Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000423.1 Hibiscus syriacus cultivar Beakdansim tig00000774_pilon, whole genome shotgun sequence
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: 69775
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3326 original size:42 final size:43
Alignment explanation
Indices: 3260--3340 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 43
3250 AATTAGTAAG
*
3260 TCATTTGGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCATTTGGGGCCATCAGTAAGTCTTTCGAGCAAGATGATTAAA
* * *
3303 TCATTT-GGGTCATCTGTAAGTCTTTTGAGCAAGATGAT
1 TCATTTGGGGCCATCAGTAAGTCTTTCGAGCAAGATGAT
3341 AAGCCCTTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 28 0.82
43 6 0.18
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (43 bp):
TCATTTGGGGCCATCAGTAAGTCTTTCGAGCAAGATGATTAAA
Found at i:3351 original size:254 final size:253
Alignment explanation
Indices: 2880--3996 Score: 1220
Period size: 254 Copynumber: 4.5 Consensus size: 253
2870 CATTAAGTTG
*
2880 TTTTG-AAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATGATATTTT
1 TTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTG-AAATGA-AATTT
* * *
2944 TGAAAAGTAAGAAGGTGATTTCCAAAGTTTCTTACCCAGTAAATTAGTTCCAAAACTAGTAAGTC
64 TGAAAAGTAAGAA-GTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTAGTAAGTC
* * * * * * * *
3009 ATTCGGGCTATCAGTAAGTCTTTCGAGCATGATTATTAAATCCTTCAGGTCATATTTCAGTATTT
128 TTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAAT-CTTCGGGTCATCTGTAAGTCTTT
*
3074 CGAGCAAGATGATAAGTCCTTCGGGCCATTCATAAGACCTTCGAGCAGGATGTTTCCACATGA
192 CGAGCAAGATGATAAGTCCTTCGGGCCA-TCATAAGACCTTCGGGCAGGATGTTTCCACATGA
* * * *
3137 -TTTGAAAAATGAGAAAGCGAATTCCAAAGGTTCTCATTT-AA-CGTTTTCAGAAATAAAAGTTT
1 TTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATC-TTTTCTGAAATGAAA-TTT
*
3199 TGAAAAGTAAG-AGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAGTAAGTCA
64 TGAAAAGTAAGAAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTAGTAAGTC-
* *
3263 TTTGGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTTGGGTCATCTGTAAGTCTTT
128 TTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATC-TTCGGGTCATCTGTAAGTCTTT
* * * * * *
3328 TGAGCAAGATGATAAGCCCTTCGGGCCATCCGTAAGAGCTTCGGGGGTAGGATGTTTTCACATGA
192 CGAGCAAGATGATAAGTCCTTCGGGCCAT-CATAAGACCTTC--GGGCAGGATGTTTCCACATGA
* * * *
3393 ATTTGAAAAAATGGGATAGCGATTTTCAAAGTTTCTCATTT-AATCTTTTCTGAAAATGAAATTT
1 TTTTG-AAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTG-AAATGAAATTT
*** *
3457 TCGAAAAGTAAGAAAACAATTTCCAAAGTTTC-T------T--AC---TT-----A--GGTAAGT
64 T-GAAAAGTAAG-AAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTAGTAAGT
* * * *
3503 CTTTTGGGCCATCAGTAAGTCTTTCAAGCATGATGCTTAAATTTTCGGGTCATCTGTAAGTCTTT
127 CTTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTCGGGTCATCTGTAAGTCTTT
* * * *
3568 CGAGCAAGATGATAA-TCATTAGGGCCATCTATAAGACCTTCGGGTAGGACGTTTCCACATGA
192 CGAGCAAGATGATAAGTCCTTCGGGCCATC-ATAAGACCTTCGGGCAGGATGTTTCCACATGA
* * *
3630 TTTTCAAAAAAGAGAAAGAGATTTCCAAA-TTTCTCATTTAAATCTTTT-TAGAAATGAAATTTT
1 TTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCT-GAAATGAAATTTT
* * ** *
3693 GAAAAGTAA-AAGCGATTTCCAAAGTTT-TTACCCTGTAAACTATTTTGAAAATTGGTAAGTCTT
65 GAAAAGTAAGAAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTAGTAAGTCTT
* * * * *
3756 TCGGGCCATCAGTATGTCTTTTGATCATGATGATTAAATCTTCGGGTTATCTGTCAGTCTTTCGA
130 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTCGGGTCATCTGTAAGTCTTTCGA
* * * * *
3821 GTAAGATGATAAGTCCTTCAGG-CAT-ATAAGACCTTCGGACAGGATGTTTTCACATTA
195 GCAAGATGATAAGTCCTTCGGGCCATCATAAGACCTTCGGGCAGGATGTTTCCACATGA
*
3878 TTTTCGAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAACATGAAATG
1 TTTT-G-AAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAA-ATGAAATT
* * * *
3943 TTGAAAAGTAAGAAAATAATTTCTAAAGTTT-TTACCTAGTAAACTATTTCCAAA
63 TTGAAAAGTAAG-AAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAA
3997 TTGGTTAATT
Statistics
Matches: 727, Mismatches: 88, Indels: 93
0.80 0.10 0.10
Matches are distributed among these distances:
232 17 0.02
234 9 0.01
235 23 0.03
236 28 0.04
237 22 0.03
238 2 0.00
239 19 0.03
240 37 0.05
241 38 0.05
242 7 0.01
243 2 0.00
244 1 0.00
248 32 0.04
249 2 0.00
250 102 0.14
251 28 0.04
252 20 0.03
253 51 0.07
254 125 0.17
255 20 0.03
256 30 0.04
257 36 0.05
258 42 0.06
259 18 0.02
260 1 0.00
261 15 0.02
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (253 bp):
TTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAATGAAATTTTG
AAAAGTAAGAAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTAGTAAGTCTTT
CGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTCGGGTCATCTGTAAGTCTTTCGAG
CAAGATGATAAGTCCTTCGGGCCATCATAAGACCTTCGGGCAGGATGTTTCCACATGA
Found at i:3802 original size:250 final size:254
Alignment explanation
Indices: 3496--3991 Score: 670
Period size: 250 Copynumber: 2.0 Consensus size: 254
3486 TTCTTACTTA
* * *
3496 GGTAAGTCTTTTGGGCCATCAGTAAGTCTTTCAAGCATGATGCTTAAATTTTCGGGTCATCTGTA
1 GGTAAGTCTTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCTTCGGGTCATCTGTA
**
3561 AGTCTTTCGAGCAAGATGATAA-TCATT-AGGGCCATCTATAAGACCTTCGGGTAGGACGTTTCC
66 AGTCTTTCGAGCAAGATGATAAGTCATTCA-GG-CA--TATAAGACCTTCGGACAGGACGTTTCC
3624 ACATGATTTTC-AAAAAA-GAGAAAGAGATTTCCAAA-TTTCTCATTTAAATCTTTT-TAGAA-A
127 ACATGATTTTCGAAAAAATGAGAAAGAGATTTCCAAAGTTTCTCATTTAAATCTTTTCT-GAACA
* * *
3684 TGAAATTTTGAAAAGT-A-AAAGCGATTTCCAAAGTTTTTACCCT-GTAAACTATTTTGAAAATT
191 TGAAATGTTGAAAAGTAAGAAAACAATTTCCAAAGTTTTTA-CCTAGTAAACTATTTTGAAAATT
* ** * * *
3746 GGTAAGTCTTTCGGGCCATCAGTATGTCTTTTGATCATGATGATTAAATCTTCGGGTTATCTGTC
1 GGTAAGTCTTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCTTCGGGTCATCTGTA
* * * *
3811 AGTCTTTCGAGTAAGATGATAAGTCCTTCAGGCATATAAGACCTTCGGACAGGATGTTTTCACAT
66 AGTCTTTCGAGCAAGATGATAAGTCATTCAGGCATATAAGACCTTCGGACAGGACGTTTCCACAT
* *
3876 TATTTTCGAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAACATGAAA
131 GATTTTCGAAAAAATGAGAAAGAGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAACATGAAA
* *
3941 TGTTGAAAAGTAAGAAAATAATTTCTAAAGTTTTTACCTAGTAAACTATTT
196 TGTTGAAAAGTAAGAAAACAATTTCCAAAGTTTTTACCTAGTAAACTATTT
3992 CCAAATTGGT
Statistics
Matches: 214, Mismatches: 22, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
248 33 0.15
249 6 0.03
250 96 0.45
251 28 0.13
252 18 0.08
253 4 0.02
254 29 0.14
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (254 bp):
GGTAAGTCTTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCTTCGGGTCATCTGTA
AGTCTTTCGAGCAAGATGATAAGTCATTCAGGCATATAAGACCTTCGGACAGGACGTTTCCACAT
GATTTTCGAAAAAATGAGAAAGAGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAACATGAAA
TGTTGAAAAGTAAGAAAACAATTTCCAAAGTTTTTACCTAGTAAACTATTTTGAAAATT
Found at i:8506 original size:2 final size:2
Alignment explanation
Indices: 8499--8556 Score: 95
Period size: 2 Copynumber: 30.5 Consensus size: 2
8489 TTAACTTCAA
8499 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8539 A- AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
8557 ACTTAAAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.06
2 50 0.94
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8508 original size:31 final size:29
Alignment explanation
Indices: 8442--8506 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
8432 TTATTCGAAC
* *
8442 AATATATTTTATTCTTTTATTAACTTAAA
1 AATATATTTTATTATTATATTAACTTAAA
*
8471 AATATATTTT-TTATTATCTTAACTTCAAA
1 AATATATTTTATTATTATATTAACTT-AAA
*
8500 TATATAT
1 AATATAT
8507 ATATAATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 12 0.39
29 19 0.61
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (29 bp):
AATATATTTTATTATTATATTAACTTAAA
Found at i:8543 original size:28 final size:27
Alignment explanation
Indices: 8499--8556 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 27
8489 TTAACTTCAA
8499 ATATATATATATAATATATATATATAT
1 ATATATATATATAATATATATATATAT
8526 ATATATATTATATAATATATATATATAT
1 ATATATA-TATATAATATATATATATAT
8554 ATA
1 ATA
8557 ACTTAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATATATATATAATATATATATATAT
Found at i:8619 original size:29 final size:30
Alignment explanation
Indices: 8586--8670 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 30
8576 TTATTACCTT
*
8586 AAGTTAATA-AAAGAATAAAATAT-TTTTTA
1 AAGTTAAGATAAA-AATAAAATATATTTTTA
*
8615 AAGTTAAGATAAAAATTAAATATATTTTT-
1 AAGTTAAGATAAAAATAAAATATATTTTTA
* *
8644 AACTT-AGAACAAAAATAAAATATATTT
1 AAGTTAAG-ATAAAAATAAAATATATTT
8671 AATGAGTAGA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
28 2 0.04
29 38 0.79
30 8 0.17
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.36
Consensus pattern (30 bp):
AAGTTAAGATAAAAATAAAATATATTTTTA
Found at i:9052 original size:23 final size:23
Alignment explanation
Indices: 9026--9084 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
9016 ATCAAGCACA
* * *
9026 ATAACATATTAGGTAGCGTTTAT
1 ATAACATAATAGGCAGCGCTTAT
*
9049 ATAACGTAATAGGCAGCGCTTAT
1 ATAACATAATAGGCAGCGCTTAT
* *
9072 ATAATAAAATAGG
1 ATAACATAATAGG
9085 TTAATTATCT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.31
Consensus pattern (23 bp):
ATAACATAATAGGCAGCGCTTAT
Found at i:9238 original size:23 final size:23
Alignment explanation
Indices: 9191--9239 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
9181 AATAGCATAT
**
9191 TAGGTAGCGCTTATATAACGTAA
1 TAGGTAGCGCTTATATAACAAAA
*
9214 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAACAAAA
9237 TAG
1 TAG
9240 ATTAATTACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAACAAAA
Found at i:9247 original size:156 final size:155
Alignment explanation
Indices: 8892--9377 Score: 704
Period size: 156 Copynumber: 3.1 Consensus size: 155
8882 ATCAAATACA
*
8892 ATAACATATTAGGTAGCGCTTATATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATA
1 ATAACATAATAGGTAGCGCTTATATAATAAAATAGGTTAATTAC-TAATTTGTTATTACAACATA
* * *
8957 TTAGGTAAACACCTAAAATGTTACCAAGATAACATAATCGATTAATTACTGGAAACATTATCAAG
65 TTAGGTAAACGCCTAAAATGTTACCAAGATAACATAACCGATTAATTACTGG-AACATTATCAAA
*
9022 CACAATAACATATTAGGTAGCGTTTAT
129 CACAATAACATATTAGGTAGCGCTTAT
* * *
9049 ATAACGTAATAGGCAGCGCTTATATAATAAAATAGGTTAATTATCTAATTTGTTACTACAACATA
1 ATAACATAATAGGTAGCGCTTATATAATAAAATAGGTTAATTA-CTAATTTGTTATTACAACATA
* *
9114 TTAGGTAAATGCCTAAAATGTTACCAAGGATAACATAACCGGTTAATTACTGGAA-ATTATCAAA
65 TTAGGTAAACGCCTAAAATGTTACCAA-GATAACATAACCGATTAATTACTGGAACATTATCAAA
*
9178 CACAATAGCATATTAGGTAGCGCTTAT
129 CACAATAACATATTAGGTAGCGCTTAT
* *
9205 ATAACGTAATAGGTAGCGCTTATATAATAAAATAGATTAATTACCTAATTTGTTATTACAACATA
1 ATAACATAATAGGTAGCGCTTATATAATAAAATAGGTTAATTA-CTAATTTGTTATTACAACATA
* * *
9270 TTAGGTAAACGCTTAAAATGTTATCAATGATAACATAACCGATTAATTACTGAAAACATTATCAA
65 TTAGGTAAACGCCTAAAATGTTACCAA-GATAACATAACCGATTAATTACTG-GAACATTATCAA
* * * *
9335 TCATAATAACATATTAAGTAGTGCTTAT
128 ACACAATAACATATTAGGTAGCGCTTAT
* *
9363 GTAACAAAATAGGTA
1 ATAACATAATAGGTA
9378 ATTACTTACT
Statistics
Matches: 296, Mismatches: 29, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
156 141 0.48
157 88 0.30
158 67 0.23
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (155 bp):
ATAACATAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAATTTGTTATTACAACATAT
TAGGTAAACGCCTAAAATGTTACCAAGATAACATAACCGATTAATTACTGGAACATTATCAAACA
CAATAACATATTAGGTAGCGCTTAT
Found at i:9603 original size:72 final size:74
Alignment explanation
Indices: 9446--9619 Score: 273
Period size: 75 Copynumber: 2.4 Consensus size: 74
9436 AAAATTTAAA
*
9446 CTACCTATTACATTAAAATACATACCGTTTTTTTTTAAAGGTTGTTAATAATGTAAACGGTAAAA
1 CTACCTATTACATTAAAATACATACCGTTTTTTTTTAAAGGTTGCTAATAATGTAAACGGTAAAA
9511 AAAATTGACG
66 AAAA-TGACG
*
9521 CTACCTATTACATTAAAATACTTACCTGTTTTTTTTT-AAGGTTGCTAATAATGTAAACGGT-AA
1 CTACCTATTACATTAAAATACATACC-GTTTTTTTTTAAAGGTTGCTAATAATGTAAACGGTAAA
9584 AAAAA-GACG
65 AAAAATGACG
* *
9593 CTACCTATTACATTAAACTACCTACCG
1 CTACCTATTACATTAAAATACATACCG
9620 GATATGTTGA
Statistics
Matches: 94, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
71 1 0.01
72 28 0.30
74 7 0.07
75 48 0.51
76 10 0.11
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (74 bp):
CTACCTATTACATTAAAATACATACCGTTTTTTTTTAAAGGTTGCTAATAATGTAAACGGTAAAA
AAAATGACG
Found at i:9886 original size:92 final size:92
Alignment explanation
Indices: 9775--10070 Score: 405
Period size: 92 Copynumber: 3.1 Consensus size: 92
9765 TTAGTTTCAT
* * *
9775 ACAAAACCGGTAAAAAGCTACTTGAAATGTTGAAAATATCGATACTTTATAAAAATGTATCGATA
1 ACAAAACCGGTAAAGAGCTACTTGATATGTTGAAAGTATCGATACTTTATAAAAATGTATCGATA
9840 CTTTACAATATAACAGGTAAAAATATG
66 CTTTACAATATAACAGGTAAAAATATG
*
9867 ACAAAACCGGTAAAGAGCTACCTGATATGTTGAAAGTATCGATACTTTATAAAAATGTATCGATA
1 ACAAAACCGGTAAAGAGCTACTTGATATGTTGAAAGTATCGATACTTTATAAAAATGTATCGATA
9932 CTTTACAATATAACAGGTAAAAATATGATTTTCATTATG
66 CTTTACAATATAACAGGT---AA-A--A-----A-TATG
*
9971 ACAAAACCGGTAAAGAGCTA-TATGATATGTTGAAAGTATCGATCCTTTTATAAAAAATGTATCG
1 ACAAAACCGGTAAAGAGCTACT-TGATATGTTGAAAGTATCGATAC-TTTAT-AAAAATGTATCG
10035 ATACTTTACAATATAACAGGTAAAAATATG
63 ATACTTTACAATATAACAGGTAAAAATATG
10065 ACAAAA
1 ACAAAA
10071 TCCATTTTCA
Statistics
Matches: 183, Mismatches: 6, Indels: 28
0.84 0.03 0.13
Matches are distributed among these distances:
92 79 0.43
94 10 0.05
95 3 0.02
96 1 0.01
98 1 0.01
100 1 0.01
102 1 0.01
103 3 0.02
104 46 0.25
105 5 0.03
106 33 0.18
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (92 bp):
ACAAAACCGGTAAAGAGCTACTTGATATGTTGAAAGTATCGATACTTTATAAAAATGTATCGATA
CTTTACAATATAACAGGTAAAAATATG
Found at i:10063 original size:198 final size:196
Alignment explanation
Indices: 9700--10070 Score: 570
Period size: 198 Copynumber: 1.9 Consensus size: 196
9690 TAGCGCCTAT
*
9700 AAAGTATCGATACTTTATAAAATGTATTGATACTTTACAATATAACAGGTAAAAATATGACAAAA
1 AAAGTATCGATACTTTATAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATG--AAAA
9765 TTAGTTTCATACAAAACCGGTAAAAAGCTACTTGAAATGTTGAAAATATCGATACTTTATAAAAA
64 TTAG-TTCATACAAAACCGGTAAAAAGCTACTTGAAATGTTGAAAATATCGATACTTTATAAAAA
9830 TGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCGGTAAAGAGCTACCTGATAT
128 TGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCGGTAAAGAGCTACCTGATAT
9895 GTTG
193 GTTG
**
9899 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATG-ATTT
1 AAAGTATCGATACTTTAT-AAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGAAAAT
* * * *
9963 TCA-TT-ATGACAAAACCGGTAAAGAGCTA-TATGATATGTTGAAAGTATCGATCCTTTTATAAA
65 T-AGTTCAT-ACAAAACCGGTAAAAAGCTACT-TGAAATGTTGAAAATATCGATAC-TTTAT-AA
10025 AAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAA
125 AAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAA
10071 TCCATTTTCA
Statistics
Matches: 159, Mismatches: 7, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
195 3 0.02
196 41 0.26
197 8 0.05
198 49 0.31
199 18 0.11
200 40 0.25
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (196 bp):
AAAGTATCGATACTTTATAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGAAAATT
AGTTCATACAAAACCGGTAAAAAGCTACTTGAAATGTTGAAAATATCGATACTTTATAAAAATGT
ATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCGGTAAAGAGCTACCTGATATGTT
G
Found at i:10287 original size:115 final size:112
Alignment explanation
Indices: 9959--10530 Score: 650
Period size: 115 Copynumber: 4.9 Consensus size: 112
9949 TAAAAATATG
* * *
9959 ATTTTCATTATGACAAAACCGGTAAAGAGCTATATGATATGTTGAAAGTATCGATCCTTTTATAA
1 ATTTACATTATGAC-AAACCGGTAAAGAGCTATCTGATATGTTGAAAGTATCGATAC-TTTAT-A
* *
10024 AAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAATCC
63 AAAATGTATCAATACTTTACAATATAACAGGTAAAAATATGACAAAATTC
* * *
10074 ATTTTCATTATGACAAAACCCGGTAAAGAGCTATATGATATGTTGAAAGTATCGATCCTTTTATA
1 ATTTACATTATGAC-AAA-CCGGTAAAGAGCTATCTGATATGTTGAAAGTATCGATAC-TTTATA
*
10139 AAAATGTAT-TATACTTTACAATATAACAGGTAAAAATATGACAAAATTTC
63 AAAATGTATCAATACTTTACAATATAACAGGTAAAAATATGACAAAA-TTC
*
10189 ATTATGACATTATGACAAACCGGTAAAGAGCTATCTGATATGTTGAAAGTATCAATACTTTATAA
1 ATT-T-ACATTATGACAAACCGGTAAAGAGCTATCTGATATGTTGAAAGTATCGATACTTTATAA
* * *
10254 AAATGTATCGATACTTTACAATATAACATGTAAAAATATGACAAAATCC
64 AAATGTATCAATACTTTACAATATAACAGGTAAAAATATGACAAAATTC
* * *
10303 AGTTT-CATTATGACAAAACCAATTATGACACCGGTAAAGAGCTACCTGATATGTTTAAGGTATC
1 A-TTTACATTATG-----A-C----A--A-ACCGGTAAAGAGCTATCTGATATGTTGAAAGTATC
*
10367 GATCATTTTTATAAAAATGTATCAATAC-TTACAATATAACAGGTAAAAATATGACAAAA-TC
52 GAT-A-CTTTATAAAAATGTATCAATACTTTACAATATAACAGGTAAAAATATGACAAAATTC
* ** *
10428 AGTTT-CATTATGAAAAATCCAGGTAAAGAGCTGCCTGATATGTTGAAAGTATCAATACTTTATA
1 A-TTTACATTATGACAAA-CC-GGTAAAGAGCTATCTGATATGTTGAAAGTATCGATACTTTATA
*
10492 GAAATGTATCAATACTTTACAATATAACAGGTACAAAAT
63 AAAATGTATCAATACTTTACAATATAACAGGTA-AAAAT
10531 CAGTTTCATC
Statistics
Matches: 408, Mismatches: 24, Indels: 51
0.84 0.05 0.11
Matches are distributed among these distances:
112 28 0.07
113 21 0.05
114 91 0.22
115 107 0.26
116 49 0.12
117 10 0.02
118 1 0.00
120 1 0.00
122 1 0.00
124 1 0.00
125 47 0.12
126 31 0.08
127 20 0.05
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (112 bp):
ATTTACATTATGACAAACCGGTAAAGAGCTATCTGATATGTTGAAAGTATCGATACTTTATAAAA
ATGTATCAATACTTTACAATATAACAGGTAAAAATATGACAAAATTC
Found at i:10500 original size:21 final size:20
Alignment explanation
Indices: 10472--10510 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
10462 CTGATATGTT
10472 GAAAGTATCAATACTTTATA
1 GAAAGTATCAATACTTTATA
10492 GAAATGTATCAATACTTTA
1 GAAA-GTATCAATACTTTA
10511 CAATATAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (20 bp):
GAAAGTATCAATACTTTATA
Found at i:10510 original size:239 final size:239
Alignment explanation
Indices: 10093--10530 Score: 670
Period size: 239 Copynumber: 1.8 Consensus size: 239
10083 ATGACAAAAC
* *
10093 CCGGTAAAGAGCTATATGATATGTTGAAAGTATCGATCCTTTTATAAAAATGTATTATACTTTAC
1 CCGGTAAAGAGCTACATGATATGTTGAAAGTATCGATCCTTTTATAAAAATGTATAATACTTTAC
* *
10158 AATATAACAGGTAAAAATATGACAAAATTTCATTATGACATTATGACAAACCGGTAAAGAGCTAT
66 AATATAACAGGTAAAAATATGACAAAA-TTCATTAT-ACATTATGAAAAACCGGTAAAGAGCTAC
* *
10223 CTGATATGTTGAAAGTATCAATACTTTATAAAAATGTATCGATACTTTACAATATAACATGTA-A
129 CTGATATGTTGAAAGTATCAATACTTTATAAAAATGTATCAATACTTTACAATATAACAGGTACA
10287 AAATATGACAAAATCCAGTTTCATTATGACAAAACCAATTATGACA
194 AAATATGACAAAATCCAGTTTCATTATGACAAAACCAATTATGACA
* * * *
10333 CCGGTAAAGAGCTACCTGATATGTTTAAGGTATCGATCATTTTTATAAAAATGTATCAATAC-TT
1 CCGGTAAAGAGCTACATGATATGTTGAAAGTATCGATC-CTTTTATAAAAATGTAT-AATACTTT
10397 ACAATATAACAGGTAAAAATATGACAAAA-TCAGTT-T-CATTATGAAAAATCCAGGTAAAGAGC
64 ACAATATAACAGGTAAAAATATGACAAAATTCA-TTATACATTATGAAAAA-CC-GGTAAAGAGC
* *
10459 TGCCTGATATGTTGAAAGTATCAATACTTTATAGAAATGTATCAATACTTTACAATATAACAGGT
126 TACCTGATATGTTGAAAGTATCAATACTTTATAAAAATGTATCAATACTTTACAATATAACAGGT
10524 ACAAAAT
191 ACAAAAT
10531 CAGTTTCATC
Statistics
Matches: 180, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
237 11 0.06
238 2 0.01
239 75 0.42
240 41 0.23
241 47 0.26
242 4 0.02
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (239 bp):
CCGGTAAAGAGCTACATGATATGTTGAAAGTATCGATCCTTTTATAAAAATGTATAATACTTTAC
AATATAACAGGTAAAAATATGACAAAATTCATTATACATTATGAAAAACCGGTAAAGAGCTACCT
GATATGTTGAAAGTATCAATACTTTATAAAAATGTATCAATACTTTACAATATAACAGGTACAAA
ATATGACAAAATCCAGTTTCATTATGACAAAACCAATTATGACA
Found at i:11552 original size:20 final size:21
Alignment explanation
Indices: 11524--11574 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
11514 TTACACCTCC
11524 TCCTAAAATTTTATAAT-T-ACT
1 TCCT-AAATTTT-TAATATAACT
11545 TCCTAAATTTTTAATATAACT
1 TCCTAAATTTTTAATATAACT
*
11566 TCTTAAATT
1 TCCTAAATT
11575 CTCATACCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 4 0.15
20 8 0.30
21 15 0.56
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (21 bp):
TCCTAAATTTTTAATATAACT
Found at i:21840 original size:125 final size:125
Alignment explanation
Indices: 21618--21878 Score: 432
Period size: 125 Copynumber: 2.1 Consensus size: 125
21608 GGTAGTATCA
* *
21618 GTTTTGTTATTGTTGTGCATAACAAAATCAGTAAAAATTACCGAAAACATCATTATTTCTACATC
1 GTTTTGTTATTGTTGTGCATAACAAAACCAGTAAAAATTACCGAAAACATCATTATTTCTACAGC
*
21683 TTTTGTTATTATTTTGGTATTTTACCGGGTTTCGTAACAAAACCGGTAAAAGCGCTACCG
66 TTTTGTTATTATTTTGGCATTTTACCGGGTTTCGTAACAAAACCGGTAAAAGCGCTACCG
* * * *
21743 GTTTTGTTATTGTTGTGCATAACAAAACCGGTAAAAATTACCGAAAACATTATTATTTCTACCGG
1 GTTTTGTTATTGTTGTGCATAACAAAACCAGTAAAAATTACCGAAAACATCATTATTTCTACAGC
* *
21808 TTTTGTTATTATTTTGGCATTTTATCGGGTTTCTTAACAAAACCGGTAAAAGCGCTACCG
66 TTTTGTTATTATTTTGGCATTTTACCGGGTTTCGTAACAAAACCGGTAAAAGCGCTACCG
*
21868 ATTTTGTTATT
1 GTTTTGTTATT
21879 TTTTTAACGG
Statistics
Matches: 126, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
125 126 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (125 bp):
GTTTTGTTATTGTTGTGCATAACAAAACCAGTAAAAATTACCGAAAACATCATTATTTCTACAGC
TTTTGTTATTATTTTGGCATTTTACCGGGTTTCGTAACAAAACCGGTAAAAGCGCTACCG
Found at i:22206 original size:23 final size:23
Alignment explanation
Indices: 22177--22224 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
22167 AAATATGTCA
* *
22177 ATATAAGTGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
*
22200 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
22223 AT
1 AT
22225 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:22282 original size:87 final size:87
Alignment explanation
Indices: 22177--22339 Score: 299
Period size: 87 Copynumber: 1.9 Consensus size: 87
22167 AAATATGTCA
*
22177 ATATAAGTGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
22242 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* *
22264 ATATAAGCGCTACTTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
22329 CCGGTTAAATG
66 CCGGTTAAATG
22340 ATATAACATA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.41
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:22311 original size:23 final size:23
Alignment explanation
Indices: 22261--22305 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
22251 TGCCTATTTT
* *
22261 ATTATATAAGCGCTACTTATTAC
1 ATTATATAAGCGCTACCTAATAC
22284 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
22306 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:27402 original size:8 final size:8
Alignment explanation
Indices: 27391--27419 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
27381 ACTTATTTAT
27391 TTTTAAAA
1 TTTTAAAA
27399 TTTTAAAA
1 TTTTAAAA
27407 TTTTAAAA
1 TTTTAAAA
27415 TTTTA
1 TTTTA
27420 TCTCTCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
TTTTAAAA
Found at i:28869 original size:6 final size:7
Alignment explanation
Indices: 28852--28880 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
28842 TTTTAATGAT
28852 TTTTTAA
1 TTTTTAA
28859 TTTTTAA
1 TTTTTAA
28866 TTTTTAA
1 TTTTTAA
28873 -TTTTAA
1 TTTTTAA
28879 TT
1 TT
28881 AAACATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTTAA
Found at i:36423 original size:41 final size:39
Alignment explanation
Indices: 36321--36434 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 39
36311 TACATATAAG
*
36321 TACTTTAGTGGCGTTTTTAAACAAACGCCGCCAAAAAATC
1 TACTTTAGTAGCGTTTTTAAACAAACGCCG-CAAAAAATC
* * *
36361 TACTTTAATAGTGTTTCTAAACAAACGCCGCAAAAGAATC
1 TACTTTAGTAGCGTTTTTAAACAAACGCCGCAAAA-AATC
* * *
36401 ATTCTTTAGTAGCATTTTTAAACAAACTCCGCAA
1 -TACTTTAGTAGCGTTTTTAAACAAACGCCGCAA
36435 TAGGATATAT
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
39 5 0.08
40 30 0.48
41 27 0.44
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (39 bp):
TACTTTAGTAGCGTTTTTAAACAAACGCCGCAAAAAATC
Found at i:38539 original size:42 final size:42
Alignment explanation
Indices: 38490--38602 Score: 172
Period size: 42 Copynumber: 2.7 Consensus size: 42
38480 TTTTCCAAAA
* *
38490 TCCCGTGTTTGTTTCATGTAATTTATTTTTTGAAAAATATTT
1 TCCCGTGTTTGTTTCACGTAATTCATTTTTTGAAAAATATTT
* * *
38532 TTCCGTGTTTGTTTCACGTAATTCGTTTTTTGGAAAATATTT
1 TCCCGTGTTTGTTTCACGTAATTCATTTTTTGAAAAATATTT
*
38574 TCCCGTGTTTGTTTCACGTAATTCGTTTT
1 TCCCGTGTTTGTTTCACGTAATTCATTTT
38603 CCGGAACGTA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.19, C:0.13, G:0.15, T:0.53
Consensus pattern (42 bp):
TCCCGTGTTTGTTTCACGTAATTCATTTTTTGAAAAATATTT
Found at i:38681 original size:18 final size:18
Alignment explanation
Indices: 38654--38690 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38644 TGTTTTCTGT
*
38654 AAAATGACTTACAGATTC
1 AAAATAACTTACAGATTC
*
38672 AAAATAACTTACGGATTC
1 AAAATAACTTACAGATTC
38690 A
1 A
38691 TTTTTCGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (18 bp):
AAAATAACTTACAGATTC
Found at i:38983 original size:28 final size:27
Alignment explanation
Indices: 38901--38991 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 27
38891 TTATAATAAT
* *
38901 ATAAGATATTATATTTTT-TAT-TTTA
1 ATAATATATAATATTTTTATATATTTA
38926 ATAATATATAATAATTTTTTATATATTTA
1 ATAATATATAAT-A-TTTTTATATATTTA
38955 ATAATGA-ATAATATTATTTATATATTTA
1 ATAAT-ATATAATATT-TTTATATATTTA
*
38983 A-AACATATA
1 ATAATATATA
38992 CTAGTAAAGA
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
25 10 0.18
26 2 0.04
27 12 0.21
28 17 0.30
29 14 0.25
30 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (27 bp):
ATAATATATAATATTTTTATATATTTA
Found at i:39017 original size:23 final size:23
Alignment explanation
Indices: 38976--39037 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
38966 TATTATTTAT
*
38976 ATATTTAAAACATATACTAGTAAAG
1 ATATTT-AAA-ATATACTAATAAAG
* *
39001 ATATTTAAAATATACTAATTAAT
1 ATATTTAAAATATACTAATAAAG
*
39024 ATTTTTAAAATATA
1 ATATTTAAAATATA
39038 ATATAACACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 24 0.73
24 3 0.09
25 6 0.18
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (23 bp):
ATATTTAAAATATACTAATAAAG
Found at i:39351 original size:20 final size:20
Alignment explanation
Indices: 39314--39352 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39304 TTTCCAGATG
**
39314 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
39334 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
39353 CAGTAATTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:39366 original size:29 final size:30
Alignment explanation
Indices: 39326--39398 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
39316 TTCCAGAAAT
39326 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
39355 GTAATTTATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
39385 GTAATTCATTTTCC
1 GTAATTCATTTTCC
39399 GAAAAATCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 15 0.37
30 26 0.63
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:39368 original size:15 final size:15
Alignment explanation
Indices: 39326--39398 Score: 94
Period size: 15 Copynumber: 4.9 Consensus size: 15
39316 TTCCAGAAAT
39326 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
39341 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
39355 GTAATTTATTTTCCA
1 GTAATTCATTTTCCA
**
39370 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
39385 GTAATTCATTTTCC
1 GTAATTCATTTTCC
39399 GAAAAATCAA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
14 12 0.26
15 35 0.74
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:44817 original size:26 final size:28
Alignment explanation
Indices: 44778--44831 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
44768 GATGATGATA
44778 ATAAATATTTTATA-ATTT-AAAAAAAT
1 ATAAATATTTTATATATTTGAAAAAAAT
*
44804 ATAAAT-TTTATATATTTTTGAAAAAAAT
1 ATAAATATTT-TATATATTTGAAAAAAAT
44832 GACTTTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.12
26 10 0.42
27 3 0.12
28 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
ATAAATATTTTATATATTTGAAAAAAAT
Found at i:44901 original size:21 final size:21
Alignment explanation
Indices: 44857--44903 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
44847 TTGTATTAAA
*
44857 TTTTATTCACTTTTAATTCTT
1 TTTTATTCACTTTTAATTCAT
*
44878 TTTTATTGCACTTTT-ATTGAT
1 TTTTATT-CACTTTTAATTCAT
44899 TTTTA
1 TTTTA
44904 AAAAAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.19, C:0.11, G:0.04, T:0.66
Consensus pattern (21 bp):
TTTTATTCACTTTTAATTCAT
Found at i:44901 original size:22 final size:21
Alignment explanation
Indices: 44857--44902 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
44847 TTGTATTAAA
*
44857 TTTTATTCACTTTTAATTCTT
1 TTTTATTCACTTTTAATTATT
44878 TTTTATTGCACTTTT-ATTGATT
1 TTTTATT-CACTTTTAATT-ATT
44900 TTT
1 TTT
44903 AAAAAAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.17, C:0.11, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTTATTCACTTTTAATTATT
Found at i:45233 original size:211 final size:210
Alignment explanation
Indices: 44855--45235 Score: 457
Period size: 211 Copynumber: 1.8 Consensus size: 210
44845 TTTTGTATTA
* *
44855 AATTTTATTCACTTTTAATTCTTTTTTATTGCACTTTTATTGATTTTTAAAAAAATGAATACTAA
1 AATTTTATTCACTTTTAATTCTTTTTTATTGCACTTTTATTGATTTTAAAAAAAATGAATAATAA
* * ** *** * * * *
44920 TTCATTTGATCTATCAATTGTAATTAAAAGTTTATTTTAATAATTTTATATTTTTAAATAATTAA
66 TTCATTTGATCTATCAATTGTAATTAAAAGTTAAATGCAATAATAAAATATATTAAAAGAAATAA
* * * * ***
44985 TATTAAAAGTCAATAAGCATTATTAGCTGTTAAAAAATAATATCACAAAAAAATAAATCAATAAG
131 AATTAAAAG-CAAAAAGAATTATAAGCTCAAAAAAAATAATATCACAAAAAAATAAATCAATAAG
45050 GTTGACATTTTAAATG
195 GTTGACATTTTAAATG
*
45066 AATTTTATTCACTTTTAATTCTTTTTTATTGCATTTTTATTGATTTTAAAAAAAATGAATAATAA
1 AATTTTATTCACTTTTAATTCTTTTTTATTGCACTTTTATTGATTTTAAAAAAAATGAATAATAA
*
45131 TTTATTTGATCTATCAATTGTAATTAAAAGTATAAAAATGCAATAA-AAAATA-ATTAAAAGAGA
66 TTCATTTGATCTATCAATTGTAATTAAAAGT-T--AAATGCAATAATAAAATATATTAAAAGA-A
*
45194 ATAAAATTCAATA-CAAAAAGAA-TATAAAG-TCAAAAAAAATAA
127 ATAAAATT-AAAAGCAAAAAGAATTAT-AAGCTCAAAAAAAATAA
45236 AAAAATTATA
Statistics
Matches: 141, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
211 105 0.74
212 16 0.11
213 10 0.07
214 10 0.07
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (210 bp):
AATTTTATTCACTTTTAATTCTTTTTTATTGCACTTTTATTGATTTTAAAAAAAATGAATAATAA
TTCATTTGATCTATCAATTGTAATTAAAAGTTAAATGCAATAATAAAATATATTAAAAGAAATAA
AATTAAAAGCAAAAAGAATTATAAGCTCAAAAAAAATAATATCACAAAAAAATAAATCAATAAGG
TTGACATTTTAAATG
Found at i:45641 original size:17 final size:17
Alignment explanation
Indices: 45619--45658 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
45609 CGCTTCAGGG
45619 GGCGCCTTACCCCACGT
1 GGCGCCTTACCCCACGT
*
45636 GGCGCCTTACTCCACGT
1 GGCGCCTTACCCCACGT
*
45653 GACGCC
1 GGCGCC
45659 CGATCAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.12, C:0.45, G:0.25, T:0.17
Consensus pattern (17 bp):
GGCGCCTTACCCCACGT
Found at i:46820 original size:39 final size:40
Alignment explanation
Indices: 46759--46853 Score: 102
Period size: 42 Copynumber: 2.4 Consensus size: 40
46749 CCTATCTTTT
*
46759 TTTGTTATGCTCACAAAACTGAA-TTTTCTTCTTCTCAAA
1 TTTGTTATGCCCACAAAACTGAACTTTTCTTCTTCTCAAA
* * * * *
46798 TTTGTTATGCCCATAGAGCTGAACTCTTTTTTTCTTCTTAAA
1 TTTGTTATGCCCACAAAACTGAA--CTTTTCTTCTTCTCAAA
*
46840 TATGTTATGCCCAC
1 TTTGTTATGCCCAC
46854 GGAATATAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
39 19 0.42
42 26 0.58
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.44
Consensus pattern (40 bp):
TTTGTTATGCCCACAAAACTGAACTTTTCTTCTTCTCAAA
Found at i:50640 original size:104 final size:104
Alignment explanation
Indices: 50521--50727 Score: 351
Period size: 104 Copynumber: 2.0 Consensus size: 104
50511 TTTGGTAAAA
*
50521 TATACATTTCAATAATCTTTTATTCCTTTAACCAAACATTTTAATCTTACATTCCTGCTAAACCA
1 TATACATTCCAATAATCTTTTATTCCTTTAACCAAACATTTTAATCTTACATTCCTGCTAAACCA
* * *
50586 ACCAAACACAAAATACAGCATTCTTAGTAATCCTATTCC
66 ACCAAACACAAAATACAACATTCTCAGTAATCATATTCC
* * *
50625 TATACATTCCAATAATTTTTTATTCCTTTAACCAAACATTTTAATCTTACATTCTTGTTAAACCA
1 TATACATTCCAATAATCTTTTATTCCTTTAACCAAACATTTTAATCTTACATTCCTGCTAAACCA
50690 ACCAAACACAAAATACAACATTCTCAGTAATCATATTC
66 ACCAAACACAAAATACAACATTCTCAGTAATCATATTC
50728 TTCGATAATC
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
104 96 1.00
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (104 bp):
TATACATTCCAATAATCTTTTATTCCTTTAACCAAACATTTTAATCTTACATTCCTGCTAAACCA
ACCAAACACAAAATACAACATTCTCAGTAATCATATTCC
Found at i:57210 original size:93 final size:94
Alignment explanation
Indices: 57028--57241 Score: 225
Period size: 93 Copynumber: 2.3 Consensus size: 94
57018 GAGATGCCAG
* * ** * * ** *
57028 ATGTACATTTCTGATGCTATGTGACCCCGGGCCTCATTCGATGTAGAGTGTATTTTCCTGATGTT
1 ATGTACGTTCCTGATGCTATGTGACCCCAAGCCTCACTCGATATAGAGTGTACGTTCCTGATGCT
* * * *
57093 ATGTTATCCCATGCCTTACTCGATGTC-A
66 ATGTGACCCCAGGCCTCACTCGATGTCGA
* * * * *
57121 GGTGTATGTTCCTGATGCTATGTGATCTCAAGCCTCACTCGATAT-GAGTGTACGTTCTTGATGC
1 -ATGTACGTTCCTGATGCTATGTGACCCCAAGCCTCACTCGATATAGAGTGTACGTTCCTGATGC
*
57185 TATGTGACCCCAGGTCTCACTCGATGTCGA
65 TATGTGACCCCAGGCCTCACTCGATGTCGA
*
57215 ATGTACGTTCCTAATGCTATGTGACCC
1 ATGTACGTTCCTGATGCTATGTGACCC
57242 TAGGTCTCAT
Statistics
Matches: 95, Mismatches: 24, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
93 60 0.63
94 35 0.37
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (94 bp):
ATGTACGTTCCTGATGCTATGTGACCCCAAGCCTCACTCGATATAGAGTGTACGTTCCTGATGCT
ATGTGACCCCAGGCCTCACTCGATGTCGA
Found at i:57239 original size:47 final size:47
Alignment explanation
Indices: 57029--57250 Score: 214
Period size: 47 Copynumber: 4.7 Consensus size: 47
57019 AGATGCCAGA
* * * * *
57029 TGTACATTTCTGATGCTATGTGACCCCGGGCCTCATTCGATGTAGAG
1 TGTACGTTCCTGATGCTATGTGACCCCAGGCCTCACTCGATGTCGAG
** * * * * *
57076 TGTATTTTCCTGATGTTATGTTATCCCATGCCTTACTCGATGTC-AGG
1 TGTACGTTCCTGATGCTATGTGACCCCAGGCCTCACTCGATGTCGA-G
* * * * *
57123 TGTATGTTCCTGATGCTATGTGATCTCAAGCCTCACTCGATAT-GAG
1 TGTACGTTCCTGATGCTATGTGACCCCAGGCCTCACTCGATGTCGAG
* * *
57169 TGTACGTTCTTGATGCTATGTGACCCCAGGTCTCACTCGATGTCGAA
1 TGTACGTTCCTGATGCTATGTGACCCCAGGCCTCACTCGATGTCGAG
* * *
57216 TGTACGTTCCTAATGCTATGTGACCCTAGGTCTCA
1 TGTACGTTCCTGATGCTATGTGACCCCAGGCCTCA
57251 TCCGAGGATA
Statistics
Matches: 143, Mismatches: 29, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
46 38 0.27
47 105 0.73
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.35
Consensus pattern (47 bp):
TGTACGTTCCTGATGCTATGTGACCCCAGGCCTCACTCGATGTCGAG
Found at i:58748 original size:11 final size:11
Alignment explanation
Indices: 58734--58781 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
58724 AAAAGAAAGA
58734 TAAACAAACAC
1 TAAACAAACAC
*
58745 TAAACAAACGC
1 TAAACAAACAC
* *
58756 TACACGAACAC
1 TAAACAAACAC
*
58767 TAAATAAACAC
1 TAAACAAACAC
58778 TAAA
1 TAAA
58782 AGAATGCTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.58, C:0.25, G:0.04, T:0.12
Consensus pattern (11 bp):
TAAACAAACAC
Found at i:58781 original size:33 final size:33
Alignment explanation
Indices: 58734--58798 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
58724 AAAAGAAAGA
*
58734 TAAACAAACACTAAACA-AACGCTACACGAACAC
1 TAAACAAACACTAAA-AGAACGCTAAACGAACAC
* *
58767 TAAATAAACACTAAAAGAATGCTAAACGAACA
1 TAAACAAACACTAAAAGAACGCTAAACGAACA
58799 TGTTCGTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.57, C:0.23, G:0.08, T:0.12
Consensus pattern (33 bp):
TAAACAAACACTAAAAGAACGCTAAACGAACAC
Found at i:58815 original size:23 final size:23
Alignment explanation
Indices: 58789--58845 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
58779 AAAAGAATGC
**
58789 TAAACGAACATGTTCGTAAACAT
1 TAAACGAACATGTTCACAAACAT
* * *
58812 TAAATGCACACGTTCACAAACAT
1 TAAACGAACATGTTCACAAACAT
58835 TAAACGAACAT
1 TAAACGAACAT
58846 ATTTACTAAC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.23
Consensus pattern (23 bp):
TAAACGAACATGTTCACAAACAT
Found at i:59712 original size:4 final size:4
Alignment explanation
Indices: 59703--59727 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
59693 CCCACTGAAC
59703 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
59728 TCTTTTGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:60324 original size:23 final size:21
Alignment explanation
Indices: 60268--60326 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
60258 AAACGACCGA
*
60268 AAATGTGCCATAAAAACAAAG
1 AAATGTGCCATAAAGACAAAG
**
60289 AAATGTGTTATAAAGACAGAAG
1 AAATGTGCCATAAAGACA-AAG
60311 AAGATGTGCCATAAAG
1 AA-ATGTGCCATAAAG
60327 TAAAAATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 15 0.48
22 5 0.16
23 11 0.35
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.19
Consensus pattern (21 bp):
AAATGTGCCATAAAGACAAAG
Found at i:61574 original size:23 final size:22
Alignment explanation
Indices: 61531--61575 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
61521 AAACATTATA
*
61531 TTAATTATAATAGAAATATTTT
1 TTAATTATAATAGAAAAATTTT
61553 TTAATTAATAATA-ATAAAATTTT
1 TTAATT-ATAATAGA-AAAATTTT
61576 AAAGCATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATTATAATAGAAAAATTTT
Found at i:64562 original size:15 final size:15
Alignment explanation
Indices: 64542--64571 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
64532 CATGAACGTC
*
64542 TAATTATAATTTGTA
1 TAATTATAACTTGTA
64557 TAATTATAACTTGTA
1 TAATTATAACTTGTA
64572 ATTTTATAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (15 bp):
TAATTATAACTTGTA
Found at i:66333 original size:25 final size:25
Alignment explanation
Indices: 66305--66359 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
66295 AAAATGAAAG
66305 TTAATTTAATTTAATTA-ATAATTAA
1 TTAATTTAATTTAATTATAT-ATTAA
* * *
66330 TTAAGTTAATTTCATTATATTTTAA
1 TTAATTTAATTTAATTATATATTAA
66355 TTAAT
1 TTAAT
66360 GAATATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
TTAATTTAATTTAATTATATATTAA
Found at i:69240 original size:15 final size:15
Alignment explanation
Indices: 69222--69251 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
69212 CCTATAAAAT
*
69222 TACAAGTTATAATTA
1 TACAAATTATAATTA
69237 TACAAATTATAATTA
1 TACAAATTATAATTA
69252 GACGTTCATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (15 bp):
TACAAATTATAATTA
Done.