Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 102 of 163
Found at i:28989823 original size:46 final size:48
Alignment explanation
Indices: 28989723--28989829 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 48
28989713 TATTACAAAT
* * *
28989723 TAGTAGTACACCACATGATAACTACAAATAATATTATCCAAGTACATAAT
1 TAGTAGTACACAACATGATAACT--AAATAATATTATCAAAGTACATAAC
* * *
28989773 TAGTAGTACACAACATTATAACT-AA-AATATTGTCAAAGTGCATAAC
1 TAGTAGTACACAACATGATAACTAAATAATATTATCAAAGTACATAAC
*
28989819 TAGTACTACAC
1 TAGTAGTACAC
28989830 CATATAATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
46 27 0.54
47 2 0.04
50 21 0.42
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.28
Consensus pattern (48 bp):
TAGTAGTACACAACATGATAACTAAATAATATTATCAAAGTACATAAC
Found at i:29008392 original size:22 final size:22
Alignment explanation
Indices: 29008360--29008405 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
29008350 AAGCCAAACA
29008360 AAAATAAAAAATAAAAAAAATT
1 AAAATAAAAAATAAAAAAAATT
* *
29008382 AAAATAGAAAATAAAAAAATTT
1 AAAATAAAAAATAAAAAAAATT
29008404 AA
1 AA
29008406 CATCGTGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (22 bp):
AAAATAAAAAATAAAAAAAATT
Found at i:29011658 original size:859 final size:860
Alignment explanation
Indices: 29009997--29011724 Score: 2114
Period size: 859 Copynumber: 2.0 Consensus size: 860
29009987 TTTATGCAAA
* *
29009997 ATAATTATCTTTCATGCTTGTTTCTTTTTATCCTTTCATTGTTTTTGCACTGGCAAGCTCAAACA
1 ATAATTATCTTTCATGCTTGTTTCATTTTATCCTTTAATTGTTTTTGCACTGGCAAGCTCAAACA
* * *
29010062 ACAAAATAGTGGAAAACAAAAAATTGGGATTAAGATCATTGAAAATGAGGATGATTGGCACATCT
66 ACAAAATAGGGGAAAACAAAAAACTGAGATTAAGATCATTGAAAATGAGGATGATTGGCACATCT
* * * *
29010127 CATTTTTAAAACTTCGTACAAGAATTTATAAGAAAATCACTAAGCTCTCCACTTTATGTGGTAGT
131 CATTTTCAAAACATCGTACAAGAATATATAAAAAAATCACTAAGCTCTCCACTTTATGTGGTAGT
* * * * * * * *
29010192 GAGATTGTTTTTATTATTTTTTCACGATCTTGTAAGGCTTATTAGTTTGGTTATCTTTCTATTGA
196 GAGATTCTTTTTATTATTTTCTCACCATCTTATAAGGCTTATTAGTTTGGTCAACCTTATATTGA
* * *
29010257 ATCTGTCGCTAAACTATTTTTGAACCAAAACCAAGCTCTTAATGAAACCACTCATGCTCGTATTA
261 ATATATCGCTAAACGATTTTTGAACCAAAACCAAGCTCTTAATGAAACCACTCATGCTCGTATTA
* *
29010322 AGGCGTACCGTAAGGTAAGAATCAACTTACTTGTCAAATATTTCAATGAGGTCCACGACCTACCA
326 AGGCGTAACGTAAGGTAAGAATAAACTTACTTGTCAAATATTTCAATGAGGTCCACGACCTACCA
* ** * *
29010387 GATGCATCAAAAGAAAAACAAAGGGTGATTTCTTTGGCCAAGTAATCACATGGAAAAGAAACTCA
391 GATCCATCAAAAGAAAAACAAAGGGAAATTTCCTTGGCCAAGCAATCACATGGAAAAGAAACTCA
* * * *
29010452 TCATTAATGGAAAACTCGCAAGGATGAGCTTAATCCGAGGAGCTCTACGAATGATTAGAACATTT
456 TCATTAATGGAAAACTCCCAAGGATCAGCTTAACCCGAGGAGCTCTACGAATGATCAGAACATTT
* *
29010517 CACAGAGTTTATAAATTTTATCTCTGTCACGACGAAGAAGAAGATTGCAAATATTTCCTCAATGA
521 CACAGAGTTTATAAATTTTATCTCCGTCACGACGAACAAGAAGATTGCAAATATTTCCTCAATGA
* * * ** *
29010582 AGGCTTCAATGGATAAGGATGCCCTTTCTGCCTTTCCTCTTAGATTTGGCCTTTCTGTCAATGGA
586 AGGATACAATGGATAAGGATGCCCTTTCTGACTTTCCTCAAAGATATGGCCTTTCTGTCAATGGA
* * * * * *
29010647 TCAAGGCTCGGAAATGCTACAATGGAGACCAAATATAATATGTTTGTTGGCTACATGAACATGTT
651 TCAAGGCTCAGAAATGCTACAATAGAGACCAAATACAATATGTTTGTTAGCGACACGAACATGTT
* * * * *
29010712 CCTGTATGCCTTGAATACTCCCAAGATTAACAAGGCTAACAAACATAGAAAATAAAACAATAAAA
716 CATGTATGCCTTGAAGACTCCCAAGATTAACAAGCCAAACAAACATAAAAAATAAAACAATAAAA
* * *
29010777 ATAAAATTTAACATCGTGGACTTTGAGGTACAAAACTATTGCTGACTAAGGCCATATCTAGGGGG
781 ATAAAATTTAACATCATGGACTTTGAGGTACAAAACTATTGCTAACTAAGGCCATATCTAGGAGG
*
29010842 AAAGGCATAAGGGAC
846 AAAGGCATAAGGAAC
* * * ** **
29010857 ATAATTATCTTTCTTGCTTGTTTCATTTTGTCTTTTAATCT-TTTTT-CTGTGGCAAGCTCAAGT
1 ATAATTATCTTTCATGCTTGTTTCATTTTATCCTTTAAT-TGTTTTTGCACTGGCAAGCTCAAAC
* * * * * *
29010920 AAGAAAGCTGGGGGAAAAGAAAAAACTGAGATTAAGATTATTGAAAATGAGGATGATTGGCTCAT
65 AACAAA-ATAGGGGAAAACAAAAAACTGAGATTAAGATCATTGAAAATGAGGATGATTGGCACAT
* * *
29010985 GTCATTTTCAAAACATCGTACAAGAATATATAAAAAAATCTCTAAGCTCT-CACTTTATGTGGTG
129 CTCATTTTCAAAACATCGTACAAGAATATATAAAAAAATCACTAAGCTCTCCACTTTATGTGGTA
* * * * *
29011049 GTGAGATTCTTTTTATTATTTTCTCGCCATCTTATAAGTCTTTTTTGTTTGGTCAACCTTATGTT
194 GTGAGATTCTTTTTATTATTTTCTCACCATCTTATAAGGCTTATTAGTTTGGTCAACCTTATATT
* * * * *
29011114 GAATATATCGCTAAACGATTTTTGAACCCAAACCAATCTCTTAATGAAATCGCTTATGCTTC-TA
259 GAATATATCGCTAAACGATTTTTGAACCAAAACCAAGCTCTTAATGAAACCACTCATGC-TCGTA
* * * * * * * * *
29011178 TTGAGGCTTAACGTATGGTAAGAATAAACTTGCTTTTC-AATGATTTTAATGAGGTCCATGGCGT
323 TTAAGGCGTAACGTAAGGTAAGAATAAACTTACTTGTCAAAT-ATTTCAATGAGGTCCACGACCT
** * * *
29011242 ACTTGATCCATCAGAAGAAAAACAAAGGGAAATTTCCTTGGCCCAA-CAGTCACATGGAAATGAA
387 ACCAGATCCATCAAAAGAAAAACAAAGGGAAATTTCCTTGG-CCAAGCAATCACATGGAAAAGAA
** ** * *
29011306 ACTCATCATTGGTGGAAAACTCCCATTGATCAGCTTAACCCGTGGAAGCTTTACG-ATCGAGTCA
451 ACTCATCATTAATGGAAAACTCCCAAGGATCAGCTTAACCCGAGG-AGCTCTACGAAT-GA-TCA
** * * * * * *
29011370 -AAGGTTTCACAGAGTTTATCAATTTTCTCTCCGTCACGAGGGACAAGAAGATTGTAGATATTTC
513 GAACATTTCACAGAGTTTATAAATTTTATCTCCGTCACGACGAACAAGAAGATTGCAAATATTTC
* *
29011434 CTCAATGTA-GATACAATGGATTAGGATGTCCCTTT-T-ACTTATCCTCAAAGATATGGCCTTTC
578 CTCAATGAAGGATACAATGGATAAGGATG-CCCTTTCTGACTT-TCCTCAAAGATATGGCCTTT-
** *
29011496 CT-TCAATGGATCAAGGCTCTAG-AATGCTACAATAGAGACCATTTACCATATGTTTGTTAGCGA
640 CTGTCAATGGATCAAGGCTC-AGAAATGCTACAATAGAGACCAAATACAATATGTTTGTTAGCGA
* * * * * *** * *
29011559 CACGAACATGTTCATTTATGCCTTGAGGATTCTCTAGATTGGTAAGCCAAATAAGCATAAAAAAT
704 CACGAACATGTTCATGTATGCCTTGAAGACTCCCAAGATTAACAAGCCAAACAAACATAAAAAAT
* * * *
29011624 AAAATAATAAAAATAATATTTAACATCATGGACTTTGAGGTACAAAATTATTGCTAACTAGGGCC
769 AAAACAATAAAAATAAAATTTAACATCATGGACTTTGAGGTACAAAACTATTGCTAACTAAGGCC
29011689 ATATCTAGGAGGAAAGGCATAAGGAAC
834 ATATCTAGGAGGAAAGGCATAAGGAAC
29011716 ATAATTATC
1 ATAATTATC
29011725 CAATGGAGCA
Statistics
Matches: 729, Mismatches: 127, Indels: 25
0.83 0.14 0.03
Matches are distributed among these distances:
858 6 0.01
859 500 0.69
860 220 0.30
861 3 0.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Consensus pattern (860 bp):
ATAATTATCTTTCATGCTTGTTTCATTTTATCCTTTAATTGTTTTTGCACTGGCAAGCTCAAACA
ACAAAATAGGGGAAAACAAAAAACTGAGATTAAGATCATTGAAAATGAGGATGATTGGCACATCT
CATTTTCAAAACATCGTACAAGAATATATAAAAAAATCACTAAGCTCTCCACTTTATGTGGTAGT
GAGATTCTTTTTATTATTTTCTCACCATCTTATAAGGCTTATTAGTTTGGTCAACCTTATATTGA
ATATATCGCTAAACGATTTTTGAACCAAAACCAAGCTCTTAATGAAACCACTCATGCTCGTATTA
AGGCGTAACGTAAGGTAAGAATAAACTTACTTGTCAAATATTTCAATGAGGTCCACGACCTACCA
GATCCATCAAAAGAAAAACAAAGGGAAATTTCCTTGGCCAAGCAATCACATGGAAAAGAAACTCA
TCATTAATGGAAAACTCCCAAGGATCAGCTTAACCCGAGGAGCTCTACGAATGATCAGAACATTT
CACAGAGTTTATAAATTTTATCTCCGTCACGACGAACAAGAAGATTGCAAATATTTCCTCAATGA
AGGATACAATGGATAAGGATGCCCTTTCTGACTTTCCTCAAAGATATGGCCTTTCTGTCAATGGA
TCAAGGCTCAGAAATGCTACAATAGAGACCAAATACAATATGTTTGTTAGCGACACGAACATGTT
CATGTATGCCTTGAAGACTCCCAAGATTAACAAGCCAAACAAACATAAAAAATAAAACAATAAAA
ATAAAATTTAACATCATGGACTTTGAGGTACAAAACTATTGCTAACTAAGGCCATATCTAGGAGG
AAAGGCATAAGGAAC
Found at i:29022719 original size:17 final size:17
Alignment explanation
Indices: 29022697--29022733 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
29022687 TTGTAGTATA
* *
29022697 ATTGTCCCTACATTTTT
1 ATTGTCACTACACTTTT
29022714 ATTGTCACTACACTTTT
1 ATTGTCACTACACTTTT
29022731 ATT
1 ATT
29022734 TTCGTTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.51
Consensus pattern (17 bp):
ATTGTCACTACACTTTT
Found at i:29026529 original size:17 final size:17
Alignment explanation
Indices: 29026507--29026540 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29026497 ACTCATTTTC
*
29026507 TTTTTCTTTTTTCACTA
1 TTTTTCTTTTTTAACTA
29026524 TTTTTCTTTTTTAACTA
1 TTTTTCTTTTTTAACTA
29026541 GGCCAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTCTTTTTTAACTA
Found at i:29039901 original size:23 final size:22
Alignment explanation
Indices: 29039865--29039908 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
29039855 TAAATATTTC
*
29039865 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
29039888 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
29039909 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:29052997 original size:3 final size:3
Alignment explanation
Indices: 29052989--29053032 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
29052979 CCTTATTCAC
* *
29052989 AAT AAT AAT ATT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29053033 AAGAGAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29058539 original size:17 final size:18
Alignment explanation
Indices: 29058517--29058554 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
29058507 GGGTGACTAG
*
29058517 AATTCA-TGTTAAAATAA
1 AATTCAGTGGTAAAATAA
*
29058534 AATTCAGTGGTAGAATAA
1 AATTCAGTGGTAAAATAA
29058552 AAT
1 AAT
29058555 AAAAGTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (18 bp):
AATTCAGTGGTAAAATAA
Found at i:29059887 original size:191 final size:193
Alignment explanation
Indices: 29059536--29059910 Score: 560
Period size: 191 Copynumber: 1.9 Consensus size: 193
29059526 CTAAACTAGA
* *
29059536 ATCACGTGCAATTGTTTAATTTTAGGTGTTCAACTTTCATTTAACTACTTGTTAATATTACAATT
1 ATCACATGCAATAGTTTAATTTTAGGTGTTCAACTTTCATTTAACTA--TGTTAATATTACAATT
* *
29059601 TGCAGTAACGATAAGAGTTGAATTATTAAGACTTAGAACAATTTGATTTTTTTCATCTATTCTTC
64 CGCAGTAACGATAAGAGTTGAATTATTAAAACTTAGAACAATTTGATTTTTTTCATCTATTCTTC
* *
29059666 TCTATTTAGCTCTCAAGAAGACATTGTGATATTTCATGCATTGTAAAATAAAATTTGATTTTCTT
129 TCTATATAACTCTCAAGAAGACATTGTGATATTTCATGCATTGTAAAATAAAATTTGATTTTCTT
* *
29059731 ATCACATGCAATAGTTTAATTTT-GGTGTTCATCTTTCATTTAACTA-GTTAAT-TCTGCAATTC
1 ATCACATGCAATAGTTTAATTTTAGGTGTTCAACTTTCATTTAACTATGTTAATAT-TACAATTC
* * * * *
29059793 GTAGTAATGTTAAGAGTTGAATTCTTAAAACTTAGTACAATTTGATTTTCTTT-ATCTATTCTTC
65 GCAGTAACGATAAGAGTTGAATTATTAAAACTTAGAACAATTTGATTTT-TTTCATCTATTCTTC
*
29059857 TCTATATAACTCTGAAGAAGACATTGTGATATTTCATGCATTGTAAAATAAAAT
129 TCTATATAACTCTCAAGAAGACATTGTGATATTTCATGCATTGTAAAATAAAAT
29059911 CAAGTAGAGA
Statistics
Matches: 164, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
190 1 0.01
191 117 0.71
192 3 0.02
194 22 0.13
195 21 0.13
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (193 bp):
ATCACATGCAATAGTTTAATTTTAGGTGTTCAACTTTCATTTAACTATGTTAATATTACAATTCG
CAGTAACGATAAGAGTTGAATTATTAAAACTTAGAACAATTTGATTTTTTTCATCTATTCTTCTC
TATATAACTCTCAAGAAGACATTGTGATATTTCATGCATTGTAAAATAAAATTTGATTTTCTT
Found at i:29074877 original size:32 final size:32
Alignment explanation
Indices: 29074835--29074913 Score: 131
Period size: 32 Copynumber: 2.5 Consensus size: 32
29074825 GTTCTTCTTT
*
29074835 GATATCGTTATTCTGTAAAATAACAAAAAATC
1 GATATCGTTATTCTGTAAAATAACAAAAAATA
* *
29074867 GATATTGTTATTCTGTAAAATTACAAAAAATA
1 GATATCGTTATTCTGTAAAATAACAAAAAATA
29074899 GATATCGTTATTCTG
1 GATATCGTTATTCTG
29074914 AAATATTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (32 bp):
GATATCGTTATTCTGTAAAATAACAAAAAATA
Found at i:29085702 original size:16 final size:16
Alignment explanation
Indices: 29085681--29085734 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
29085671 ATATCGGTAG
29085681 AAGGAACAGCATCATT
1 AAGGAACAGCATCATT
*
29085697 AAGGAACAGC-TC-GT
1 AAGGAACAGCATCATT
*
29085711 --GTGAGCAGCATCATT
1 AAG-GAACAGCATCATT
29085726 AAGGAACAG
1 AAGGAACAG
29085735 TTTATAGTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
12 1 0.03
13 6 0.21
14 3 0.10
15 3 0.10
16 15 0.52
17 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.17
Consensus pattern (16 bp):
AAGGAACAGCATCATT
Found at i:29087045 original size:12 final size:12
Alignment explanation
Indices: 29087028--29087059 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
29087018 GAATTTAATT
29087028 ATTGATTGGTGG
1 ATTGATTGGTGG
*
29087040 ATTGATTGTTGG
1 ATTGATTGGTGG
29087052 ATTGATTG
1 ATTGATTG
29087060 ATTTAAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (12 bp):
ATTGATTGGTGG
Found at i:29099097 original size:29 final size:27
Alignment explanation
Indices: 29099028--29099097 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 27
29099018 CAAACAAAAG
* *
29099028 AAATAATAAAAAAATAAAAACAGTTTT
1 AAATAAAAAAAAAATAAAAACAGATTT
29099055 AAA-AAAAAATAAAATATGAAAACAGATTT
1 AAATAAAAAA-AAAATA--AAAACAGATTT
*
29099084 AAATAACAAAAAAA
1 AAATAAAAAAAAAA
29099098 GGGTTTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 5 0.14
27 9 0.25
29 17 0.47
30 5 0.14
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20
Consensus pattern (27 bp):
AAATAAAAAAAAAATAAAAACAGATTT
Found at i:29099979 original size:32 final size:30
Alignment explanation
Indices: 29099872--29100039 Score: 167
Period size: 30 Copynumber: 5.5 Consensus size: 30
29099862 TTAACAATCT
* * * *
29099872 AAAAATTACATTTTTAACCCTTAAAATTTGC
1 AAAAATCACA-TTTTAACCCTCAAACTTTTC
* * * *
29099903 AAAAATTACGTTTTAACACTTAAACTTTTC
1 AAAAATCACATTTTAACCCTCAAACTTTTC
29099933 -AAAATCACATTTTAACCCTCAAACTTTTC
1 AAAAATCACATTTTAACCCTCAAACTTTTC
* *
29099962 AAAAAAAACACATTTTAACCCTCAAACTTCTC
1 --AAAAATCACATTTTAACCCTCAAACTTTTC
* *
29099994 AAAAATCACATTTTGACCCTCGAACTTTTC
1 AAAAATCACATTTTAACCCTCAAACTTTTC
* * *
29100024 CAAAATTATATTTTAA
1 AAAAATCACATTTTAA
29100040 TCTCGAACCT
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
29 25 0.22
30 55 0.47
31 9 0.08
32 27 0.23
ACGTcount: A:0.41, C:0.21, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAAATCACATTTTAACCCTCAAACTTTTC
Found at i:29100013 original size:62 final size:61
Alignment explanation
Indices: 29099913--29100028 Score: 169
Period size: 62 Copynumber: 1.9 Consensus size: 61
29099903 AAAAATTACG
* *
29099913 TTTTAACACTTAAACTTTTCAAAATCACATTTTAACCCTCAAACTTTTCAAAAAAAACACA
1 TTTTAACACTCAAACTTCTCAAAATCACATTTTAACCCTCAAACTTTTCAAAAAAAACACA
* * * *
29099974 TTTTAACCCTCAAACTTCTCAAAAATCACATTTTGACCCTCGAACTTTTCCAAAA
1 TTTTAACACTCAAACTTCTC-AAAATCACATTTTAACCCTCAAACTTTTCAAAAA
29100029 TTATATTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
61 17 0.35
62 31 0.65
ACGTcount: A:0.40, C:0.26, G:0.02, T:0.33
Consensus pattern (61 bp):
TTTTAACACTCAAACTTCTCAAAATCACATTTTAACCCTCAAACTTTTCAAAAAAAACACA
Found at i:29100045 original size:29 final size:31
Alignment explanation
Indices: 29099873--29100097 Score: 122
Period size: 30 Copynumber: 7.5 Consensus size: 31
29099863 TAACAATCTA
* ** * * *
29099873 AAAATTACATTTTTAACCCTTAAAATTTGCA
1 AAAATTACATTTTTAACTCTCGAACTTTTCC
* * **
29099904 AAAATTAC-GTTTTAACACTTAAACTTTT-C
1 AAAATTACATTTTTAACTCTCGAACTTTTCC
* * * *
29099933 AAAATCACA-TTTTAACCCTCAAACTTTTCA
1 AAAATTACATTTTTAACTCTCGAACTTTTCC
** * * * * *
29099963 AAAAAAACACATTTTAACCCTCAAACTTCTCA
1 AAAATTACA-TTTTTAACTCTCGAACTTTTCC
* * *
29099995 AAAATCACA-TTTTGACCCTCGAACTTTTCC
1 AAAATTACATTTTTAACTCTCGAACTTTTCC
* *
29100025 AAAATTATA-TTTTAA-TCTCGAACCTTTCC
1 AAAATTACATTTTTAACTCTCGAACTTTTCC
* * *
29100054 -AAATTACATTTTTAACTCCCAAACTTTCCC
1 AAAATTACATTTTTAACTCTCGAACTTTTCC
*
29100084 AAAATTGCATTTTT
1 AAAATTACATTTTT
29100098 GCTTCCCAAA
Statistics
Matches: 158, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
28 7 0.04
29 42 0.27
30 62 0.39
31 20 0.13
32 27 0.17
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (31 bp):
AAAATTACATTTTTAACTCTCGAACTTTTCC
Found at i:29106006 original size:3 final size:3
Alignment explanation
Indices: 29105998--29106060 Score: 62
Period size: 3 Copynumber: 21.3 Consensus size: 3
29105988 TATTAAGGTA
29105998 AAG AAG AAG AAAG AA- AAG AAG AAG -AG AAAG AAG AA- AAG AAG AA-
1 AAG AAG AAG -AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG
*
29106041 AAGG AAG AAA AAG AAG AAG A
1 AA-G AAG AAG AAG AAG AAG A
29106061 TGTTGCCCTG
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
2 8 0.16
3 36 0.71
4 7 0.14
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29106058 original size:9 final size:9
Alignment explanation
Indices: 29105997--29106058 Score: 74
Period size: 9 Copynumber: 7.0 Consensus size: 9
29105987 GTATTAAGGT
29105997 AAAGAAGAA
1 AAAGAAGAA
29106006 GAAAGAA-AA
1 -AAAGAAGAA
* *
29106015 GAAGAAGAG
1 AAAGAAGAA
29106024 AAAGAAG-A
1 AAAGAAGAA
29106032 AAAGAAGAA
1 AAAGAAGAA
*
29106041 AAGGAAGAA
1 AAAGAAGAA
29106050 AAAGAAGAA
1 AAAGAAGAA
29106059 GATGTTGCCC
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
8 12 0.27
9 26 0.59
10 6 0.14
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (9 bp):
AAAGAAGAA
Found at i:29109098 original size:16 final size:16
Alignment explanation
Indices: 29109077--29109123 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
29109067 GCTGTCGACA
29109077 AAATAATTGTGCAT-AT
1 AAATAATTGTG-ATAAT
*
29109093 AAATAAATGTGATAAT
1 AAATAATTGTGATAAT
29109109 AAGTATAATTGTGAT
1 AA--ATAATTGTGAT
29109124 TGTAACTGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 2 0.08
16 14 0.54
18 10 0.38
ACGTcount: A:0.47, C:0.02, G:0.15, T:0.36
Consensus pattern (16 bp):
AAATAATTGTGATAAT
Found at i:29119956 original size:24 final size:24
Alignment explanation
Indices: 29119928--29119991 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
29119918 AAACTATATG
*
29119928 AAACCCAAAGATGGAAGGTTT-AAT
1 AAACCCAAAGATGGAA-GTTTCAAC
* *
29119952 AAACCAAAATGATTGAAGTTTCAAC
1 AAACCCAAA-GATGGAAGTTTCAAC
*
29119977 AAACCCAAAAATGGA
1 AAACCCAAAGATGGA
29119992 TGTGAAATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 16 0.50
25 16 0.50
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (24 bp):
AAACCCAAAGATGGAAGTTTCAAC
Found at i:29120027 original size:91 final size:92
Alignment explanation
Indices: 29119817--29120245 Score: 306
Period size: 92 Copynumber: 4.7 Consensus size: 92
29119807 AAGACTCAAC
*
29119817 ATGCTTGGGAAGCTTTATGAAACCCAAAGATGTG-AGCTTTAAGAAACCACAAATGGAGTAAGCT
1 ATGCTTGGGAAGCTTTATGAAACCCAAAGATG-GAAGGTTTAAGAAACCACAAATGGAGTAAGCT
29119881 TAAAAATACCCATAAAAGGAGGTGAAAT
65 TAAAAATACCCATAAAAGGAGGTGAAAT
* * * * * *
29119909 ATGCTTGGAAAACTATATGAAACCCAAAGATGGAAGGTTTAATAAACCA-AAAT-GATTGAAGTT
1 ATGCTTGGGAAGCTTTATGAAACCCAAAGATGGAAGGTTTAAGAAACCACAAATGGAGT-AAGCT
* *
29119972 TCAACAA-ACCCA-AAAATGGATGTGAAAT
65 T-AAAAATACCCATAAAA-GGAGGTGAAAT
* * * * * * *
29120000 GTGGTTGGGAAGCTTTATGAAATCCAAATATGGAAGGTTTAAGAAACAACAAACGGAGGAAGCTT
1 ATGCTTGGGAAGCTTTATGAAACCCAAAGATGGAAGGTTTAAGAAACCACAAATGGAGTAAGC-T
* * *
29120065 TAAGAA-ACCCATAAATGCAGGTGAAAT
65 TAAAAATACCCATAAAAGGAGGTGAAAT
* * ** ** * ** * * * *
29120092 GTGCTTAGGAAAATTTATGAAA--C-TTGATAGAAACTTTAAGATACCAAAAATAGAGAAAGCTT
1 ATGCTTGGGAAGCTTTATGAAACCCAAAGATGGAAGGTTTAAGAAACCACAAATGGAGTAAGCTT
* * *
29120154 CAATAAA-A-TCATAAATGGAGGAGAAAT
66 -AA-AAATACCCATAAAAGGAGGTGAAAT
** * *** * * *
29120181 ATGCTTATGAAACTTTACCCAACCCAAAGATGAAAGCTTTAAGAAACCATAAATAGG-GTAAGCT
1 ATGCTTGGGAAGCTTTATGAAACCCAAAGATGGAAGGTTTAAGAAACCACAAAT-GGAGTAAGCT
29120245 T
65 T
29120246 CAAGAAACCA
Statistics
Matches: 262, Mismatches: 61, Indels: 28
0.75 0.17 0.08
Matches are distributed among these distances:
88 2 0.01
89 59 0.23
90 11 0.04
91 66 0.25
92 116 0.44
93 8 0.03
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (92 bp):
ATGCTTGGGAAGCTTTATGAAACCCAAAGATGGAAGGTTTAAGAAACCACAAATGGAGTAAGCTT
AAAAATACCCATAAAAGGAGGTGAAAT
Found at i:29127523 original size:12 final size:12
Alignment explanation
Indices: 29127503--29127533 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29127493 TGTAGTCAGA
*
29127503 TGCATCTCCAAT
1 TGCAACTCCAAT
29127515 TGCAACTCCAAT
1 TGCAACTCCAAT
29127527 TGCAACT
1 TGCAACT
29127534 AATAAGAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.32, G:0.10, T:0.29
Consensus pattern (12 bp):
TGCAACTCCAAT
Found at i:29135809 original size:2 final size:2
Alignment explanation
Indices: 29135802--29135830 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29135792 AAAATAAAAC
29135802 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
29135831 ACTAACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:29137045 original size:18 final size:18
Alignment explanation
Indices: 29137024--29137058 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29137014 AAAAGAATTT
*
29137024 AAAATTTAAAAATTTAAA
1 AAAAATTAAAAATTTAAA
*
29137042 AAAAATTAATAATTTAA
1 AAAAATTAAAAATTTAA
29137059 TGAGTTTGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATTAAAAATTTAAA
Found at i:29137048 original size:26 final size:27
Alignment explanation
Indices: 29137003--29137058 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
29136993 TAAAAATATA
* *
29137003 TAAAATTTCTAAAAAGAATTTAA-AATT
1 TAAAAATTCTAAAAA-AAATTAATAATT
29137030 TAAAAATT-TAAAAAAAATTAATAATT
1 TAAAAATTCTAAAAAAAATTAATAATT
29137056 TAA
1 TAA
29137059 TGAGTTTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 6 0.23
26 13 0.50
27 7 0.27
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (27 bp):
TAAAAATTCTAAAAAAAATTAATAATT
Found at i:29137869 original size:21 final size:19
Alignment explanation
Indices: 29137837--29137877 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
29137827 ATTCAAAATG
*
29137837 ATAACATGTGATATGCTCA
1 ATAACATGTGATATGATCA
29137856 ATAAGCATGATGATATGATCA
1 ATAA-CATG-TGATATGATCA
29137877 A
1 A
29137878 CAAGGCATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 4 0.21
21 11 0.58
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (19 bp):
ATAACATGTGATATGATCA
Found at i:29138892 original size:87 final size:87
Alignment explanation
Indices: 29138737--29138934 Score: 209
Period size: 87 Copynumber: 2.3 Consensus size: 87
29138727 CCCAAATAGT
* * * *
29138737 TAAGTTTATGGATGAACCACCAGTATTTGCAGATAAAATGCCAGTAGGTTGTGGATGCATAACAT
1 TAAGTTTATGGATGAACCACCAGTATTTGCAAATAAAATACCAGTAGGTTGTGAATGCACAACAT
* *
29138802 ATTTGTCGATAAAGGCTACCAA
66 ATTTGTAGATAAAAGCTACCAA
* ** * * **
29138824 TAAGTTTGTGGATGAATTACCAGTGA-TTGCAAATAAACTACTAGTAGGTTGTGAATGCACAATG
1 TAAGTTTATGGATGAACCACCAGT-ATTTGCAAATAAAATACCAGTAGGTTGTGAATGCACAACA
** *
29138888 TATTTGTAGATAAAAGCTATTAG
65 TATTTGTAGATAAAAGCTACCAA
* * *
29138911 TAAATTTATGGATAAACCGCCAGT
1 TAAGTTTATGGATGAACCACCAGT
29138935 GTTGCAGATT
Statistics
Matches: 88, Mismatches: 22, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
87 87 0.99
88 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (87 bp):
TAAGTTTATGGATGAACCACCAGTATTTGCAAATAAAATACCAGTAGGTTGTGAATGCACAACAT
ATTTGTAGATAAAAGCTACCAA
Found at i:29143061 original size:19 final size:20
Alignment explanation
Indices: 29143039--29143083 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
29143029 TTATATTAGG
29143039 ATTTAAT-ATTTAAGATAT-T
1 ATTTAATCATTTAA-ATATGT
*
29143058 ATTT-ATCATTTAAATTTGT
1 ATTTAATCATTTAAATATGT
29143077 ATTTAAT
1 ATTTAAT
29143084 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 5 0.23
19 15 0.68
20 2 0.09
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
ATTTAATCATTTAAATATGT
Found at i:29143919 original size:22 final size:21
Alignment explanation
Indices: 29143894--29143940 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
29143884 TTTCTATTTC
29143894 TTTTAATTATACTTTCTTCTAT
1 TTTTAATTAT-CTTTCTTCTAT
* *
29143916 TTTTAATTCTGTTTCTTCTAT
1 TTTTAATTATCTTTCTTCTAT
29143937 TTTT
1 TTTT
29143941 CCTTAGATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.17, C:0.13, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTAATTATCTTTCTTCTAT
Found at i:29146608 original size:108 final size:108
Alignment explanation
Indices: 29146415--29146630 Score: 396
Period size: 108 Copynumber: 2.0 Consensus size: 108
29146405 AACCGTGTCG
29146415 ATATAGTGAAATCCTTAGTAGAAGAGACTTCCAAATCACTCCATAAAAATGAACCTAAAATATTG
1 ATATAGTGAAATCCTTAGTAGAAGAGACTTCCAAATCACTCCATAAAAATGAACCTAAAATATTG
* *
29146480 TTTGATGATTTAGATCCATCTTGCAAATCTGTTAAGAAGTTAT
66 TTTGATGATTTAAATCCATCTTGCAAATCTGTTAAGAAATTAT
*
29146523 ATATAGTGGAATCCTTAGTAGAAGAGACTTCCAAATCACTCCATAAAAATGAACCTAAAATATTG
1 ATATAGTGAAATCCTTAGTAGAAGAGACTTCCAAATCACTCCATAAAAATGAACCTAAAATATTG
*
29146588 TTTGATGATTTAAATTCATCTTGCAAATCTGTTAAGAAATTAT
66 TTTGATGATTTAAATCCATCTTGCAAATCTGTTAAGAAATTAT
29146631 TGCCCCCTAT
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 104 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Consensus pattern (108 bp):
ATATAGTGAAATCCTTAGTAGAAGAGACTTCCAAATCACTCCATAAAAATGAACCTAAAATATTG
TTTGATGATTTAAATCCATCTTGCAAATCTGTTAAGAAATTAT
Found at i:29146799 original size:4 final size:4
Alignment explanation
Indices: 29146790--29146845 Score: 62
Period size: 4 Copynumber: 13.8 Consensus size: 4
29146780 CCCAATTATT
*
29146790 TTTA TTTA TTT- TTTA TTTT TTTA TTT- TTCTA TCTTA TTTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA T-TTA -TTTA TTTA TTTA
29146839 TTTA TTT
1 TTTA TTT
29146846 TTGTCCAGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
3 5 0.11
4 32 0.71
5 6 0.13
6 2 0.04
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:29147805 original size:104 final size:101
Alignment explanation
Indices: 29147637--29147829 Score: 244
Period size: 104 Copynumber: 1.9 Consensus size: 101
29147627 ATGTGTTAGA
* * *
29147637 CTGAGTAACCGGGGTGGAGTGCTTTGTCGTCATTTCACTTCGCGTCAAAAGGGCTAACACATTCT
1 CTGAGTAACCGGGATGGAGTGCTTGGTCGTCATTTCACTTCGCGTCAAAAGGGCCAACACATTCT
29147702 ACAAAAAAAAAAAGAAGAAAAAATTGAGAGCATGTGGGG
66 --AAAAAAAAAAAG-AGAAAAAATTGAGAGCATGTGGGG
* * * ***
29147741 CTGAGTAACCGGGATGGAGTGCTTGGGT-GTCATTTCATTTCGCGTTAAAAGGTCCAATGTATTC
1 CTGAGTAACCGGGATGGAGTGCTT-GGTCGTCATTTCACTTCGCGTCAAAAGGGCCAACACATTC
**
29147805 TTTAAAAAAAAAGAGAAAAAATTGA
65 TAAAAAAAAAAAGAGAAAAAATTGA
29147830 AAAAATAAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
101 12 0.16
102 10 0.13
104 53 0.69
105 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (101 bp):
CTGAGTAACCGGGATGGAGTGCTTGGTCGTCATTTCACTTCGCGTCAAAAGGGCCAACACATTCT
AAAAAAAAAAAGAGAAAAAATTGAGAGCATGTGGGG
Found at i:29149278 original size:15 final size:15
Alignment explanation
Indices: 29149229--29149278 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
29149219 CTTCAACTTC
29149229 TTTATTTTCTATTTCT
1 TTTATTTT-TATTTCT
* *
29149245 TTTAATTATACTTTCT
1 TTTATTTTTA-TTTCT
29149261 TTTATTTTTATTTCT
1 TTTATTTTTATTTCT
29149276 TTT
1 TTT
29149279 GGAAACGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTTTTATTTCT
Found at i:29195453 original size:30 final size:30
Alignment explanation
Indices: 29195405--29195472 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
29195395 TATCTTTAAA
*
29195405 ATTTTT-AAAAGATTAAATTAAATTTTTATT
1 ATTTTTAAAAAGATCAAATT-AATTTTTATT
*
29195435 ATTTTTAAAAAG-TCAAATTTATTTTTATT
1 ATTTTTAAAAAGATCAAATTAATTTTTATT
*
29195464 A-ATTTAAAA
1 ATTTTTAAAA
29195473 TTTTTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.21
29 10 0.29
30 12 0.35
31 5 0.15
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (30 bp):
ATTTTTAAAAAGATCAAATTAATTTTTATT
Found at i:29195990 original size:29 final size:27
Alignment explanation
Indices: 29195950--29196006 Score: 62
Period size: 27 Copynumber: 2.0 Consensus size: 27
29195940 TAGTAATAAT
* *
29195950 AAAATTATATTTTATTCTTTTTAAAGATA
1 AAAATTATA-TTTAAT-TTTTTAAAAATA
29195979 AAAATT-TGATTTAATTTTTTAAAAATA
1 AAAATTAT-ATTTAATTTTTTAAAAATA
29196006 A
1 A
29196007 TAAAGATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 12 0.48
28 6 0.24
29 7 0.28
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (27 bp):
AAAATTATATTTAATTTTTTAAAAATA
Found at i:29197084 original size:18 final size:18
Alignment explanation
Indices: 29197045--29197101 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
29197035 CAATATAAAT
29197045 AATTTTTAT-T-TTTTTGA
1 AATTTTTATATATTTTT-A
29197062 CAATTTTTATATATTTTTA
1 -AATTTTTATATATTTTTA
29197081 AA-TTTTATTATATTTTATA
1 AATTTTTA-TATATTTT-TA
29197100 AA
1 AA
29197102 ACATTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.14
18 19 0.54
19 6 0.17
20 5 0.14
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
AATTTTTATATATTTTTA
Found at i:29197086 original size:17 final size:19
Alignment explanation
Indices: 29197066--29197101 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
29197056 TTTTGACAAT
29197066 TTTTA-TATATTTT-TAAA
1 TTTTATTATATTTTATAAA
29197083 TTTTATTATATTTTATAAA
1 TTTTATTATATTTTATAAA
29197102 ACATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 8 0.47
19 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTATTATATTTTATAAA
Found at i:29200348 original size:15 final size:16
Alignment explanation
Indices: 29200328--29200360 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
29200318 GCTTTTGAGG
29200328 TTTTGATA-AAATTTA
1 TTTTGATATAAATTTA
*
29200343 TTTTGATATGAATTTA
1 TTTTGATATAAATTTA
29200359 TT
1 TT
29200361 GATTTGTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (16 bp):
TTTTGATATAAATTTA
Found at i:29201463 original size:3 final size:3
Alignment explanation
Indices: 29201455--29201480 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29201445 CTTCTCTCTT
29201455 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
29201481 TTCTTTCTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:29212659 original size:24 final size:24
Alignment explanation
Indices: 29212627--29212674 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
29212617 TTTCGTTTTC
*
29212627 TTTACAATATTTCTTCATTGTCGA
1 TTTACAATATTTCCTCATTGTCGA
29212651 TTTACAATATTTCCTCATTGTCGA
1 TTTACAATATTTCCTCATTGTCGA
29212675 CACTCAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (24 bp):
TTTACAATATTTCCTCATTGTCGA
Found at i:29212682 original size:24 final size:24
Alignment explanation
Indices: 29212629--29212682 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
29212619 TCGTTTTCTT
* **
29212629 TACAATATTTCTTCATTGTCGATT
1 TACAATATTTCCTCATTGTCGAAC
29212653 TACAATATTTCCTCATTGTCGACAC
1 TACAATATTTCCTCATTGTCGA-AC
29212678 T-CAAT
1 TACAAT
29212683 TTTAATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (24 bp):
TACAATATTTCCTCATTGTCGAAC
Found at i:29216769 original size:4 final size:4
Alignment explanation
Indices: 29216760--29216784 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
29216750 AAGAAAAGGG
29216760 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
29216785 AAGTTTGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:29220865 original size:26 final size:26
Alignment explanation
Indices: 29220822--29220899 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
29220812 AATAAATAAA
* *
29220822 AAATAATAAAAGAGATAACAATAAAAT
1 AAATAA-AAAATAAATAACAATAAAAT
* * *
29220849 GACAT-GAAAATAAATAACAATAAGAT
1 -AAATAAAAAATAAATAACAATAAAAT
*
29220875 AAATAAAAAATAAATAAAAATAAAA
1 AAATAAAAAATAAATAACAATAAAA
29220900 ATTAAATGCT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
25 3 0.08
26 34 0.85
28 3 0.08
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (26 bp):
AAATAAAAAATAAATAACAATAAAAT
Found at i:29220984 original size:19 final size:19
Alignment explanation
Indices: 29220960--29221017 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
29220950 TTAGGCGTGA
29220960 AAATAAATGACAAATAAAT
1 AAATAAATGACAAATAAAT
** * *
29220979 AAATAAACAAAAAATCAAT
1 AAATAAATGACAAATAAAT
*
29220998 AAATTAAATGTCAAAATAAA
1 AAA-TAAATGAC-AAATAAA
29221018 CAACTTAATA
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
19 18 0.64
20 4 0.14
21 6 0.21
ACGTcount: A:0.69, C:0.07, G:0.03, T:0.21
Consensus pattern (19 bp):
AAATAAATGACAAATAAAT
Found at i:29220993 original size:15 final size:15
Alignment explanation
Indices: 29220959--29221000 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
29220949 ATTAGGCGTG
*
29220959 AAAATAAAT-GACAA
1 AAAATAAATAAACAA
29220973 ATAAATAAATAAACAA
1 A-AAATAAATAAACAA
*
29220989 AAAATCAATAAA
1 AAAATAAATAAA
29221001 TTAAATGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.75
16 5 0.21
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.17
Consensus pattern (15 bp):
AAAATAAATAAACAA
Found at i:29221133 original size:49 final size:50
Alignment explanation
Indices: 29221080--29221190 Score: 138
Period size: 49 Copynumber: 2.3 Consensus size: 50
29221070 CTCTTTTTGG
** * * *
29221080 TTTTAGGGTGTTAA-ATCTGTCGTTGTGGCTTTAAT-TTATTCCTCTTCGA
1 TTTTAGGGTGTTAAGATCTACCGTGGCGACTTTAATCTT-TTCCTCTTCGA
*
29221129 TTTTAGGGTG-TAAGATCTACCGTGGCGACTTTAATCTTTTCCTCTTTGA
1 TTTTAGGGTGTTAAGATCTACCGTGGCGACTTTAATCTTTTCCTCTTCGA
29221178 TTTTAGGGTGTTA
1 TTTTAGGGTGTTA
29221191 GGTCCACTGT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
48 3 0.06
49 46 0.87
50 4 0.08
ACGTcount: A:0.17, C:0.14, G:0.22, T:0.47
Consensus pattern (50 bp):
TTTTAGGGTGTTAAGATCTACCGTGGCGACTTTAATCTTTTCCTCTTCGA
Found at i:29221222 original size:98 final size:96
Alignment explanation
Indices: 29221120--29221439 Score: 316
Period size: 98 Copynumber: 3.3 Consensus size: 96
29221110 TTAATTTATT
** *
29221120 CCTCTTCGATTTTAGGGTGTAAGATCTACCGTGGCGACTTTAATCTTTTCCTCTTTGATTTTAGG
1 CCTCTTCGATTTTAGGGTGTAAGATCTACCGTTACGA-TTTAATCTTTTCCTCTTAGATTTTAGG
*
29221185 GTGTTAGGTCCAC-TGT-CGTAGCTTTTACCTATC
65 GTGTTAGGTCCACAT-TACG-A-CTTTAACCTATC
* * *
29221218 CCTCTTCAATTTTAAGGTGTAAGAT-T-CGTCATTACGGATTTAATCTTTTCGC-CTTAGATTTT
1 CCTCTTCGATTTTAGGGTGTAAGATCTAC--CGTTAC-GATTTAATCTTTTC-CTCTTAGATTTT
*
29221280 AGGGTGTTAGATCCACCATTACGACTTTAACCTA-C
62 AGGGTGTTAGGTCCA-CATTACGACTTTAACCTATC
** * * * *
29221315 TCCTCTTCGATTTTAGCTTATAACATC-AGCCGTTACGA-TTAATCTTTCCCTCTTCGATTTTAG
1 -CCTCTTCGATTTTAGGGTGTAAGATCTA-CCGTTACGATTTAATCTTTTCCTCTTAGATTTTAG
* *
29221378 AGTGTTAGGTCCGCCATTACGACTTTAACCTATC
64 GGTGTTAGGTCC-ACATTACGACTTTAACCTATC
29221412 CCTCTTC-AGTTTTAGGGTGTAAGATCTA
1 CCTCTTCGA-TTTTAGGGTGTAAGATCTA
29221440 ACGGCTTTAG
Statistics
Matches: 182, Mismatches: 24, Indels: 33
0.76 0.10 0.14
Matches are distributed among these distances:
95 2 0.01
96 70 0.38
97 6 0.03
98 94 0.52
99 6 0.03
100 4 0.02
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.40
Consensus pattern (96 bp):
CCTCTTCGATTTTAGGGTGTAAGATCTACCGTTACGATTTAATCTTTTCCTCTTAGATTTTAGGG
TGTTAGGTCCACATTACGACTTTAACCTATC
Found at i:29221309 original size:49 final size:49
Alignment explanation
Indices: 29221108--29221437 Score: 187
Period size: 49 Copynumber: 6.8 Consensus size: 49
29221098 GTCGTTGTGG
* * * **
29221108 CTTTAAT-TTATTCCTCTTCGATTTTAGGGTGTAAGATCTACCGTGGCGA
1 CTTTAATCTT-TTCCTCTTAGATTTTAGGGTGTAAGATCCACCATTACGA
* * *
29221157 CTTTAATCTTTTCCTCTTTGATTTTAGGGTGTTAGGTCCA-C-TGT-CGTA
1 CTTTAATCTTTTCCTCTTAGATTTTAGGGTGTAAGATCCACCAT-TACG-A
* * * * * * **
29221205 GCTTTTACCTATCCCTCTTCA-ATTTTAAGGTGTAAGATTCGTCATTACGGA
1 -CTTTAATCTTTTCCTCTT-AGATTTTAGGGTGTAAGATCCACCATTAC-GA
*
29221256 -TTTAATCTTTTCGC-CTTAGATTTTAGGGTGTTAGATCCACCATTACGA
1 CTTTAATCTTTTC-CTCTTAGATTTTAGGGTGTAAGATCCACCATTACGA
* ** * ** * * *
29221304 CTTTAACCTACTCCTCTTCGATTTTAGCTTATAACAT-CAGCCGTTACGA
1 CTTTAATCTTTTCCTCTTAGATTTTAGGGTGTAAGATCCA-CCATTACGA
* * * * * *
29221353 --TTAATCTTTCCCTCTTCGATTTTAGAGTGTTAGGTCCGCCATTACGA
1 CTTTAATCTTTTCCTCTTAGATTTTAGGGTGTAAGATCCACCATTACGA
* * *
29221400 CTTTAACCTATCCCTCTTCAG-TTTTAGGGTGTAAGATC
1 CTTTAATCTTTTCCTCTT-AGATTTTAGGGTGTAAGATC
29221438 TAACGGCTTT
Statistics
Matches: 211, Mismatches: 52, Indels: 36
0.71 0.17 0.12
Matches are distributed among these distances:
47 36 0.17
48 9 0.04
49 156 0.74
50 6 0.03
51 3 0.01
52 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (49 bp):
CTTTAATCTTTTCCTCTTAGATTTTAGGGTGTAAGATCCACCATTACGA
Found at i:29222505 original size:3 final size:3
Alignment explanation
Indices: 29222497--29222522 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29222487 CTTTTTTGTT
29222497 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
29222523 GTGCTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:29225010 original size:265 final size:265
Alignment explanation
Indices: 29224512--29225037 Score: 811
Period size: 265 Copynumber: 2.0 Consensus size: 265
29224502 ATGCAGTTAA
*
29224512 CCCCATCATGAACTTAAGAGGATCCAATTTTGATATCAACCAAGTTGAATGGTATAACATGTACT
1 CCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAACCAAGTTGAATGGTATAACATGTACT
* * * *
29224577 TCCTCAACATTCGAGTAGTCCAGACTAAAGCGCAACATAATTTCTCGATTGGCGAATATCTTATC
66 GCCTCAACATTCGAGTAGTCCAGACCAAAGCGCAACACAATTTCTCGATTGGCGAATATATTATC
* * *
29224642 TCGCATTCAGTGAACTTCTTGCTCAGATAATAAATTGCTCTTTCTTTTTTTTCTTAACTCATTAT
131 TCACATTCAGTGAACTTCTTGCTCAGATAATAAATTGCTCTTTCTTTTTTTTCCTAACTCATCAT
* * ** *
29224707 GTTAGCCCAATACGCATCCCATAAAGTTTTTGAATACGACTAAGTACAGGATCAAAGGTTTATCA
196 GTTAGCCCAATACGCATCCAATAAAGTGTTCAAATACGACTAAGTACAGGATCAAAAGTTTATCA
29224772 GTCGG
261 GTCGG
*
29224777 CCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAACCAAGTTGTATGGTATAACATGTACT
1 CCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAACCAAGTTGAATGGTATAACATGTACT
* * * *
29224842 GCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACAATTTCTTGATTGGCGAATATATTATC
66 GCCTCAACATTCGAGTAGTCCAGACCAAAGCGCAACACAATTTCTCGATTGGCGAATATATTATC
* *
29224907 TCACATTCAGTGAACTTCTTGCTGAGATAATAAATTGCTCTTTC-TTTTTTTCCTGACTCATCAT
131 TCACATTCAGTGAACTTCTTGCTCAGATAATAAATTGCTCTTTCTTTTTTTTCCTAACTCATCAT
* * * * *
29224971 GTTGGCCCAGTACGTATCCAAATAGAGTGTTCAAATACGACTAAGTACATGATCAAAAGTTTATC
196 GTTAGCCCAATACGCATCC-AATAAAGTGTTCAAATACGACTAAGTACAGGATCAAAAGTTTATC
29225036 AG
260 AG
29225038 GATTTGGTGG
Statistics
Matches: 235, Mismatches: 25, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
264 33 0.14
265 202 0.86
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (265 bp):
CCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAACCAAGTTGAATGGTATAACATGTACT
GCCTCAACATTCGAGTAGTCCAGACCAAAGCGCAACACAATTTCTCGATTGGCGAATATATTATC
TCACATTCAGTGAACTTCTTGCTCAGATAATAAATTGCTCTTTCTTTTTTTTCCTAACTCATCAT
GTTAGCCCAATACGCATCCAATAAAGTGTTCAAATACGACTAAGTACAGGATCAAAAGTTTATCA
GTCGG
Found at i:29225471 original size:330 final size:330
Alignment explanation
Indices: 29224751--29225747 Score: 1616
Period size: 333 Copynumber: 3.0 Consensus size: 330
29224741 TACGACTAAG
*
29224751 TACAGGATCAAAGGTTTATCAGTCGGCCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAA
1 TACAGGATCAAAGGTTTATCAGTCGACCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAA
29224816 CCAAGTTGTATGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACA
66 CCAAGTTGTATGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACA
*
29224881 ATTTCTTGATTGGCGAATATATTATCTCACATTCAGTGAACTTCTTGCTGAGATAATAAATTGCT
131 ATTTCTAGATTGGCGAATATATTATCTCACATTCAGTGAACTTCTTGCTGAGATAATAAATTGCT
*
29224946 CTTTCTTTTTTTCCTGACTCATCATGTTGGCCCAGTACGTATCCAAATAGAGTGTTCAAATACGA
196 CTTT-TTTTTTT-CTGACTCATCATGTTGGCCCAGTACGCATCCAAATAGAGT-TTCAAATACGA
* * *
29225011 CTAAGTACATGATCAAAAGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGGACAAGTAA
258 CTAAGTACAGGATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGGACAAATAA
29225076 TGTTTAAC
323 TGTTTAAC
* * *
29225084 TACAGGATCAAAGGTTTATCAGTTGACCCCATCATGACCTTAAGAAGATCCAATTTTGAAATCAA
1 TACAGGATCAAAGGTTTATCAGTCGACCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAA
*
29225149 CCAAGTTGTATGGTATAACATGTAATGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACA
66 CCAAGTTGTATGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACA
** * * * *
29225214 ATTTCTAGATTGGTAAATATTTTATCACTCATTCAGTGAACTTCTTGTTGAGATAATAAATTGCT
131 ATTTCTAGATTGGCGAATATATTATCTCACATTCAGTGAACTTCTTGCTGAGATAATAAATTGCT
* * *
29225279 CTTTTTTTTTTCTTACTCATCATGTTAGCCCAGTACACATCCAAATAGAGTTTCAAATACGACTA
196 CTTTTTTTTTTCTGACTCATCATGTTGGCCCAGTACGCATCCAAATAGAGTTTCAAATACGACTA
* * *
29225344 AGTATAGGATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGAAGTGTTGGACAAATAATGT
261 AGTACAGGATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGGACAAATAATGT
29225409 TTAAC
326 TTAAC
*
29225414 TACAGGATCAAAGGTTTATCAGTCGACCCCATCATGAACTTAAGAGGATCTAATTTTGAAATCAA
1 TACAGGATCAAAGGTTTATCAGTCGACCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAA
29225479 CCAAGTTGTATGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACA
66 CCAAGTTGTATGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACA
* * * * **
29225544 ATTTCTCGATTGGCGAATATCTTATCTCGCATTCAGTGAACTTCTTGCTGAAATAATAAATTATT
131 ATTTCTAGATTGGCGAATATATTATCTCACATTCAGTGAACTTCTTGCTGAGATAATAAATT-GC
* * *
29225609 TTTTCTTTTTTTTCTGACTCATCATGTTGGCCCAATTCGCATCCAAATAGAGTTTTCAAATACGA
195 TCTT-TTTTTTTTCTGACTCATCATGTTGGCCCAGTACGCATCCAAATAGAG-TTTCAAATACGA
* *
29225674 TTAAGTACAGAATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGGACAAATAA
258 CTAAGTACAGGATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGGACAAATAA
**
29225739 AATTTAAC
323 TGTTTAAC
29225747 T
1 T
29225748 TTTTCAAAGG
Statistics
Matches: 611, Mismatches: 50, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
330 257 0.42
331 39 0.06
332 49 0.08
333 266 0.44
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (330 bp):
TACAGGATCAAAGGTTTATCAGTCGACCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAA
CCAAGTTGTATGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACA
ATTTCTAGATTGGCGAATATATTATCTCACATTCAGTGAACTTCTTGCTGAGATAATAAATTGCT
CTTTTTTTTTTCTGACTCATCATGTTGGCCCAGTACGCATCCAAATAGAGTTTCAAATACGACTA
AGTACAGGATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGGACAAATAATGT
TTAAC
Found at i:29225757 original size:330 final size:329
Alignment explanation
Indices: 29224754--29225747 Score: 1553
Period size: 330 Copynumber: 3.0 Consensus size: 329
29224744 GACTAAGTAC
*
29224754 AGGATCAAAGGTTTATCAGTCGGCCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAACCA
1 AGGATCAAAGGTTTATCAGTCGACCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAACCA
29224819 AGTTGTATGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACAATT
66 AGTTGTATGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACAATT
* *
29224884 TCTTGATTGGCGAATATATTATCTCACATTCAGTGAACTTCTTGCTGAGATAATAAATTGCTCTT
131 TCTAGATTGGCGAATATATTATCTCACATTCAGTGAACTTCTTGCTGAGATAATAAATT-CTTTT
* * *
29224949 TCTTTTTTTCCTGACTCATCATGTTGGCCCAGTACGTATCCAAATAGAGTGTTCAAATACGACTA
195 TCTTTTTTTTCTGACTCATCATGTTGGCCCAGTACGCATCCAAATAGAGTTTTCAAATACGACTA
* *
29225014 AGTACATGATCAAAAGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGGACAAGTAATGT
260 AGTACA-GATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGGACAAATAATGT
29225079 TTAACT
324 TTAACT
* * *
29225085 ACAGGATCAAAGGTTTATCAGTTGACCCCATCATGACCTTAAGAAGATCCAATTTTGAAATCAAC
1 --AGGATCAAAGGTTTATCAGTCGACCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAAC
*
29225150 CAAGTTGTATGGTATAACATGTAATGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACAA
64 CAAGTTGTATGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACAA
** * * * *
29225215 TTTCTAGATTGGTAAATATTTTATCACTCATTCAGTGAACTTCTTGTTGAGATAATAAATTGC-T
129 TTTCTAGATTGGCGAATATATTATCTCACATTCAGTGAACTTCTTGCTGAGATAATAAATT-CTT
* * * *
29225279 CTT-TTTTTTTTCTTACTCATCATGTTAGCCCAGTACACATCCAAATAGAG-TTTCAAATACGAC
193 TTTCTTTTTTTTCTGACTCATCATGTTGGCCCAGTACGCATCCAAATAGAGTTTTCAAATACGAC
* * *
29225342 TAAGTATAGGATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGAAGTGTTGGACAAATAAT
258 TAAGTACA-GATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGGACAAATAAT
29225407 GTTTAACT
322 GTTTAACT
*
29225415 ACAGGATCAAAGGTTTATCAGTCGACCCCATCATGAACTTAAGAGGATCTAATTTTGAAATCAAC
1 --AGGATCAAAGGTTTATCAGTCGACCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAAC
29225480 CAAGTTGTATGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACAA
64 CAAGTTGTATGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACAA
* * * * *
29225545 TTTCTCGATTGGCGAATATCTTATCTCGCATTCAGTGAACTTCTTGCTGAAATAATAAATTATTT
129 TTTCTAGATTGGCGAATATATTATCTCACATTCAGTGAACTTCTTGCTGAGATAATAAATT-CTT
* * *
29225610 TTTCTTTTTTTTCTGACTCATCATGTTGGCCCAATTCGCATCCAAATAGAGTTTTCAAATACGAT
193 TTTCTTTTTTTTCTGACTCATCATGTTGGCCCAGTACGCATCCAAATAGAGTTTTCAAATACGAC
*
29225675 TAAGTACAGAATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGGACAAATAAA
258 TAAGTACAG-ATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGGACAAATAAT
*
29225740 ATTTAACT
322 GTTTAACT
29225748 TTTTCAAAGG
Statistics
Matches: 604, Mismatches: 53, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
330 257 0.43
331 45 0.07
332 45 0.07
333 257 0.43
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (329 bp):
AGGATCAAAGGTTTATCAGTCGACCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAACCA
AGTTGTATGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACAATT
TCTAGATTGGCGAATATATTATCTCACATTCAGTGAACTTCTTGCTGAGATAATAAATTCTTTTT
CTTTTTTTTCTGACTCATCATGTTGGCCCAGTACGCATCCAAATAGAGTTTTCAAATACGACTAA
GTACAGATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGGACAAATAATGTTT
AACT
Found at i:29227441 original size:14 final size:15
Alignment explanation
Indices: 29227415--29227444 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29227405 AGGATTTTTA
29227415 TTTTATTTATTATTT
1 TTTTATTTATTATTT
29227430 TTTTATTT-TTATTT
1 TTTTATTTATTATTT
29227444 T
1 T
29227445 GAAATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTATTTATTATTT
Found at i:29229922 original size:2 final size:2
Alignment explanation
Indices: 29229915--29229950 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
29229905 TGGAAATAGG
29229915 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29229951 TCATAGATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29233549 original size:23 final size:23
Alignment explanation
Indices: 29233522--29233650 Score: 134
Period size: 23 Copynumber: 5.5 Consensus size: 23
29233512 GAACACTAGC
29233522 GTGCTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGTTTAGCACTGTGT
*
29233545 GTGCTCTCTGTTTAGCAC-GTCT
1 GTGCTCTCTGTTTAGCACTGTGT
*
29233567 CGTGCTCTCTATTTTTAGCACTGTGT
1 -GTGCTCTC--TGTTTAGCACTGTGT
** * *
29233593 GTGCTCTCTAATTAGTACTTTGT
1 GTGCTCTCTGTTTAGCACTGTGT
* * *
29233616 GTACTTTCTATTTAGCACTGTGT
1 GTGCTCTCTGTTTAGCACTGTGT
*
29233639 GTGCTCTTTGTT
1 GTGCTCTCTGTT
29233651 GCCCAGCACT
Statistics
Matches: 86, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
22 3 0.03
23 63 0.73
25 17 0.20
26 3 0.03
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.47
Consensus pattern (23 bp):
GTGCTCTCTGTTTAGCACTGTGT
Found at i:29234741 original size:19 final size:21
Alignment explanation
Indices: 29234699--29234743 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
29234689 GAAAACATAG
*
29234699 ACATA-TATATAGCAATATCA
1 ACATATTATATAGCAATAGCA
29234719 ACATATTAT-TAGCAA-AGCA
1 ACATATTATATAGCAATAGCA
29234738 ACATAT
1 ACATAT
29234744 AAAAAACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 11 0.48
21 3 0.13
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.29
Consensus pattern (21 bp):
ACATATTATATAGCAATAGCA
Found at i:29235573 original size:22 final size:22
Alignment explanation
Indices: 29235543--29235603 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
29235533 AAAATACATG
*
29235543 AATATAAATAATTAAATGAAGAC
1 AATA-AAATAATTAAATGAACAC
*
29235566 AATCAAATGCAATT-AAT-AACAC
1 AATAAAAT--AATTAAATGAACAC
29235588 AATAAAATAA-TAAATG
1 AATAAAATAATTAAATG
29235604 GGAGTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
19 1 0.03
20 5 0.16
22 15 0.48
23 6 0.19
24 4 0.13
ACGTcount: A:0.61, C:0.08, G:0.07, T:0.25
Consensus pattern (22 bp):
AATAAAATAATTAAATGAACAC
Found at i:29236008 original size:8 final size:8
Alignment explanation
Indices: 29235995--29236028 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
29235985 TAACAATAAG
29235995 ATAAAAAA
1 ATAAAAAA
29236003 ATAAAAAA
1 ATAAAAAA
29236011 ATAAAAAA
1 ATAAAAAA
29236019 A-AAATAAA
1 ATAAA-AAA
29236027 AT
1 AT
29236029 GTTAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 3 0.12
8 21 0.88
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
ATAAAAAA
Found at i:29236016 original size:16 final size:16
Alignment explanation
Indices: 29235989--29236028 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
29235979 AATAAATAAC
*
29235989 AATAAGATAAAAAAATA
1 AATAAAATAAAAAAA-A
29236006 AA-AAAATAAAAAAAA
1 AATAAAATAAAAAAAA
29236021 AATAAAAT
1 AATAAAAT
29236029 GTTAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 16 0.76
17 2 0.10
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (16 bp):
AATAAAATAAAAAAAA
Found at i:29236020 original size:19 final size:22
Alignment explanation
Indices: 29235978--29236027 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 22
29235968 AAATGACATG
29235978 AAATAAATAACAATAAGATAAAA
1 AAATAAA-AACAATAAGATAAAA
29236001 AAATAAAAA-AATAA-A-AAAA
1 AAATAAAAACAATAAGATAAAA
29236020 AAATAAAA
1 AAATAAAA
29236028 TGTTAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 12 0.44
20 1 0.04
21 5 0.19
22 2 0.07
23 7 0.26
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.14
Consensus pattern (22 bp):
AAATAAAAACAATAAGATAAAA
Found at i:29236106 original size:19 final size:19
Alignment explanation
Indices: 29236082--29236162 Score: 65
Period size: 19 Copynumber: 4.2 Consensus size: 19
29236072 TTAGACATGA
*
29236082 AAATAAATGAAAAATAAAT
1 AAATAAATAAAAAATAAAT
* *
29236101 AAATAAACAAAAAATCAAT
1 AAATAAATAAAAAATAAAT
** *
29236120 AAATTAAATCCAAAATAAAC
1 AAA-TAAATAAAAAATAAAT
*
29236140 AATTAAATATAAATAAT-AAT
1 AAATAAATA-AAA-AATAAAT
29236160 AAA
1 AAA
29236163 AAAGAAGACG
Statistics
Matches: 46, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
19 24 0.52
20 19 0.41
21 3 0.07
ACGTcount: A:0.70, C:0.06, G:0.01, T:0.22
Consensus pattern (19 bp):
AAATAAATAAAAAATAAAT
Found at i:29236223 original size:27 final size:27
Alignment explanation
Indices: 29236185--29236238 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
29236175 CTCCGAGCAA
*
29236185 ACCCGAAGGAAACCATAGGTCTCACAT
1 ACCCGAAAGAAACCATAGGTCTCACAT
*
29236212 ACCCGAAAGAAACCATGGGTCTCACAT
1 ACCCGAAAGAAACCATAGGTCTCACAT
29236239 CAAAACCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.37, C:0.30, G:0.19, T:0.15
Consensus pattern (27 bp):
ACCCGAAAGAAACCATAGGTCTCACAT
Found at i:29238887 original size:17 final size:18
Alignment explanation
Indices: 29238857--29238898 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
29238847 CAAAAGTTAT
29238857 TAAAATGTATAAT-ATTA
1 TAAAATGTATAATAATTA
29238874 TAAAATGT-TCAATAAATTA
1 TAAAATGTAT-AAT-AATTA
29238893 TAAAAT
1 TAAAAT
29238899 TTACTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.05
17 11 0.50
19 10 0.45
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (18 bp):
TAAAATGTATAATAATTA
Found at i:29239633 original size:30 final size:30
Alignment explanation
Indices: 29239598--29239654 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
29239588 TTTTTTATTC
** *
29239598 AATTTGATATTTAAACTTGACATTTTTCCT
1 AATTTGATACCTAAACTTGACACTTTTCCT
*
29239628 AATTTGGTACCTAAACTTGACACTTTT
1 AATTTGATACCTAAACTTGACACTTTT
29239655 ATTTTAAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.46
Consensus pattern (30 bp):
AATTTGATACCTAAACTTGACACTTTTCCT
Found at i:29239675 original size:32 final size:30
Alignment explanation
Indices: 29239608--29239677 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 30
29239598 AATTTGATAT
*
29239608 TTAAACTTGACATTTTTCCTAATTTGGTAC
1 TTAAACTTGACATTTTTCCTAAGTTGGTAC
* **
29239638 CTAAACTTGACACTTTTATTTTAAGTTGGTAC
1 TTAAACTTGACA-TTTT-TCCTAAGTTGGTAC
29239670 TTAAACTT
1 TTAAACTT
29239678 TTTGGGGTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 11 0.33
31 4 0.12
32 18 0.55
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.46
Consensus pattern (30 bp):
TTAAACTTGACATTTTTCCTAAGTTGGTAC
Found at i:29239982 original size:61 final size:59
Alignment explanation
Indices: 29239900--29240073 Score: 172
Period size: 60 Copynumber: 2.9 Consensus size: 59
29239890 AATTGAATCT
* * * *
29239900 AAAAAAAGCTTAGGTACCAAATTAGGAAAAAAAATGTTAAGTTCAAGTACCGAATTGGGTC
1 AAAAAAAG-TTAGGTAACAAATTA-GAAAAAAAATGTCAAGTTCAAGTACCAAATTAGGTC
* * *
29239961 CAAAAAAGTATAGGTAACAAATTAGAAAAAAATTGTCAAGTTCAGGTACCAAATTAGGTC
1 AAAAAAAGT-TAGGTAACAAATTAGAAAAAAAATGTCAAGTTCAAGTACCAAATTAGGTC
** * * *
29240021 AAATAAAAGTTTAAATACCAAAATA-AAAAAAAATATCAAGTTC-AGATACCAAA
1 AAA-AAAAG-TTAGGTAACAAATTAGAAAAAAAATGTCAAGTTCAAG-TACCAAA
29240074 AGTTATAGCC
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
59 1 0.01
60 57 0.61
61 35 0.37
62 1 0.01
ACGTcount: A:0.52, C:0.11, G:0.14, T:0.22
Consensus pattern (59 bp):
AAAAAAAGTTAGGTAACAAATTAGAAAAAAAATGTCAAGTTCAAGTACCAAATTAGGTC
Found at i:29240158 original size:2 final size:2
Alignment explanation
Indices: 29240151--29240205 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
29240141 TAACGACATC
*
29240151 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
29240193 AT GT AT AT A- AT AT
1 AT AT AT AT AT AT AT
29240206 TTTTAAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:29240250 original size:18 final size:18
Alignment explanation
Indices: 29240213--29240260 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
29240203 TATTTTTAAA
**
29240213 TAAATTTTATAATATTTTT
1 TAAATTTT-TAATAACTTT
29240232 TAAATTTTTAATAACTTT
1 TAAATTTTTAATAACTTT
*
29240250 TGAATCTTTTA
1 TAAAT-TTTTA
29240261 TATTTTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (18 bp):
TAAATTTTTAATAACTTT
Found at i:29240268 original size:18 final size:17
Alignment explanation
Indices: 29240224--29240277 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
29240214 AAATTTTATA
*
29240224 ATATTTTTTAAATTTTT
1 ATATTTTTTGAATTTTT
**
29240241 AATAACTTTTGAATCTTTT
1 -ATATTTTTTGAAT-TTTT
29240260 ATATTTTTTGAATTTTT
1 ATATTTTTTGAATTTTT
29240277 A
1 A
29240278 GAATTAGGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 5 0.17
18 21 0.70
19 4 0.13
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (17 bp):
ATATTTTTTGAATTTTT
Found at i:29240408 original size:23 final size:24
Alignment explanation
Indices: 29240369--29240416 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
29240359 TTTATTTGAT
29240369 AATATGTTTTGATATAACAAATTAA
1 AATATGTTTTGATATAA-AAATTAA
*
29240394 AATAT-TTTTGA-ATAAAAGTTAA
1 AATATGTTTTGATATAAAAATTAA
29240416 A
1 A
29240417 GTTAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 6 0.27
25 5 0.23
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (24 bp):
AATATGTTTTGATATAAAAATTAA
Found at i:29242369 original size:60 final size:60
Alignment explanation
Indices: 29242294--29242498 Score: 211
Period size: 60 Copynumber: 3.4 Consensus size: 60
29242284 AAATCAAGTG
* * * * *
29242294 TTGACCCCTAAACTTTCTAAAAATTTAGATTTAACCCTCATACTTTCCAAAAA-TTAAAT
1 TTGACCCCTAAACTTTCCAAAAATTCAAATTTAACCCTCAAACTTTCCAAAAATTTAGAT
* * * * * *
29242353 TTAGACCCCTATACTTTCCATAAATTCATATTTGACCATCAAACTTTCCAAAAATTTGGAT
1 TT-GACCCCTAAACTTTCCAAAAATTCAAATTTAACCCTCAAACTTTCCAAAAATTTAGAT
* * *
29242414 TTGACTCCCGT--AC-TTCTTAAAAATTCAAATTTAACCCTTAAATTTTCCAAAAATTTAGAT
1 TTGAC-CCC-TAAACTTTC-CAAAAATTCAAATTTAACCCTCAAACTTTCCAAAAATTTAGAT
*
29242474 TTGACCCTTAAACTTTCCAAAAATT
1 TTGACCCCTAAACTTTCCAAAAATT
29242499 ATGTTTTGGC
Statistics
Matches: 118, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
58 1 0.01
59 7 0.06
60 97 0.82
61 12 0.10
62 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.37
Consensus pattern (60 bp):
TTGACCCCTAAACTTTCCAAAAATTCAAATTTAACCCTCAAACTTTCCAAAAATTTAGAT
Found at i:29242407 original size:90 final size:90
Alignment explanation
Indices: 29242303--29242498 Score: 227
Period size: 90 Copynumber: 2.2 Consensus size: 90
29242293 GTTGACCCCT
* *
29242303 AAACTTTCTAAAAATTTAGATTTAAC-CCTCATACTT-TCCAAAAATT-AAATTTAGACCCCTAT
1 AAACTTTCCAAAAATTTAGATTTAACTCC-CATACTTCT-CAAAAATTCAAATTTA-ACCCCTAA
* *
29242365 ACTTTCCATAAATTCATATTTGACCATC
63 ACTTTCCAAAAATTCAGATTTGACCATC
* * * * * *
29242393 AAACTTTCCAAAAATTTGGATTTGACTCCCGTACTTCTTAAAAATTCAAATTTAACCCTTAAATT
1 AAACTTTCCAAAAATTTAGATTTAACTCCCATACTTCTCAAAAATTCAAATTTAACCCCTAAACT
* * *
29242458 TTCCAAAAATTTAGATTTGACCCTT
66 TTCCAAAAATTCAGATTTGACCATC
29242483 AAACTTTCCAAAAATT
1 AAACTTTCCAAAAATT
29242499 ATGTTTTGGC
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
90 80 0.89
91 10 0.11
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (90 bp):
AAACTTTCCAAAAATTTAGATTTAACTCCCATACTTCTCAAAAATTCAAATTTAACCCCTAAACT
TTCCAAAAATTCAGATTTGACCATC
Found at i:29242515 original size:29 final size:30
Alignment explanation
Indices: 29242294--29242519 Score: 167
Period size: 30 Copynumber: 7.6 Consensus size: 30
29242284 AAATCAAGTG
* *
29242294 TTGACCCCTAAACTTTCTAAAAATTTAGAT
1 TTGACCCTTAAACTTTCCAAAAATTTAGAT
* * * *
29242324 TTAACCCTCATACTTTCCAAAAA-TTAAAT
1 TTGACCCTTAAACTTTCCAAAAATTTAGAT
* * * * *
29242353 TTAGACCCCTATACTTTCCATAAATTCATAT
1 TT-GACCCTTAAACTTTCCAAAAATTTAGAT
* * *
29242384 TTGACCATCAAACTTTCCAAAAATTTGGAT
1 TTGACCCTTAAACTTTCCAAAAATTTAGAT
* * * *
29242414 TTGACTCCCGT--AC-TTCTTAAAAATTCAAAT
1 TTGA--CCCTTAAACTTTC-CAAAAATTTAGAT
* *
29242444 TTAACCCTTAAATTTTCCAAAAATTTAGAT
1 TTGACCCTTAAACTTTCCAAAAATTTAGAT
*
29242474 TTGACCCTTAAACTTTCCAAAAA-TTATGTT
1 TTGACCCTTAAACTTTCCAAAAATTTA-GAT
*
29242504 TTGGCCC-TAAACTTTC
1 TTGACCCTTAAACTTTC
29242520 TAAACTTTCA
Statistics
Matches: 150, Mismatches: 37, Indels: 19
0.73 0.18 0.09
Matches are distributed among these distances:
28 4 0.03
29 22 0.15
30 113 0.75
31 9 0.06
32 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (30 bp):
TTGACCCTTAAACTTTCCAAAAATTTAGAT
Found at i:29246888 original size:50 final size:50
Alignment explanation
Indices: 29246632--29247218 Score: 210
Period size: 49 Copynumber: 11.9 Consensus size: 50
29246622 AGTTGAAAAT
* * * * *
29246632 AACCCTATACCTTAAAAGATGTGATGGGAAAGATTGAGGCCGCAACGATG
1 AACCCTGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCCGTAACGACG
** * * * * * * *
29246682 AATTCGGTACCATA-AAGATATGAAAGGAAAGG-TTGAGGCTGCAACGACG
1 AACCCTGTACCTTAGAAGATGTG-ATGGGAAGGATTGAGGCCGTAACGACG
* ** * * *
29246731 AACCCTGTACCTTATAAGACATGATGGGAAAGATCGAGGCCGTAACAACG
1 AACCCTGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCCGTAACGACG
* * * * * * * * * *
29246781 GA-TCTAGCACCAT-GAA-A-ATAAAGGGAAAGG-TTGAGGCCGCAA-GTGCA
1 AACCCT-GTACCTTAGAAGATGTGATGGG-AAGGATTGAGGCCGTAACG-ACG
* **
29246828 AACCCTGTACCTTAAAAGATGTGATGGGAAGGATTGAGGCCGTAACGGTG
1 AACCCTGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCCGTAACGACG
* * * * **
29246878 AA-TCTAGTACCAT-GAAGATATGAAGGGAAAGG-TTGAGATCGTAACGACG
1 AACCCT-GTACCTTAGAAGATGTGATGGG-AAGGATTGAGGCCGTAACGACG
* * *** *
29246927 AACCCTGTACCTTAGAAGATGTAATAGGAAGGATTGAGGCTACAACGGCG
1 AACCCTGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCCGTAACGACG
* * * * * * * *
29246977 AATCCGGTACCATAGAA-ATATAAAGGGAAAGG-CTGAGGCCGCAACGACG
1 AACCCTGTACCTTAGAAGATGTGATGGG-AAGGATTGAGGCCGTAACGACG
* ** * *
29247026 AA-CTTGATATCC-TAGAA-ACATGATGGGAAAGATTGAGGCTGTAACGACG
1 AACCCTG-TA-CCTTAGAAGATGTGATGGGAAGGATTGAGGCCGTAACGACG
* * * * * * * ** *
29247075 AA-TCTAATACCATGGAA-ATATAAAGGGAAAGG-TTGAGGCCACAACGGCG
1 AACCCT-GTACCTTAGAAGATGTGATGGG-AAGGATTGAGGCCGTAACGACG
* * **
29247124 AA-CCTGGTACCTTAGAA-ACGTGATGGGAAAGG-TTGAGGCCGCAACGATA
1 AACCCT-GTACCTTAGAAGATGTGATGGG-AAGGATTGAGGCCGTAACGACG
* * * * *
29247173 AACCTTGTCCCTTAGAAGATGTGACGGGAAGGATCGAGGCCATAAC
1 AACCCTGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCCGTAAC
29247219 TGCAGATCTA
Statistics
Matches: 391, Mismatches: 119, Indels: 54
0.69 0.21 0.10
Matches are distributed among these distances:
47 23 0.06
48 15 0.04
49 216 0.55
50 136 0.35
51 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (50 bp):
AACCCTGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCCGTAACGACG
Found at i:29246946 original size:99 final size:98
Alignment explanation
Indices: 29246632--29247170 Score: 529
Period size: 99 Copynumber: 5.5 Consensus size: 98
29246622 AGTTGAAAAT
* * * * * *
29246632 AACCCTATACCTTAAAAGATGTGATGGGAAAGATTGAGGCCGCAACGATGAAT-TCGGTACCATA
1 AACCCTGTACCTTAGAAGACGTGATGGGAAAGATTGAGGCCGCAACGACGAATCT-AGTACCATG
*
29246696 AAGATATGAAA-GGAAAGGTTGAGGCTGCAACGACG
65 AA-ATAT-AAAGGGAAAGGTTGAGGCCGCAACGACG
* * * * * * *
29246731 AACCCTGTACCTTATAAGACATGATGGGAAAGATCGAGGCCGTAACAACGGATCTAGCACCATGA
1 AACCCTGTACCTTAGAAGACGTGATGGGAAAGATTGAGGCCGCAACGACGAATCTAGTACCATGA
* *
29246796 AA-ATAAAGGGAAAGGTTGAGGCCGCAA-GTGCA
66 AATATAAAGGGAAAGGTTGAGGCCGCAACG-ACG
* * * * **
29246828 AACCCTGTACCTTAAAAGATGTGATGGGAAGGATTGAGGCCGTAACGGTGAATCTAGTACCATGA
1 AACCCTGTACCTTAGAAGACGTGATGGGAAAGATTGAGGCCGCAACGACGAATCTAGTACCATGA
* ** *
29246893 AGATATGAAGGGAAAGGTTGAGATCGTAACGACG
66 A-ATATAAAGGGAAAGGTTGAGGCCGCAACGACG
* * * * ** * **
29246927 AACCCTGTACCTTAGAAGATGTAATAGGAAGGATTGAGGCTACAACGGCGAATCCGGTACCATAG
1 AACCCTGTACCTTAGAAGACGTGATGGGAAAGATTGAGGCCGCAACGACGAATCTAGTACCAT-G
*
29246992 AAATATAAAGGGAAAGGCTGAGGCCGCAACGACG
65 AAATATAAAGGGAAAGGTTGAGGCCGCAACGACG
* * * * *
29247026 AA-CTTGATATCC-TAGAA-ACATGATGGGAAAGATTGAGGCTGTAACGACGAATCTAATACCAT
1 AACCCTG-TA-CCTTAGAAGACGTGATGGGAAAGATTGAGGCCGCAACGACGAATCTAGTACCAT
* *
29247088 GGAAATATAAAGGGAAAGGTTGAGGCCACAACGGCG
64 -GAAATATAAAGGGAAAGGTTGAGGCCGCAACGACG
*
29247124 AA-CCTGGTACCTTAGAA-ACGTGATGGGAAAGGTTGAGGCCGCAACGA
1 AACCCT-GTACCTTAGAAGACGTGATGGGAAAGATTGAGGCCGCAACGA
29247171 TAAACCTTGT
Statistics
Matches: 363, Mismatches: 66, Indels: 23
0.80 0.15 0.05
Matches are distributed among these distances:
96 4 0.01
97 79 0.22
98 108 0.30
99 165 0.45
100 7 0.02
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.18
Consensus pattern (98 bp):
AACCCTGTACCTTAGAAGACGTGATGGGAAAGATTGAGGCCGCAACGACGAATCTAGTACCATGA
AATATAAAGGGAAAGGTTGAGGCCGCAACGACG
Found at i:29247177 original size:49 final size:49
Alignment explanation
Indices: 29246653--29247170 Score: 224
Period size: 49 Copynumber: 10.6 Consensus size: 49
29246643 TTAAAAGATG
* * * * * *
29246653 TGATGGGAAAGATTGAGGCCGCAACGATGAA-TTCGGTACCATA-AAGATA
1 TGATGGGAAAGGTTGAGGCCGCAACGACGAACCT-GATACCTTAGAA-ACA
** * *
29246702 TGAAAGGAAAGGTTGAGGCTGCAACGACGAACCCTG-TACCTTATAAGACA
1 TGATGGGAAAGGTTGAGGCCGCAACGACGAA-CCTGATACCTTAGAA-ACA
* * * * * * * *
29246752 TGATGGGAAAGATCGAGGCCGTAACAACGGATCT-AGCACCAT-GAAA-A
1 TGATGGGAAAGGTTGAGGCCGCAACGACGAACCTGA-TACCTTAGAAACA
* * * * *
29246799 TAAAGGGAAAGGTTGAGGCCGCAA-GTGCAAACCCTG-TACCTTA-AAAGA
1 TGATGGGAAAGGTTGAGGCCGCAACG-ACGAA-CCTGATACCTTAGAAACA
* ** * * *
29246847 TGTGATGGG-AAGGATTGAGGCCGTAACGGTGAATCT-AGTACCAT-GAAGATA
1 --TGATGGGAAAGG-TTGAGGCCGCAACGACGAACCTGA-TACCTTAGAA-ACA
* ** * *
29246898 TGAAGGGAAAGGTTGAGATCGTAACGACGAACCCTG-TACCTTAG-AAGA
1 TGATGGGAAAGGTTGAGGCCGCAACGACGAA-CCTGATACCTTAGAAACA
* ** * * * *
29246946 TGTAATAGG-AAGGATTGAGGCTACAACGGCGAATCC-GGTACCATAGAAATA
1 TG--ATGGGAAAGG-TTGAGGCCGCAACGACGAA-CCTGATACCTTAGAAACA
* * * *
29246997 TAAAGGGAAAGGCTGAGGCCGCAACGACGAACTTGATATCC-TAGAAACA
1 TGATGGGAAAGGTTGAGGCCGCAACGACGAACCTGATA-CCTTAGAAACA
* * * * * * * *
29247046 TGATGGGAAAGATTGAGGCTGTAACGACGAATCTAATACCATGGAAATA
1 TGATGGGAAAGGTTGAGGCCGCAACGACGAACCTGATACCTTAGAAACA
* * * * * *
29247095 TAAAGGGAAAGGTTGAGGCCACAACGGCGAACCTGGTACCTTAGAAACG
1 TGATGGGAAAGGTTGAGGCCGCAACGACGAACCTGATACCTTAGAAACA
29247144 TGATGGGAAAGGTTGAGGCCGCAACGA
1 TGATGGGAAAGGTTGAGGCCGCAACGA
29247171 TAAACCTTGT
Statistics
Matches: 340, Mismatches: 98, Indels: 62
0.68 0.20 0.12
Matches are distributed among these distances:
47 29 0.09
48 11 0.03
49 195 0.57
50 97 0.29
51 8 0.02
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.18
Consensus pattern (49 bp):
TGATGGGAAAGGTTGAGGCCGCAACGACGAACCTGATACCTTAGAAACA
Found at i:29247603 original size:114 final size:114
Alignment explanation
Indices: 29247388--29247683 Score: 371
Period size: 114 Copynumber: 2.6 Consensus size: 114
29247378 ACCTTAAAGT
* * * *
29247388 TACAGTAGAATGGAGTGAGACTTCAAACCCCATCTTCCTCG-TGAGGTATAGAGAAGTGGGTCAA
1 TACAATAGAATGGAGTGAGACTTCAAATCCCATCTTCCT-GATGAGGTATAGAAAAGTGGGTTAA
* * * *
29247452 AACAGTATGTTAAATCAAAATAATGAAGTTGAGCTCAACGTCCCTGAGGA
65 AACAGTATGTTAAATCAAAACAACGAAGTCGAGCTCAACGTCCATGAGGA
* * * *
29247502 TACAATGGAATGGGGTGAGACTTCAAATCTCATCTTCCTGATGAGGTATAGAAAAGTGGGTTAAG
1 TACAATAGAATGGAGTGAGACTTCAAATCCCATCTTCCTGATGAGGTATAGAAAAGTGGGTTAAA
* * *
29247567 ACAGTATGTTGAATCAAAACAGCGAAGTCGATCTCAACGTCCATGAGGA
66 ACAGTATGTTAAATCAAAACAACGAAGTCGAGCTCAACGTCCATGAGGA
* * * * * *
29247616 TACAGTAGAGTGAAGTGAGACTTTAAATCCCATCTTCCT-AGTGAGGTACAAAAAAGTGGGTTAA
1 TACAATAGAATGGAGTGAGACTTCAAATCCCATCTTCCTGA-TGAGGTATAGAAAAGTGGGTTAA
29247680 AACA
65 AACA
29247684 AATAGCGAAT
Statistics
Matches: 155, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
113 2 0.01
114 153 0.99
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (114 bp):
TACAATAGAATGGAGTGAGACTTCAAATCCCATCTTCCTGATGAGGTATAGAAAAGTGGGTTAAA
ACAGTATGTTAAATCAAAACAACGAAGTCGAGCTCAACGTCCATGAGGA
Found at i:29249484 original size:30 final size:30
Alignment explanation
Indices: 29249431--29249539 Score: 94
Period size: 30 Copynumber: 3.6 Consensus size: 30
29249421 GAAATTTCTT
* * *
29249431 TTTGACCCCCAAA-TTATCCAAAAATTAAGT
1 TTTGACCCTCAAACTT-TCTAAAAATTAAGA
* *
29249461 TTTGACCCTCAAACTTTCTAAAAAATATGGA
1 TTTGACCCTCAAACTTTCTAAAAATTA-AGA
** * *
29249492 TTTGACCCTCGTACTTCCTAAAAATTCAGA
1 TTTGACCCTCAAACTTTCTAAAAATTAAGA
* *
29249522 TTTAACCGTCAAACTTTC
1 TTTGACCCTCAAACTTTC
29249540 CTTAGATCCC
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
30 36 0.59
31 25 0.41
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (30 bp):
TTTGACCCTCAAACTTTCTAAAAATTAAGA
Found at i:29249626 original size:60 final size:59
Alignment explanation
Indices: 29249547--29249697 Score: 169
Period size: 60 Copynumber: 2.5 Consensus size: 59
29249537 TTCCTTAGAT
* * * * *
29249547 CCCTGTACTTTCCATAAATTCGTATTTGACCTTTAAACTTTCTAAAAATTTGGATTTGA
1 CCCTGTACTTTCCAAAAATTCGTATTTGACCTTCAAACTTCCCAAAAATTTGGATTTAA
* *
29249606 CCCTCGTACTTTCCAAAAATTCAG-ATTTGACCCTCAAACTTCCCAAAAATTTTGATTTAA
1 CCCT-GTACTTTCCAAAAATTC-GTATTTGACCTTCAAACTTCCCAAAAATTTGGATTTAA
** * * *
29249666 CCCTAAACTTTCCAAAATTTTGTTTTTGACCT
1 CCCTGTACTTTCCAAAAATTCGTATTTGACCT
29249698 CATTTTTCCT
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
58 1 0.01
59 24 0.32
60 50 0.66
61 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (59 bp):
CCCTGTACTTTCCAAAAATTCGTATTTGACCTTCAAACTTCCCAAAAATTTGGATTTAA
Found at i:29249673 original size:29 final size:30
Alignment explanation
Indices: 29249553--29249696 Score: 132
Period size: 30 Copynumber: 4.8 Consensus size: 30
29249543 AGATCCCTGT
* * * *
29249553 ACTTTCCATAAA-TTCGTATTTGACCTTTAA
1 ACTTTCCAAAAATTTTG-ATTTGACCCTCAA
* * **
29249583 ACTTTCTAAAAATTTGGATTTGACCCTCGT
1 ACTTTCCAAAAATTTTGATTTGACCCTCAA
**
29249613 ACTTTCCAAAAATTCAGATTTGACCCTCAA
1 ACTTTCCAAAAATTTTGATTTGACCCTCAA
* *
29249643 ACTTCCCAAAAATTTTGATTTAACCCT-AA
1 ACTTTCCAAAAATTTTGATTTGACCCTCAA
*
29249672 ACTTTCC-AAAATTTTGTTTTTGACC
1 ACTTTCCAAAAATTTTG-ATTTGACC
29249697 TCATTTTTCC
Statistics
Matches: 93, Mismatches: 19, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
28 9 0.10
29 14 0.15
30 67 0.72
31 3 0.03
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (30 bp):
ACTTTCCAAAAATTTTGATTTGACCCTCAA
Found at i:29271295 original size:116 final size:116
Alignment explanation
Indices: 29271091--29271322 Score: 428
Period size: 116 Copynumber: 2.0 Consensus size: 116
29271081 AGCTAAAGAA
* * *
29271091 TCTCTTAAACATATCTCTATGTCAATTCAACCGATTAATTAACAATCATAAGCATGTAAAGGATC
1 TCTCTTAAAAATATCTCTATGCCAATTCAACCGACTAATTAACAATCATAAGCATGTAAAGGATC
*
29271156 AAGTGAAGTAACAATCATATCTCTATGTTGAAACAATTTAATCACAAAAAT
66 AAGTGAAGTAACAATCATATCTCTATATTGAAACAATTTAATCACAAAAAT
29271207 TCTCTTAAAAATATCTCTATGCCAATTCAACCGACTAATTAACAATCATAAGCATGTAAAGGATC
1 TCTCTTAAAAATATCTCTATGCCAATTCAACCGACTAATTAACAATCATAAGCATGTAAAGGATC
29271272 AAGTGAAGTAACAATCATATCTCTATATTGAAACAATTTAATCACAAAAAT
66 AAGTGAAGTAACAATCATATCTCTATATTGAAACAATTTAATCACAAAAAT
29271323 CCTACAAGTT
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 112 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (116 bp):
TCTCTTAAAAATATCTCTATGCCAATTCAACCGACTAATTAACAATCATAAGCATGTAAAGGATC
AAGTGAAGTAACAATCATATCTCTATATTGAAACAATTTAATCACAAAAAT
Found at i:29274020 original size:24 final size:24
Alignment explanation
Indices: 29273993--29274042 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
29273983 TCAACAAGTG
29273993 TCCATAAAATTTAAACATGTAAAT
1 TCCATAAAATTTAAACATGTAAAT
29274017 TCCATAAAATTTAAACATGTAAAT
1 TCCATAAAATTTAAACATGTAAAT
29274041 TC
1 TC
29274043 AATCATTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.34
Consensus pattern (24 bp):
TCCATAAAATTTAAACATGTAAAT
Found at i:29287529 original size:6 final size:6
Alignment explanation
Indices: 29287518--29287555 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
29287508 ACCAAACCTT
* *
29287518 ATCTTG ATCTTG ATCTTG ATCTTT ATCTTG ATATTG AT
1 ATCTTG ATCTTG ATCTTG ATCTTG ATCTTG ATCTTG AT
29287556 GGACATCCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.53
Consensus pattern (6 bp):
ATCTTG
Found at i:29292943 original size:154 final size:154
Alignment explanation
Indices: 29292694--29292993 Score: 528
Period size: 154 Copynumber: 1.9 Consensus size: 154
29292684 GGGCATGGTG
* *
29292694 TTTCGAGGTCTTCACACTAAAGAACATTGTTTCTTTTCTTTGGTCTTAAAATCCTTTGTATATAT
1 TTTCGAAGTCTTCACACGAAAGAACATTGTTTCTTTTCTTTGGTCTTAAAATCCTTTGTATATAT
* *
29292759 AAGATTGAAGAGCGTTTGGAAAACTTTTGAAAAGGATATTCGATTTCCGTGAATTACGAAAATCA
66 AAGATTGAAGAGCATTTGGAAAACTGTTGAAAAGGATATTCGATTTCCGTGAATTACGAAAATCA
29292824 CACTTAACTCGTTAAAGTGCGATT
131 CACTTAACTCGTTAAAGTGCGATT
* *
29292848 TTTCGAAGTTTTCACACGAAAGAATATTGTTTCTTTTCTTTGGTCTTAAAATCCTTTGTATATAT
1 TTTCGAAGTCTTCACACGAAAGAACATTGTTTCTTTTCTTTGGTCTTAAAATCCTTTGTATATAT
* *
29292913 AAGATTTAAGAGCATTTGGAAAACTGTTGAAAAGGATATTCGATTTGCGTGAATTACGAAAATCA
66 AAGATTGAAGAGCATTTGGAAAACTGTTGAAAAGGATATTCGATTTCCGTGAATTACGAAAATCA
29292978 CACTTAACTCGTTAAA
131 CACTTAACTCGTTAAA
29292994 ATGCAATCCT
Statistics
Matches: 138, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
154 138 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.37
Consensus pattern (154 bp):
TTTCGAAGTCTTCACACGAAAGAACATTGTTTCTTTTCTTTGGTCTTAAAATCCTTTGTATATAT
AAGATTGAAGAGCATTTGGAAAACTGTTGAAAAGGATATTCGATTTCCGTGAATTACGAAAATCA
CACTTAACTCGTTAAAGTGCGATT
Found at i:29293468 original size:29 final size:28
Alignment explanation
Indices: 29293435--29293495 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
29293425 AAACGGGACC
* *
29293435 TTTGAATGCCTGGGGGTGAAATGGTAATT
1 TTTGAATGCC-GGGGGTAAAATGATAATT
* **
29293464 TTTGACTTTCGGGGGTAAAATGATAATT
1 TTTGAATGCCGGGGGTAAAATGATAATT
29293492 TTTG
1 TTTG
29293496 GTGAAATCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 20 0.74
29 7 0.26
ACGTcount: A:0.25, C:0.07, G:0.30, T:0.39
Consensus pattern (28 bp):
TTTGAATGCCGGGGGTAAAATGATAATT
Found at i:29293542 original size:29 final size:29
Alignment explanation
Indices: 29293509--29293658 Score: 71
Period size: 29 Copynumber: 5.2 Consensus size: 29
29293499 AAATCAAAGT
29293509 TAAAAATGGGATTTTAGAAAGTTTAAGGG
1 TAAAAATGGGATTTTAGAAAGTTTAAGGG
** * **
29293538 T-AAAATGATAATTTTTGGTGAAA---TCGGGG
1 TAAAAATG-GGA-TTTT--AGAAAGTTTAAGGG
* *
29293567 TTAAAAATGGGATTTTGGAAAGTTTAGGGG
1 T-AAAAATGGGATTTTAGAAAGTTTAAGGG
** *
29293597 T-AAAATGTAATTTTTAGTAAA-ATT-AGGG
1 TAAAAATGGGA-TTTTAG-AAAGTTTAAGGG
* * *
29293625 TTAAAATGGGATTTTGGAAAGTTTGAGGG
1 TAAAAATGGGATTTTAGAAAGTTTAAGGG
29293654 TAAAA
1 TAAAA
29293659 TGGTAATTTT
Statistics
Matches: 88, Mismatches: 19, Indels: 28
0.65 0.14 0.21
Matches are distributed among these distances:
27 7 0.08
28 24 0.27
29 33 0.38
30 14 0.16
31 6 0.07
32 4 0.05
ACGTcount: A:0.38, C:0.01, G:0.27, T:0.34
Consensus pattern (29 bp):
TAAAAATGGGATTTTAGAAAGTTTAAGGG
Found at i:29293545 original size:59 final size:59
Alignment explanation
Indices: 29293475--29293816 Score: 476
Period size: 59 Copynumber: 5.8 Consensus size: 59
29293465 TTGACTTTCG
* * * * *
29293475 GGGGTAAAATGATAATTTTTGGTGAAATCAAAGTTAAAAATGGGATTTTAGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTA
* * * *
29293534 AGGGTAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTA
* *
29293593 GGGGTAAAAT-GTAATTTTTAGTAAAAT-TAGGGTT-AAAATGGGATTTTGGAAAGTTT-
1 GGGGTAAAATGGTAATTTTTAGTGAAATCGA-GGTTAAAAATGGGATTTTGGAAAGTTTA
*
29293649 GAGGGTAAAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTG
1 G-GGGTAAAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTA
* * * *
29293709 GGGGTAAAATGGTAATTTTTGGTTAAATCGAGGTTAAAAATGGAATTTTGGAATGTTTA
1 GGGGTAAAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTA
* *
29293768 GGGGTAAAATGGTAATTTTTAGTGAAATCGAGGTTAAAATTGGAATTTT
1 GGGGTAAAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGGGATTTT
29293817 AGGGAGTTTG
Statistics
Matches: 256, Mismatches: 21, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
56 1 0.00
57 31 0.12
58 38 0.15
59 185 0.72
60 1 0.00
ACGTcount: A:0.36, C:0.01, G:0.27, T:0.35
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTA
Found at i:29293654 original size:116 final size:116
Alignment explanation
Indices: 29293475--29293816 Score: 472
Period size: 116 Copynumber: 2.9 Consensus size: 116
29293465 TTGACTTTCG
* * ** *
29293475 GGGGTAAAATGATAATTTTTGGTGAAATCAAAGTTAAAAATGGGATTTTAGAAAGTTTAAGGGTA
1 GGGGTAAAATG-TAATTTTTGGTAAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTT-AGGGTA
* * *
29293540 AAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
64 AAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTA
*
29293593 GGGGTAAAATGTAATTTTTAGTAAAATTAGGGTT-AAAATGGGATTTTGGAAAGTTTGAGGGTAA
1 GGGGTAAAATGTAATTTTTGGTAAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTT-AGGGTAA
*
29293657 AATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTG
65 AATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTA
* * * *
29293709 GGGGTAAAATGGTAATTTTTGGTTAAA-TCGAGGTTAAAAATGGAATTTTGGAATGTTTAGGGGT
1 GGGGTAAAAT-GTAATTTTTGGTAAAATTAG-GGTTAAAAATGGGATTTTGGAAAGTTTA-GGGT
* *
29293773 AAAATGGTAATTTTTAGTGAAATCGAGGTTAAAATTGGAATTTT
63 AAAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGGGATTTT
29293817 AGGGAGTTTG
Statistics
Matches: 202, Mismatches: 18, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
116 88 0.44
117 37 0.18
118 77 0.38
ACGTcount: A:0.36, C:0.01, G:0.27, T:0.35
Consensus pattern (116 bp):
GGGGTAAAATGTAATTTTTGGTAAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGTAAA
ATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTA
Found at i:29293769 original size:175 final size:176
Alignment explanation
Indices: 29293476--29293795 Score: 516
Period size: 175 Copynumber: 1.8 Consensus size: 176
29293466 TGACTTTCGG
*
29293476 GGGTAAAATGATAATTTTTGGTGAAATCAAAGTTAAAAATGGGATTTTAGAAAGTTTAAGGGTAA
1 GGGTAAAATGATAATTTTTAGTGAAATCAAAGTTAAAAATGGGATTTTAGAAAGTTTAAGGGTAA
* *
29293541 AATGATAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAAT-GT
66 AATGATAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGT
29293605 AATTTTTAGTAAAATTAGGGTTAAAATGGGATTTTGGAAAGTTTGA
131 AATTTTTAGTAAAATTAGGGTTAAAATGGGATTTTGGAAAGTTTGA
* * * * **
29293651 GGGTAAAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTGGGGGTAA
1 GGGTAAAATGATAATTTTTAGTGAAATCAAAGTTAAAAATGGGATTTTAGAAAGTTTAAGGGTAA
* * *
29293716 AATGGTAATTTTTGGTTAAATCGAGGTTAAAAATGGAATTTTGGAATGTTTAGGGGTAAAATGGT
66 AATGATAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGT
*
29293781 AATTTTTAGTGAAAT
131 AATTTTTAGTAAAAT
29293796 CGAGGTTAAA
Statistics
Matches: 131, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
175 115 0.88
176 16 0.12
ACGTcount: A:0.36, C:0.01, G:0.27, T:0.35
Consensus pattern (176 bp):
GGGTAAAATGATAATTTTTAGTGAAATCAAAGTTAAAAATGGGATTTTAGAAAGTTTAAGGGTAA
AATGATAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGT
AATTTTTAGTAAAATTAGGGTTAAAATGGGATTTTGGAAAGTTTGA
Found at i:29293807 original size:30 final size:28
Alignment explanation
Indices: 29293534--29293816 Score: 118
Period size: 29 Copynumber: 9.6 Consensus size: 28
29293524 AGAAAGTTTA
*
29293534 AGGGTAAAATGATAATTTTTGGTGAAATCG
1 AGGGTAAAATG-GAATTTTT-GTGAAATCG
* **
29293564 -GGGTTAAAAATGGGA-TTTTG-GAAAGTTT
1 AGGG-T-AAAATGGAATTTTTGTGAAA-TCG
* * *
29293592 AGGGGTAAAATGTAATTTTTAGTAAAAT-T
1 A-GGGTAAAATGGAATTTTT-GTGAAATCG
* *
29293621 AGGGTTAAAATGGGA-TTTTG-GAAAGTTTG
1 AGGG-TAAAATGGAATTTTTGTGAAA--TCG
29293650 AGGGTAAAATGGTAATTTTTAGTGAAATCG
1 AGGGTAAAATGG-AATTTTT-GTGAAATCG
* * *
29293680 AGGTTAAAAATGGGA-TTTTG-GAAAGTTTG
1 AGGGT-AAAATGGAATTTTTGTGAAA--TCG
* *
29293709 GGGGTAAAATGGTAATTTTTGGTTAAATCG
1 AGGGTAAAATGG-AATTTTT-GTGAAATCG
* * **
29293739 AGGTTAAAAATGGAA-TTTTG-GAATGTTT
1 AGGGT-AAAATGGAATTTTTGTGAA-ATCG
29293767 AGGGGTAAAATGGTAATTTTTAGTGAAATCG
1 A-GGGTAAAATGG-AATTTTT-GTGAAATCG
*
29293798 AGGTTAAAATTGGAATTTT
1 AGGGTAAAA-TGGAATTTT
29293817 AGGGAGTTTG
Statistics
Matches: 190, Mismatches: 32, Indels: 62
0.67 0.11 0.22
Matches are distributed among these distances:
26 3 0.02
27 11 0.06
28 43 0.23
29 46 0.24
30 46 0.24
31 31 0.16
32 10 0.05
ACGTcount: A:0.35, C:0.01, G:0.28, T:0.36
Consensus pattern (28 bp):
AGGGTAAAATGGAATTTTTGTGAAATCG
Found at i:29293898 original size:86 final size:85
Alignment explanation
Indices: 29293744--29293912 Score: 216
Period size: 86 Copynumber: 2.0 Consensus size: 85
29293734 AATCGAGGTT
* * * *
29293744 AAAAATGGAATTTTGGAATGTTTAGGGGTAAAATGGTAATTTTTAGTGAAATCGAGGTTAAAATT
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAG-GAAATCAAGGTCAAAAAT
29293809 GGAATTTTAGGG-AGTTTGGTC
65 GGAATTTT-GGGAAGTTTGGTC
* * * *
29293830 AAAAATGGGATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTA-GAAGTTTAAGGGTCAAAAA
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAGGAA-ATCAA-GGTCAAAAA
29293894 TGGAATTTTGGGAAGTTTG
64 TGGAATTTTGGGAAGTTTG
29293913 AGGACTAGAG
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
84 3 0.04
85 5 0.07
86 64 0.89
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (85 bp):
AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAGGAAATCAAGGTCAAAAATG
GAATTTTGGGAAGTTTGGTC
Found at i:29293909 original size:30 final size:28
Alignment explanation
Indices: 29293803--29293912 Score: 98
Period size: 27 Copynumber: 3.9 Consensus size: 28
29293793 AATCGAGGTT
*
29293803 AAAATTGGAATTTTAGGG-AGTTT-GGTC
1 AAAAATGGAATTTT-GGGAAGTTTGGGTC
* * **
29293830 AAAAATGGGATTTTGGAAAGTTTGGGGG
1 AAAAATGGAATTTTGGGAAGTTTGGGTC
* **
29293858 TAAAATGGTAATTTTTAGAAGTTTAAGGGTC
1 AAAAATGG-AATTTTGGGAAGTTT--GGGTC
29293889 AAAAATGGAATTTTGGGAAGTTTG
1 AAAAATGGAATTTTGGGAAGTTTG
29293913 AGGACTAGAG
Statistics
Matches: 63, Mismatches: 15, Indels: 9
0.72 0.17 0.10
Matches are distributed among these distances:
26 2 0.03
27 17 0.27
28 10 0.16
29 11 0.17
30 13 0.21
31 10 0.16
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.35
Consensus pattern (28 bp):
AAAAATGGAATTTTGGGAAGTTTGGGTC
Found at i:29294949 original size:23 final size:23
Alignment explanation
Indices: 29294888--29294960 Score: 58
Period size: 26 Copynumber: 3.0 Consensus size: 23
29294878 ATTTCCTTTT
*
29294888 TTATTAAATATTTATTTA-TTATCA
1 TTATTAAATA-TTA-TTAGTTATTA
*
29294912 TTAATAATATTTATTATTAGTTATTA
1 TTATTAA-A--TATTATTAGTTATTA
* *
29294938 TTATTAAATATTAATAGATATTA
1 TTATTAAATATTATTAGTTATTA
29294961 AGAGCATTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
23 13 0.32
24 6 0.15
25 5 0.12
26 14 0.35
27 2 0.05
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (23 bp):
TTATTAAATATTATTAGTTATTA
Found at i:29295746 original size:11 final size:11
Alignment explanation
Indices: 29295714--29295768 Score: 58
Period size: 11 Copynumber: 5.1 Consensus size: 11
29295704 TAAATGTATT
29295714 TAAATTTAAAA
1 TAAATTTAAAA
*
29295725 CAAATTT-AAA
1 TAAATTTAAAA
29295735 TAAATTTAAAA
1 TAAATTTAAAA
* * *
29295746 TTAATTCAAAC
1 TAAATTTAAAA
*
29295757 TTAATTTAAAA
1 TAAATTTAAAA
29295768 T
1 T
29295769 CCAAGTTGGG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
10 9 0.25
11 27 0.75
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:29295751 original size:21 final size:22
Alignment explanation
Indices: 29295714--29295768 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
29295704 TAAATGTATT
* *
29295714 TAAATTTAAAACAAATTTAAA-
1 TAAATTTAAAATAAATTCAAAC
*
29295735 TAAATTTAAAATTAATTCAAAC
1 TAAATTTAAAATAAATTCAAAC
*
29295757 TTAATTTAAAAT
1 TAAATTTAAAAT
29295769 CCAAGTTGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTTAAAATAAATTCAAAC
Found at i:29295991 original size:12 final size:12
Alignment explanation
Indices: 29295968--29296001 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
29295958 ATACTAAACC
29295968 TTATCTTGATCT
1 TTATCTTGATCT
* *
29295980 TGATCTTTATCT
1 TTATCTTGATCT
29295992 TTATCTTGAT
1 TTATCTTGAT
29296002 GTTGATGGAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.59
Consensus pattern (12 bp):
TTATCTTGATCT
Found at i:29296231 original size:21 final size:22
Alignment explanation
Indices: 29296207--29296252 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
29296197 GTTTGTTTAG
**
29296207 AATTTTAGGTTTTTTA-AAAAC
1 AATTTTAGAATTTTTAGAAAAC
29296228 AA-TTTAGAATTTTTAGAAAAC
1 AATTTTAGAATTTTTAGAAAAC
29296249 AATT
1 AATT
29296253 AATAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 11 0.52
21 9 0.43
22 1 0.05
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (22 bp):
AATTTTAGAATTTTTAGAAAAC
Found at i:29296261 original size:20 final size:20
Alignment explanation
Indices: 29296217--29296261 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
29296207 AATTTTAGGT
*
29296217 TTTTTAAAAACAATTTAGAA
1 TTTTTAAAAACAATTAAGAA
*
29296237 TTTTTAGAAAACAATTAATAA
1 TTTTTA-AAAACAATTAAGAA
29296258 TTTT
1 TTTT
29296262 ATGATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (20 bp):
TTTTTAAAAACAATTAAGAA
Found at i:29302985 original size:2 final size:2
Alignment explanation
Indices: 29302980--29303011 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29302970 TATATATATA
29302980 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
29303012 AGGTTCGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:29303754 original size:18 final size:18
Alignment explanation
Indices: 29303733--29303786 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
29303723 GAGTGAGGAG
*
29303733 AGGTTGAAATGTGAGTTT
1 AGGTTGAGATGTGAGTTT
29303751 AGGTTGAGATGTGAGTTT
1 AGGTTGAGATGTGAGTTT
*
29303769 AGGTTGAGATTTGAGTTT
1 AGGTTGAGATGTGAGTTT
29303787 GGTCATCGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (18 bp):
AGGTTGAGATGTGAGTTT
Found at i:29318130 original size:8 final size:8
Alignment explanation
Indices: 29318119--29318164 Score: 65
Period size: 8 Copynumber: 5.8 Consensus size: 8
29318109 AAAGAGAAAG
29318119 AGAGAGCA
1 AGAGAGCA
*
29318127 AGAGCGCA
1 AGAGAGCA
*
29318135 AGAGCGCA
1 AGAGAGCA
*
29318143 AGAGCGCA
1 AGAGAGCA
29318151 AGAGAGCA
1 AGAGAGCA
29318159 AGAGAG
1 AGAGAG
29318165 AGAGTATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.43, C:0.17, G:0.39, T:0.00
Consensus pattern (8 bp):
AGAGAGCA
Found at i:29318138 original size:16 final size:16
Alignment explanation
Indices: 29318119--29318162 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
29318109 AAAGAGAAAG
29318119 AGAGAGCAAGAGCGCA
1 AGAGAGCAAGAGCGCA
*
29318135 AGAGCGCAAGAGCGCA
1 AGAGAGCAAGAGCGCA
29318151 AGAGAGCAAGAG
1 AGAGAGCAAGAG
29318163 AGAGAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.43, C:0.18, G:0.39, T:0.00
Consensus pattern (16 bp):
AGAGAGCAAGAGCGCA
Found at i:29319181 original size:3 final size:3
Alignment explanation
Indices: 29319173--29319202 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
29319163 AAAGTGTAAA
29319173 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29319203 TGAATATACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:29328365 original size:21 final size:21
Alignment explanation
Indices: 29328330--29328384 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
29328320 AAAAATTTAA
29328330 AAATATATAAATACATAAAAAT
1 AAATATAT-AATACATAAAAAT
* *
29328352 TAATATATAATACATATAAAT
1 AAATATATAATACATAAAAAT
*
29328373 AAATAAATAATA
1 AAATATATAATA
29328385 GACAAAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATATATAATACATAAAAAT
Found at i:29330198 original size:24 final size:24
Alignment explanation
Indices: 29330143--29330198 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
29330133 TAGACTAATA
** *
29330143 AGAGTTTAACTGAAATAAATAAAT
1 AGAGTTTATTTGAAACAAATAAAT
*
29330167 AGATTTTATTTGAAACAAATAAAT
1 AGAGTTTATTTGAAACAAATAAAT
*
29330191 AGGGTTTA
1 AGAGTTTA
29330199 ACTCGAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.04, G:0.14, T:0.34
Consensus pattern (24 bp):
AGAGTTTATTTGAAACAAATAAAT
Found at i:29330491 original size:22 final size:23
Alignment explanation
Indices: 29330460--29330506 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
29330450 ACCTGCATCT
*
29330460 AAAAGAGAACCTCTTTTCAACAA
1 AAAAGAGAACCTCTCTTCAACAA
29330483 AAAAG-GAACCTCTCTTCAACAA
1 AAAAGAGAACCTCTCTTCAACAA
29330505 AA
1 AA
29330507 CAGTCATACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.49, C:0.23, G:0.09, T:0.19
Consensus pattern (23 bp):
AAAAGAGAACCTCTCTTCAACAA
Found at i:29332333 original size:23 final size:23
Alignment explanation
Indices: 29332300--29332356 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
29332290 CGGGGAGTAC
* *
29332300 CAAAGTACTAAACAGATAGCACA
1 CAAAGTGCTAAACAGAGAGCACA
** *
29332323 CGCAGTGCTAAACAGAGAGTACA
1 CAAAGTGCTAAACAGAGAGCACA
29332346 CAAAGTGCTAA
1 CAAAGTGCTAA
29332357 TAATGGAGAG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.14
Consensus pattern (23 bp):
CAAAGTGCTAAACAGAGAGCACA
Found at i:29334981 original size:24 final size:24
Alignment explanation
Indices: 29334953--29335011 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
29334943 TAGACTAATA
29334953 AGAGTTTAACTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
29334977 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
29335001 AAAGTTTAACT
1 AGAGTTTAACT
29335012 CGAAGAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:29335313 original size:25 final size:25
Alignment explanation
Indices: 29335253--29335313 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
29335243 TAAATATACT
* *
29335253 AAAAATATTAAAATAAATGTTTACCA
1 AAAAAT-TTTAAATAAATGTTTACAA
* *
29335279 ACAAATTTTAAATAAATTTTTA-AA
1 AAAAATTTTAAATAAATGTTTACAA
29335303 AAAAATCTTTA
1 AAAAAT-TTTA
29335314 CACTTAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 6 0.21
25 18 0.62
26 5 0.17
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (25 bp):
AAAAATTTTAAATAAATGTTTACAA
Found at i:29342770 original size:23 final size:24
Alignment explanation
Indices: 29342741--29342793 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
29342731 AGAGTGCCAT
*
29342741 TTAGAATAAAGAAGAAAACTCCTC
1 TTAGAATAAAGAAAAAAACTCCTC
29342765 -TAGAATAAAGAAAAAAACTCCTC
1 TTAGAATAAAGAAAAAAACTCCTC
29342788 TTAGAA
1 TTAGAA
29342794 CCCTTCCCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.53, C:0.15, G:0.11, T:0.21
Consensus pattern (24 bp):
TTAGAATAAAGAAAAAAACTCCTC
Found at i:29351008 original size:53 final size:53
Alignment explanation
Indices: 29350895--29350999 Score: 135
Period size: 53 Copynumber: 2.0 Consensus size: 53
29350885 GATATTTATG
* * * *
29350895 TTATTTTTCAATCAGTTTGATTTTTTATTTTGTATAACACTTTGTTATTTGAA
1 TTATTTTTCAATCAGTTTCACTTTTTATTTTGTATAACACTTCGTTATTTCAA
* *
29350948 TTATTTTTCTATCGGTTTCACTTTTTATTTTGTAT-A-A-TTCGTTATTTCAA
1 TTATTTTTCAATCAGTTTCACTTTTTATTTTGTATAACACTTCGTTATTTCAA
29350998 TT
1 TT
29351000 CAATTTTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
50 13 0.28
51 1 0.02
52 1 0.02
53 31 0.67
ACGTcount: A:0.22, C:0.10, G:0.09, T:0.60
Consensus pattern (53 bp):
TTATTTTTCAATCAGTTTCACTTTTTATTTTGTATAACACTTCGTTATTTCAA
Found at i:29354332 original size:36 final size:36
Alignment explanation
Indices: 29354256--29354490 Score: 217
Period size: 36 Copynumber: 6.6 Consensus size: 36
29354246 ATGGCTTTAT
* * * *
29354256 GCTCTAATCGAGACATAAGTAGTCA-ATTAGCATTAC
1 GCTCTAATCGAGACGTAAGCAATTACA-TAGCATTAC
* * * * *
29354292 GCTCTAACCGAGACGTAAGAAATTACATAGTAATAA
1 GCTCTAATCGAGACGTAAGCAATTACATAGCATTAC
* *
29354328 GCTCTAATCGAGATGTATA-CAATCACATAGCATTAC
1 GCTCTAATCGAGACGTA-AGCAATTACATAGCATTAC
* *
29354364 GCTCTAATCGAGA-GTAAGCAATCT-CTTAGCATTAT
1 GCTCTAATCGAGACGTAAGCAAT-TACATAGCATTAC
* * *
29354399 GCTCTAATCGAGACGTAAGAAATTACATAGCAATAT
1 GCTCTAATCGAGACGTAAGCAATTACATAGCATTAC
* * * * * *
29354435 GCTCTAACCGAGAAGTATGCACTCACATAGTATTAC
1 GCTCTAATCGAGACGTAAGCAATTACATAGCATTAC
29354471 GCTCTAATCGAGACGTAAGC
1 GCTCTAATCGAGACGTAAGC
29354491 TTTCCATAGA
Statistics
Matches: 160, Mismatches: 33, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
34 1 0.01
35 30 0.19
36 127 0.79
37 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (36 bp):
GCTCTAATCGAGACGTAAGCAATTACATAGCATTAC
Found at i:29354470 original size:107 final size:108
Alignment explanation
Indices: 29354256--29354490 Score: 337
Period size: 107 Copynumber: 2.2 Consensus size: 108
29354246 ATGGCTTTAT
* * * **
29354256 GCTCTAATCGAGACATAAGTAGTCAATTAGCATTACGCTCTAACCGAGACGTAAGAAATTACATA
1 GCTCTAATCGAGACGTAAGCAATCTCTTAGCATTACGCTCTAACCGAGACGTAAGAAATTACATA
* * *
29354321 GTAATAAGCTCTAATCGAGATGTATACAATCACATAGCATTAC
66 GCAATAAGCTCTAACCGAGAAGTATACAATCACATAGCATTAC
* *
29354364 GCTCTAATCGAGA-GTAAGCAATCTCTTAGCATTATGCTCTAATCGAGACGTAAGAAATTACATA
1 GCTCTAATCGAGACGTAAGCAATCTCTTAGCATTACGCTCTAACCGAGACGTAAGAAATTACATA
* * * *
29354428 GCAATATGCTCTAACCGAGAAGTATGCACTCACATAGTATTAC
66 GCAATAAGCTCTAACCGAGAAGTATACAATCACATAGCATTAC
29354471 GCTCTAATCGAGACGTAAGC
1 GCTCTAATCGAGACGTAAGC
29354491 TTTCCATAGA
Statistics
Matches: 112, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
107 93 0.83
108 19 0.17
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (108 bp):
GCTCTAATCGAGACGTAAGCAATCTCTTAGCATTACGCTCTAACCGAGACGTAAGAAATTACATA
GCAATAAGCTCTAACCGAGAAGTATACAATCACATAGCATTAC
Found at i:29360133 original size:17 final size:17
Alignment explanation
Indices: 29360113--29360154 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
29360103 TACTTTGAGA
29360113 TTAAATTTATCTTAAAT
1 TTAAATTTATCTTAAAT
* *
29360130 TTAAATGTATTTTAAAT
1 TTAAATTTATCTTAAAT
29360147 TT-AATTTA
1 TTAAATTTA
29360155 AGTTTGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAAATTTATCTTAAAT
Found at i:29360135 original size:6 final size:6
Alignment explanation
Indices: 29360124--29360178 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
29360114 TAAATTTATC
* * * *
29360124 TTAAAT TTAAAT GT-ATT TTAAAT TT-AAT TTAAGT TTGAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
29360169 TTAAAT TTAA
1 TTAAAT TTAA
29360179 TATTATTATA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
5 13 0.33
6 26 0.67
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:29360149 original size:45 final size:45
Alignment explanation
Indices: 29360093--29360197 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 45
29360083 GGCCTAAACC
* * *
29360093 ATTTTTAATTTACTTTGAGATTAAATTT-ATCTTAAATTTAA-ATGT
1 ATTTTAAATTTAATTTAAGATTAAATTTAAT-TTAAATTTAATAT-T
* *
29360138 ATTTTAAATTTAATTTAAGTTTGAATTTAATTTAAATTTAATATT
1 ATTTTAAATTTAATTTAAGATTAAATTTAATTTAAATTTAATATT
*
29360183 ATTATAAATTTAATT
1 ATTTTAAATTTAATT
29360198 AAATCCAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
45 48 0.92
46 4 0.08
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (45 bp):
ATTTTAAATTTAATTTAAGATTAAATTTAATTTAAATTTAATATT
Found at i:29360154 original size:11 final size:11
Alignment explanation
Indices: 29360127--29360201 Score: 59
Period size: 11 Copynumber: 6.8 Consensus size: 11
29360117 ATTTATCTTA
*
29360127 AATTTAAATGT
1 AATTTAAATTT
*
29360138 ATTTTAAATTT
1 AATTTAAATTT
*
29360149 AATTTAAGTTT
1 AATTTAAATTT
29360160 GAATTT-AATTT
1 -AATTTAAATTT
29360171 AAATTT-AATATT
1 -AATTTAAAT-TT
29360183 -ATTATAAATTT
1 AATT-TAAATTT
29360194 AA-TTAAAT
1 AATTTAAAT
29360202 CCAAAAGTCC
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
10 8 0.15
11 34 0.64
12 11 0.21
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:29360192 original size:28 final size:28
Alignment explanation
Indices: 29360113--29360201 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 28
29360103 TACTTTGAGA
* * *
29360113 TTAAATTT-ATCTTAAATTTAAATGTATT
1 TTAAATTTAAT-TTAAGTTTAAATTTAAT
*
29360141 TTAAATTTAATTTAAGTTTGAATTTAAT
1 TTAAATTTAATTTAAGTTTAAATTTAAT
29360169 TTAAATTTAATATT-A-TTATAAATTTAA-
1 TTAAATTTAAT-TTAAGTT-TAAATTTAAT
29360196 TTAAAT
1 TTAAAT
29360202 CCAAAAGTCC
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
27 8 0.15
28 41 0.77
29 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (28 bp):
TTAAATTTAATTTAAGTTTAAATTTAAT
Found at i:29361805 original size:10 final size:10
Alignment explanation
Indices: 29361790--29361814 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29361780 CGTGGATCGG
29361790 CCCGATCCGA
1 CCCGATCCGA
29361800 CCCGATCCGA
1 CCCGATCCGA
29361810 CCCGA
1 CCCGA
29361815 CCTAGGATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.52, G:0.20, T:0.08
Consensus pattern (10 bp):
CCCGATCCGA
Found at i:29362258 original size:30 final size:29
Alignment explanation
Indices: 29362192--29362425 Score: 181
Period size: 29 Copynumber: 7.9 Consensus size: 29
29362182 GGAGCTCCTT
** *
29362192 AAACTATCCAAAAATTGTATTTTGACCCCT-
1 AAACT-TCCAAAAATTACATTTTTA-CCCTA
* *
29362222 AAACTTCAAAAAATTCCATTTTTATCCCTA
1 AAACTTCCAAAAATTACATTTTTA-CCCTA
* *
29362252 AAACTTCCAAAAATTACAATTTTACCCTC
1 AAACTTCCAAAAATTACATTTTTACCCTA
*
29362281 AAACTTCCAAAAAATT-CTATTTTTAACCCCA
1 AAACTTCC-AAAAATTAC-ATTTTT-ACCCTA
* * *
29362312 AAACTTTTC-AAAATTACATTTCTACCCTT
1 AAAC-TTCCAAAAATTACATTTTTACCCTA
* * *
29362341 GAACTTCCAAAAATTCCATTTTGA-CCTCA
1 AAACTTCCAAAAATTACATTTTTACCCT-A
* * *
29362370 AAATTTCCCAAAATTACATTTTTACCCCA
1 AAACTTCCAAAAATTACATTTTTACCCTA
* *
29362399 AAA-TTTCAAAAATTTCATTTTTGACCC
1 AAACTTCCAAAAATTACATTTTT-ACCC
29362426 CGATACTTTC
Statistics
Matches: 163, Mismatches: 31, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
28 22 0.13
29 78 0.48
30 51 0.31
31 9 0.06
32 3 0.02
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTACCCTA
Done.