Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_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: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 38
Found at i:1165824 original size:20 final size:20
Alignment explanation
Indices: 1165799--1165843 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1165789 TCAAATAGTT
1165799 TTTAAT-TTATATAATATAAA
1 TTTAATATT-TATAATATAAA
1165819 TTTAATATTTATAATATAAA
1 TTTAATATTTATAATATAAA
*
1165839 ATTAA
1 TTTAA
1165844 AAGATGATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAATATTTATAATATAAA
Found at i:1169922 original size:2 final size:2
Alignment explanation
Indices: 1169915--1169939 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1169905 ATTACACAAA
1169915 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
1169940 ATACTTTTTA
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:1172210 original size:16 final size:17
Alignment explanation
Indices: 1172176--1172210 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1172166 TGATAAAAAA
1172176 TTAAATAAATTATTTGT
1 TTAAATAAATTATTTGT
1172193 TTAAATAAATTA-TTGT
1 TTAAATAAATTATTTGT
1172209 TT
1 TT
1172211 CTTTAACCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TTAAATAAATTATTTGT
Found at i:1172293 original size:69 final size:68
Alignment explanation
Indices: 1172199--1172447 Score: 287
Period size: 69 Copynumber: 3.6 Consensus size: 68
1172189 TTGTTTAAAT
*
1172199 AAATTATTGTTTCTTTAACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAACCCGAA
1 AAATT-TT-TTTCTTTAACCATTAATCGAACCGAAATTTATTTGAAAATTATTAACCAA-CCGAA
1172264 TTAATC
63 TTAATC
* * *
1172270 AAATTTTTTTCTTTAACCATTAATCGAACCGAAATTTATCTGGAAATTATT----AACCGAATAA
1 AAATTTTTTTCTTTAACCATTAATCGAACCGAAATTTATTTGAAAATTATTAACCAACCGAAT-T
1172331 AAT-
65 AATC
* *
1172334 AAATTATTTTTTCTTTAACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAA
1 AAA-T-TTTTTTCTTTAACCATTAATCGAACCGAAATTTATTTGAAAATTATTAACC-AACCGAA
*
1172399 TTAACC
63 TTAATC
**
1172405 GATTTTTTTTTTCTTTAA-CATTAATCGAACCGAAA-TTATTTGA
1 -A-AATTTTTTTCTTTAACCATTAATCGAACCGAAATTTATTTGA
1172448 CCGTTAATCG
Statistics
Matches: 154, Mismatches: 13, Indels: 24
0.81 0.07 0.13
Matches are distributed among these distances:
64 9 0.06
65 6 0.04
66 44 0.29
69 49 0.32
70 20 0.13
71 24 0.16
72 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (68 bp):
AAATTTTTTTCTTTAACCATTAATCGAACCGAAATTTATTTGAAAATTATTAACCAACCGAATTA
ATC
Found at i:1172357 original size:135 final size:136
Alignment explanation
Indices: 1172195--1172441 Score: 410
Period size: 135 Copynumber: 1.8 Consensus size: 136
1172185 TTATTTGTTT
1172195 AAATAAATTATTGTTTCTTTAACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACC-AAC
1 AAATAAATTATTGTTTCTTTAACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAA-
* *
1172259 CCGAATTAATC-A-AATTTTTTTCTTTAACCATTAATCGAACCGAAATTTATCTGGAAATTATTA
65 CCAAATTAACCGATAATTTTTTTCTTTAA-CATTAATCGAACCGAAATTTATCTGGAAATTATTA
1172322 ACCGAATA
129 ACCGAATA
*
1172330 AAATAAATTATTTTTTCTTTAACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAAC
1 AAATAAATTATTGTTTCTTTAACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAAC
**
1172395 CAAATTAACCGATTTTTTTTTTCTTTAACATTAATCGAACCGAAATT
66 CAAATTAACCGATAATTTTTTTCTTTAACATTAATCGAACCGAAATT
1172442 ATTTGACCGT
Statistics
Matches: 104, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
135 69 0.66
136 22 0.21
137 13 0.12
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (136 bp):
AAATAAATTATTGTTTCTTTAACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAAC
CAAATTAACCGATAATTTTTTTCTTTAACATTAATCGAACCGAAATTTATCTGGAAATTATTAAC
CGAATA
Found at i:1172372 original size:66 final size:66
Alignment explanation
Indices: 1172195--1172447 Score: 291
Period size: 66 Copynumber: 3.7 Consensus size: 66
1172185 TTATTTGTTT
* *
1172195 AAATAAATTATTGTTTCTTTAACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAACC
1 AAATAAATTATTTTTTCTTTAACCATTAATCGAACCGAAATTTATTTGAAAATTATT----AA-C
1172260 CGAAT-
61 CGAATA
* * *
1172265 TAATCAAA-T-TTTTTTCTTTAACCATTAATCGAACCGAAATTTATCTGGAAATTATTAACCGAA
1 AAAT-AAATTATTTTTTCTTTAACCATTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAA
1172328 TA
65 TA
*
1172330 AAATAAATTATTTTTTCTTTAACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAAC
1 AAATAAATTATTTTTTCTTTAACCATTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAA-
*
1172395 CA
65 TA
* *
1172397 AATTAACCGATTTTTTTTTTCTTTAA-CATTAATCGAACCGAAA-TTATTTGA
1 AAATAA---A-TTATTTTTTCTTTAACCATTAATCGAACCGAAATTTATTTGA
1172448 CCGTTAATCG
Statistics
Matches: 161, Mismatches: 13, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
64 9 0.06
65 6 0.04
66 51 0.32
67 6 0.04
69 51 0.32
70 21 0.13
71 17 0.11
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (66 bp):
AAATAAATTATTTTTTCTTTAACCATTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAAT
A
Found at i:1172664 original size:95 final size:94
Alignment explanation
Indices: 1172351--1172726 Score: 528
Period size: 94 Copynumber: 4.0 Consensus size: 94
1172341 TTTTTCTTTA
*
1172351 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTTT
1 ACCGTTAATAGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGA--TTTTTTT
1172416 TCTTTAACATTAATCGAACCGAAATTATTTG
64 TCTTTAACATTAATCGAACCGAAATTATTTG
* * * *
1172447 ACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTA
1 ACCGTTAATAGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTTC
*
1172512 TTTAACATTAATCGAAACGAAATTATTTG
66 TTTAACATTAATCGAACCGAAATTATTTG
*
1172541 ACCGTTAATCA-AACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGATTTTTTTT
1 ACCGTTAAT-AGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTT
1172605 CTTTAACCATTAATCGAACCGAAATTATTTG
65 CTTTAA-CATTAATCGAACCGAAATTATTTG
* * * * * *
1172636 ACAGTTAATAGAATCGAAATTTATTTGAAAATTATTAATCGAA-TAAAATAA---ATTATTTTTC
1 ACCGTTAATAGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTTC
* *
1172697 CTTAACTGTTAATCGAACCGAAATTTATTT
66 TTTAAC-ATTAATCGAACCGAAA-TTATTT
1172727 AAAAATTATT
Statistics
Matches: 256, Mismatches: 19, Indels: 14
0.89 0.07 0.05
Matches are distributed among these distances:
90 1 0.00
91 28 0.11
92 6 0.02
94 105 0.41
95 61 0.24
96 55 0.21
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (94 bp):
ACCGTTAATAGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTTC
TTTAACATTAATCGAACCGAAATTATTTG
Found at i:1173773 original size:334 final size:334
Alignment explanation
Indices: 1173164--1173838 Score: 1217
Period size: 334 Copynumber: 2.0 Consensus size: 334
1173154 AATATTAAGG
*
1173164 ACCAAATATATAATTATACCAATTTTATTAACGGACACGTCACCAACTCTGTTAAAAATTAACGG
1 ACCAAATATATAATTATACCAATTTTATTAACGGACACGTCACCAACTCTGTTAAAAATTAACGA
* * * *
1173229 CCAATGGTTTGATTGAATCAATTAAATAGTTTGGTGGTCACATTGACTTTTGACTATAGTTTAAT
66 CCAATGATTTAATTGAATCAATTAAATAGTTTGGTGATCACATTAACTTTTGACTATAGTTTAAT
1173294 AGTCTCCCGTCTAGTTTACCCTTTTTTTTAATAGACCATCTATTTTTACGCTCATAATATTCTTC
131 AGTCTCCCGTCTAGTTTACCCTTTTTTTTAATAGACCATCTATTTTTACGCTCATAATATTCTTC
1173359 TTATATTCATGAATAGCAGACGAAACAACCTCTCCAAATCCTTGTATATTGAACCAATAGTTGAT
196 TTATATTCATGAATAGCAGACGAAACAACCTCTCCAAATCCTTGTATATTGAACCAATAGTTGAT
1173424 GCATTAAAAAGGTCAACGACCCCAATTGTGTACATCTTCACATATCAACTAACTA-ACTAGGGTG
261 GCATTAAAAAGGTCAACGACCCCAATTGTGTACATCTTCACATATCAACTAACTACA-TAGGGTG
*
1173488 CGTTTGGTTA
325 CGTTTGATTA
* * * *
1173498 ACCAAATATATAATTATACTAATTTTATTAATGGACACGTCACTAATTCTGTTAAAAATTAACGA
1 ACCAAATATATAATTATACCAATTTTATTAACGGACACGTCACCAACTCTGTTAAAAATTAACGA
* *
1173563 CCAATGATTTAATTGAATCAATTAAATAGTTTTGTGATCATATTAACTTTTGACTATAGTTTAAT
66 CCAATGATTTAATTGAATCAATTAAATAGTTTGGTGATCACATTAACTTTTGACTATAGTTTAAT
1173628 AGTCTCCCGTCTAGTTTACCCTTTTTTTTAATAGACCATCTATTTTTACGCTCATAATATTCTTC
131 AGTCTCCCGTCTAGTTTACCCTTTTTTTTAATAGACCATCTATTTTTACGCTCATAATATTCTTC
1173693 TTATATTCATGAATAGCAGACGAAACAACCTCTCCAAATCCTTGTATATTGAACCAATAGTTGAT
196 TTATATTCATGAATAGCAGACGAAACAACCTCTCCAAATCCTTGTATATTGAACCAATAGTTGAT
1173758 GCATTAAAAAGGTCAACGACCCCAATTGTGTACATCTTCACATATCAACTAACTACATAGGGTGC
261 GCATTAAAAAGGTCAACGACCCCAATTGTGTACATCTTCACATATCAACTAACTACATAGGGTGC
1173823 GTTTGATTA
326 GTTTGATTA
*
1173832 ACGAAAT
1 ACCAAAT
1173839 GTAAGATTAC
Statistics
Matches: 327, Mismatches: 13, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
334 326 1.00
335 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (334 bp):
ACCAAATATATAATTATACCAATTTTATTAACGGACACGTCACCAACTCTGTTAAAAATTAACGA
CCAATGATTTAATTGAATCAATTAAATAGTTTGGTGATCACATTAACTTTTGACTATAGTTTAAT
AGTCTCCCGTCTAGTTTACCCTTTTTTTTAATAGACCATCTATTTTTACGCTCATAATATTCTTC
TTATATTCATGAATAGCAGACGAAACAACCTCTCCAAATCCTTGTATATTGAACCAATAGTTGAT
GCATTAAAAAGGTCAACGACCCCAATTGTGTACATCTTCACATATCAACTAACTACATAGGGTGC
GTTTGATTA
Found at i:1173863 original size:18 final size:18
Alignment explanation
Indices: 1173840--1173902 Score: 108
Period size: 18 Copynumber: 3.5 Consensus size: 18
1173830 TAACGAAATG
1173840 TAAGATTACCGGCGGGAA
1 TAAGATTACCGGCGGGAA
*
1173858 TAAGATTACCGACGGGAA
1 TAAGATTACCGGCGGGAA
*
1173876 TAAGATTACCGGCAGGAA
1 TAAGATTACCGGCGGGAA
1173894 TAAGATTAC
1 TAAGATTAC
1173903 TGCAAATGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.19
Consensus pattern (18 bp):
TAAGATTACCGGCGGGAA
Found at i:1179309 original size:2 final size:2
Alignment explanation
Indices: 1179293--1179357 Score: 98
Period size: 2 Copynumber: 33.0 Consensus size: 2
1179283 GAGTAATAAA
*
1179293 AT AT A- AT AC AT AT AT AT -T 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 AT AT
1179333 AT AT AT AT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT
1179358 GCTATGTGTA
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 2 0.03
2 54 0.93
3 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1180000 original size:68 final size:68
Alignment explanation
Indices: 1179886--1180070 Score: 187
Period size: 65 Copynumber: 2.7 Consensus size: 68
1179876 GGAAACGCTC
* * * * *
1179886 TCAAAGATATTTGTTGTTTCATGAGAAACGGTCTCAAGGTAAACAAAATTTTGTTTTAAGGAAAA
1 TCAAAGAT-TTT-TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGAAAA
1179951 TAAAT
64 TAAAT
* * * * **
1179956 TCAAAGATTTTTTGTTTCAAGAGAAACTATCTCAGGGGAGACAAAA-CTTGTTTCAGGGGGAATA
1 TCAAAGATTTTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGAAAATA
*
1180020 TAT
66 AAT
* * * *
1180023 TC-AA-ATATTTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATTTT
1 TCAAAGATTTTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1180071 TAAGAGAAAG
Statistics
Matches: 95, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
65 34 0.36
66 4 0.04
67 17 0.18
68 29 0.31
69 3 0.03
70 8 0.08
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (68 bp):
TCAAAGATTTTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGAAAATA
AAT
Found at i:1180072 original size:33 final size:33
Alignment explanation
Indices: 1180035--1180138 Score: 136
Period size: 33 Copynumber: 3.1 Consensus size: 33
1180025 AAATATTTTG
*
1180035 TTTTAAGGGAAACTGTCTCAAGAGAGACAAAAT
1 TTTTAAGAGAAACTGTCTCAAGAGAGACAAAAT
*
1180068 TTTTAAGAGAAAGTGTCTCAAGAGAGACAAAATTT
1 TTTTAAGAGAAACTGTCTCAAGAGAGACAAAA--T
* * *
1180103 ATTTTAAAAGAAACTGTCTCAAGGGAGACGAAAT
1 -TTTTAAGAGAAACTGTCTCAAGAGAGACAAAAT
1180137 TT
1 TT
1180139 ATTTCAAGGA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
33 32 0.52
34 1 0.02
35 1 0.02
36 28 0.45
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (33 bp):
TTTTAAGAGAAACTGTCTCAAGAGAGACAAAAT
Found at i:1180115 original size:36 final size:36
Alignment explanation
Indices: 1180043--1180142 Score: 143
Period size: 36 Copynumber: 2.9 Consensus size: 36
1180033 TGTTTTAAGG
*
1180043 GAAACTGTCTCAAGAGAGACAAAA--T-TTTTAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTTATTTTAAAA
*
1180076 GAAAGTGTCTCAAGAGAGACAAAATTTATTTTAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTTATTTTAAAA
* *
1180112 GAAACTGTCTCAAGGGAGACGAAATTTATTT
1 GAAACTGTCTCAAGAGAGACAAAATTTATTT
1180143 CAAGGAAAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
33 23 0.39
35 1 0.02
36 35 0.59
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTTATTTTAAAA
Found at i:1180218 original size:29 final size:29
Alignment explanation
Indices: 1180140--1180210 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
1180130 ACGAAATTTA
*
1180140 TTTCAAGGAAAACAGAATCAAAGATTTTG
1 TTTCAAGGAAAACAGATTCAAAGATTTTG
1180169 TTTCAAGGAAAACAGATTCAAAGATTTTG
1 TTTCAAGGAAAACAGATTCAAAGATTTTG
*
1180198 TTTCAAGGGAAAC
1 TTTCAAGGAAAAC
1180211 TGTCTCAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.28
Consensus pattern (29 bp):
TTTCAAGGAAAACAGATTCAAAGATTTTG
Found at i:1180251 original size:36 final size:36
Alignment explanation
Indices: 1180194--1180317 Score: 151
Period size: 36 Copynumber: 3.5 Consensus size: 36
1180184 ATTCAAAGAT
* *
1180194 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAA
* *
1180230 TTTGTTTTAAGAGAAAATGTCTTAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAA
* * * * * *
1180266 TTTGTTTTAAAAGAAATTGTTTCAAGGGAGACGAAA
1 TTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAA
1180302 TTTGTTTCAAG-GAAAA
1 TTTGTTTCAAGAGAAAA
1180318 CAGATTCAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
35 4 0.05
36 71 0.95
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAA
Found at i:1180301 original size:166 final size:161
Alignment explanation
Indices: 1180021--1180432 Score: 584
Period size: 166 Copynumber: 2.6 Consensus size: 161
1180011 GGGGGAATAT
*
1180021 ATTCAAATATTTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAA--T-TTTTAAGAGAAAGTG
1 ATTCAAA-ATTTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATG
1180083 TCTCAAGAGAGACAAAATTTATTTTAAAAGAAACTGTCTCAAGGGAGACGAAATTTATTTCAAGG
65 TCTCAAGAGAGACAAAATTTATTTTAAAAGAAACTGTCTCAAGGGAGACGAAATTTATTTCAAGG
1180148 AAAACAGAATCAAAGATTTTGTTTCAAGGAAAACAG
130 AAAACAGAATCAAAGATTTTGTTTCAA-G---ACAG
*
1180184 ATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATG
1 ATTCAAA-ATTTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATG
* * * * *
1180249 TCTTAAGAGAGACAAAATTTGTTTTAAAAGAAATTGTTTCAAGGGAGACGAAATTTGTTTCAAGG
65 TCTCAAGAGAGACAAAATTTATTTTAAAAGAAACTGTCTCAAGGGAGACGAAATTTATTTCAAGG
* *
1180314 AAAACAGATTCAAAGATTTTGTTTCAAGAGAG
130 AAAACAGAATCAAAGATTTTGTTTCAAGACAG
* ** * *
1180346 A--CCAAA-TTTGTTTTAAAAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGT
1 ATTCAAAATTTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGT
*
1180408 CTCAAGAGAGATAAAACTTTATTTT
66 CTCAAGAGAGACAAAA-TTTATTTT
1180433 GAGTAAATTA
Statistics
Matches: 226, Mismatches: 19, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
158 65 0.29
159 8 0.04
160 3 0.01
162 4 0.02
163 44 0.19
165 2 0.01
166 100 0.44
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (161 bp):
ATTCAAAATTTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGT
CTCAAGAGAGACAAAATTTATTTTAAAAGAAACTGTCTCAAGGGAGACGAAATTTATTTCAAGGA
AAACAGAATCAAAGATTTTGTTTCAAGACAG
Found at i:1180377 original size:36 final size:36
Alignment explanation
Indices: 1180337--1180432 Score: 138
Period size: 36 Copynumber: 2.6 Consensus size: 36
1180327 AGATTTTGTT
*
1180337 TCAAGAGAGACCAAATTTGTTTTAAAAGAAAATGTC
1 TCAAGAGAGACAAAATTTGTTTTAAAAGAAAATGTC
* *
1180373 TCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTC
1 TCAAGAGAGACAAAATTTGTTTTAAAAGAAAATGTC
* *
1180409 TCAAGAGAGATAAAACTTTATTTT
1 TCAAGAGAGACAAAA-TTTGTTTT
1180433 GAGTAAATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 47 0.87
37 7 0.13
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (36 bp):
TCAAGAGAGACAAAATTTGTTTTAAAAGAAAATGTC
Found at i:1181834 original size:95 final size:97
Alignment explanation
Indices: 1181626--1181880 Score: 347
Period size: 95 Copynumber: 2.6 Consensus size: 97
1181616 AGCTTGCTAG
* * *
1181626 ATCCATAAAGCCGAGGCGTTTAACCAATTCCTCTAGAGGGACAGCTC-AG-TATTATTGTATAGA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAGCTCAAGCT-TTATTGTATAG-
* * *
1181689 TATAATTATCACATTTATCAGGCTAGTTGAATATT
64 -ATAATGATCACATTTATCAGGCTAGCTGAATATC
* *
1181724 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATAG-T
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAGCTCAAGCTTTATTGTATAGAT
* * *
1181788 -ATGATCACCTTTATCAGGCTAGCTGACTCTC
66 AATGATCACATTTATCAGGCTAGCTGAATATC
*
1181819 ATCCATAAAGCCGGGGCATTTAACCAATTGCTTTAGAGGGACAGCTCAAGCTTTATTGTATA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAGCTCAAGCTTTATTGTATA
1181881 TATATATATA
Statistics
Matches: 141, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
95 84 0.60
96 1 0.01
98 42 0.30
99 13 0.09
100 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (97 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAGCTCAAGCTTTATTGTATAGAT
AATGATCACATTTATCAGGCTAGCTGAATATC
Found at i:1188949 original size:21 final size:21
Alignment explanation
Indices: 1188923--1188964 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1188913 CCAGAATGGG
*
1188923 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1188944 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1188965 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1189145 original size:35 final size:34
Alignment explanation
Indices: 1189077--1189162 Score: 129
Period size: 34 Copynumber: 2.5 Consensus size: 34
1189067 AAACCATGCA
*
1189077 GGGGGGAATCTGTACCCAGGGAATCGATACCCCT
1 GGGGGGAATCTGTTCCCAGGGAATCGATACCCCT
1189111 GGGGGGAATCTGTTCCC-GAGGAATCGATACCCCCT
1 GGGGGGAATCTGTTCCCAG-GGAATCGATA-CCCCT
*
1189146 AGGGGGAATCTGTTCCC
1 GGGGGGAATCTGTTCCC
1189163 CCTGGACAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
33 1 0.02
34 26 0.54
35 21 0.44
ACGTcount: A:0.21, C:0.27, G:0.33, T:0.20
Consensus pattern (34 bp):
GGGGGGAATCTGTTCCCAGGGAATCGATACCCCT
Found at i:1192512 original size:21 final size:21
Alignment explanation
Indices: 1192486--1192527 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1192476 CCAGAATGGG
*
1192486 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1192507 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1192528 ATATTCAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1192681 original size:20 final size:19
Alignment explanation
Indices: 1192656--1192715 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 19
1192646 ATCTGTACCC
*
1192656 GGGGAATCGATACCCCCTGG
1 GGGGAATTG-TACCCCCTGG
*
1192676 GGGGAATATGTTCCCCCTGG
1 GGGGAAT-TGTACCCCCTGG
1192696 GGGGAATTTGTACCCCCTGG
1 GGGGAA-TTGTACCCCCTGG
1192716 ACAATCTGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 33 0.94
21 2 0.06
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (19 bp):
GGGGAATTGTACCCCCTGG
Found at i:1199819 original size:16 final size:16
Alignment explanation
Indices: 1199795--1199825 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1199785 TATATATATA
1199795 ATATAATGGATTATTT
1 ATATAATGGATTATTT
*
1199811 ATATTATGGATTATT
1 ATATAATGGATTATT
1199826 AGATTTTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (16 bp):
ATATAATGGATTATTT
Found at i:1208618 original size:21 final size:21
Alignment explanation
Indices: 1208594--1208633 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1208584 ACATTTATAA
*
1208594 TATTTATTATAAAAAATTAAT
1 TATTAATTATAAAAAATTAAT
* *
1208615 TATTAATTTTAAAATATTA
1 TATTAATTATAAAAAATTA
1208634 TAATCATTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTAATTATAAAAAATTAAT
Found at i:1210071 original size:3 final size:3
Alignment explanation
Indices: 1210056--1210099 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
1210046 AGACAAAAAA
* * *
1210056 TAT TAT TAA TAT TATT TAT TAT TAT TAT TAA TAT TTT TAT TAT T
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1210100 TTGCAGGGCC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1210845 original size:20 final size:20
Alignment explanation
Indices: 1210820--1210893 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
1210810 TTTTCCCAAT
*
1210820 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
1210840 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
1210861 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
1210881 TCGCAACGCGAAT
1 TCGCAACGCGAAT
1210894 TGGGAAAACC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:1210863 original size:21 final size:21
Alignment explanation
Indices: 1210837--1210912 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1210827 GCGAATAAGT
1210837 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
1210858 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
1210878 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* *
1210899 AAACCGCAATGCGA
1 AAATCGCAACGCGA
1210913 TACTGACTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:1210865 original size:41 final size:41
Alignment explanation
Indices: 1210820--1210912 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1210810 TTTTCCCAAT
1210820 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1210861 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
1210902 CCGCAATGCGA
1 TCGCAATGCGA
1210913 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1210928 original size:20 final size:20
Alignment explanation
Indices: 1210903--1210995 Score: 87
Period size: 20 Copynumber: 4.6 Consensus size: 20
1210893 TTGGGAAAAC
*
1210903 CGCAATGCGATACTGACTAT
1 CGCAACGCGATACTGACTAT
* * * **
1210923 CGCAATGCGATAATAAAAAAT
1 CGCAACGCGATACT-GACTAT
* * *
1210944 CGCAACGAGATACTTACTTT
1 CGCAACGCGATACTGACTAT
*
1210964 CGCAACGCGATACTGACTTT
1 CGCAACGCGATACTGACTAT
1210984 CGCAACGCGATA
1 CGCAACGCGATA
1210996 ATACATAATC
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
CGCAACGCGATACTGACTAT
Found at i:1210948 original size:41 final size:41
Alignment explanation
Indices: 1210898--1210975 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
1210888 GCGAATTGGG
* * *
1210898 AAAACCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAACCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* * *
1210939 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAACCGCAACGAGATACTGACTATCGCAACGCGATA
1210976 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21
Consensus pattern (41 bp):
AAAACCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:1211211 original size:22 final size:22
Alignment explanation
Indices: 1211183--1211226 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1211173 CACTCTCTCA
*
1211183 CCCATCTCCGACGAAATTCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1211205 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1211227 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1211515 original size:20 final size:20
Alignment explanation
Indices: 1211490--1211527 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1211480 CGATTCTCTC
1211490 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1211510 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1211528 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1212865 original size:18 final size:18
Alignment explanation
Indices: 1212844--1212888 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1212834 TCCACTTCGG
*
1212844 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1212862 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1212880 GAGCCATCA
1 GAGCCATCA
1212889 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1213417 original size:19 final size:20
Alignment explanation
Indices: 1213363--1213429 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1213353 TAGTTTACTT
* *
1213363 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1213383 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1213403 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1213422 TCGCAACG
1 TCGCAACG
1213430 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1213496 original size:14 final size:14
Alignment explanation
Indices: 1213477--1213534 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1213467 TTGTGTTTCG
1213477 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1213491 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1213507 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1213523 CGTTGCGATTTT
1 CGTTGCGATTTT
1213535 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1213515 original size:32 final size:33
Alignment explanation
Indices: 1213472--1213550 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1213462 GCGATTTGTG
*
1213472 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1213504 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1213537 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1213551 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 26 0.58
33 19 0.42
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1213557 original size:19 final size:19
Alignment explanation
Indices: 1213535--1213589 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1213525 TTGCGATTTT
*
1213535 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
* *
1213554 CATTTCCGTGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1213574 CATTTTGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1213590 TTTAAGTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1215473 original size:14 final size:14
Alignment explanation
Indices: 1215454--1215489 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1215444 ATTGTTTAAT
1215454 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1215468 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1215482 TGATTTGT
1 TGATTTGT
1215490 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1215628 original size:19 final size:19
Alignment explanation
Indices: 1215606--1215673 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1215596 ATCGCAACGA
1215606 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1215625 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1215644 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1215658 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1215674 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1215749 original size:20 final size:20
Alignment explanation
Indices: 1215692--1215749 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1215682 TCGCATTGCG
* *
1215692 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
1215712 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1215732 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1215750 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1216838 original size:24 final size:24
Alignment explanation
Indices: 1216811--1216864 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1216801 GTATTCGAAA
* *
1216811 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1216835 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1216859 TTTGAT
1 TTTGAT
1216865 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1219399 original size:33 final size:33
Alignment explanation
Indices: 1219356--1219479 Score: 169
Period size: 33 Copynumber: 3.8 Consensus size: 33
1219346 AATTACTATT
*
1219356 GCAATGCGAAATGAAAATTGCAACGAGAGAATC
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
* * ** *
1219389 ACAATGCGAAATGAAGATCGCAACGCTA-ATTTC
1 GCAATGCGAAATGAAAATCGCAACGAGAGA-ATC
*
1219422 GCAATGCGAAATGAAAATCGCAACGAGGGAATC
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
1219455 GCAATGCGAAATGAAAATCGCAACG
1 GCAATGCGAAATGAAAATCGCAACG
1219480 CGAATTTAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
32 1 0.01
33 75 0.97
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
GCAATGCGAAATGAAAATCGCAACGAGAGAATC
Found at i:1219438 original size:66 final size:66
Alignment explanation
Indices: 1219356--1219486 Score: 217
Period size: 66 Copynumber: 2.0 Consensus size: 66
1219346 AATTACTATT
* * *
1219356 GCAATGCGAAATGAAAATTGCAACGAGAGAATCACAATGCGAAATGAAGATCGCAACGCTAATTT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAATTT
1219421 C
66 C
* *
1219422 GCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAATTT
1219487 AATTTCGCGT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (66 bp):
GCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAATTT
C
Found at i:1219444 original size:19 final size:19
Alignment explanation
Indices: 1219420--1219483 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
1219410 AACGCTAATT
1219420 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
**
1219439 TCGCAA--CG--A-GGGAA
1 TCGCAATGCGAAATGAAAA
1219453 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
1219472 TCGCAACGCGAA
1 TCGCAATGCGAA
1219484 TTTAATTTCG
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
14 9 0.26
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 20 0.57
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.12
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:1219501 original size:19 final size:20
Alignment explanation
Indices: 1219479--1219521 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1219469 AAATCGCAAC
1219479 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
1219498 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1219518 GCGA
1 GCGA
1219522 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1219506 original size:14 final size:14
Alignment explanation
Indices: 1219507--1219540 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1219497 TGCGATTTTC
1219507 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
1219521 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
1219535 ATTTTC
1 ATTTTC
1219541 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1219681 original size:14 final size:14
Alignment explanation
Indices: 1219662--1219698 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1219652 CATCAATTAA
1219662 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1219676 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1219690 ACAAATCAA
1 ACAAATCAA
1219699 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1221122 original size:21 final size:21
Alignment explanation
Indices: 1221056--1221122 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1221046 GTGAATCGGG
*
1221056 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1221076 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1221098 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1221119 CTCT
1 CTCT
1221123 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1221161 original size:41 final size:41
Alignment explanation
Indices: 1221095--1221177 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
1221085 CGATGACAGT
* * *
1221095 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAG
* * *
1221136 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAG
1221177 G
1 G
1221178 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.22
Consensus pattern (41 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAG
Found at i:1223270 original size:19 final size:19
Alignment explanation
Indices: 1223179--1223349 Score: 190
Period size: 19 Copynumber: 9.1 Consensus size: 19
1223169 TCTTTTGGTT
*
1223179 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1223198 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1223218 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1223236 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1223252 GAAATGACTATCGCGACGC
1 GAAATGAAAATCGCAACGC
1223271 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1223291 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1223310 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1223329 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1223348 GA
1 GA
1223350 TTTTGGTTTC
Statistics
Matches: 129, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
14 9 0.07
15 1 0.01
16 2 0.02
17 1 0.01
18 2 0.02
19 67 0.52
20 45 0.35
21 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1223304 original size:39 final size:38
Alignment explanation
Indices: 1223179--1223349 Score: 190
Period size: 39 Copynumber: 4.6 Consensus size: 38
1223169 TCTTTTGGTT
* *
1223179 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** *
1223218 GGAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** *
1223252 GAAATGACTATCGCGACGCGAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAA-CGC
*
1223291 GAAATAAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
*
1223329 GAAATGAAAATCGCAATGCGA
1 GAAATGAAAATCGCAACGCGA
1223350 TTTTGGTTTC
Statistics
Matches: 114, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
33 15 0.13
34 14 0.12
35 3 0.03
37 1 0.01
38 33 0.29
39 34 0.30
40 14 0.12
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:1223367 original size:19 final size:19
Alignment explanation
Indices: 1223345--1223411 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
1223335 AAAATCGCAA
* *
1223345 TGCGATTTTGGTTTCGTGT
1 TGCGATTTTGATTTCGCGT
*
1223364 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
1223383 TGCGATAGTT-ATTTCCGCGT
1 TGCGAT-TTTGATTT-CGCGT
1223403 TGCGATTTT
1 TGCGATTTT
1223412 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 28 0.68
20 13 0.32
ACGTcount: A:0.10, C:0.15, G:0.25, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:1223953 original size:20 final size:20
Alignment explanation
Indices: 1223928--1223980 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1223918 ACGCTATGTA
1223928 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
*
1223948 AATCGCGTTACGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1223968 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1223981 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1224014 original size:20 final size:20
Alignment explanation
Indices: 1223989--1224042 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1223979 GATTTTGTAT
1223989 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1224009 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1224029 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1224043 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1224027 original size:61 final size:61
Alignment explanation
Indices: 1223929--1224045 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
1223919 CGCTATGTAA
* * * * *
1223929 ATCGCGTTGCGAAAGTCAGAATCGCGTTACGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * * *
1223990 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTT
1224046 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1224061 original size:61 final size:61
Alignment explanation
Indices: 1223929--1224063 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
1223919 CGCTATGTAA
* * * * * ** *
1223929 ATCGCGTTGCGAAAGTCAGAATCGCGTTACGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * * *
1223990 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
1224052 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1224064 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1224153 original size:21 final size:21
Alignment explanation
Indices: 1224113--1224153 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1224103 ATTGTATACC
**
1224113 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1224134 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1224154 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1224407 original size:15 final size:14
Alignment explanation
Indices: 1224385--1224426 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1224375 CACCTTCCTT
1224385 TTTTTATTTTTATC
1 TTTTTATTTTTATC
*
1224399 TTCTTTATTTTTTTC
1 TT-TTTATTTTTATC
*
1224414 TTTTTATATTTAT
1 TTTTTATTTTTAT
1224427 TTAATTTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTATTTTTATC
Found at i:1224526 original size:18 final size:18
Alignment explanation
Indices: 1224487--1224531 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1224477 AATATATATT
**
1224487 ATTTTCATTATTTTATTT
1 ATTTTCATTATTTTATAC
1224505 ATTTTCATCTATTTT-TAC
1 ATTTTCAT-TATTTTATAC
1224523 ATTTTCATT
1 ATTTTCATT
1224532 TCTTTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 17 0.71
19 6 0.25
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTCATTATTTTATAC
Found at i:1225651 original size:17 final size:17
Alignment explanation
Indices: 1225629--1225697 Score: 52
Period size: 17 Copynumber: 3.9 Consensus size: 17
1225619 ACAGTCAGAG
1225629 TAGAGATCATGTCTGGA
1 TAGAGATCATGTCTGGA
* * *
1225646 TAGAGACCATGTCCGGG
1 TAGAGATCATGTCTGGA
*
1225663 TAGAAATTAACATG-C-GAGA
1 TAGAGA-T--CATGTCTG-GA
1225682 TAGAGATCATGTCTGG
1 TAGAGATCATGTCTGG
1225698 GTAGGAATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
16 4 0.10
17 21 0.54
18 3 0.08
19 7 0.18
20 4 0.10
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (17 bp):
TAGAGATCATGTCTGGA
Found at i:1225670 original size:53 final size:53
Alignment explanation
Indices: 1225590--1225697 Score: 157
Period size: 53 Copynumber: 2.0 Consensus size: 53
1225580 TTAACATGCG
*
1225590 GGATAAAGATCATATCCGGGTAGAAATTAACA-GTC-AGAGTAGAGATCATGTCT
1 GGATAAAGACCATATCCGGGTAGAAATTAACATG-CGAGA-TAGAGATCATGTCT
* *
1225643 GGATAGAGACCATGTCCGGGTAGAAATTAACATGCGAGATAGAGATCATGTCT
1 GGATAAAGACCATATCCGGGTAGAAATTAACATGCGAGATAGAGATCATGTCT
1225696 GG
1 GG
1225698 GTAGGAATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
53 46 0.92
54 4 0.08
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (53 bp):
GGATAAAGACCATATCCGGGTAGAAATTAACATGCGAGATAGAGATCATGTCT
Found at i:1227531 original size:66 final size:66
Alignment explanation
Indices: 1227423--1227550 Score: 220
Period size: 66 Copynumber: 1.9 Consensus size: 66
1227413 CTCTAAGGCA
* *
1227423 TCAAGGTTCAACTTCACAACGAAGGGACCATCCACGATTTCAACTTCACGATGAAGGATATCCAA
1 TCAAGGCTCAACTTCACAACGAAGGGACCATCCACGACTTCAACTTCACGATGAAGGATATCCAA
1227488 T
66 T
**
1227489 TCAAGGCTCAACTTCACAACGAAGGGGTCATCCACGACTTCAACTTCACGATGAAGGATATC
1 TCAAGGCTCAACTTCACAACGAAGGGACCATCCACGACTTCAACTTCACGATGAAGGATATC
1227551 GTTTCCACCA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (66 bp):
TCAAGGCTCAACTTCACAACGAAGGGACCATCCACGACTTCAACTTCACGATGAAGGATATCCAA
T
Found at i:1227545 original size:32 final size:32
Alignment explanation
Indices: 1227429--1227537 Score: 103
Period size: 32 Copynumber: 3.3 Consensus size: 32
1227419 GGCATCAAGG
* *
1227429 TTCAACTTCACAACGAAGGGACCATCCACGAT
1 TTCAACTTCACAACGAAGGGATCATCCACGAC
* * * * * *
1227461 TTCAACTTCACGATGAAGGATATCCAATTCAAGGC
1 TTCAACTTCACAACGAAGG-GAT-C-ATCCACGAC
*
1227496 -TCAACTTCACAACGAAGGGGTCATCCACGAC
1 TTCAACTTCACAACGAAGGGATCATCCACGAC
1227527 TTCAACTTCAC
1 TTCAACTTCAC
1227538 GATGAAGGAT
Statistics
Matches: 58, Mismatches: 15, Indels: 8
0.72 0.19 0.10
Matches are distributed among these distances:
31 6 0.10
32 28 0.48
33 2 0.03
34 17 0.29
35 5 0.09
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (32 bp):
TTCAACTTCACAACGAAGGGATCATCCACGAC
Found at i:1236509 original size:17 final size:18
Alignment explanation
Indices: 1236484--1236524 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1236474 TATTTTTTCC
*
1236484 TTTTATATTT-ATTTAAT
1 TTTTCTATTTAATTTAAT
*
1236501 TTTTCTATTTAATTTTAT
1 TTTTCTATTTAATTTAAT
1236519 TTTTCT
1 TTTTCT
1236525 CGTGATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTCTATTTAATTTAAT
Found at i:1236511 original size:23 final size:23
Alignment explanation
Indices: 1236472--1236520 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
1236462 CTTTTTTCTC
*
1236472 TTTATTTTTTCCTTTT-ATATTTA
1 TTTAATTTTTCCTTTTAAT-TTTA
1236495 TTTAATTTTT-CTATTTAATTTTA
1 TTTAATTTTTCCT-TTTAATTTTA
1236518 TTT
1 TTT
1236521 TTCTCGTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 2 0.09
23 19 0.83
24 2 0.09
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTAATTTTTCCTTTTAATTTTA
Found at i:1236588 original size:10 final size:9
Alignment explanation
Indices: 1236553--1236579 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1236543 TTTAATATAT
1236553 ATTATTTTC
1 ATTATTTTC
1236562 ATTATTTTC
1 ATTATTTTC
1236571 ATTATTTTC
1 ATTATTTTC
1236580 TTCTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (9 bp):
ATTATTTTC
Found at i:1236713 original size:21 final size:21
Alignment explanation
Indices: 1236663--1236713 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
1236653 TATCTCACCT
* * *
1236663 TTTTATTTGATTTTTATGTTC
1 TTTTATTTAATTTTAATGTTA
*
1236684 TTTGT-TTTAATTTTAATTTTA
1 TTT-TATTTAATTTTAATGTTA
1236705 TTTTATTTA
1 TTTTATTTA
1236714 TTATCTAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.73
Consensus pattern (21 bp):
TTTTATTTAATTTTAATGTTA
Found at i:1239846 original size:36 final size:36
Alignment explanation
Indices: 1239776--1240021 Score: 179
Period size: 36 Copynumber: 6.8 Consensus size: 36
1239766 AGACCTGTAA
* *
1239776 AAAATTATA-TATATATATTTTCAAAAGAT-G-TTTT
1 AAAACTATATTATATATGTTTTCAAAA-ATCGTTTTT
*
1239810 AAAACTATATTATATACGTTTTCAAAAATCGTTTTT
1 AAAACTATATTATATATGTTTTCAAAAATCGTTTTT
* * * *
1239846 AAAACTATGTAAAGTATACGTTTTCAAAAATGCGTTTTC
1 AAAACTATAT-TA-TATATGTTTTCAAAAAT-CGTTTTT
* * *
1239885 AAAATTATATAATATATGTTTTCAAAAA-CGTATTTG
1 AAAACTATATTATATATGTTTTCAAAAATCGT-TTTT
* *
1239921 AAAACCATATTATATA--TTTT-AAAAAACTGATTTTT
1 AAAACTATATTATATATGTTTTCAAAAATC-G-TTTTT
* * *
1239956 AAAAACTATA-TATTATATGCTTTCAATAA-CATTTTCT
1 -AAAACTATATTA-TATATGTTTTCAAAAATCGTTTT-T
1239993 GAAAACTATA-TATTATATGTTTTCAAAAA
1 -AAAACTATATTA-TATATGTTTTCAAAAA
1240022 ATATTTTAAA
Statistics
Matches: 175, Mismatches: 21, Indels: 29
0.78 0.09 0.13
Matches are distributed among these distances:
33 5 0.03
34 15 0.09
35 25 0.14
36 46 0.26
37 43 0.25
38 23 0.13
39 18 0.10
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.42
Consensus pattern (36 bp):
AAAACTATATTATATATGTTTTCAAAAATCGTTTTT
Found at i:1245445 original size:55 final size:55
Alignment explanation
Indices: 1245361--1245471 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
1245351 TAATAGATGG
*
1245361 ATCCTAGTCCTATCACTATCTTCAATGCCATCCGTTATTATAGCATTGATGCTCA
1 ATCCTAGTCCTATCACTATCTTCAATGCCATCCGTTATTATAGAATTGATGCTCA
*
1245416 ATCCTAGTCCTATCACTATCTTCAATGCCATCCGTTGTTATAGAATTGATGCTCA
1 ATCCTAGTCCTATCACTATCTTCAATGCCATCCGTTATTATAGAATTGATGCTCA
1245471 A
1 A
1245472 GTCTTTCAGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (55 bp):
ATCCTAGTCCTATCACTATCTTCAATGCCATCCGTTATTATAGAATTGATGCTCA
Found at i:1248359 original size:24 final size:24
Alignment explanation
Indices: 1248323--1248368 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1248313 TTGGATATAG
*
1248323 AAGCTTGTACTTTTACAGCAGACT
1 AAGCTTGTACTTTCACAGCAGACT
* *
1248347 AAGCTTGTGCTTTCATAGCAGA
1 AAGCTTGTACTTTCACAGCAGA
1248369 TGCGTCCCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (24 bp):
AAGCTTGTACTTTCACAGCAGACT
Found at i:1253579 original size:5 final size:6
Alignment explanation
Indices: 1253564--1253589 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1253554 GGACCTGTAA
1253564 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
1253590 TATATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:1253638 original size:17 final size:17
Alignment explanation
Indices: 1253618--1253650 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1253608 TAATATTATA
1253618 TTTTCAAAAATAATATG
1 TTTTCAAAAATAATATG
*
1253635 TTTTCAAAAATTATAT
1 TTTTCAAAAATAATAT
1253651 ATTATATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTTCAAAAATAATATG
Found at i:1253651 original size:42 final size:40
Alignment explanation
Indices: 1253598--1253749 Score: 116
Period size: 42 Copynumber: 3.7 Consensus size: 40
1253588 AATATATAAT
1253598 AAAAACTATATAATATTATATTTTCAAAAATAATATGTTTTC
1 AAAAACTATATAATA-TATATTTTCAAAAA-AATATGTTTTC
* * * * *
1253640 AAAAATTATATATTATATATGTTTCCAAAAAAT-CGTTTATAG
1 AAAAACTATATAATATATAT-TTTCAAAAAAATATGTTT-T-C
1253682 AAAAACTATATATATATATATATATTC---AAAATATGTTTTC
1 AAAAACTATATA-ATATATAT-T-TTCAAAAAAATATGTTTTC
* * **
1253722 -AAAATTATATTATATACGTTTTCAAAAA
1 AAAAACTATATAATATATATTTTCAAAAA
1253750 TCCTTTTTAA
Statistics
Matches: 87, Mismatches: 14, Indels: 21
0.71 0.11 0.17
Matches are distributed among these distances:
36 3 0.03
37 1 0.01
38 6 0.07
39 11 0.13
40 4 0.05
41 15 0.17
42 36 0.41
43 8 0.09
44 3 0.03
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.41
Consensus pattern (40 bp):
AAAAACTATATAATATATATTTTCAAAAAAATATGTTTTC
Found at i:1253824 original size:37 final size:37
Alignment explanation
Indices: 1253783--1253918 Score: 111
Period size: 37 Copynumber: 3.8 Consensus size: 37
1253773 ATACGTTTTC
* *
1253783 AAAACTATAAAATATATGTTTTCAAAAACGTATTATC
1 AAAACTATATAATATATGTTTTCAAAAACGTATTATA
* *
1253820 AAAAC--CATAATATA--TTTTCAAAAATCG-ATTTTTA
1 AAAACTATATAATATATGTTTTCAAAAA-CGTA-TTATA
* * * * * *
1253854 AAAATTATATATTATAGGCTTTCAAAAACGTTTTCTA
1 AAAACTATATAATATATGTTTTCAAAAACGTATTATA
* *
1253891 AAAACTATATATTATATGTTTTTAAAAA
1 AAAACTATATAATATATGTTTTCAAAAA
1253919 TATTTTTAAA
Statistics
Matches: 78, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
33 11 0.14
34 9 0.12
35 7 0.09
36 7 0.09
37 35 0.45
38 9 0.12
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (37 bp):
AAAACTATATAATATATGTTTTCAAAAACGTATTATA
Found at i:1255109 original size:21 final size:22
Alignment explanation
Indices: 1255079--1255122 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1255069 AATTTTATTT
1255079 ATGAATTAT-AAACAAATAGTAA
1 ATGAATTATAAAACAAATA-TAA
1255101 ATGAA-TATAAAACAAATATAA
1 ATGAATTATAAAACAAATATAA
1255122 A
1 A
1255123 AAAATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.25
Consensus pattern (22 bp):
ATGAATTATAAAACAAATATAA
Found at i:1255132 original size:21 final size:22
Alignment explanation
Indices: 1255088--1255132 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1255078 TATGAATTAT
**
1255088 AAACAAATAGTAAATGAATATA
1 AAACAAATAGTAAAAAAATATA
*
1255110 AAACAAATA-TAAAAAAATTTA
1 AAACAAATAGTAAAAAAATATA
1255131 AA
1 AA
1255133 TATATTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (22 bp):
AAACAAATAGTAAAAAAATATA
Found at i:1256447 original size:12 final size:12
Alignment explanation
Indices: 1256426--1256455 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1256416 CCATTGTCAT
*
1256426 TTGCCATTGCCG
1 TTGCCTTTGCCG
1256438 TTGCCTTTGCCG
1 TTGCCTTTGCCG
1256450 TTGCCT
1 TTGCCT
1256456 GGACTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.03, C:0.33, G:0.23, T:0.40
Consensus pattern (12 bp):
TTGCCTTTGCCG
Found at i:1259652 original size:12 final size:12
Alignment explanation
Indices: 1259635--1259660 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1259625 AGCCTTAGAG
1259635 CAGAAACACTGT
1 CAGAAACACTGT
1259647 CAGAAACACTGT
1 CAGAAACACTGT
1259659 CA
1 CA
1259661 ACAAGCTTAG
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:0.42, C:0.27, G:0.15, T:0.15
Consensus pattern (12 bp):
CAGAAACACTGT
Found at i:1263568 original size:21 final size:21
Alignment explanation
Indices: 1263534--1263623 Score: 103
Period size: 21 Copynumber: 4.4 Consensus size: 21
1263524 ACTTCGACTA
*
1263534 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
* * *
1263555 TTGCGTTACGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
** *
1263576 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATAGTCCAAGT
1263597 T--CGTTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
1263616 TCGCGTTG
1 TCGCGTTG
1263624 TGATTTATTC
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
19 16 0.30
21 38 0.70
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:1263603 original size:19 final size:19
Alignment explanation
Indices: 1263579--1263648 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
1263569 TCGAAGTTCG
1263579 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
** *
1263598 CGTTGCGATAGTCCAAGTT
1 CGTTGCGATTTTCCAAATT
*
1263617 CGCGTTGTGATTTATTCCAAATT
1 --CGTTGCGA-TT-TTCCAAATT
*
1263640 TGTTGCGAT
1 CGTTGCGAT
1263649 AGTCCAAAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
19 16 0.42
20 1 0.03
21 13 0.34
22 1 0.03
23 7 0.18
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:1263616 original size:40 final size:42
Alignment explanation
Indices: 1263558--1263655 Score: 146
Period size: 40 Copynumber: 2.4 Consensus size: 42
1263548 TCCAAGTTTG
* *
1263558 CGTTACGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
1263598 CGTTGCGATAGTCCAAGTTCGCGTTGTGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
1263640 TGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
1263656 AATCGCAACG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 26 0.50
41 2 0.04
42 24 0.46
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (42 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:1263755 original size:6 final size:6
Alignment explanation
Indices: 1263745--1263781 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
1263735 GACACGTATT
*
1263745 ACCACT ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1263782 GACGAGATGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.35, C:0.49, G:0.14, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:1264563 original size:42 final size:42
Alignment explanation
Indices: 1264516--1264789 Score: 399
Period size: 42 Copynumber: 6.5 Consensus size: 42
1264506 TGCGATTTTG
* *
1264516 GACTATCGCAACGAATTTGGAATAAATCGTAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1264558 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1264600 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1264642 GACTATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
1264684 GACTATCGCAACGCGAACTTGGACT--ATCGCAACGCGAACTTG
1 GACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
* * * * * *
1264726 GACTATCACAACGAATTTGGAATAAATTGAAACGTGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1264768 GACTATCGCAACGAATTTGGAA
1 GACTATCGCAACGAACTTGGAA
1264790 AATTGCATTG
Statistics
Matches: 213, Mismatches: 15, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
40 10 0.05
42 192 0.90
44 11 0.05
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:1264565 original size:21 final size:21
Alignment explanation
Indices: 1264513--1264780 Score: 223
Period size: 21 Copynumber: 12.8 Consensus size: 21
1264503 CGTTGCGATT
*
1264513 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
1264532 TTGGAATAAATCGTAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
1264555 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
1264574 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
1264597 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
1264616 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
1264639 TTTGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
* *
1264658 TTGGAATAAATCGCAACGCAAAC
1 TTGGACT--ATCGCAACGCGAAC
*
1264681 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
1264702 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* *
1264723 TTGGACTATCACAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* * * *
1264742 TTGGAATAAATTGAAACGTGAAC
1 TTGGACT--ATCGCAACGCGAAC
1264765 TTGGACTATCGCAACG
1 TTGGACTATCGCAACG
1264781 AATTTGGAAA
Statistics
Matches: 197, Mismatches: 32, Indels: 38
0.74 0.12 0.14
Matches are distributed among these distances:
19 46 0.23
21 104 0.53
23 47 0.24
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:1264823 original size:21 final size:21
Alignment explanation
Indices: 1264797--1264844 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1264787 GAAAATTGCA
1264797 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
*
1264818 TTGCGATAGTCGATGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
1264839 TTGCGA
1 TTGCGA
1264845 ATTTGGAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (21 bp):
TTGCGATAGTCGAAGTTCGCG
Found at i:1267489 original size:22 final size:22
Alignment explanation
Indices: 1267444--1267506 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
1267434 ATATGAAATT
*
1267444 TGTCCTGAAGGACCTCA--TATA
1 TGTCCCGAAGGACCT-ATGTATA
1267465 TGTCCCGAAGGACCTATGTATA
1 TGTCCCGAAGGACCTATGTATA
*
1267487 TGTCCCGAATGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
1267507 ACCACAACTC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 1 0.03
21 14 0.37
22 23 0.61
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATGTATA
Found at i:1268613 original size:23 final size:23
Alignment explanation
Indices: 1268587--1268645 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
1268577 CGTATAATTA
**
1268587 CACCGAAGTGCTGCGTAGAAATG
1 CACCGAAGTGCCACGTAGAAATG
* * *
1268610 CACCGTAGTGCCACGTAGGATTG
1 CACCGAAGTGCCACGTAGAAATG
*
1268633 TACCGAAGTGCCA
1 CACCGAAGTGCCA
1268646 TATAAAATGT
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:0.27, C:0.25, G:0.29, T:0.19
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAAATG
Found at i:1270219 original size:24 final size:24
Alignment explanation
Indices: 1270187--1270247 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
1270177 TCCCCTTGAA
1270187 GTGCATCGATGCATTCTTTAACAT
1 GTGCATCGATGCATTCTTTAACAT
1270211 GTGCATCGATGCATTCTTTAACAT
1 GTGCATCGATGCATTCTTTAACAT
1270235 GTGCATCGATGCA
1 GTGCATCGATGCA
1270248 CTACCCATGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (24 bp):
GTGCATCGATGCATTCTTTAACAT
Found at i:1271610 original size:18 final size:19
Alignment explanation
Indices: 1271587--1271623 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1271577 TGGTATCGGT
1271587 ACCCTT-GGTATCAATACG
1 ACCCTTAGGTATCAATACG
1271605 ACCCTTCAGGTATCAATAC
1 ACCCTT-AGGTATCAATAC
1271624 CTTATGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.27
Consensus pattern (19 bp):
ACCCTTAGGTATCAATACG
Found at i:1277852 original size:22 final size:22
Alignment explanation
Indices: 1277825--1277868 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1277815 GGACCTCATG
1277825 TATGTCCCGAAGAACCTATGTA
1 TATGTCCCGAAGAACCTATGTA
* *
1277847 TATGTCCTGAAGGACCTATGTA
1 TATGTCCCGAAGAACCTATGTA
1277869 ACCCTCAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (22 bp):
TATGTCCCGAAGAACCTATGTA
Found at i:1279794 original size:45 final size:45
Alignment explanation
Indices: 1279745--1279977 Score: 265
Period size: 45 Copynumber: 5.2 Consensus size: 45
1279735 AATACTTCAT
* * *
1279745 TATGCATTTTAAATTATAACAT-CTTTTCTGTTGATAATGCACCCA
1 TATGCA-TTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCA
* * *
1279790 TATGCATTTCAACTATAGTATACTTTTATGTTGATAATGTACCCA
1 TATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCA
* * *
1279835 TATACATTTCAACCATAGTATACTTTTCTGTTGATAATGCACCCA
1 TATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCA
* * *
1279880 TATGCATTT-ACACTTTAACATACTTTTCTGTTGAAAATGCACCCA
1 TATGCATTTCA-ACTATAGCATACTTTTCTGTTGATAATGCACCCA
* * ***
1279925 TATGCATTTCAACTATGGCAT-CCTTTCATGCCAATAATGCACCCA
1 TATGCATTTCAACTATAGCATACTTTTC-TGTTGATAATGCACCCA
1279970 TATGCATT
1 TATGCATT
1279978 ATTCTTTTAC
Statistics
Matches: 160, Mismatches: 24, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
44 17 0.11
45 142 0.89
46 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (45 bp):
TATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCA
Found at i:1280033 original size:79 final size:79
Alignment explanation
Indices: 1279915--1280066 Score: 243
Period size: 79 Copynumber: 1.9 Consensus size: 79
1279905 TTCTGTTGAA
*
1279915 AATGCACCCATATGCATTTCAACTATGGCATCCTTTCATG-CCAATAATGCACCCATATGCATTA
1 AATGCACCCATATACATTTCAACTATGGCATCCTTTCATGACC-ATAATGCACCCATATGCATTA
1279979 TTCTTTTACGCTGAC
65 TTCTTTTACGCTGAC
* ** *
1279994 AATGTACCCATATACATTTCAGTTATGGCATCCTTTCATGACCATAATGCACTCATATGCATTAT
1 AATGCACCCATATACATTTCAACTATGGCATCCTTTCATGACCATAATGCACCCATATGCATTAT
1280059 TCTTTTAC
66 TCTTTTAC
1280067 ATTTGTTTTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
79 65 0.97
80 2 0.03
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.36
Consensus pattern (79 bp):
AATGCACCCATATACATTTCAACTATGGCATCCTTTCATGACCATAATGCACCCATATGCATTAT
TCTTTTACGCTGAC
Found at i:1280519 original size:22 final size:21
Alignment explanation
Indices: 1280466--1280543 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 21
1280456 ATTTCTGGCC
1280466 CTTA-GGTATCGATACCCCTA
1 CTTAGGGTATCGATACCCCTA
* *
1280486 CTTATGGTATCGATACTATCCTA
1 CTTAGGGTATCGATAC--CCCTA
1280509 -TTAGGGTATCGATACCCC--
1 CTTAGGGTATCGATACCCCTA
**
1280527 CTTAATGTATCGATACC
1 CTTAGGGTATCGATACC
1280544 TAAATTAGCT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
19 14 0.29
20 6 0.12
21 11 0.22
22 14 0.29
23 4 0.08
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (21 bp):
CTTAGGGTATCGATACCCCTA
Found at i:1280611 original size:22 final size:20
Alignment explanation
Indices: 1280565--1280638 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
1280555 CAAACTAGCC
* *
1280565 TGGTATCAATACCCTCAT-CA
1 TGGTATCGATACCC-CATATA
1280585 TGGTATCGATACCCCTATACTA
1 TGGTATCGATACCCC-ATA-TA
*
1280607 TGGTATCGATACCCCCTATA
1 TGGTATCGATACCCCATATA
1280627 -GGTATCGATACC
1 TGGTATCGATACC
1280639 TAATTTAGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
19 13 0.27
20 17 0.35
21 2 0.04
22 16 0.33
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (20 bp):
TGGTATCGATACCCCATATA
Found at i:1280632 original size:19 final size:22
Alignment explanation
Indices: 1280584--1280638 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
1280574 TACCCTCATC
1280584 ATGGTATCGATACCCCTATACT
1 ATGGTATCGATACCCCTATACT
*
1280606 ATGGTATCGATACCCC-CTA-T
1 ATGGTATCGATACCCCTATACT
1280626 A-GGTATCGATACC
1 ATGGTATCGATACC
1280639 TAATTTAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 12 0.38
20 2 0.06
21 2 0.06
22 16 0.50
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (22 bp):
ATGGTATCGATACCCCTATACT
Found at i:1280713 original size:95 final size:95
Alignment explanation
Indices: 1280513--1280694 Score: 249
Period size: 95 Copynumber: 1.9 Consensus size: 95
1280503 ATCCTATTAG
* * *
1280513 GGTATCGATACCCCCTTAATGTATCGATACCTAAATTAGCTTCAAACTAGCCTGGTATCAATACC
1 GGTATCGATACCCCCTTAAGGTATCGATACCTAAATTAGATTCAAACTAGACTGGTATCAATACC
1280578 CTCATCATGGTATCGATACCCCTATACTAT
66 CTCATCATGGTATCGATACCCCTATACTAT
* ** ** *
1280608 GGTATCGATACCCCC-TATAGGTATCGATACCTAATTTAGATTCAATGTTTACTGGTATCGATAC
1 GGTATCGATACCCCCTTA-AGGTATCGATACCTAAATTAGATTCAAACTAGACTGGTATCAATAC
* *
1280672 CCTTATCTTGGTATCGATACCCC
65 CCTCATCATGGTATCGATACCCC
1280695 ATTACTTGGG
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
94 2 0.03
95 73 0.97
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.32
Consensus pattern (95 bp):
GGTATCGATACCCCCTTAAGGTATCGATACCTAAATTAGATTCAAACTAGACTGGTATCAATACC
CTCATCATGGTATCGATACCCCTATACTAT
Found at i:1288606 original size:90 final size:90
Alignment explanation
Indices: 1288491--1288661 Score: 279
Period size: 90 Copynumber: 1.9 Consensus size: 90
1288481 ATTCTAACAT
* * *
1288491 CTTTTCTATTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTATGTTGATAATGTAC
1 CTTTTATATTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTATGTTGATAATGCAC
1288556 CCATATACATTTCAACCATAATATA
66 CCATATACATTTCAACCATAATATA
* * *
1288581 CTTTTATATTGATAATGCACTCATATGCATTTCAACTTTAGCATACTTTTCTGTTGATAATGCAC
1 CTTTTATATTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTATGTTGATAATGCAC
*
1288646 CCATATGCATTTCAAC
66 CCATATACATTTCAAC
1288662 TATGGAACCC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 74 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (90 bp):
CTTTTATATTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTATGTTGATAATGCAC
CCATATACATTTCAACCATAATATA
Found at i:1288658 original size:45 final size:45
Alignment explanation
Indices: 1288485--1288664 Score: 236
Period size: 45 Copynumber: 4.0 Consensus size: 45
1288475 TTTTAAATTC
*
1288485 TAACAT-CTTTTCTATTGATAATGCACCCATATGCATTTCAACTA
1 TAACATACTTTTATATTGATAATGCACCCATATGCATTTCAACTA
** * * * *
1288529 TAGTATACTTTTATGTTGATAATGTACCCATATACATTTCAACCA
1 TAACATACTTTTATATTGATAATGCACCCATATGCATTTCAACTA
* * *
1288574 TAATATACTTTTATATTGATAATGCACTCATATGCATTTCAACTT
1 TAACATACTTTTATATTGATAATGCACCCATATGCATTTCAACTA
* * *
1288619 TAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTA
1 TAACATACTTTTATATTGATAATGCACCCATATGCATTTCAACTA
1288664 T
1 T
1288665 GGAACCCTTT
Statistics
Matches: 115, Mismatches: 20, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
44 4 0.03
45 111 0.97
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (45 bp):
TAACATACTTTTATATTGATAATGCACCCATATGCATTTCAACTA
Found at i:1288686 original size:90 final size:90
Alignment explanation
Indices: 1288502--1288701 Score: 249
Period size: 90 Copynumber: 2.2 Consensus size: 90
1288492 TTTTCTATTG
* *
1288502 ATAATGCACCCATATGCATTTCAACTATAGTATACTTTTATGTTGATAATGTACCCATATACATT
1 ATAATGCACCCATATGCATTTCAACTATAGCATACTTTTATGTTGATAATGCACCCATATACATT
* * ***
1288567 TCAACCATAATATACTTTTATATTG
66 TCAACCATAATACACTTTCATACCA
* * * *
1288592 ATAATGCACTCATATGCATTTCAACTTTAGCATACTTTTCTGTTGATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATTTCAACTATAGCATACTTTTATGTTGATAATGCACCCATATACATT
* * * *
1288657 TCAACTATGGA-ACCCTTTCATGCCA
66 TCAACCAT-AATACACTTTCATACCA
1288682 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATT
1288702 ATTCTTTTAC
Statistics
Matches: 93, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
90 92 0.99
91 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (90 bp):
ATAATGCACCCATATGCATTTCAACTATAGCATACTTTTATGTTGATAATGCACCCATATACATT
TCAACCATAATACACTTTCATACCA
Found at i:1288757 original size:79 final size:79
Alignment explanation
Indices: 1288639--1288791 Score: 243
Period size: 79 Copynumber: 1.9 Consensus size: 79
1288629 TTCTGTTGAT
* *
1288639 AATGCACCCATATGCATTTCAACTATGGAACCCTTTCATGCCAATAATGCACCCATATGCATTAT
1 AATGCACCCATATACATTTCAACTATGGAACCATTTCATGCCAATAATGCACCCATATGCATTAT
1288704 TCTTTTACACTAAC
66 TCTTTTACACTAAC
* * * * *
1288718 AATGTACCCATATACATTTCAGCTATGGCATCATTTCATGCCTATAATGCACCCATATGCATTAT
1 AATGCACCCATATACATTTCAACTATGGAACCATTTCATGCCAATAATGCACCCATATGCATTAT
1288783 TCTTTTACA
66 TCTTTTACA
1288792 TTCGTTTTAG
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 67 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (79 bp):
AATGCACCCATATACATTTCAACTATGGAACCATTTCATGCCAATAATGCACCCATATGCATTAT
TCTTTTACACTAAC
Found at i:1289454 original size:15 final size:15
Alignment explanation
Indices: 1289434--1289468 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1289424 ATAGGGTATC
* *
1289434 GGTACTGTTTCATAG
1 GGTACTATTCCATAG
1289449 GGTACTATTCCATAG
1 GGTACTATTCCATAG
1289464 GGTAC
1 GGTAC
1289469 CGATACTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (15 bp):
GGTACTATTCCATAG
Found at i:1293018 original size:22 final size:22
Alignment explanation
Indices: 1292993--1293038 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1292983 GTATCGATAT
1292993 CATAGTATAGAAGTATCAGTAC
1 CATAGTATAGAAGTATCAGTAC
*
1293015 CATAGTATAGAAGTATCGGTAC
1 CATAGTATAGAAGTATCAGTAC
1293037 CA
1 CA
1293039 GGGTAGTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (22 bp):
CATAGTATAGAAGTATCAGTAC
Found at i:1293702 original size:138 final size:138
Alignment explanation
Indices: 1293442--1293942 Score: 686
Period size: 138 Copynumber: 3.6 Consensus size: 138
1293432 TAAACCAAAT
* * *
1293442 CCATAACTAAAACGCATGAAATGATGCATTAAGCCATGAAAGGATACCATAATTAAAATGCATG-
1 CCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGA
* * * *
1293506 AACGAATGCATTAAGGCATGAAAGGATGAGATAACTAAAATGCTTGAA-AGGATGCATTAAGGCA
66 AAAG-ATGCATTAAGGCATGAAAGGATGACATAATTAAAATGCATGAACA-GATGCATTAAGGCA
*
1293570 TGAAAAGATG
129 TGAAAGGATG
* * *
1293580 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATACATGA
1 CCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGA
*
1293645 AAAGATGCATTAAGGCATGAAAGGATGACATAATTAAAATGCATGAACAGATACATTAAGGCATG
66 AAAGATGCATTAAGGCATGAAAGGATGACATAATTAAAATGCATGAACAGATGCATTAAGGCATG
1293710 AAAGGATG
131 AAAGGATG
** *
1293718 ATATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGTCATAATTAAAATGCATGA
1 CCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGA
** * *
1293783 ATGGATGCATTAAGGTATGAAAGGATG-CGATAATTAAAATGTATGAAC-GAATGCATTAAGGCA
66 AAAGATGCATTAAGGCATGAAAGGATGAC-ATAATTAAAATGCATGAACAG-ATGCATTAAGGCA
1293846 TGAAAGGATG
129 TGAAAGGATG
* * * * * *
1293856 CCATAACAAAAATGCATGAAATGATGCTTTAGGGCGTGAAAAGATGCCATGATTAAAATGCATGA
1 CCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGA
* * *
1293921 ACATATGCATTAATGCATGAAA
66 AAAGATGCATTAAGGCATGAAA
1293943 AGAGACAACG
Statistics
Matches: 322, Mismatches: 37, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
137 2 0.01
138 316 0.98
139 4 0.01
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.23
Consensus pattern (138 bp):
CCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGA
AAAGATGCATTAAGGCATGAAAGGATGACATAATTAAAATGCATGAACAGATGCATTAAGGCATG
AAAGGATG
Found at i:1293808 original size:20 final size:20
Alignment explanation
Indices: 1293455--1293856 Score: 122
Period size: 20 Copynumber: 17.7 Consensus size: 20
1293445 TAACTAAAAC
*
1293455 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * *
1293475 CCATGAAAGGATACCATAATTAAAAT
1 GCATGAAAGGAT-GC---ATT--AAG
* *
1293501 GCATGAACGAATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1293521 GCATGAAAGGATGAGATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
1293547 GCTTGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1293567 GCATGAAAAGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
1293593 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1293613 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
* *
1293639 ACATGAAAAGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1293659 GCATGAAAGGATGACATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
1293685 GCATGAACA-GATACATTAAG
1 GCATGAA-AGGATGCATTAAG
* *
1293705 GCATGAAAGGATGATATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
1293731 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1293751 GCATGAAAGGATGTCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
1293777 GCATGAATGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1293797 GTATGAAAGGATGCGATAATTAAAAT
1 GCATGAAAGGATGC----ATT--AAG
* * *
1293823 GTATGAACGAATGCATTAAG
1 GCATGAAAGGATGCATTAAG
1293843 GCATGAAAGGATGC
1 GCATGAAAGGATGC
1293857 CATAACAAAA
Statistics
Matches: 283, Mismatches: 49, Indels: 100
0.66 0.11 0.23
Matches are distributed among these distances:
19 1 0.00
20 117 0.41
21 13 0.05
22 16 0.06
24 16 0.06
25 13 0.05
26 106 0.37
27 1 0.00
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:1293945 original size:46 final size:45
Alignment explanation
Indices: 1293442--1293942 Score: 615
Period size: 46 Copynumber: 10.9 Consensus size: 45
1293432 TAAACCAAAT
* * *
1293442 CCATAACTAAAACGCATGAAATGATGCATTAAGCCATGAAAGGATA
1 CCATAACTAAAATGCATGAAA-GATGCATTAAGGCATGAAAGGATG
* *
1293488 CCATAATTAAAATGCATGAACGAATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAG-ATGCATTAAGGCATGAAAGGATG
** * *
1293534 AGATAACTAAAATGCTTGAAAGGATGCATTAAGGCATGAAAAGATG
1 CCATAACTAAAATGCATGAAA-GATGCATTAAGGCATGAAAGGATG
1293580 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAA-GATGCATTAAGGCATGAAAGGATG
*
1293626 CCATAACTAAAATACATGAAAAGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATG-AAAGATGCATTAAGGCATGAAAGGATG
* * *
1293672 ACATAATTAAAATGCATGAACAGATACATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAA-AGATGCATTAAGGCATGAAAGGATG
**
1293718 ATATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAA-GATGCATTAAGGCATGAAAGGATG
* * * *
1293764 TCATAATTAAAATGCATGAATGGATGCATTAAGGTATGAAAGGATG
1 CCATAACTAAAATGCATGAA-AGATGCATTAAGGCATGAAAGGATG
* * * *
1293810 CGATAATTAAAATGTATGAACGAATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAG-ATGCATTAAGGCATGAAAGGATG
* * * * *
1293856 CCATAACAAAAATGCATGAAATGATGCTTTAGGGCGTGAAAAGATG
1 CCATAACTAAAATGCATGAAA-GATGCATTAAGGCATGAAAGGATG
* * * *
1293902 CCATGATTAAAATGCATGAACATATGCATTAATGCATGAAA
1 CCATAACTAAAATGCATGAA-AGATGCATTAAGGCATGAAA
1293943 AGAGACAACG
Statistics
Matches: 396, Mismatches: 50, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
45 5 0.01
46 385 0.97
47 6 0.02
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.23
Consensus pattern (45 bp):
CCATAACTAAAATGCATGAAAGATGCATTAAGGCATGAAAGGATG
Found at i:1299584 original size:26 final size:25
Alignment explanation
Indices: 1299554--1299871 Score: 166
Period size: 26 Copynumber: 13.4 Consensus size: 25
1299544 GCATTAAGGT
*
1299554 ATGAAAGGATTCCATAATTAAAAAGC
1 ATGAAAGGATT-CATAATTAAAATGC
* * *
1299580 ATGAACGGATGC---ATT--AAGGC
1 ATGAAAGGATTCATAATTAAAATGC
* *
1299600 ATGAAAGGATGCCATAACTAAAATGC
1 ATGAAAGGAT-TCATAATTAAAATGC
*
1299626 ATGAAAGGATGTCATAACTAAAATGC
1 ATGAAAGGAT-TCATAATTAAAATGC
* * *
1299652 ATGAAATGATGC---ATT--AAGGC
1 ATGAAAGGATTCATAATTAAAATGC
*
1299672 ATGAAAGGATGTCATAACTAAAATGC
1 ATGAAAGGAT-TCATAATTAAAATGC
1299698 ATGAAAGGATGTCATAATTAAAATGC
1 ATGAAAGGAT-TCATAATTAAAATGC
* * *
1299724 ATGAACGGATGC---ATT--AAGGC
1 ATGAAAGGATTCATAATTAAAATGC
*
1299744 ATGAAAGGATGCCATAATTAAAATGC
1 ATGAAAGGAT-TCATAATTAAAATGC
* * *
1299770 ATGAAAGGATGC---ATT--AAGGA
1 ATGAAAGGATTCATAATTAAAATGC
*
1299790 ATGAAAGGATGCCATAATTAAAATGC
1 ATGAAAGGAT-TCATAATTAAAATGC
* *
1299816 ATGAATGGATGC---ATT---ATGGC
1 ATGAAAGGATTCATAATTAAAAT-GC
*
1299836 ATGAAAGGATGCCATAATTAAAATGC
1 ATGAAAGGAT-TCATAATTAAAATGC
*
1299862 ATGAATGGAT
1 ATGAAAGGAT
1299872 GCATTAAGGC
Statistics
Matches: 226, Mismatches: 34, Indels: 64
0.70 0.10 0.20
Matches are distributed among these distances:
19 2 0.01
20 63 0.28
21 5 0.02
22 14 0.06
24 13 0.06
25 5 0.02
26 122 0.54
27 2 0.01
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.23
Consensus pattern (25 bp):
ATGAAAGGATTCATAATTAAAATGC
Found at i:1299590 original size:46 final size:46
Alignment explanation
Indices: 1299519--1299975 Score: 532
Period size: 46 Copynumber: 9.8 Consensus size: 46
1299509 TAAACCAAAT
* * *
1299519 CCATAACTAAAATGCATGAAAGGATGCATTAAGGTATGAAAGGATT
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
1299565 CCATAATTAAAAAGCATGAACGGATGCATTAAGGCATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
1299611 CCATAACTAAAATGCATGAAAGGATGTCATAACTAAAATGCATGAAATGATG
1 CCATAATTAAAATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATG
* *
1299663 -C---ATT--AAGGCATGAAAGGATGTCATAACTAAAATGCATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATG
* *
1299709 TCATAATTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
1299755 CCATAATTAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
1299801 CCATAATTAAAATGCATGAATGGATGCATTATGGCATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
1299847 CCATAATTAAAATGCATGAATGGATGCATTAAGGCTTGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* ** * *
1299893 ACATAACAAAAATGCATGAAATGATGCATTAGGGCATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
1299939 CCATAATTAAAATGCATGAACA-GATGTATTAATGCAT
1 CCATAATTAAAATGCATGAA-AGGATGCATTAAGGCAT
1299976 TAAAAGAGAG
Statistics
Matches: 361, Mismatches: 37, Indels: 26
0.85 0.09 0.06
Matches are distributed among these distances:
46 317 0.88
47 5 0.01
48 3 0.01
50 4 0.01
51 4 0.01
52 28 0.08
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.23
Consensus pattern (46 bp):
CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:1299648 original size:72 final size:72
Alignment explanation
Indices: 1299554--1299918 Score: 407
Period size: 72 Copynumber: 5.2 Consensus size: 72
1299544 GCATTAAGGT
* *
1299554 ATGAAAGGAT-TCCATAATTAAAAAGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAAC
1 ATGAAAGGATGT-CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAC
1299618 TAAAATGC
65 TAAAATGC
* * *
1299626 ATGAAAGGATGTCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGTCATAACT
1 ATGAAAGGATGTCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACT
1299691 AAAATGC
66 AAAATGC
* *
1299698 ATGAAAGGATGTCATAATTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAATT
1 ATGAAAGGATGTCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACT
1299763 AAAATGC
66 AAAATGC
* * * *
1299770 ATGAAAGGATG-C---ATT--AAGGAATGAAAGGATGCCATAATTAAAATGCATGAATGGATG-C
1 ATGAAAGGATGTCATAATTAAAATGCATGAAAGGATG-C---ATT--AAGGCATGAAAGGATGCC
1299828 AT---T---ATGGC
60 ATAACTAAAAT-GC
* * * * *
1299836 ATGAAAGGATGCCATAATTAAAATGCATGAATGGATGCATTAAGGCTTGAAAGGATGACATAACA
1 ATGAAAGGATGTCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACT
1299901 AAAATGC
66 AAAATGC
*
1299908 ATGAAATGATG
1 ATGAAAGGATG
1299919 CATTAGGGCA
Statistics
Matches: 249, Mismatches: 23, Indels: 42
0.79 0.07 0.13
Matches are distributed among these distances:
65 2 0.01
66 39 0.16
67 5 0.02
68 7 0.03
70 6 0.02
71 5 0.02
72 182 0.73
73 3 0.01
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (72 bp):
ATGAAAGGATGTCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACT
AAAATGC
Found at i:1299747 original size:20 final size:20
Alignment explanation
Indices: 1299722--1299939 Score: 103
Period size: 20 Copynumber: 9.7 Consensus size: 20
1299712 TAATTAAAAT
*
1299722 GCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1299742 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
1299768 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1299788 GAATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
* *
1299814 GCATGAATGGATGCATTATG
1 GCATGAAAGGATGCATTAAG
*
1299834 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
1299860 GCATGAATGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * *
1299880 GCTTGAAAGGATGACATAACAAAAAT
1 GCATGAAAGGATG-CAT-----TAAG
* *
1299906 GCATGAAATGATGCATTAGG
1 GCATGAAAGGATGCATTAAG
1299926 GCATGAAAGGATGC
1 GCATGAAAGGATGC
1299940 CATAATTAAA
Statistics
Matches: 150, Mismatches: 24, Indels: 48
0.68 0.11 0.22
Matches are distributed among these distances:
20 66 0.44
21 6 0.04
22 9 0.06
24 9 0.06
25 6 0.04
26 54 0.36
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:1299864 original size:118 final size:118
Alignment explanation
Indices: 1299519--1299873 Score: 454
Period size: 118 Copynumber: 3.0 Consensus size: 118
1299509 TAAACCAAAT
* * *
1299519 CCATAACTAAAATGCATGAAAGGATGCATTAAGGTATGAAAGGATTCCATAATTAAAAAGCATGA
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCCATAATTAAAATGCATGA
* * *
1299584 ACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATG
66 AAGGATGCATTATGGCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATG
* * * * *
1299637 TCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGA
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCCATAATTAAAATGCATGA
* *
1299702 AAGGATGTCATAATTAAAAT-GCATGAACGGATG-C---ATT--AAGGCATGAAAGGATG
66 AAGGATG-C---ATT---ATGGCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATG
*
1299755 CCATAATTAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCCATAATTAAAATGCATGA
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCCATAATTAAAATGCATGA
* *
1299820 ATGGATGCATTATGGCATGAAAGGATGCCATAATTAAAATGCATGAATGGATG
66 AAGGATGCATTATGGCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATG
1299873 C
1 C
1299874 ATTAAGGCTT
Statistics
Matches: 201, Mismatches: 22, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
111 2 0.01
112 12 0.06
113 1 0.00
114 3 0.01
116 3 0.01
117 1 0.00
118 159 0.79
119 1 0.00
120 2 0.01
122 3 0.01
123 1 0.00
124 12 0.06
125 1 0.00
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (118 bp):
CCATAACTAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCCATAATTAAAATGCATGA
AAGGATGCATTATGGCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATG
Found at i:1306525 original size:46 final size:46
Alignment explanation
Indices: 1306454--1306841 Score: 542
Period size: 46 Copynumber: 8.4 Consensus size: 46
1306444 TAAATCGAAT
*
1306454 CCATAATTAAAATCCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* ** *
1306500 CCATAATTAAATTGCATGATCGGATGCATTAAGGCATGAGAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * * * *
1306546 TCGTAACTAAAATGCATGAAAGGATACATTAAGGCATAAAAGTATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
1306592 TCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
1306638 CCATAATTAAAATGCATGAAAGGATGCATTAAGTCATGAAAGGATA
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
1306684 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAACGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
1306730 CCATAATTAAAATGCATGAACGGGTGCATTAAGGCATGAAAGGAAG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
** * *
1306776 CCATAACAAAAATGCATGAAAGGATGCATTAGGGCATGAAAAGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
1306822 CCATGATTAAAATGCATGAA
1 CCATAATTAAAATGCATGAA
1306842 CAGATGTATT
Statistics
Matches: 298, Mismatches: 44, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 298 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (46 bp):
CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:1315145 original size:20 final size:20
Alignment explanation
Indices: 1315120--1315168 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1315110 TTGAATGTGT
1315120 ATCGATGCACATGGTCATGC
1 ATCGATGCACATGGTCATGC
1315140 ATCGATGCACATGGTCATGC
1 ATCGATGCACATGGTCATGC
1315160 ATCGATGCA
1 ATCGATGCA
1315169 TCCGTCGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (20 bp):
ATCGATGCACATGGTCATGC
Found at i:1317691 original size:42 final size:41
Alignment explanation
Indices: 1317645--1317727 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 41
1317635 ATTTTGAACC
1317645 AAAATCAAGCCTAAAATCAATTTTTCAGAGTGAATGCACCGA
1 AAAATCAAGCCTAAAATCAATTTTTCAGAGTG-ATGCACCGA
1317687 AAAATCAAGCCTAAAATCAATTTTTCAGAGTGATGCACCGA
1 AAAATCAAGCCTAAAATCAATTTTTCAGAGTGATGCACCGA
1317728 TGCACCAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 9 0.22
42 32 0.78
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.24
Consensus pattern (41 bp):
AAAATCAAGCCTAAAATCAATTTTTCAGAGTGATGCACCGA
Found at i:1317872 original size:65 final size:65
Alignment explanation
Indices: 1317717--1317926 Score: 182
Period size: 65 Copynumber: 3.2 Consensus size: 65
1317707 TTTTTCAGAG
* * * * *
1317717 TGATGCACCGATGCACCAATAC-ATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCAAACG
1 TGATGCATCGATGCACC-ATACAATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATG
1317778 CATT
62 CATT
* * * *
1317782 TCAAGCATCGATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACCATACAATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCA
1317845 TT
64 TT
* * * * *
1317847 TGATGCATCGATGCACCA-GCAATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCATACAATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
*
1317911 TGATGCATCAATGCAC
1 TGATGCATCGATGCAC
1317927 TCTTAGTGCA
Statistics
Matches: 119, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 44 0.37
65 63 0.53
66 5 0.04
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (65 bp):
TGATGCATCGATGCACCATACAATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:1317946 original size:64 final size:65
Alignment explanation
Indices: 1317803--1317926 Score: 171
Period size: 64 Copynumber: 1.9 Consensus size: 65
1317793 TGCACATACC
* * *
1317803 ATGCACCGATGCACTGAGGATTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGCA
1 ATGCACCGATGCACTCAGGATTTTATGAAAACATCGAATGCACTTGATGCATCAATGCACCAGCA
* * *
1317868 ATGCATCGATGCACTCTGGCTATTT-TG-AAACATCGAATGCACTTGATGCATCAATGCAC
1 ATGCACCGATGCACTCAGGAT-TTTATGAAAACATCGAATGCACTTGATGCATCAATGCAC
1317927 TCTTAGTGCA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 30 0.58
65 19 0.37
66 3 0.06
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Consensus pattern (65 bp):
ATGCACCGATGCACTCAGGATTTTATGAAAACATCGAATGCACTTGATGCATCAATGCACCAGCA
Found at i:1321845 original size:30 final size:30
Alignment explanation
Indices: 1321805--1321915 Score: 125
Period size: 30 Copynumber: 3.7 Consensus size: 30
1321795 TCGAATTAGC
1321805 ACTATAGTGTGTAAGGACACTTAGTGCAAG
1 ACTATAGTGTGTAAGGACACTTAGTGCAAG
* *
1321835 ACTATGGTGTGTAAGGACACTTAGTAC-AG
1 ACTATAGTGTGTAAGGACACTTAGTGCAAG
* ** * *
1321864 AACTGTAGTGTGTAAGGATGCTCAGTGCAAC
1 -ACTATAGTGTGTAAGGACACTTAGTGCAAG
* *
1321895 ACTGTGGTGTGTAAGGACACT
1 ACTATAGTGTGTAAGGACACT
1321916 AATTGCATAT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 2 0.03
30 64 0.96
31 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (30 bp):
ACTATAGTGTGTAAGGACACTTAGTGCAAG
Found at i:1323533 original size:22 final size:22
Alignment explanation
Indices: 1323475--1323534 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
1323465 ATTGAATATA
*
1323475 TAAATGAACGATAAACAAACAC
1 TAAATAAACGATAAACAAACAC
* * *
1323497 TAAAAAAATGTTAAACAAACAC
1 TAAATAAACGATAAACAAACAC
*
1323519 TAAATAAACAATAAAC
1 TAAATAAACGATAAAC
1323535 GAACTTGTTC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.63, C:0.15, G:0.05, T:0.17
Consensus pattern (22 bp):
TAAATAAACGATAAACAAACAC
Found at i:1323574 original size:24 final size:23
Alignment explanation
Indices: 1323547--1323593 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1323537 ACTTGTTCAT
*
1323547 GAACATGTTCGTGAACATATAAAC
1 GAACACGTTCGTGAACAT-TAAAC
*
1323571 GAACACGTTTGTGAACATTAAAC
1 GAACACGTTCGTGAACATTAAAC
1323594 TAACCTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (23 bp):
GAACACGTTCGTGAACATTAAAC
Found at i:1323656 original size:69 final size:69
Alignment explanation
Indices: 1323530--1323661 Score: 169
Period size: 69 Copynumber: 1.9 Consensus size: 69
1323520 AAATAAACAA
* ** * * * *
1323530 TAAACGAACTTGTTCATGAACATGTTCGTGAACATATAAACGAACACGTTTGTGAACATTAAACT
1 TAAACGAACATGTTCATGAACACATTCATAAACATATAAACGAACACATTTCTGAACATTAAACT
1323595 AACC
66 AACC
1323599 TAAACGAACATGTTCATGAACACATTCATAAACATATAAAC-AA-ACATATTCTCGAACATTAAA
1 TAAACGAACATGTTCATGAACACATTCATAAACATATAAACGAACACAT-TTCT-GAACATTAAA
1323662 TGAACATGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
67 3 0.06
68 5 0.09
69 46 0.85
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.27
Consensus pattern (69 bp):
TAAACGAACATGTTCATGAACACATTCATAAACATATAAACGAACACATTTCTGAACATTAAACT
AACC
Found at i:1329185 original size:22 final size:22
Alignment explanation
Indices: 1329169--1329212 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1329159 TTAATCCTTT
*
1329169 AAAATAACTAAAATAATTTTATA
1 AAAATAA-TAAAATAATCTTATA
1329192 AAAATAATAAAATAAT-TTATA
1 AAAATAATAAAATAATCTTATA
1329213 TCTAAGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.24
22 9 0.43
23 7 0.33
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATAATAAAATAATCTTATA
Done.