Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold211
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: 2157208
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 20444 characters in sequence are not A, C, G, or T
File 9 of 15
Found at i:1264070 original size:15 final size:14
Alignment explanation
Indices: 1264030--1264070 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
1264020 AAAAGTATAG
1264030 ATAATATTAAATAC
1 ATAATATTAAATAC
1264044 A-ATATATT-AATAC
1 ATA-ATATTAAATAC
1264057 ATAATATGTAAATA
1 ATAATAT-TAAATA
1264071 AAATCATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.48
14 8 0.35
15 4 0.17
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (14 bp):
ATAATATTAAATAC
Found at i:1266648 original size:65 final size:62
Alignment explanation
Indices: 1266515--1266655 Score: 142
Period size: 65 Copynumber: 2.2 Consensus size: 62
1266505 TAAATTATTT
** *
1266515 CAAATCTAAAATAATCAGAACTTGAAAAAAATTATAACTTAAATAGTCAGAATTAAATTGTTC
1 CAAATCTAAAATAATCAGAACTTGAAAAAAATTATAACTTAAATAGTCAGAACCAAATAG-TC
* * * *
1266578 TAAATCTAAAATAATCCA-AACTTGAAAAAAAAATTATAACTTAAATGGTTAGAGCCCAAGATAG
1 CAAATCTAAAATAAT-CAGAACTTG--AAAAAAATTATAACTTAAATAGTCAGA-ACCAA-ATAG
1266642 -C
61 TC
1266643 CAAATCTGAAAAT
1 CAAATCT-AAAAT
1266656 CAAATTAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
63 20 0.31
64 2 0.03
65 32 0.50
66 7 0.11
67 3 0.05
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.27
Consensus pattern (62 bp):
CAAATCTAAAATAATCAGAACTTGAAAAAAATTATAACTTAAATAGTCAGAACCAAATAGTC
Found at i:1266711 original size:16 final size:16
Alignment explanation
Indices: 1266672--1266755 Score: 107
Period size: 17 Copynumber: 5.2 Consensus size: 16
1266662 AAAAGATAAA
1266672 TAAATTTAAAAT-ATT
1 TAAATTTAAAATAATT
* *
1266687 TATACTTAAAATAATT
1 TAAATTTAAAATAATT
1266703 TAAATTTAAAATAAATT
1 TAAATTTAAAAT-AATT
*
1266720 TTAATTTAAAATAATT
1 TAAATTTAAAATAATT
*
1266736 AAAATCTTAAAATAATT
1 TAAAT-TTAAAATAATT
1266753 TAA
1 TAA
1266756 TTCGAATCCG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
15 10 0.17
16 20 0.34
17 28 0.48
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTTAAAATAATT
Found at i:1266734 original size:33 final size:31
Alignment explanation
Indices: 1266672--1266757 Score: 111
Period size: 33 Copynumber: 2.7 Consensus size: 31
1266662 AAAAGATAAA
*
1266672 TAAATTTAAAAT-ATTTATACTTAAAATAATT
1 TAAATTTAAAATAATTTA-ATTTAAAATAATT
1266703 TAAATTTAAAATAAATTTTAATTTAAAATAATT
1 TAAATTTAAAAT-AA-TTTAATTTAAAATAATT
*
1266736 AAAATCTTAAAATAATTTAATT
1 TAAAT-TTAAAATAATTTAATT
1266758 CGAATCCGCT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
31 12 0.24
32 7 0.14
33 19 0.39
34 11 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (31 bp):
TAAATTTAAAATAATTTAATTTAAAATAATT
Found at i:1268660 original size:13 final size:13
Alignment explanation
Indices: 1268644--1268668 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1268634 TATTCAAATT
1268644 TTAATTAATTAAG
1 TTAATTAATTAAG
1268657 TTAATTAATTAA
1 TTAATTAATTAA
1268669 TTCAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TTAATTAATTAAG
Found at i:1269353 original size:109 final size:109
Alignment explanation
Indices: 1269168--1269598 Score: 415
Period size: 109 Copynumber: 4.0 Consensus size: 109
1269158 ATTGATCTCA
* * * * *
1269168 AAATAAATCATTGTCTAGAGTCGCAAAACGGCATACAAACGCCTTTTACATAAGAAAATTCATTT
1 AAATAAATCATCGTCTAGAGTCGTAAAACAGCATACAAACGCCCTTTACATAAGATAATTCATTT
* * * *
1269233 TCGTATCAATTACGTAATATTCGGGCACTAAAGGATTGACCTTG
66 TTGTATTAATTACGTAATATTCGGGCACCAAAAGATTGACCTTG
* * * * * ** * *
1269277 AAATAAATCATTGTCTAGAGTCGTAAAACGGCGTACGAATGCTTTTTACATAGGACAATTCATTT
1 AAATAAATCATCGTCTAGAGTCGTAAAACAGCATACAAACGCCCTTTACATAAGATAATTCATTT
* * * * *
1269342 TTGTATTAATTACGTAATATTCGGGCACCCAAGGATTGGCCCTA
66 TTGTATTAATTACGTAATATTCGGGCACCAAAAGATTGACCTTG
** * *
1269386 AAATAAATCATCGTCTAGAGTCGTAAAACAGCAT-TGAACGCCCTTTATATAAGATAATTTATTT
1 AAATAAATCATCGTCTAGAGTCGTAAAACAGCATACAAACGCCCTTTACATAAGATAATTCATTT
* * *
1269450 TTGCATTAATTACGTAA-ATTTC-GACACCAAAAGATTGA-CTCCG
66 TTGTATTAATTACGTAATA-TTCGGGCACCAAAAGATTGACCT-TG
** ** * ** * * * *
1269493 AAATAGGTCATCGTCTAGAGTTATAAAGCAGTGTACAAATGCTCTTTATATAGGATAATTCATTT
1 AAATAAATCATCGTCTAGAGTCGTAAAACAGCATACAAACGCCCTTTACATAAGATAATTCATTT
1269558 TT-TACATTAATTACGT-ATATTCGGGCACCAAAAGATTGACC
66 TTGT--ATTAATTACGTAATATTCGGGCACCAAAAGATTGACC
1269599 CCGAAAAAGG
Statistics
Matches: 266, Mismatches: 48, Indels: 15
0.81 0.15 0.05
Matches are distributed among these distances:
106 1 0.00
107 40 0.15
108 71 0.27
109 153 0.58
110 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (109 bp):
AAATAAATCATCGTCTAGAGTCGTAAAACAGCATACAAACGCCCTTTACATAAGATAATTCATTT
TTGTATTAATTACGTAATATTCGGGCACCAAAAGATTGACCTTG
Found at i:1269580 original size:216 final size:218
Alignment explanation
Indices: 1269167--1269595 Score: 510
Period size: 216 Copynumber: 2.0 Consensus size: 218
1269157 AATTGATCTC
* * *
1269167 AAAATAAATCATTGTCTAGAGTCGCAAAACGGCATACAAACGCCTTTTACATAAGAAAATTCATT
1 AAAATAAATCATCGTCTAGAGTCGCAAAACAGCATACAAACGCCCTTTACATAAGAAAATTCATT
* * * * * *
1269232 TTCGTATCAATTACGTAATATTCGGGCACTAAAGGATTGACCTTGAAATAAATCATTGTCTAGAG
66 TTCGCATCAATTACGTAATATTCGGACACCAAAAGATTGACCTCGAAATAAATCATCGTCTAGAG
* * * *
1269297 TCGTAAAACGGCGTACGAATGCTTTTTACATAGGACAATTCATTTTTGTATTAATTACGTAATAT
131 TCATAAAACAGCGTACAAATGCTCTTTACATAGGACAATTCATTTTTGTATTAATTACGTAATAT
* *
1269362 TCGGGCACCCAAGGATTGGCCCT
196 TCGGGCACCAAAAGATTGGCCCT
* ** * * *
1269385 AAAATAAATCATCGTCTAGAGTCGTAAAACAGCAT-TGAACGCCCTTTATATAAGATAATTTATT
1 AAAATAAATCATCGTCTAGAGTCGCAAAACAGCATACAAACGCCCTTTACATAAGAAAATTCATT
* * **
1269449 TTTGCATTAATTACGTAA-ATTTC-GACACCAAAAGATTGA-CTCCGAAATAGGTCATCGTCTAG
66 TTCGCATCAATTACGTAATA-TTCGGACACCAAAAGATTGACCT-CGAAATAAATCATCGTCTAG
* * * * *
1269511 AGTTATAAAGCAGTGTACAAATGCTCTTTATATAGGATAATTCATTTTT-TACATTAATTACGT-
129 AGTCATAAAACAGCGTACAAATGCTCTTTACATAGGACAATTCATTTTTGT--ATTAATTACGTA
1269574 ATATTCGGGCACCAAAAGATTG
192 ATATTCGGGCACCAAAAGATTG
1269596 ACCCCGAAAA
Statistics
Matches: 177, Mismatches: 30, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
215 3 0.02
216 90 0.51
217 52 0.29
218 32 0.18
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (218 bp):
AAAATAAATCATCGTCTAGAGTCGCAAAACAGCATACAAACGCCCTTTACATAAGAAAATTCATT
TTCGCATCAATTACGTAATATTCGGACACCAAAAGATTGACCTCGAAATAAATCATCGTCTAGAG
TCATAAAACAGCGTACAAATGCTCTTTACATAGGACAATTCATTTTTGTATTAATTACGTAATAT
TCGGGCACCAAAAGATTGGCCCT
Found at i:1269637 original size:109 final size:108
Alignment explanation
Indices: 1269212--1269697 Score: 364
Period size: 109 Copynumber: 4.5 Consensus size: 108
1269202 ACAAACGCCT
* * * * * * **
1269212 TTTACATAAGAAAATTCATTTTCGT-ATCAATTACGTAATATTCGGGCACTAAAGGATTGACCTT
1 TTTATATAAGATAATTCATTTT-TTCATTAATTACGTAATATTCGGGCACCAAAAGATTGACCCC
* * * * *
1269276 GAAATAA-ATCATTGTCTAGAGTCGTAAAACGG-CGTACGAATGCTT
65 GAAA-AAGATCATCGTCTAGAGTCAT-AAA-GGATGTACGAACGCTC
* * * * * *
1269321 TTTACATAGGACAATTCATTTTTGT-ATTAATTACGTAATATTCGGGCACCCAAGGATTG-GCCC
1 TTTATATAAGATAATTCATTTTT-TCATTAATTACGTAATATTCGGGCACCAAAAGATTGACCCC
* * * ** * * *
1269384 TAAAATAAATCATCGTCTAGAGTCGTAAAACA-GCATTGAACGCCC
65 GAAAA-AGATCATCGTCTAGAGTCATAAAGGATGTA-CGAACGCTC
* * * *
1269429 TTTATATAAGATAATTTATTTTTGCATTAATTACGTAA-ATTTC-GACACCAAAAGATTGACTCC
1 TTTATATAAGATAATTCATTTTTTCATTAATTACGTAATA-TTCGGGCACCAAAAGATTGACCCC
* * * * * *
1269492 GAAATAGGTCATCGTCTAGAGTTATAAAGCAGTGTACAAATGCTC
65 GAAAAAGATCATCGTCTAGAGTCATAAAGGA-TGTACGAACGCTC
*
1269537 TTTATATAGGATAATTCATTTTTTACATTAATTACGT-ATATTCGGGCACCAAAAGATTGACCCC
1 TTTATATAAGATAATTCATTTTTT-CATTAATTACGTAATATTCGGGCACCAAAAGATTGACCCC
* * *
1269601 GAAAAAGGTCATCGTCTAAAGTCATAAAGTGATGTACGCACG-TCC
65 GAAAAAGATCATCGTCTAGAGTCATAAAG-GATGTACGAACGCT-C
* ** *
1269646 TTTATATAAGATAACTCA-TTTTTCATGTAAATTACACAATATTCCGGCACCA
1 TTTATATAAGATAATTCATTTTTTCAT-T-AATTACGTAATATTCGGGCACCA
1269698 TGGAATTGGC
Statistics
Matches: 302, Mismatches: 57, Indels: 35
0.77 0.14 0.09
Matches are distributed among these distances:
107 40 0.13
108 90 0.30
109 158 0.52
110 14 0.05
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (108 bp):
TTTATATAAGATAATTCATTTTTTCATTAATTACGTAATATTCGGGCACCAAAAGATTGACCCCG
AAAAAGATCATCGTCTAGAGTCATAAAGGATGTACGAACGCTC
Found at i:1272849 original size:18 final size:18
Alignment explanation
Indices: 1272822--1272865 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1272812 AAATTCAAAT
*
1272822 TTAAAAATTATCTATTTC
1 TTAAAAATTATCCATTTC
*
1272840 TTAAAGATTATCCATTTC
1 TTAAAAATTATCCATTTC
1272858 TTAAAAAT
1 TTAAAAAT
1272866 GACTTAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.45
Consensus pattern (18 bp):
TTAAAAATTATCCATTTC
Found at i:1276059 original size:34 final size:34
Alignment explanation
Indices: 1276002--1276220 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 34
1275992 GCCTGTTGTT
*
1276002 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1276035 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1276069 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
1276103 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1276137 ATTATCGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1276171 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
1276205 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1276221 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 17 0.11
34 142 0.89
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:1276177 original size:102 final size:101
Alignment explanation
Indices: 1276002--1276220 Score: 339
Period size: 102 Copynumber: 2.2 Consensus size: 101
1275992 GCCTGTTGTT
** * * * * *
1276002 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATCGATTAAATGGGTGATTTGGTGGCTTA
1276067 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1276103 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATCGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATCGATTAAATGGGTGATTTGGTGGCTT
* * *
1276168 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1276205 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1276221 TGGTTTTTAC
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATCGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:1280684 original size:34 final size:34
Alignment explanation
Indices: 1280627--1280845 Score: 253
Period size: 34 Copynumber: 6.5 Consensus size: 34
1280617 AAGTGGGAGA
* *
1280627 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACT
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1280660 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1280694 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
1280728 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1280762 ATTATCGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
1280796 ATTGTTGACTAAAT-GATAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
*
1280830 ATTATTGATTAAATGG
1 ATTGTTGATTAAATGG
1280846 TGGTTTTTAC
Statistics
Matches: 157, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
33 16 0.10
34 140 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:1280778 original size:102 final size:101
Alignment explanation
Indices: 1280627--1280845 Score: 312
Period size: 102 Copynumber: 2.2 Consensus size: 101
1280617 AAGTGGGAGA
** * * * * * *
1280627 ATTGTTGATTAAATGGTGATTTGGTAGTTTACTATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATCGATTAAATGGGTGATTTGGTGGCTTA
*
1280692 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGAGAGATTTGGTAGCTTACC
1280728 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATCGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATCGATTAAATGGGTGATTTGGTGGCTT
* * *
1280793 ACCATTGTTGACTAAATGATAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGAGAGATTTGGTAGCTTACC
*
1280830 ATTATTGATTAAATGG
1 ATTGTTGATTAAATGG
1280846 TGGTTTTTAC
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 16 0.15
102 88 0.85
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATCGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGAGAGATTTGGTAGCTTACC
Found at i:1285699 original size:22 final size:23
Alignment explanation
Indices: 1285671--1285721 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
1285661 TAATTATAAA
1285671 TAATTTTTTTA-AAAAATAAAAT
1 TAATTTTTTTATAAAAATAAAAT
**
1285693 TAA-TTTTTTATAAAAATTTAAT
1 TAATTTTTTTATAAAAATAAAAT
1285715 TAATTTT
1 TAATTTT
1285722 AAATCAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.28
22 15 0.60
23 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TAATTTTTTTATAAAAATAAAAT
Found at i:1289195 original size:22 final size:22
Alignment explanation
Indices: 1289163--1289204 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1289153 TAAAATAACC
1289163 TAAACTCAATTAATCTAAATGT
1 TAAACTCAATTAATCTAAATGT
* *
1289185 TAAACTTAATTAATGTAAAT
1 TAAACTCAATTAATCTAAAT
1289205 CCAAAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.38
Consensus pattern (22 bp):
TAAACTCAATTAATCTAAATGT
Found at i:1291914 original size:2 final size:2
Alignment explanation
Indices: 1291907--1291953 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1291897 GACCAAGTGT
1291907 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1291949 TA TA T
1 TA TA T
1291954 GAAATTTGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1295223 original size:22 final size:21
Alignment explanation
Indices: 1295180--1295226 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
1295170 ATTTAACAAT
*
1295180 ATTTACTTAAATTATAATATA
1 ATTTACTTAAATTATAAGATA
* *
1295201 ATTTAGTTAGAATTTTAAGATA
1 ATTTACTTA-AATTATAAGATA
1295223 ATTT
1 ATTT
1295227 TAAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (21 bp):
ATTTACTTAAATTATAAGATA
Found at i:1295853 original size:16 final size:16
Alignment explanation
Indices: 1295787--1295853 Score: 64
Period size: 16 Copynumber: 4.2 Consensus size: 16
1295777 CGAAAGTCTT
1295787 AATTTAAAAAAATTCA
1 AATTTAAAAAAATTCA
* * *
1295803 AACTCAAAAAAATTCG
1 AATTTAAAAAAATTCA
* * *
1295819 AATGTGAGAAAA-TCTA
1 AATTTAAAAAAATTC-A
1295835 AATTTAAAAAAATTCA
1 AATTTAAAAAAATTCA
1295851 AAT
1 AAT
1295854 AAAATCTAAA
Statistics
Matches: 37, Mismatches: 12, Indels: 4
0.70 0.23 0.08
Matches are distributed among these distances:
15 2 0.05
16 33 0.89
17 2 0.05
ACGTcount: A:0.58, C:0.09, G:0.06, T:0.27
Consensus pattern (16 bp):
AATTTAAAAAAATTCA
Found at i:1297415 original size:15 final size:15
Alignment explanation
Indices: 1297395--1297435 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 15
1297385 CTCATGATAT
1297395 TTTATATTTATTTTA
1 TTTATATTTATTTTA
1297410 TTTATA-TTATTTTA
1 TTTATATTTATTTTA
1297424 --TAT-TTTATTTTA
1 TTTATATTTATTTTA
1297436 GCTCACTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 11 0.44
14 8 0.32
15 6 0.24
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATATTTATTTTA
Found at i:1297698 original size:16 final size:18
Alignment explanation
Indices: 1297677--1297739 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 18
1297667 AATAAGATTA
1297677 TTATATAATTTTA-T-AT
1 TTATATAATTTTATTAAT
1297693 TTATATAAATATTTATTAAT
1 TTATAT-AAT-TTTATTAAT
1297713 TTAT-TAA-TTT-TTAAT
1 TTATATAATTTTATTAAT
1297728 TT-TAGTAATTTT
1 TTATA-TAATTTT
1297740 GTAATTACGT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
14 1 0.03
15 7 0.17
16 12 0.30
17 6 0.15
18 6 0.15
19 2 0.05
20 6 0.15
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTATATAATTTTATTAAT
Found at i:1297923 original size:15 final size:15
Alignment explanation
Indices: 1297898--1297949 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
1297888 TCGATATAAC
*
1297898 TCAATTTTAAAAAAT
1 TCAAATTTAAAAAAT
*
1297913 TTAAATTTAAAAATAT
1 TCAAATTTAAAAA-AT
1297929 TCAAATTTAAAATAAT
1 TCAAATTTAAAA-AAT
1297945 TCAAA
1 TCAAA
1297950 ACTTAACTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 11 0.34
16 20 0.62
17 1 0.03
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (15 bp):
TCAAATTTAAAAAAT
Found at i:1302646 original size:88 final size:88
Alignment explanation
Indices: 1302497--1302690 Score: 343
Period size: 88 Copynumber: 2.2 Consensus size: 88
1302487 TTGCAGAAAA
1302497 ACCAACACAAAGCGAAAGCAAAAGCGAAAGCCCAAGCTCGTAAAGTAAAAAGGGTTAGCCGATTA
1 ACCAACACAAAGCGAAAGCAAAAGCGAAAGCCCAAGCTCGTAAAGTAAAAAGGGTTAGCCGATTA
*
1302562 GGGACAGGGCAGGTCATTTACTT
66 GGGACAGGGCAGGTCATTAACTT
* *
1302585 ACCAACACAAAGCGAAAGCAAAAGCGAAAGCCCAAGCTCGTCATGTAAAAAGGGTTAGCCGATTA
1 ACCAACACAAAGCGAAAGCAAAAGCGAAAGCCCAAGCTCGTAAAGTAAAAAGGGTTAGCCGATTA
*
1302650 GGGACAGGGCAGGTCATTAAGTT
66 GGGACAGGGCAGGTCATTAACTT
*
1302673 ACCAACACAAAGCAAAAG
1 ACCAACACAAAGCGAAAG
1302691 TCCACTACTA
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 101 1.00
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.13
Consensus pattern (88 bp):
ACCAACACAAAGCGAAAGCAAAAGCGAAAGCCCAAGCTCGTAAAGTAAAAAGGGTTAGCCGATTA
GGGACAGGGCAGGTCATTAACTT
Found at i:1303156 original size:12 final size:13
Alignment explanation
Indices: 1303139--1303169 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1303129 CCCATATTTA
1303139 AAATTTTTTATT-
1 AAATTTTTTATTC
1303151 AAATTTTTTATTC
1 AAATTTTTTATTC
1303164 AAATTT
1 AAATTT
1303170 AATATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
AAATTTTTTATTC
Found at i:1303394 original size:28 final size:28
Alignment explanation
Indices: 1303341--1303425 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 28
1303331 TAACTTTTTT
* *
1303341 TATTTTATTAATTTATTTTTTA-AAATAA
1 TATTTTAATAA-TTATTTATTATAAATAA
* *
1303369 TATTTTAATAATTATTTAATATAAATAT
1 TATTTTAATAATTATTTATTATAAATAA
* *
1303397 TTTTTTAATATATAATTTATTATATAATA
1 TATTTTAATA-ATTATTTATTATA-AATA
1303426 TAAAAATAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
27 8 0.17
28 24 0.51
29 11 0.23
30 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TATTTTAATAATTATTTATTATAAATAA
Found at i:1303406 original size:36 final size:36
Alignment explanation
Indices: 1303366--1303447 Score: 85
Period size: 36 Copynumber: 2.2 Consensus size: 36
1303356 TTTTTTAAAA
* * **
1303366 TAATATTTTAA-TAATTATTTAATATAAATATTTTTT
1 TAATA-TTTAATTAATTATATAATATAAAAATAATTT
* *
1303402 TAATATATAATTTATTATATAATATAAAAATAATTT
1 TAATATTTAATTAATTATATAATATAAAAATAATTT
1303438 TAATAATTTA
1 TAAT-ATTTA
1303448 TTTTTAATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
35 4 0.11
36 29 0.78
37 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
TAATATTTAATTAATTATATAATATAAAAATAATTT
Found at i:1303441 original size:17 final size:17
Alignment explanation
Indices: 1303378--1303442 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
1303368 ATATTTTAAT
1303378 AATTA-TTTAATATAAA
1 AATTATTTTAATATAAA
* * *
1303394 TATTTTTTTAATATATA
1 AATTATTTTAATATAAA
*
1303411 ATTTATTATATAATATAAA
1 AATTATT-T-TAATATAAA
*
1303430 AATAATTTTAATA
1 AATTATTTTAATA
1303443 ATTTATTTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
16 3 0.08
17 19 0.51
18 2 0.05
19 13 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTATTTTAATATAAA
Found at i:1303532 original size:101 final size:106
Alignment explanation
Indices: 1303364--1303551 Score: 278
Period size: 102 Copynumber: 1.8 Consensus size: 106
1303354 TATTTTTTAA
* *
1303364 AATAATATTTTAATAATTATTTAATATAAATATTTTTTTAATATATAATTTATTATATAATATAA
1 AATAATATTTTAATAATTATTCAATATAAATATATTTTTAATATATAATTTATTATATAATATAA
1303429 AAAT-AATTTTAATAATTTATTTTTAATTTAAATACAGTGT
66 AAATAAATTTTAATAATTTATTTTTAATTTAAATACAGTGT
* * * *
1303469 AATAAT-TTTTAATTATTATTCAA-ATAAATATATTTTT-ATTTAT-TTTTATTATTTAATATAA
1 AATAATATTTTAATAATTATTCAATATAAATATATTTTTAATATATAATTTATTATATAATATAA
*
1303530 AAATAAATTTTAATTATTTATT
66 AAATAAATTTTAATAATTTATT
1303552 ATAAATATAT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
101 20 0.27
102 21 0.28
103 13 0.17
104 15 0.20
105 6 0.08
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (106 bp):
AATAATATTTTAATAATTATTCAATATAAATATATTTTTAATATATAATTTATTATATAATATAA
AAATAAATTTTAATAATTTATTTTTAATTTAAATACAGTGT
Found at i:1304091 original size:14 final size:15
Alignment explanation
Indices: 1304055--1304101 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 15
1304045 AAAAAAATAC
1304055 ATATAATATAAATATAT
1 ATATAATATAAAT-T-T
1304072 AAATATAATA-AAATTT
1 --ATATAATATAAATTT
1304088 ATATAATATAAATT
1 ATATAATATAAATT
1304102 ATCAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.30
15 5 0.19
16 1 0.04
17 1 0.04
18 4 0.15
19 8 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATAATATAAATTT
Found at i:1304118 original size:32 final size:33
Alignment explanation
Indices: 1304055--1304176 Score: 103
Period size: 32 Copynumber: 3.8 Consensus size: 33
1304045 AAAAAAATAC
*
1304055 ATATAATATAAATATATAAATATAATAAAATTT
1 ATATAATATAAATATATAAATATAATAAAATTA
* * *
1304088 ATATAATATAAAT-TATCAATATATTTAAATTA
1 ATATAATATAAATATATAAATATAATAAAATTA
* * * *
1304120 ATAAAATATTTAATATTTTAAATATAAT--TATT-
1 ATATAATA-TAAATA-TATAAATATAATAAAATTA
*
1304152 ATAT--TAAAAATATATAAATATAATA
1 ATATAATATAAATATATAAATATAATA
1304177 TTAAAAACAT
Statistics
Matches: 71, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
28 11 0.15
29 4 0.06
30 2 0.03
32 25 0.35
33 20 0.28
35 9 0.13
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.43
Consensus pattern (33 bp):
ATATAATATAAATATATAAATATAATAAAATTA
Found at i:1304126 original size:26 final size:27
Alignment explanation
Indices: 1304088--1304147 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
1304078 AATAAAATTT
1304088 ATATAATATAAAT-TATCAATATATTTAA
1 ATATAATATAAATAT-TCAATAT-TTTAA
*
1304116 AT-TAATA-AAATATTTAATATTTTAA
1 ATATAATATAAATATTCAATATTTTAA
1304141 ATATAAT
1 ATATAAT
1304148 TATTATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
25 7 0.24
26 14 0.48
27 6 0.21
28 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATAATATAAATATTCAATATTTTAA
Found at i:1304166 original size:22 final size:22
Alignment explanation
Indices: 1304141--1304196 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
1304131 AATATTTTAA
*
1304141 ATATAATTATTATATTAAAAAT
1 ATATAATTATTATATTAAAAAC
* *
1304163 ATATAAATATAATATTAAAAAC
1 ATATAATTATTATATTAAAAAC
*
1304185 ATTTAATT-TTAT
1 ATATAATTATTAT
1304197 CCGAATTTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATAATTATTATATTAAAAAC
Found at i:1304171 original size:44 final size:49
Alignment explanation
Indices: 1304055--1304176 Score: 121
Period size: 50 Copynumber: 2.6 Consensus size: 49
1304045 AAAAAAATAC
* *
1304055 ATATAATATAAATATATAAATATAATAAAATTTATATAATATAAATTAT
1 ATATATTAAAAATATATAAATATAATAAAATTTATATAATATAAATTAT
* * * *
1304104 CAATATATTTAAATTA-ATAAA-ATATTTAATATTT-TA-AATAT-AATTAT
1 --ATATATTAAAAATATATAAATATA-ATAAAATTTATATAATATAAATTAT
1304151 -TATATTAAAAATATATAAATATAATA
1 ATATATTAAAAATATATAAATATAATA
1304177 TTAAAAACAT
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
44 11 0.19
45 7 0.12
46 3 0.05
47 6 0.10
48 5 0.08
49 5 0.08
50 12 0.20
51 10 0.17
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.43
Consensus pattern (49 bp):
ATATATTAAAAATATATAAATATAATAAAATTTATATAATATAAATTAT
Found at i:1307600 original size:23 final size:23
Alignment explanation
Indices: 1307547--1307602 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
1307537 TATTTATTTA
*
1307547 AATAAATAAATTTATATACGAAT
1 AATAAATAAATATATATACGAAT
** * * *
1307570 GTTTAATAAATATATTTATGAAT
1 AATAAATAAATATATATACGAAT
1307593 AATAAATAAA
1 AATAAATAAA
1307603 CAAATAAACA
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (23 bp):
AATAAATAAATATATATACGAAT
Found at i:1308023 original size:56 final size:57
Alignment explanation
Indices: 1307931--1308054 Score: 144
Period size: 56 Copynumber: 2.2 Consensus size: 57
1307921 ATTCATGAAC
* * * * *
1307931 AAATTTACTTATAAATCTTTAAAATCTATTTTTTATTTAATTATAATATTATT-ATT
1 AAATTTATTTATAAATCATTAAAATCTATTTATTATTTAATTAGAACATTATTGATT
* *
1307987 AAATTTATTTATAAATCATTAAAAT-TCGTTTATTATTTGATTAGAACATTATTGATT
1 AAATTTATTTATAAATCATTAAAATCT-ATTTATTATTTAATTAGAACATTATTGATT
1308044 ATAATATTATT
1 A-AAT-TTATT
1308055 ATTATTTATG
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
55 1 0.02
56 44 0.77
57 4 0.07
58 3 0.05
59 5 0.09
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (57 bp):
AAATTTATTTATAAATCATTAAAATCTATTTATTATTTAATTAGAACATTATTGATT
Found at i:1308445 original size:11 final size:11
Alignment explanation
Indices: 1308429--1308461 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1308419 ATATAATACG
1308429 ATATAAAAATA
1 ATATAAAAATA
*
1308440 ATATAAATATA
1 ATATAAAAATA
1308451 ATATAAAAATA
1 ATATAAAAATA
1308462 TAAATATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:1308485 original size:33 final size:34
Alignment explanation
Indices: 1308446--1308521 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 34
1308436 AATAATATAA
1308446 ATATAATATAAAAAT-ATAAATATATCAAAATTT
1 ATATAATATAAAAATGATAAATATATCAAAATTT
* * * *
1308479 ATAT-A-ATACAAATGATTAATTTATTAAAATTT
1 ATATAATATAAAAATGATAAATATATCAAAATTT
1308511 ATATAAATATA
1 ATAT-AATATA
1308522 TAATAAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
31 7 0.20
32 20 0.57
33 4 0.11
34 1 0.03
35 3 0.09
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (34 bp):
ATATAATATAAAAATGATAAATATATCAAAATTT
Found at i:1309033 original size:5 final size:5
Alignment explanation
Indices: 1309025--1309098 Score: 58
Period size: 5 Copynumber: 14.0 Consensus size: 5
1309015 TATTTACTTT
* ** * *
1309025 AATAA AATAA AATAA AATAA TAATAA AATAA TTATTT TATAAA AATAG
1 AATAA AATAA AATAA AATAA -AATAA AATAA -AATAA AAT-AA AATAA
*
1309073 AATAA AATTAA AATAA AATAT AATAA
1 AATAA AA-TAA AATAA AATAA AATAA
1309099 TTATAATCAT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
5 41 0.75
6 14 0.25
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (5 bp):
AATAA
Found at i:1309051 original size:11 final size:11
Alignment explanation
Indices: 1309024--1309104 Score: 60
Period size: 11 Copynumber: 7.5 Consensus size: 11
1309014 ATATTTACTT
1309024 TAATAAAATAA
1 TAATAAAATAA
1309035 -AATAAAATAA
1 TAATAAAATAA
1309045 TAATAAAATAA
1 TAATAAAATAA
* ***
1309056 TTATTTTATAA
1 TAATAAAATAA
* *
1309067 AAATAGAATAA
1 TAATAAAATAA
1309078 -AATTAAAATAA
1 TAA-TAAAATAA
*
1309089 -AATATAATAA
1 TAATAAAATAA
*
1309099 TTATAA
1 TAATAA
1309105 TCATAATTTA
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
10 19 0.35
11 35 0.65
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:1309051 original size:16 final size:16
Alignment explanation
Indices: 1309025--1309098 Score: 57
Period size: 16 Copynumber: 4.7 Consensus size: 16
1309015 TATTTACTTT
1309025 AATAA-AATAAAATAA
1 AATAATAATAAAATAA
1309040 AATAATAATAAAAT-A
1 AATAATAATAAAATAA
* * * *
1309055 ATTATTTTATAAAAATAG
1 AATA-ATAAT-AAAATAA
1309073 AATAA-AATTAAAATAA
1 AATAATAA-TAAAATAA
1309089 AAT-ATAATAA
1 AATAATAATAA
1309099 TTATAATCAT
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
15 13 0.29
16 23 0.51
17 6 0.13
18 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (16 bp):
AATAATAATAAAATAA
Found at i:1309103 original size:38 final size:38
Alignment explanation
Indices: 1309028--1309104 Score: 95
Period size: 38 Copynumber: 2.0 Consensus size: 38
1309018 TTACTTTAAT
* *
1309028 AAAATAAAATAAAATAATAATAAAATAATTATTTTATA
1 AAAATAAAATAAAATAATAATAAAATAAATATATTATA
*
1309066 AAAATAGAATAAAATTAA-AATAAAATATAATA-ATTATA
1 AAAATAAAATAAAA-TAATAATAAAATA-AATATATTATA
1309104 A
1 A
1309105 TCATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 28 0.82
39 6 0.18
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (38 bp):
AAAATAAAATAAAATAATAATAAAATAAATATATTATA
Found at i:1309178 original size:20 final size:20
Alignment explanation
Indices: 1309133--1309176 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1309123 AAATATTATA
1309133 AATTTAAATTTTTAATAAAA-
1 AATTTAAATTTTT-ATAAAAT
1309153 AATTTAAATTTTT-TAAAAT
1 AATTTAAATTTTTATAAAAT
1309172 AATTT
1 AATTT
1309177 TATCCTACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.22
19 5 0.22
20 13 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTTAAATTTTTATAAAAT
Found at i:1315126 original size:18 final size:17
Alignment explanation
Indices: 1315095--1315128 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1315085 TACTCTTTTT
*
1315095 AATATTTATGCTAATAA
1 AATATTTATACTAATAA
1315112 AATATATTATACTAATA
1 AATAT-TTATACTAATA
1315129 CTATTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (17 bp):
AATATTTATACTAATAA
Found at i:1315592 original size:34 final size:34
Alignment explanation
Indices: 1315540--1315672 Score: 185
Period size: 34 Copynumber: 3.9 Consensus size: 34
1315530 TAATTTAGTG
* *
1315540 GTTTATCATTATTTATTAAATGAGAGTTTTGATA
1 GTTTATCATTATTGATTAAATGAGAGATTTGATA
* * *
1315574 GTTTGTCATTATTGATTAAATGAGTGATTTGGTA
1 GTTTATCATTATTGATTAAATGAGAGATTTGATA
* *
1315608 ATTTGTCATTATTGATTAAATGAGAGATTTGATA
1 GTTTATCATTATTGATTAAATGAGAGATTTGATA
* *
1315642 GTTTATCATTGTTGATTAAATGAGTGATTTG
1 GTTTATCATTATTGATTAAATGAGAGATTTG
1315673 GTGATTTTTA
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 87 1.00
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (34 bp):
GTTTATCATTATTGATTAAATGAGAGATTTGATA
Found at i:1315657 original size:68 final size:68
Alignment explanation
Indices: 1315545--1315679 Score: 225
Period size: 68 Copynumber: 2.0 Consensus size: 68
1315535 TAGTGGTTTA
* * *
1315545 TCATTATTTATTAAATGAGAGTTTTGATAGTTTGTCATTATTGATTAAATGAGTGATTTGGTAAT
1 TCATTATTGATTAAATGAGAGATTTGATAGTTTATCATTATTGATTAAATGAGTGATTTGGTAAT
1315610 TTG
66 TTG
* *
1315613 TCATTATTGATTAAATGAGAGATTTGATAGTTTATCATTGTTGATTAAATGAGTGATTTGGTGAT
1 TCATTATTGATTAAATGAGAGATTTGATAGTTTATCATTATTGATTAAATGAGTGATTTGGTAAT
1315678 TT
66 TT
1315680 TTACCAAATC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (68 bp):
TCATTATTGATTAAATGAGAGATTTGATAGTTTATCATTATTGATTAAATGAGTGATTTGGTAAT
TTG
Found at i:1316019 original size:21 final size:21
Alignment explanation
Indices: 1315993--1316032 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1315983 ATGTATATAA
*
1315993 GTACTATTTACATATACGGGG
1 GTACTATTCACATATACGGGG
*
1316014 GTACTATTCACGTATACGG
1 GTACTATTCACATATACGG
1316033 TATTGTGCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (21 bp):
GTACTATTCACATATACGGGG
Found at i:1319467 original size:34 final size:34
Alignment explanation
Indices: 1319421--1319563 Score: 169
Period size: 34 Copynumber: 4.2 Consensus size: 34
1319411 TTTACCATTA
* *
1319421 ATTTGGTGGTTTGCCATTATTGACTAAATGAGAG
1 ATTTGGTAGTTTGCCATTATTGACTAAATGGGAG
* * * *
1319455 TTTTGGTAGTTTGCCATTGTTGATTAAATGGGTG
1 ATTTGGTAGTTTGCCATTATTGACTAAATGGGAG
* *
1319489 ATTTGGTGGTTTGTCATTATTGACTAAATGGGAG
1 ATTTGGTAGTTTGCCATTATTGACTAAATGGGAG
* * * * *
1319523 ATTTGATAGTTTGCCATTGTTGATTAAATCGGTG
1 ATTTGGTAGTTTGCCATTATTGACTAAATGGGAG
1319557 ATTTGGT
1 ATTTGGT
1319564 GATTTTTACC
Statistics
Matches: 89, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 89 1.00
ACGTcount: A:0.22, C:0.07, G:0.27, T:0.43
Consensus pattern (34 bp):
ATTTGGTAGTTTGCCATTATTGACTAAATGGGAG
Found at i:1319507 original size:68 final size:68
Alignment explanation
Indices: 1319421--1319564 Score: 243
Period size: 68 Copynumber: 2.1 Consensus size: 68
1319411 TTTACCATTA
* * *
1319421 ATTTGGTGGTTTGCCATTATTGACTAAATGAGAGTTTTGGTAGTTTGCCATTGTTGATTAAATGG
1 ATTTGGTGGTTTGCCATTATTGACTAAATGAGAGATTTGATAGTTTGCCATTGTTGATTAAATCG
1319486 GTG
66 GTG
* *
1319489 ATTTGGTGGTTTGTCATTATTGACTAAATGGGAGATTTGATAGTTTGCCATTGTTGATTAAATCG
1 ATTTGGTGGTTTGCCATTATTGACTAAATGAGAGATTTGATAGTTTGCCATTGTTGATTAAATCG
1319554 GTG
66 GTG
1319557 ATTTGGTG
1 ATTTGGTG
1319565 ATTTTTACCA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.22, C:0.07, G:0.28, T:0.43
Consensus pattern (68 bp):
ATTTGGTGGTTTGCCATTATTGACTAAATGAGAGATTTGATAGTTTGCCATTGTTGATTAAATCG
GTG
Found at i:1319889 original size:10 final size:10
Alignment explanation
Indices: 1319874--1319999 Score: 62
Period size: 10 Copynumber: 12.6 Consensus size: 10
1319864 AATATTGACA
1319874 TTATTTATAT
1 TTATTTATAT
*
1319884 TTATTTAAAT
1 TTATTTATAT
1319894 TTGATTTA-AT
1 TT-ATTTATAT
**
1319904 TT-TAAATAT
1 TTATTTATAT
* *
1319913 TAATTTTAAATT
1 TTA-TTTATA-T
1319925 TTATTTATAT
1 TTATTTATAT
*
1319935 TTTTTTATAT
1 TTATTTATAT
** *
1319945 TTATAAATAA
1 TTATTTATAT
* *
1319955 TAATTTAAAT
1 TTATTTATAT
* *
1319965 CTATTTAGAT
1 TTATTTATAT
1319975 CTT-TTTATAT
1 -TTATTTATAT
*
1319985 TTTTTTA-AT
1 TTATTTATAT
1319994 TTATTT
1 TTATTT
1320000 TTTAAAAAAT
Statistics
Matches: 84, Mismatches: 25, Indels: 15
0.68 0.20 0.12
Matches are distributed among these distances:
8 2 0.02
9 12 0.14
10 53 0.63
11 14 0.17
12 3 0.04
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (10 bp):
TTATTTATAT
Found at i:1319917 original size:13 final size:13
Alignment explanation
Indices: 1319899--1319923 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1319889 TAAATTTGAT
1319899 TTAATTTTAAATA
1 TTAATTTTAAATA
1319912 TTAATTTTAAAT
1 TTAATTTTAAAT
1319924 TTTATTTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATTTTAAATA
Found at i:1319930 original size:41 final size:41
Alignment explanation
Indices: 1319883--1319986 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
1319873 ATTATTTATA
*
1319883 TTTATTTAAATTTGATTTA-ATTT-TAAATATTAATTTTAAAT
1 TTTATTTAAATTT-ATTTATATTTATAAATAATAA-TTTAAAT
* *
1319924 TTTATTTATATTTTTTTATATTTATAAATAATAATTTAAA-
1 TTTATTTAAATTTATTTATATTTATAAATAATAATTTAAAT
* *
1319964 TCTATTTAGATCTT-TTTATATTT
1 TTTATTTAAAT-TTATTTATATTT
1319987 TTTTAATTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
40 22 0.40
41 24 0.44
42 9 0.16
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (41 bp):
TTTATTTAAATTTATTTATATTTATAAATAATAATTTAAAT
Found at i:1319981 original size:40 final size:41
Alignment explanation
Indices: 1319898--1319987 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 41
1319888 TTAAATTTGA
* * * *
1319898 TTTA-ATTTTAAATATTAATTTTAAATTTTATTTATATTTT
1 TTTATATTTTAAATAATAATTTTAAATTCTATTTAGATCTT
1319938 TTTATATTTATAAATAATAA-TTTAAA-TCTATTTAGATCTT
1 TTTATATTT-TAAATAATAATTTTAAATTCTATTTAGATCTT
1319978 TTTATATTTT
1 TTTATATTTT
1319988 TTTAATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
39 1 0.02
40 24 0.55
41 10 0.23
42 9 0.20
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (41 bp):
TTTATATTTTAAATAATAATTTTAAATTCTATTTAGATCTT
Found at i:1320055 original size:35 final size:36
Alignment explanation
Indices: 1320007--1320089 Score: 84
Period size: 35 Copynumber: 2.4 Consensus size: 36
1319997 TTTTTTAAAA
* * * *
1320007 AATATA-TATTTAAAAATTT-AATTTTTAGTAATTT
1 AATATATTTTTTAAAAATTTAAAATTTAAATAATTT
*
1320041 AATAT-TTTTATT-AAATTTTAAAATTTAAATAATTT
1 AATATATTTT-TTAAAAATTTAAAATTTAAATAATTT
1320076 AATATATTTTTTAA
1 AATATATTTTTTAA
1320090 TATTGACATT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
34 13 0.33
35 21 0.54
36 5 0.13
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (36 bp):
AATATATTTTTTAAAAATTTAAAATTTAAATAATTT
Found at i:1320326 original size:19 final size:18
Alignment explanation
Indices: 1320302--1320338 Score: 65
Period size: 18 Copynumber: 2.0 Consensus size: 18
1320292 ATTTAAATTC
1320302 TTTTAAATATTAAATAAAT
1 TTTTAAAT-TTAAATAAAT
1320321 TTTTAAATTTAAATAAAT
1 TTTTAAATTTAAATAAAT
1320339 AATTTAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTAAATTTAAATAAAT
Found at i:1320344 original size:19 final size:18
Alignment explanation
Indices: 1320303--1320359 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 18
1320293 TTTAAATTCT
*
1320303 TTTAAATATTAAATAAATT
1 TTTAAAT-TTAAATAAATA
1320322 TTTAAATTTAAATAAATAA
1 TTTAAATTTAAATAAAT-A
*
1320341 TTTAACTTT--ATAAATA
1 TTTAAATTTAAATAAATA
1320357 TTT
1 TTT
1320360 TTAATAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 4 0.11
17 6 0.17
18 10 0.29
19 15 0.43
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAAATTTAAATAAATA
Found at i:1320366 original size:13 final size:13
Alignment explanation
Indices: 1320350--1320380 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1320340 ATTTAACTTT
*
1320350 ATAAATATTTTTA
1 ATAAATACTTTTA
1320363 ATAAATACTTTTA
1 ATAAATACTTTTA
1320376 ATAAA
1 ATAAA
1320381 GAGTGACAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (13 bp):
ATAAATACTTTTA
Found at i:1320669 original size:27 final size:28
Alignment explanation
Indices: 1320639--1320723 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 28
1320629 ATAAATTATT
1320639 AATATATTAAAAT-TTATATAAAAATAA
1 AATATATTAAAATATTATATAAAAATAA
* *
1320666 AATATTTTAAATATAATTATA-ATATAATAA
1 AATATATTAAA-AT-ATTATATA-AAAATAA
*
1320696 AATATA-T-AAATATAATATAAATAATAA
1 AATATATTAAAATATTATATAAA-AATAA
1320723 A
1 A
1320724 TTTTCAAGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
26 6 0.13
27 19 0.40
28 4 0.09
29 2 0.04
30 16 0.34
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
AATATATTAAAATATTATATAAAAATAA
Found at i:1320693 original size:5 final size:5
Alignment explanation
Indices: 1320675--1320721 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
1320665 AAATATTTTA
*
1320675 AATAT AATTAT AATAT AATAA AATAT -ATA- AATAT AATAT AA-AT AATA
1 AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATA
1320722 AATTTTCAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
4 10 0.28
5 21 0.58
6 5 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:1320709 original size:18 final size:18
Alignment explanation
Indices: 1320686--1320724 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1320676 ATATAATTAT
1320686 AATATAATA-AAATATATA
1 AATATAATATAAATA-ATA
1320704 AATATAATATAAATAATA
1 AATATAATATAAATAATA
1320722 AAT
1 AAT
1320725 TTTCAAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATAATATAAATAATA
Found at i:1320718 original size:29 final size:30
Alignment explanation
Indices: 1320661--1320723 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
1320651 TTTATATAAA
*
1320661 AATAAAATATTTTAAATATAATTATAATAT
1 AATAAAATATTATAAATATAATTATAATAT
1320691 AATAAAATA-TATAAATATAA-TATAA-AT
1 AATAAAATATTATAAATATAATTATAATAT
1320718 AATAAA
1 AATAAA
1320724 TTTTCAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 8 0.25
28 5 0.16
29 10 0.31
30 9 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (30 bp):
AATAAAATATTATAAATATAATTATAATAT
Found at i:1320719 original size:9 final size:10
Alignment explanation
Indices: 1320675--1320721 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 10
1320665 AAATATTTTA
1320675 AATATAATTAT
1 AATATAA-TAT
*
1320686 AATATAATAA
1 AATATAATAT
1320696 AATAT-ATA-
1 AATATAATAT
1320704 AATATAATAT
1 AATATAATAT
1320714 AA-ATAATA
1 AATATAATA
1320722 AATTTTCAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 5 0.15
9 12 0.36
10 9 0.27
11 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AATATAATAT
Found at i:1321560 original size:6 final size:6
Alignment explanation
Indices: 1321507--1321565 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
1321497 AATGTATGTA
* * * *
1321507 TTATAT TTTTAT TTAAAT TT-TTT TATATAT TTAATAA TTATA- TTATAT
1 TTATAT TTATAT TTATAT TTATAT T-TATAT TT-ATAT TTATAT TTATAT
1321555 TTATAT TTATA
1 TTATAT TTATA
1321566 CTATTAAGAC
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 7 0.17
6 27 0.64
7 8 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
TTATAT
Found at i:1321769 original size:2 final size:2
Alignment explanation
Indices: 1321758--1321788 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1321748 AATAAGAAAT
1321758 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1321789 GTGATTTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1322789 original size:39 final size:38
Alignment explanation
Indices: 1322746--1322834 Score: 90
Period size: 39 Copynumber: 2.3 Consensus size: 38
1322736 AATATTTTTC
* * *
1322746 ATTTTTTATTCAATTATTATGTA-AAATAATAAAAAATTT
1 ATTTTTTATT-AATAATTATATATAAAT-ATAAAAAAATT
* *
1322785 ATTTTTATATTAATAATTTTATATAAATTTAAAAAAATT
1 ATTTTT-TATTAATAATTATATATAAATATAAAAAAATT
1322824 ATTATTTTATT
1 ATT-TTTTATT
1322835 TATTAAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
39 31 0.74
40 11 0.26
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (38 bp):
ATTTTTTATTAATAATTATATATAAATATAAAAAAATT
Found at i:1323088 original size:2 final size:2
Alignment explanation
Indices: 1323083--1323107 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1323073 TGATGAAAAA
1323083 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1323108 ATTTTAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1323276 original size:9 final size:9
Alignment explanation
Indices: 1323249--1323296 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 9
1323239 AAATTATTTT
1323249 ATTTAA-AA
1 ATTTAATAA
1323257 ATTT-A-AA
1 ATTTAATAA
1323264 ATTTAATAA
1 ATTTAATAA
*
1323273 ATTTTAT-A
1 ATTTAATAA
1323281 ATTTAATAA
1 ATTTAATAA
1323290 ATTTAAT
1 ATTTAAT
1323297 TAATATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
7 7 0.20
8 12 0.34
9 16 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
ATTTAATAA
Found at i:1323283 original size:17 final size:17
Alignment explanation
Indices: 1323249--1323293 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
1323239 AAATTATTTT
1323249 ATTTAA-AAA-TTTAAA
1 ATTTAATAAATTTTAAA
*
1323264 ATTTAATAAATTTTATA
1 ATTTAATAAATTTTAAA
1323281 ATTTAATAAATTT
1 ATTTAATAAATTT
1323294 AATTAATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 6 0.22
16 3 0.11
17 18 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTAATAAATTTTAAA
Found at i:1323900 original size:30 final size:29
Alignment explanation
Indices: 1323857--1324013 Score: 89
Period size: 28 Copynumber: 5.4 Consensus size: 29
1323847 TTTTTATAAA
1323857 TATAATAAGTATAAAATAATTAATATATAATT
1 TATAAT-A-TATAAAATAATTAA-ATATAATT
* * *
1323889 TATATTATAT-AAATTATAAAATA-AATT
1 TATAATATATAAAATAATTAAATATAATT
* * *
1323916 ATATATTAT-TAATAT-ATT-AA-A-AATA
1 -TATAATATATAAAATAATTAAATATAATT
*
1323941 TATAA-ATATAAAATATTTTAAATATAA-T
1 TATAATATATAAAATA-ATTAAATATAATT
* *
1323969 TATAATATAATAAAATATATAAATATATAAAT
1 TATAATAT-ATAAAATA-ATTAA-ATATAATT
1324001 TATTAATATATAA
1 TA-TAATATATAA
1324014 TCATTAGAGA
Statistics
Matches: 100, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
23 2 0.02
24 9 0.09
25 4 0.04
26 4 0.04
27 9 0.09
28 20 0.20
29 12 0.12
30 15 0.15
31 7 0.07
32 12 0.12
33 6 0.06
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (29 bp):
TATAATATATAAAATAATTAAATATAATT
Found at i:1323943 original size:45 final size:45
Alignment explanation
Indices: 1323894--1323999 Score: 128
Period size: 45 Copynumber: 2.3 Consensus size: 45
1323884 TAATTTATAT
*
1323894 TATATAAATTATAAAATAAATT-ATAT-ATTATTAATATATTAAAAA
1 TATATAAATTATAAAATAAATTAATATAATTA-TAATATAAT-AAAA
**
1323939 TATATAAA-TATAAAATATTTTAAATATAATTATAATATAATAAAA
1 TATATAAATTATAAAATAAATT-AATATAATTATAATATAATAAAA
1323984 TATATAAATATATAAA
1 TATATAAAT-TATAAA
1324000 TTATTAATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
44 11 0.21
45 20 0.38
46 12 0.23
47 10 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (45 bp):
TATATAAATTATAAAATAAATTAATATAATTATAATATAATAAAA
Found at i:1323965 original size:35 final size:38
Alignment explanation
Indices: 1323904--1324014 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 38
1323894 TATATAAATT
* *
1323904 ATAAAATAAATTATATATTATT-AATATATTAAAAATAT-
1 ATAAAATATA-TAAATATT-TTAAATATATTAAAAATATA
*
1323942 AT-AAATATA-AAATATTTTAAATATAATT-ATAATATA
1 ATAAAATATATAAATATTTTAAATAT-ATTAAAAATATA
* *
1323978 ATAAAATATATAAATA-TATAAAT-TATT-AATATATA
1 ATAAAATATATAAATATTTTAAATATATTAAAAATATA
1324013 AT
1 AT
1324015 CATTAGAGAT
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
34 2 0.03
35 28 0.45
36 6 0.10
37 19 0.31
38 7 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (38 bp):
ATAAAATATATAAATATTTTAAATATATTAAAAATATA
Found at i:1324000 original size:37 final size:37
Alignment explanation
Indices: 1323851--1324000 Score: 107
Period size: 37 Copynumber: 4.0 Consensus size: 37
1323841 AATATTTTTT
* *
1323851 TATAAATATAATAAGTATAAAATA-ATTAATA-TAT-AA
1 TATAATTATAA-AA-TATAAAATATATAAATATTATAAA
* * * *
1323887 TTTATATTATATAAATTATAAAATAAATTATATATTATTAA
1 TATA-ATTATA-AAA-TATAAAATATA-TAAATATTATAAA
*
1323928 TAT-ATTA-AAAATATATAAATATA-AAATATTTTAAA
1 TATAATTATAAAATATA-AAATATATAAATATTATAAA
*
1323963 TATAATTATAATATAATAAAATATATAAATA-TATAAA
1 TATAATTATAAAAT-ATAAAATATATAAATATTATAAA
1324000 T
1 T
1324001 TATTAATATA
Statistics
Matches: 91, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
35 12 0.13
36 11 0.12
37 42 0.46
38 11 0.12
39 8 0.09
40 3 0.03
41 4 0.04
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (37 bp):
TATAATTATAAAATATAAAATATATAAATATTATAAA
Found at i:1324012 original size:81 final size:81
Alignment explanation
Indices: 1323854--1324011 Score: 200
Period size: 81 Copynumber: 2.0 Consensus size: 81
1323844 ATTTTTTTAT
* * *
1323854 AAATATAATAAGTATAAAATAATTAATATATAATTTATATTATATAAATTATAAAATAAATTATA
1 AAATATAATAAATATAAAATAATTAATATATAATTTATAATATATAAAATATAAAAT-AATTATA
*
1323919 TATTATTAATATATTAA
65 AATTATTAATATATTAA
*
1323936 AAATAT-ATAAATATAAAATATTTTAA-ATATAA-TTATAATATAATAAAATATATAAAT-A-TA
1 AAATATAATAAATATAAAATA-ATTAATATATAATTTATAATAT-ATAAAATATA-AAATAATTA
1323996 TAAATTATTAATATAT
63 TAAATTATTAATATAT
1324012 AATCATTAGA
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
79 17 0.25
80 9 0.13
81 28 0.41
82 14 0.21
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.42
Consensus pattern (81 bp):
AAATATAATAAATATAAAATAATTAATATATAATTTATAATATATAAAATATAAAATAATTATAA
ATTATTAATATATTAA
Found at i:1324222 original size:13 final size:13
Alignment explanation
Indices: 1324204--1324228 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1324194 AATATTTATC
1324204 ATAAAAAATAAAT
1 ATAAAAAATAAAT
1324217 ATAAAAAATAAA
1 ATAAAAAATAAA
1324229 AAATTTATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
ATAAAAAATAAAT
Found at i:1325269 original size:19 final size:19
Alignment explanation
Indices: 1325245--1325281 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1325235 ACAACAGCTA
*
1325245 AAATGATGAAATTTATCTT
1 AAATGATAAAATTTATCTT
1325264 AAATGATAAAATTTATCT
1 AAATGATAAAATTTATCT
1325282 AACTATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
AAATGATAAAATTTATCTT
Found at i:1331081 original size:4 final size:4
Alignment explanation
Indices: 1331072--1331105 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
1331062 TTTTGAATAT
1331072 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA AT
1331106 ATATGCTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:1331448 original size:18 final size:18
Alignment explanation
Indices: 1331427--1331492 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
1331417 TTTTCAAAAA
1331427 AATAATTTTTAATAATTT
1 AATAATTTTTAATAATTT
*
1331445 AATAATTTTTATTAAATTT
1 AATAATTTTTAAT-AATTT
* * *
1331464 TAT-ATTTTAAATAACTT
1 AATAATTTTTAATAATTT
1331481 AA-ATATTTTTAA
1 AATA-ATTTTTAA
1331493 ATCTTCCTAC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
17 5 0.13
18 26 0.68
19 7 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
AATAATTTTTAATAATTT
Found at i:1332260 original size:2 final size:2
Alignment explanation
Indices: 1332255--1332292 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1332245 CTTTTTTGTA
1332255 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1332293 TGCATTTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1335168 original size:2 final size:2
Alignment explanation
Indices: 1335161--1335193 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1335151 GCATGCTTTG
1335161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1335194 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1335198 original size:2 final size:2
Alignment explanation
Indices: 1335193--1335225 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1335183 ATATATATAT
1335193 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1335226 CACACACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1336841 original size:27 final size:26
Alignment explanation
Indices: 1336810--1336865 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
1336800 TTTTTATATA
*
1336810 TAATAATTAAATGATAAATATTTATTT
1 TAATAATTAAATAATAAATATTT-TTT
**
1336837 TAATAATTTTATAATAAATATTTTTT
1 TAATAATTAAATAATAAATATTTTTT
1336863 TAA
1 TAA
1336866 AAAAAATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
TAATAATTAAATAATAAATATTTTTT
Found at i:1337415 original size:21 final size:21
Alignment explanation
Indices: 1337391--1337430 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1337381 TTTTGATTAT
* *
1337391 AAAAATTATATTTTTTTATTC
1 AAAAAGTATATATTTTTATTC
1337412 AAAAAGTATATATTTTTAT
1 AAAAAGTATATATTTTTAT
1337431 CCAACTAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (21 bp):
AAAAAGTATATATTTTTATTC
Found at i:1342191 original size:12 final size:13
Alignment explanation
Indices: 1342173--1342210 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1342163 TAGTAAACAC
1342173 TAATAATTTTGAA
1 TAATAATTTTGAA
1342186 -AATAATTTTTGAA
1 TAATAA-TTTTGAA
*
1342199 TAAAAATTTTGA
1 TAATAATTTTGA
1342211 CAATTGAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 5 0.23
13 13 0.59
14 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (13 bp):
TAATAATTTTGAA
Found at i:1342348 original size:21 final size:22
Alignment explanation
Indices: 1342307--1342353 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
1342297 AGTTATATTT
*
1342307 TTTTCATCCAAAAAGTTCATC-
1 TTTTCATCCAAAAAGTGCATCA
*
1342328 TTTTCATCCAATCAA-TGCATCA
1 TTTTCATCCAA-AAAGTGCATCA
1342350 TTTT
1 TTTT
1342354 ATCTAAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.43
Consensus pattern (22 bp):
TTTTCATCCAAAAAGTGCATCA
Found at i:1343588 original size:28 final size:28
Alignment explanation
Indices: 1343556--1343613 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
1343546 GCCAAAAGAA
* *
1343556 ATTTTAGAAGAGTTTAAAAATTGATGAC
1 ATTTTAGAAAAGTTTAAAAATTGACGAC
1343584 ATTTTAGAAAAGTTTAAAAATTGACGAC
1 ATTTTAGAAAAGTTTAAAAATTGACGAC
1343612 AT
1 AT
1343614 AGTCAATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (28 bp):
ATTTTAGAAAAGTTTAAAAATTGACGAC
Found at i:1347547 original size:2 final size:2
Alignment explanation
Indices: 1347540--1347575 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1347530 AGAAACTACA
1347540 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1347576 TGAAGCCTTA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1349299 original size:16 final size:16
Alignment explanation
Indices: 1349278--1349311 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1349268 CGAGTTTGGA
1349278 CTCGTTCAGGTTCGGG
1 CTCGTTCAGGTTCGGG
1349294 CTCGTTCAGGTTCGGG
1 CTCGTTCAGGTTCGGG
1349310 CT
1 CT
1349312 TATTCGGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.26, G:0.35, T:0.32
Consensus pattern (16 bp):
CTCGTTCAGGTTCGGG
Found at i:1349315 original size:48 final size:48
Alignment explanation
Indices: 1349231--1349360 Score: 136
Period size: 48 Copynumber: 2.7 Consensus size: 48
1349221 GGGTTCAAGT
* * * *
1349231 TCGTTTAGGTTCGGGTTCATTCAGGTTCTAGTTTATTCGAGTTTG-GAC
1 TCGTTCAGGTTCGGGCTCATTCAGGTTCGAGCTTATTCGAGTTTGAG-C
* * *
1349279 TCGTTCAGGTTCGGGCTCGTTCAGGTTCGGGCTTATTCGGGTTTGAGC
1 TCGTTCAGGTTCGGGCTCATTCAGGTTCGAGCTTATTCGAGTTTGAGC
* * * * *
1349327 TTGTTCGGGTTCGGACTAATTCGGGTTCGAGCTT
1 TCGTTCAGGTTCGGGCTCATTCAGGTTCGAGCTT
1349361 CTTTGGGGTT
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
48 66 0.99
49 1 0.01
ACGTcount: A:0.12, C:0.18, G:0.32, T:0.39
Consensus pattern (48 bp):
TCGTTCAGGTTCGGGCTCATTCAGGTTCGAGCTTATTCGAGTTTGAGC
Found at i:1349321 original size:16 final size:16
Alignment explanation
Indices: 1349286--1349360 Score: 69
Period size: 16 Copynumber: 4.7 Consensus size: 16
1349276 GACTCGTTCA
** *
1349286 GGTTCGGGCTCGTTCA
1 GGTTCGGGCTTATTCG
1349302 GGTTCGGGCTTATTCG
1 GGTTCGGGCTTATTCG
* * *
1349318 GGTTTGAGCTTGTTCG
1 GGTTCGGGCTTATTCG
* *
1349334 GGTTCGGACTAATTCG
1 GGTTCGGGCTTATTCG
*
1349350 GGTTCGAGCTT
1 GGTTCGGGCTT
1349361 CTTTGGGGTT
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.09, C:0.19, G:0.36, T:0.36
Consensus pattern (16 bp):
GGTTCGGGCTTATTCG
Found at i:1349349 original size:32 final size:32
Alignment explanation
Indices: 1349286--1349360 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
1349276 GACTCGTTCA
* * * *
1349286 GGTTCGGGCTCGTTCAGGTTCGGGCTTATTCG
1 GGTTCGAGCTTGTTCAGGTTCGGACTAATTCG
* *
1349318 GGTTTGAGCTTGTTCGGGTTCGGACTAATTCG
1 GGTTCGAGCTTGTTCAGGTTCGGACTAATTCG
1349350 GGTTCGAGCTT
1 GGTTCGAGCTT
1349361 CTTTGGGGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.09, C:0.19, G:0.36, T:0.36
Consensus pattern (32 bp):
GGTTCGAGCTTGTTCAGGTTCGGACTAATTCG
Found at i:1349392 original size:23 final size:23
Alignment explanation
Indices: 1349366--1349419 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
1349356 AGCTTCTTTG
1349366 GGGTTCAAGTTCGAGTCGGTTTT
1 GGGTTCAAGTTCGAGTCGGTTTT
* * *
1349389 GGGTTCGAGTTCGGGTTGGTTTT
1 GGGTTCAAGTTCGAGTCGGTTTT
1349412 GGGTTCAA
1 GGGTTCAA
1349420 ATTTATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.11, C:0.11, G:0.39, T:0.39
Consensus pattern (23 bp):
GGGTTCAAGTTCGAGTCGGTTTT
Found at i:1349784 original size:12 final size:11
Alignment explanation
Indices: 1349748--1349791 Score: 56
Period size: 12 Copynumber: 4.1 Consensus size: 11
1349738 ACACTGAATT
1349748 AATATTT-AAA
1 AATATTTAAAA
1349758 AAT-TTTAAAA
1 AATATTTAAAA
*
1349768 TATATTTAATAA
1 AATATTTAA-AA
1349780 AATATTTAAAA
1 AATATTTAAAA
1349791 A
1 A
1349792 TTCATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 3 0.10
10 8 0.28
11 8 0.28
12 10 0.34
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATATTTAAAA
Found at i:1349787 original size:23 final size:20
Alignment explanation
Indices: 1349749--1349790 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 20
1349739 CACTGAATTA
1349749 ATATTTAAAAATTTTAAAAT
1 ATATTTAAAAATTTTAAAAT
1349769 ATATTTAATAAAATATTTAAAA
1 ATATTT-A-AAAAT-TTTAAAA
1349791 ATTCATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 1 0.05
22 5 0.26
23 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATTTAAAAATTTTAAAAT
Found at i:1349791 original size:24 final size:23
Alignment explanation
Indices: 1349754--1349801 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
1349744 AATTAATATT
*
1349754 TAAAAATTTTAAAATAT-ATTTAA
1 TAAAAATTTAAAAAT-TCATTTAA
1349777 TAAAATATTTAAAAATTCATTTAA
1 TAAAA-ATTTAAAAATTCATTTAA
1349801 T
1 T
1349802 CTTAACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAAAATTTAAAAATTCATTTAA
Found at i:1350289 original size:20 final size:21
Alignment explanation
Indices: 1350207--1350293 Score: 74
Period size: 20 Copynumber: 4.3 Consensus size: 21
1350197 TGTCATCAAA
*
1350207 TCTGTCATAACTTGTGACA-T
1 TCTGTCACAACTTGTGACAGT
** *
1350227 TCCATCACAATTTGTGA-AGT
1 TCTGTCACAACTTGTGACAGT
* * * *
1350247 CCCGTCATAACTTGT-AAAGT
1 TCTGTCACAACTTGTGACAGT
1350267 TCTGTCACAACTTGTGACA-T
1 TCTGTCACAACTTGTGACAGT
1350287 TCTGTCA
1 TCTGTCA
1350294 TAATTTTTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
19 2 0.04
20 48 0.92
21 2 0.04
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (21 bp):
TCTGTCACAACTTGTGACAGT
Found at i:1350294 original size:40 final size:40
Alignment explanation
Indices: 1350207--1350296 Score: 94
Period size: 40 Copynumber: 2.2 Consensus size: 40
1350197 TGTCATCAAA
* *
1350207 TCTGTCATAACTTGTGACATTCCATCACAATTTGTGAAGT
1 TCTGTCATAACTTGTGAAATTCCATCACAACTTGTGAAGT
* * **
1350247 CCCGTCATAACTTGT-AAAGTTCTGTCACAACTTGTGACA-T
1 TCTGTCATAACTTGTGAAA-TTCCATCACAACTTGTGA-AGT
1350287 TCTGTCATAA
1 TCTGTCATAA
1350297 TTTTTTTCAC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
39 2 0.05
40 37 0.93
41 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (40 bp):
TCTGTCATAACTTGTGAAATTCCATCACAACTTGTGAAGT
Found at i:1352404 original size:10 final size:10
Alignment explanation
Indices: 1352378--1352415 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1352368 CACTCATTCA
*
1352378 TTTATTCTTTT
1 TTTATT-TTTG
1352389 TTTATTTTTG
1 TTTATTTTTG
1352399 TTTATTTTTG
1 TTTATTTTTG
1352409 TTT-TTTT
1 TTTATTTT
1352416 GTATTTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 4 0.15
10 16 0.62
11 6 0.23
ACGTcount: A:0.08, C:0.03, G:0.05, T:0.84
Consensus pattern (10 bp):
TTTATTTTTG
Found at i:1352637 original size:16 final size:15
Alignment explanation
Indices: 1352610--1352639 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1352600 ATGTTAACTT
1352610 TATATTCTATTCTAC
1 TATATTCTATTCTAC
1352625 TATATTACTATTCTA
1 TATATT-CTATTCTA
1352640 AGTGTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATTCTATTCTAC
Found at i:1353156 original size:16 final size:17
Alignment explanation
Indices: 1353137--1353181 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
1353127 CAGATTCGAG
1353137 TTTTTTCGAGTTCAAAT
1 TTTTTTCGAGTTCAAAT
*
1353154 TTTTTTCGAATTCAAA-
1 TTTTTTCGAGTTCAAAT
*
1353170 CTTTTTCGAGTT
1 TTTTTTCGAGTT
1353182 TAACTTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.53
Consensus pattern (17 bp):
TTTTTTCGAGTTCAAAT
Found at i:1353258 original size:6 final size:6
Alignment explanation
Indices: 1353247--1353325 Score: 52
Period size: 6 Copynumber: 14.2 Consensus size: 6
1353237 AATTCGATTC
1353247 AAATTT AAATTT AAATTT AAATTT ---TTT AAA--T AAATTTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAA--TTT AAATTT
1353292 AAATTT ---TTT AAA--T AAATTTTT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAA--TTT AAATTT AAATTT A
1353326 TTTTACCATC
Statistics
Matches: 59, Mismatches: 0, Indels: 28
0.68 0.00 0.32
Matches are distributed among these distances:
3 6 0.10
4 8 0.14
6 37 0.63
8 8 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:1353277 original size:27 final size:26
Alignment explanation
Indices: 1353252--1353324 Score: 121
Period size: 27 Copynumber: 2.8 Consensus size: 26
1353242 GATTCAAATT
1353252 TAAA-TTTAAATTTAAATTTTTTAAA
1 TAAATTTTAAATTTAAATTTTTTAAA
1353277 TAAATTTTTAAATTTAAATTTTTTAAA
1 TAAA-TTTTAAATTTAAATTTTTTAAA
1353304 TAAATTTTTAAATTTAAATTT
1 TAAA-TTTTAAATTTAAATTT
1353325 ATTTTACCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
25 4 0.09
27 42 0.91
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TAAATTTTAAATTTAAATTTTTTAAA
Found at i:1353282 original size:13 final size:12
Alignment explanation
Indices: 1353264--1353316 Score: 70
Period size: 12 Copynumber: 4.1 Consensus size: 12
1353254 AATTTAAATT
1353264 TAAATTTTTTAAA
1 TAAA-TTTTTAAA
1353277 TAAATTTTTAAA
1 TAAATTTTTAAA
1353289 TTTAAATTTTTTAAA
1 --TAAA-TTTTTAAA
1353304 TAAATTTTTAAA
1 TAAATTTTTAAA
1353316 T
1 T
1353317 TTAAATTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
12 17 0.46
13 8 0.22
14 4 0.11
15 8 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TAAATTTTTAAA
Found at i:1353933 original size:20 final size:20
Alignment explanation
Indices: 1353886--1353934 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1353876 TATTAAAATT
*
1353886 AAATTATTTTAAATTAATAA
1 AAATTAATTTAAATTAATAA
* *
1353906 AAAGTTAATTTAACTTATTAA
1 AAA-TTAATTTAAATTAATAA
1353927 AAATTAAT
1 AAATTAAT
1353935 AAAAGTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
AAATTAATTTAAATTAATAA
Found at i:1354006 original size:12 final size:12
Alignment explanation
Indices: 1353989--1354014 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1353979 TTTAAACTCA
1353989 TTAAATTTAATT
1 TTAAATTTAATT
1354001 TTAAATTTAATT
1 TTAAATTTAATT
1354013 TT
1 TT
1354015 TTTAAAATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTAAATTTAATT
Found at i:1354113 original size:17 final size:17
Alignment explanation
Indices: 1354091--1354187 Score: 52
Period size: 17 Copynumber: 6.0 Consensus size: 17
1354081 AGTTGCATAA
1354091 ATTTAATAATTTTATAT
1 ATTTAATAATTTTATAT
*
1354108 ATTTAA-ATATTTTATTT
1 ATTTAATA-ATTTTATAT
*
1354125 AATT-ATAA---T-TAT
1 ATTTAATAATTTTATAT
1354137 ATTTAA-AATATTT-TAT
1 ATTTAATAAT-TTTATAT
*
1354153 TTTTATATAAATTTTA-AT
1 ATTTA-AT-AATTTTATAT
1354171 ATATTAATAA-TTTATAT
1 AT-TTAATAATTTTATAT
1354188 TATATAAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 26
0.66 0.06 0.28
Matches are distributed among these distances:
12 7 0.11
13 2 0.03
16 15 0.25
17 23 0.38
18 8 0.13
19 6 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTAATAATTTTATAT
Found at i:1354125 original size:30 final size:30
Alignment explanation
Indices: 1354091--1354154 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
1354081 AGTTGCATAA
* *
1354091 ATTTAATAAT-TTTATATATTTAAATATTTT
1 ATTTAATAATAATTATAT-TTAAAATATTTT
*
1354121 ATTTAATTATAATTATATTTAAAATATTTT
1 ATTTAATAATAATTATATTTAAAATATTTT
1354151 ATTT
1 ATTT
1354155 TTATATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
ATTTAATAATAATTATATTTAAAATATTTT
Found at i:1354171 original size:25 final size:24
Alignment explanation
Indices: 1354100--1354172 Score: 67
Period size: 30 Copynumber: 2.8 Consensus size: 24
1354090 AATTTAATAA
1354100 TTTTATAT-ATTTAAATATTTTAT
1 TTTTATATAATTTAAATATTTTAT
1354123 TTAATTATAATTATATTTAAAATATTTTAT
1 TT--TTAT-A-TA-ATTT-AAATATTTTAT
*
1354153 TTTTATATAAATTTTAATAT
1 TTTTATAT-AATTTAAATAT
1354173 ATTAATAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
23 2 0.05
25 9 0.22
26 6 0.15
27 3 0.07
28 4 0.10
29 4 0.10
30 13 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTATATAATTTAAATATTTTAT
Found at i:1354526 original size:6 final size:6
Alignment explanation
Indices: 1354515--1354557 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
1354505 TGCCTCTCAC
*
1354515 CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT CCCCTT C
1 CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT C
1354558 ATCGTCTTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (6 bp):
CTCCTT
Found at i:1356744 original size:32 final size:32
Alignment explanation
Indices: 1356703--1356790 Score: 81
Period size: 32 Copynumber: 2.8 Consensus size: 32
1356693 GATTAATTTG
1356703 AACTCAAAATAATTTGAATTTAGAA-TGATTCA
1 AACTCAAAATAATTTGAATTTA-AAGTGATTCA
* ** *
1356735 AACTTAAAATTTTTTGAATTTAAAGTGATTTGA
1 AACTCAAAATAATTTGAATTTAAAGTGA-TTCA
** *
1356768 AACT-AAAACGACTTGAATTTAAA
1 AACTCAAAATAATTTGAATTTAAA
1356791 AATTAAAAAC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 2 0.04
32 37 0.80
33 7 0.15
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.36
Consensus pattern (32 bp):
AACTCAAAATAATTTGAATTTAAAGTGATTCA
Found at i:1358832 original size:22 final size:22
Alignment explanation
Indices: 1358804--1358846 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1358794 TAAAATATTA
1358804 TTTTAT-ATTAATATTTAAATAT
1 TTTTATAATTAA-ATTTAAATAT
1358826 TTTTATAATTAAATTTAAATA
1 TTTTATAATTAAATTTAAATA
1358847 AAAATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTATAATTAAATTTAAATAT
Found at i:1359732 original size:9 final size:9
Alignment explanation
Indices: 1359720--1359745 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1359710 ATAATAAATA
1359720 TTATTATAT
1 TTATTATAT
1359729 TTATTATAT
1 TTATTATAT
1359738 TTATTATA
1 TTATTATA
1359746 AAATTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTATTATAT
Found at i:1359866 original size:27 final size:27
Alignment explanation
Indices: 1359831--1359883 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1359821 TATAATTTTT
1359831 ATATATTAT-A-AATTAAATTTATATTAC
1 ATATATTATGATAA-TAAATTTA-ATTAC
*
1359858 ATATTTTATGATAATAAATTTAATTA
1 ATATATTATGATAATAAATTTAATTA
1359884 TTATAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 12 0.52
28 9 0.39
29 2 0.09
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATATTATGATAATAAATTTAATTAC
Found at i:1360891 original size:18 final size:18
Alignment explanation
Indices: 1360870--1360908 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1360860 CTGGTGGTTT
*
1360870 TGGAGGAGGAGGTGGAGG
1 TGGAGAAGGAGGTGGAGG
* *
1360888 TGGAGAAGGTGTTGGAGG
1 TGGAGAAGGAGGTGGAGG
1360906 TGG
1 TGG
1360909 GGCTGATGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.62, T:0.18
Consensus pattern (18 bp):
TGGAGAAGGAGGTGGAGG
Found at i:1360994 original size:18 final size:18
Alignment explanation
Indices: 1360973--1361014 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
1360963 AGCTGAGACT
1360973 GGTGGAGGAGGG-GGTGGA
1 GGTGGA-GAGGGTGGTGGA
1360991 GGTGGAGAGGGTGGTGGA
1 GGTGGAGAGGGTGGTGGA
1361009 GGTGGA
1 GGTGGA
1361015 AGTGGTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.17, C:0.00, G:0.69, T:0.14
Consensus pattern (18 bp):
GGTGGAGAGGGTGGTGGA
Found at i:1361132 original size:21 final size:21
Alignment explanation
Indices: 1361090--1361141 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1361080 AGGAGGAGAG
*
1361090 GGAGGTGGTGGTGGAAGCGGT
1 GGAGGTGGTGGGGGAAGCGGT
*
1361111 GGAGGTGGTGGGGGTGAG-GGT
1 GGAGGTGGTGGGGG-AAGCGGT
*
1361132 GGTGGTGGTG
1 GGAGGTGGTG
1361142 CTGGTAAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.10, C:0.02, G:0.67, T:0.21
Consensus pattern (21 bp):
GGAGGTGGTGGGGGAAGCGGT
Found at i:1363424 original size:16 final size:14
Alignment explanation
Indices: 1363400--1363441 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
1363390 AAAAATAATT
1363400 AAAATATATAATATA
1 AAAATATATAA-ATA
1363415 AAAATAATATAAATA
1 AAAAT-ATATAAATA
1363430 AAAA-AT-TAAATA
1 AAAATATATAAATA
1363442 TATAAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.23
13 2 0.08
15 12 0.46
16 6 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATATATAAATA
Found at i:1363441 original size:29 final size:27
Alignment explanation
Indices: 1363381--1363449 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 27
1363371 TAATAAGTTG
* *
1363381 TAAATAT-AAAA-AAATAATTAAAATA
1 TAAATATAAAAATAAATAAATAAAAAA
1363406 TATAATATAAAAATAATATAAATAAAAAA
1 TA-AATATAAAAATAA-ATAAATAAAAAA
*
1363435 TTAAATATATAAATA
1 -TAAATATAAAAATA
1363450 TTTTAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 2 0.06
26 5 0.14
27 4 0.11
28 2 0.06
29 21 0.58
30 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (27 bp):
TAAATATAAAAATAAATAAATAAAAAA
Found at i:1364875 original size:15 final size:17
Alignment explanation
Indices: 1364844--1364884 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1364834 TAACCTCAAT
*
1364844 TTAAAATGATCTAAAAC
1 TTAAAATAATCTAAAAC
1364861 -TAAAATAAT-TAAAAC
1 TTAAAATAATCTAAAAC
1364876 TTAAAATAA
1 TTAAAATAA
1364885 CTCAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.29
Consensus pattern (17 bp):
TTAAAATAATCTAAAAC
Found at i:1364891 original size:26 final size:26
Alignment explanation
Indices: 1364858--1364939 Score: 96
Period size: 26 Copynumber: 3.2 Consensus size: 26
1364848 AATGATCTAA
*
1364858 AACT-AAAATAATTAAAACTTAAAAT
1 AACTCAAAATAATTAAAATTTAAAAT
*
1364883 AACTCAAAATAATTTAAATTTAAAAT
1 AACTCAAAATAATTAAAATTTAAAAT
* * *
1364909 AATTCAAAA-ATTTATAAATTTAAATT
1 AACTCAAAATAATTA-AAATTTAAAAT
1364935 AACTC
1 AACTC
1364940 GACCTATCCA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
25 7 0.15
26 41 0.85
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (26 bp):
AACTCAAAATAATTAAAATTTAAAAT
Found at i:1375114 original size:14 final size:14
Alignment explanation
Indices: 1375095--1375122 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1375085 CCTGAAATCA
1375095 TTGAAAATTAAAAG
1 TTGAAAATTAAAAG
1375109 TTGAAAATTAAAAG
1 TTGAAAATTAAAAG
1375123 AACCCAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (14 bp):
TTGAAAATTAAAAG
Found at i:1380061 original size:25 final size:25
Alignment explanation
Indices: 1379999--1380068 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
1379989 AATAAAAATT
*
1379999 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
1380023 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
1380048 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
1380069 CAAAGGAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:1380114 original size:27 final size:27
Alignment explanation
Indices: 1380053--1380123 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
1380043 AAACAAGCCT
* *
1380053 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
1380081 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
1380108 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
1380124 AATGAGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Done.