Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008914.1 Hibiscus syriacus cultivar Beakdansim tig00112217_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: 1601432
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1137682 original size:125 final size:122
Alignment explanation
Indices: 1137419--1137978 Score: 505
Period size: 125 Copynumber: 4.5 Consensus size: 122
1137409 AACTTTAGCA
* ** **
1137419 GCGTTTTTATAAAAACGCCGC-AATAGGTTCAT-CGATAGTGGCGTTTTT-TCAACAAACGCCGC
1 GCGTTTTTATACAAACGCCGCTAA-AGACTCATACTTTAGTGGCGTTTTTAT--ACAAACGCCGC
* * * * *
1137481 AAAAGAGTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAATTTAGCG
63 TAAAGACT-GTACTTTAGTGACATTTTTATACAAACGCCGCTAAAGACTCATAATTTAGTG
* * * * ** * *
1137542 GCATTGTTATACAAACGCCGCTATAGAATTGTACTTTAGTGGCGTTTTTATACAAACGCCGTTAT
1 GCGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACGCCGCTAA
* * * * *
1137607 ACACATGTACTATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCATAATTTAGTG
66 AGAC-TGTACTTTAGTGACATTT-T-TATACAAACGCCGCTAAAGACTCATAATTTAGTG
* *
1137667 GCGTTTTTATACAAACGCCGCTAAAGACTCATTCTTTAGTGGCGTTTTTATACAAACTCCGCTAA
1 GCGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACGCCGCTAA
* * * * * * ** * *
1137732 AGACGCGTACTTTAGTGACATTTTTATTCAAACGTCGTTATACACTTGTACTATAGTG
66 AGAC-TGTACTTTAGTGACATTTTTATACAAACGCCGCTAAAGACTCATAATTTAGTG
* * * * * *
1137790 GCGTTTGTGTTTACAAACGTCACTAAAGACTCATAATTTAGTGGCATTTTTATACAAACGCCACT
1 GCGTTT-T-TATACAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACGCCGCT
* * * *
1137855 AAAGACTCGTACTTTATTGATATTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTG
64 AAAGACT-GTACTTTAGTGACATTTTTATACAAACGCCGCTAAAGACTCATAATTTAGTG
* * * * ** * *
1137915 GCGTTTTTATTCAAATGCCGCTATACACTTGTACTATAGTGGCGTTTGTGTTTACAAACGCCGC
1 GCGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTT-T-TATACAAACGCCGC
1137979 AAGTTTACAA
Statistics
Matches: 350, Mismatches: 76, Indels: 20
0.78 0.17 0.04
Matches are distributed among these distances:
123 109 0.31
124 21 0.06
125 220 0.63
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (122 bp):
GCGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACGCCGCTAA
AGACTGTACTTTAGTGACATTTTTATACAAACGCCGCTAAAGACTCATAATTTAGTG
Found at i:1141188 original size:86 final size:86
Alignment explanation
Indices: 1141013--1141337 Score: 356
Period size: 86 Copynumber: 3.8 Consensus size: 86
1141003 AAGGTAATTA
* * * *
1141013 GCGGTGTTTGTATCCAAAAACGCCGCTATAGGTCTGACTTTTTGCGGTGTTTGTGT-TCAAAAAC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGT-TCT-AAAAAC
*
1141077 GCCGTTATATGTCTAAC-CTTTT
64 GCCGCTATATGTCTAACTCTTTT
* * * *
1141099 GCGGCGTTTGTGTCCAAAAAACGCCGCTATAGGTTTAACCTTTTGCGGCGTTTGTTCTAAAAACG
1 GCGGCGTTTGTATCC-AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAACG
* *
1141164 CCAG-TATAGGTCT-TCTCTTTT
65 CC-GCTATATGTCTAACTCTTTT
* * *
1141185 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTTTTCTAGAAACGC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAACGC
*
1141250 CGCTATATATCATAACT-TTTT
66 CGCTATATGTC-TAACTCTTTT
* * ** * * *
1141271 GCGGCATTTAT-TCCAAAAGTGCCGCTATAGATATCGACCTTTTGCAGCGTTTGTTCAAAAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTTCTAAAAACG
1141335 CCG
65 CCG
1141338 TAATAGATAT
Statistics
Matches: 205, Mismatches: 26, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
84 1 0.00
85 73 0.36
86 92 0.45
87 39 0.19
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (86 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAACGC
CGCTATATGTCTAACTCTTTT
Found at i:1141344 original size:43 final size:42
Alignment explanation
Indices: 1141013--1141365 Score: 266
Period size: 43 Copynumber: 8.2 Consensus size: 42
1141003 AAGGTAATTA
* * * * *
1141013 GCGGTGTTTGTATCCAAAAACGCCGCTATAGGTCTGACTTTTT
1 GCGGCGTTTGT-TCAAAAAACGCCGCTATAGATATGACCTTTT
* * * *
1141056 GCGGTGTTTGTGTTC-AAAAACGCCGTTATATG-TCTAACCTTTT
1 GCGGCG-TT-TGTTCAAAAAACGCCGCTATA-GATATGACCTTTT
* * *
1141099 GCGGCGTTTGTGTCCAAAAAACGCCGCTATAGGTTTAACCTTTT
1 GCGGCGTTTGT-T-CAAAAAACGCCGCTATAGATATGACCTTTT
* * * *
1141143 GCGGCGTTTGTTCTAAAAACGCCAG-TATAGGTCT-TCTCTTTT
1 GCGGCGTTTGTTCAAAAAACGCC-GCTATAGATATGAC-CTTTT
* * *
1141185 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGT-TCAAAAAACGCCGCTATAGATATGACCTTTT
* * * * * *
1141228 GCGGCGTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGAT-ATGACCTTTT
* * * **
1141271 GCGGCATTTATTCCAAAAGTGCCGCTATAGATATCGACCTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGATAT-GACCTTTT
* *
1141314 GCAGCGTTTGTTCAAAAAACGCCG-TAATAGATATTGACCTATT
1 GCGGCGTTTGTTCAAAAAACGCCGCT-ATAGATA-TGACCTTTT
1141357 GCGGCGTTT
1 GCGGCGTTT
1141366 TTTGTTCTCA
Statistics
Matches: 256, Mismatches: 38, Indels: 32
0.79 0.12 0.10
Matches are distributed among these distances:
41 4 0.02
42 58 0.23
43 149 0.58
44 42 0.16
45 3 0.01
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (42 bp):
GCGGCGTTTGTTCAAAAAACGCCGCTATAGATATGACCTTTT
Found at i:1147808 original size:32 final size:32
Alignment explanation
Indices: 1147725--1147846 Score: 99
Period size: 31 Copynumber: 3.9 Consensus size: 32
1147715 CTAAGGGAAC
* * *
1147725 ATCTTAGGGCCTG-AGAGCCTACCCAAGATA-G
1 ATCTCAGGGCC-GCAGAGCCTACCTAAGAAATG
* * **
1147756 ATTTCGGGGCCGTGGAGCCTACCTAAGAACAT-
1 ATCTCAGGGCCGCAGAGCCTACCTAAGAA-ATG
* * **
1147788 ATCTTAGGGCCGCAGGGCCTACCCGAG-AATG
1 ATCTCAGGGCCGCAGAGCCTACCTAAGAAATG
1147819 ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ATCTCAGGGCCGCAGAGCCTACCTAAGA
1147847 GTCACATTAG
Statistics
Matches: 68, Mismatches: 18, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
30 3 0.04
31 45 0.66
32 20 0.29
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (32 bp):
ATCTCAGGGCCGCAGAGCCTACCTAAGAAATG
Found at i:1147829 original size:63 final size:63
Alignment explanation
Indices: 1147725--1147846 Score: 158
Period size: 63 Copynumber: 1.9 Consensus size: 63
1147715 CTAAGGGAAC
* * **
1147725 ATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGAGCCTACCTAAGAACAT
1 ATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAACAT
* *
1147788 ATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
1147847 GTCACATTAG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (63 bp):
ATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAACAT
Found at i:1148757 original size:29 final size:29
Alignment explanation
Indices: 1148730--1148894 Score: 260
Period size: 29 Copynumber: 5.6 Consensus size: 29
1148720 CACATTCAAA
*
1148730 AATTCCCAAAATGTCACATTTTTTTCAAAAT
1 AATTCCCAAAATGTCAC--CTTTTTCAAAAT
*
1148761 AATTCCCAGAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
*
1148790 AATT-CCAAGAATGTCAGCTTTTTCAAAAT
1 AATTCCCAA-AATGTCACCTTTTTCAAAAT
1148819 AATTCCCAAAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
*
1148848 AATTCTCAAAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
1148877 AATTCCCAAAATGTCACC
1 AATTCCCAAAATGTCACC
1148895 GGGTCGGGTC
Statistics
Matches: 125, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
28 3 0.02
29 102 0.82
30 4 0.03
31 16 0.13
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (29 bp):
AATTCCCAAAATGTCACCTTTTTCAAAAT
Found at i:1148847 original size:17 final size:17
Alignment explanation
Indices: 1148825--1148876 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
1148815 AAATAATTCC
1148825 CAAAATGTCACCTTTTT
1 CAAAATGTCACCTTTTT
* *
1148842 CAAAA--T-A--ATTCT
1 CAAAATGTCACCTTTTT
1148854 CAAAATGTCACCTTTTT
1 CAAAATGTCACCTTTTT
1148871 CAAAAT
1 CAAAAT
1148877 AATTCCCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 10
0.65 0.10 0.25
Matches are distributed among these distances:
12 8 0.31
14 2 0.08
15 2 0.08
17 14 0.54
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.37
Consensus pattern (17 bp):
CAAAATGTCACCTTTTT
Found at i:1155159 original size:32 final size:31
Alignment explanation
Indices: 1155065--1155197 Score: 88
Period size: 31 Copynumber: 4.2 Consensus size: 31
1155055 AAAGAGTTAC
* *
1155065 CCTAAGAGAACATCTTAGGGCTTG-AGAGCCTA
1 CCTAAGA-AACATCTCAGGGC-CGCAGAGCCTA
* * * * * **
1155097 CCCAAGATAGATTTCGGGGCCGTGGAGCCTA
1 CCTAAGAAACATCTCAGGGCCGCAGAGCCTA
* *
1155128 CCTAAGAACACATCTTAGGGCCGCAGGGCCTA
1 CCTAAGAA-ACATCTCAGGGCCGCAGAGCCTA
** **
1155160 CCCGAGAATGATCTCAGGGCCGCAGAGCCTA
1 CCTAAGAAACATCTCAGGGCCGCAGAGCCTA
*
1155191 TCTAAGA
1 CCTAAGA
1155198 GTCACATTAG
Statistics
Matches: 73, Mismatches: 26, Indels: 5
0.70 0.25 0.05
Matches are distributed among these distances:
30 1 0.01
31 44 0.60
32 28 0.38
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (31 bp):
CCTAAGAAACATCTCAGGGCCGCAGAGCCTA
Found at i:1155180 original size:63 final size:63
Alignment explanation
Indices: 1155065--1155198 Score: 148
Period size: 63 Copynumber: 2.1 Consensus size: 63
1155055 AAAGAGTTAC
* * * **
1155065 CCTAAGAGAACATCTTAGGGCTTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGAGCCTA
1 CCTAAGAGAACATCTTAGGGCTCGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTA
* *
1155128 CCTAAGA-ACACATCTTAGGGC-CGCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCT
1 CCTAAGAGA-ACATCTTAGGGCTCG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCT
1155190 A
63 A
*
1155191 TCTAAGAG
1 CCTAAGAG
1155199 TCACATTAGG
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
62 3 0.05
63 56 0.95
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.18
Consensus pattern (63 bp):
CCTAAGAGAACATCTTAGGGCTCGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTA
Found at i:1156120 original size:29 final size:29
Alignment explanation
Indices: 1156068--1156257 Score: 267
Period size: 29 Copynumber: 6.6 Consensus size: 29
1156058 CACATTCAAA
**
1156068 AATTCCCAAAATGTCATATTTTTTTCAAAAT
1 AATTCCCAAAATGTC--ACCTTTTTCAAAAT
*
1156099 AATTCCCAGAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
*
1156128 AATTCCCAAAATGTCAAC-TTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* *
1156156 AATTCTCAAAATGTCACATTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* *
1156185 AATTCCCAGAATATCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
*
1156214 AATTCCCAAAATATCA-CTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
1156242 AATTCCCAAAATGTCA
1 AATTCCCAAAATGTCA
1156258 TCGGGTCGGG
Statistics
Matches: 144, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
28 52 0.36
29 78 0.54
31 14 0.10
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (29 bp):
AATTCCCAAAATGTCACCTTTTTCAAAAT
Found at i:1156156 original size:57 final size:57
Alignment explanation
Indices: 1156068--1156257 Score: 265
Period size: 57 Copynumber: 3.3 Consensus size: 57
1156058 CACATTCAAA
* *
1156068 AATTCCCAAAATGTCATATTTTTTTCAAAATAATTCCCAGAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCA-A--CTTTTCAAAATAATTCCCAAAATGTCACCTTTTTCAAAAT
* *
1156128 AATTCCCAAAATGTCAACTTTTCAAAATAATTCTCAAAATGTCACATTTTTCAAAAT
1 AATTCCCAAAATGTCAACTTTTCAAAATAATTCCCAAAATGTCACCTTTTTCAAAAT
* * * *
1156185 AATTCCCAGAATATCACCTTTTTCAAAATAATTCCCAAAATATCA-CTTTTTCAAAAT
1 AATTCCCAAAATGTCAAC-TTTTCAAAATAATTCCCAAAATGTCACCTTTTTCAAAAT
1156242 AATTCCCAAAATGTCA
1 AATTCCCAAAATGTCA
1156258 TCGGGTCGGG
Statistics
Matches: 117, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
57 76 0.65
58 24 0.21
59 1 0.01
60 16 0.14
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (57 bp):
AATTCCCAAAATGTCAACTTTTCAAAATAATTCCCAAAATGTCACCTTTTTCAAAAT
Found at i:1156207 original size:86 final size:87
Alignment explanation
Indices: 1156068--1156257 Score: 312
Period size: 86 Copynumber: 2.2 Consensus size: 87
1156058 CACATTCAAA
* *
1156068 AATTCCCAAAATGTCATATTTTTTTCAAAATAATTCCCAGAATGTCACCTTTTTCAAAATAATTC
1 AATTCCCAAAATGTCACA-TTTTTTCAAAATAATTCCCAGAATATCACCTTTTTCAAAATAATTC
*
1156133 CCAAAATGTCAAC-TTTTCAAAAT
65 CCAAAATATC-ACTTTTTCAAAAT
*
1156156 AATTCTCAAAATGTCACA-TTTTTCAAAATAATTCCCAGAATATCACCTTTTTCAAAATAATTCC
1 AATTCCCAAAATGTCACATTTTTTCAAAATAATTCCCAGAATATCACCTTTTTCAAAATAATTCC
1156220 CAAAATATCACTTTTTCAAAAT
66 CAAAATATCACTTTTTCAAAAT
1156242 AATTCCCAAAATGTCA
1 AATTCCCAAAATGTCA
1156258 TCGGGTCGGG
Statistics
Matches: 96, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
85 2 0.02
86 78 0.81
88 16 0.17
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (87 bp):
AATTCCCAAAATGTCACATTTTTTCAAAATAATTCCCAGAATATCACCTTTTTCAAAATAATTCC
CAAAATATCACTTTTTCAAAAT
Found at i:1156317 original size:19 final size:19
Alignment explanation
Indices: 1156293--1156336 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1156283 GTCGGGTCAG
*
1156293 ACCGGTTCGGACCGGTCAA
1 ACCGGTTCGGACCGATCAA
*
1156312 ATCGGTTCGGACCGATCAA
1 ACCGGTTCGGACCGATCAA
1156331 ACCGGT
1 ACCGGT
1156337 CAACTATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.18
Consensus pattern (19 bp):
ACCGGTTCGGACCGATCAA
Found at i:1159422 original size:6 final size:6
Alignment explanation
Indices: 1159411--1160817 Score: 596
Period size: 6 Copynumber: 235.0 Consensus size: 6
1159401 TGTTAAATCC
* * * * *
1159411 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT CCTCCT CCTCCT TCTCCT
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT
* * * * * * *
1159459 TCTCCT TC-TCT TGTTTCT CCTGT-T TCTCCT TCTTCT CCTCCT TCTCCT
1 TCTTCT TCTTCT T-CTTCT TCT-TCT TCTTCT TCTTCT TCTTCT TCTTCT
* * * * * * * *
1159507 CCTCCT TCTCCT TCTCCT TCTCCT TCTCCT TCTCCT TCTCCT TCTTC-
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT
* * * * *
1159554 TCATTCT CCTTCT TCTTCT CCTTCT CCTTCT TTTTCT CCTTCT TCTTCT
1 TC-TTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT
* * * * * * * * *
1159603 CCTCCT TCTCCT CCTCCT TCTTCT TCTTCT TCTTAT CCTCCT TC-TCC
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT
*
1159650 TCTTTCT TC-TCAT TCTTCT TCTTCT TCTTCT T-TTCCT TCTCCT TC-TCAT
1 TC-TTCT TCTTC-T TCTTCT TCTTCT TCTTCT TCTT-CT TCTTCT TCTTC-T
* * * * * * *
1159699 TCTCCT CCTTGT TCTTCT CCATCT CCTTCT TCTTCT TCTTCT ACTTCT
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT
* * * * * * *
1159747 CCTTC- TCATTCT CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT
1 TCTTCT TC-TTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT
* * * * * * * * *
1159795 CCTTCT CCTTCT CCTTCT CCTTC- TCATTCT TCTTCC CCTTCC CCTTCC
1 TCTTCT TCTTCT TCTTCT TCTTCT TC-TTCT TCTTCT TCTTCT TCTTCT
* * * * * * * * *
1159843 CCTTCC CCTTC- CCTTTCT CCTTCC CCTTCT CCTTCT CCTTC- TCATTC-
1 TCTTCT TCTTCT TC-TTCT TCTTCT TCTTCT TCTTCT TCTTCT TC-TTCT
* * *
1159890 TCATTCT CCTTCT CCTTC- TCATTC- TCATTC- TCATTC- TCATTCT CCTTCT
1 TC-TTCT TCTTCT TCTTCT TC-TTCT TC-TTCT TC-TTCT TC-TTCT TCTTCT
* *
1159939 CCTTCT TCTTCT TCTTCT TCTTCT TC-TCAT TC-CCTT TCTTCT TCTTCT
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTC-T TCTTC-T TCTTCT TCTTCT
* * * * * *
1159987 TCTT-T TCTTCT TCTTCT TCTTCT CCTTCT CCTTCT CCTCCT CCTCCT
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT
* * * * * * * * *
1160034 CCTCCT CCTCCT CCTTCT CCTTCT T-TTCT CCTTCT TCTTAT TCTCCT
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT
* * * *
1160081 TCTCCT TCTCCT TCTCCT TC-TCAT TCTCCT TC-TCAT TC-TCAT TCTTCT
1 TCTTCT TCTTCT TCTTCT TCTTC-T TCTTCT TCTTC-T TCTTC-T TCTTCT
* * * * * * * *
1160129 TCTACT TCTACT TCTCCT TCTACT TCTCCT TCTCCT TCTCCT TCTCCT
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT
* * * * * * *
1160177 TCTCCT TCTTCT TCTCCT ACTTAT TATTC- TCTTTCT TCTTCT CCTACT
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TC-TTCT TCTTCT TCTTCT
* * * *
1160225 TATTCT TC-TCTT TCTCCT TC-TCTT TCTCCT T-TTCTT TCTTCT TCTCCT
1 TCTTCT TCTTC-T TCTTCT TCTTC-T TCTTCT TCTTC-T TCTTCT TCTTCT
* * *
1160273 TATTTT TCTTCT TCTTCT TCTCCT TC-TCAT TCTTC- TCATTCT TC-TCAT
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTC-T TCTTCT TC-TTCT TCTTC-T
* * * *
1160321 TCTTCT TCTTCT TCTTCT TCTTCT TCTTTCT TC-TCT CCTCCT CCTCCT
1 TCTTCT TCTTCT TCTTCT TCTTCT TC-TTCT TCTTCT TCTTCT TCTTCT
* * * * * * *
1160369 CCTCCT CCTTCT TCTTCT TCTCCT TCTTCT TCTCCT TCTCCT TCTCCT
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT
* * * * * *
1160417 TCTTCT CCTTCT CCTTCT CCTTC- TCTCCT TCTCCT TCTCCT TCTTCT
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT
* * **
1160464 TCTTCT CCTTCT TCTTC- TCATTCT CCTTCT TCTTCT TCTTAA TCTTCT
1 TCTTCT TCTTCT TCTTCT TC-TTCT TCTTCT TCTTCT TCTTCT TCTTCT
* * * * *
1160512 TCTCCT TCTTCT TCTTCT TC-TCT TCTCCT TCTCCT TCTCCT CCTTCT
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT
* * * * * * * *
1160559 CCTCCT TCTCCT TCTCCT TCTCCT CCTTCT CCTTCT CCTTC- TCTTTCT
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TC-TTCT
* * * * * * * *
1160607 CCTCCT CCTTCT CCTTCT CCTTC- TCATTC- TCCTCAT TCTCCT TCTCCT
1 TCTTCT TCTTCT TCTTCT TCTTCT TC-TTCT TCTTC-T TCTTCT TCTTCT
* * * * * * * * *
1160655 CCTTC- TCATCCT TC-TCC TCCTCC TCCTCC TCATTCT CCTTCT TCTGCT
1 TCTTCT TC-TTCT TCTTCT TCTTCT TCTTCT TC-TTCT TCTTCT TCTTCT
* * *
1160703 TCTGCT TC-TCAT TCTTCT TCTTCT TC-TCAT TCTTCT CCTTCT TCTTAT
1 TCTTCT TCTTC-T TCTTCT TCTTCT TCTTC-T TCTTCT TCTTCT TCTTCT
* * ** *
1160751 TCTTC- TCATTCT TCTTCT TCTTAT TATATAAA T-TTCT CCTTCT TCTTCT
1 TCTTCT TC-TTCT TCTTCT TCTTCT TCT-T-CT TCTTCT TCTTCT TCTTCT
*
1160800 TCTTCT TTTTCT TCTTCT
1 TCTTCT TCTTCT TCTTCT
1160818 CAAACACATA
Statistics
Matches: 1159, Mismatches: 172, Indels: 140
0.79 0.12 0.10
Matches are distributed among these distances:
5 70 0.06
6 1026 0.89
7 61 0.05
8 2 0.00
ACGTcount: A:0.03, C:0.42, G:0.00, T:0.54
Consensus pattern (6 bp):
TCTTCT
Found at i:1160829 original size:49 final size:49
Alignment explanation
Indices: 1160735--1160832 Score: 117
Period size: 49 Copynumber: 2.0 Consensus size: 49
1160725 CTTCTCATTC
** **
1160735 TTCTCCTTCTTCTTATTCTTCTCATTCTTCTTCTTCTTATTATATAAAT
1 TTCTCCTTCTTCTTATTCTTCTCATTCTTCTTCTTCAAAACATATAAAT
* **
1160784 TTCTCCTTCTTCTTCTTCTTCTTTTTCTTCTTC-TCAAACACATATAAAT
1 TTCTCCTTCTTCTTATTCTTCTCATTCTTCTTCTTCAAA-ACATATAAAT
1160833 AACTACCTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 3 0.07
49 38 0.93
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.56
Consensus pattern (49 bp):
TTCTCCTTCTTCTTATTCTTCTCATTCTTCTTCTTCAAAACATATAAAT
Found at i:1163011 original size:20 final size:20
Alignment explanation
Indices: 1162986--1163035 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1162976 GCGAAATAAA
1162986 AATCGCAACGC-GATCTCCAG
1 AATCGCAACGCAGATC-CCAG
** *
1163006 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGCAGATCCCAG
1163026 AATCGCAACG
1 AATCGCAACG
1163036 TGATTATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.34, C:0.32, G:0.18, T:0.16
Consensus pattern (20 bp):
AATCGCAACGCAGATCCCAG
Found at i:1163101 original size:21 final size:21
Alignment explanation
Indices: 1162986--1163101 Score: 58
Period size: 21 Copynumber: 5.6 Consensus size: 21
1162976 GCGAAATAAA
*
1162986 AATCGCAACGCGA-TCTCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
1163006 AATCGCAAATC-AGTTCCCAG
1 AATCGCAACGCGATTTTCCAG
* * **
1163026 AATCGCAACGTGATTATGAAG
1 AATCGCAACGCGATTTTCCAG
* ** *
1163047 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
* **
1163067 AATTAGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
1163089 AATCGCAACGCGA
1 AATCGCAACGCGA
1163102 ACATATAAAT
Statistics
Matches: 66, Mismatches: 26, Indels: 7
0.67 0.26 0.07
Matches are distributed among these distances:
19 1 0.02
20 24 0.36
21 39 0.59
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:1163156 original size:21 final size:21
Alignment explanation
Indices: 1163130--1163233 Score: 122
Period size: 21 Copynumber: 5.0 Consensus size: 21
1163120 GATTCTGACT
1163130 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGTAAA
** *
1163151 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGTAAA
* *
1163172 ATCGCAACGCGTATACGTAAA
1 ATCGCAACGAGTATCCGTAAA
1163193 ATCGCAACGCA-TATCCGT-AA
1 ATCGCAACG-AGTATCCGTAAA
* *
1163213 ATCGTAACGCGTATCCGTAAA
1 ATCGCAACGAGTATCCGTAAA
1163234 TAGCAATACG
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
20 17 0.24
21 53 0.76
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (21 bp):
ATCGCAACGAGTATCCGTAAA
Found at i:1163216 original size:20 final size:20
Alignment explanation
Indices: 1163130--1163320 Score: 144
Period size: 20 Copynumber: 9.3 Consensus size: 20
1163120 GATTCTGACT
*
1163130 ATCGCAACG-AGTATCCGTAAA
1 ATCGCAACGCA-TATACGT-AA
1163151 ATCGCAACGACA-ATACGTAAA
1 ATCGCAACG-CATATACGT-AA
*
1163172 ATCGCAACGCGTATACGTAAA
1 ATCGCAACGCATATACGT-AA
*
1163193 ATCGCAACGCATATCCGTAA
1 ATCGCAACGCATATACGTAA
* * *
1163213 ATCGTAACGCGTATCCGTAA
1 ATCGCAACGCATATACGTAA
*
1163233 ATAGCAATACG-A-ATACGTAA
1 ATCGC-A-ACGCATATACGTAA
* *
1163253 ATCGCAATGTGAT-TACGTAA
1 ATCGCAACG-CATATACGTAA
*
1163273 ATCGCAATGCGA-ATACGTAA
1 ATCGCAACGC-ATATACGTAA
1163293 ATCGCAACGACA-ATACGTAAA
1 ATCGCAACG-CATATACGT-AA
1163314 ATCGCAA
1 ATCGCAA
1163321 TGCGATTTTT
Statistics
Matches: 144, Mismatches: 14, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.01
19 1 0.01
20 75 0.52
21 62 0.43
22 3 0.02
23 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCATATACGTAA
Found at i:1163272 original size:60 final size:61
Alignment explanation
Indices: 1163149--1163327 Score: 179
Period size: 60 Copynumber: 2.9 Consensus size: 61
1163139 AGTATCCGTA
* * * *
1163149 AAATCGCAACGAC-AATACGTAAAATCGCAACG-CGTATACGTAAAATCGCAACGC-ATATCCGT
1 AAATCGCAACG-CGAATACGT-AAATAGCAACGAC-AATACGTAAAATCGCAATGCGAT-TACGT
* * * * *
1163211 AAATCGTAACGCGTATCCGTAAATAGCAA-TACGAATACGT-AAATCGCAATGTGATTACGT
1 AAATCGCAACGCGAATACGTAAATAGCAACGAC-AATACGTAAAATCGCAATGCGATTACGT
* *
1163271 AAATCGCAATGCGAATACGTAAATCGCAACGACAATACGTAAAATCGCAATGCGATT
1 AAATCGCAACGCGAATACGTAAATAGCAACGACAATACGTAAAATCGCAATGCGATT
1163328 TTTAAAGCGC
Statistics
Matches: 96, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
60 45 0.47
61 36 0.38
62 15 0.16
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (61 bp):
AAATCGCAACGCGAATACGTAAATAGCAACGACAATACGTAAAATCGCAATGCGATTACGT
Found at i:1163310 original size:40 final size:40
Alignment explanation
Indices: 1163130--1163325 Score: 177
Period size: 40 Copynumber: 4.8 Consensus size: 40
1163120 GATTCTGACT
* * *
1163130 ATCGCAACGAGTATCCGTAAAATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CTATACGTAAAATCGCAATG-CGAATACGT-AA
* *
1163172 ATCGCAACGCGTATACGTAAAATCGCAACGC-ATATCCGTAA
1 ATCGCAACGC-TATACGTAAAATCGCAATGCGA-ATACGTAA
* * * *
1163213 ATCGTAACGCGTATCCGT-AAATAGCAATACGAATACGTAA
1 ATCGCAACGC-TATACGTAAAATCGCAATGCGAATACGTAA
*
1163253 ATCGCAATG-TGATTACGT-AAATCGCAATGCGAATACGTAA
1 ATCGCAACGCT-A-TACGTAAAATCGCAATGCGAATACGTAA
*
1163293 ATCGCAACGACAATACGTAAAATCGCAATGCGA
1 ATCGCAACG-CTATACGTAAAATCGCAATGCGA
1163326 TTTTTAAAGC
Statistics
Matches: 130, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 60 0.46
41 36 0.28
42 32 0.25
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (40 bp):
ATCGCAACGCTATACGTAAAATCGCAATGCGAATACGTAA
Found at i:1163942 original size:21 final size:20
Alignment explanation
Indices: 1163881--1163956 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
1163871 TTCTAAACTT
1163881 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGA-GAAAATG
1163901 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGA-GAAAATG
**
1163921 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGA-AAATG
*
1163942 AAAATCACAACGAGA
1 AAAATCGCAACGAGA
1163957 TAATCGCAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 30 0.62
21 18 0.38
ACGTcount: A:0.53, C:0.18, G:0.17, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGAGAAAATG
Found at i:1164007 original size:19 final size:19
Alignment explanation
Indices: 1163980--1164125 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
1163970 AAACCAAAAA
*
1163980 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1163999 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
*
1164018 TCGCGTTGCGATTCTC--T
1 TCGCGTTGCGATTTTCATT
1164035 T---GTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1164051 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
1164065 TCTCGTTGCAATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
1164084 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
1164104 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1164124 TC
1 TC
1164126 AACGAAAAGA
Statistics
Matches: 102, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
14 20 0.20
16 4 0.04
17 5 0.05
19 41 0.40
20 31 0.30
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1164045 original size:33 final size:33
Alignment explanation
Indices: 1164002--1164125 Score: 140
Period size: 33 Copynumber: 3.5 Consensus size: 33
1163992 TTTCATTTCG
*
1164002 CGTTGCGATTTTAATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
1164035 TGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* **
1164068 CGTTGCAATAGTCATTTCCGCGTTGCGATAGTCATTCTCT
1 CGTTGCGATTTTCATTT-CGCGTTGC----G--ATTCTCT
1164108 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
1164126 AACGAAAAGA
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
33 44 0.59
34 8 0.11
38 1 0.01
39 1 0.01
40 21 0.28
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:1164111 original size:20 final size:20
Alignment explanation
Indices: 1164061--1164116 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1164051 TCGCGTTGCG
*
1164061 ATTCTCTCGTTGCAATAGTC
1 ATTCTCTCGTTGCGATAGTC
*
1164081 ATT-TCCGCGTTGCGATAGTC
1 ATTCT-CTCGTTGCGATAGTC
1164101 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
1164117 TTTCATTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:1165974 original size:94 final size:94
Alignment explanation
Indices: 1165812--1166190 Score: 620
Period size: 94 Copynumber: 4.1 Consensus size: 94
1165802 TAGATTGCTT
* * *
1165812 AGTAAATTTATTCGATTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1165877 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
* *
1165906 AGTAAATTTATTCGGTTGTTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1165971 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
1166000 AGTAAATTTGTTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1166065 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
1166094 AGTAAATTTGTTCGGTTGTTGTCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1166159 ATTTGTCTTTGTTTTGTC-TTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1166186 AGTAA
1 AGTAA
1166191 TGCAATCCAT
Statistics
Matches: 270, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
92 6 0.02
93 28 0.10
94 236 0.87
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1166293 original size:19 final size:17
Alignment explanation
Indices: 1166277--1166335 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 17
1166267 AAAAATGATT
1166277 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
*
1166294 ATCGCAA--CGAGA-GA
1 ATCGCAACGCGAAATGA
1166308 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATG--A
1166327 ATCGCAACG
1 ATCGCAACG
1166336 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 9 0.26
15 4 0.11
16 4 0.11
17 8 0.23
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.10
Consensus pattern (17 bp):
ATCGCAACGCGAAATGA
Found at i:1166311 original size:14 final size:14
Alignment explanation
Indices: 1166292--1166363 Score: 72
Period size: 14 Copynumber: 4.8 Consensus size: 14
1166282 AACGCGAAAT
1166292 GAATCGCAACGAGA
1 GAATCGCAACGAGA
1166306 GAATCGCAACGCGAAATGA
1 GAATCGCAA--CG--A-GA
*
1166325 AAATCGCAACGAGA
1 GAATCGCAACGAGA
*
1166339 GAATCGCAACGACA
1 GAATCGCAACGAGA
*
1166353 AAATCGCAACG
1 GAATCGCAACG
1166364 CGAAACTATA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
14 33 0.67
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 10 0.20
ACGTcount: A:0.44, C:0.24, G:0.24, T:0.08
Consensus pattern (14 bp):
GAATCGCAACGAGA
Found at i:1166315 original size:31 final size:32
Alignment explanation
Indices: 1166277--1166349 Score: 130
Period size: 33 Copynumber: 2.3 Consensus size: 32
1166267 AAAAATGATT
1166277 ATCGCAACGCGAAATG-AATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAATCGCAACGAGAGA
1166308 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATG-AAATCGCAACGAGAGA
1166341 ATCGCAACG
1 ATCGCAACG
1166350 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 16 0.40
33 24 0.60
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGAGAGA
Found at i:1166397 original size:19 final size:19
Alignment explanation
Indices: 1166375--1166495 Score: 82
Period size: 19 Copynumber: 6.8 Consensus size: 19
1166365 GAAACTATAA
1166375 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1166394 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1166408 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1166427 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1166441 TCTCGTTGCAATATTCATT
1 TCGCGTTGCGATTTTCATT
**
1166460 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
1166481 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
1166496 AAGTTCCAGA
Statistics
Matches: 78, Mismatches: 12, Indels: 22
0.70 0.11 0.20
Matches are distributed among these distances:
14 18 0.23
16 6 0.08
17 6 0.08
19 34 0.44
21 14 0.18
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1166420 original size:33 final size:33
Alignment explanation
Indices: 1166378--1166471 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
1166368 ACTATAATCG
*
1166378 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1166411 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
1166444 CGTTGCAATATTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
1166472 AGTCATTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:1168384 original size:14 final size:14
Alignment explanation
Indices: 1168365--1168400 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1168355 ATTGTTTAAT
1168365 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1168379 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1168393 TGATTTGT
1 TGATTTGT
1168401 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1168523 original size:19 final size:17
Alignment explanation
Indices: 1168507--1168557 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
1168497 AAAAATGACT
1168507 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
1168526 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
1168540 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
1168557 A
1 A
1168558 AATCGCAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
16 5 0.19
17 7 0.26
19 7 0.26
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:1168549 original size:33 final size:33
Alignment explanation
Indices: 1168507--1168586 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
1168497 AAAAATGACT
* *
1168507 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1168540 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1168573 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1168587 CTAAATTCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1168563 original size:19 final size:19
Alignment explanation
Indices: 1168507--1168565 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1168497 AAAAATGACT
1168507 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1168526 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1168540 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1168559 ATCGCAA
1 ATCGCAA
1168566 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1168614 original size:19 final size:19
Alignment explanation
Indices: 1168592--1168689 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
1168582 CGAAACTAAA
*
1168592 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
1168611 TTCGCTTTGTGA--TTC--
1 TTCGCATTGCGATTTTCAT
*
1168626 -TCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1168644 TTCGTATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
1168660 ATCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1168677 TTCGCATTGCGAT
1 TTCGCATTGCGAT
1168690 AGACATTAAG
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 14 0.23
16 10 0.17
17 10 0.17
19 26 0.43
ACGTcount: A:0.13, C:0.20, G:0.18, T:0.48
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1168640 original size:33 final size:34
Alignment explanation
Indices: 1168598--1168689 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 34
1168588 TAAATTCGCG
* *
1168598 TTGCGATTTTCATTTCGCT-TTGTGATTCTCTCA
1 TTGCGATTTTCATTTCGCTATTGCGATTCTATCA
*
1168631 TTGCGATTTTCATTTCG-TATTGCGATTCTATCG
1 TTGCGATTTTCATTTCGCTATTGCGATTCTATCA
1168664 TTGCGATTTTCATTTCGC-ATTGCGAT
1 TTGCGATTTTCATTTCGCTATTGCGAT
1168690 AGACATTAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
32 1 0.02
33 53 0.98
ACGTcount: A:0.14, C:0.20, G:0.17, T:0.49
Consensus pattern (34 bp):
TTGCGATTTTCATTTCGCTATTGCGATTCTATCA
Found at i:1171222 original size:24 final size:24
Alignment explanation
Indices: 1171188--1171241 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1171178 CTGAAAAATC
1171188 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1171212 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1171236 ATCAAA
1 ATCAAA
1171242 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1171255 original size:24 final size:24
Alignment explanation
Indices: 1171188--1171255 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1171178 CTGAAAAATC
* * *
1171188 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1171212 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1171236 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1171256 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1172122 original size:20 final size:21
Alignment explanation
Indices: 1172099--1172186 Score: 110
Period size: 21 Copynumber: 4.3 Consensus size: 21
1172089 GTCAGAATCT
1172099 CGTTGCGA-TTTACGGATACG
1 CGTTGCGATTTTACGGATACG
* *
1172119 CGTTGCGATTTTACGTAT-TG
1 CGTTGCGATTTTACGGATACG
*
1172139 TCGTTGCGA-TTTACGAATACG
1 -CGTTGCGATTTTACGGATACG
*
1172160 CGTTGCGATTTTACGGATACT
1 CGTTGCGATTTTACGGATACG
1172181 CGTTGC
1 CGTTGC
1172187 AATAGTCAGA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
20 25 0.43
21 33 0.57
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.36
Consensus pattern (21 bp):
CGTTGCGATTTTACGGATACG
Found at i:1172184 original size:41 final size:41
Alignment explanation
Indices: 1172097--1172186 Score: 144
Period size: 41 Copynumber: 2.2 Consensus size: 41
1172087 TAGTCAGAAT
* * *
1172097 CTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATT
1 CTCGTTGCGATTTACGAATACGCGTTGCGATTTTACGGATA
*
1172138 GTCGTTGCGATTTACGAATACGCGTTGCGATTTTACGGATA
1 CTCGTTGCGATTTACGAATACGCGTTGCGATTTTACGGATA
1172179 CTCGTTGC
1 CTCGTTGC
1172187 AATAGTCAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.37
Consensus pattern (41 bp):
CTCGTTGCGATTTACGAATACGCGTTGCGATTTTACGGATA
Found at i:1172228 original size:20 final size:20
Alignment explanation
Indices: 1172201--1172270 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
1172191 GTCAGAATCA
1172201 CGTTGCGATTTATATGTTCG
1 CGTTGCGATTTATATGTTCG
* *
1172221 CATTGCGATTTATATGTTTG
1 CGTTGCGATTTATATGTTCG
1172241 CGTTGCGATTTATATGTTCG
1 CGTTGCGATTTATATGTTCG
1172261 CGTTGCGATT
1 CGTTGCGATT
1172271 CTGGAAAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.16, C:0.14, G:0.24, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTATATGTTCG
Found at i:1176879 original size:18 final size:18
Alignment explanation
Indices: 1176856--1176893 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1176846 AATAAAATAA
*
1176856 AATAAAAGTAACG-AAAGT
1 AATAAAAATAA-GAAAAGT
1176874 AATAAAAATAAGAAAAGT
1 AATAAAAATAAGAAAAGT
1176892 AA
1 AA
1176894 ATTGTAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.68, C:0.03, G:0.13, T:0.16
Consensus pattern (18 bp):
AATAAAAATAAGAAAAGT
Found at i:1177642 original size:18 final size:18
Alignment explanation
Indices: 1177619--1177659 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1177609 GCTTGAGAAA
*
1177619 ACCTAAGGAAAATAAAAT
1 ACCTAAAGAAAATAAAAT
1177637 ACCTAAAGAAAATAAAAT
1 ACCTAAAGAAAATAAAAT
1177655 -CCTAA
1 ACCTAA
1177660 TAAAACTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.61, C:0.15, G:0.07, T:0.17
Consensus pattern (18 bp):
ACCTAAAGAAAATAAAAT
Found at i:1177661 original size:29 final size:30
Alignment explanation
Indices: 1177629--1177718 Score: 116
Period size: 29 Copynumber: 3.1 Consensus size: 30
1177619 ACCTAAGGAA
**
1177629 AATAAAATACCTAAAG-AAAATAAAATCCT
1 AATAAAATACCTTTAGCAAAATAAAATCCT
1177658 AAT-AAA-ACTCTTTAGCAAAATAAAATCCT
1 AATAAAATAC-CTTTAGCAAAATAAAATCCT
*
1177687 AATAAAAT-TCTTTAGCAAAATAAAATCCT
1 AATAAAATACCTTTAGCAAAATAAAATCCT
1177716 AAT
1 AAT
1177719 TAGTTAAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
27 2 0.04
28 7 0.13
29 42 0.78
30 3 0.06
ACGTcount: A:0.56, C:0.14, G:0.03, T:0.27
Consensus pattern (30 bp):
AATAAAATACCTTTAGCAAAATAAAATCCT
Found at i:1179050 original size:2 final size:2
Alignment explanation
Indices: 1179043--1179077 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1179033 CGTATACAAT
1179043 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1179078 CTTAAACTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1186435 original size:23 final size:23
Alignment explanation
Indices: 1186409--1186455 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1186399 TAATCATAAA
1186409 AGCCCTACTTTGAGTAGATTTTT
1 AGCCCTACTTTGAGTAGATTTTT
1186432 AGCCCTACTTTGAGTAGATTTTT
1 AGCCCTACTTTGAGTAGATTTTT
1186455 A
1 A
1186456 TTAAATAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (23 bp):
AGCCCTACTTTGAGTAGATTTTT
Found at i:1186741 original size:19 final size:19
Alignment explanation
Indices: 1186717--1186762 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1186707 AGAGGTCACC
1186717 AAATTATTATT-AATATTTT
1 AAATTATTATTGAA-ATTTT
*
1186736 AAATTAGTATTGAAATTTT
1 AAATTATTATTGAAATTTT
*
1186755 AAAATATT
1 AAATTATT
1186763 CTATATAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (19 bp):
AAATTATTATTGAAATTTT
Found at i:1192567 original size:57 final size:57
Alignment explanation
Indices: 1192466--1192576 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 57
1192456 CCTCAGAATA
* * *
1192466 GCACTCCTTTGCATAATGCCCATGCTTGCCGCAATTATAACACTCGAGATTTGATTT
1 GCACTCCTTTGCATAATGCCCATGCTTACCGCAATTATAACACTCAACATTTGATTT
* * * * * *
1192523 GCACTCTTTTTCATAGTGCCCATGCTTACCGCAGTTGTAGCACTCAACATTTGA
1 GCACTCCTTTGCATAATGCCCATGCTTACCGCAATTATAACACTCAACATTTGA
1192577 ATGATTTGAC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.33
Consensus pattern (57 bp):
GCACTCCTTTGCATAATGCCCATGCTTACCGCAATTATAACACTCAACATTTGATTT
Found at i:1206604 original size:20 final size:19
Alignment explanation
Indices: 1206579--1206616 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1206569 ATTCTGCTAG
*
1206579 AGAGGTTTTGAAACACCCTC
1 AGAGGTTTCGAAAC-CCCTC
1206599 AGAGGTTTCGAAACCCCT
1 AGAGGTTTCGAAACCCCT
1206617 ACCCAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (19 bp):
AGAGGTTTCGAAACCCCTC
Found at i:1214007 original size:24 final size:24
Alignment explanation
Indices: 1213972--1214020 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1213962 AGAATATACT
1213972 AGTTATACCTTGAACTTTAAATGA
1 AGTTATACCTTGAACTTTAAATGA
* *
1213996 AGTTATAGCTTGAACTTTAGATGA
1 AGTTATACCTTGAACTTTAAATGA
1214020 A
1 A
1214021 ACATCATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (24 bp):
AGTTATACCTTGAACTTTAAATGA
Found at i:1214385 original size:34 final size:33
Alignment explanation
Indices: 1214332--1214420 Score: 94
Period size: 34 Copynumber: 2.6 Consensus size: 33
1214322 TATTTTAATT
*
1214332 TTTTTTAAAATTTAGATTAATTGAA-AATTT-A
1 TTTTTTAAAATTTAAATTAATTGAATAATTTGA
1214363 TTTTTTAAAATATAATAAATTAATTGAATTAATTTGA
1 TTTTTTAAAAT-T--TAAATTAATTGAA-TAATTTGA
1214400 -TTTTTATAAATTTAATATTAA
1 TTTTTTA-AAATTTAA-ATTAA
1214421 ATGTGAGTCA
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
31 11 0.22
32 1 0.02
34 15 0.31
35 5 0.10
36 12 0.24
37 5 0.10
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (33 bp):
TTTTTTAAAATTTAAATTAATTGAATAATTTGA
Found at i:1215676 original size:3 final size:3
Alignment explanation
Indices: 1215668--1215697 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1215658 CACAGTCGAG
1215668 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1215698 TCATCGAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1216234 original size:23 final size:23
Alignment explanation
Indices: 1216208--1216252 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1216198 CTTTTTTTAG
1216208 GTTCTTAGTATATTTGTTTTGCA
1 GTTCTTAGTATATTTGTTTTGCA
1216231 GTTCTTAGTATATTTGTTTTGC
1 GTTCTTAGTATATTTGTTTTGC
1216253 TTTACGATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.16, C:0.09, G:0.18, T:0.58
Consensus pattern (23 bp):
GTTCTTAGTATATTTGTTTTGCA
Found at i:1218583 original size:31 final size:31
Alignment explanation
Indices: 1218548--1218614 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
1218538 AATATTAAAA
*
1218548 AGTTTGAGGAGTAATTTAGAATGAAGATCAT
1 AGTTTGAGGACTAATTTAGAATGAAGATCAT
* *
1218579 AGTTTGGGGACTAATTTAGAATGAATATCAT
1 AGTTTGAGGACTAATTTAGAATGAAGATCAT
1218610 AGTTT
1 AGTTT
1218615 AGATGAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (31 bp):
AGTTTGAGGACTAATTTAGAATGAAGATCAT
Found at i:1218654 original size:58 final size:59
Alignment explanation
Indices: 1218590--1218705 Score: 166
Period size: 58 Copynumber: 2.0 Consensus size: 59
1218580 GTTTGGGGAC
* * *
1218590 TAATTTAGAATGAATATCATAGTTT-A-GATGAAATTAAAAT-TTTCAAAAGTTTGAAGAT
1 TAATTTAGAATGAAAACCATAATTTAAGGATGAAATTAAAATATTT-AAAAGTTT-AAGAT
1218648 TAATTTAGAATGAAAACCATAATTTAAGGATGAAATTAAAATATTTAAAAGTTTAAGA
1 TAATTTAGAATGAAAACCATAATTTAAGGATGAAATTAAAATATTTAAAAGTTTAAGA
1218706 ACAAATTTAG
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
58 22 0.42
59 5 0.10
60 22 0.42
61 3 0.06
ACGTcount: A:0.48, C:0.03, G:0.13, T:0.35
Consensus pattern (59 bp):
TAATTTAGAATGAAAACCATAATTTAAGGATGAAATTAAAATATTTAAAAGTTTAAGAT
Found at i:1218713 original size:60 final size:58
Alignment explanation
Indices: 1218591--1218717 Score: 159
Period size: 60 Copynumber: 2.2 Consensus size: 58
1218581 TTTGGGGACT
* * * **
1218591 AATTTAGAATGAATATCATAGTTTAGATGAAATTAAAATTTTCAAAAGTTTGAAGATT
1 AATTTAGAATGAAAACCATAATTTAGATGAAATTAAAATTTTCAAAAGTTTGAAGACA
1218649 AATTTAGAATGAAAACCATAATTTAAGGATGAAATTAAAATATTT-AAAAGTTT-AAGAACA
1 AATTTAGAATGAAAACCATAATTT-A-GATGAAATTAAAAT-TTTCAAAAGTTTGAAG-ACA
1218709 AATTTAGAA
1 AATTTAGAA
1218718 GTTAACTCTT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
58 21 0.35
59 4 0.07
60 32 0.53
61 3 0.05
ACGTcount: A:0.50, C:0.04, G:0.13, T:0.34
Consensus pattern (58 bp):
AATTTAGAATGAAAACCATAATTTAGATGAAATTAAAATTTTCAAAAGTTTGAAGACA
Found at i:1228057 original size:21 final size:21
Alignment explanation
Indices: 1228031--1228070 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1228021 CAGAAATAAG
1228031 TCAAAATCAAAT-AACCAAATC
1 TCAAAA-CAAATCAACCAAATC
*
1228052 TCAAAACAACTCAACCAAA
1 TCAAAACAAATCAACCAAA
1228071 CTCGTAACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.57, C:0.28, G:0.00, T:0.15
Consensus pattern (21 bp):
TCAAAACAAATCAACCAAATC
Found at i:1234508 original size:16 final size:16
Alignment explanation
Indices: 1234487--1234519 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1234477 TTAATGTTTA
1234487 TTAATTATCCTATTAT
1 TTAATTATCCTATTAT
*
1234503 TTAATTATCTTATTAT
1 TTAATTATCCTATTAT
1234519 T
1 T
1234520 CTTATTGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATTATCCTATTAT
Found at i:1234594 original size:17 final size:17
Alignment explanation
Indices: 1234578--1234610 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1234568 GTGGTTTTTA
1234578 ACTT-TTTATAAAATTT
1 ACTTATTTATAAAATTT
*
1234594 ACTTATTTATTAAATTT
1 ACTTATTTATAAAATTT
1234611 TTATATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
ACTTATTTATAAAATTT
Found at i:1236131 original size:18 final size:18
Alignment explanation
Indices: 1236108--1236144 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1236098 GAATGTCACT
1236108 TTCAGATTCAGTGGTCTC
1 TTCAGATTCAGTGGTCTC
1236126 TTCAGATTCAGTGGTCTC
1 TTCAGATTCAGTGGTCTC
1236144 T
1 T
1236145 ACCTTTGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.41
Consensus pattern (18 bp):
TTCAGATTCAGTGGTCTC
Found at i:1239122 original size:19 final size:19
Alignment explanation
Indices: 1239098--1239139 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1239088 AAATCCAGAA
1239098 CCCTA-GGGGATATCGATTC
1 CCCTAGGGGGA-ATCGATTC
*
1239117 CCCTAGGGGGAATCGGTTC
1 CCCTAGGGGGAATCGATTC
1239136 CCCT
1 CCCT
1239140 TCAAAGGGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.17, C:0.31, G:0.29, T:0.24
Consensus pattern (19 bp):
CCCTAGGGGGAATCGATTC
Found at i:1243027 original size:22 final size:21
Alignment explanation
Indices: 1242985--1243024 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1242975 GAGTTTATTT
*
1242985 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1243006 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1243025 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1248209 original size:27 final size:27
Alignment explanation
Indices: 1248153--1248215 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 27
1248143 AATTGGAAGT
* * *
1248153 TCAA-GGTATTTTGGTCCTTGTATTAT
1 TCAAGGGTATTTTGGTCATTGTAATAC
* *
1248179 TCAAGGGTATTTTGGTTATTTTAATAC
1 TCAAGGGTATTTTGGTCATTGTAATAC
*
1248206 TCAAGCGTAT
1 TCAAGGGTAT
1248216 ATCGATCATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (27 bp):
TCAAGGGTATTTTGGTCATTGTAATAC
Found at i:1249039 original size:21 final size:21
Alignment explanation
Indices: 1249015--1249055 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1249005 ATTGACTTTT
*
1249015 TGGTTAAAGTCAATGGTCAAG
1 TGGTCAAAGTCAATGGTCAAG
* *
1249036 TGGTCAAGGTTAATGGTCAA
1 TGGTCAAAGTCAATGGTCAA
1249056 TGCTAGTGAG
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:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (21 bp):
TGGTCAAAGTCAATGGTCAAG
Found at i:1259702 original size:20 final size:20
Alignment explanation
Indices: 1259665--1259702 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1259655 ATTTGTTTTA
*
1259665 AAAGAAAGTAAAGGGAAATC
1 AAAGAAAGTAAAGAGAAATC
1259685 AAAGAAAGATAAA-AGAAA
1 AAAGAAAG-TAAAGAGAAA
1259703 ATACCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.68, C:0.03, G:0.21, T:0.08
Consensus pattern (20 bp):
AAAGAAAGTAAAGAGAAATC
Found at i:1270883 original size:77 final size:79
Alignment explanation
Indices: 1270743--1270889 Score: 185
Period size: 77 Copynumber: 1.9 Consensus size: 79
1270733 ATATAGTAAG
1270743 TAAACATTAAAAGAATGTAATTATAATTACAACTCTTTTAATCGATATTTAATTCGGAATAATTA
1 TAAACATTAAAAGAATGTAATTATAATTACAACTCTTTTAATCGATATTTAATTCGGAATAATTA
1270808 AATAAGAGTTTAAA
66 AATAAGAGTTTAAA
* * * * * * *
1270822 TAAACGTT-AAAGATTGTAATTCTGATTATAAGTC-TTTAAT-GTATATTTAATT-TGAATTAAT
1 TAAACATTAAAAGAATGTAATTATAATTACAACTCTTTTAATCG-ATATTTAATTCGGAA-TAAT
1270883 TAAATAA
64 TAAATAA
1270890 TGTTTTGATC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
76 4 0.07
77 27 0.46
78 21 0.36
79 7 0.12
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (79 bp):
TAAACATTAAAAGAATGTAATTATAATTACAACTCTTTTAATCGATATTTAATTCGGAATAATTA
AATAAGAGTTTAAA
Found at i:1271586 original size:19 final size:20
Alignment explanation
Indices: 1271549--1271586 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1271539 AGTGTTAATG
*
1271549 AATTTTAAGATTTTATATTA
1 AATTTTAAGATTATATATTA
1271569 AATTTTAA-ATTATATATT
1 AATTTTAAGATTATATATT
1271587 CGATTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
AATTTTAAGATTATATATTA
Found at i:1273140 original size:19 final size:20
Alignment explanation
Indices: 1273116--1273163 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1273106 AACGATTTTC
*
1273116 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1273135 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1273155 TTTTGAAAA
1 TTTTGAAAA
1273164 ATGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1274802 original size:21 final size:21
Alignment explanation
Indices: 1274776--1274825 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
1274766 AATTGATTCT
1274776 CATCCCCAAATGGCTCAAAAA
1 CATCCCCAAATGGCTCAAAAA
*
1274797 CATCCCC-AATGGCTCCAAAA
1 CATCCCCAAATGGCTCAAAAA
1274817 CATCCCCAA
1 CATCCCCAA
1274826 CGGCTATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.38, C:0.40, G:0.08, T:0.14
Consensus pattern (21 bp):
CATCCCCAAATGGCTCAAAAA
Found at i:1276630 original size:64 final size:65
Alignment explanation
Indices: 1276522--1276731 Score: 227
Period size: 64 Copynumber: 3.3 Consensus size: 65
1276512 TGCATAAATA
* * *
1276522 CCATGCATCGATGCA-TCAATGGA-TAAATTGAAACATCGAATGCATTTTATGCACCGATGCACT
1 CCATGCATCGATGCACTC-AT-GATTTAATTGAAACATCGAATGCATTTGATGCATCGATGCACT
1276585 CT
64 CT
*
1276587 CCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTTGATGCATCGATGCAC-CA
1 CCATGCATCGATGCACTCATGATTTAATTGAAACATCGAATGCATTTGATGCATCGATGCACTC-
*
1276650 G
65 T
** * *
1276651 CCATGCATCGATGCACTCGGGCTATT--TTGAAACATCGAATGCACTTGATGCATCGATGCACTC
1 CCATGCATCGATGCACTCATGAT-TTAATTGAAACATCGAATGCATTTGATGCATCGATGCACTC
1276714 T
65 T
* *
1276715 -TAGTGCACCGATGCACT
1 CCA-TGCATCGATGCACT
1276732 AAGGGTCCAA
Statistics
Matches: 126, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
63 4 0.03
64 100 0.79
65 18 0.14
66 4 0.03
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (65 bp):
CCATGCATCGATGCACTCATGATTTAATTGAAACATCGAATGCATTTGATGCATCGATGCACTCT
Found at i:1276711 original size:17 final size:19
Alignment explanation
Indices: 1276683--1276731 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1276673 TATTTTGAAA
1276683 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1276701 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1276720 CACCGATGCACT
1 CATCGATGCACT
1276732 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1283580 original size:2 final size:2
Alignment explanation
Indices: 1283573--1283667 Score: 183
Period size: 2 Copynumber: 48.0 Consensus size: 2
1283563 TAGCAGCCTA
1283573 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1283615 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1283656 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1283668 CAATTGGCTA
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 91 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1284259 original size:64 final size:65
Alignment explanation
Indices: 1284151--1284340 Score: 185
Period size: 64 Copynumber: 3.0 Consensus size: 65
1284141 TGGATAAATA
* *
1284151 CCATGCATCGATGCA-TCAATGGATAAATTGAAACATCGAATGCATTCT-ATGCACCGATGCACT
1 CCATGCATCGATGCACTC-ATGGATAAATTAAAACATCGAATGCATT-TGATACACCGATGCAC-
*
1284214 C-T
63 CAG
* *
1284216 CCATGCATCGATGCACTC-T-GATTTAATTAAAACATCGAATGCATTTGATACATCGATGCACCA
1 CCATGCATCGATGCACTCATGGA-TAAATTAAAACATCGAATGCATTTGATACACCGATGCACCA
1284279 G
65 G
* * ** * * * *
1284280 CCATGCATCGATGCACTC-GGGCTATTTTGAAACATCGAATGCACTTGATGCATCGATGCAC
1 CCATGCATCGATGCACTCATGGATAAATTAAAACATCGAATGCATTTGATACACCGATGCAC
1284341 TCTTAGTGCA
Statistics
Matches: 107, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
63 4 0.04
64 85 0.79
65 16 0.15
66 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (65 bp):
CCATGCATCGATGCACTCATGGATAAATTAAAACATCGAATGCATTTGATACACCGATGCACCAG
Found at i:1284340 original size:17 final size:19
Alignment explanation
Indices: 1284312--1284360 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1284302 TATTTTGAAA
1284312 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1284330 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1284349 CACCGATGCACT
1 CATCGATGCACT
1284361 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1284356 original size:64 final size:61
Alignment explanation
Indices: 1284177--1284360 Score: 169
Period size: 64 Copynumber: 2.9 Consensus size: 61
1284167 CAATGGATAA
* * *
1284177 ATTGAAACATCGAATGCATTCTATGCACCGATGCACTCTCCA-TGCATCGATGCACTCTGATTT
1 ATTGAAACATCGAATGCATT-GATGCATCGATGCACTCT--AGTGCATCGATGCACTCGGATTT
* * *
1284240 AATTAAAACATCGAATGCATTTGATACATCGATGCAC-C-AGCCATGCATCGATGCACTCGGGCT
1 -ATTGAAACATCGAATGCA-TTGATGCATCGATGCACTCTAG---TGCATCGATGCACTC-GGAT
1284303 ATT
60 -TT
*
1284306 -TTGAAACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 ATTGAAACATCGAATGCA-TTGATGCATCGATGCACTC-TAGTGCATCGATGCACT
1284361 AAGGGTCCAA
Statistics
Matches: 100, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
60 1 0.01
63 1 0.01
64 89 0.89
65 5 0.05
66 2 0.02
67 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (61 bp):
ATTGAAACATCGAATGCATTGATGCATCGATGCACTCTAGTGCATCGATGCACTCGGATTT
Found at i:1287173 original size:69 final size:69
Alignment explanation
Indices: 1286968--1287177 Score: 285
Period size: 69 Copynumber: 3.0 Consensus size: 69
1286958 ATTCTGGTAA
* * * * * * *
1286968 CTCGCATGAGAGCCTCGAAGGGTTAGAACGACTCGCACAGGAGCGCTTAATCAAATGTATTCCAG
1 CTCGCATGGGAGCCCCGAAGGGTTAGAGCGACTCACACGGGAGCGCCTAATCAAATGTATTCCGG
*
1287033 GAGT
66 GTGT
* * * * * *
1287037 CACGCACGGGAGCCCTGAATGGTTAGAGCGATTCACACGGGAGCGCCTAATCAAATGTATTCAGG
1 CTCGCATGGGAGCCCCGAAGGGTTAGAGCGACTCACACGGGAGCGCCTAATCAAATGTATTCCGG
1287102 GTGT
66 GTGT
*
1287106 CTCGCATGGGAGCCCCGAAGGGTTAGAGCGACTCACTCGGGAGCGCCTAATCAAATGTATTCCGG
1 CTCGCATGGGAGCCCCGAAGGGTTAGAGCGACTCACACGGGAGCGCCTAATCAAATGTATTCCGG
1287171 GTGT
66 GTGT
1287175 CTC
1 CTC
1287178 TCACGAGAGC
Statistics
Matches: 120, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 120 1.00
ACGTcount: A:0.25, C:0.25, G:0.30, T:0.20
Consensus pattern (69 bp):
CTCGCATGGGAGCCCCGAAGGGTTAGAGCGACTCACACGGGAGCGCCTAATCAAATGTATTCCGG
GTGT
Found at i:1291870 original size:423 final size:424
Alignment explanation
Indices: 1291115--1292931 Score: 1721
Period size: 427 Copynumber: 4.3 Consensus size: 424
1291105 GTTTAGAGCG
* * * * * *
1291115 TCATCTCTGTTTTTGTGTTACACA--TCTCTTTATATCGAGGGATTGATCGAGAAAAGAAGAGAT
1 TCATCTCTTTTTTTGTGTTAGACATCTCTCTTTATATTGAGGGATCGATTGAGAAAATAAGAGAT
* * *
1291178 AATTATCTTTAAAAAATTTATATAA-TTTA-AT--TAT----A-AATTATGCGTTTAATACTTAA
66 AATTATCTTT-AAAAATTT-TA-AACTTTACATAATATAAGGATAATTACGCATTTAATACCTAA
* ** * * *
1291234 ACTATTAATTTTGATATGTAT-TTTTTACTT-AAGATTTTAAGTTTTTCGAAATCATACTTCAAA
128 ACTATCAATTCGGAT-T-TATATTTTTACTTAAAG-TTTCAA-TTTTTCAAAATCATACTTAAAA
** *
1291297 TTTAGTTTTT-TTTTTTTTTAGTACCCATTCAAAATTTAACGTTAAGTTTTGAAAAGAAAAATGG
189 TTTAGTTTTTGTTTCATTTTAGTACCC-TTCAAAATTTAACGTTAAGTTTTGAAAATAAAAA---
* * * * *
1291361 AAGTTTAGATACTTAAATGAACCAAAACTGATAGTTTAGATACTAAACACGTGAAGA--TTTTAA
250 AAGTTTAGATACTAAAACGGATCAAAACTGATAGTTTAGATACTAAACGCGTGAA-ATTTTTTAA
* * * *
1291424 TGGTGGGAATACTAAAATGAAATAAAACTAAATATTAAATATAATTTAAAAAAAACAAAAGTTAA
314 CGGTGGG-ATACTAAAATGAAATAAAACTAAATATTAGATATAATTTAAAAAAAATAAAAGTTTA
* * * *
1291489 GGTATTAAAACTTGTACATTACGTATTTGTTTAGAGCATAGATAAAT
378 GATACTAAAACTTGTACATTACATATTTGTTTAGAGCGTAGATAAAT
* **
1291536 TCATTTCTTTTTTGTGTGTTAGACATCTCTCTTTATATTGAGGGATCGAACGAGAAAATAAGAGA
1 TCATCTCTTTTTT-TGTGTTAGACATCTCTCTTTATATTGAGGGATCGATTGAGAAAATAAGAGA
*
1291601 TAATTATCTTTAAAAATTTTAAACTTTACATAATATAAGGATAATTGCGCATTTAATACCTAAAC
65 TAATTATCTTTAAAAATTTTAAACTTTACATAATATAAGGATAATTACGCATTTAATACCTAAAC
* * *
1291666 TATCAGTTCGGATTTATATTTTTACTTAAAGTTTCAATTTTCTCAAAACCATAATTAAAATTTAG
130 TATCAATTCGGATTTATATTTTTACTTAAAGTTTCAATTTT-TCAAAATCATACTTAAAATTTAG
*** *
1291731 -TTTT-TTT-ATTTTAGTACCCTGGGGGAAATTTAACGTTATGTTTTG-AAA-AAAAAAAGTTTA
194 TTTTTGTTTCATTTTAGTACCCT--TCAAAATTTAACGTTAAGTTTTGAAAATAAAAAAAGTTTA
* * * **
1291791 GGA-ACTAAAACGGATCAGAATTGATAGTTTAGATACTAAACGCGTTAAATTTTTTAACGGTTTG
257 -GATACTAAAACGGATCAAAACTGATAGTTTAGATACTAAACGCGTGAAATTTTTTAACGGTGGG
* * * * *
1291855 ATATTAAAATGAAATAAAAACTAAATGTTAGGTATAATTTTGAGAAAAATTAAAAGTTTAGATAC
321 ATACTAAAATGAAAT-AAAACTAAATATTAGATATAA-TTT-AAAAAAAATAAAAGTTTAGATAC
*
1291920 TAAAACTTGTACATTACATATTTGTTTAGAGTGTAGATAAAT
383 TAAAACTTGTACATTACATATTTGTTTAGAGCGTAGATAAAT
* * *
1291962 TCATCTCTCTTTTTTTATGTTAGGCATCTCTCTTTATATTGAGGGATCGATT-AGAGAATAAGAG
1 TCA--TCTCTTTTTTTGTGTTAGACATCTCTCTTTATATTGAGGGATCGATTGAGAAAATAAGAG
* * ** *
1292026 ATAATTATCTTTAAAAA-TTTAAACTTTTACATAATTTAAGGGTATATTACGTGTTTAGTACCTA
64 ATAATTATCTTTAAAAATTTTAAAC-TTTACATAATATAAGGATA-ATTACGCATTTAATACCTA
* * * * * * * *
1292090 AACCACCAATTC-TAGTATGTACTTTTACTTAAAGTTTCAATTTTTTCAAAATCATATTTAAATT
127 AACTATCAATTCGGA-TTTATATTTTTACTTAAAGTTTCAA-TTTTTCAAAATCATACTTAAAAT
* * ***
1292154 TTAGTTTTTGTTTCATTTTAGTAACTCATTCAAAATTTAACGTTAAGTTTTGATTATTATTTTTT
190 TTAGTTTTTGTTTCATTTTAGT-AC-CCTTCAAAATTTAACGTTAAGTTTTGA--A--A-ATAAA
* * * * * *
1292219 GAAAGTCTAGATACTAAAAAGGATCAAAACTAAAAGTTTAGATACTAAACGCGTG-AAGTTTTTA
248 AAAAGTTTAGATACTAAAACGGATCAAAACTGATAGTTTAGATACTAAACGCGTGAAATTTTTTA
* * * * * * * * * * *
1292283 TCGGTGAGATACTAAAATAAAACAAAAAATAAATGTCAGATATATTTTGAAAATATTAAAAGTTT
313 ACGGTGGGATACTAAAATGAAA-TAAAACTAAATATTAGATATAATTTAAAAAAAATAAAAGTTT
* * *
1292348 AGATACTAAAACTTTTACATTACATGTTT-TATAGAGCGTAGATAAAT
377 AGATACTAAAACTTGTACATTACATATTTGTTTAGAGCGTAGATAAAT
1292395 TCATCTC-TTTTTTGTGTTAGACATCTCTCTTTATATTGAGGGATCGATTGAGAAAATAAGAGAT
1 TCATCTCTTTTTTTGTGTTAGACATCTCTCTTTATATTGAGGGATCGATTGAGAAAATAAGAGAT
* * * * *
1292459 AA--ATCTTTTAAAAA---AAATATTTTGCATAATATAAGGTTAAATTACGCATTTACTACCTAA
66 AATTATC-TTTAAAAATTTTAA-ACTTTACATAATATAAGGAT-AATTACGCATTTAATACCTAA
* * * * * ** *
1292519 AATGTTAGTTTCGG-TCTATAACTTTACTTAAAGTTTCAATTTTTCAAAATCATACTTATAATTT
128 ACTATCA-ATTCGGATTTATATTTTTACTTAAAGTTTCAATTTTTCAAAATCATACTTAAAATTT
* * * *
1292583 AGTTTTTGTTTCATTTTTGTACCCCATTCAAAATATAATGTTAAATTTTGAAAA-AAAATGAAAG
192 AGTTTTTGTTTCATTTTAGTA-CCC-TTCAAAATTTAACGTTAAGTTTTGAAAATAAAA--AAAG
* * * * *
1292647 TTTAGGTACTAAAACGGATCAAAACTGATAGTATAGATATTAAACGCATGAAATTTTTT-ACGGC
253 TTTAGATACTAAAACGGATCAAAACTGATAGTTTAGATACTAAACGCGTGAAATTTTTTAACGGT
* * * * *
1292711 GGG-TACTAAAATGAAATAAAACCTAAACATTAGGTATGATTTTAAAAAAATAAAAAGTTT-GGT
318 GGGATACTAAAATGAAATAAAA-CTAAATATTAGATATAATTTAAAAAAAAT-AAAAGTTTAGAT
* * * *
1292774 ATTAAAACTTGGACATTGCGTATTTGTTTAGAGCGTAGATAAAT
381 ACTAAAACTTGTACATTACATATTTGTTTAGAGCGTAGATAAAT
* * * * * * *
1292818 TCATCTATTTTTGTGTGTTAGAGATCTTTCTTTATATTGAGGGATCGATTAAGAAAACAAGAGTT
1 TCATCTCTTTTTTTGTGTTAGACATCTCTCTTTATATTGAGGGATCGATTGAGAAAATAAGAGAT
* * * *
1292883 AATTATCTCTAAAAATTTTAAACTTTTACGTAATTTAAGGGTAAATTAC
66 AATTATCTTTAAAAATTTTAAAC-TTTACATAATATAAGGAT-AATTAC
1292932 ACGTTTAGTG
Statistics
Matches: 1145, Mismatches: 187, Indels: 121
0.79 0.13 0.08
Matches are distributed among these distances:
421 17 0.01
422 69 0.06
423 151 0.13
424 135 0.12
425 21 0.02
426 116 0.10
427 178 0.16
428 130 0.11
429 46 0.04
430 106 0.09
431 21 0.02
432 2 0.00
433 20 0.02
434 41 0.04
435 4 0.00
436 44 0.04
437 44 0.04
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (424 bp):
TCATCTCTTTTTTTGTGTTAGACATCTCTCTTTATATTGAGGGATCGATTGAGAAAATAAGAGAT
AATTATCTTTAAAAATTTTAAACTTTACATAATATAAGGATAATTACGCATTTAATACCTAAACT
ATCAATTCGGATTTATATTTTTACTTAAAGTTTCAATTTTTCAAAATCATACTTAAAATTTAGTT
TTTGTTTCATTTTAGTACCCTTCAAAATTTAACGTTAAGTTTTGAAAATAAAAAAAGTTTAGATA
CTAAAACGGATCAAAACTGATAGTTTAGATACTAAACGCGTGAAATTTTTTAACGGTGGGATACT
AAAATGAAATAAAACTAAATATTAGATATAATTTAAAAAAAATAAAAGTTTAGATACTAAAACTT
GTACATTACATATTTGTTTAGAGCGTAGATAAAT
Found at i:1293617 original size:142 final size:141
Alignment explanation
Indices: 1293414--1293680 Score: 354
Period size: 142 Copynumber: 1.9 Consensus size: 141
1293404 AACCTAAAAA
* * ** ** *
1293414 TGGAGACTCTAATATTTATCCTAATTCATTTTATTCAATTATTGAATTGAATAATGGAAATGGAC
1 TGGAGACTCTAATATTAATCCTAATTCATTTTAATCAATTATTGAATCAAATAATCAAAATGAAC
** * *
1293479 TGTCGGGCATTTTAATGCGAGAGCCAAATCAAATTATTCCAAAAAATTAAGAGACTAAAGTTAAA
66 CATCAGACATTTTAATGCGAGAGCCAAATCAAATTATTCC-AAAAATTAAGAGACTAAAGTTAAA
1293544 TTAAGCCTAAAG
130 TTAAGCCTAAAG
* * *
1293556 TGGAGACTCTAATATTAATTCTAATTTATTTTAATCAATTATTGAATCAAATGATCAAAATGAAC
1 TGGAGACTCTAATATTAATCCTAATTCATTTTAATCAATTATTGAATCAAATAATCAAAATGAAC
* * ** *
1293621 CATCATACATTTTAATGCGAGAGCCAAATCGAATTATTCCCTAAATTAAGGGACTAAAGT
66 CATCAGACATTTTAATGCGAGAGCCAAATCAAATTATTCCAAAAATTAAGAGACTAAAGT
1293681 GTGAGAAATC
Statistics
Matches: 106, Mismatches: 19, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
141 17 0.16
142 89 0.84
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (141 bp):
TGGAGACTCTAATATTAATCCTAATTCATTTTAATCAATTATTGAATCAAATAATCAAAATGAAC
CATCAGACATTTTAATGCGAGAGCCAAATCAAATTATTCCAAAAATTAAGAGACTAAAGTTAAAT
TAAGCCTAAAG
Found at i:1294327 original size:21 final size:21
Alignment explanation
Indices: 1294301--1294350 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1294291 CGACTATCGT
1294301 ATTGCGATAGTCCAAGTTCAC
1 ATTGCGATAGTCCAAGTTCAC
* *
1294322 ATTGCGATAGTCGAAGTTCGC
1 ATTGCGATAGTCCAAGTTCAC
*
1294343 GTTGCGAT
1 ATTGCGAT
1294351 TTTCCAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (21 bp):
ATTGCGATAGTCCAAGTTCAC
Found at i:1295182 original size:21 final size:21
Alignment explanation
Indices: 1295156--1295210 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
1295146 GATTTATATA
1295156 TTCGCATTGCGATAGTTC-AAG
1 TTCGCATTGCGATAG-TCGAAG
1295177 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
1295198 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
1295211 TTTCCAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:1295210 original size:42 final size:42
Alignment explanation
Indices: 1295177--1295452 Score: 205
Period size: 42 Copynumber: 6.4 Consensus size: 42
1295167 ATAGTTCAAG
1295177 TTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAA
1 TTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAA
* * * *
1295219 TTCGACTATCGC-A-ACG-CGAACTTCGACTATCGCATTGCGA-TTTACATA
1 TTCG-C-ATTGCGATA-GTCGAA----G--T-TCGCGTTGCGATTTTCCAAA
* * * *
1295267 TTCGCATTGCGATAGTCCAAGTTCGCATTGC-ATTCCGATTTACATA
1 TTCGCATTGCGATAGTCGAAGTTCGCGTTGCGA-T----TTTCCAAA
*
1295313 TTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAA
1 TTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAA
* *
1295355 TTCG--TTGTGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAA
1 TTCGCATTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAA
1295397 TTCG--TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAA
1 TTCGCATTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAA
1295439 TTCG--TTGCGATAGT
1 TTCGCATTGCGATAGT
1295453 TCAAAATCGC
Statistics
Matches: 198, Mismatches: 14, Indels: 44
0.77 0.05 0.17
Matches are distributed among these distances:
40 25 0.13
41 11 0.06
42 81 0.41
43 3 0.02
44 5 0.03
46 44 0.22
47 4 0.02
48 15 0.08
49 10 0.05
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (42 bp):
TTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAA
Found at i:1295273 original size:20 final size:20
Alignment explanation
Indices: 1295248--1295325 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
1295238 ACTTCGACTA
1295248 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* *
1295268 TCGCATTGCGATAGTCCA-AGT
1 TCGCATTGCGAT-TTACATA-T
1295289 TCGCATTGCATTCCGATTTACATAT
1 TCGCATTG-----CGATTTACATAT
1295314 TCGCATTGCGAT
1 TCGCATTGCGAT
1295326 AGTCCAAGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
20 17 0.37
21 12 0.26
25 12 0.26
26 5 0.11
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1295293 original size:21 final size:21
Alignment explanation
Indices: 1295267--1295428 Score: 84
Period size: 21 Copynumber: 7.6 Consensus size: 21
1295257 GATTTACATA
1295267 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
1295288 TTCGCATTGC-ATTCCGATTTACATA-
1 TTCGCATTGCGA-T---A-GTCCA-AG
1295313 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* ** *
1295334 TTCGCGTTGCGATTTTCCAAA
1 TTCGCATTGCGATAGTCCAAG
* *
1295355 TTCG--TTGTGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
** * *
1295374 TTCGTGTTGCGATTTATTCCAAA
1 TTCGCATTGCGA--TAGTCCAAG
*
1295397 TTCG--TTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
1295416 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
1295429 TTATTCCAAA
Statistics
Matches: 107, Mismatches: 20, Indels: 28
0.69 0.13 0.18
Matches are distributed among these distances:
19 24 0.22
20 2 0.02
21 53 0.50
22 1 0.01
23 10 0.09
24 1 0.01
25 14 0.13
26 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:1295306 original size:46 final size:46
Alignment explanation
Indices: 1295250--1295343 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
1295240 TTCGACTATC
*
1295250 GCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATT
1 GCATTCCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATT
*
1295296 GCATTCCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCGTT
1 GCATTCCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATT
1295342 GC
1 GC
1295344 GATTTTCCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.34
Consensus pattern (46 bp):
GCATTCCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATT
Found at i:1295444 original size:21 final size:20
Alignment explanation
Indices: 1295338--1295449 Score: 86
Period size: 21 Copynumber: 5.5 Consensus size: 20
1295328 TCCAAGTTCG
1295338 CGTTGCGATT-TTCCAAATT
1 CGTTGCGATTATTCCAAATT
* * * *
1295357 CGTTGTGA-TAGTCGAAGTT
1 CGTTGCGATTATTCCAAATT
1295376 CGTGTTGCGATTTATTCCAAATT
1 C--GTTGCGA-TTATTCCAAATT
* * *
1295399 CGTTGCGA-TAGTCGAAGTT
1 CGTTGCGATTATTCCAAATT
1295418 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TTATTCCAAATT
1295441 CGTTGCGAT
1 CGTTGCGAT
1295450 AGTTCAAAAT
Statistics
Matches: 70, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
18 1 0.01
19 22 0.31
20 1 0.01
21 29 0.41
23 17 0.24
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTATTCCAAATT
Found at i:1296177 original size:21 final size:21
Alignment explanation
Indices: 1296153--1296257 Score: 119
Period size: 21 Copynumber: 5.1 Consensus size: 21
1296143 ACCGTCGTTG
*
1296153 CGAATTTGGAATAAATCGCAA
1 CGAACTTGGAATAAATCGCAA
*
1296174 CGAACTTGGACT--ATCGCAA
1 CGAACTTGGAATAAATCGCAA
*
1296193 CGAATTTGGAATAAATCGCAA
1 CGAACTTGGAATAAATCGCAA
* *
1296214 CGCGAACTTCGACT--ATCGCAA
1 --CGAACTTGGAATAAATCGCAA
1296235 CGAACTTGGAATAAATCGCAA
1 CGAACTTGGAATAAATCGCAA
1296256 CG
1 CG
1296258 CGAACTTCGA
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
19 27 0.39
21 33 0.48
23 9 0.13
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (21 bp):
CGAACTTGGAATAAATCGCAA
Found at i:1296191 original size:19 final size:19
Alignment explanation
Indices: 1296167--1296276 Score: 103
Period size: 21 Copynumber: 5.4 Consensus size: 19
1296157 TTTGGAATAA
1296167 ATCGCAACGAACTTGGACT
1 ATCGCAACGAACTTGGACT
* *
1296186 ATCGCAACGAATTTGGAAT
1 ATCGCAACGAACTTGGACT
*
1296205 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAA--CGAACTTGGACT
*
1296228 ATCGCAACGAACTTGGAAT
1 ATCGCAACGAACTTGGACT
*
1296247 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAA--CGAACTTGGACT
1296270 ATCGCAA
1 ATCGCAA
1296277 TGCGAATATG
Statistics
Matches: 74, Mismatches: 9, Indels: 14
0.76 0.09 0.14
Matches are distributed among these distances:
19 27 0.36
21 28 0.38
23 19 0.26
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (19 bp):
ATCGCAACGAACTTGGACT
Found at i:1296233 original size:42 final size:42
Alignment explanation
Indices: 1296153--1296276 Score: 216
Period size: 42 Copynumber: 3.0 Consensus size: 42
1296143 ACCGTCGTTG
*
1296153 CGAATTTGGAATAAATCGCAA--CGAACTTGGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1296193 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
*
1296235 CGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1296277 TGCGAATATG
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
40 21 0.26
42 59 0.74
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (42 bp):
CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
Found at i:1298075 original size:36 final size:36
Alignment explanation
Indices: 1298000--1298105 Score: 140
Period size: 36 Copynumber: 2.9 Consensus size: 36
1297990 AGAGGGATGC
*
1298000 AATTTGTTTTAAGAAAAAACAATATCAAGAGAGACAA
1 AATTTGTTTTAAG-AAAAACAATATCAAGTGAGACAA
* * * * *
1298037 AATTTGCTTTAAGAAAAACAATTTCGAGTGATATAA
1 AATTTGTTTTAAGAAAAACAATATCAAGTGAGACAA
*
1298073 AATTCGTTTTAAGAAAAACAATATCAAGTGAGA
1 AATTTGTTTTAAGAAAAACAATATCAAGTGAGA
1298106 TTATTTCTTG
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
36 46 0.79
37 12 0.21
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.28
Consensus pattern (36 bp):
AATTTGTTTTAAGAAAAACAATATCAAGTGAGACAA
Found at i:1298207 original size:44 final size:44
Alignment explanation
Indices: 1298158--1298390 Score: 306
Period size: 44 Copynumber: 5.3 Consensus size: 44
1298148 TCTCAAGCAA
*
1298158 GATGATGTTGATCCAACTCCTTATGTTATGGAATCGAGCGAAAT
1 GATGATGTTGATCCAACTCCTTATGTGATGGAATCGAGCGAAAT
** * * *
1298202 GATGATACTGATCCAATTCCTTATGCGATGGAATCGAGCAAAAT
1 GATGATGTTGATCCAACTCCTTATGTGATGGAATCGAGCGAAAT
* ** * * **
1298246 TATGATACTGATCCAACTCCCTATGTGAAGGAATCGAGAAAAAT
1 GATGATGTTGATCCAACTCCTTATGTGATGGAATCGAGCGAAAT
*
1298290 GTTGATGTTGATCCAACTCCTTATGTGATGGAATCGAGCGAAAAT
1 GATGATGTTGATCCAACTCCTTATGTGATGGAATCGAGCG-AAAT
1298335 GATGATGTTGATCCAACTCCTTATGTGATGGAATCGAGCGAAAAT
1 GATGATGTTGATCCAACTCCTTATGTGATGGAATCGAGCG-AAAT
*
1298380 GA-AATGTTGAT
1 GATGATGTTGAT
1298391 ACACCTTCTT
Statistics
Matches: 166, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
44 116 0.70
45 50 0.30
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (44 bp):
GATGATGTTGATCCAACTCCTTATGTGATGGAATCGAGCGAAAT
Found at i:1300866 original size:65 final size:65
Alignment explanation
Indices: 1300706--1300866 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 65
1300696 TTGTTCAAGG
* * * ** *
1300706 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATATGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
1300769 A
65 A
*
1300770 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
1300834 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
1300867 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:1301379 original size:18 final size:18
Alignment explanation
Indices: 1301356--1301390 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1301346 CTAGGAGATT
1301356 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1301374 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1301391 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1302460 original size:149 final size:149
Alignment explanation
Indices: 1302289--1302603 Score: 594
Period size: 149 Copynumber: 2.1 Consensus size: 149
1302279 GAGTCGAGGG
1302289 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACAAAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACAAAT
1302354 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1302419 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
1302438 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACAAAT
*
1302503 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1302568 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
1302587 TCTACACGGTACTTCGG
1 TCTACGCGGTCCTTCGG
1302604 TGTAATTATA
Statistics
Matches: 162, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 162 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACAAAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1305659 original size:65 final size:65
Alignment explanation
Indices: 1305499--1305659 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 65
1305489 TTGTTCAAGG
* * * ** *
1305499 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATATGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
1305562 A
65 A
*
1305563 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
1305627 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
1305660 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:1306174 original size:18 final size:18
Alignment explanation
Indices: 1306151--1306185 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1306141 CTAGGAGATT
1306151 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1306169 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1306186 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1307350 original size:149 final size:149
Alignment explanation
Indices: 1307080--1307386 Score: 587
Period size: 149 Copynumber: 2.1 Consensus size: 149
1307070 GAGTCGAGGG
*
1307080 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTCTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTAGGGATATATATATATTCTGTGGAACATGTCTGAAGTCTTGAAAGACACAT
*
1307145 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAACATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1307210 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1307229 TCTACGCGGTCCTTAGGGATATATATATATTCTGTGGAACATGTCTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTAGGGATATATATATATTCTGTGGAACATGTCTGAAGTCTTGAAAGACACAT
*
1307294 ACTTGATCCCTAACATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAACATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1307359 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1307378 TCTACGCGG
1 TCTACGCGG
1307387 CACTTCGGTG
Statistics
Matches: 155, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 155 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTAGGGATATATATATATTCTGTGGAACATGTCTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAACATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1307395 original size:23 final size:23
Alignment explanation
Indices: 1307362--1307406 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1307352 ATTATTATAT
*
1307362 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
1307385 GGCACTTCGGTGTAATTATACG
1 GGCACTACGGTGCAATTATACG
1307407 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1310447 original size:65 final size:65
Alignment explanation
Indices: 1310287--1310447 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 65
1310277 TTTTTCAAGG
* * * ** *
1310287 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATATGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
1310350 A
65 A
*
1310351 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
1310415 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
1310448 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:1310962 original size:18 final size:18
Alignment explanation
Indices: 1310939--1310973 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1310929 CTAGGAGATT
1310939 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1310957 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1310974 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1311107 original size:2 final size:2
Alignment explanation
Indices: 1311100--1311153 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1311090 CAGATTAGAT
1311100 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1311142 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1311154 AGAAATAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1312084 original size:149 final size:149
Alignment explanation
Indices: 1311909--1312214 Score: 576
Period size: 149 Copynumber: 2.1 Consensus size: 149
1311899 GAGTCGAGGG
* *
1311909 TCTATGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGATCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1311974 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTAGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTAGTCCTTATGGACATCATTA
1312039 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1312058 TCTACGCGATCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGATCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
1312123 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTAGTCCTTATGGACATCATTA
1312188 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1312207 TCTACGCG
1 TCTACGCG
1312215 GCACTTCGGT
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGATCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTAGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1312224 original size:23 final size:23
Alignment explanation
Indices: 1312191--1312235 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1312181 ATTATTATAT
*
1312191 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
1312214 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
1312236 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1312860 original size:39 final size:40
Alignment explanation
Indices: 1312806--1312884 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 40
1312796 CTTAATCCTG
* *
1312806 GGCATTATCGCCTTTATTAAATTCATCATCCTCA-TTTTA
1 GGCATTATCACCTTTATTAAACTCATCATCCTCACTTTTA
* *
1312845 GGCATTATCACCTTTATTGAACTCGTCATCCTCACTTTTA
1 GGCATTATCACCTTTATTAAACTCATCATCCTCACTTTTA
1312885 CCTCATGTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
39 30 0.86
40 5 0.14
ACGTcount: A:0.24, C:0.25, G:0.09, T:0.42
Consensus pattern (40 bp):
GGCATTATCACCTTTATTAAACTCATCATCCTCACTTTTA
Found at i:1316950 original size:235 final size:236
Alignment explanation
Indices: 1316539--1317001 Score: 883
Period size: 235 Copynumber: 2.0 Consensus size: 236
1316529 AGTTGATGCG
1316539 AAACGATAAGACACCAAGTGCATCAGAAGCATGCAAAAACAAATGGTGATTGAAATCGAGCAAGG
1 AAACGATAAGACACCAAGTGCATCAGAAGCATGCAAAAACAAATGGTGATTGAAATCGAGCAAGG
1316604 AAGTTTCCATGGCAAAAAGAGGGGGGAAAAGAGGGAAAAACCCAAAATCAATTTTGATCGAGAGA
66 AAGTTTCCATGGCAAAAAGAGGGGGGAAAAGAGGGAAAAACCCAAAATCAATTTTGATCGAGAGA
*
1316669 AACGAATTCACGGGAAACAGATCGAATGACTCATGATACCATGTTAAAAGGAAAATTTAC-AAAA
131 AACGAATTCACGGGAAACAGATAGAATGACTCATGATACCATGTTAAAAGGAAAATTTACAAAAA
1316733 AGGTACTTCATCTATTTCATTCATCTCAATATACCATGTTA
196 AGGTACTTCATCTATTTCATTCATCTCAATATACCATGTTA
*
1316774 AAACGATAAGACACCAAGTGCATGAGAAGCATGCAAAAACAAATGGTGATTGAAATCGAGCAAGG
1 AAACGATAAGACACCAAGTGCATCAGAAGCATGCAAAAACAAATGGTGATTGAAATCGAGCAAGG
1316839 AAGTTTCCATGGCAAAAAGAGGGGGGAAAAGAGGGAAAAACCCAAAATCAATTTTGATCGAGAGA
66 AAGTTTCCATGGCAAAAAGAGGGGGGAAAAGAGGGAAAAACCCAAAATCAATTTTGATCGAGAGA
*
1316904 AACGAATTCACGGGAAACAGATAGAATGCCTCATGATACCATGTTAAAAGGAAAATTTACAAAAA
131 AACGAATTCACGGGAAACAGATAGAATGACTCATGATACCATGTTAAAAGGAAAATTTACAAAAA
*
1316969 AGGTACTTCGTCTATTTCATTCATCTCAATATA
196 AGGTACTTCATCTATTTCATTCATCTCAATATA
1317002 TAGTTTACAA
Statistics
Matches: 223, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
235 187 0.84
236 36 0.16
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.21
Consensus pattern (236 bp):
AAACGATAAGACACCAAGTGCATCAGAAGCATGCAAAAACAAATGGTGATTGAAATCGAGCAAGG
AAGTTTCCATGGCAAAAAGAGGGGGGAAAAGAGGGAAAAACCCAAAATCAATTTTGATCGAGAGA
AACGAATTCACGGGAAACAGATAGAATGACTCATGATACCATGTTAAAAGGAAAATTTACAAAAA
AGGTACTTCATCTATTTCATTCATCTCAATATACCATGTTA
Found at i:1321058 original size:27 final size:27
Alignment explanation
Indices: 1321049--1321103 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1321039 TCTGGTATGC
1321049 TTTTGAAAAAAAATAATAGTTGGATGA
1 TTTTGAAAAAAAATAATAGTTGGATGA
1321076 TTTTGAAAAAAAATAATAGTTGGATGA
1 TTTTGAAAAAAAATAATAGTTGGATGA
1321103 T
1 T
1321104 CCAAACAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (27 bp):
TTTTGAAAAAAAATAATAGTTGGATGA
Found at i:1326983 original size:87 final size:88
Alignment explanation
Indices: 1326827--1327005 Score: 279
Period size: 87 Copynumber: 2.0 Consensus size: 88
1326817 TACTCATTCT
* * *
1326827 TTTTTGCTTTGCTGTTTGTTGTTTCTTCTTGGCATGGTAGTGTATATTCGTCTCAAGAGTACTAA
1 TTTTTGCTTTGCTGTTTGTTGTTTCTTCTTGCCATGGTAGGGTAGATTCGTCTCAAGAGTACTAA
1326892 TTCTCATGAATATGTAACCAGTA
66 TTCTCATGAATATGTAACCAGTA
* * *
1326915 TTTTT-CTTTGCTGTTTGTTGTTTCTTCTTGCCATGGTAGGGTAGATTCGTCTCTAGAGTATTAG
1 TTTTTGCTTTGCTGTTTGTTGTTTCTTCTTGCCATGGTAGGGTAGATTCGTCTCAAGAGTACTAA
* *
1326979 TTCTCATTAATATGTAACTAGTA
66 TTCTCATGAATATGTAACCAGTA
1327002 TTTT
1 TTTT
1327006 GCAGAAATTA
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 78 0.94
88 5 0.06
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.48
Consensus pattern (88 bp):
TTTTTGCTTTGCTGTTTGTTGTTTCTTCTTGCCATGGTAGGGTAGATTCGTCTCAAGAGTACTAA
TTCTCATGAATATGTAACCAGTA
Found at i:1331321 original size:22 final size:21
Alignment explanation
Indices: 1331293--1331334 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1331283 CCGGAAATGA
*
1331293 TAAAAAACATTAATATTTTAGG
1 TAAAAAA-AATAATATTTTAGG
*
1331315 TAAAAAAAATAATGTTTTAG
1 TAAAAAAAATAATATTTTAG
1331335 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (21 bp):
TAAAAAAAATAATATTTTAGG
Found at i:1344311 original size:26 final size:26
Alignment explanation
Indices: 1344282--1344385 Score: 83
Period size: 26 Copynumber: 4.1 Consensus size: 26
1344272 TTTCTAATAA
1344282 TATAATATTATAATAAAATAATCA-AT
1 TATAATATTATAATAAAATAAT-ATAT
* *
1344308 TATATTATTATAATAATATAATATAT
1 TATAATATTATAATAAAATAATATAT
** **
1344334 TAT-ATATT-TTTTTTAATAATATAT
1 TATAATATTATAATAAAATAATATAT
* *
1344358 AATAA-ATTATTAATAAAAT-TTATAT
1 TATAATATTA-TAATAAAATAATATAT
1344383 TAT
1 TAT
1344386 TTATTAATTT
Statistics
Matches: 59, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
24 16 0.27
25 13 0.22
26 30 0.51
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (26 bp):
TATAATATTATAATAAAATAATATAT
Found at i:1344440 original size:19 final size:18
Alignment explanation
Indices: 1344267--1344484 Score: 53
Period size: 19 Copynumber: 11.8 Consensus size: 18
1344257 ATATATTTAT
1344267 TAATATT-TCTAATAAT-A
1 TAATATTAT-TAATAATAA
1344284 TAATATTA-TAATAA-AA
1 TAATATTATTAATAATAA
* *
1344300 TAATCAATTATATTATTATAA
1 TAAT--ATTAT-TAATAATAA
* *
1344321 TAATA-TAAT-ATATTATA
1 TAATATTATTAATAATA-A
* * *
1344338 TATTTTTTTTAATAATATA
1 TAATATTATTAATAATA-A
1344357 TAATAAATTATTAATAA-AA
1 TAAT--ATTATTAATAATAA
* * *
1344376 TTTATATTATTTATTAAT-T
1 -TAATATTA-TTAATAATAA
* ** * * *
1344395 TCATAGAAATAATATTAT
1 TAATATTATTAATAATAA
1344413 TAA-ATTATTAATAATGAA
1 TAATATTATTAATAAT-AA
* *
1344431 TAATATTATTTAT-ATAT
1 TAATATTATTAATAATAA
1344448 TAAATATTAATATAATAATCTAA
1 T-AATATT-AT-TAATAA--TAA
1344471 TAATATT-TTAATAA
1 TAATATTATTAATAA
1344485 AGATATTTAA
Statistics
Matches: 145, Mismatches: 32, Indels: 46
0.65 0.14 0.21
Matches are distributed among these distances:
16 15 0.10
17 27 0.19
18 32 0.22
19 34 0.23
20 12 0.08
21 16 0.11
22 6 0.04
23 3 0.02
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.48
Consensus pattern (18 bp):
TAATATTATTAATAATAA
Found at i:1353800 original size:13 final size:13
Alignment explanation
Indices: 1353760--1353793 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1353750 ACTTCTATAT
1353760 AAAT-AATTAATC
1 AAATCAATTAATC
1353772 AAATCAATTAATC
1 AAATCAATTAATC
1353785 AAATCAATT
1 AAATCAATT
1353794 GGTCAAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATCAATTAATC
Found at i:1355257 original size:2 final size:2
Alignment explanation
Indices: 1355250--1355285 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1355240 ATAAACTTTA
1355250 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1355286 CACTACAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1361366 original size:8 final size:8
Alignment explanation
Indices: 1361355--1361453 Score: 76
Period size: 8 Copynumber: 12.0 Consensus size: 8
1361345 ATATATACTA
1361355 TTTTTTATT
1 TTTTTTA-T
1361364 TTTTTTAT
1 TTTTTTAT
1361372 TTTTTTAT
1 TTTTTTAT
* * * *
1361380 ATATATAA
1 TTTTTTAT
*
1361388 TTTTTTAC
1 TTTTTTAT
1361396 TTTTTTA-
1 TTTTTTAT
*
1361403 -TTATTAT
1 TTTTTTAT
1361410 TTTATTTAT
1 TTT-TTTAT
1361419 TTGTTTTAT
1 TT-TTTTAT
*
1361428 TTATATATAT
1 TT-T-TTTAT
1361438 TTTTTTAT
1 TTTTTTAT
1361446 TTTTTTAT
1 TTTTTTAT
1361454 ATTTATTTTA
Statistics
Matches: 72, Mismatches: 13, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
6 5 0.07
8 38 0.53
9 22 0.31
10 7 0.10
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.77
Consensus pattern (8 bp):
TTTTTTAT
Found at i:1361381 original size:35 final size:34
Alignment explanation
Indices: 1361342--1361455 Score: 104
Period size: 35 Copynumber: 3.1 Consensus size: 34
1361332 TTTATATATA
1361342 TATATATATACTATTTTTTATTTTTTTTATTTTTT
1 TATATATATA-TATTTTTTATTTTTTTTATTTTTT
1361377 TATATATATA-ATTTTTTACTTTTTTATTATTATTTT
1 TATATATATATATTTTTTA-TTTTTT-TTATT-TTTT
* * * * *
1361413 ATTTATTTGTTTTATTTATATATATTTTTTTATTTTTT
1 -TATATAT-ATATATTT-TTTAT-TTTTTTTATTTTTT
1361451 TATAT
1 TATAT
1361456 TTATTTTACT
Statistics
Matches: 65, Mismatches: 6, Indels: 14
0.76 0.07 0.16
Matches are distributed among these distances:
33 8 0.12
34 6 0.09
35 15 0.23
36 4 0.06
37 9 0.14
38 5 0.08
39 10 0.15
40 8 0.12
ACGTcount: A:0.25, C:0.02, G:0.01, T:0.73
Consensus pattern (34 bp):
TATATATATATATTTTTTATTTTTTTTATTTTTT
Found at i:1361391 original size:33 final size:36
Alignment explanation
Indices: 1361342--1361414 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 36
1361332 TTTATATATA
*
1361342 TATATATATACTATTTTTTA-TTTTTT-TTATTTTTT
1 TATATATATAC-ATTTTTTACTTTTTTATTATTATTT
1361377 TATATATATA-ATTTTTTACTTTTTTATTATTATTT
1 TATATATATACATTTTTTACTTTTTTATTATTATTT
1361412 TAT
1 TAT
1361415 TTATTTGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
33 8 0.23
34 6 0.17
35 21 0.60
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (36 bp):
TATATATATACATTTTTTACTTTTTTATTATTATTT
Found at i:1361399 original size:24 final size:24
Alignment explanation
Indices: 1361363--1361462 Score: 118
Period size: 24 Copynumber: 4.2 Consensus size: 24
1361353 TATTTTTTAT
1361363 TTTTTTTATTTTTTTATATATATA
1 TTTTTTTATTTTTTTATATATATA
* *
1361387 ATTTTTTACTTTTTTAT-TAT-TA
1 TTTTTTTATTTTTTTATATATATA
1361409 TTTTATTTATTTGTTTTATTTATATATA
1 TTTT-TTTATTT-TTTTA--TATATATA
1361437 TTTTTTTATTTTTTTATAT-T-TA
1 TTTTTTTATTTTTTTATATATATA
1361459 TTTT
1 TTTT
1361463 ACTTACTATT
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
22 11 0.17
23 10 0.15
24 23 0.35
26 6 0.09
27 10 0.15
28 6 0.09
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.76
Consensus pattern (24 bp):
TTTTTTTATTTTTTTATATATATA
Found at i:1361413 original size:52 final size:49
Alignment explanation
Indices: 1361359--1361463 Score: 144
Period size: 50 Copynumber: 2.2 Consensus size: 49
1361349 ATACTATTTT
* *
1361359 TTATTTTTTTTATTT-TTTTA--TATATATAATTTTTTACTTTTTTATTA
1 TTATTTTATTTATTTGTTTTATTTATATATATTTTTTTACTTTTTTA-TA
*
1361406 TTATTTTATTTATTTGTTTTATTTATATATATTTTTTTATTTTTTTATA
1 TTATTTTATTTATTTGTTTTATTTATATATATTTTTTTACTTTTTTATA
1361455 TTTATTTTA
1 -TTATTTTA
1361464 CTTACTATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
47 14 0.27
48 5 0.10
49 2 0.04
50 30 0.59
ACGTcount: A:0.23, C:0.01, G:0.01, T:0.75
Consensus pattern (49 bp):
TTATTTTATTTATTTGTTTTATTTATATATATTTTTTTACTTTTTTATA
Found at i:1364616 original size:14 final size:13
Alignment explanation
Indices: 1364597--1364645 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
1364587 ATCAAAGAAA
1364597 AAAGAGAAAAAAGC
1 AAAGAGAAAAAA-C
1364611 AAAGAGAACAAAA-
1 AAAGAGAA-AAAAC
*
1364624 AAAGAAAAAAAAC
1 AAAGAGAAAAAAC
1364637 AAAG-GAAAA
1 AAAGAGAAAA
1364646 TTGAAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 8 0.26
13 11 0.35
14 8 0.26
15 4 0.13
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAGAGAAAAAAC
Found at i:1364855 original size:69 final size:69
Alignment explanation
Indices: 1364718--1364855 Score: 179
Period size: 69 Copynumber: 2.0 Consensus size: 69
1364708 GATTCAAACT
* * **
1364718 ATGAAATTGAACAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAGAGTA
1 ATGAAATTGAACAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCAAAGATCATAGACCA
1364783 TCAA
66 TCAA
* * * * *
1364787 ATGAGATTGATCAAGCACAATCATTTCTGAATTACTGAATCACTCCACTCAAAGATCAT-GCACC
1 ATGAAATTGAACAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCAAAGATCATAG-ACC
1364851 ATCAA
65 ATCAA
1364856 GAGAAAGACA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
68 1 0.02
69 58 0.98
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (69 bp):
ATGAAATTGAACAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCAAAGATCATAGACCA
TCAA
Found at i:1365816 original size:32 final size:31
Alignment explanation
Indices: 1365780--1365886 Score: 133
Period size: 32 Copynumber: 3.4 Consensus size: 31
1365770 GGAACAATGA
1365780 GGGCATCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTG-AGATTCAACATCAAATGTTG
* * *
1365812 GGGCATTTTTTTAGATTTAACATCAAATGTTG
1 GGGCA-TCTTTGAGATTCAACATCAAATGTTG
* * *
1365844 GGGCATTTTTTGAGATTCAACATCGAATATTG
1 GGGCA-TCTTTGAGATTCAACATCAAATGTTG
1365876 GGGCATCTTTG
1 GGGCATCTTTG
1365887 GGAATTAAAC
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
31 5 0.08
32 57 0.86
33 4 0.06
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (31 bp):
GGGCATCTTTGAGATTCAACATCAAATGTTG
Done.