Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001739.1 Hibiscus syriacus cultivar Beakdansim tig00003518_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: 329412
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
File 2 of 2
Found at i:227785 original size:97 final size:98
Alignment explanation
Indices: 227613--227807 Score: 302
Period size: 97 Copynumber: 2.0 Consensus size: 98
227603 CAGAATTCTG
* *
227613 CTACAGAGGAAACAAAGAAACACTAGCTACAAACAAAGGCAACTAATAACCTTATACAACCAATC
1 CTACAGAGGAAACAAAGAAACACTAGCTACAAACAAAGGCAACTAACAACCCTATACAACCAATC
*
227678 CCAATGAACAACCAACAGCTATACAAACAAGGA
66 CCAATGAACAACCAACAGCTAAACAAACAAGGA
* * * *
227711 CTACAGAGGAAACAAATAAACACTAGCTACTAAC-AAGGCAACTAACGACCCTATACAACCATTC
1 CTACAGAGGAAACAAAGAAACACTAGCTACAAACAAAGGCAACTAACAACCCTATACAACCAATC
* *
227775 CCAATGAACAACTAGCAGCTAAACAAACAAGGA
66 CCAATGAACAACCAACAGCTAAACAAACAAGGA
227808 ATTATAACAA
Statistics
Matches: 88, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
97 56 0.64
98 32 0.36
ACGTcount: A:0.49, C:0.26, G:0.12, T:0.13
Consensus pattern (98 bp):
CTACAGAGGAAACAAAGAAACACTAGCTACAAACAAAGGCAACTAACAACCCTATACAACCAATC
CCAATGAACAACCAACAGCTAAACAAACAAGGA
Found at i:228153 original size:17 final size:17
Alignment explanation
Indices: 228131--228185 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
228121 TGTTTTTTTA
*
228131 GGTTTGGGTTTGGGTTT-
1 GGTTT-GGTTCGGGTTTG
228148 GGTTTGGTTCGGGTTTG
1 GGTTTGGTTCGGGTTTG
**
228165 GGTTCAGTTCGGGTTTG
1 GGTTTGGTTCGGGTTTG
228182 GGTT
1 GGTT
228186 ACAAAAGATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 10 0.29
17 24 0.71
ACGTcount: A:0.02, C:0.05, G:0.45, T:0.47
Consensus pattern (17 bp):
GGTTTGGTTCGGGTTTG
Found at i:228185 original size:6 final size:6
Alignment explanation
Indices: 228131--228168 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
228121 TGTTTTTTTA
*
228131 GGTTTG GGTTTG GGTTT- GGTTT- GGTTCG GGTTTG GGTT
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTT
228169 CAGTTCGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 9 0.31
6 20 0.69
ACGTcount: A:0.00, C:0.03, G:0.47, T:0.50
Consensus pattern (6 bp):
GGTTTG
Found at i:229336 original size:46 final size:45
Alignment explanation
Indices: 229286--229373 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 45
229276 TTACGTTTTA
*
229286 TTTATGGCATCA-TTTCATGCCTTTTTATACACCGTTATACATTTCG
1 TTTATGGCAT-ATTTTCATGCC-TTTTATACACCATTATACATTTCG
229332 TTTATGGCATATTTTCATGCCTTTTATACACCATTATACATT
1 TTTATGGCATATTTTCATGCCTTTTATACACCATTATACATT
229374 GTTATACATC
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
45 21 0.52
46 19 0.47
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.47
Consensus pattern (45 bp):
TTTATGGCATATTTTCATGCCTTTTATACACCATTATACATTTCG
Found at i:229372 original size:45 final size:46
Alignment explanation
Indices: 229259--229373 Score: 144
Period size: 46 Copynumber: 2.5 Consensus size: 46
229249 AAACCTTTCA
* * * * **
229259 CCTTTTTATATACTATTTTACGTTTTATTTATGGCATCATTTCATG
1 CCTTTTTATACACCATTATACATTTCGTTTATGGCATCATTTCATG
*
229305 CCTTTTTATACACCGTTATACATTTCGTTTATGGCAT-ATTTTCATG
1 CCTTTTTATACACCATTATACATTTCGTTTATGGCATCA-TTTCATG
229351 CC-TTTTATACACCATTATACATT
1 CCTTTTTATACACCATTATACATT
229374 GTTATACATC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
45 21 0.35
46 39 0.65
ACGTcount: A:0.23, C:0.19, G:0.08, T:0.50
Consensus pattern (46 bp):
CCTTTTTATACACCATTATACATTTCGTTTATGGCATCATTTCATG
Found at i:229479 original size:68 final size:68
Alignment explanation
Indices: 229394--229599 Score: 331
Period size: 68 Copynumber: 3.0 Consensus size: 68
229384 TAGTCTTTTA
* * **
229394 CTCAAAGGCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTA
1 CTCAAAGGCACTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
229459 GGC
66 GGC
* *
229462 CTCAAAGGCACTTAACCTTTCATCTAGCTGGCATAATTGACACCTTTCTGTCAAATGCAGAGTTA
1 CTCAAAGGCACTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
*
229527 GGT
66 GGC
* *
229530 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGAAACCTTTCTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
229595 GGC
66 GGC
229598 CT
1 CT
229600 TTAACTTTTT
Statistics
Matches: 126, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 126 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (68 bp):
CTCAAAGGCACTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
GGC
Found at i:230011 original size:59 final size:59
Alignment explanation
Indices: 229943--230469 Score: 822
Period size: 59 Copynumber: 8.9 Consensus size: 59
229933 TTTCTCATAA
* * * ** * * *
229943 GGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGTGCAC-AAGGTTCCCCATTT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAA-GTGCCCTATAT
* * *
230002 GGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
* * **
230061 GAAAATTCATACGCTTAGTATGAATTTATTCTCATGTTAGCACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
* *
230120 GAAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAACACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
*
230179 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACAAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
230238 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
230297 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
** * * *
230356 TTAAATCCATACACTTAGTATTAATTCCTTCTCATGCTAGCACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
*
230415 GGAAATTCATACACTTAGTATGAATTCCTTCTCGTGTTAGCACACGAAGTGCCCT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
230470 TTTGGTAATC
Statistics
Matches: 438, Mismatches: 29, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
59 436 1.00
60 2 0.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
Found at i:230926 original size:93 final size:94
Alignment explanation
Indices: 230803--231009 Score: 245
Period size: 94 Copynumber: 2.2 Consensus size: 94
230793 TCAATACTAC
* * * * * *** *
230803 TACCCTGGTACCGATACTTCTATGCTATGGTACCAATACCT-TTTTTGTATCGATACTAATTTTA
1 TACCATGGTATCGATACTACTATACCATGGTACCAATACCTCTTCCGGTATCGATACCAATTTTA
* * *
230867 GGTTCGATGTTGCCTGGCATCGATACCTT
66 GATTCGATGTTGCCTGGCATAGATACCCT
** * *
230896 TACTTTGGTATCGATACTACTATACCATGGTACCGATACCTCTTCCGGTATCGATACCAATTTTT
1 TACCATGGTATCGATACTACTATACCATGGTACCAATACCTCTTCCGGTATCGATACCAATTTTA
* *
230961 GATTCGATGTTTCCTGGTATAGATACCCT
66 GATTCGATGTTGCCTGGCATAGATACCCT
230990 TACCATGGTATCGATACTAC
1 TACCATGGTATCGATACTAC
231010 CTCTTCGGTA
Statistics
Matches: 94, Mismatches: 19, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
93 34 0.36
94 60 0.64
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (94 bp):
TACCATGGTATCGATACTACTATACCATGGTACCAATACCTCTTCCGGTATCGATACCAATTTTA
GATTCGATGTTGCCTGGCATAGATACCCT
Found at i:232135 original size:20 final size:20
Alignment explanation
Indices: 232110--232148 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
232100 TTCATCCCTA
232110 TATAATTTATATTAATAAAC
1 TATAATTTATATTAATAAAC
232130 TATAATTTATATTAATAAA
1 TATAATTTATATTAATAAA
232149 TATTTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
TATAATTTATATTAATAAAC
Found at i:232202 original size:29 final size:30
Alignment explanation
Indices: 232165--232332 Score: 97
Period size: 30 Copynumber: 5.8 Consensus size: 30
232155 ATTAATAGAT
*
232165 TTAATATAAACTATCA-TTTAT-AATTAATA
1 TTAATATAAAATAT-AGTTTATAAATTAATA
232194 TTAATATAAAATATAGTTTATAAAATTAATA
1 TTAATATAAAATATAGTTTAT-AAATTAATA
** * * *
232225 TTAATATAGTATAT-GATATATAGACT-ATAA
1 TTAATATAAAATATAG-TTTATAAATTAAT-A
* *
232255 TTAATAT-TAATACTA---TAT--ACT-ATA
1 TTAATATAAAATA-TAGTTTATAAATTAATA
* **
232279 TTAATATAAAATATAGTTAATATGTTAATA
1 TTAATATAAAATATAGTTTATAAATTAATA
* *
232309 TTAATGTAAACTATAGTTTATAAA
1 TTAATATAAAATATAGTTTATAAA
232333 ATATCTACTA
Statistics
Matches: 108, Mismatches: 17, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
24 10 0.09
25 9 0.08
27 5 0.05
28 1 0.01
29 24 0.22
30 35 0.32
31 24 0.22
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.43
Consensus pattern (30 bp):
TTAATATAAAATATAGTTTATAAATTAATA
Found at i:232224 original size:31 final size:29
Alignment explanation
Indices: 232165--232232 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
232155 ATTAATAGAT
*
232165 TTAATATAAACTATCATTTATAATTAATA
1 TTAATATAAAATATCATTTATAATTAATA
232194 TTAATATAAAATAT-AGTTTATAAAATTAATA
1 TTAATATAAAATATCA-TTTAT--AATTAATA
232225 TTAATATA
1 TTAATATA
232233 GTATATGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
28 1 0.03
29 18 0.51
31 16 0.46
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (29 bp):
TTAATATAAAATATCATTTATAATTAATA
Found at i:232348 original size:36 final size:36
Alignment explanation
Indices: 232308--232398 Score: 119
Period size: 36 Copynumber: 2.5 Consensus size: 36
232298 ATATGTTAAT
* * *
232308 ATTAATGTAAACTATAGTTTATAAAATATCTACTAC
1 ATTAATATAAATTATAGTTTATAAAATATATACTAC
* * *
232344 ATTAATACAAATTATAGTTTATAAACTATATACTAT
1 ATTAATATAAATTATAGTTTATAAAATATATACTAC
*
232380 ATTGATATAAATTATAGTT
1 ATTAATATAAATTATAGTT
232399 AAGATAATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (36 bp):
ATTAATATAAATTATAGTTTATAAAATATATACTAC
Found at i:232395 original size:15 final size:15
Alignment explanation
Indices: 232377--232427 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
232367 AACTATATAC
*
232377 TATATTGATATAAAT
1 TATATTAATATAAAT
*
232392 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
*
232407 TAACATTAATATAAAT
1 T-ATATTAATATAAAT
232423 TATAT
1 TATAT
232428 AGTACATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:232427 original size:53 final size:55
Alignment explanation
Indices: 232362--232503 Score: 139
Period size: 53 Copynumber: 2.6 Consensus size: 55
232352 AAATTATAGT
*
232362 TTATAAACTATATACTATATTGATATAAATTATAGTTAAGATAATTA-ACATTA-A
1 TTATAAATTATATACTATATTGATATAAATTATAGTTAAGA-AATTATACATTATA
* * * * * * *
232416 -TATAAATTATATAGTACATTAATATAAAATATAGTTTATAAATTATATATTATA
1 TTATAAATTATATACTATATTGATATAAATTATAGTTAAGAAATTATACATTATA
* *
232470 GTTTATAAATTATATACTATA-GGTTATAAATTAT
1 --TTATAAATTATATACTATATTGATATAAATTAT
232504 TTAGTACACT
Statistics
Matches: 69, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
52 5 0.07
53 38 0.55
54 1 0.01
56 9 0.13
57 16 0.23
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.44
Consensus pattern (55 bp):
TTATAAATTATATACTATATTGATATAAATTATAGTTAAGAAATTATACATTATA
Found at i:232449 original size:20 final size:21
Alignment explanation
Indices: 232409--232450 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
232399 AAGATAATTA
232409 ACATTAATATAAATTATATAGT
1 ACATTAATATAAA-TATATAGT
232431 ACATTAATATAAA-ATATAGT
1 ACATTAATATAAATATATAGT
232451 TTATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
22 13 0.65
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
ACATTAATATAAATATATAGT
Found at i:232469 original size:21 final size:21
Alignment explanation
Indices: 232445--232503 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
232435 TAATATAAAA
*
232445 TATAGTTTATAAATTATATAT
1 TATAGTTTATAAATTATATAC
232466 TATAGTTTATAAATTATATAC
1 TATAGTTTATAAATTATATAC
*
232487 TATAGGTTATAAATTAT
1 TATAGTTTATAAATTAT
232504 TTAGTACACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (21 bp):
TATAGTTTATAAATTATATAC
Found at i:232614 original size:44 final size:44
Alignment explanation
Indices: 232566--232716 Score: 116
Period size: 44 Copynumber: 3.4 Consensus size: 44
232556 AATAAATTGT
232566 ATATATACATAATATATATACTATAAGTTACATATATAGTTTAC
1 ATATATACATAATATATATACTATAAGTTACATATATAGTTTAC
* ** * * * *
232610 ATATAAATAGATTGTATATATAC-ATATACTT--GTATATACTATAC
1 ATAT--ATACATAATATATATACTATA-AGTTACATATATAGTTTAC
* *
232654 ATAGT-T-TATACATACATATACTATAAGTTACATATATAGTTTAC
1 ATA-TATACATA-ATATATATACTATAAGTTACATATATAGTTTAC
*
232698 ATGTATACAT-ATACTATAT
1 ATATATACATAATA-TATAT
232717 GTTATATATA
Statistics
Matches: 78, Mismatches: 18, Indels: 22
0.66 0.15 0.19
Matches are distributed among these distances:
41 2 0.03
42 12 0.15
43 7 0.09
44 34 0.44
45 6 0.08
46 17 0.22
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (44 bp):
ATATATACATAATATATATACTATAAGTTACATATATAGTTTAC
Found at i:232647 original size:16 final size:17
Alignment explanation
Indices: 232626--232667 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
232616 ATAGATTGTA
*
232626 TATATACATATAC-TTG
1 TATATACATATACATAG
232642 TATATAC-TATACATAG
1 TATATACATATACATAG
*
232658 TTTATACATA
1 TATATACATA
232668 CATATACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 5 0.23
16 15 0.68
17 2 0.09
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (17 bp):
TATATACATATACATAG
Found at i:232647 original size:64 final size:61
Alignment explanation
Indices: 232515--232635 Score: 165
Period size: 64 Copynumber: 2.0 Consensus size: 61
232505 TAGTACACTA
* *
232515 ATATAAACTATAGGTTACATATATAGTTTATATAAATTGTAAATAAATTGTATATATACATAAT
1 ATATAAACTATAAGTTACATATATAGTTTACAT-AA-T-TAAATAAATTGTATATATACATAAT
* *
232579 ATATATACTATAAGTTACATATATAGTTTACAT-A-TAAATAGATTGTATATATACATA
1 ATATAAACTATAAGTTACATATATAGTTTACATAATTAAATAAATTGTATATATACATA
232636 TACTTGTATA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
59 22 0.42
62 1 0.02
64 30 0.57
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.40
Consensus pattern (61 bp):
ATATAAACTATAAGTTACATATATAGTTTACATAATTAAATAAATTGTATATATACATAAT
Found at i:232888 original size:13 final size:13
Alignment explanation
Indices: 232870--232895 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
232860 GTTTATAGAC
232870 TATAGGTTATATA
1 TATAGGTTATATA
232883 TATAGGTTATATA
1 TATAGGTTATATA
232896 AATTATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TATAGGTTATATA
Found at i:232893 original size:54 final size:55
Alignment explanation
Indices: 232824--232940 Score: 184
Period size: 54 Copynumber: 2.2 Consensus size: 55
232814 CTGTGTCTAC
* * *
232824 ACATATAT-GGTTTATATAAATTATATATCAACTATTGTTTATAGACTATAGGTT
1 ACATATATAGGTTTATATAAATTATATATAAACTATTCTTTATAAACTATAGGTT
*
232878 ATATATATAGG-TTATATAAATTATATATAAACTATTCTTTATAAACTATAGGTT
1 ACATATATAGGTTTATATAAATTATATATAAACTATTCTTTATAAACTATAGGTT
232932 ACATATATA
1 ACATATATA
232941 TATATAATTT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 55 0.96
55 2 0.04
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.44
Consensus pattern (55 bp):
ACATATATAGGTTTATATAAATTATATATAAACTATTCTTTATAAACTATAGGTT
Found at i:233029 original size:13 final size:15
Alignment explanation
Indices: 233002--233300 Score: 152
Period size: 13 Copynumber: 20.4 Consensus size: 15
232992 CTATATACTT
233002 TATATAGTTTATATA
1 TATATAGTTTATATA
*
233017 TATATATTTTATATAAA
1 TATATAGTTTATAT--A
* *
233034 CTATATAG-AT-TACA
1 -TATATAGTTTATATA
* *
233048 TACATAGTTTATACA
1 TATATAGTTTATATA
* *
233063 TATGTAG---CT-TA
1 TATATAGTTTATATA
*
233074 TATATAGATTATATA
1 TATATAGTTTATATA
*
233089 TATA-A-TTTATATC
1 TATATAGTTTATATA
*
233102 TATATAGTTGAT-T-
1 TATATAGTTTATATA
*
233115 TATATAATTTATATA
1 TATATAGTTTATATA
* *
233130 CATAT--TTTATACA
1 TATATAGTTTATATA
* *
233143 TATGTAGTTTATATC
1 TATATAGTTTATATA
*
233158 TATATAGTTGAT-T-
1 TATATAGTTTATATA
*
233171 TATATAATTTATATA
1 TATATAGTTTATATA
* *
233186 CATAT--TTTATACA
1 TATATAGTTTATATA
*
233199 TATGTAGTTTATATAAA
1 TATATAGTTTATAT--A
233216 CTATATAG-TT-TATA
1 -TATATAGTTTATATA
233230 TATATAGTTTATAATA
1 TATATAGTTTAT-ATA
233246 TCCATATAG-TT-TATA
1 T--ATATAGTTTATATA
233261 TATATAGTTTATAATAA
1 TATATAGTTTAT-AT-A
*
233278 CTATATAATTTATATTA
1 -TATATAGTTTATA-TA
233295 TATATA
1 TATATA
233301 TAGTTTATGC
Statistics
Matches: 217, Mismatches: 34, Indels: 65
0.69 0.11 0.21
Matches are distributed among these distances:
11 7 0.03
12 1 0.00
13 69 0.32
14 14 0.06
15 68 0.31
16 18 0.08
17 10 0.05
18 30 0.14
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:233038 original size:24 final size:24
Alignment explanation
Indices: 232993--233040 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
232983 TTTTATAAAC
***
232993 TATATACTTTATATAGTTTATATA
1 TATATACTTTATATAAACTATATA
*
233017 TATATATTTTATATAAACTATATA
1 TATATACTTTATATAAACTATATA
233041 GATTACATAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (24 bp):
TATATACTTTATATAAACTATATA
Found at i:233140 original size:11 final size:12
Alignment explanation
Indices: 233121--233201 Score: 50
Period size: 11 Copynumber: 7.2 Consensus size: 12
233111 GATTTATATA
233121 ATTTATATACAT
1 ATTTATATACAT
233133 ATTT-TATACAT
1 ATTTATATACAT
* *
233144 ATGTAGT-T-TAT
1 ATTTA-TATACAT
* **
233155 ATCTATATAGTT
1 ATTTATATACAT
233167 GATTTATAT--A-
1 -ATTTATATACAT
233177 ATTTATATACAT
1 ATTTATATACAT
233189 ATTT-TATACAT
1 ATTTATATACAT
233200 AT
1 AT
233202 GTAGTTTATA
Statistics
Matches: 54, Mismatches: 7, Indels: 17
0.69 0.09 0.22
Matches are distributed among these distances:
9 8 0.15
10 1 0.02
11 27 0.50
12 10 0.19
13 8 0.15
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (12 bp):
ATTTATATACAT
Found at i:233160 original size:56 final size:56
Alignment explanation
Indices: 233094--233242 Score: 244
Period size: 56 Copynumber: 2.6 Consensus size: 56
233084 ATATATATAA
233094 TTTATATCTATATAGTTGATTTATATAATTTATATACATATTTTATACATATGTAG
1 TTTATATCTATATAGTTGATTTATATAATTTATATACATATTTTATACATATGTAG
233150 TTTATATCTATATAGTTGATTTATATAATTTATATACATATTTTATACATATGTAG
1 TTTATATCTATATAGTTGATTTATATAATTTATATACATATTTTATACATATGTAG
* * *
233206 TTTATATAAACTATATAGTTTATATATATAGTTTATA
1 TTTATAT---CTATATAGTTGATTTATATAATTTATA
233243 ATATCCATAT
Statistics
Matches: 87, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
56 63 0.72
59 24 0.28
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.52
Consensus pattern (56 bp):
TTTATATCTATATAGTTGATTTATATAATTTATATACATATTTTATACATATGTAG
Found at i:233254 original size:18 final size:18
Alignment explanation
Indices: 233230--233308 Score: 78
Period size: 18 Copynumber: 4.7 Consensus size: 18
233220 ATAGTTTATA
233230 TATATAGTTTATAATATC
1 TATATAGTTTATAATATC
*
233248 CATATAG-TT-T-ATA--
1 TATATAGTTTATAATATC
*
233261 TATATAGTTTATAATAAC
1 TATATAGTTTATAATATC
* * *
233279 TATATAATTTATATTATA
1 TATATAGTTTATAATATC
233297 TATATAGTTTAT
1 TATATAGTTTAT
233309 GCATAGTATT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
13 6 0.12
14 2 0.04
15 4 0.08
16 4 0.08
17 2 0.04
18 31 0.63
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.51
Consensus pattern (18 bp):
TATATAGTTTATAATATC
Found at i:233480 original size:68 final size:69
Alignment explanation
Indices: 233380--233525 Score: 233
Period size: 68 Copynumber: 2.1 Consensus size: 69
233370 ATATATTAGT
233380 TATACATACATATATATATACTATATTAATATAAATTATAATTTATAAACTATATAC-TTTATAT
1 TATACATACA-ATATATATACTATATTAATATAAATTATAATTTATAAACTATATACATTT-TAT
233444 AGTTTA
64 AGTTTA
* *
233450 TATACATAC-ATATATATACTATATTAATATAAATTATAGTTTATAAATTATATACATTTTATAG
1 TATACATACAATATATATACTATATTAATATAAATTATAATTTATAAACTATATACATTTTATAG
233514 TTTA
66 TTTA
*
233518 TACACATA
1 TATACATA
233526 GTTTATATAA
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
68 60 0.83
69 3 0.04
70 9 0.12
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (69 bp):
TATACATACAATATATATACTATATTAATATAAATTATAATTTATAAACTATATACATTTTATAG
TTTA
Found at i:233528 original size:13 final size:13
Alignment explanation
Indices: 233510--233561 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
233500 TATACATTTT
*
233510 ATAGTTTATACAC
1 ATAGTTTATAAAC
233523 ATAGTTTATATAAAC
1 ATAG-TT-TATAAAC
* *
233538 ATAGTTTATATAT
1 ATAGTTTATAAAC
*
233551 ATAGCTTATAA
1 ATAGTTTATAA
233562 TAATTATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 18 0.56
14 4 0.12
15 10 0.31
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (13 bp):
ATAGTTTATAAAC
Found at i:233551 original size:17 final size:15
Alignment explanation
Indices: 233516--233549 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
233506 TTTTATAGTT
*
233516 TATACACATAGTTTA
1 TATAAACATAGTTTA
233531 TATAAACATAGTTTA
1 TATAAACATAGTTTA
233546 TATA
1 TATA
233550 TATAGCTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (15 bp):
TATAAACATAGTTTA
Found at i:233554 original size:28 final size:29
Alignment explanation
Indices: 233510--233591 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 29
233500 TATACATTTT
* *
233510 ATAGTTTATACACATAGTTTATATAA-AC
1 ATAGTTTATATATATAGTTTATATAATAC
* *
233538 ATAGTTTATATATATAGCTTATAATAATTAT
1 ATAGTTTATATATATAGTTTAT-ATAA-TAC
233569 ATAGTTTATATATA-A-TTTATATA
1 ATAGTTTATATATATAGTTTATATA
233592 TAAACTTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
28 22 0.48
29 8 0.17
30 1 0.02
31 15 0.33
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (29 bp):
ATAGTTTATATATATAGTTTATATAATAC
Found at i:233571 original size:18 final size:20
Alignment explanation
Indices: 233548--233591 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
233538 ATAGTTTATA
233548 TATATAGCTTATA-ATAA-T
1 TATATAGCTTATATATAATT
*
233566 TATATAGTTTATATATAATT
1 TATATAGCTTATATATAATT
233586 TATATA
1 TATATA
233592 TAAACTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.52
19 4 0.17
20 7 0.30
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (20 bp):
TATATAGCTTATATATAATT
Found at i:233637 original size:17 final size:18
Alignment explanation
Indices: 233617--233651 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
233607 TTAATATAAA
233617 TTATATACTTTA-ATATT
1 TTATATACTTTATATATT
*
233634 TTATATAGTTTATATATT
1 TTATATACTTTATATATT
233652 GTTTACACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
TTATATACTTTATATATT
Found at i:233839 original size:11 final size:11
Alignment explanation
Indices: 233822--233857 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
233812 TAGTTTATTA
233822 ATAAACTACAT
1 ATAAACTACAT
*
233833 GTAAACTACAT
1 ATAAACTACAT
*
233844 ATAAACTATAT
1 ATAAACTACAT
233855 ATA
1 ATA
233858 TATATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.31
Consensus pattern (11 bp):
ATAAACTACAT
Found at i:237811 original size:15 final size:15
Alignment explanation
Indices: 237791--237822 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
237781 TTAGCTGGGT
*
237791 GGCGGATGTGGGGCG
1 GGCGGATGCGGGGCG
237806 GGCGGATGCGGGGCG
1 GGCGGATGCGGGGCG
237821 GG
1 GG
237823 TAATGTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.16, G:0.69, T:0.09
Consensus pattern (15 bp):
GGCGGATGCGGGGCG
Found at i:239440 original size:17 final size:17
Alignment explanation
Indices: 239414--239450 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
239404 AACGGTCAAC
239414 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
239431 GGTCAGCGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
239448 GGT
1 GGT
239451 TGGGTCAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.08, C:0.22, G:0.51, T:0.19
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:239441 original size:7 final size:7
Alignment explanation
Indices: 239394--239424 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
239384 GTCAAAGAAA
*
239394 GTCAACA
1 GTCAACG
239401 GTCAACG
1 GTCAACG
239408 GTCAACG
1 GTCAACG
239415 GTCAACG
1 GTCAACG
239422 GTC
1 GTC
239425 GGGTCGGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:247699 original size:31 final size:30
Alignment explanation
Indices: 247626--247813 Score: 166
Period size: 32 Copynumber: 6.1 Consensus size: 30
247616 GGAGTCGAGG
*
247626 GTATACCTATGTTCTACG-GAACATATGGACA
1 GTATACCTATGTT-TTCGAG-ACATATGGACA
*
247657 GAATTACCTATGTCTTTCGAGACATATGGACA
1 GTA-TACCTATGT-TTTCGAGACATATGGACA
*
247689 GTATACCTATGTTCTACG-GAACATATGGACA
1 GTATACCTATGTT-TTCGAG-ACATATGGACA
*
247720 GAATTACCTATGTCTTTCGAGACATATGGACA
1 GTA-TACCTATGT-TTTCGAGACATATGGACA
* ***
247752 ATATACCTATGTTAAGGA-ACATATGGACA
1 GTATACCTATGTTTTCGAGACATATGGACA
* * * *
247781 GTTTACCTAGGTTCTTCGAAACCTATGGACA
1 GTATACCTATGTT-TTCGAGACATATGGACA
247812 GT
1 GT
247814 TGCCGAGGAT
Statistics
Matches: 129, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
29 21 0.16
30 7 0.05
31 48 0.37
32 49 0.38
33 4 0.03
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (30 bp):
GTATACCTATGTTTTCGAGACATATGGACA
Found at i:247704 original size:63 final size:63
Alignment explanation
Indices: 247626--247813 Score: 285
Period size: 63 Copynumber: 3.0 Consensus size: 63
247616 GGAGTCGAGG
247626 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
247689 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* * * * * *
247752 ATATACCTATG-T-TAAGGAACATATGGACAG-TTTACCTAGGT-TCTTCGAAACCTATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCT-TTCGAGACATATGGACA
247812 GT
1 GT
247814 TGCCGAGGAT
Statistics
Matches: 117, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
59 1 0.01
60 25 0.21
61 17 0.15
62 1 0.01
63 73 0.62
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:247814 original size:31 final size:30
Alignment explanation
Indices: 247629--247814 Score: 158
Period size: 31 Copynumber: 6.0 Consensus size: 30
247619 GTCGAGGGTA
* *
247629 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATG-TCTACGAAACATATGGACAG-TT
* * *
247661 TACCTATGTCTTTCGAGACATATGGACAGTA
1 TACCTATGTC-TACGAAACATATGGACAGTT
* *
247692 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATG-TCTACGAAACATATGGACAG-TT
* * * *
247724 TACCTATGTCTTTCGAGACATATGGACAATA
1 TACCTATGTC-TACGAAACATATGGACAGTT
* *
247755 TACCTATGT-TAAGGAACATATGGACAGTT
1 TACCTATGTCTACGAAACATATGGACAGTT
* * *
247784 TACCTAGGTTCTTCGAAACCTATGGACAGTT
1 TACCTATG-TCTACGAAACATATGGACAGTT
247815 GCCGAGGATC
Statistics
Matches: 121, Mismatches: 27, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
29 21 0.17
30 1 0.01
31 52 0.43
32 47 0.39
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (30 bp):
TACCTATGTCTACGAAACATATGGACAGTT
Found at i:252525 original size:31 final size:31
Alignment explanation
Indices: 252452--252617 Score: 171
Period size: 32 Copynumber: 5.3 Consensus size: 31
252442 GGAGTCGAGT
252452 GTATACCTATGT-TCTACG-GAACATATGGACA
1 GTATACCTATGTCT-TACGAG-ACATATGGACA
* *
252483 GAATTACCTATGTCTTTCGAGACATATGGACA
1 GTA-TACCTATGTCTTACGAGACATATGGACA
252515 GTATACCTATGT-TCTACG-GAACATATGGACA
1 GTATACCTATGTCT-TACGAG-ACATATGGACA
* *
252546 GAATTACCTATGTCTTTCGAGACATATGGACA
1 GTA-TACCTATGTCTTACGAGACATATGGACA
* *
252578 GTATACCTATGTTCTAAGGA-ACATATGGACA
1 GTATACCTATG-TCTTACGAGACATATGGACA
*
252609 GTTTACCTA
1 GTATACCTA
252618 GGTTCTTCGA
Statistics
Matches: 115, Mismatches: 11, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
30 2 0.02
31 54 0.47
32 55 0.48
33 4 0.03
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTCTTACGAGACATATGGACA
Found at i:252530 original size:63 final size:63
Alignment explanation
Indices: 252452--252617 Score: 307
Period size: 63 Copynumber: 2.7 Consensus size: 63
252442 GGAGTCGAGT
252452 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
252515 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* *
252578 GTATACCTATGTTCTAAGGAACATATGGACAG-TTTACCTA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTA
252618 GGTTCTTCGA
Statistics
Matches: 101, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
62 7 0.07
63 94 0.93
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:252623 original size:31 final size:31
Alignment explanation
Indices: 252455--252623 Score: 184
Period size: 31 Copynumber: 5.4 Consensus size: 31
252445 GTCGAGTGTA
*
252455 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
* *
252487 TACCTATG-TCTTTC-GAGACATATGGACAGTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
252518 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
* *
252550 TACCTATG-TCTTTC-GAGACATATGGACAGTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
252581 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
*
252612 TACCTAGGTTCT
1 TACCTATGTTCT
252624 TCGAAACCTA
Statistics
Matches: 115, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
31 63 0.55
32 52 0.45
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:252678 original size:30 final size:30
Alignment explanation
Indices: 252629--252700 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
252619 GTTCTTCGAA
* * *
252629 ACCTATGGTTAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
252659 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
*
252689 ACATCTGGATAG
1 ACCTCTGGATAG
252701 GTCCTTCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:265186 original size:20 final size:20
Alignment explanation
Indices: 265161--265198 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
265151 TTTGGTTCAC
265161 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
265181 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
265199 GGAATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:265208 original size:16 final size:18
Alignment explanation
Indices: 265161--265211 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
265151 TTTGGTTCAC
265161 GGAATGTAAGATTACCAGTG
1 GGAA-GTAAGATTACCAG-G
265181 GGAATGTAAGATTACCA-G
1 GGAA-GTAAGATTACCAGG
265199 GGAA-TAAGATTAC
1 GGAAGTAAGATTAC
265212 TGAGAATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.29
18 5 0.16
20 17 0.55
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (18 bp):
GGAAGTAAGATTACCAGG
Found at i:269349 original size:18 final size:18
Alignment explanation
Indices: 269323--269382 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
269313 CAACTAATGA
*
269323 TTCAACTGACAAGGTTGG
1 TTCAGCTGACAAGGTTGG
269341 TTCAGCTGACAAGGTTGG
1 TTCAGCTGACAAGGTTGG
*
269359 TTCAG--GGCAAGGTTGG
1 TTCAGCTGACAAGGTTGG
269375 TTCAGCTG
1 TTCAGCTG
269383 GTTCGGTTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.39
18 23 0.61
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (18 bp):
TTCAGCTGACAAGGTTGG
Found at i:273487 original size:43 final size:43
Alignment explanation
Indices: 273429--273933 Score: 651
Period size: 43 Copynumber: 11.8 Consensus size: 43
273419 AGGTCTTATA
* * *
273429 CTTGCACATAGCAAAAGAGCCTGGGGAAATTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
* *
273472 CTTGCACACAACAAAAGAA-CTTGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
* * *
273514 TTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
*
273557 CTTGCACACAGC-AAAGAGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGA-ACCTGGGGAAACTGTAAGGCTTACC
* *
273600 CTTGCATACAGCAAAAGAACCT-GGGAAACTGTAAAGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
273642 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
* * * *
273685 CTCGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
* * * *
273728 CTCGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
** * ** * *
273771 CTCACACACAACAATGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
* * *
273814 TTTGGACACAACAAAAGAACCT-GGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
* *
273856 CTTACACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
* * *
273899 CTTGCACACAACAAAGGGACCTAGGGG-AACTGTAA
1 CTTGCACACAGCAAAAGAACCT-GGGGAAACTGTAA
273934 CGGTAATTAA
Statistics
Matches: 416, Mismatches: 40, Indels: 12
0.89 0.09 0.03
Matches are distributed among these distances:
42 117 0.28
43 290 0.70
44 9 0.02
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.17
Consensus pattern (43 bp):
CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
Found at i:273616 original size:128 final size:127
Alignment explanation
Indices: 273429--273933 Score: 665
Period size: 128 Copynumber: 3.9 Consensus size: 127
273419 AGGTCTTATA
* * * *
273429 CTTGCACATAGCAAAAGAGCCTGGGGAAATTGTAAGGCTTACCCTTGCACACAACAAAAGAACTT
1 CTTGCACACAGCAAAAGA-CCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAACTG
*
273494 GGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACC
65 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACC
* *
273557 CTTGCACACAGCAAAGAGACCTGGGGGAACTGTAAGGCTTACCCTTGCATACAGCAAAAGAACCT
1 CTTGCACACAGCAAA-AGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAA-CT
* * *
273622 -GGGAAACTGTAAAGCTTACCCTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
64 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACC
* * * * * *
273685 CTCGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTCGCACACAGCAAAGGGACCT
1 CTTGCACACAGCAAA-AGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAA-AGAACT
* ** * * *
273750 GGGGGAACTGTAAGGCTTACCCTCACACACAACAATGGGACCTGGGGGAACTGTAAGGCTTACC
64 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACC
* * * * *
273814 TTTGGACACAACAAAAGAACCT-GGGAAACTGTAAGGCTTACCCTTACACACAGCAAAGGAACCT
1 CTTGCACACAGCAAAAG-ACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAA-CT
*
273878 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTAGGGG-AACTGTAA
64 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCT-GGGGAAACTGTAA
273934 CGGTAATTAA
Statistics
Matches: 333, Mismatches: 37, Indels: 14
0.87 0.10 0.04
Matches are distributed among these distances:
127 3 0.01
128 250 0.75
129 80 0.24
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.17
Consensus pattern (127 bp):
CTTGCACACAGCAAAAGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAACTGG
GGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACC
Found at i:273723 original size:171 final size:171
Alignment explanation
Indices: 273429--273933 Score: 760
Period size: 171 Copynumber: 3.0 Consensus size: 171
273419 AGGTCTTATA
* * * *
273429 CTTGCACATAGCAAAAGAGCCTGGGGAAATTGTAAGGCTTACCCTTGCACACAACAAAAGAACTT
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAAGAACCT
* *
273494 GGGAAACTGTAAGGCTTACCTTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACCCT
66 GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCT
*
273559 TGCACACAGCAAAGAGACCTGGGGGAACTGTAAGGCTTACC
131 TGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
* * *
273600 CTTGCATACAGCAAAAGAACCT-GGGAAACTGTAAAGCTTACCCTTGCACACAGCAAAAGAACCT
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAAGAACCT
* * *
273664 GGGGAAACTGTAAGGCTTACCCTCGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCC
66 -GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACCC
*
273729 TCGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
130 TTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
** * ** * * * *
273771 CTCACACACAACAATGGGACCTGGGGGAACTGTAAGGCTTACCTTTGGACACAACAAAAGAACCT
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAAGAACCT
*
273836 GGGAAACTGTAAGGCTTACCCTTACACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCT
66 GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCT
* *
273901 TGCACACAACAAAGGGACCTAGGGGAACTGTAA
131 TGCACACAGCAAAGGGACCTGGGGGAACTGTAA
273934 CGGTAATTAA
Statistics
Matches: 299, Mismatches: 33, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
170 38 0.13
171 224 0.75
172 37 0.12
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.17
Consensus pattern (171 bp):
CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAAGAACCT
GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCT
TGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
Found at i:276758 original size:13 final size:13
Alignment explanation
Indices: 276740--276778 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
276730 CAACGATCAA
276740 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
276753 CGGGTCAACAGGT
1 CGGGTCAACGGGT
*
276766 CGGGTAAACGGGT
1 CGGGTCAACGGGT
276779 AGGGATATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.44, T:0.15
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:281285 original size:23 final size:26
Alignment explanation
Indices: 281216--281287 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 26
281206 ACCATATAAC
* *
281216 TTAATCTATTTTTCTTAAGAATACTAA
1 TTAATTTACTTTTCTTAA-AATACTAA
* *
281243 TTTATTTACTTTACGTTAAAATA-T-A
1 TTAATTTACTTTTC-TTAAAATACTAA
281268 TTAATTTA-TTTTCTTAAAAT
1 TTAATTTACTTTTCTTAAAAT
281288 TGATGAATGG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
23 7 0.18
24 4 0.11
25 8 0.21
26 1 0.03
27 14 0.37
28 4 0.11
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (26 bp):
TTAATTTACTTTTCTTAAAATACTAA
Found at i:281528 original size:2 final size:2
Alignment explanation
Indices: 281516--281550 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
281506 CCTAAAAATC
281516 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
281551 GTTCAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:281916 original size:19 final size:19
Alignment explanation
Indices: 281880--281930 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
281870 AATAACGTTT
* * *
281880 TAAATATTTGTAGAATATG
1 TAAATATTTTTTGAATATC
*
281899 TAAATATTTTTTGTATATC
1 TAAATATTTTTTGAATATC
281918 TGAAATATTTTTT
1 T-AAATATTTTTT
281931 TAAATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.53
Consensus pattern (19 bp):
TAAATATTTTTTGAATATC
Found at i:283829 original size:23 final size:24
Alignment explanation
Indices: 283803--283856 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
283793 CTAAAAGATA
* *
283803 AGTATAATTTAAA-AAAATAAAAT
1 AGTATAAATAAAATAAAATAAAAT
283826 AGTA-AAATAAAATAAAATAAAAT
1 AGTATAAATAAAATAAAATAAAAT
*
283849 ACTATAAA
1 AGTATAAA
283857 AATAGAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 6 0.23
23 17 0.65
24 3 0.12
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.26
Consensus pattern (24 bp):
AGTATAAATAAAATAAAATAAAAT
Found at i:283882 original size:26 final size:25
Alignment explanation
Indices: 283816--283892 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 25
283806 ATAATTTAAA
* *
283816 AAAATAAAATA--GTAAAATAAAAT
1 AAAATAAAATACTATAAAATAGAAT
283839 AAAATAAAATACTATAAAAATAGAAT
1 AAAATAAAATACTAT-AAAATAGAAT
* *
283865 AAAACTTAAATA-TTTAAAA-AGAAT
1 AAAA-TAAAATACTATAAAATAGAAT
283889 AAAA
1 AAAA
283893 GTAATACTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
23 11 0.24
24 9 0.20
25 5 0.11
26 15 0.33
27 6 0.13
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.23
Consensus pattern (25 bp):
AAAATAAAATACTATAAAATAGAAT
Found at i:285405 original size:21 final size:21
Alignment explanation
Indices: 285380--285431 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
285370 CAAAGAGGTA
285380 GTATCGGTACCATTGGTTATG
1 GTATCGGTACCATTGGTTATG
285401 GTATCGGTACCATTGGTTATG
1 GTATCGGTACCATTGGTTATG
285422 GTATCGGTAC
1 GTATCGGTAC
285432 TACTATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.15, G:0.29, T:0.37
Consensus pattern (21 bp):
GTATCGGTACCATTGGTTATG
Found at i:285709 original size:18 final size:18
Alignment explanation
Indices: 285686--285721 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
285676 ATTCGAATAA
285686 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
285704 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
285722 CTTAAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (18 bp):
TTGAATCGAATATAAAAT
Found at i:288291 original size:15 final size:16
Alignment explanation
Indices: 288271--288316 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
288261 ATCAAACATT
288271 CAAAACACAAAATATC
1 CAAAACACAAAATATC
*
288287 C-AAACAACCAAA-ATC
1 CAAAAC-ACAAAATATC
288302 CAAAACACATAAATA
1 CAAAACACA-AAATA
288317 CATCAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
15 10 0.42
16 13 0.54
17 1 0.04
ACGTcount: A:0.63, C:0.26, G:0.00, T:0.11
Consensus pattern (16 bp):
CAAAACACAAAATATC
Found at i:296747 original size:24 final size:24
Alignment explanation
Indices: 296720--296775 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
296710 ATCTACACTT
*
296720 TTATAAATAAAAAAAATTAAATTA
1 TTATAAATAAAAAAAATAAAATTA
** * **
296744 TTATATTTTATTAAAATAAAATTA
1 TTATAAATAAAAAAAATAAAATTA
296768 TTATAAAT
1 TTATAAAT
296776 TATTTATTAA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TTATAAATAAAAAAAATAAAATTA
Found at i:296778 original size:24 final size:24
Alignment explanation
Indices: 296732--296779 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
296722 ATAAATAAAA
* **
296732 AAAATTAAATTATTATATTTTATT
1 AAAATAAAATTATTATAAATTATT
296756 AAAATAAAATTATTATAAATTATT
1 AAAATAAAATTATTATAAATTATT
296780 TATTAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATAAAATTATTATAAATTATT
Found at i:296810 original size:26 final size:26
Alignment explanation
Indices: 296732--296806 Score: 77
Period size: 28 Copynumber: 2.9 Consensus size: 26
296722 ATAAATAAAA
*
296732 AAAATTAAATTAT-TATATT-TTATT
1 AAAATAAAATTATATATATTATTATT
*
296756 AAAATAAAATTATTATAAATTATTTATT
1 AAAATAAAATTA-TATATATTA-TTATT
296784 AAAATAAGAA-TA-ATATATTATTA
1 AAAATAA-AATTATATATATTATTA
296807 ATTATACTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
24 11 0.26
25 4 0.09
26 12 0.28
28 14 0.33
29 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (26 bp):
AAAATAAAATTATATATATTATTATT
Found at i:296852 original size:8 final size:8
Alignment explanation
Indices: 296822--296881 Score: 63
Period size: 8 Copynumber: 7.6 Consensus size: 8
296812 ACTAAATACT
296822 TATTAAAA
1 TATTAAAA
* *
296830 TAATAAGAT
1 TATTAA-AA
296839 TATTAAAA
1 TATTAAAA
296847 TATTAAAA
1 TATTAAAA
296855 -ATTATAAA
1 TATTA-AAA
296863 TATTAAAA
1 TATTAAAA
296871 TA--AAAA
1 TATTAAAA
296877 TATTA
1 TATTA
296882 TATTATATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 6 0.14
7 4 0.09
8 23 0.53
9 10 0.23
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (8 bp):
TATTAAAA
Found at i:296865 original size:16 final size:15
Alignment explanation
Indices: 296840--296881 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
296830 TAATAAGATT
296840 ATTAAAATATTAAAA
1 ATTAAAATATTAAAA
296855 ATTATAAATATT-AAA
1 ATTA-AAATATTAAAA
*
296870 ATAAAAATATTA
1 ATTAAAATATTA
296882 TATTATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 7 0.29
15 10 0.42
16 7 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATTAAAATATTAAAA
Found at i:297607 original size:41 final size:43
Alignment explanation
Indices: 297493--297872 Score: 362
Period size: 43 Copynumber: 8.9 Consensus size: 43
297483 AATTTATAAA
* * * * *
297493 ATTGAAAAAAATAGGGGTCTAAATTATAAAGGTAAAAAGTGAC
1 ATTGAAAAAATTAAGAGTCTCAATTATAAAGGTAAAAAGTGAG
* * * * * *
297536 AATGAAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGCGGG
1 ATTG--AAAAAATTAAGAGTCTCAATTATAAAGGTAAAAAGTGAG
** * * *
297581 ATTGAAAATTTTTAGA-TCTCAA-TATAAATGCAAAAAGT-AG
1 ATTGAAAAAATTAAGAGTCTCAATTATAAAGGTAAAAAGTGAG
* * *
297621 TATT--AAAAATTAGGAGACTCAATTATAAATGTAAAAAGTGAG
1 -ATTGAAAAAATTAAGAGTCTCAATTATAAAGGTAAAAAGTGAG
*
297663 ATTGAAAAAATTAAGAGCCTCAATTATAAAGGTAAAAAGTGAG
1 ATTGAAAAAATTAAGAGTCTCAATTATAAAGGTAAAAAGTGAG
*
297706 ATTGAAAAAATTAAGAGTATCAATTATAAAGGTAAAAAGTGAG
1 ATTGAAAAAATTAAGAGTCTCAATTATAAAGGTAAAAAGTGAG
*
297749 ATTGAAAAAATTAAGAGTCTCAATTATAAAGATAAAAAGTGAG
1 ATTGAAAAAATTAAGAGTCTCAATTATAAAGGTAAAAAGTGAG
* * * * *
297792 ATTAAAAAAATTTAAGA--CATCAATTACAAAGATAAAAAGTAAA
1 ATTGAAAAAA-TTAAGAGTC-TCAATTATAAAGGTAAAAAGTGAG
* * * * *
297835 ATT-ACAAAAACTAAAAATTTCAATTATAAAAGTAAAAA
1 ATTGA-AAAAATTAAGAGTCTCAATTATAAAGGTAAAAA
297873 ATTAAAATAA
Statistics
Matches: 283, Mismatches: 41, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
39 7 0.02
40 6 0.02
41 34 0.12
42 13 0.05
43 181 0.64
44 6 0.02
45 36 0.13
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (43 bp):
ATTGAAAAAATTAAGAGTCTCAATTATAAAGGTAAAAAGTGAG
Found at i:297859 original size:22 final size:21
Alignment explanation
Indices: 297811--297872 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
297801 ATTTAAGACA
*
297811 TCAATTACAAAGATAAAAAGT
1 TCAATTACAAAAATAAAAAGT
** *
297832 AAAATTACAAAAACTAAAAATT
1 TCAATTACAAAAA-TAAAAAGT
* *
297854 TCAATTATAAAAGTAAAAA
1 TCAATTACAAAAATAAAAA
297873 ATTAAAATAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.63, C:0.08, G:0.05, T:0.24
Consensus pattern (21 bp):
TCAATTACAAAAATAAAAAGT
Found at i:297886 original size:129 final size:128
Alignment explanation
Indices: 297625--297908 Score: 324
Period size: 129 Copynumber: 2.2 Consensus size: 128
297615 AAGTAGTATT
* * * *
297625 AAAAATTAGGAGACTCAATTATAAATGTAAAAAGTGAGATTGAAAAAATTAAGAGCCTCAATTAT
1 AAAAATTAAGAGACTCAATTATAAA-GTAAAAAGTGAGATTAAAAAAATTAAGAGCATCAATTAC
* * * * * * * * * * *
297690 AAAGGTAAAAAGTGAGATTGAAAAAATTAAGAGTATCAATTATAAAGGTAAAAAGTGAGATTGA
65 AAAGATAAAAAGTAAAATTGAAAAAACTAAAAATATCAATTATAAAAGTAAAAAATGAAAATAA
*
297754 AAAAATTAAGAGTCTCAATTATAAAGATAAAAAGTGAGATTAAAAAAATTTAAGA-CATCAATTA
1 AAAAATTAAGAGACTCAATTATAAAG-TAAAAAGTGAGATTAAAAAAA-TTAAGAGCATCAATTA
* *
297818 CAAAGATAAAAAGTAAAATT-ACAAAAACTAAAAATTTCAATTATAAAAGTAAAAAATTAAAATA
64 CAAAGATAAAAAGTAAAATTGA-AAAAACTAAAAATATCAATTATAAAAGTAAAAAATGAAAATA
297882 A
128 A
*
297883 AAAAATCAAGA-ACCTCAATTA-AAAGT
1 AAAAATTAAGAGA-CTCAATTATAAAGT
297909 GATTTTAAGA
Statistics
Matches: 131, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
127 1 0.01
128 6 0.05
129 118 0.90
130 6 0.05
ACGTcount: A:0.57, C:0.06, G:0.13, T:0.24
Consensus pattern (128 bp):
AAAAATTAAGAGACTCAATTATAAAGTAAAAAGTGAGATTAAAAAAATTAAGAGCATCAATTACA
AAGATAAAAAGTAAAATTGAAAAAACTAAAAATATCAATTATAAAAGTAAAAAATGAAAATAA
Found at i:299028 original size:22 final size:22
Alignment explanation
Indices: 298971--299036 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
298961 TTGAATAGAG
*
298971 ATTTAAATTAATGGAATT--AA
1 ATTTAAATTAATTGAATTGAAA
*
298991 A-TAAAGATCTAATTGAATTGAAA
1 ATTTAA-AT-TAATTGAATTGAAA
299014 ATTTAAATTAATTGAATTGAAA
1 ATTTAAATTAATTGAATTGAAA
299036 A
1 A
299037 AAAACCCAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.08
20 3 0.08
21 9 0.24
22 15 0.39
23 5 0.13
24 3 0.08
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.36
Consensus pattern (22 bp):
ATTTAAATTAATTGAATTGAAA
Found at i:299052 original size:43 final size:43
Alignment explanation
Indices: 298949--299053 Score: 106
Period size: 43 Copynumber: 2.5 Consensus size: 43
298939 ATTGCATAGG
* * * *
298949 ATAAAAACCAAATTGAATAG-AGATTTAAATTAATGGAATTAA
1 ATAAAAACCCAATCGAATTGAAAATTTAAATTAATGGAATTAA
* * * * *
298991 ATAAAGATCTAATTGAATTGAAAATTTAAATTAATTGAATTGAA
1 ATAAAAACCCAATCGAATTGAAAATTTAAATTAATGGAATT-AA
299035 A-AAAAACCCAATCGAATTG
1 ATAAAAACCCAATCGAATTG
299054 CCTAGGATAA
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
42 16 0.31
43 32 0.63
44 3 0.06
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (43 bp):
ATAAAAACCCAATCGAATTGAAAATTTAAATTAATGGAATTAA
Found at i:300275 original size:17 final size:17
Alignment explanation
Indices: 300253--300286 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
300243 TGGTTGGAAA
300253 GATAATTGAATTATATT
1 GATAATTGAATTATATT
300270 GATAATTGAATTATATT
1 GATAATTGAATTATATT
300287 TCTAAGGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
GATAATTGAATTATATT
Found at i:300911 original size:41 final size:41
Alignment explanation
Indices: 300865--301021 Score: 216
Period size: 41 Copynumber: 3.9 Consensus size: 41
300855 TGAATTAGGG
*
300865 ATTATTGCATGCTGCCATGATCGAATT-AAGTTGAATTGTGA
1 ATTATTGCATGCTGCCATGATCGAATTGAA-TCGAATTGTGA
*
300906 ATTATTGCATGCTGCC---AT-GAATTGAATCGAATGGTGA
1 ATTATTGCATGCTGCCATGATCGAATTGAATCGAATTGTGA
* *
300943 ATTATTGCATGATGCCATGATTGAATTGAATCGAATTGTGA
1 ATTATTGCATGCTGCCATGATCGAATTGAATCGAATTGTGA
* *
300984 ATTATTGCATGCTGCCATGATCGAATTTAATTGAATTG
1 ATTATTGCATGCTGCCATGATCGAATTGAATCGAATTG
301022 AAATCTTGAA
Statistics
Matches: 103, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
37 29 0.28
38 4 0.04
40 2 0.02
41 68 0.66
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (41 bp):
ATTATTGCATGCTGCCATGATCGAATTGAATCGAATTGTGA
Found at i:300943 original size:37 final size:38
Alignment explanation
Indices: 300823--301000 Score: 168
Period size: 41 Copynumber: 4.6 Consensus size: 38
300813 TTAATTTGGT
* * * * *
300823 TTGTGAATAAATGCATGTTGCC-ATG-ACTGAATTGAA
1 TTGTGAATTATTGCATGCTGCCAATGAATTGAATCGAA
* *
300859 TTAG-GGATTATTGCATGCTGCCATGATCGAATT-AAGTTGAA
1 TT-GTGAATTATTGCATGCTGCCA--AT-GAATTGAA-TCGAA
300900 TTGTGAATTATTGCATGCTGCC-ATGAATTGAATCGAA
1 TTGTGAATTATTGCATGCTGCCAATGAATTGAATCGAA
* *
300937 TGGTGAATTATTGCATGATGCCATGATTGAATTGAATCGAA
1 TTGTGAATTATTGCATGCTGCCA--A-TGAATTGAATCGAA
300978 TTGTGAATTATTGCATGCTGCCA
1 TTGTGAATTATTGCATGCTGCCA
301001 TGATCGAATT
Statistics
Matches: 118, Mismatches: 11, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
36 16 0.14
37 30 0.25
38 4 0.03
39 2 0.02
40 5 0.04
41 61 0.52
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (38 bp):
TTGTGAATTATTGCATGCTGCCAATGAATTGAATCGAA
Found at i:300969 original size:78 final size:77
Alignment explanation
Indices: 300770--301003 Score: 242
Period size: 78 Copynumber: 3.0 Consensus size: 77
300760 CCTTTATTTA
* * * * * * ** * *
300770 AATTGAATTGGATTGTGAATTAATACATGTTACCATGATAT-AATTAATTTGGTTTGTGAATAAA
1 AATTGAATTGAATGGTGAATTATTGCATGATGCCATGAT-TGAATTAA-TTGAATTGTGAATTAT
*
300834 TGCATGTTGCCATG
64 TGCATGCTGCCATG
* * *
300848 -ACTGAATTGAATTAGG-G-ATTATTGCATGCTGCCATGATCGAATTAAGTTGAATTGTGAATTA
1 AATTGAATTGAA-T-GGTGAATTATTGCATGATGCCATGATTGAATTAA-TTGAATTGTGAATTA
300910 TTGCATGCTGCCATG
63 TTGCATGCTGCCATG
* *
300925 AATTGAATCGAATGGTGAATTATTGCATGATGCCATGATTGAATTGAATCGAATTGTGAATTATT
1 AATTGAATTGAATGGTGAATTATTGCATGATGCCATGATTGAATT-AATTGAATTGTGAATTATT
300990 GCATGCTGCCATG
65 GCATGCTGCCATG
301003 A
1 A
301004 TCGAATTTAA
Statistics
Matches: 130, Mismatches: 19, Indels: 14
0.80 0.12 0.09
Matches are distributed among these distances:
76 2 0.02
77 59 0.45
78 66 0.51
79 3 0.02
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (77 bp):
AATTGAATTGAATGGTGAATTATTGCATGATGCCATGATTGAATTAATTGAATTGTGAATTATTG
CATGCTGCCATG
Found at i:302126 original size:2 final size:2
Alignment explanation
Indices: 302121--302151 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
302111 TCTTTTTTGG
*
302121 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
302152 GGGTTATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:308869 original size:54 final size:54
Alignment explanation
Indices: 308453--308837 Score: 590
Period size: 54 Copynumber: 7.1 Consensus size: 54
308443 CATTTATCCA
* * *
308453 ATTGGCACTATCTGTGCAACCTAAGAAATTCATAATAAATTTATGAATTTTCGT
1 ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGT
*
308507 ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGT
1 ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGT
* * * *
308561 ATTGGTACTATGTTTGCAACCTAAGAAATTAATAATAAATTTATGAATTTCCGT
1 ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGT
* * * * *
308615 ATTGGCATTATGTGTGCAACCTAAGAAATTAAAAATTAGTTTATGAATTTCAGT
1 ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGT
* *
308669 ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATTAATTTCCAT
1 ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGT
* *
308723 ATTGACACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGT
1 ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGT
* * *
308777 ATTGGCACTGTGTGTGCAACATAAGAAATTCATAATGAGTTTATGAATTTCCGT
1 ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGT
308831 ATTGGCA
1 ATTGGCA
308838 TTAGATGTGC
Statistics
Matches: 299, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 299 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (54 bp):
ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGT
Found at i:314974 original size:95 final size:94
Alignment explanation
Indices: 314861--315060 Score: 267
Period size: 94 Copynumber: 2.1 Consensus size: 94
314851 TACTGAAGTG
**
314861 AGTATCGATACTAAGAG-AAAGATATAGATACCTTGGAATCCAAAAGGTAGAAATGGTATCGATA
1 AGTATCGATACTAAGAGAAAAG-TATAGATACCAAGG-ATCCAAAAGGTAGAAATGGTATCGATA
* *
314925 TTGAAAGGGAGTATCGGTACCATAGTATAAA
64 CTGAAAGGGAGTATCGGTACCATAATATAAA
* * * * * *
314956 AGTATCGGTACTAGGAGAAAAGTATCGATACCAAGGATCTAGAATGTAGAAATGGTATCGATACT
1 AGTATCGATACTAAGAGAAAAGTATAGATACCAAGGATCCAAAAGGTAGAAATGGTATCGATACT
* *
315021 GAAGGGGAGTATCGGTACCATAATATAGA
66 GAAAGGGAGTATCGGTACCATAATATAAA
315050 AGTATCGATAC
1 AGTATCGATAC
315061 CATGGTAGGG
Statistics
Matches: 91, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
94 61 0.67
95 26 0.29
96 4 0.04
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (94 bp):
AGTATCGATACTAAGAGAAAAGTATAGATACCAAGGATCCAAAAGGTAGAAATGGTATCGATACT
GAAAGGGAGTATCGGTACCATAATATAAA
Found at i:314978 original size:20 final size:22
Alignment explanation
Indices: 314934--314992 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 22
314924 ATTGAAAGGG
* *
314934 AGTATCGGTACCATAGTATAAA
1 AGTATCGGTACCATAGGAGAAA
314956 AGTATCGGTA-C-TAGGAGAAA
1 AGTATCGGTACCATAGGAGAAA
*
314976 AGTATCGATACCA-AGGA
1 AGTATCGGTACCATAGGA
314993 TCTAGAATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 16 0.50
21 6 0.19
22 10 0.31
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.22
Consensus pattern (22 bp):
AGTATCGGTACCATAGGAGAAA
Found at i:315667 original size:161 final size:162
Alignment explanation
Indices: 315402--315780 Score: 618
Period size: 161 Copynumber: 2.3 Consensus size: 162
315392 TTTACCCAAC
* * ** *
315402 TGGCACTATGTGTGCAACCTAAGAAACTCATAATAAGTTTATAAATTTCTATATTGGCACTCTGT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGACACTCTGT
* *
315467 GTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACCTAA
66 GTGAAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACCTAA
* * *
315532 GAAATTCAT-ATGAGTTTATGAATTTTCGTAT
131 GAAATTCATAATAAGTTTATAAATTTCCGTAT
315563 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGACAC-CATG
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGACACTC-TG
315627 TGTGAAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACCTA
65 TGTGAAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACCTA
315692 AGAAATTCATAATAAGTTTATAAATTTCCGTAT
130 AGAAATTCATAATAAGTTTATAAATTTCCGTAT
* * *
315725 TGGCACTGTGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTG
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
315781 GCATTAGATG
Statistics
Matches: 203, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
160 1 0.00
161 130 0.64
162 72 0.35
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (162 bp):
TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGACACTCTGT
GTGAAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACCTAA
GAAATTCATAATAAGTTTATAAATTTCCGTAT
Found at i:315794 original size:54 final size:54
Alignment explanation
Indices: 315402--315783 Score: 622
Period size: 54 Copynumber: 7.1 Consensus size: 54
315392 TTTACCCAAC
* * **
315402 TGGCACTATGTGTGCAACCTAAGAAACTCATAATAAGTTTATAAATTTCTATAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* *
315456 TGGCACTCTGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* *
315510 TGGCACTATGTGTGCAACCTAAGAAATTCAT-ATGAGTTTATGAATTTTCGTAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
315563 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * *
315617 TGACACCATGTGTGAAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
*
315671 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATAAATTTCCGTAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * *
315725 TGGCACTGTGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTTCGTAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
315779 TGGCA
1 TGGCA
315784 TTAGATGTGC
Statistics
Matches: 306, Mismatches: 21, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
53 52 0.17
54 254 0.83
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (54 bp):
TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
Found at i:323703 original size:12 final size:12
Alignment explanation
Indices: 323688--323712 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
323678 TATATATATA
323688 TATGTGTGTGTG
1 TATGTGTGTGTG
323700 TATGTGTGTGTG
1 TATGTGTGTGTG
323712 T
1 T
323713 GTGAGAGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.40, T:0.52
Consensus pattern (12 bp):
TATGTGTGTGTG
Done.