (25 bp):
TTTGATTTGGATCATAGAGAGCAAC
Found at i:44401516 original size:25 final size:24
Alignment explanation
Indices: 44401482--44401862 Score: 122
Period size: 25 Copynumber: 15.6 Consensus size: 24
44401472 AAATGAATTA
*
44401482 AAATAATATAAAAATATTTAAAAGT
1 AAATAATATAAAAAGATTTAAAA-T
* * *
44401507 AAATAGTATAACAAGGTTTAAAAT
1 AAATAATATAAAAAGATTTAAAAT
* ** * *
44401531 AAATGATGAATAAAACCA-ATAAAGT
1 AAATAAT--ATAAAAAGATTTAAAAT
* *
44401556 --ACAACATAAAAAG-TTTAAAAT
1 AAATAATATAAAAAGATTTAAAAT
*
44401577 AAATAATATATAAAAAGGTTTAAAAT
1 AAAT-A-ATATAAAAAGATTTAAAAT
* * *
44401603 AAATAATATATGAAACGATTCAGAAT
1 AAATAATATA--AAAAGATTTAAAAT
* * *
44401629 AAACAATATATAAA-TTTTAAAAT
1 AAATAATATAAAAAGATTTAAAAT
* ** *
44401652 -AA-AGTATAAATCGATTTGAAAT
1 AAATAATATAAAAAGATTTAAAAT
* * * *
44401674 AAATAGTTTATAAAGCAATTTAAAGT
1 AAATAATATAAAAAG--ATTTAAAAT
* *
44401700 TAATAATATATAAAATAATTTAAAAT
1 AAATAATATA-AAAA-GATTTAAAAT
** *
44401726 -AATAATGCAAAACA-AATTAAAAT
1 AAATAATATAAAA-AGATTTAAAAT
* *
44401749 AAATAATGTGTTAAAACA-ATTTAAAAC
1 AAATAA--T-ATAAAA-AGATTTAAAAT
* *
44401776 AAATACTATATGAAAA-ACTTAAAAT
1 AAATA--ATATAAAAAGATTTAAAAT
* *
44401801 AAATAATAATAAAACTG-TTCAAAAT
1 AAATAAT-ATAAAA-AGATTTAAAAT
* * *
44401826 AAATACTAT-GAAAGATTTATAAT
1 AAATAATATAAAAAGATTTAAAAT
*
44401849 AAATAAAATAAAAA
1 AAATAATATAAAAA
44401863 AGAATACAAT
Statistics
Matches: 255, Mismatches: 72, Indels: 59
0.66 0.19 0.15
Matches are distributed among these distances:
21 17 0.07
22 10 0.04
23 36 0.14
24 39 0.15
25 67 0.26
26 63 0.25
27 22 0.09
29 1 0.00
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (24 bp):
AAATAATATAAAAAGATTTAAAAT
Found at i:44401611 original size:26 final size:26
Alignment explanation
Indices: 44401561--44401642 Score: 103
Period size: 26 Copynumber: 3.2 Consensus size: 26
44401551 AAAGTACAAC
44401561 ATAAAAA-GTTTAAAATAAATAATAT
1 ATAAAAAGGTTTAAAATAAATAATAT
44401586 ATAAAAAGGTTTAAAATAAATAATAT
1 ATAAAAAGGTTTAAAATAAATAATAT
* * * * * *
44401612 ATGAAACGATTCAGAATAAACAATAT
1 ATAAAAAGGTTTAAAATAAATAATAT
44401638 ATAAA
1 ATAAA
44401643 TTTTAAAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 7 0.14
26 42 0.86
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (26 bp):
ATAAAAAGGTTTAAAATAAATAATAT
Found at i:44401752 original size:27 final size:26
Alignment explanation
Indices: 44401722--44401815 Score: 79
Period size: 27 Copynumber: 3.6 Consensus size: 26
44401712 AAATAATTTA
44401722 AAATAATAATGCAAAACAAATTAAAAT
1 AAATAATAATG-AAAACAAATTAAAAT
* * *
44401749 AAATAAT-GTGTTAAAACAATTTAAAAC
1 AAATAATAATG--AAAACAAATTAAAAT
* *
44401776 AAATACTATATG-AAA-AACTTAAAAT
1 AAATAATA-ATGAAAACAAATTAAAAT
44401801 AAATAATAAT-AAAAC
1 AAATAATAATGAAAAC
44401816 TGTTCAAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
24 5 0.09
25 15 0.28
26 5 0.09
27 26 0.49
29 2 0.04
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (26 bp):
AAATAATAATGAAAACAAATTAAAAT
Found at i:44401814 original size:50 final size:48
Alignment explanation
Indices: 44401742--44401861 Score: 116
Period size: 48 Copynumber: 2.4 Consensus size: 48
44401732 GCAAAACAAA
** *
44401742 TTAAAATAAATAATGTGTTAAAACAATTTAAAACAAATACTATATGAAAAAC
1 TTAAAATAAATAA--TAATAAAACAATTCAAAACAAATAC--TATGAAAAAC
** * * *
44401794 TTAAAATAAATAATAATAAAACTGTTCAAAATAAATACTATGAAAGAT
1 TTAAAATAAATAATAATAAAACAATTCAAAACAAATACTATGAAAAAC
*
44401842 TTATAATAAATAA-AATAAAA
1 TTAAAATAAATAATAATAAAA
44401862 AAGAATACAA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
47 7 0.12
48 20 0.34
50 19 0.32
52 13 0.22
ACGTcount: A:0.60, C:0.06, G:0.05, T:0.29
Consensus pattern (48 bp):
TTAAAATAAATAATAATAAAACAATTCAAAACAAATACTATGAAAAAC
Found at i:44402138 original size:11 final size:11
Alignment explanation
Indices: 44402124--44402166 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
44402114 TGTTTTCTCC
*
44402124 CTATTTTGCTA
1 CTATTTTACTA
44402135 CTATTTTACTA
1 CTATTTTACTA
* *
44402146 TTATGTTACTA
1 CTATTTTACTA
44402157 CTATTTTACT
1 CTATTTTACT
44402167 GTTATTGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.23, C:0.16, G:0.05, T:0.56
Consensus pattern (11 bp):
CTATTTTACTA
Found at i:44402172 original size:11 final size:11
Alignment explanation
Indices: 44402125--44402172 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
44402115 GTTTTCTCCC
* *
44402125 TATTTTGCTAC
1 TATTTTACTAT
44402136 TATTTTACTAT
1 TATTTTACTAT
* *
44402147 TATGTTACTAC
1 TATTTTACTAT
*
44402158 TATTTTACTGT
1 TATTTTACTAT
44402169 TATT
1 TATT
44402173 GTTTGGATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.23, C:0.12, G:0.06, T:0.58
Consensus pattern (11 bp):
TATTTTACTAT
Found at i:44404097 original size:44 final size:44
Alignment explanation
Indices: 44404038--44404434 Score: 244
Period size: 44 Copynumber: 8.7 Consensus size: 44
44404028 AGCTTCAATA
44404038 TGCTCCACTGCAACTTCAGGGAGATAAGGCTTGTAACTTCAACC
1 TGCTCCACTGCAACTTCAGGGAGATAAGGCTTGTAACTTCAACC
* * * * *
44404082 TGCTCCACTGTAACTTTAGTGAGATAAGGTTTGTGATTTGTAGCTTCAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGGCTTGT-A-----A-CTTCAACC
* * * * ** **
44404133 TACTCCACTGCAACTTTAGGGAGATAA-GATTCACTATTTTCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGGCTT--GTAACTTCAACC
** *
44404178 TGCTCCACTATAACTTCAGGGAGATAAGACTTGTAACTTCGAA-C
1 TGCTCCACTGCAACTTCAGGGAGATAAGGCTTGTAACTTC-AACC
* * * **
44404222 TGCCCCACTGCAACTTTAGGGGGATAAGG-TTCGTGGCTTCAACC
1 TGCTCCACTGCAACTTCAGGGAGATAAGGCTT-GTAACTTCAACC
* *
44404266 TGCTCCACTACAACTTCAGGGAGATAAGGTTTGTGATTTGTAGCTTCAATCC
1 TGCTCCACTGCAACTTCAGGGAGATAAGGCTTGT-A-----A-CTTCAA-CC
* * ** * * **
44404318 -ACTCCACTGCAACTTCAGAGAGATAAGATTCTCTATCTTCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGGCT-TGTAACTTCAACC
* * * * *
44404362 TGCTCCATTGCAACTTCAAGGAGATGAGACTTGTAAATTCAACC
1 TGCTCCACTGCAACTTCAGGGAGATAAGGCTTGTAACTTCAACC
* *
44404406 TACTCCACTGCAACTTCAGGAAGATAAGG
1 TGCTCCACTGCAACTTCAGGGAGATAAGG
44404435 TTAGGGGCTT
Statistics
Matches: 267, Mismatches: 62, Indels: 48
0.71 0.16 0.13
Matches are distributed among these distances:
43 4 0.01
44 125 0.47
45 62 0.23
46 2 0.01
50 4 0.01
51 65 0.24
52 5 0.02
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGGCTTGTAACTTCAACC
Found at i:44404248 original size:89 final size:87
Alignment explanation
Indices: 44404119--44404433 Score: 279
Period size: 89 Copynumber: 3.5 Consensus size: 87
44404109 GGTTTGTGAT
* * *
44404119 TTGTAGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAGATTCACTATTTTCAGTCTGCTCC
1 TTGTAACTTCAA-CTACCCCACTGCAACTTTAGGGAGATAAGATTC-CTATCTTCAGTCTGCTCC
*
44404184 ACTATAACTTCAGGGAGATAAGAC
64 ACTACAACTTCAGGGAGATAAGAC
* * * * ** **
44404208 TTGTAACTTCGAACTGCCCCACTGCAACTTTAGGGGGATAAGGTTCGTGGCTTCAACCTGCTCCA
1 TTGTAACTTC-AACTACCCCACTGCAACTTTAGGGAGATAAGATTCCTATCTTCAGTCTGCTCCA
*
44404273 CTACAACTTCAGGGAGATAAGGTTTGTGAT
65 CTACAACTTCAGGGAGATAA-------GAC
* * * * *
44404303 TTGTAGCTTCAATCCACTCCACTGCAACTTCAGAGAGATAAGATTCTCTATCTTCAGTCTGCTCC
1 TTGTAACTTCAA-CTACCCCACTGCAACTTTAGGGAGATAAGATTC-CTATCTTCAGTCTGCTCC
* * * *
44404368 ATTGCAACTTCAAGGAGATGAGAC
64 ACTACAACTTCAGGGAGATAAGAC
* * * *
44404392 TTGTAAATTCAACCTACTCCACTGCAACTTCAGGAAGATAAG
1 TTGTAACTTCAA-CTACCCCACTGCAACTTTAGGGAGATAAG
44404434 GTTAGGGGCT
Statistics
Matches: 179, Mismatches: 37, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
88 32 0.18
89 76 0.42
90 2 0.01
94 2 0.01
95 37 0.21
96 30 0.17
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (87 bp):
TTGTAACTTCAACTACCCCACTGCAACTTTAGGGAGATAAGATTCCTATCTTCAGTCTGCTCCAC
TACAACTTCAGGGAGATAAGAC
Found at i:44404361 original size:184 final size:183
Alignment explanation
Indices: 44404042--44404477 Score: 586
Period size: 184 Copynumber: 2.4 Consensus size: 183
44404032 TCAATATGCT
** * *
44404042 CCACTGCAACTTCAGGGAGATAAGGCTTGTAACTTCAACCTGCTCCACTGTAACTTTAGTGAGAT
1 CCACTGCAACTTCAGGGAGATAAGG-TTGTGGCTTCAACCTGCTCCACTGCAACTTTAGGGAGAT
* * * *
44404107 AAGGTTTGTGATTTGTAGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAGATTCACTATTT
65 AAGGTTTGTGATTTGTAGCTTCAATCCACTCCACTGCAACTTCAGAGAGATAAGATTCACTATCT
* * * *
44404172 TCAGTCTGCTCCACTATAACTTCAGGGAGATAAGACTTGTAACTTCGAA-CTGCC
130 TCAGTCTGCTCCACTACAACTTCAAGGAGATAAGACTTGTAAATTC-AACCTACC
* * * *
44404226 CCACTGCAACTTTAGGGGGATAAGGTTCGTGGCTTCAACCTGCTCCACTACAACTTCAGGGAGAT
1 CCACTGCAACTTCAGGGAGATAAGGTT-GTGGCTTCAACCTGCTCCACTGCAACTTTAGGGAGAT
*
44404291 AAGGTTTGTGATTTGTAGCTTCAATCCACTCCACTGCAACTTCAGAGAGATAAGATTCTCTATCT
65 AAGGTTTGTGATTTGTAGCTTCAATCCACTCCACTGCAACTTCAGAGAGATAAGATTCACTATCT
* * * *
44404356 TCAGTCTGCTCCATTGCAACTTCAAGGAGATGAGACTTGTAAATTCAACCTACT
130 TCAGTCTGCTCCACTACAACTTCAAGGAGATAAGACTTGTAAATTCAACCTACC
* * * * * *
44404410 CCACTGCAACTTCAGGAAGATAAGGTTAGGGGCTTCGATCTGCTCTACTGCAACTTTAAGGAGAT
1 CCACTGCAACTTCAGGGAGATAAGGTT-GTGGCTTCAACCTGCTCCACTGCAACTTTAGGGAGAT
44404475 AAG
65 AAG
44404478 ATTCGCCATG
Statistics
Matches: 218, Mismatches: 32, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
183 4 0.02
184 214 0.98
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (183 bp):
CCACTGCAACTTCAGGGAGATAAGGTTGTGGCTTCAACCTGCTCCACTGCAACTTTAGGGAGATA
AGGTTTGTGATTTGTAGCTTCAATCCACTCCACTGCAACTTCAGAGAGATAAGATTCACTATCTT
CAGTCTGCTCCACTACAACTTCAAGGAGATAAGACTTGTAAATTCAACCTACC
Found at i:44404871 original size:44 final size:44
Alignment explanation
Indices: 44404737--44405281 Score: 266
Period size: 44 Copynumber: 12.4 Consensus size: 44
44404727 TCCCTAGAAC
* * *
44404737 TTCAAGGAGATAAGAATTATGGCTTCGAGCTGCTCCAATACCAT
1 TTCAAGGAGATAAGAATTGTGGCTTCGAGCTACTCCAATGCCAT
* * * * ** ** *
44404781 TTC-AGG-GAGAAGAGA-TGTAGCTTCAATCTACTCCGCTGGAAC
1 TTCAAGGAGATAAGA-ATTGTGGCTTCGAGCTACTCCAATGCCAT
* * *
44404823 TTCAAAGAGATAAGAATTGTGGCTTCGAGCCACTCCAATCCCAT
1 TTCAAGGAGATAAGAATTGTGGCTTCGAGCTACTCCAATGCCAT
* * * * ** * *
44404867 TTCAAGGAGA-AGAGATTTGTAGCTTCAATCTACTCCGCTAG-AAC
1 TTCAAGGAGATA-AGAATTGTGGCTTCGAGCTACTCCAAT-GCCAT
* **
44404911 TTCAAGGAGATACGAATTGTGGCTTCGAGCCGCTCCAATGCCAT
1 TTCAAGGAGATAAGAATTGTGGCTTCGAGCTACTCCAATGCCAT
* * * ** ** *
44404955 TTC-AGG-GAGAAGAGATCTGTAGCTTCGATCTACTCCGCTGGAAC
1 TTCAAGGAGATAAGA-AT-TGTGGCTTCGAGCTACTCCAATGCCAT
* ** * *
44404999 TTCAAGGAGATATGAATTGTGGCTTCGAGCCGCTCCTATTCCAT
1 TTCAAGGAGATAAGAATTGTGGCTTCGAGCTACTCCAATGCCAT
* * * * * ** ** *
44405043 TTCAAGAAGA-AGAGATTTGTAGTTTCGATCTACTCCGCTGGAAC
1 TTCAAGGAGATA-AGAATTGTGGCTTCGAGCTACTCCAATGCCAT
* * *
44405087 TTCAAGGAGATATGAATTGTGGCTTCGAGCTGCTCCAATTCCAT
1 TTCAAGGAGATAAGAATTGTGGCTTCGAGCTACTCCAATGCCAT
* * * * * *** **
44405131 TTCAAGGAGAAAAGATTTGTAGTTTCGATCTACTCTGCTGGAACT
1 TTCAAGGAGATAAGAATTGTGGCTTCGAGCTACTCCAATGCCA-T
* ** *
44405176 TT-AAGGAGATACGAATTGTGGCTTCGAGCCGCTCCAATGTCAT
1 TTCAAGGAGATAAGAATTGTGGCTTCGAGCTACTCCAATGCCAT
* * * * * * *
44405219 TTCAGGGAGA-AGAGATTTGTAGCTTCGATCTACTCCATTAG-AAC
1 TTCAAGGAGATA-AGAATTGTGGCTTCGAGCTACTCCAAT-GCCAT
*
44405263 TTCAAGGAGATAATAATTG
1 TTCAAGGAGATAAGAATTG
44405282 ATGATTTCAA
Statistics
Matches: 347, Mismatches: 135, Indels: 38
0.67 0.26 0.07
Matches are distributed among these distances:
42 30 0.09
43 19 0.05
44 281 0.81
45 12 0.03
46 5 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
TTCAAGGAGATAAGAATTGTGGCTTCGAGCTACTCCAATGCCAT
Found at i:44404928 original size:88 final size:88
Alignment explanation
Indices: 44404692--44405281 Score: 853
Period size: 88 Copynumber: 6.7 Consensus size: 88
44404682 TTTCATTGTA
* * *
44404692 ATTTCAGGGAGAAGAGATTTGTAGTTTCGATCTACTCC-CTAGAACTTCAAGGAGATAAGAATTA
1 ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGATAAGAATTG
* *
44404756 TGGCTTCGAGCTGCTCCAATACC
66 TGGCTTCGAGCCGCTCCAATGCC
* *
44404779 ATTTCAGGGAGAAGAGA--TGTAGCTTCAATCTACTCCGCTGGAACTTCAAAGAGATAAGAATTG
1 ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGATAAGAATTG
* *
44404842 TGGCTTCGAGCCACTCCAATCCC
66 TGGCTTCGAGCCGCTCCAATGCC
* * * *
44404865 ATTTCAAGGAGAAGAGATTTGTAGCTTCAATCTACTCCGCTAGAACTTCAAGGAGATACGAATTG
1 ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGATAAGAATTG
44404930 TGGCTTCGAGCCGCTCCAATGCC
66 TGGCTTCGAGCCGCTCCAATGCC
* *
44404953 ATTTCAGGGAGAAGAGATCTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGATATGAATTG
1 ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGATAAGAATTG
* *
44405018 TGGCTTCGAGCCGCTCCTATTCC
66 TGGCTTCGAGCCGCTCCAATGCC
* * * *
44405041 ATTTCAAGAAGAAGAGATTTGTAGTTTCGATCTACTCCGCTGGAACTTCAAGGAGATATGAATTG
1 ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGATAAGAATTG
* *
44405106 TGGCTTCGAGCTGCTCCAATTCC
66 TGGCTTCGAGCCGCTCCAATGCC
* * * * * *
44405129 ATTTCAAGGAGAAAAGATTTGTAGTTTCGATCTACTCTGCTGGAACTTTAAGGAGATACGAATTG
1 ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGATAAGAATTG
*
44405194 TGGCTTCGAGCCGCTCCAATGTC
66 TGGCTTCGAGCCGCTCCAATGCC
** * *
44405217 ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCATTAGAACTTCAAGGAGATAATAATTG
1 ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGATAAGAATTG
44405282 ATGATTTCAA
Statistics
Matches: 455, Mismatches: 45, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
85 17 0.04
86 59 0.13
87 17 0.04
88 362 0.80
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (88 bp):
ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGATAAGAATTG
TGGCTTCGAGCCGCTCCAATGCC
Found at i:44405443 original size:130 final size:130
Alignment explanation
Indices: 44405287--44406096 Score: 1125
Period size: 130 Copynumber: 6.2 Consensus size: 130
44405277 AATTGATGAT
* * * * * *
44405287 TTCAACCTGCTCCACTACTGCTTAGGGGGATAGGATGGTGACTTAAATCTGCTCCACTACTCCTT
1 TTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATAGTGGCTTAAATCTGCTCCACTACTGCTT
* * * * * * **
44405352 AGGGAGACAAGATTTGTTATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACAATC
66 AGGGAGACAAGATTCGTCATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATC
* *
44405417 TTTAGCCTACTCCACTACTGCTTAGGGAGATAGGATAGTGGCTTAAATTTGCTCCACTACTGCTT
1 TTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATAGTGGCTTAAATCTGCTCCACTACTGCTT
* ** *
44405482 AGGGAGATAAGATTCGTTGTCTACGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATC
66 AGGGAGACAAGATTCGTCATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATC
* *
44405547 TTCAGCCTATTCCACTACTGCTTAGGGAGATAGGATAGTGGCTTAAATTTGCTCCACTACTGCTT
1 TTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATAGTGGCTTAAATCTGCTCCACTACTGCTT
* ** * *
44405612 AGGGAGATAAGATTCGTTGTCTACGATCTACTCCACTACTACTTAGGGAGATAAGATCTGTAATC
66 AGGGAGACAAGATTCGTCATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATC
* *
44405677 TTCAGCCTATTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACTGCTT
1 TTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATAGTGGCTTAAATCTGCTCCACTACTGCTT
* * * * * *
44405742 AGGGAGATAATATTCGTCATCTTTGATCTGCTCTACTACTGCTTAGGGAGATAAGATATGTAATC
66 AGGGAGACAAGATTCGTCATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATC
* * * *
44405807 TTCAGCCTATTCCACTACTGCTTAGGGAGATAGGATTGTGGCTTAAATATGCTCCACTATTGCTT
1 TTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATAGTGGCTTAAATCTGCTCCACTACTGCTT
* * * * * *
44405872 AGGGTGACAAAATTCGCCATTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATT
66 AGGGAGACAAGATTCGTCATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATC
* *
44405937 TTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATTGTGGCTTAAATCTGCTCCACTACTGCAT
1 TTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATAGTGGCTTAAATCTGCTCCACTACTGCTT
* * * ** * **
44406002 AGGGAAACAATATTCGTCGTCTTCGATCTATTCTACTACTACTTAGGGAGATAAGATCTACAATC
66 AGGGAGACAAGATTCGTCATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATC
44406067 TTCAGCCTACTCCACTACTGCTTAGGGAGA
1 TTCAGCCTACTCCACTACTGCTTAGGGAGA
44406097 CAAGATTCGT
Statistics
Matches: 619, Mismatches: 61, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 619 1.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (130 bp):
TTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATAGTGGCTTAAATCTGCTCCACTACTGCTT
AGGGAGACAAGATTCGTCATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATC
Found at i:44411761 original size:26 final size:27
Alignment explanation
Indices: 44411732--44411825 Score: 70
Period size: 26 Copynumber: 3.5 Consensus size: 27
44411722 TAAAACCATT
*
44411732 TAAAATACA-AAATAAAGA-GTTTAAAA
1 TAAAATA-ATAAATAAAAAGGTTTAAAA
*
44411758 T-AAATAATATATAAAAAGGTTTAAAA
1 TAAAATAATAAATAAAAAGGTTTAAAA
* * *
44411784 T-AAATAATATATGAAACGGTTTAGAACA
1 TAAAATAATAAATAAAAAGGTTTA-AA-A
*
44411812 AAAAATATATAAAT
1 TAAAATA-ATAAAT
44411826 TTTAAAATAA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.02
25 12 0.21
26 30 0.54
27 2 0.04
28 1 0.02
29 5 0.09
30 5 0.09
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.28
Consensus pattern (27 bp):
TAAAATAATAAATAAAAAGGTTTAAAA
Found at i:44411817 original size:73 final size:73
Alignment explanation
Indices: 44411679--44411836 Score: 169
Period size: 73 Copynumber: 2.2 Consensus size: 73
44411669 TATAAAAATA
* * * *
44411679 TTTAAAAGTAAATAATATAACAAGGTTTAAAATAAATGATGAATAAAACCATTTAAAATACAAAA
1 TTTAAAA-TAAATAATATAAAAAGGTTTAAAATAAATAATGAATAAAACCATTTAAAACAAAAAA
*
44411744 TA-A-AGAG
65 TATATAAAG
* ** *
44411751 TTTAAAATAAATAATATATAAAAAGGTTTAAAATAAATAAT-ATATGAAACGGTTTAGAACAAAA
1 TTTAAAATAAAT-A-ATATAAAAAGGTTTAAAATAAATAATGA-ATAAAACCATTTAAAACAAAA
*
44411815 AATATATAAAT
63 AATATATAAAG
44411826 TTTAAAATAAA
1 TTTAAAATAAA
44411837 GTATAAATCA
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
71 5 0.07
72 9 0.13
73 43 0.61
74 1 0.01
75 13 0.18
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (73 bp):
TTTAAAATAAATAATATAAAAAGGTTTAAAATAAATAATGAATAAAACCATTTAAAACAAAAAAT
ATATAAAG
Found at i:44411886 original size:26 final size:25
Alignment explanation
Indices: 44411755--44411997 Score: 109
Period size: 26 Copynumber: 9.8 Consensus size: 25
44411745 AAAGAGTTTA
*
44411755 AAATAAATAATATATAAAA-AGGTTT
1 AAATAAATAATATATAAAACA-ATTT
* **
44411780 AAAATAAATAATATATGAAACGGTTT
1 -AAATAAATAATATATAAAACAATTT
* *
44411806 AGAACAAA-AA-ATAT-ATA-AATTT
1 A-AATAAATAATATATAAAACAATTT
* *
44411828 -TA-AAATAA-AGTATAAATCAATTT
1 AAATAAATAATA-TATAAAACAATTT
* *
44411851 GAAATAAATAGTTTATAAAACAATTT
1 -AAATAAATAATATATAAAACAATTT
* *
44411877 AAAGTGAATAATATATAAAATAATTT
1 AAA-TAAATAATATATAAAACAATTT
*
44411903 --A-AAATAATA-ATACAATACAAATTA
1 AAATAAATAATATATA-AA-AC-AATTT
* *
44411927 AAATAAATAATGTGATAAAAAAATTT
1 AAATAAATAATAT-ATAAAACAATTT
* * * *
44411953 AAAACAAATACTATATGAAAA-ACTTA
1 -AAATAAATAATATAT-AAAACAATTT
44411979 AAATAAATAATA-ATAAAAC
1 AAATAAATAATATATAAAAC
44411998 TGTTCAAAAT
Statistics
Matches: 165, Mismatches: 30, Indels: 46
0.68 0.12 0.19
Matches are distributed among these distances:
19 3 0.02
20 4 0.02
21 6 0.04
22 13 0.08
23 12 0.07
24 11 0.07
25 17 0.10
26 72 0.44
27 22 0.13
28 2 0.01
29 3 0.02
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (25 bp):
AAATAAATAATATATAAAACAATTT
Found at i:44411995 original size:50 final size:48
Alignment explanation
Indices: 44411883--44412045 Score: 127
Period size: 50 Copynumber: 3.3 Consensus size: 48
44411873 ATTTAAAGTG
* *
44411883 AATAATATATAAAATAATTTAAAATAATAATACA-AT-ACAAATTAAAATA
1 AATAATA-ATAAAAAAATTTAAAA-AA-AATACATATGAAAAATTAAAATA
* *
44411932 AATAATGTGATAAAAAAATTTAAAACAAATACTATATGAAAAACTTAAAATA
1 AATAA--TAATAAAAAAATTTAAAAAAAATAC-ATATGAAAAA-TTAAAATA
*** * * * *
44411984 AATAATAATAAAACTGTTCAAAATAAATAC-TATGAAAGATTTATAATA
1 AATAATAATAAAAAAATTTAAAAAAAATACATATGAAA-AATTAAAATA
44412032 AATAA-AATAAAAAA
1 AATAATAATAAAAAA
44412046 GAATACAAAA
Statistics
Matches: 93, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
47 7 0.08
48 24 0.26
49 8 0.09
50 36 0.39
51 5 0.05
52 13 0.14
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (48 bp):
AATAATAATAAAAAAATTTAAAAAAAATACATATGAAAAATTAAAATA
Found at i:44412055 original size:12 final size:12
Alignment explanation
Indices: 44412040--44412065 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44412030 TAAATAAAAT
44412040 AAAAAAGAATAC
1 AAAAAAGAATAC
44412052 AAAAAAGAATAC
1 AAAAAAGAATAC
44412064 AA
1 AA
44412066 TATAATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAAGAATAC
Found at i:44414286 original size:35 final size:35
Alignment explanation
Indices: 44414219--44414287 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
44414209 GACAATGTTT
* *
44414219 GTTATGACCATTTAAAGAATTCAAACATATTTTTA
1 GTTATGACCATCTAAAGAATTCAAACACATTTTTA
44414254 GTTATGACCATCTAAAGAATTCAAA-AGCATTTTT
1 GTTATGACCATCTAAAGAATTCAAACA-CATTTTT
44414288 CTTTACAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 1 0.03
35 30 0.97
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (35 bp):
GTTATGACCATCTAAAGAATTCAAACACATTTTTA
Found at i:44415838 original size:27 final size:28
Alignment explanation
Indices: 44415808--44415868 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
44415798 TTTCTGTATT
*
44415808 TTTTTATATTT-GAATTTAGTATCTCTA
1 TTTTTATATTTGGAATTTAATATCTCTA
* *
44415835 TTTTTATTTTTGGGAATTTAATTTCTCTA
1 TTTTTATATTT-GGAATTTAATATCTCTA
44415864 TTTTT
1 TTTTT
44415869 TAAGTTTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 10 0.34
29 19 0.66
ACGTcount: A:0.21, C:0.07, G:0.08, T:0.64
Consensus pattern (28 bp):
TTTTTATATTTGGAATTTAATATCTCTA
Found at i:44416938 original size:17 final size:19
Alignment explanation
Indices: 44416900--44416940 Score: 59
Period size: 17 Copynumber: 2.2 Consensus size: 19
44416890 ATGAATAAAA
44416900 TAATATTTAGTCTCTAAATT
1 TAATATTTAGTCTC-AAATT
44416920 TAATATTT-GTCTC-AATT
1 TAATATTTAGTCTCAAATT
44416937 TAAT
1 TAAT
44416941 CTATAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
19 5 0.24
20 8 0.38
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (19 bp):
TAATATTTAGTCTCAAATT
Found at i:44417575 original size:28 final size:28
Alignment explanation
Indices: 44417535--44417625 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
44417525 GTCATTATCA
44417535 ACCCCATAAGTTATAAAACTCTTCTTAT
1 ACCCCATAAGTTATAAAACTCTTCTTAT
44417563 ACCCCATAAGTTATAAAACTCTT-TCTAT
1 ACCCCATAAGTTATAAAACTCTTCT-TAT
* * *
44417591 ACCCCATAAGTTATAAGACTTTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCTTAT
44417619 ACCCCAT
1 ACCCCAT
44417626 TAATATGGGA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
27 1 0.02
28 57 0.98
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.34
Consensus pattern (28 bp):
ACCCCATAAGTTATAAAACTCTTCTTAT
Found at i:44420943 original size:6 final size:6
Alignment explanation
Indices: 44420932--44420973 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
44420922 CATATATGAA
*
44420932 AAATAT AAATAT AAATAT AAATAT AAATAC AAATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
44420974 CACATAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATAT
Found at i:44423227 original size:25 final size:25
Alignment explanation
Indices: 44423178--44423227 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
44423168 TCATGTGTCT
*
44423178 CATTTTCATGTTTCAATTCACTATCC
1 CATTTTCA-GTTTCAATTCAATATCC
44423204 CATTTTCA-TTTCACATTCAATATC
1 CATTTTCAGTTTCA-ATTCAATATC
44423228 ATCCAATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 9 0.41
26 8 0.36
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.46
Consensus pattern (25 bp):
CATTTTCAGTTTCAATTCAATATCC
Found at i:44424339 original size:21 final size:22
Alignment explanation
Indices: 44424305--44424349 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
44424295 TGGCCGTGAG
44424305 TTCTTCTTCCTTTCTTTCCCTTT
1 TTCTTCTTCCTTTCTTT-CCTTT
44424328 TTCTT-TT-CTTTCTTTCCTTT
1 TTCTTCTTCCTTTCTTTCCTTT
44424348 TT
1 TT
44424350 AATTTCGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 8 0.36
22 2 0.09
23 5 0.23
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (22 bp):
TTCTTCTTCCTTTCTTTCCTTT
Found at i:44424355 original size:20 final size:21
Alignment explanation
Indices: 44424314--44424355 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
44424304 GTTCTTCTTC
**
44424314 CTTTCTTTCCCTTTTTCTTTT
1 CTTTCTTTCCCTTTTTAATTT
44424335 CTTTCTTT-CCTTTTTAATTT
1 CTTTCTTTCCCTTTTTAATTT
44424355 C
1 C
44424356 GTTGCCTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (21 bp):
CTTTCTTTCCCTTTTTAATTT
Found at i:44424371 original size:2 final size:2
Alignment explanation
Indices: 44424364--44424394 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44424354 TCGTTGCCTT
44424364 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
44424395 TTTATTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:44428272 original size:13 final size:13
Alignment explanation
Indices: 44428254--44428317 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
44428244 AGTTTAACAT
44428254 TGTTTTTGAAAAA
1 TGTTTTTGAAAAA
44428267 TGTTTTT-AAAAA
1 TGTTTTTGAAAAA
* * *
44428279 GTGTTGTGGAAAAG
1 -TGTTTTTGAAAAA
*
44428293 TGTTTTTGAGAAA
1 TGTTTTTGAAAAA
**
44428306 TACTTTTGAAAA
1 TGTTTTTGAAAA
44428318 GTTTAGTTTA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
12 5 0.13
13 30 0.77
14 4 0.10
ACGTcount: A:0.36, C:0.02, G:0.20, T:0.42
Consensus pattern (13 bp):
TGTTTTTGAAAAA
Found at i:44446395 original size:20 final size:19
Alignment explanation
Indices: 44446357--44446403 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
44446347 TTTTAATTTA
44446357 TTTGGTTTTATTTATTGTT
1 TTTGGTTTTATTTATTGTT
44446376 TTTGGTTTCTATTT-TCTGTT
1 TTTGGTTT-TATTTAT-TGTT
44446396 TTT-GTTTT
1 TTTGGTTTT
44446404 TGTATGGGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.04
19 13 0.50
20 12 0.46
ACGTcount: A:0.06, C:0.04, G:0.15, T:0.74
Consensus pattern (19 bp):
TTTGGTTTTATTTATTGTT
Found at i:44446658 original size:2 final size:2
Alignment explanation
Indices: 44446651--44446683 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
44446641 TTCGAATCCT
44446651 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
44446684 ATAATATTGA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:44447409 original size:18 final size:18
Alignment explanation
Indices: 44447303--44447400 Score: 56
Period size: 18 Copynumber: 5.3 Consensus size: 18
44447293 AGTATCTAGC
*
44447303 ATTATAAAATACTATTAATAT
1 ATTATAAAA-A-TATTAA-AA
*
44447324 ATTATAAAAATATGAAAA
1 ATTATAAAAATATTAAAA
* * *
44447342 ATCATTGAAATTATTAACAA
1 ATTA-TAAAAATATTAA-AA
** *
44447362 A--ATAGGAACATTAAAA
1 ATTATAAAAATATTAAAA
*
44447378 ATTATAAAAATATTAAAT
1 ATTATAAAAATATTAAAA
44447396 ATTAT
1 ATTAT
44447401 TAATATATTG
Statistics
Matches: 58, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
16 3 0.05
17 7 0.12
18 21 0.36
19 14 0.24
20 4 0.07
21 9 0.16
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (18 bp):
ATTATAAAAATATTAAAA
Found at i:44450383 original size:19 final size:19
Alignment explanation
Indices: 44450359--44450414 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
44450349 ATTGGTGTAA
44450359 ATTT-AAACTTTTTCTATTT
1 ATTTAAAACTTTTT-TATTT
**
44450378 ATTTAAAACCATTTTATTT
1 ATTTAAAACTTTTTTATTT
* *
44450397 ATTTCAAACTTTTGTATT
1 ATTTAAAACTTTTTTATT
44450415 GAGTTATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 23 0.77
20 7 0.23
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTTAAAACTTTTTTATTT
Found at i:44454772 original size:39 final size:39
Alignment explanation
Indices: 44454700--44454774 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
44454690 TTTATATATA
* * *
44454700 TTATGTATATATTTTTTAATGCCATTAGTTATATATTTC
1 TTATGTATATATTCTTAAATACCATTAGTTATATATTTC
*
44454739 TTATGTATATATTCTTAAATACTATTA-TATATATAT
1 TTATGTATATATTCTTAAATACCATTAGT-TATATAT
44454775 ATATATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.03
39 30 0.97
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (39 bp):
TTATGTATATATTCTTAAATACCATTAGTTATATATTTC
Found at i:44457357 original size:24 final size:24
Alignment explanation
Indices: 44457314--44457363 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
44457304 TTCCTTTCTT
*
44457314 TTGCATTCATTCCATACATTTGCA
1 TTGCATTCATTCCATACATTGGCA
*
44457338 TTGCATTGCATTGCAT-CATTGGCA
1 TTGCATT-CATTCCATACATTGGCA
44457362 TT
1 TT
44457364 AAACTTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (24 bp):
TTGCATTCATTCCATACATTGGCA
Found at i:44458694 original size:30 final size:30
Alignment explanation
Indices: 44458660--44458719 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
44458650 AGCCGTACCA
*
44458660 TGGAAATATGACGTCAATATCGTCACACCT
1 TGGAAATACGACGTCAATATCGTCACACCT
44458690 TGGAAATACGACGTCAATATCGTCACACCT
1 TGGAAATACGACGTCAATATCGTCACACCT
44458720 GAAGATGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (30 bp):
TGGAAATACGACGTCAATATCGTCACACCT
Found at i:44462743 original size:30 final size:30
Alignment explanation
Indices: 44462707--44462763 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
44462697 AATTTCCCCG
*
44462707 AAAGCTTCTAATGGACATCGATTCATTCCA
1 AAAGCTTCTAATGGACACCGATTCATTCCA
*
44462737 AAAGCTTCTAATGGATACCGATTCATT
1 AAAGCTTCTAATGGACACCGATTCATT
44462764 TTTGTGGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (30 bp):
AAAGCTTCTAATGGACACCGATTCATTCCA
Found at i:44464143 original size:18 final size:18
Alignment explanation
Indices: 44464108--44464141 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
44464098 GTACAAGAGC
44464108 CTCAACGCAAGGACAAAG
1 CTCAACGCAAGGACAAAG
*
44464126 CTCAAC-CAAGGGCAAA
1 CTCAACGCAAGGACAAA
44464142 AGAGTGATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.29, G:0.21, T:0.06
Consensus pattern (18 bp):
CTCAACGCAAGGACAAAG
Found at i:44466390 original size:19 final size:19
Alignment explanation
Indices: 44466304--44466390 Score: 61
Period size: 19 Copynumber: 4.3 Consensus size: 19
44466294 AATAATTTCA
*
44466304 TTTATTGTAGATATTATTAT
1 TTTA-TGTACATATTATTAT
44466324 TATTAT-TACATACTT-TTAT
1 T-TTATGTACATA-TTATTAT
* *
44466343 TATATGCACATATATATATGTATT
1 TTTATGTAC--ATAT-TAT-TA-T
44466367 TTTATGTACATATTATTAT
1 TTTATGTACATATTATTAT
44466386 TTTAT
1 TTTAT
44466391 ATTATTATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 19
0.69 0.06 0.25
Matches are distributed among these distances:
18 3 0.06
19 18 0.34
20 7 0.13
21 10 0.19
22 5 0.09
23 2 0.04
24 8 0.15
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTATGTACATATTATTAT
Found at i:44468344 original size:31 final size:30
Alignment explanation
Indices: 44468299--44468392 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 30
44468289 AATTATTTAA
* *
44468299 GATTTAAT-TTAATTTTATACATTAACTTT
1 GATTTAATGTCAATTTTATACATGAACTTT
* * * *
44468328 GTTTTCATGTGCAATTTGATATATGAACTTT
1 GATTTAATGT-CAATTTTATACATGAACTTT
* *
44468359 GATTTAATGTC-ATTATATACATGAAACTTG
1 GATTTAATGTCAATTTTATACATG-AACTTT
44468389 GATT
1 GATT
44468393 GCGGTTCATA
Statistics
Matches: 50, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
29 15 0.30
30 11 0.22
31 24 0.48
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.48
Consensus pattern (30 bp):
GATTTAATGTCAATTTTATACATGAACTTT
Found at i:44468621 original size:29 final size:30
Alignment explanation
Indices: 44468589--44468651 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
44468579 AATTTAATGG
*
44468589 ATAAAATAACACA-AAATTAAAGTTCATGT
1 ATAAAATAACACATAAATCAAAGTTCATGT
* * *
44468618 ATAACATTACACATTAGATCAAAGTTCATGT
1 ATAAAATAACACA-TAAATCAAAGTTCATGT
44468649 ATA
1 ATA
44468652 GTTTTAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 11 0.39
31 17 0.61
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.30
Consensus pattern (30 bp):
ATAAAATAACACATAAATCAAAGTTCATGT
Found at i:44469147 original size:22 final size:23
Alignment explanation
Indices: 44469093--44469157 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
44469083 TGCTACTGTT
* *
44469093 TTACTATTGTTTGTTATTTTTTTG
1 TTACTATT-TTTGTTATTATATTG
* *
44469117 CTACCA-TTTTGTTATTATATTG
1 TTACTATTTTTGTTATTATATTG
*
44469139 TTACTATTTTTGTTGTTAT
1 TTACTATTTTTGTTATTAT
44469158 TGTTTGGATA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 17 0.52
23 12 0.36
24 4 0.12
ACGTcount: A:0.17, C:0.08, G:0.11, T:0.65
Consensus pattern (23 bp):
TTACTATTTTTGTTATTATATTG
Found at i:44470731 original size:207 final size:207
Alignment explanation
Indices: 44470376--44470788 Score: 736
Period size: 207 Copynumber: 2.0 Consensus size: 207
44470366 CCGAGATCCG
*
44470376 ACCCAAGACCCCCAAGATCTGCGTGTTTTTGGACTAAGGGTCTATTTACCCTTTCAGTCCTTTCA
1 ACCCAAGACCCCCAAGATCCGCGTGTTTTTGGACTAAGGGTCTATTTACCCTTTCAGTCCTTTCA
*
44470441 CTTTTTGGATGATTTACAATGTAGTTTCTTTTTCTTTTTAATTTTTACCCCTTAATTTTATTTTT
66 CTTTTTGGACGATTTACAATGTAGTTTCTTTTTCTTTTTAATTTTTACCCCTTAATTTTATTTTT
* * *
44470506 TTTTCATTTTGGTCCCTATGGAATGGCGCGTTTAAGGAGTTCGAGATAATTTCATATTTAGTCCT
131 CTTTCATTTTGGTCCCTATGGAATGGCACGTTTAAGGAGTTCGAGATAATTTCATATTTAGTCCC
44470571 TATTTCTTTTCC
196 TATTTCTTTTCC
* * *
44470583 ACCCAAGACCCCCAAGCTCCGCGTGTTTTTGGACTAATGGTCTATTTACCCTTTCAGTCCTTTCG
1 ACCCAAGACCCCCAAGATCCGCGTGTTTTTGGACTAAGGGTCTATTTACCCTTTCAGTCCTTTCA
*
44470648 CTTTTTGGACGTTTTACAATGTAGTTTCTTTTTCTTTTTAATTTTTACCCCTTAATTTTATTTTT
66 CTTTTTGGACGATTTACAATGTAGTTTCTTTTTCTTTTTAATTTTTACCCCTTAATTTTATTTTT
*
44470713 CTTTCATTTTGGTCCCTATGGAATGGCACGTTTAAGGAGTTCGGGATAATTTCATATTTAGTCCC
131 CTTTCATTTTGGTCCCTATGGAATGGCACGTTTAAGGAGTTCGAGATAATTTCATATTTAGTCCC
44470778 TATTTCTTTTC
196 TATTTCTTTTC
44470789 GCGCGCTTCA
Statistics
Matches: 196, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
207 196 1.00
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.46
Consensus pattern (207 bp):
ACCCAAGACCCCCAAGATCCGCGTGTTTTTGGACTAAGGGTCTATTTACCCTTTCAGTCCTTTCA
CTTTTTGGACGATTTACAATGTAGTTTCTTTTTCTTTTTAATTTTTACCCCTTAATTTTATTTTT
CTTTCATTTTGGTCCCTATGGAATGGCACGTTTAAGGAGTTCGAGATAATTTCATATTTAGTCCC
TATTTCTTTTCC
Found at i:44470834 original size:12 final size:12
Alignment explanation
Indices: 44470817--44470843 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
44470807 CCTTATTCTG
44470817 TTTTATTAATTA
1 TTTTATTAATTA
44470829 TTTTATTAATTA
1 TTTTATTAATTA
44470841 TTT
1 TTT
44470844 ACAATTCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTATTAATTA
Found at i:44471997 original size:18 final size:18
Alignment explanation
Indices: 44471974--44472010 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
44471964 ACTCAATATA
44471974 AGCCCTTTATAAATATCT
1 AGCCCTTTATAAATATCT
44471992 AGCCCTTTATAAATATCT
1 AGCCCTTTATAAATATCT
44472010 A
1 A
44472011 ACATTCTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (18 bp):
AGCCCTTTATAAATATCT
Found at i:44473855 original size:27 final size:27
Alignment explanation
Indices: 44473825--44473963 Score: 142
Period size: 27 Copynumber: 5.1 Consensus size: 27
44473815 ATGACGAAGT
44473825 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATATTGTGGCAGAGC
* *
44473852 CACCATA-ACAGATATATGTGGAAGAGC
1 CACCAGATACAGATAT-TGTGGCAGAGC
* * * *
44473879 TACTAGAT-TAGATAATTGTGGCATAGC
1 CACCAGATACAGAT-ATTGTGGCAGAGC
*
44473906 CACCA-AGACAGATATATGTGGCAGAGC
1 CACCAGATACAGATAT-TGTGGCAGAGC
*
44473933 CACCAGAT-CAGATAATTGTGGCATAGC
1 CACCAGATACAGAT-ATTGTGGCAGAGC
44473960 CACC
1 CACC
44473964 TGGACGCTTC
Statistics
Matches: 90, Mismatches: 15, Indels: 14
0.76 0.13 0.12
Matches are distributed among these distances:
26 11 0.12
27 74 0.82
28 5 0.06
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (27 bp):
CACCAGATACAGATATTGTGGCAGAGC
Found at i:44473907 original size:54 final size:54
Alignment explanation
Indices: 44473825--44473963 Score: 201
Period size: 54 Copynumber: 2.6 Consensus size: 54
44473815 ATGACGAAGT
*
44473825 CACCAGATACAGAT-ATTGTGGCAGAGCCACCATA-ACAGATATATGTGGAAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCA-AGACAGATATATGTGGAAGAGC
* * * *
44473879 TACTAGATTAGATAATTGTGGCATAGCCACCAAGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAAGACAGATATATGTGGAAGAGC
44473933 CACCAGATCAGATAATTGTGGCATAGCCACC
1 CACCAGATCAGATAATTGTGGCATAGCCACC
44473964 TGGACGCTTC
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
53 5 0.07
54 70 0.93
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAAGACAGATATATGTGGAAGAGC
Found at i:44474097 original size:27 final size:26
Alignment explanation
Indices: 44474071--44474144 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
44474061 AAATTAACCT
*
44474071 TAGGGGTATAACGGTAATTTTGCACC
1 TAGGGGTATAACAGTAATTTTGCACC
* *
44474097 TAGGGGTATAACAGTAATTTTCCATACA
1 TAGGGGTATAACAGTAATTTTGC--ACC
* *
44474125 TAGGGGTATTATAGTAATTT
1 TAGGGGTATAACAGTAATTT
44474145 AGCTACTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
26 21 0.51
28 20 0.49
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (26 bp):
TAGGGGTATAACAGTAATTTTGCACC
Found at i:44474404 original size:16 final size:15
Alignment explanation
Indices: 44474383--44474412 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
44474373 AAAATACCGA
44474383 CTTTTCGGCATTTTGG
1 CTTTTCGGC-TTTTGG
44474399 CTTTTCGGCTTTTG
1 CTTTTCGGCTTTTG
44474413 CCAATCTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.03, C:0.20, G:0.23, T:0.53
Consensus pattern (15 bp):
CTTTTCGGCTTTTGG
Found at i:44475619 original size:26 final size:26
Alignment explanation
Indices: 44475588--44475695 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
44475578 TGAAATGCCC
*
44475588 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
44475614 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
44475640 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
44475666 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
44475692 ATCA
1 ATCA
44475696 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:44482336 original size:26 final size:26
Alignment explanation
Indices: 44482305--44482412 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
44482295 TGAAATGCCC
*
44482305 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
44482331 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
44482357 ATCATAGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
44482383 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
44482409 ATCA
1 ATCA
44482413 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:44485629 original size:22 final size:22
Alignment explanation
Indices: 44485600--44485667 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
44485590 TGTACAAACG
44485600 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* *
44485622 TACAGAGAGCAC-ATATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
* *
44485644 AACAAAGAGCACTTAACGTGCTA
1 AACAGAGAGCAC-TAAAGTGCTA
44485667 A
1 A
44485668 TAATAGAACG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 28 0.74
23 8 0.21
24 1 0.03
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.18
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:44486509 original size:26 final size:26
Alignment explanation
Indices: 44486473--44486684 Score: 381
Period size: 26 Copynumber: 8.2 Consensus size: 26
44486463 TGATACAAAT
44486473 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
44486499 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
44486525 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
44486551 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
44486577 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
44486603 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
44486629 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
44486655 TGATAAT-GGTTTAGGTAAATGTTCCA
1 TGATAATAGG-TTAGGTAAATGTTCCA
44486681 TGAT
1 TGAT
44486685 GGGCATTTCA
Statistics
Matches: 184, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
25 2 0.01
26 182 0.99
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:44496828 original size:29 final size:30
Alignment explanation
Indices: 44496795--44496873 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 30
44496785 ATTATTTAAT
*
44496795 TAATAAATATCT-TTTAACTT-AATAATAAG
1 TAATAAATATCTATTT-ACTTAAATAAAAAG
44496824 TAATAAATATCTATTTACTTAAATAAAAAG
1 TAATAAATATCTATTTACTTAAATAAAAAG
*
44496854 TAATTAAATATTTATGTTAC
1 TAA-TAAATATCTAT-TTAC
44496874 AATTGTATAC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
29 16 0.36
30 14 0.32
31 10 0.23
32 4 0.09
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (30 bp):
TAATAAATATCTATTTACTTAAATAAAAAG
Found at i:44499778 original size:24 final size:22
Alignment explanation
Indices: 44499751--44499794 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
44499741 AAAAACTAAA
44499751 AAAATAAATGATATAAAAAAGATT
1 AAAATAAAT-A-ATAAAAAAGATT
*
44499775 AAAATAAGTAATAAAAAAGA
1 AAAATAAATAATAAAAAAGA
44499795 GAAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 1 0.05
24 8 0.42
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (22 bp):
AAAATAAATAATAAAAAAGATT
Found at i:44499802 original size:24 final size:24
Alignment explanation
Indices: 44499748--44499807 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
44499738 AAAAAAAACT
*
44499748 AAAAAAATAAATGATATAAAAAAG
1 AAAAAAATAAATAATATAAAAAAG
** *
44499772 ATTAAAATAAGTAATA-AAAAAGAG
1 AAAAAAATAAATAATATAAAAA-AG
44499796 AAAAAAAATAAA
1 -AAAAAAATAAA
44499808 GGTTTAAAAC
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
23 5 0.19
24 14 0.52
25 8 0.30
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (24 bp):
AAAAAAATAAATAATATAAAAAAG
Found at i:44499899 original size:30 final size:28
Alignment explanation
Indices: 44499865--44499921 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
44499855 AAACTATTGT
44499865 AAACAAGATGAAAATATATAATA-TATAACA
1 AAACAA-ATGAAAA-ATA-AATACTATAACA
*
44499895 AAACAAATTAAAAATAAATACTATAAC
1 AAACAAATGAAAAATAAATACTATAAC
44499922 TGGCAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 4 0.16
28 9 0.36
29 6 0.24
30 6 0.24
ACGTcount: A:0.65, C:0.09, G:0.04, T:0.23
Consensus pattern (28 bp):
AAACAAATGAAAAATAAATACTATAACA
Found at i:44500584 original size:14 final size:14
Alignment explanation
Indices: 44500561--44500590 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
44500551 AAATTGAAAA
44500561 ATAAAGATAAATTG
1 ATAAAGATAAATTG
*
44500575 ATAAATATAAATTG
1 ATAAAGATAAATTG
44500589 AT
1 AT
44500591 TTGAAAGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (14 bp):
ATAAAGATAAATTG
Found at i:44503729 original size:176 final size:176
Alignment explanation
Indices: 44503359--44503864 Score: 683
Period size: 176 Copynumber: 2.9 Consensus size: 176
44503349 TGATTATTTG
* * * *
44503359 CTACCTCAAGAAGATAAGACTACAATCTTCAACCTACTTTCTTTCTACCTCAGAGAGATAAGGCT
1 CTACCTCAGGAAGATAAGACTACAATCTTCAACCTGCTCTC-TTGTACCTCAGAGAGATAAGGCT
* * * * * *
44503424 GGTGGCTAAAATGTACTCCTCTACTATCTTGGGAAGATAAGATTCGCTATCTTCGATCTGCTCCA
65 GGTGGCTAAAATCTACTCCCCTGCTACCTCGGGAAGATAAGATTCGCTATCTTTGATCTGCTCCA
* * *
44503489 CTATTGCTTAGGGAGATAAGATC-ACAATCCTCAGTTTGCTTCCTTG
130 CTACTGCTTAGGGAGATAAGATCTACAATCCTCAGTCTGCTTCCTTA
* * *
44503535 CTACCTCAGGAAGATAAGACTACAATCTTCAACCTGCTCTCTTGTACCTCAAAGAGATAATGTTG
1 CTACCTCAGGAAGATAAGACTACAATCTTCAACCTGCTCTCTTGTACCTCAGAGAGATAAGGCTG
* * ** * * *
44503600 GTAGCTAAAATCTACTCCCCTGTTACCTCGAAAAGATAAGATTCGCCACCTTTGATCTACTCCAC
66 GTGGCTAAAATCTACTCCCCTGCTACCTCGGGAAGATAAGATTCGCTATCTTTGATCTGCTCCAC
* *
44503665 TACTGCTTAGGGAGATAAGATCTACAATCTTTAGTCTGCTTCCTTA
131 TACTGCTTAGGGAGATAAGATCTACAATCCTCAGTCTGCTTCCTTA
* * *
44503711 TTACTTCAGGAAGATAAGACTACAATC-TCAACTTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
1 CTACCTCAGGAAGATAAGACTACAATCTTCAACCTGCTCTCTTG-TACCTCAGAGAGATAAGGCT
* *
44503775 GGTGGCTAAAATCTACTCCCCTGCTACCTCGGGAAGATAAGATTCACTATTTTTCGATCTGCTCC
65 GGTGGCTAAAATCTACTCCCCTGCTACCTCGGGAAGATAAGATTCGCTATCTTT-GATCTGCTCC
* *
44503840 TCTACTACTTAGGGAGATAAGATCT
129 ACTACTGCTTAGGGAGATAAGATCT
44503865 TACTTCACCG
Statistics
Matches: 285, Mismatches: 42, Indels: 5
0.86 0.13 0.02
Matches are distributed among these distances:
175 108 0.38
176 145 0.51
177 32 0.11
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (176 bp):
CTACCTCAGGAAGATAAGACTACAATCTTCAACCTGCTCTCTTGTACCTCAGAGAGATAAGGCTG
GTGGCTAAAATCTACTCCCCTGCTACCTCGGGAAGATAAGATTCGCTATCTTTGATCTGCTCCAC
TACTGCTTAGGGAGATAAGATCTACAATCCTCAGTCTGCTTCCTTA
Found at i:44506355 original size:46 final size:47
Alignment explanation
Indices: 44506267--44506360 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 47
44506257 TGATAGCAGG
**
44506267 GATGAGGAGTGTAAACTCCTTGCACCACCATGACCACACAACA-AGA
1 GATGAGGAGTGTAAACTCCTCACACCACCATGACCACACAACAGAGA
* * *
44506313 GATGAGGAGTGTAAACTCCTCACACCACTATGACCGCGCAACAGAGA
1 GATGAGGAGTGTAAACTCCTCACACCACCATGACCACACAACAGAGA
44506360 G
1 G
44506361 GTAAGTCTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
46 38 0.90
47 4 0.10
ACGTcount: A:0.35, C:0.28, G:0.22, T:0.15
Consensus pattern (47 bp):
GATGAGGAGTGTAAACTCCTCACACCACCATGACCACACAACAGAGA
Done.