Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1967
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: 158123
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
File 2 of 2
Found at i:132101 original size:11 final size:11
Alignment explanation
Indices: 132087--132123 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
132077 TATTTTCTCT
132087 TTTTTTCTTTC
1 TTTTTTCTTTC
132098 TTTTTTCTTTC
1 TTTTTTCTTTC
*
132109 TTTTTTTTTTC
1 TTTTTTCTTTC
132120 TTTT
1 TTTT
132124 CTTTCTCTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:132110 original size:15 final size:15
Alignment explanation
Indices: 132080--132129 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
132070 TTCACTATAT
*
132080 TTTCTCTTTT-TTTC
1 TTTCTTTTTTCTTTC
132094 TTTCTTTTTTCTTTC
1 TTTCTTTTTTCTTTC
*
132109 TTTTTTTTTTCTTTTC
1 TTTCTTTTTTC-TTTC
132125 TTTCT
1 TTTCT
132130 CTCGTTTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 9 0.29
15 14 0.45
16 8 0.26
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTCTTTTTTCTTTC
Found at i:132112 original size:22 final size:21
Alignment explanation
Indices: 132079--132123 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
132069 TTTCACTATA
132079 TTTTCTCTTTTTTTCTTTCTT
1 TTTTCTCTTTTTTTCTTTCTT
132100 TTTTCTTTCTTTTTTT-TTTCTT
1 TTTTC--TCTTTTTTTCTTTCTT
132122 TT
1 TT
132124 CTTTCTCTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.23
22 8 0.36
23 9 0.41
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTCTCTTTTTTTCTTTCTT
Found at i:133545 original size:167 final size:167
Alignment explanation
Indices: 132770--133856 Score: 1437
Period size: 166 Copynumber: 6.5 Consensus size: 167
132760 AGAAAATGGG
* * * * *
132770 GTTTCAAAGCAAAAATTCAAAAACTCATGAAGATGAATGAATTTTTGAAAATTGAATTAATATGA
1 GTTTC-AAGGAAAAAATAAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGA
*
132835 AATAAATAATGATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATT
65 AATAAATAATAATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATT
* * *
132900 TACAGAGTAGAAAACACCGTAT-TCCA-AAAAAA-TGAA
130 TACGGAGTAGAAAACACCATATCT-CAGAAAAAAGGGAA
* * * *
132936 GTTTCAAGGAAAAATTCAAAAACTCATGAAAATTAATGAATTTTTGAAAACTGAATTACTATGAA
1 GTTTCAAGGAAAAAATAAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAA
* * * * * *
133001 ATAAATAATAATGTTTTATAAATTTTAAAATTTTAAAACTAAGAAAAAT-CCTTCCGAAAAAATT
66 ATAAATAATAATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCT-CGAAAAAATT
**
133065 TATAGAGTAGAAAACACCATATCTCA-AAAAAAGGGAA
130 TACGGAGTAGAAAACACCATATCTCAGAAAAAAGGGAA
* * * *
133102 GTTTCAAGAAAAAAATCAAAAACTCATGAAAATTAATGAATTTTTGAAAA-TGGAATTAATATGT
1 GTTTCAAGGAAAAAATAAAAAACTCATGAAAATGAATGAATTTTTGAAAACT-GAATTAATATGA
* **
133166 AATAAATAATAATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAACTCCCCTTAAAAAAATT
65 AATAAATAATAATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATT
* * * *
133231 TACGGAGTAGAAAACACCGTATCTC-GGAACAAGGGTA
130 TACGGAGTAGAAAACACCATATCTCAGAAAAAAGGGAA
* *
133268 GTTTCAAGGAAAAAATAAAAAAACTCATG-AAATGAATGAATTTTTGAAAACTAAATTACTATGA
1 GTTTCAAGGAAAAAAT-AAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGA
* *
133332 AATAAATTATAATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCTCCTCGAAAAAATT
65 AATAAATAATAATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATT
*
133397 TACGGAGTAGAAAATACCATATCTCAGAAAAAA-GGAA
130 TACGGAGTAGAAAACACCATATCTCAGAAAAAAGGGAA
* *
133434 GTTTCAAGGAAAAAATAAAAAAGCTCATGAAAATGAATGAATTTATAAAAACTGAATTAATATGA
1 GTTTCAAGGAAAAAATAAAAAA-CTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGA
* *
133499 AATAAATGATAATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATTCCCTCGAAAAAATT
65 AATAAATAATAATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATT
* * * *
133564 TACGGAGTAGAAAACACCGTATCT-AAAAAAAATGGTA
130 TACGGAGTAGAAAACACCATATCTCAGAAAAAAGGGAA
* * *
133601 GTTTCAAGGAAAAAAATAAAAAACTCATGAAAATGAATGAATTTTTTAAAACTAAATTAATATGG
1 GTTTCAAGG-AAAAAATAAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGA
* *
133666 AATAAATGATAATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCAAAAAAATT
65 AATAAATAATAATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATT
* * * **
133731 TACGAAGTAGAAAATATCATAT-TTTGAAAAAATGGGAA
130 TACGGAGTAGAAAACACCATATCTCAGAAAAAA-GGGAA
* * * *
133769 -TTTCAA-GAAAAAATCAAAAGCTCTTGAAAATGATTGAATTTTTGAAAACTGAATTAATAAT-A
1 GTTTCAAGGAAAAAATAAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAAT-ATGA
* * *
133831 AATAAATGATAATATATGATGAATTT
65 AATAAATAATAATGTTTGATGAATTT
133857 CGATGCTTGA
Statistics
Matches: 821, Mismatches: 84, Indels: 33
0.88 0.09 0.04
Matches are distributed among these distances:
164 3 0.00
165 212 0.26
166 312 0.38
167 278 0.34
168 16 0.02
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (167 bp):
GTTTCAAGGAAAAAATAAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAA
ATAAATAATAATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTT
ACGGAGTAGAAAACACCATATCTCAGAAAAAAGGGAA
Found at i:135261 original size:83 final size:83
Alignment explanation
Indices: 135099--135367 Score: 228
Period size: 83 Copynumber: 3.2 Consensus size: 83
135089 ATCGGGACTG
* * * * ** * *
135099 AAAGGATAAAAGATTTACCTAGGACTAAGCCAACAGGTAAATAAAGGAAGAAAAGTTGA-CTAGG
1 AAAGGAGAAAAGATTTACCCAGGATTAAGCCAACAAGTAAACGATGGATGAAAAGTTGATC-AGG
* *
135163 -GCTGAACCGATAAGTCAAC
65 ATC-GAACCGACAAGTCAAC
* *
135182 AAAGGGCGAGAAA-ATTTA-CTAGGGATTAAGCCAACAAGTAAAC-A-GGA-GAAGAAAGTTGAT
1 AAA-GGAGA-AAAGATTTACCCA-GGATTAAGCCAACAAGTAAACGATGGATG-A-AAAGTTGAT
135242 CAGGATCGAACCGACAAGTCAAC
61 CAGGATCGAACCGACAAGTCAAC
* * *
135265 ATAGGATAAAAGATTTACCCAGGATTAAGCCAACAGGTAAACGATGGATGAAAAGTTGATCAGGA
1 AAAGGAGAAAAGATTTACCCAGGATTAAGCCAACAAGTAAACGATGGATGAAAAGTTGATCAGGA
* * * *
135330 TTGAACTGTCAAGTTAAC
66 TCGAACCGACAAGTCAAC
* * *
135348 AAGGGATAAAGGATTTACCC
1 AAAGGAGAAAAGATTTACCC
135368 GGGACTAGGT
Statistics
Matches: 155, Mismatches: 19, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
81 4 0.03
82 32 0.21
83 83 0.54
84 32 0.21
85 4 0.03
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.18
Consensus pattern (83 bp):
AAAGGAGAAAAGATTTACCCAGGATTAAGCCAACAAGTAAACGATGGATGAAAAGTTGATCAGGA
TCGAACCGACAAGTCAAC
Found at i:135670 original size:83 final size:83
Alignment explanation
Indices: 135454--135822 Score: 366
Period size: 83 Copynumber: 4.4 Consensus size: 83
135444 GAAGTACCTG
* * * * * ** *
135454 GGACCAAGCCGATAGGTGAATAAAGGATAAAGGTTGATAAGAGACTGAGCTGACAAGTCACCATA
1 GGACTAAGCCGACAGGTAAATAATGGATGAAGGTTGACCAGAGACTGAGCTGACAGGTCACCATA
*
135519 AGGGTAATGGGCTCACCACA
66 AGGGTAATGGG-TTACCA-A
* * * *
135539 -GACTAAGCCAACATGTAAATAATGGATGAAGGTTGATCAGAGATTGAGCTGACAGGTCACCATA
1 GGACTAAGCCGACAGGTAAATAATGGATGAAGGTTGACCAGAGACTGAGCTGACAGGTCACCATA
*
135603 AGGGTAATAGGTTACCAA
66 AGGGTAATGGGTTACCAA
* **
135621 GGACTAAGCCGACAGGTAAATAATGGATGAAGGTTGACCGGAGACTGAGCTGATGGGTCACCATA
1 GGACTAAGCCGACAGGTAAATAATGGATGAAGGTTGACCAGAGACTGAGCTGACAGGTCACCATA
* **
135686 TGGGTAATGGGTTACCGG
66 AGGGTAATGGGTTACCAA
* * * * *
135704 GGACTAAGCCGACTA-GTAAACAATGGATGAAGGTTGA-CTGAAGATTAAGCTGATAGGTCACCA
1 GGACTAAGCCGAC-AGGTAAATAATGGATGAAGGTTGACCAG-AGACTGAGCTGACAGGTCACCA
* * *
135767 TAAGGGTGATGGGTTTATCAG
64 TAAGGGTAATGGG-TTACCAA
*** * * *
135788 GGACTAAATTGACTGGTAAACAATAGATGAAGGTT
1 GGACTAAGCCGACAGGTAAATAATGGATGAAGGTT
135823 ATTTCCCAAG
Statistics
Matches: 242, Mismatches: 37, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
82 3 0.01
83 140 0.58
84 99 0.41
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.21
Consensus pattern (83 bp):
GGACTAAGCCGACAGGTAAATAATGGATGAAGGTTGACCAGAGACTGAGCTGACAGGTCACCATA
AGGGTAATGGGTTACCAA
Found at i:135794 original size:167 final size:167
Alignment explanation
Indices: 135448--135822 Score: 414
Period size: 167 Copynumber: 2.2 Consensus size: 167
135438 TAAAAGGAAG
* * * * * * *
135448 TACCTGGGACCAAGCCGATAGGTGAATAAAGGATAAAGGTTGATAAGAGACTGAGCTGACAAGTC
1 TACCAGGGACTAAGCCGACAGGTAAATAATGGATGAAGGTTGACAAGAGACTGAGCTGACAAGTC
*
135513 ACCATAAGGGTAATGGGCTCACCACAGACTAAGCCAACATGTAAATAATGGATGAAGGTTGATCA
66 ACCATAAGGGTAATGGGCTCACCACAGACTAAGCCAACATGTAAACAATGGATGAAGGTTGATCA
*
135578 GAGATTGAGCTGACAGGTCACCATAAGGGTAATAGGT
131 GAGATTAAGCTGACAGGTCACCATAAGGGTAATAGGT
* ** ***
135615 TACCAAGGACTAAGCCGACAGGTAAATAATGGATGAAGGTTGACCGGAGACTGAGCTGATGGGTC
1 TACCAGGGACTAAGCCGACAGGTAAATAATGGATGAAGGTTGACAAGAGACTGAGCTGACAAGTC
* * *** *
135680 ACCATATGGGTAATGGG-TTACCGGGGACTAAGCCGAC-TAGTAAACAATGGATGAAGGTTGA-C
66 ACCATAAGGGTAATGGGCTCACCACAGACTAAGCCAACAT-GTAAACAATGGATGAAGGTTGATC
* * * *
135742 TGAAGATTAAGCTGATAGGTCACCATAAGGGTGATGGGTT
130 AG-AGATTAAGCTGACAGGTCACCATAAGGGTAATAGG-T
* *** * * *
135782 TATCAGGGACTAAATTGACTGGTAAACAATAGATGAAGGTT
1 TACCAGGGACTAAGCCGACAGGTAAATAATGGATGAAGGTT
135823 ATTTCCCAAG
Statistics
Matches: 172, Mismatches: 33, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
165 3 0.02
166 67 0.39
167 102 0.59
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.21
Consensus pattern (167 bp):
TACCAGGGACTAAGCCGACAGGTAAATAATGGATGAAGGTTGACAAGAGACTGAGCTGACAAGTC
ACCATAAGGGTAATGGGCTCACCACAGACTAAGCCAACATGTAAACAATGGATGAAGGTTGATCA
GAGATTAAGCTGACAGGTCACCATAAGGGTAATAGGT
Found at i:136201 original size:85 final size:85
Alignment explanation
Indices: 136109--137203 Score: 645
Period size: 85 Copynumber: 12.9 Consensus size: 85
136099 GGCAAACAAT
* *
136109 TGATGAAAAAGTCTCCCGAGTCTGAGCCGACGGGCAGATGATGGATAAAGAAAGTCTCTCGGGTC
1 TGATGAAAAAGTCTCCCGAGTCTAAGCCGACGGGCAGATGATTGATAAAGAAAGTCTCTCGGGTC
*
136174 TGAGCCGACGGGCAGACGAA
66 TAAGCCGACGGGCAGACGAA
** * * *** * * * *
136194 TGATGAAAAAGTCTCTTGGGTCTAAGCCGTCACACAGATGATTGATAAAGGAAGTCCCCCTGGTC
1 TGATGAAAAAGTCTCCCGAGTCTAAGCCGACGGGCAGATGATTGATAAAGAAAGTCTCTCGGGTC
* * ** * *
136259 TGAGTCGATAGGCAGATGAT
66 TAAGCCGACGGGCAGACGAA
* * * * * * * **
136279 TGATGGAAAAGTCTCTCGAGTCTAAGCCGACGGGCATAAGATAGATAAAGGAAGTCTCCCATGTC
1 TGATGAAAAAGTCTCCCGAGTCTAAGCCGACGGGCAGATGATTGATAAAGAAAGTCTCTCGGGTC
* * *
136344 TAAGTCGACGGGTAGATGAA
66 TAAGCCGACGGGCAGACGAA
* * * * * *
136364 TGATGGAAAAGTCTCTCGAGTCTAAGTCGACGGGCAGATGATTGATAAAGGAAGTCCCCCGGGTC
1 TGATGAAAAAGTCTCCCGAGTCTAAGCCGACGGGCAGATGATTGATAAAGAAAGTCTCTCGGGTC
* * *
136429 TGAGCCGACGGGCAGATGAT
66 TAAGCCGACGGGCAGACGAA
* * * * * *
136449 TGAT-AAAGGAAGTC-CCTCG-GATCTGAGTCGATGAGCAGATGATTGATAAA-AGAAGTCCCCC
1 TGATGAAA--AAGTCTCC-CGAG-TCTAAGCCGACGGGCAGATGATTGATAAAGA-AAGTCTCTC
** * * *
136510 AAGTCTAAGCCGACAGGAAGA-TAA
61 GGGTCTAAGCCGACGGGCAGACGAA
* * * * * *
136534 TTGATGGAAAAGTCTCCAG-GTCTAAGCCGACGGGCAAATGATTGACAAAGGAAGTCTC-CTGAG
1 -TGATGAAAAAGTCTCCCGAGTCTAAGCCGACGGGCAGATGATTGATAAAGAAAGTCTCTC-GGG
* *
136597 TCTAAGCCGATGGGCAGATGAA
64 TCTAAGCCGACGGGCAGACGAA
* * ** * * *
136619 TGATGAAAAAGTCTCTCGAGTCTAAGCCAAAAGGCAGATGACTGATGAA-AAAGTCTCTCGAGTC
1 TGATGAAAAAGTCTCCCGAGTCTAAGCCGACGGGCAGATGATTGATAAAGAAAGTCTCTCGGGTC
* * *
136683 TAAGCCGATGGGCAAACGAT
66 TAAGCCGACGGGCAGACGAA
** * * * ** * *
136703 TGATGAAAAAGTCTTTCG-GATCTAAGCTGACAGGTAGACAATTGACAAAGGAAA-TCTCTCGAG
1 TGATGAAAAAGTCTCCCGAG-TCTAAGCCGACGGGCAGATGATTGATAAA-GAAAGTCTCTCGGG
* *
136766 TCT-AGCCGACTGGCAGACGAT
64 TCTAAGCCGACGGGCAGACGAA
* * ** * * * * * *
136787 TGAT-AAAGGAAGTCTCCTGAGTCTAATCC-AATGGTAAATGATTGATGAAAAAAAATCTCCCGA
1 TGATGAAA--AAGTCTCCCGAGTCTAAGCCGACGGGCAGATGATTGAT-AAAGAAAGTCTCTCGG
* ** *
136850 GTCTAAGCTGATAGGCAGACGAT
63 GTCTAAGCCGACGGGCAGACGAA
* * ** *
136873 TGATGAAAAAGTCTCTC-AGGTCTAAGCTGACGGGCAGACAATTGACAAA-AGAAGTCTCTCGGG
1 TGATGAAAAAGTCTCCCGA-GTCTAAGCCGACGGGCAGATGATTGATAAAGA-AAGTCTCTCGGG
* * * *
136936 TCTAAGCCAACGAGTAAAC-AA
64 TCTAAGCCGACGGGCAGACGAA
* * * * * * * * *
136957 TTGATAAAAGAAG-CCCCCTGGGTTTGAGCTGA-TGGCTAGACGATTG-TCAAAGGAAGTCTCT-
1 -TGATGAAA-AAGTCTCCC-GAGTCTAAGCCGACGGGC-AGATGATTGAT-AAAGAAAGTCTCTC
* *
137018 GAGGTCTAAGCCAACAGGCAGACG-A
61 G-GGTCTAAGCCGACGGGCAGACGAA
* * * * *
137043 TGGAT-AGAAAAGTCT-CTGAGGTCTAAGTCGATGGGCAGATGATGGATAGA-AAAGTCTCTCGG
1 T-GATGA-AAAAGTCTCCCGA-GTCTAAGCCGACGGGCAGATGATTGATAAAGAAAGTCTCTCGG
* * *
137105 GTCTAAGCCGACGGCCAGATGAT
63 GTCTAAGCCGACGGGCAGACGAA
* * * * * *
137128 TGATGAAAAAATCTCCCGGGTCTAAGCCAACGGGCAGATGATTGACAAAGGAAGTCTCTCTGGTC
1 TGATGAAAAAGTCTCCCGAGTCTAAGCCGACGGGCAGATGATTGATAAAGAAAGTCTCTCGGGTC
*
137193 TAAGCCAACGG
66 TAAGCCGACGG
137204 TTAAACGATT
Statistics
Matches: 781, Mismatches: 183, Indels: 92
0.74 0.17 0.09
Matches are distributed among these distances:
83 5 0.01
84 226 0.29
85 389 0.50
86 156 0.20
87 5 0.01
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (85 bp):
TGATGAAAAAGTCTCCCGAGTCTAAGCCGACGGGCAGATGATTGATAAAGAAAGTCTCTCGGGTC
TAAGCCGACGGGCAGACGAA
Found at i:136222 original size:42 final size:42
Alignment explanation
Indices: 136107--137203 Score: 623
Period size: 42 Copynumber: 25.8 Consensus size: 42
136097 AAGGCAAACA
* * *
136107 ATTGATGAAAAAGTCTCCCGAGTCTGAGCCGACGGGCAGATG
1 ATTGATGAAAAAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * * *
136149 ATGGATAAAGAAAGTCTCTCGGGTCTGAGCCGACGGGCAGACG
1 ATTGATGAA-AAAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * * ***
136192 AATGATGAAAAAGTCTCTTGGGTCTAAGCCGTCACACAGATG
1 ATTGATGAAAAAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * * * * **
136234 ATTGAT-AAAGGAAGTCCCCCTGGTCTGAGTCGATAGGCAGATG
1 ATTGATGAAA--AAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * * *
136277 ATTGATGGAAAAGTCTCTCGAGTCTAAGCCGACGGGCATAAG
1 ATTGATGAAAAAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * ** * *
136319 ATAGAT-AAAGGAAGTCTCCCATGTCTAAGTCGACGGGTAGATG
1 ATTGATGAAA--AAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * * *
136362 AATGATGGAAAAGTCTCTCGAGTCTAAGTCGACGGGCAGATG
1 ATTGATGAAAAAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * *
136404 ATTGAT-AAAGGAAGTCCCCCGGGTCTGAGCCGACGGGCAGATG
1 ATTGATGAAA--AAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * * * * *
136447 ATTGAT-AAAGGAAGTCCCTCGGATCTGAGTCGATGAGCAGATG
1 ATTGATGAAA--AAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * * ** * * *
136490 ATTGATAAAAGAAGTCCCCCAAGTCTAAGCCGACAGGAAGATA
1 ATTGATGAAA-AAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * *
136533 ATTGATGGAAAAGTCTC-CAGGTCTAAGCCGACGGGCAAATG
1 ATTGATGAAAAAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * *
136574 ATTGA-CAAAGGAAGTCTC-CTGAGTCTAAGCCGATGGGCAGATG
1 ATTGATGAAA--AAGTCTCTC-GGGTCTAAGCCGACGGGCAGATG
* * * **
136617 AATGATGAAAAAGTCTCTCGAGTCTAAGCCAAAAGGCAGATG
1 ATTGATGAAAAAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * * * *
136659 ACTGATGAAAAAGTCTCTCGAGTCTAAGCCGATGGGCAAACG
1 ATTGATGAAAAAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * * * * **
136701 ATTGATGAAAAAGTCTTTCGGATCTAAGCTGACAGGTAGACA
1 ATTGATGAAAAAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * * * *
136743 ATTGA-CAAAGGAAATCTCTCGAGTCT-AGCCGACTGGCAGACG
1 ATTGATGAAA--AAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * ** * *
136785 ATTGAT-AAAGGAAGTCTC-CTGAGTCTAATCC-AATGGTAAATG
1 ATTGATGAAA--AAGTCTCTC-GGGTCTAAGCCGACGGGCAGATG
* * * * ** *
136827 ATTGATGAAAAAAAATCTCCCGAGTCTAAGCTGATAGGCAGACG
1 ATTGATG--AAAAAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * **
136871 ATTGATGAAAAAGTCTCTCAGGTCTAAGCTGACGGGCAGACA
1 ATTGATGAAAAAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
** * * * * **
136913 ATTGACAAAAGAAGTCTCTCGGGTCTAAGCCAACGAGTAAACA
1 ATTGATGAAA-AAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * * * * * * *
136956 ATTGATAAAAGAAG-CCCCCTGGGTTTGAGCTGA-TGGCTAGACG
1 ATTGATGAAA-AAGTCTCTC-GGGTCTAAGCCGACGGGC-AGATG
* * * *
136999 ATTG-TCAAAGGAAGTCTCT-GAGGTCTAAGCCAACAGGCAGACG
1 ATTGATGAAA--AAGTCTCTCG-GGTCTAAGCCGACGGGCAGATG
* * *
137042 ATGGAT-AGAAAAGTCTCT-GAGGTCTAAGTCGATGGGCAGATG
1 ATTGATGA-AAAAGTCTCTCG-GGTCTAAGCCGACGGGCAGATG
* *
137084 ATGGAT-AGAAAAGTCTCTCGGGTCTAAGCCGACGGCCAGATG
1 ATTGATGA-AAAAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * *
137126 ATTGATGAAAAAATCTCCCGGGTCTAAGCCAACGGGCAGATG
1 ATTGATGAAAAAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
* * *
137168 ATTGA-CAAAGGAAGTCTCTCTGGTCTAAGCCAACGG
1 ATTGATGAAA--AAGTCTCTCGGGTCTAAGCCGACGG
137204 TTAAACGATT
Statistics
Matches: 830, Mismatches: 187, Indels: 75
0.76 0.17 0.07
Matches are distributed among these distances:
40 2 0.00
41 38 0.05
42 408 0.49
43 347 0.42
44 32 0.04
45 3 0.00
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (42 bp):
ATTGATGAAAAAGTCTCTCGGGTCTAAGCCGACGGGCAGATG
Found at i:137230 original size:22 final size:22
Alignment explanation
Indices: 137200--137244 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
137190 GTCTAAGCCA
* *
137200 ACGGTTAAACGATTGATAAAGG
1 ACGGGTAAACAATTGATAAAGG
137222 ACGGGTAAACAATTGATAAAGG
1 ACGGGTAAACAATTGATAAAGG
137244 A
1 A
137245 AGTCCCCCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.27, T:0.20
Consensus pattern (22 bp):
ACGGGTAAACAATTGATAAAGG
Found at i:137462 original size:277 final size:275
Alignment explanation
Indices: 136949--137497 Score: 609
Period size: 277 Copynumber: 2.0 Consensus size: 275
136939 AAGCCAACGA
* * * *
136949 GTAAACAATTGATAAAAGAAGCCCCCTGGGTTTGAGCTGATGGCTAGACGATTGTCAAAGGAAGT
1 GTAAACAATTGATAAAAGAAGCCCCCTAGGTATGAGCTGAAGGCTAGACGATTGACAAAGGAAGT
* * *
137014 CTCTGAGGTCTAAGCCAACAGGCAGACGATGGATAGAAAAGTCTCTGAGGTCTAAGTCGATGGGC
66 CTCCGAGGTCTAAGCCAACAGGCAAACGATAGATAGAAAAGTCTCTGAGGTCTAAGTCGATGGGC
** * **
137079 AGATGATGGATAGAAAAGTCTCTCGGGTCTAAGCCGACGGCCAGATGATTGATGAAAAAATCTCC
131 AGATGAAAGATAAAAAAGTCTCTCGGGTCTAAGCCGACGGCCAGACAATTGATGAAAAAATCTCC
* * *
137144 CGGGTCTAAGCCAACGGGCAGATGATTGACAAAGGAAGTCTCTCTG-GTCTAAGCCAACGGTTAA
196 CGGGTCTAAGCCAACGAGCAGATGATTGA-AAA-GAAGTCTC-CCGAGTCTAAGCCAACGGGTAA
137208 ACGATTGATAAAGGACGG
258 ACGATTGATAAAGGACGG
*
137226 GTAAACAATTGATAAAGGAAGTCCCCC-AGGTATGAGCTGACAGG-TAGACGATTGACAAAGGAA
1 GTAAACAATTGATAAAAGAAG-CCCCCTAGGTATGAGCTGA-AGGCTAGACGATTGACAAAGGAA
* * *
137289 GTCTCCCGA-GTCTGAGCCAACAGGCAAATGATAGAT-GAAGAAGTCTCTTGA-GTCTATG-CTG
64 GTCT-CCGAGGTCTAAGCCAACAGGCAAACGATAGATAGAA-AAGTCTC-TGAGGTCTAAGTC-G
* *
137350 ATGGGTAGATGAAAGATGAAAAAAGTCTC-CTGGGTCTAAGCCGACGAG-CATACAATTGAT-AA
125 ATGGGCAGATGAAAGAT-AAAAAAGTCTCTC-GGGTCTAAGCCGACG-GCCAGACAATTGATGAA
* * * * * *
137412 AGAAGTCTCCCGGGTCTGAGCCGATGAGCAAACGATGGTTG-AAA-AAGTCTCCCGAGTCTGAGC
187 A-AAATCTCCCGGGTCTAAGCCAACGAGC--A-GATGATTGAAAAGAAGTCTCCCGAGTCTAAGC
* *
137475 CGACGGGTAGACGATTGATAAAG
248 CAACGGGTAAACGATTGATAAAG
137498 AAGTCTCGTG
Statistics
Matches: 229, Mismatches: 29, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
276 6 0.03
277 142 0.62
278 69 0.30
279 4 0.02
280 1 0.00
281 7 0.03
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (275 bp):
GTAAACAATTGATAAAAGAAGCCCCCTAGGTATGAGCTGAAGGCTAGACGATTGACAAAGGAAGT
CTCCGAGGTCTAAGCCAACAGGCAAACGATAGATAGAAAAGTCTCTGAGGTCTAAGTCGATGGGC
AGATGAAAGATAAAAAAGTCTCTCGGGTCTAAGCCGACGGCCAGACAATTGATGAAAAAATCTCC
CGGGTCTAAGCCAACGAGCAGATGATTGAAAAGAAGTCTCCCGAGTCTAAGCCAACGGGTAAACG
ATTGATAAAGGACGG
Found at i:137511 original size:42 final size:42
Alignment explanation
Indices: 137233--137516 Score: 169
Period size: 42 Copynumber: 6.7 Consensus size: 42
137223 CGGGTAAACA
* * * * *
137233 ATTGATAAAGGAAGTC-CCCCAGGTATGAGCTGACAGGTAGACG
1 ATTGATAAA-GAAGTCTCCCGA-GTCTGAGCCGACGGGCAGACG
* * * * *
137276 ATTGACAAAGGAAGTCTCCCGAGTCTGAGCCAACAGGCAAATG
1 ATTGATAAA-GAAGTCTCCCGAGTCTGAGCCGACGGGCAGACG
* * ** * * * *
137319 ATAGATGAAGAAGTCTCTTGAGTCT-ATGCTGATGGGTAGATG
1 ATTGATAAAGAAGTCTCCCGAGTCTGA-GCCGACGGGCAGACG
** * * * * * * *
137361 AAAGATGAAAAAAGTCTCCTGGGTCTAAGCCGACGAGCATACA
1 ATTGAT-AAAGAAGTCTCCCGAGTCTGAGCCGACGGGCAGACG
* * * *
137404 ATTGATAAAGAAGTCTCCCGGGTCTGAGCCGATGAGCAAACG
1 ATTGATAAAGAAGTCTCCCGAGTCTGAGCCGACGGGCAGACG
* * *
137446 ATGGTTGAAA-AAGTCTCCCGAGTCTGAGCCGACGGGTAGACG
1 ATTGAT-AAAGAAGTCTCCCGAGTCTGAGCCGACGGGCAGACG
**
137488 ATTGATAAAGAAGTCTCGTGAGTCTGAGC
1 ATTGATAAAGAAGTCTCCCGAGTCTGAGC
137517 TTGTACGCTC
Statistics
Matches: 185, Mismatches: 50, Indels: 13
0.75 0.20 0.05
Matches are distributed among these distances:
41 4 0.02
42 110 0.59
43 66 0.36
44 5 0.03
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.21
Consensus pattern (42 bp):
ATTGATAAAGAAGTCTCCCGAGTCTGAGCCGACGGGCAGACG
Found at i:138359 original size:13 final size:13
Alignment explanation
Indices: 138341--138367 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
138331 TACAATGAGC
138341 ATGTATCGATACA
1 ATGTATCGATACA
138354 ATGTATCGATACA
1 ATGTATCGATACA
138367 A
1 A
138368 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:142288 original size:17 final size:15
Alignment explanation
Indices: 142253--142292 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
142243 GAGTTTTATC
142253 AAAATTTTCTCTATT
1 AAAATTTTCTCTATT
*
142268 AAAATCTTTTTCTATT
1 AAAAT-TTTCTCTATT
142284 AAAAATTTT
1 -AAAATTTT
142293 GAAAGTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 12 0.55
17 5 0.23
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (15 bp):
AAAATTTTCTCTATT
Found at i:145320 original size:15 final size:15
Alignment explanation
Indices: 145302--145333 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
145292 TGAGTCAACT
145302 TCATCATCATCATTA
1 TCATCATCATCATTA
*
145317 TCATCATCTTCATTA
1 TCATCATCATCATTA
145332 TC
1 TC
145334 TTTGATGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (15 bp):
TCATCATCATCATTA
Found at i:146924 original size:33 final size:33
Alignment explanation
Indices: 146887--146953 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
146877 CGTTAGGCAT
*
146887 AATGTATCGATACAATTCTTC-ATGTATCGATAC
1 AATGTATCGATAC-ATTCTCCTATGTATCGATAC
*
146920 AATGTATCGATACATTGTCCTATGTATCGATAC
1 AATGTATCGATACATTCTCCTATGTATCGATAC
146953 A
1 A
146954 TTTCACTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 5 0.16
33 26 0.84
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (33 bp):
AATGTATCGATACATTCTCCTATGTATCGATAC
Found at i:146926 original size:13 final size:13
Alignment explanation
Indices: 146908--146933 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
146898 ACAATTCTTC
146908 ATGTATCGATACA
1 ATGTATCGATACA
146921 ATGTATCGATACA
1 ATGTATCGATACA
146934 TTGTCCTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:147025 original size:19 final size:19
Alignment explanation
Indices: 146982--147037 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
146972 CTAGCAGTTT
146982 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAG
*
147002 TATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
147021 CATGTATCGATACAATG
1 CATGTATCGATACAATG
147038 TATGATACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:147524 original size:42 final size:42
Alignment explanation
Indices: 147446--147531 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 42
147436 GTTTGAATTA
* * * *
147446 ACGGGTAGACAATGGATGAAGAAGTCTCCCGAGTCAACGTCG
1 ACGGGTAGACAAAGGATAAAGAAGTCTCCAGAGTCAAAGTCG
147488 ACGGGTAGACAAAGGATAAAGAAGTCTCCTAG-GTCAAAGTCG
1 ACGGGTAGACAAAGGATAAAGAAGTCTCC-AGAGTCAAAGTCG
147530 AC
1 AC
147532 AGGAAAACTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 38 0.97
43 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.16
Consensus pattern (42 bp):
ACGGGTAGACAAAGGATAAAGAAGTCTCCAGAGTCAAAGTCG
Found at i:147614 original size:43 final size:43
Alignment explanation
Indices: 147506--148144 Score: 636
Period size: 43 Copynumber: 14.9 Consensus size: 43
147496 ACAAAGGATA
* * * **
147506 AAGAAGTCTCCTA-GGTCAAAGTCGACAGGAAAACTTAAGGGCA
1 AAGAAGTCTCC-AGGGTCAAAGCCGACAGGCAGACTTAAGGGGG
* *
147549 AAGAAAGTCTCCAGGGTCAAAGCCGATAGGCAAACTTAAGGGGG
1 AAG-AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGGGG
* *
147593 AAGAAGTCTCCAGGGTCAAAGCCGACATGCAGACTTAAGGGCG
1 AAGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGGGG
* * *
147636 AAGAAGTCTCCAAGGTCAAAGCTGACAGGCAGACTTAAGCGGG
1 AAGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGGGG
* *
147679 AAGAAGTCTCCATGGTCAAAGCCGACAGGCAGACTTAAGCGGG
1 AAGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGGGG
* * * *
147722 AAGACGTCTCAAGGGTCAAAGCCGATAGGCAGAATTAAGGGGG
1 AAGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGGGG
* * * * *
147765 AAAAAGTCTCCAAGGTCAAATCCGATAGGCCGACTTAAGGGGG
1 AAGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGGGG
* * *
147808 AAGAAGTCTCTAGGGTCAAAGTCGACAGGCAAACTT-AGAGGGG
1 AAGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG-GGGG
* * * * * **
147851 AAGAAGTCTCCAAGGTTAAAGTCGACAGGTAGACTTGAGGATG
1 AAGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGGGG
* * * * *
147894 AAGAAGTCTCCAAGGTCAAAGCCGACTGGTAGACTTGAGGGCG
1 AAGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGGGG
* ** * *
147937 AAGAAGTCTCCAAGGTC-AAGTTGACAAGCAGACTTAAGGGGA
1 AAGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGGGG
* * * * **
147979 AAGAAGTCTCTAGAGTCAAAGCCAACAGGTAGACTTAAAAGGG
1 AAGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGGGG
* * * * ***
148022 AAGAAGTCACTAGGGTCAAAGCCGACAAGCAGACTTGAGGTCA
1 AAGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGGGG
** * **
148065 AAGAAGTCTCCAGGGTCAAAGCTAACAGGCAGACTTAAAGAAG
1 AAGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGGGG
** * * *
148108 AAGAAGTCTTTAAGGTCAAAGCTGACAAGCAGACTTA
1 AAGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTA
148145 TGGTGAAGCA
Statistics
Matches: 497, Mismatches: 94, Indels: 10
0.83 0.16 0.02
Matches are distributed among these distances:
42 33 0.07
43 426 0.86
44 38 0.08
ACGTcount: A:0.36, C:0.19, G:0.29, T:0.16
Consensus pattern (43 bp):
AAGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGGGG
Found at i:148256 original size:42 final size:42
Alignment explanation
Indices: 148210--148355 Score: 150
Period size: 42 Copynumber: 3.5 Consensus size: 42
148200 TCTCGGGTCA
* *
148210 AAGCCAATGGGCAGACGAAGGATAAAGAAGTCTCCTAGGCCT
1 AAGCCGATGGGCAGACAAAGGATAAAGAAGTCTCCTAGGCCT
* ** **
148252 AAGCCGACGGGCAGACAAAGGACGAAGAAGTC-CCCGGGCCT
1 AAGCCGATGGGCAGACAAAGGATAAAGAAGTCTCCTAGGCCT
* * * * * *
148293 AAGCTGATGGGCAAATAAAAGATAGAGAAGTCTCCTAGGTCT
1 AAGCCGATGGGCAGACAAAGGATAAAGAAGTCTCCTAGGCCT
* *
148335 AAGCCGACGGGTAGACAAAGG
1 AAGCCGATGGGCAGACAAAGG
148356 GTACAAAAAG
Statistics
Matches: 79, Mismatches: 24, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
41 31 0.39
42 48 0.61
ACGTcount: A:0.36, C:0.21, G:0.31, T:0.12
Consensus pattern (42 bp):
AAGCCGATGGGCAGACAAAGGATAAAGAAGTCTCCTAGGCCT
Found at i:148538 original size:44 final size:44
Alignment explanation
Indices: 148479--148635 Score: 129
Period size: 44 Copynumber: 3.6 Consensus size: 44
148469 GCAAATTGTT
*
148479 TGACTAGGGTGGTAACCATACGTCAAATCGAAATAAAAAAAGTC
1 TGACCAGGGTGGTAACCATACGTCAAATCGAAATAAAAAAAGTC
* * * * * * * ** *
148523 TGACCAGGGTTGTAACCATATGTTAGATAGGAAT-GAAGCAGATT
1 TGACCAGGGTGGTAACCATACGTCAAATCGAAATAAAAAAAG-TC
* * *
148567 TGACTAGGGTGGTAAACATACATCAAATCGAAATAAAAAGAA-TC
1 TGACCAGGGTGGTAACCATACGTCAAATCGAAATAAAAA-AAGTC
* * *
148611 TAACCAAGGTGGTAACCATGCGTCA
1 TGACCAGGGTGGTAACCATACGTCA
148636 GACAGGAAAA
Statistics
Matches: 80, Mismatches: 30, Indels: 6
0.69 0.26 0.05
Matches are distributed among these distances:
43 4 0.05
44 73 0.91
45 2 0.03
46 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.22
Consensus pattern (44 bp):
TGACCAGGGTGGTAACCATACGTCAAATCGAAATAAAAAAAGTC
Found at i:148643 original size:88 final size:88
Alignment explanation
Indices: 148477--148643 Score: 237
Period size: 88 Copynumber: 1.9 Consensus size: 88
148467 ATGCAAATTG
* * * * *
148477 TTTGACTAGGGTGGTAACCATACGTCAAATCGAAATAAAAAAAGTCTGACCAGGGTTGTAACCAT
1 TTTGACTAGGGTGGTAAACATACATCAAATCGAAATAAAAAAAGTCTAACCAAGGTGGTAACCAT
* * *
148542 ATGTTAGATAGGAATGAAGCAGA
66 ACGTCAGACAGGAATGAAGCAGA
148565 TTTGACTAGGGTGGTAAACATACATCAAATCGAAATAAAAAGAA-TCTAACCAAGGTGGTAACCA
1 TTTGACTAGGGTGGTAAACATACATCAAATCGAAATAAAAA-AAGTCTAACCAAGGTGGTAACCA
*
148629 TGCGTCAGACAGGAA
65 TACGTCAGACAGGAA
148644 AAAGGAGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
88 67 0.97
89 2 0.03
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (88 bp):
TTTGACTAGGGTGGTAAACATACATCAAATCGAAATAAAAAAAGTCTAACCAAGGTGGTAACCAT
ACGTCAGACAGGAATGAAGCAGA
Found at i:148659 original size:88 final size:88
Alignment explanation
Indices: 148479--148662 Score: 228
Period size: 88 Copynumber: 2.1 Consensus size: 88
148469 GCAAATTGTT
* * * * * *
148479 TGACTAGGGTGGTAACCATACGTCAAATCGAAATAAAAAAAGTCTGACCAGGGTTGTAACCATAT
1 TGACTAGGGTGGTAAACATACATCAAATCGAAATAAAAAAAGTCTAACCAAGGTGGTAACCATAC
* * * *
148544 GTTAGATAGGAATGAAGCAGATT
66 GTCAGACAGGAATAAAGCAGATC
*
148567 TGACTAGGGTGGTAAACATACATCAAATCGAAATAAAAAGAA-TCTAACCAAGGTGGTAACCATG
1 TGACTAGGGTGGTAAACATACATCAAATCGAAATAAAAA-AAGTCTAACCAAGGTGGTAACCATA
*
148631 CGTCAGACAGGAA-AAAGGAGAGTC
65 CGTCAGACAGGAATAAAGCAGA-TC
148655 TGACTAGG
1 TGACTAGG
148663 CCCTAACACC
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
87 6 0.07
88 74 0.90
89 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (88 bp):
TGACTAGGGTGGTAAACATACATCAAATCGAAATAAAAAAAGTCTAACCAAGGTGGTAACCATAC
GTCAGACAGGAATAAAGCAGATC
Found at i:154589 original size:160 final size:156
Alignment explanation
Indices: 154238--154672 Score: 439
Period size: 160 Copynumber: 2.7 Consensus size: 156
154228 GCTAAGTTAA
* * * *
154238 AGAAAAATTATGAAAATGCCCCTAAAG-ATACCTTCGATGTAAAAGTATCCTAACAGCCCT-AAA
1 AGAAAAATTATGAAAATGCCCCTAGAGTATACCTTCGACGTAAAAGTATCCTAGCAACCCTAAAA
* * * ** *
154301 GAACCTAAAAAGACTCATAAAAGGGAAGAACCTATTTTAAATGCCCACCTTCGGCATAAAAGTGG
66 G-ACTTAAAAAGACTCATAAAAAGGAAGAACCTATTGTAAATGCCCACCTTCAACATAAAAGTAG
* **
154366 ACCCGGTATGACCTTGGGGTTGGTTCT
130 ACCCGGTATGACCTAGGCATTGGTTCT
** * * *
154393 A-AAAAATTACCAAAATACCCCTAGGATTATGTATACCTTCGACATAAAAGTATCTTAGCAACCC
1 AGAAAAATTATGAAAATGCCCCTA-G---A-GTATACCTTCGACGTAAAAGTATCCTAGCAACCC
* **
154457 TAAAAGACTTAAAAAGACTCATAAAAAGGATA-AACCTATATCGTATATGCCCATTTTCAACATA
61 TAAAAGACTTAAAAAGACTCATAAAAAGGA-AGAACCTAT-T-GTAAATGCCCACCTTCAACATA
154521 AAAGTAGACCCGGTGATGACCTAGGCATTGGTTCT
123 AAAGTAGACCCGGT-ATGACCTAGGCATTGGTTCT
* * * *
154556 AGAAAAATTATGAAAATGTCCTTACGAGTATACCTTCGACGTAAAAGTATCCCAGTAACCCTAAA
1 AGAAAAATTATGAAAATGCCCCTA-GAGTATACCTTCGACGTAAAAGTATCCTAGCAACCCTAAA
* * * ** *
154621 GGACTTAAAAAGACT-AGAAAATAGTGATGAACCTATCCTAAATTCCCACCTT
65 AGACTTAAAAAGACTCATAAAA-AG-GAAGAACCTATTGTAAATGCCCACCTT
154673 TGGCATTAAA
Statistics
Matches: 225, Mismatches: 40, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
154 19 0.08
155 1 0.00
158 1 0.00
159 16 0.07
160 107 0.48
161 16 0.07
162 29 0.13
163 18 0.08
164 18 0.08
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (156 bp):
AGAAAAATTATGAAAATGCCCCTAGAGTATACCTTCGACGTAAAAGTATCCTAGCAACCCTAAAA
GACTTAAAAAGACTCATAAAAAGGAAGAACCTATTGTAAATGCCCACCTTCAACATAAAAGTAGA
CCCGGTATGACCTAGGCATTGGTTCT
Found at i:155022 original size:152 final size:152
Alignment explanation
Indices: 154558--155039 Score: 433
Period size: 152 Copynumber: 3.1 Consensus size: 152
154548 TTGGTTCTAG
** * * **
154558 AAAAATTATGAAAATGTCCTTACGAGTATACCTTCGACGTAAAAGTATCCCAGTAACCCTAAAGG
1 AAAAATTATGAAAATACCCTTA-GAG-ATACTTTCGACGTGAAAGTATCCTGGT-ACCCTAAAGG
* * *
154623 ACTTAAAAAGACTAGAAAATAGTGATGAACCTATCCTAAATTCCCACCTTTGGCATTAAAGAGGA
63 ACTTAAAAAGACTAG-AAATGGTGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGAGGA
* * * *
154688 CTCAGTGCCAACCTCGGACTCGGTTTT
127 CCCAGTGACAACCTAGGACT-AGTTTT
* * * **
154715 AGGAAAACTATGAAAATGCGCC-TAGAGGACACCTTT-GATATGAAAGTATCCTGGTACCCTTAA
1 A--AAAATTATGAAAATAC-CCTTAGA-GATA-CTTTCGACGTGAAAGTATCCTGGTACCC-TAA
* * * * *
154778 AGGGCTT-AAATGACTATCAAAAGG-G-TGAACCTATCCTAAGTACCCACCTTTGGCATAAAAGA
60 AGGACTTAAAAAGACTA-GAAATGGTGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGA
* * *
154840 GGACCTAGT-ATTAACCTAGGACTCGATTTT
124 GGACCCAGTGA-CAACCTAGGACTAG-TTTT
* * *
154870 -AAAATTACGAAAATACCCTTAGGAGATACTTTCGACGTGAAAGTATCCTGGTACACTAAAAGAC
1 AAAAATTATGAAAATACCCTTA-GAGATACTTTCGACGTGAAAGTATCCTGGTACCCTAAAGGAC
* * *
154934 TTAAAAAGACCAGAAATGGTGATGAACCTATCCTAAATGCCCACC-TTCGCATAAAAGCA-GACC
65 TTAAAAAGACTAGAAATGGTGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAG-AGGACC
* *
154997 CAGTGACAGCCTAAGACTAAGTTTT
129 CAGTGACAACCTAGGACT-AGTTTT
155022 AAGAAATTATGAAAATAC
1 AA-AAATTATGAAAATAC
155040 ACCTATGGGT
Statistics
Matches: 260, Mismatches: 45, Indels: 43
0.75 0.13 0.12
Matches are distributed among these distances:
151 19 0.07
152 77 0.30
153 27 0.10
154 15 0.06
155 55 0.21
156 1 0.00
157 17 0.07
158 27 0.10
159 20 0.08
160 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (152 bp):
AAAAATTATGAAAATACCCTTAGAGATACTTTCGACGTGAAAGTATCCTGGTACCCTAAAGGACT
TAAAAAGACTAGAAATGGTGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGAGGACCCA
GTGACAACCTAGGACTAGTTTT
Found at i:157352 original size:16 final size:16
Alignment explanation
Indices: 157330--157367 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
157320 AAAAACATCC
*
157330 ATGAAAAGTAATGAAT
1 ATGAAAAATAATGAAT
*
157346 TTGAAAAATAATGAAT
1 ATGAAAAATAATGAAT
157362 ATGAAA
1 ATGAAA
157368 TAAATGATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (16 bp):
ATGAAAAATAATGAAT
Done.