Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011496.1 Kokia drynarioides strain JFW-HI SEQ_126481, 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: 296730
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 150 characters in sequence are not A, C, G, or T
Found at i:118 original size:9 final size:9
Alignment explanation
Indices: 101--132 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
91 CTTTTTTTTC
101 CTTCTCCTT
1 CTTCTCCTT
*
110 CTTCCCCTT
1 CTTCTCCTT
119 CTTCTCCTT
1 CTTCTCCTT
128 CTTCT
1 CTTCT
133 TTCTTCTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (9 bp):
CTTCTCCTT
Found at i:151 original size:17 final size:17
Alignment explanation
Indices: 129--168 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
119 CTTCTCCTTC
129 TTCTTTCT-TCTTTCTCT
1 TTCTTTCTCT-TTTCTCT
*
146 TTCTTTCTCTTTTTTCT
1 TTCTTTCTCTTTTCTCT
163 TTCTTT
1 TTCTTT
169 TTTCCTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TTCTTTCTCTTTTCTCT
Found at i:8797 original size:25 final size:24
Alignment explanation
Indices: 8742--8797 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
8732 AAAGTTGGTA
*
8742 AAAAAAATTTAACCTTTAAAAATT
1 AAAAAAATTGAACCTTTAAAAATT
*
8766 AACAAAAATTGGACCTCTTAAAAATT
1 AA-AAAAATTGAACCT-TTAAAAATT
*
8792 GAAAAA
1 AAAAAA
8798 CAATATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.07
25 15 0.56
26 10 0.37
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (24 bp):
AAAAAAATTGAACCTTTAAAAATT
Found at i:11144 original size:2 final size:2
Alignment explanation
Indices: 11137--11168 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11127 TATTCTTTTC
11137 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
11169 GTATCATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13790 original size:18 final size:19
Alignment explanation
Indices: 13733--13822 Score: 92
Period size: 18 Copynumber: 4.4 Consensus size: 19
13723 TTTATATTGT
13733 TGTTTTGGTGTTTTTTTTAC
1 TGTTTTGGTG-TTTTTTTAC
13753 TGTTTTGGTTGCTATTTTTTAC
1 TGTTTTGG-TG-T-TTTTTTAC
*
13775 TATTTTGGTG-TTTTTTAC
1 TGTTTTGGTGTTTTTTTAC
13793 TGTTTTGGTTGCTATTTTTTTAC
1 TGTTTTGG-TG---TTTTTTTAC
13816 TGTTTTG
1 TGTTTTG
13823 ATGCTGTTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
18 15 0.25
19 2 0.03
20 8 0.13
21 5 0.08
22 15 0.25
23 15 0.25
ACGTcount: A:0.08, C:0.07, G:0.19, T:0.67
Consensus pattern (19 bp):
TGTTTTGGTGTTTTTTTAC
Found at i:13798 original size:40 final size:42
Alignment explanation
Indices: 13735--13822 Score: 144
Period size: 40 Copynumber: 2.1 Consensus size: 42
13725 TATATTGTTG
13735 TTTTGGTGTTTTTTTTACTGTTTTGGTTGCTA-TTTTTTACTA
1 TTTTGGTG-TTTTTTTACTGTTTTGGTTGCTATTTTTTTACTA
*
13777 TTTTGGTG-TTTTTTACTGTTTTGGTTGCTATTTTTTTACTG
1 TTTTGGTGTTTTTTTACTGTTTTGGTTGCTATTTTTTTACTA
13818 TTTTG
1 TTTTG
13823 ATGCTGTTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
40 22 0.50
41 14 0.32
42 8 0.18
ACGTcount: A:0.08, C:0.07, G:0.18, T:0.67
Consensus pattern (42 bp):
TTTTGGTGTTTTTTTACTGTTTTGGTTGCTATTTTTTTACTA
Found at i:13835 original size:22 final size:22
Alignment explanation
Indices: 13733--13822 Score: 111
Period size: 22 Copynumber: 4.3 Consensus size: 22
13723 TTTATATTGT
*
13733 TGTTTTGG-TG-TTTTTTTTAC
1 TGTTTTGGTTGCTATTTTTTAC
13753 TGTTTTGGTTGCTATTTTTTAC
1 TGTTTTGGTTGCTATTTTTTAC
*
13775 TATTTTGG-TG---TTTTTTAC
1 TGTTTTGGTTGCTATTTTTTAC
13793 TGTTTTGGTTGCTATTTTTTTAC
1 TGTTTTGGTTGCTA-TTTTTTAC
13816 TGTTTTG
1 TGTTTTG
13823 ATGCTGTTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
18 15 0.25
19 2 0.03
20 8 0.13
21 4 0.07
22 16 0.27
23 15 0.25
ACGTcount: A:0.08, C:0.07, G:0.19, T:0.67
Consensus pattern (22 bp):
TGTTTTGGTTGCTATTTTTTAC
Found at i:13835 original size:23 final size:23
Alignment explanation
Indices: 13733--13836 Score: 93
Period size: 22 Copynumber: 4.9 Consensus size: 23
13723 TTTATATTGT
13733 TGTTTTGG-TG-T-TTTTTTTAC
1 TGTTTTGGATGCTATTTTTTTAC
*
13753 TGTTTTGGTTGCTA-TTTTTTAC
1 TGTTTTGGATGCTATTTTTTTAC
*
13775 TATTTTGG-TG----TTTTTTAC
1 TGTTTTGGATGCTATTTTTTTAC
*
13793 TGTTTTGGTTGCTATTTTTTTAC
1 TGTTTTGGATGCTATTTTTTTAC
*
13816 TGTTTT-GATGCTGTTATTTTT
1 TGTTTTGGATGCTATT-TTTTT
13837 GTTGTTATTT
Statistics
Matches: 71, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
18 15 0.21
19 2 0.03
20 8 0.11
21 4 0.06
22 23 0.32
23 19 0.27
ACGTcount: A:0.09, C:0.07, G:0.18, T:0.66
Consensus pattern (23 bp):
TGTTTTGGATGCTATTTTTTTAC
Found at i:13859 original size:12 final size:12
Alignment explanation
Indices: 13829--13872 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
13819 TTTGATGCTG
*
13829 TTATTTTTGTTG
1 TTATTTTTGTTA
13841 TTATTTTTGTTA
1 TTATTTTTGTTA
* *
13853 TT-GTTTTGCTA
1 TTATTTTTGTTA
13864 TTATTTTTG
1 TTATTTTTG
13873 CTGATGTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.11, C:0.02, G:0.14, T:0.73
Consensus pattern (12 bp):
TTATTTTTGTTA
Found at i:13859 original size:23 final size:23
Alignment explanation
Indices: 13833--13894 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
13823 ATGCTGTTAT
*
13833 TTTTGTTGTTATTTTTG-TTATTG
1 TTTTGTTGTTATTTTTGCTGA-TG
* *
13856 TTTTGCTATTATTTTTGCTGATG
1 TTTTGTTGTTATTTTTGCTGATG
*
13879 TTTTGATTGTTCTTTT
1 TTTTG-TTGTTATTTT
13895 GGTTGTTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 22 0.71
24 9 0.29
ACGTcount: A:0.10, C:0.05, G:0.16, T:0.69
Consensus pattern (23 bp):
TTTTGTTGTTATTTTTGCTGATG
Found at i:13873 original size:12 final size:12
Alignment explanation
Indices: 13824--13874 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
13814 ACTGTTTTGA
*
13824 TGCTGTTATTTT
1 TGCTATTATTTT
* *
13836 TGTTGTTATTTT
1 TGCTATTATTTT
* *
13848 TGTTATT-GTTT
1 TGCTATTATTTT
13859 TGCTATTATTTT
1 TGCTATTATTTT
13871 TGCT
1 TGCT
13875 GATGTTTTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.10, C:0.06, G:0.16, T:0.69
Consensus pattern (12 bp):
TGCTATTATTTT
Found at i:16412 original size:190 final size:193
Alignment explanation
Indices: 15838--16633 Score: 722
Period size: 204 Copynumber: 4.0 Consensus size: 193
15828 AAAATAATAA
* * * *
15838 TTATTTAAATTTTCAATGAACGTTAATATATAC-A-T--GAAAATTTA-AGAAGATGTTCAAAAT
1 TTATTTAAATTTTCAATAAACGTTAACATATACAATTCACAAAACTTAGA-AAGATGTTCAAAAT
* * * * * * *
15898 TTAAAATTAACTCGTATATTTTTTTAAACATTACGTGTTTTCATTTAAAACACGACAAAATACAA
65 TTAAAATTAACTCATATCTTTCTTGAAACGTTCCGTGCTTTCATTTAAAACACGA-AAAATACAA
* * * *
15963 TAAAAAT-ATA--TATGTGTATTTAATAGTTATAAATAAAAAGAATAATCTATTTGTTG-CAGTT
129 TAAAAATGATATTTGTGTGTATTTAATAGTTATAAATAAAAAGAAGAATTTGTTTGTTGTCA---
**
16024 TTT
191 AAT
* * ** * * *
16027 TTTTTTTAATTTTCTGTGAACGTTAACATATACAAAAGTCTTATTCATCAAAGCTTAGAAAAATG
1 TTATTTAAATTTTCAATAAACGTTAACATATAC---A-----ATTCA-CAAAACTTAGAAAGATG
* * * *
16092 TTCAAAATTTAAAATTAACTCGTATCTTTCTTGAAACGTTCTGTGCTTTTATTTGAAACACGTAA
57 TTCAAAATTTAAAATTAACTCATATCTTTCTTGAAACGTTCCGTGCTTTCATTTAAAACACG-AA
* * *
16157 AAATACAATAAAAATTATATTTGTGTGTATTTAATTGTTATAAATAAATAGAAGAATTTGTTTGT
121 AAATACAATAAAAATGATATTTGTGTGTATTTAATAGTTATAAATAAAAAGAAGAATTTGTTTGT
16222 TGTCAAAT
186 TGTCAAAT
*
16230 TTATTTAAATTTTCAATAAACGTTAACATATAC-A-T-A-AAAACTTAGGAAGATGTTCAAAATT
1 TTATTTAAATTTTCAATAAACGTTAACATATACAATTCACAAAACTTAGAAAGATGTTCAAAATT
* * * *
16291 TAAAATTAACTCATATCTTTCTTGAAACGTT-GGATGCTTTCATTTAAAAGACGACAAATTACAG
66 TAAAATTAACTCATATCTTTCTTGAAACGTTCCG-TGCTTTCATTTAAAACACGA-AAAATACAA
* * * * * *
16355 TAAAACTGATATTTGTGTGTATTTAATAGTTATAATTAAAAAGAATAATATGTTTGTTAT-AGTT
129 TAAAAATGATATTTGTGTGTATTTAATAGTTATAAATAAAAAGAAGAATTTGTTTGTTGTCA--A
*
16419 TT
192 AT
* * * * *
16421 TTTTTTTAATTTTCAGTGAACGTTAACATATACAAAAGTTTTGTTCATCAAAGCTTAGAAAGATG
1 TTATTTAAATTTTCAATAAACGTTAACATATAC--AA------TTCA-CAAAACTTAGAAAGATG
* * * *
16486 TTTAAAATTTAAAATCAACTCATATCTTCCTTGAAAGGTTCCGTGCTTTCATTTAAAACACGATA
57 TTCAAAATTTAAAATTAACTCATATCTTTCTTGAAACGTTCCGTGCTTTCATTTAAAACACGA-A
* * *
16551 AAATACAATAAAAATGATATTTGTGTGTATTCAATAGTTATAAACAATAAGAAGAATTTGTTTGT
121 AAATACAATAAAAATGATATTTGTGTGTATTTAATAGTTATAAATAAAAAGAAGAATTTGTTTGT
16616 TGTCAAAAT
186 TGTC-AAAT
16625 TTATTTAAA
1 TTATTTAAA
16634 ATTTGGCTTA
Statistics
Matches: 490, Mismatches: 78, Indels: 63
0.78 0.12 0.10
Matches are distributed among these distances:
189 31 0.06
190 127 0.26
191 30 0.06
192 1 0.00
193 1 0.00
194 2 0.00
198 1 0.00
199 1 0.00
201 1 0.00
202 81 0.17
203 34 0.07
204 136 0.28
205 41 0.08
206 3 0.01
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (193 bp):
TTATTTAAATTTTCAATAAACGTTAACATATACAATTCACAAAACTTAGAAAGATGTTCAAAATT
TAAAATTAACTCATATCTTTCTTGAAACGTTCCGTGCTTTCATTTAAAACACGAAAAATACAATA
AAAATGATATTTGTGTGTATTTAATAGTTATAAATAAAAAGAAGAATTTGTTTGTTGTCAAAT
Found at i:16564 original size:394 final size:393
Alignment explanation
Indices: 15838--16633 Score: 1161
Period size: 394 Copynumber: 2.0 Consensus size: 393
15828 AAAATAATAA
* * * *
15838 TTATTTAAATTTTCAATGAACGTTAATATATACATGAAAATTTAAGAAGATGTTCAAAATTTAAA
1 TTATTTAAATTTTCAATAAACGTTAACATATACATAAAAACTTAAGAAGATGTTCAAAATTTAAA
* * * *
15903 ATTAACTCGTATATTTTTTTAAACATTACGTGTTTTCATTTAAAACACGACAAAATACAATAAAA
66 ATTAACTCATATATTTCTTGAAACATTACGTGCTTTCATTTAAAACACGACAAAATACAATAAAA
* *
15968 ATATATATGTGTATTTAATAGTTATAAATAAAAAGAATAATCTATTTGTTGCAGTTTTTTTTTTT
131 ATATATATGTGTATTTAATAGTTATAAATAAAAAGAATAATATATTTGTTACAGTTTTTTTTTTT
*
16033 TAATTTTCTGTGAACGTTAACATATACAAAAGTCTTATTCATCAAAGCTTAGAAAAATGTTCAAA
196 TAATTTTCAGTGAACGTTAACATATACAAAAGTCTTATTCATCAAAGCTTAGAAAAATGTTCAAA
* * * * * *
16098 ATTTAAAATTAACTCGTATCTTTCTTGAAACGTTCTGTGCTTTTATTTGAAACACGTAAAAATAC
261 ATTTAAAATCAACTCATATCTTCCTTGAAACGTTCCGTGCTTTCATTTAAAACACGTAAAAATAC
* * *
16163 AATAAAAATTATATTTGTGTGTATTTAATTGTTATAAATAAAT-AGAAGAATTTGTTTGTTGTC-
326 AATAAAAATGATATTTGTGTGTATTCAATAGTTATAAA-AAATAAGAAGAATTTGTTTGTTGTCA
16226 AAAT
390 AAAT
*
16230 TTATTTAAATTTTCAATAAACGTTAACATATACATAAAAACTTAGGAAGATGTTCAAAATTTAAA
1 TTATTTAAATTTTCAATAAACGTTAACATATACATAAAAACTTAAGAAGATGTTCAAAATTTAAA
* * * * * *
16295 ATTAACTCATATCTTTCTTGAAACGTT-GGATGCTTTCATTTAAAAGACGACAAATTACAGTAAA
66 ATTAACTCATATATTTCTTGAAACATTACG-TGCTTTCATTTAAAACACGACAAAATACAATAAA
* * * * *
16359 ACTGATATTTGTGTGTATTTAATAGTTATAATTAAAAAGAATAATATGTTTGTTATAG-TTTTTT
130 A---ATATATATGTGTATTTAATAGTTATAAATAAAAAGAATAATATATTTGTTACAGTTTTTTT
* * *
16423 TTTTTAATTTTCAGTGAACGTTAACATATACAAAAGTTTTGTTCATCAAAGCTTAGAAAGATGTT
192 TTTTTAATTTTCAGTGAACGTTAACATATACAAAAGTCTTATTCATCAAAGCTTAGAAAAATGTT
* *
16488 TAAAATTTAAAATCAACTCATATCTTCCTTGAAAGGTTCCGTGCTTTCATTTAAAACACG-ATAA
257 CAAAATTTAAAATCAACTCATATCTTCCTTGAAACGTTCCGTGCTTTCATTTAAAACACGTA-AA
*
16552 AATACAATAAAAATGATATTTGTGTGTATTCAATAGTTATAAACAATAAGAAGAATTTGTTTGTT
321 AATACAATAAAAATGATATTTGTGTGTATTCAATAGTTATAAAAAATAAGAAGAATTTGTTTGTT
16617 GTCAAAAT
386 GTCAAAAT
16625 TTATTTAAA
1 TTATTTAAA
16634 ATTTGGCTTA
Statistics
Matches: 359, Mismatches: 38, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
391 1 0.00
392 113 0.31
393 4 0.01
394 181 0.50
395 60 0.17
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (393 bp):
TTATTTAAATTTTCAATAAACGTTAACATATACATAAAAACTTAAGAAGATGTTCAAAATTTAAA
ATTAACTCATATATTTCTTGAAACATTACGTGCTTTCATTTAAAACACGACAAAATACAATAAAA
ATATATATGTGTATTTAATAGTTATAAATAAAAAGAATAATATATTTGTTACAGTTTTTTTTTTT
TAATTTTCAGTGAACGTTAACATATACAAAAGTCTTATTCATCAAAGCTTAGAAAAATGTTCAAA
ATTTAAAATCAACTCATATCTTCCTTGAAACGTTCCGTGCTTTCATTTAAAACACGTAAAAATAC
AATAAAAATGATATTTGTGTGTATTCAATAGTTATAAAAAATAAGAAGAATTTGTTTGTTGTCAA
AAT
Found at i:16727 original size:59 final size:59
Alignment explanation
Indices: 16660--16824 Score: 195
Period size: 61 Copynumber: 2.8 Consensus size: 59
16650 TATTTTATAT
* ** *
16660 CTGAACTTGACATTTTTTCTTAATTTTATATCTAAACTTTTTTTGACCAAATTTCGTAC
1 CTGAACTTGATATTTTTTCTTAATTTGGTATCTAAACTTTTTTTAACCAAATTTCGTAC
* * * *
16719 CTGAACTTGATATTTTTTTTCTAATTTGGTACCTAAACTTTTTTTTAACCCAATTTGGTAC
1 CTGAACTTGATATTTTTTCT-TAATTTGGTATCTAAAC-TTTTTTTAACCAAATTTCGTAC
* * * * *
16780 TTGAACTTGATTTTTTTTCCTAATTTGGCATCTAAGCTTTTTTTA
1 CTGAACTTGATATTTTTTCTTAATTTGGTATCTAAACTTTTTTTA
16825 GATTCAATTT
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
59 26 0.29
60 28 0.31
61 35 0.39
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (59 bp):
CTGAACTTGATATTTTTTCTTAATTTGGTATCTAAACTTTTTTTAACCAAATTTCGTAC
Found at i:16745 original size:32 final size:31
Alignment explanation
Indices: 16709--16807 Score: 112
Period size: 29 Copynumber: 3.2 Consensus size: 31
16699 TTTTTGACCA
* *
16709 AATTTCGTACCTGAACTTGATATTTTTTTTCT
1 AATTTGGTACCTGAACTTGAT-TTTTTTTCCT
* ** *
16741 AATTTGGTACCTAAACTT--TTTTTTAACCC
1 AATTTGGTACCTGAACTTGATTTTTTTTCCT
*
16770 AATTTGGTACTTGAACTTGATTTTTTTTCCT
1 AATTTGGTACCTGAACTTGATTTTTTTTCCT
16801 AATTTGG
1 AATTTGG
16808 CATCTAAGCT
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
29 22 0.41
30 1 0.02
31 15 0.28
32 16 0.30
ACGTcount: A:0.23, C:0.15, G:0.11, T:0.51
Consensus pattern (31 bp):
AATTTGGTACCTGAACTTGATTTTTTTTCCT
Found at i:16774 original size:61 final size:61
Alignment explanation
Indices: 16660--16823 Score: 199
Period size: 60 Copynumber: 2.7 Consensus size: 61
16650 TATTTTATAT
* * ** *
16660 CTGAACTTGACATTTTTTCT-TAATTTTATATCTAAAC-TTTTTTTGACCAAATTTCGTAC
1 CTGAACTTGATATTTTTTTTCTAATTTGGTATCTAAACTTTTTTTTAACCAAATTTCGTAC
* * *
16719 CTGAACTTGATATTTTTTTTCTAATTTGGTACCTAAACTTTTTTTTAACCCAATTTGGTAC
1 CTGAACTTGATATTTTTTTTCTAATTTGGTATCTAAACTTTTTTTTAACCAAATTTCGTAC
* * * *
16780 TTGAACTTGAT-TTTTTTTCCTAATTTGGCATCTAAGCTTTTTTT
1 CTGAACTTGATATTTTTTTTCTAATTTGGTATCTAAACTTTTTTT
16824 AGATTCAATT
Statistics
Matches: 90, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
59 18 0.20
60 43 0.48
61 29 0.32
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (61 bp):
CTGAACTTGATATTTTTTTTCTAATTTGGTATCTAAACTTTTTTTTAACCAAATTTCGTAC
Found at i:17545 original size:202 final size:201
Alignment explanation
Indices: 17199--18467 Score: 1182
Period size: 202 Copynumber: 6.4 Consensus size: 201
17189 CACATACATA
* * *
17199 AAAACTTCAG-AAGATGTTCAAAATTTAATATTAATTCATATATTTCTTGAAATGTTCGGTGCTT
1 AAAACTT-AGAAAGATGTTCAAAATTTAAAATTAACTCATATATTTCTTGAAACGTTCGGTGCTT
* * * * *
17263 TCATCTAAAACACGAC-AAATACAATAAAAATGATATCTGAGTGTATTCAATAGTTATAAACAAA
65 TCATTTAAAACACGACAAAATACAATAAAAATGATATTTGTGTGTATTTAATAGTTATAAATAAA
* * * * *
17327 ATGAATAATTTATTTGTTG-CTAAATTTATTTAAATTTTTAGTTAATGTTAACATATACAAAAGT
130 AAGAATAATTTATTTGTTGTC-AAATTTATTTAAATTTTCAGTGAACGTTAACATATACAAAA-A
17391 CTTGTTCATT
193 CTTGTTCA-T
* * * *
17401 AAAACTTAGAAAGATGTTCAAATTTTAAAATTAACTCATATTTTTCTTG-AACGTTCCGTACTAT
1 AAAACTTAGAAAGATGTTCAAAATTTAAAATTAACTCATATATTTCTTGAAACGTTCGGTGCT-T
* *
17465 T-ATTTAAAACATGACAAAATACAATAAAAATGATATTTGTGTTTATTTAATAGTTATAAATAAA
65 TCATTTAAAACACGACAAAATACAATAAAAATGATATTTGTGTGTATTTAATAGTTATAAATAAA
*
17529 AAGAATAATTTATTTGTTGTCAATTTTATTTAAA-TTTCTAGTGAACGTTAACATATAC----A-
130 AAGAATAATTTATTTGTTGTCAAATTTATTTAAATTTTC-AGTGAACGTTAACATATACAAAAAC
17588 ----T-A-
194 TTGTTCAT
* * * * * *
17590 AAAATTTA-AGAAGATGTTCTAAATTTAAAATTAACTCGTATCTTTCTTGAAACATTCGGTTCTT
1 AAAACTTAGA-AAGATGTTCAAAATTTAAAATTAACTCATATATTTCTTGAAACGTTCGGTGCTT
* * * * *
17654 TCATTTAATACACAATAAAATACAATAAAAAATGATATATGTATGTATTTAATAGTTATAAATAA
65 TCATTTAAAACACGACAAAATACAAT-AAAAATGATATTTGTGTGTATTTAATAGTTATAAATAA
* ** * * *
17719 ACTA-AATAATCTT-TTTGTTG-CATTTTTTTTTTTAATTTCCAGTGAACGTTAACATATACAAA
129 A-AAGAATAAT-TTATTTGTTGTCA-AATTTATTTAAATTTTCAGTGAACGTTAACATATACAAA
17781 AATCTTGTTCAT
191 AA-CTTGTTCAT
* * **
17793 CAAAACTTCGAAAGATGTTCAAAATTTAAAATTAACTCATGTATTTCTTGAAACGTTTTGTGCTT
1 -AAAACTTAGAAAGATGTTCAAAATTTAAAATTAACTCATATATTTCTTGAAACGTTCGGTGCTT
* * *
17858 TCATTTAAAACATGACAAAATACAATAAAAATGAT-TTTATATGTATTTAATAGTTATAAATAAA
65 TCATTTAAAACACGACAAAATACAATAAAAATGATATTTGTGTGTATTTAATAGTTATAAATAAA
* * * * * *
17922 AAGAAGAATTTGTTTGTTGTCAATTTTATTTAAATTTTTAGTGAGCATTAACATATAC----A--
130 AAGAATAATTTATTTGTTGTCAAATTTATTTAAATTTTCAGTGAACGTTAACATATACAAAAACT
17981 ---T-A-
195 TGTTCAT
* * * *
17983 AAAACTTAGGAAGATAG-TCAAAAGTTAAAATTAACTCGTATATTTCTCGAAACG-TCTGGTGCT
1 AAAACTTAGAAAGAT-GTTCAAAATTTAAAATTAACTCATATATTTCTTGAAACGTTC-GGTGCT
* * * *
18046 TTCATTTAAAACACAACAAAATACAATAAAAATAATATTTGAGCGTATTTAATAGTTATAAATAA
64 TTCATTTAAAACACGACAAAATACAATAAAAATGATATTTGTGTGTATTTAATAGTTATAAATAA
* * * * * * *
18111 AAAGAATGATCTATTTGTTG-CAAAATTTATTGAAATTTTCAGTCAGCATTAATATATACAAAAA
129 AAAGAATAATTTATTTGTTGTC-AAATTTATTTAAATTTTCAGTGAACGTTAACATATAC-AAAA
18175 ACATTGTTCAT
192 AC-TTGTTCAT
* * * * * ** * ** *
18186 CAAAACTTAAAAAGATATTTAAAATGTAGAATTAACTC--ATCGTTCTTGAAACATTTTGTGATT
1 -AAAACTTAGAAAGATGTTCAAAATTTAAAATTAACTCATATATTTCTTGAAACGTTCGGTGCTT
* * * * * * * *
18249 TCAATTAAAACATGGCAAAATACAATAAAAACGATATATGTGTAT-TTTAATAGTTA-CAA-GAA
65 TCATTTAAAACACGACAAAATACAATAAAAATGATATTTGTGTGTATTTAATAGTTATAAATAAA
* * * * * *
18311 AAGTATAATTTGTTTGTTGTCAAATTTATTCAAAATTTCGGTGAATGTTAACATATACAAAAACC
130 AAGAATAATTTATTTGTTGTCAAATTTATTTAAATTTTCAGTGAACGTTAACATATACAAAAA-C
*
18376 TTGTTTATT
194 TTGTTCA-T
* * * *
18385 AAAACTTAGAAAGATATTCAAAATTTCAAATTAACTCGTATATTTCTTGAAACGTTTC-ATGCTT
1 AAAACTTAGAAAGATGTTCAAAATTTAAAATTAACTCATATATTTCTTGAAACG-TTCGGTGCTT
*
18449 TCATTTAAAACACAACAAA
65 TCATTTAAAACACGACAAA
18468 TAAATTAACT
Statistics
Matches: 868, Mismatches: 143, Indels: 114
0.77 0.13 0.10
Matches are distributed among these distances:
188 2 0.00
189 129 0.15
190 105 0.12
191 79 0.09
192 8 0.01
195 2 0.00
198 44 0.05
199 48 0.06
200 34 0.04
201 45 0.05
202 255 0.29
203 13 0.01
204 103 0.12
205 1 0.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (201 bp):
AAAACTTAGAAAGATGTTCAAAATTTAAAATTAACTCATATATTTCTTGAAACGTTCGGTGCTTT
CATTTAAAACACGACAAAATACAATAAAAATGATATTTGTGTGTATTTAATAGTTATAAATAAAA
AGAATAATTTATTTGTTGTCAAATTTATTTAAATTTTCAGTGAACGTTAACATATACAAAAACTT
GTTCAT
Found at i:17738 original size:191 final size:190
Alignment explanation
Indices: 17411--18148 Score: 796
Period size: 189 Copynumber: 3.8 Consensus size: 190
17401 AAAACTTAGA
* * * *
17411 AAGATGTTCAAATTTTAAAATTAACTCATATTTTTCTTG-AACGTTCCGTACTATT-ATTTAAAA
1 AAGATGTTCAAAATTTAAAATTAACTCATATATTTCTTGAAACGTTCGGTGCT-TTCATTTAAAA
** * *
17474 CATGACAAAATACAATAAAAATGATATTTGTGTTTATTTAATAGTTATAAATAAAAAGAATAATT
65 CACAACAAAATACAATAAAAATGATATTTGTATGTATTTAATAGTTATAAATAAAAAGAATAATT
17539 TATTTGTTGTCAATTTTATTTAAATTTCTAGTGAACGTTAACATATACATAAAAATTTAAG
130 TATTTGTTGTCAATTTTATTTAAATTTCTAGTGAACGTTAACATATACATAAAAATTTAAG
* * * * * *
17600 AAGATGTTCTAAATTTAAAATTAACTCGTATCTTTCTTGAAACATTCGGTTCTTTCATTTAATAC
1 AAGATGTTCAAAATTTAAAATTAACTCATATATTTCTTGAAACGTTCGGTGCTTTCATTTAAAAC
* * *
17665 ACAATAAAATACAATAAAAAATGATATATGTATGTATTTAATAGTTATAAATAAACTA-AATAAT
66 ACAACAAAATACAAT-AAAAATGATATTTGTATGTATTTAATAGTTATAAATAAA-AAGAATAAT
* * * * *
17729 CTT-TTTGTTG-CATTTTTTTTTTTAATTTCCAGTGAACGTTAACATATACA-AAAATCTTGTTC
129 -TTATTTGTTGTCA-ATTTTATTTAAATTTCTAGTGAACGTTAACATATACATAAAA----ATT-
17791 ATCAAAACTTCG
187 -T---AA----G
* **
17803 AAAGATGTTCAAAATTTAAAATTAACTCATGTATTTCTTGAAACGTTTTGTGCTTTCATTTAAAA
1 -AAGATGTTCAAAATTTAAAATTAACTCATATATTTCTTGAAACGTTCGGTGCTTTCATTTAAAA
** * *
17868 CATGACAAAATACAATAAAAATGAT-TTTATATGTATTTAATAGTTATAAATAAAAAGAAGAATT
65 CACAACAAAATACAATAAAAATGATATTTGTATGTATTTAATAGTTATAAATAAAAAGAATAATT
* * * * * *
17932 TGTTTGTTGTCAATTTTATTTAAATTTTTAGTGAGCATTAACATATACATAAAAACTTAGG
130 TATTTGTTGTCAATTTTATTTAAATTTCTAGTGAACGTTAACATATACATAAAAATTTAAG
* * *
17993 AAGATAG-TCAAAAGTTAAAATTAACTCGTATATTTCTCGAAACG-TCTGGTGCTTTCATTTAAA
1 AAGAT-GTTCAAAATTTAAAATTAACTCATATATTTCTTGAAACGTTC-GGTGCTTTCATTTAAA
* * *
18056 ACACAACAAAATACAATAAAAATAATATTTG-AGCGTATTTAATAGTTATAAATAAAAAGAATGA
64 ACACAACAAAATACAATAAAAATGATATTTGTA-TGTATTTAATAGTTATAAATAAAAAGAATAA
* * *
18120 TCTATTTGTTG-CAAAATTTATTGAAATTT
128 TTTATTTGTTGTC-AATTTTATTTAAATTT
18149 TCAGTCAGCA
Statistics
Matches: 457, Mismatches: 63, Indels: 57
0.79 0.11 0.10
Matches are distributed among these distances:
188 1 0.00
189 115 0.25
190 92 0.20
191 82 0.18
192 3 0.01
194 3 0.01
196 1 0.00
197 1 0.00
199 3 0.01
201 3 0.01
202 69 0.15
203 16 0.04
204 68 0.15
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (190 bp):
AAGATGTTCAAAATTTAAAATTAACTCATATATTTCTTGAAACGTTCGGTGCTTTCATTTAAAAC
ACAACAAAATACAATAAAAATGATATTTGTATGTATTTAATAGTTATAAATAAAAAGAATAATTT
ATTTGTTGTCAATTTTATTTAAATTTCTAGTGAACGTTAACATATACATAAAAATTTAAG
Found at i:17808 original size:393 final size:389
Alignment explanation
Indices: 17170--18469 Score: 1424
Period size: 393 Copynumber: 3.3 Consensus size: 389
17160 TTAAACCTTA
* * * *
17170 AAATTTCAGTGAACGTTAACACATACATAAAAACTTCAGAAGATGTTCAAAATTTAATATTAATT
1 AAATTTCAGTGAACGTTAACATATACATAAAAACTTAAGAAGATGTTCAAAATTTAAAATTAACT
* * * * * *
17235 CATATATTTCTTGAAATGTTCGGTGCTTTCATCTAAAACACGACAAATACAATAAAAATGATATC
66 CGTATATTTCTTGAAA-CTTCGGTGCTTTCATTTAAAACACAAAAAATACAATAAAAATGATATA
* * *
17300 TGAGTGTATTCAATAGTTATAAACAAAATGAATAAT-TTATTTGTTGC-TAAATTTATTTAAATT
130 TGAGTGTATTTAATAGTTATAAA-TAAATAAATAATCTT-TTTGTTGCAT-AATTTATTTAAATT
* * * * * *
17363 TTTAGTTAATGTTAACATATACAAAAGTCTTGTTCATTAAAACTTAGAAAGATGTTCAAATTTTA
192 TTCAGTCAACGTTAACATATACAAAAATCTTGTTCATCAAAACTTAGAAAGATGTTCAAAATTTA
* **
17428 AAATTAACTCATATTTTTCTTG-AACGTTCCGTACTATT-ATTTAAAACATGACAAAATACAATA
257 AAATTAACTCATATATTTCTTGAAACGTTTTGTACT-TTCATTTAAAACATGACAAAATACAATA
* *
17491 AAAATGATATTTGTGTTTATTTAATAGTTATAAATAAAAAGAATAATTTATTTGTTGTCAATTTT
321 AAAATGATATTTGTGTATATTTAATAGTTATAAATAAAAAGAATAATTTGTTTGTTGTCAATTTT
17556 ATTT
386 ATTT
* *
17560 AAATTTCTAGTGAACGTTAACATATACATAAAAATTTAAGAAGATGTTCTAAATTTAAAATTAAC
1 AAATTTC-AGTGAACGTTAACATATACATAAAAACTTAAGAAGATGTTCAAAATTTAAAATTAAC
* * *
17625 TCGTATCTTTCTTGAAACATTCGGTTCTTTCATTTAATACACAATAAAATACAATAAAAAATGAT
65 TCGTATATTTCTTGAAAC-TTCGGTGCTTTCATTTAAAACACAA-AAAATACAAT-AAAAATGAT
** * *
17690 ATATGTA-TGTATTTAATAGTTATAAATAAACTAAATAATCTTTTTGTTGCATTTTTTTTTTTAA
127 ATATG-AGTGTATTTAATAGTTATAAATAAA-TAAATAATCTTTTTGTTGCATAATTTATTTAAA
* * *
17754 TTTCCAGTGAACGTTAACATATACAAAAATCTTGTTCATCAAAACTTCGAAAGATGTTCAAAATT
190 TTTTCAGTCAACGTTAACATATACAAAAATCTTGTTCATCAAAACTTAGAAAGATGTTCAAAATT
* *
17819 TAAAATTAACTCATGTATTTCTTGAAACGTTTTGTGCTTTCATTTAAAACATGACAAAATACAAT
255 TAAAATTAACTCATATATTTCTTGAAACGTTTTGTACTTTCATTTAAAACATGACAAAATACAAT
* * * *
17884 AAAAATGAT-TTTATATGTATTTAATAGTTATAAATAAAAAGAAGAATTTGTTTGTTGTCAATTT
320 AAAAATGATATTTGTGTATATTTAATAGTTATAAATAAAAAGAATAATTTGTTTGTTGTCAATTT
17948 TATTT
385 TATTT
* * * * *
17953 AAATTTTTAGTGAGCATTAACATATACATAAAAACTTAGGAAGATAG-TCAAAAGTTAAAATTAA
1 AAA-TTTCAGTGAACGTTAACATATACATAAAAACTTAAGAAGAT-GTTCAAAATTTAAAATTAA
* * *
18017 CTCGTATATTTCTCGAAACGTCTGGTGCTTTCATTTAAAACACAACAAAATACAATAAAAATAAT
64 CTCGTATATTTCTTGAAACTTC-GGTGCTTTCATTTAAAACACAA-AAAATACAATAAAAATGAT
* * * * * * *
18082 ATTTGAGCGTATTTAATAGTTATAAATAAAAAGAATGATCTATTTGTTGCAAAATTTATTGAAAT
127 ATATGAGTGTATTTAATAGTTATAAATAAATA-AATAATCTTTTTGTTGCATAATTTATTTAAAT
* * * * * * * *
18147 TTTCAGTCAGCATTAATATATACAAAAAACATTGTTCATCAAAACTTAAAAAGATATTTAAAATG
191 TTTCAGTCAACGTTAACATATACAAAAATC-TTGTTCATCAAAACTTAGAAAGATGTTCAAAATT
* ** * * *
18212 TAGAATTAACTC--ATCGTTCTTGAAACATTTTGTGA-TTTCAATTAAAACATGGCAAAATACAA
255 TAAAATTAACTCATATATTTCTTGAAACGTTTTGT-ACTTTCATTTAAAACATGACAAAATACAA
* * * * * *
18274 TAAAAACGATATATGTGTAT-TTTAATAGTTA-CAA-GAAAAGTATAATTTGTTTGTTGTCAAAT
319 TAAAAATGATATTTGTGTATATTTAATAGTTATAAATAAAAAGAATAATTTGTTTGTTGTCAATT
*
18336 TTATTCA
384 TTATT-T
* * *
18343 AAATTTCGGTGAATGTTAACATATACAAAAACCTTGTTTATTAAAACTT-AGAAAGATATTCAAA
1 AAATTTCAGTGAACGTTAACATATAC----A-------TA--AAAACTTAAG-AAGATGTTCAAA
* * *
18407 ATTTCAAATTAACTCGTATATTTCTTGAAACGTTTC-ATGCTTTCATTTAAAACACAACAAATA
52 ATTTAAAATTAACTCGTATATTTCTTGAAAC--TTCGGTGCTTTCATTTAAAACACAAAAAATA
18470 AATTAACTTA
Statistics
Matches: 766, Mismatches: 108, Indels: 61
0.82 0.12 0.07
Matches are distributed among these distances:
389 47 0.06
390 12 0.02
391 151 0.20
392 101 0.13
393 329 0.43
394 51 0.07
400 2 0.00
401 6 0.01
402 65 0.08
404 2 0.00
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.38
Consensus pattern (389 bp):
AAATTTCAGTGAACGTTAACATATACATAAAAACTTAAGAAGATGTTCAAAATTTAAAATTAACT
CGTATATTTCTTGAAACTTCGGTGCTTTCATTTAAAACACAAAAAATACAATAAAAATGATATAT
GAGTGTATTTAATAGTTATAAATAAATAAATAATCTTTTTGTTGCATAATTTATTTAAATTTTCA
GTCAACGTTAACATATACAAAAATCTTGTTCATCAAAACTTAGAAAGATGTTCAAAATTTAAAAT
TAACTCATATATTTCTTGAAACGTTTTGTACTTTCATTTAAAACATGACAAAATACAATAAAAAT
GATATTTGTGTATATTTAATAGTTATAAATAAAAAGAATAATTTGTTTGTTGTCAATTTTATTT
Found at i:19613 original size:2 final size:2
Alignment explanation
Indices: 19608--19643 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
19598 AAGCAGCTCG
*
19608 CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
19644 ATTTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:24758 original size:4 final size:4
Alignment explanation
Indices: 24749--24780 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
24739 TCCCTTCCTC
24749 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
24781 TATTGTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:39927 original size:6 final size:6
Alignment explanation
Indices: 39918--39947 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
39908 CATCAACATC
*
39918 CCATTG CCATAG CCATAG CCATAG CCATAG
1 CCATAG CCATAG CCATAG CCATAG CCATAG
39948 TGTGACCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (6 bp):
CCATAG
Found at i:54491 original size:23 final size:23
Alignment explanation
Indices: 54461--54506 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
54451 AAGACAGGTT
54461 GTAAAGCTATATTAACATTCCTG
1 GTAAAGCTATATTAACATTCCTG
54484 GTAAAGCTATATTAACATTCCTG
1 GTAAAGCTATATTAACATTCCTG
54507 ACGGCAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (23 bp):
GTAAAGCTATATTAACATTCCTG
Found at i:64601 original size:12 final size:12
Alignment explanation
Indices: 64584--64636 Score: 72
Period size: 12 Copynumber: 4.4 Consensus size: 12
64574 TTCAAATAAC
64584 AAAAATAACAAT
1 AAAAATAACAAT
*
64596 AAAAATAATAGA-
1 AAAAATAACA-AT
*
64608 AAAAATAACAAC
1 AAAAATAACAAT
64620 AAAAATAACAAT
1 AAAAATAACAAT
64632 AAAAA
1 AAAAA
64637 CAGGATCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
11 1 0.03
12 34 0.94
13 1 0.03
ACGTcount: A:0.77, C:0.08, G:0.02, T:0.13
Consensus pattern (12 bp):
AAAAATAACAAT
Found at i:64656 original size:9 final size:9
Alignment explanation
Indices: 64581--64638 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
64571 ACATTCAAAT
64581 AACAA-AAA
1 AACAATAAA
64589 TAACAATAAA
1 -AACAATAAA
*
64599 AATAATAGAA
1 AACAATA-AA
*
64609 AA-AATAAC
1 AACAATAAA
64617 AACAA-AAA
1 AACAATAAA
64625 TAACAATAAA
1 -AACAATAAA
64635 AACA
1 AACA
64639 GGATCAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
8 5 0.12
9 26 0.63
10 10 0.24
ACGTcount: A:0.76, C:0.10, G:0.02, T:0.12
Consensus pattern (9 bp):
AACAATAAA
Found at i:64660 original size:22 final size:23
Alignment explanation
Indices: 64597--64679 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 23
64587 AATAACAATA
* ** *
64597 AAAATAATAGAAAAAATAACAACA
1 AAAATAATA-AAAAAACAGTAACC
* * *
64621 AAAATAACAATAAAAACAG-GATC
1 AAAATAATAA-AAAAACAGTAACC
64644 AAAATAATAAAAAAACAGTAACC
1 AAAATAATAAAAAAACAGTAACC
*
64667 AAAACAATAAAAA
1 AAAATAATAAAAA
64680 CACAACACCA
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
22 8 0.17
23 25 0.53
24 14 0.30
ACGTcount: A:0.72, C:0.11, G:0.05, T:0.12
Consensus pattern (23 bp):
AAAATAATAAAAAAACAGTAACC
Found at i:64669 original size:23 final size:22
Alignment explanation
Indices: 64597--64692 Score: 68
Period size: 23 Copynumber: 4.2 Consensus size: 22
64587 AATAACAATA
* * *
64597 AAAATAATAGAAAAAATAACAACA
1 AAAATAATA-AAAAAA-CAGAACC
* * *
64621 AAAATAACAATAAAAACAGGATC
1 AAAATAATAA-AAAAACAGAACC
64644 AAAATAATAAAAAAACAGTAACC
1 AAAATAATAAAAAAACAG-AACC
* *
64667 AAAACAATAAAAACACA-ACACC
1 AAAATAATAAAAAAACAGA-ACC
64689 AAAA
1 AAAA
64693 CAGAAAAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
21 1 0.02
22 15 0.26
23 29 0.50
24 13 0.22
ACGTcount: A:0.71, C:0.15, G:0.04, T:0.10
Consensus pattern (22 bp):
AAAATAATAAAAAAACAGAACC
Found at i:67495 original size:6 final size:6
Alignment explanation
Indices: 67484--67519 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
67474 TTTCCATTTG
*
67484 TGCTTT TGCTTT TGCTTT TGCTTT TGCTTT TCCTTT
1 TGCTTT TGCTTT TGCTTT TGCTTT TGCTTT TGCTTT
67520 GTTTTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.19, G:0.14, T:0.67
Consensus pattern (6 bp):
TGCTTT
Found at i:67507 original size:18 final size:18
Alignment explanation
Indices: 67468--67519 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
67458 AGATGATAAA
67468 TTTT-CTTTTCCATTTGTGC
1 TTTTGCTTTTCC-TTT-TGC
*
67487 TTTTGCTTTTGCTTTTGC
1 TTTTGCTTTTCCTTTTGC
67505 TTTTGCTTTTCCTTT
1 TTTTGCTTTTCCTTT
67520 GTTTTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 17 0.57
19 7 0.23
20 6 0.20
ACGTcount: A:0.02, C:0.19, G:0.12, T:0.67
Consensus pattern (18 bp):
TTTTGCTTTTCCTTTTGC
Found at i:68835 original size:20 final size:20
Alignment explanation
Indices: 68810--68997 Score: 134
Period size: 20 Copynumber: 9.9 Consensus size: 20
68800 TTTTTAATTG
68810 ATTTGTTATTTAATATTTTT
1 ATTTGTTATTTAATATTTTT
68830 ATTTGTTATTT-A-ATTTTT
1 ATTTGTTATTTAATATTTTT
* * * *
68848 A--AGTTATTT-TTA-ATTG
1 ATTTGTTATTTAATATTTTT
*
68864 ATTTGTTATTTAATGTTTTT
1 ATTTGTTATTTAATATTTTT
*
68884 ATTTGTTATTTAATTTTTAATT
1 ATTTGTTATTTAATATTT--TT
*
68906 GATTTGTTATTTAATGTTTTT
1 -ATTTGTTATTTAATATTTTT
68927 ATTTGTTATTT-A-ATTTTT
1 ATTTGTTATTTAATATTTTT
* * * *
68945 A--AGTT-TTT-CTA-ATTG
1 ATTTGTTATTTAATATTTTT
*
68960 ATTTGTTATTTAATGTTTTT
1 ATTTGTTATTTAATATTTTT
*
68980 ATGTGTTATTTAAT-TTTT
1 ATTTGTTATTTAATATTTT
68998 AAGTTTTTCT
Statistics
Matches: 132, Mismatches: 22, Indels: 29
0.72 0.12 0.16
Matches are distributed among these distances:
15 6 0.05
16 14 0.11
17 4 0.03
18 23 0.17
19 8 0.06
20 56 0.42
21 2 0.02
22 2 0.02
23 17 0.13
ACGTcount: A:0.23, C:0.01, G:0.09, T:0.67
Consensus pattern (20 bp):
ATTTGTTATTTAATATTTTT
Found at i:68870 original size:54 final size:54
Alignment explanation
Indices: 68800--68903 Score: 199
Period size: 54 Copynumber: 1.9 Consensus size: 54
68790 TTAATTTAAT
68800 TTTTTAATTGATTTGTTATTTAATATTTTTATTTGTTATTTAATTTTTAAGTTA
1 TTTTTAATTGATTTGTTATTTAATATTTTTATTTGTTATTTAATTTTTAAGTTA
*
68854 TTTTTAATTGATTTGTTATTTAATGTTTTTATTTGTTATTTAATTTTTAA
1 TTTTTAATTGATTTGTTATTTAATATTTTTATTTGTTATTTAATTTTTAA
68904 TTGATTTGTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (54 bp):
TTTTTAATTGATTTGTTATTTAATATTTTTATTTGTTATTTAATTTTTAAGTTA
Found at i:68911 original size:43 final size:43
Alignment explanation
Indices: 68853--68946 Score: 188
Period size: 43 Copynumber: 2.2 Consensus size: 43
68843 TTTTTAAGTT
68853 ATTTTTAATTGATTTGTTATTTAATGTTTTTATTTGTTATTTA
1 ATTTTTAATTGATTTGTTATTTAATGTTTTTATTTGTTATTTA
68896 ATTTTTAATTGATTTGTTATTTAATGTTTTTATTTGTTATTTA
1 ATTTTTAATTGATTTGTTATTTAATGTTTTTATTTGTTATTTA
68939 ATTTTTAA
1 ATTTTTAA
68947 GTTTTTCTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (43 bp):
ATTTTTAATTGATTTGTTATTTAATGTTTTTATTTGTTATTTA
Found at i:68915 original size:97 final size:96
Alignment explanation
Indices: 68793--68999 Score: 369
Period size: 97 Copynumber: 2.1 Consensus size: 96
68783 GTTTTGTTTA
*
68793 ATTTAATTTTTTAATTGATTTGTTATTTAATATTTTTATTTGTTATTTAATTTTTAAGTTATTTT
1 ATTTAA-TTTTTAATTGATTTGTTATTTAATATTTTTATTTGTTATTTAATTTTTAAGTT-TTTC
*
68858 TAATTGATTTGTTATTTAATGTTTTTATTTGTT
64 TAATTGATTTGTTATTTAATGTTTTTATGTGTT
*
68891 ATTTAATTTTTAATTGATTTGTTATTTAATGTTTTTATTTGTTATTTAATTTTTAAGTTTTTCTA
1 ATTTAATTTTTAATTGATTTGTTATTTAATATTTTTATTTGTTATTTAATTTTTAAGTTTTTCTA
68956 ATTGATTTGTTATTTAATGTTTTTATGTGTT
66 ATTGATTTGTTATTTAATGTTTTTATGTGTT
68987 ATTTAATTTTTAA
1 ATTTAATTTTTAA
69000 GTTTTTCTTA
Statistics
Matches: 106, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
96 48 0.45
97 52 0.49
98 6 0.06
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (96 bp):
ATTTAATTTTTAATTGATTTGTTATTTAATATTTTTATTTGTTATTTAATTTTTAAGTTTTTCTA
ATTGATTTGTTATTTAATGTTTTTATGTGTT
Found at i:68964 original size:53 final size:53
Alignment explanation
Indices: 68897--69030 Score: 236
Period size: 53 Copynumber: 2.6 Consensus size: 53
68887 TGTTATTTAA
*
68897 TTTT-TAATTGATTTGTTATTTAATGTTTTTATTTGTTATTTAATTTTTAAGT
1 TTTTCTAATTGATTTGTTATTTAATGTTTTTATGTGTTATTTAATTTTTAAGT
68949 TTTTCTAATTGATTTGTTATTTAATGTTTTTATGTGTTATTTAATTTTTAAGT
1 TTTTCTAATTGATTTGTTATTTAATGTTTTTATGTGTTATTTAATTTTTAAGT
*
69002 TTTTCTTATTGATTTGTTATTTAAT-TTTT
1 TTTTCTAATTGATTTGTTATTTAATGTTTT
69031 CGTGTATTTT
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
52 8 0.10
53 71 0.90
ACGTcount: A:0.22, C:0.01, G:0.10, T:0.67
Consensus pattern (53 bp):
TTTTCTAATTGATTTGTTATTTAATGTTTTTATGTGTTATTTAATTTTTAAGT
Found at i:69016 original size:26 final size:26
Alignment explanation
Indices: 68934--69016 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 26
68924 TTTATTTGTT
*
68934 ATTTAATTTTTAAGTTTTTCTAATTG
1 ATTTAATTTTTAAGTTTTTCTTATTG
* * *
68960 ATTT-GTTATTTAATGTTTTTATGTGTT-
1 ATTTAATT-TTTAA-GTTTTTCT-TATTG
68987 ATTTAATTTTTAAGTTTTTCTTATTG
1 ATTTAATTTTTAAGTTTTTCTTATTG
69013 ATTT
1 ATTT
69017 GTTATTTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
25 5 0.11
26 20 0.44
27 16 0.36
28 4 0.09
ACGTcount: A:0.23, C:0.02, G:0.10, T:0.65
Consensus pattern (26 bp):
ATTTAATTTTTAAGTTTTTCTTATTG
Found at i:69049 original size:21 final size:21
Alignment explanation
Indices: 69023--69092 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
69013 ATTTGTTATT
69023 TAATTTTTCGTGTATTTTGTA
1 TAATTTTTCGTGTATTTTGTA
***
69044 TAATTTTTCAGTGT-TCAAGTA
1 TAATTTTTC-GTGTATTTTGTA
* *
69065 T--TTTTTGGTGTATTTTATA
1 TAATTTTTCGTGTATTTTGTA
69084 TAATTTTTC
1 TAATTTTTC
69093 CTTGTAATAT
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
18 4 0.11
19 9 0.25
21 19 0.53
22 4 0.11
ACGTcount: A:0.21, C:0.06, G:0.13, T:0.60
Consensus pattern (21 bp):
TAATTTTTCGTGTATTTTGTA
Found at i:69151 original size:60 final size:60
Alignment explanation
Indices: 69105--69261 Score: 232
Period size: 58 Copynumber: 2.6 Consensus size: 60
69095 TGTAATATCA
*
69105 CCATTTGATAACCCTCCACTAATATAATATTATTTTTTAT-TTTTTTT-CTGTGGTGCCG
1 CCATTTGATAACCCTCCACTAATATAATATTATTTTTTATATTTTTTTCCTGTAGTGCCG
* *
69163 CCATTTGATAA-CCTCTCACTAATATAATTTTATTTTTTTTTATTTTTTTCCTGTAGTGCCG
1 CCATTTGATAACCCTC-CACTAATATAATATTA-TTTTTTATATTTTTTTCCTGTAGTGCCG
*
69224 CCATTTGAT-GCCCTCCACTAATATAATATTATTTTTTA
1 CCATTTGATAACCCTCCACTAATATAATATTATTTTTTA
69262 ATAAATAAAT
Statistics
Matches: 88, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
57 4 0.05
58 26 0.30
59 13 0.15
60 22 0.25
61 23 0.26
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (60 bp):
CCATTTGATAACCCTCCACTAATATAATATTATTTTTTATATTTTTTTCCTGTAGTGCCG
Found at i:69169 original size:58 final size:58
Alignment explanation
Indices: 69105--69261 Score: 228
Period size: 61 Copynumber: 2.7 Consensus size: 58
69095 TGTAATATCA
* *
69105 CCATTTGATAACCCTCCACTAATATAATATTATTTTTTATTTTTTTTCTGTGGTGCCG
1 CCATTTGATAACCCTCCACTAATATAATATTATTTTTTATTTTTTTCCTGTAGTGCCG
*
69163 CCATTTGATAA-CCTCTCACTAATATAATTTTATTTTTTTTTATTTTTTTCCTGTAGTGCCG
1 CCATTTGATAACCCTC-CACTAATATAA---TATTATTTTTTATTTTTTTCCTGTAGTGCCG
*
69224 CCATTTGAT-GCCCTCCACTAATATAATATTATTTTTTA
1 CCATTTGATAACCCTCCACTAATATAATATTATTTTTTA
69262 ATAAATAAAT
Statistics
Matches: 89, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
57 15 0.17
58 22 0.25
60 11 0.12
61 41 0.46
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (58 bp):
CCATTTGATAACCCTCCACTAATATAATATTATTTTTTATTTTTTTCCTGTAGTGCCG
Found at i:74958 original size:3 final size:3
Alignment explanation
Indices: 74950--74980 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
74940 GCAAATTTTA
74950 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
74981 TACCTTTCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:75482 original size:3 final size:3
Alignment explanation
Indices: 75474--75498 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
75464 ATAATTACTT
75474 CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA C
75499 TCTTACAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:80075 original size:2 final size:2
Alignment explanation
Indices: 80068--80097 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
80058 AAAGTAAATA
80068 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
80098 GATTTCGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81337 original size:20 final size:20
Alignment explanation
Indices: 81307--81357 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
81297 ATTAATTTTT
*
81307 AAATT-TTTAAAAA-TCATTA
1 AAATTATTTAAAAAGT-ATAA
81326 AAATTATTTAAAAAGTATAA
1 AAATTATTTAAAAAGTATAA
81346 AAATTATTTAAA
1 AAATTATTTAAA
81358 TGTTGACATG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 5 0.17
20 23 0.79
21 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
AAATTATTTAAAAAGTATAA
Found at i:83468 original size:24 final size:25
Alignment explanation
Indices: 83423--83469 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
83413 TTTGATTTTT
* * *
83423 ATTTAAAAAATTAAACTTAAATTTA
1 ATTTAAAAAATAAAAATCAAATTTA
83448 ATTT-AAAAATAAAAATCAAATT
1 ATTTAAAAAATAAAAATCAAATT
83470 AATATGTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (25 bp):
ATTTAAAAAATAAAAATCAAATTTA
Found at i:84671 original size:16 final size:17
Alignment explanation
Indices: 84634--84673 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
84624 TTTTTTTTTG
84634 AATTATTTATATTTATAT
1 AATT-TTTATATTTATAT
84652 --TTTTTAT-TTTATAT
1 AATTTTTATATTTATAT
84666 AATTTTTA
1 AATTTTTA
84674 AACTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 7 0.35
15 5 0.25
16 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
AATTTTTATATTTATAT
Found at i:85171 original size:2 final size:2
Alignment explanation
Indices: 85164--85204 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
85154 ACACAGTTAC
85164 TA TA TA 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 TA TA TA T
85205 TATTTTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:105081 original size:2 final size:2
Alignment explanation
Indices: 105076--105102 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
105066 AAAAACTGTT
105076 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 T
105103 GTGTGTGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:115786 original size:25 final size:24
Alignment explanation
Indices: 115757--115831 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
115747 GTTTTTTATT
115757 TTTTTCAATATTTATTTATATTTTAC
1 TTTTT-AATA-TTATTTATATTTTAC
* * * *
115783 TTTTTAATATGATTAATATTATAT
1 TTTTTAATATTATTTATATTTTAC
115807 TTTTATAATATTATTTATTATTTTA
1 TTTT-TAATATTATTTA-TATTTTA
115832 AATATATTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 15 0.38
25 14 0.35
26 11 0.28
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (24 bp):
TTTTTAATATTATTTATATTTTAC
Found at i:117426 original size:27 final size:27
Alignment explanation
Indices: 117388--117524 Score: 274
Period size: 27 Copynumber: 5.1 Consensus size: 27
117378 TTGTTTGTTT
117388 ATGTTCGTAAACATTTAATAAACGAGC
1 ATGTTCGTAAACATTTAATAAACGAGC
117415 ATGTTCGTAAACATTTAATAAACGAGC
1 ATGTTCGTAAACATTTAATAAACGAGC
117442 ATGTTCGTAAACATTTAATAAACGAGC
1 ATGTTCGTAAACATTTAATAAACGAGC
117469 ATGTTCGTAAACATTTAATAAACGAGC
1 ATGTTCGTAAACATTTAATAAACGAGC
117496 ATGTTCGTAAACATTTAATAAACGAGC
1 ATGTTCGTAAACATTTAATAAACGAGC
117523 AT
1 AT
117525 AAACAAAAGA
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 110 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (27 bp):
ATGTTCGTAAACATTTAATAAACGAGC
Found at i:123022 original size:31 final size:31
Alignment explanation
Indices: 122987--123053 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
122977 CTCACTTCCG
* * *
122987 TCCTTAATATTATCAGACATTTTTAATTTAA
1 TCCTTAATATTATCAAACATTTTCAATTCAA
*
123018 TCCTTAATATTATCAAACGTTTTCAATTCAA
1 TCCTTAATATTATCAAACATTTTCAATTCAA
123049 TCCTT
1 TCCTT
123054 TAGATGTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.46
Consensus pattern (31 bp):
TCCTTAATATTATCAAACATTTTCAATTCAA
Found at i:127102 original size:17 final size:17
Alignment explanation
Indices: 127080--127114 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
127070 AATTGCGGTA
127080 AAGACTAGAAAATGTTT
1 AAGACTAGAAAATGTTT
127097 AAGACTAGAAAATGTTT
1 AAGACTAGAAAATGTTT
127114 A
1 A
127115 TGTTTAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.29
Consensus pattern (17 bp):
AAGACTAGAAAATGTTT
Found at i:128758 original size:23 final size:24
Alignment explanation
Indices: 128725--128894 Score: 156
Period size: 23 Copynumber: 7.4 Consensus size: 24
128715 GAAGTACTTA
*
128725 ACAGTAAGCACACACAGTGC-AAT
1 ACAGTAAGCACACAAAGTGCGAAT
* * *
128748 CCAGTAGGCACACACAGTGC-AAT
1 ACAGTAAGCACACAAAGTGCGAAT
* * * * * *
128771 CCAGTAGGCGCACATAGCGCAAAT
1 ACAGTAAGCACACAAAGTGCGAAT
* * *
128795 -TAGTAGGCACACAAGGTGCGAA-
1 ACAGTAAGCACACAAAGTGCGAAT
128817 ACAGTAAGCACACAAAGTGCGAA-
1 ACAGTAAGCACACAAAGTGCGAAT
128840 ACAGTAAGCACACAAAGTGCGAA-
1 ACAGTAAGCACACAAAGTGCGAAT
* *
128863 ACAGTAAGCACACGAAGTGTGAA-
1 ACAGTAAGCACACAAAGTGCGAAT
128886 ACAGTAAGC
1 ACAGTAAGC
128895 GCGTTAGCGT
Statistics
Matches: 129, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
23 126 0.98
24 3 0.02
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.12
Consensus pattern (24 bp):
ACAGTAAGCACACAAAGTGCGAAT
Found at i:131640 original size:2 final size:2
Alignment explanation
Indices: 131633--131657 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
131623 GAAGTAAATT
131633 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
131658 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:131663 original size:2 final size:2
Alignment explanation
Indices: 131658--131682 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
131648 ACACACACAC
131658 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 T
131683 GGTTGTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:131897 original size:17 final size:17
Alignment explanation
Indices: 131862--131903 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
131852 CTCCCTTGAC
*
131862 CTTTAACCTTCCATCTT
1 CTTTAACCTTCCATATT
131879 CTTTAACCATT-CATATT
1 CTTTAACC-TTCCATATT
131896 CTTGTAAC
1 CTT-TAAC
131904 TACTTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.24, C:0.29, G:0.02, T:0.45
Consensus pattern (17 bp):
CTTTAACCTTCCATATT
Found at i:135285 original size:22 final size:22
Alignment explanation
Indices: 135259--135319 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
135249 GAGGATCGAG
* *
135259 ATTAAATTATAATTTTTATAAT
1 ATTAAATTATAATTTTTAAAAA
*
135281 ATTAAAAATATAATTTTTAAAAA
1 ATT-AAATTATAATTTTTAAAAA
135304 ATTAAATTGA-AATTTT
1 ATTAAATT-ATAATTTT
135320 ATCATTTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTAAATTATAATTTTTAAAAA
Found at i:137304 original size:17 final size:18
Alignment explanation
Indices: 137279--137315 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
137269 ATTTTTAAAA
137279 ATTATAAAT-ATATAAATT
1 ATTATAAATGATA-AAATT
137297 ATTA-AAATGATAAAATT
1 ATTATAAATGATAAAATT
137314 AT
1 AT
137316 ATTTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTATAAATGATAAAATT
Found at i:137312 original size:25 final size:26
Alignment explanation
Indices: 137257--137317 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 26
137247 TAAATAATAG
* * *
137257 AAATTAATTTAAATTTTTAAAAATTAT
1 AAATT-ATATAAATTATTAAAAATGAT
137284 AAA-TATATAAATTATT-AAAATGAT
1 AAATTATATAAATTATTAAAAATGAT
137308 AAAATTATAT
1 -AAATTATAT
137318 TTTTATTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 7 0.24
25 13 0.45
26 6 0.21
27 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
AAATTATATAAATTATTAAAAATGAT
Found at i:143586 original size:2 final size:2
Alignment explanation
Indices: 143579--143607 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
143569 TAATTTACAT
143579 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 T
143608 TAAATGAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:144741 original size:2 final size:2
Alignment explanation
Indices: 144734--144761 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
144724 TGAAATTATG
144734 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
144762 GAAAAGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:151359 original size:6 final size:6
Alignment explanation
Indices: 151348--151372 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
151338 TACAGTATTA
151348 ACCCAT ACCCAT ACCCAT ACCCAT A
1 ACCCAT ACCCAT ACCCAT ACCCAT A
151373 GGGCTCATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (6 bp):
ACCCAT
Found at i:164769 original size:8 final size:8
Alignment explanation
Indices: 164747--164793 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
164737 AACCTTCCTC
*
164747 TCTTTCTT
1 TCTTTTTT
164755 TCTTTTTTT
1 TC-TTTTTT
164764 TCTTTTTT
1 TCTTTTTT
164772 T-TCTTTTT
1 TCT-TTTTT
164780 T-TTTTTT
1 TCTTTTTT
164787 TCTTTTT
1 TCTTTTT
164794 ATTGTTGTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
7 7 0.20
8 21 0.60
9 7 0.20
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TCTTTTTT
Found at i:164777 original size:22 final size:23
Alignment explanation
Indices: 164749--164793 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
164739 CCTTCCTCTC
164749 TTTC-TTTCTTTTTTTTCTTTTT
1 TTTCTTTTCTTTTTTTTCTTTTT
*
164771 TTTCTTTTTTTTTTTTTCTTTTT
1 TTTCTTTTCTTTTTTTTCTTTTT
164794 ATTGTTGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (23 bp):
TTTCTTTTCTTTTTTTTCTTTTT
Found at i:164783 original size:14 final size:15
Alignment explanation
Indices: 164760--164793 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
164750 TTCTTTCTTT
164760 TTTTTCTTTTTTTTC
1 TTTTTCTTTTTTTTC
164775 TTTTT-TTTTTTTTC
1 TTTTTCTTTTTTTTC
164789 TTTTT
1 TTTTT
164794 ATTGTTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (15 bp):
TTTTTCTTTTTTTTC
Found at i:164793 original size:9 final size:9
Alignment explanation
Indices: 164753--164787 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
164743 CCTCTCTTTC
164753 TTTCTTTTT
1 TTTCTTTTT
164762 TTTCTTTTT
1 TTTCTTTTT
164771 TTTCTTTTT
1 TTTCTTTTT
164780 TTT-TTTTT
1 TTTCTTTTT
164788 CTTTTTATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.19
9 21 0.81
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:172903 original size:18 final size:19
Alignment explanation
Indices: 172876--172914 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
172866 GTGGACTTTG
*
172876 ATTTGCTGAACTTTCA-GC
1 ATTTGCTGAAATTTCATGC
*
172894 ATTTGTTGAAATTTCATGC
1 ATTTGCTGAAATTTCATGC
172913 AT
1 AT
172915 GGAATTGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (19 bp):
ATTTGCTGAAATTTCATGC
Found at i:177240 original size:25 final size:28
Alignment explanation
Indices: 177212--177273 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 28
177202 ATTTTTTTTA
**
177212 TTTAATATATAATTA-GTTTTA-ATTT-
1 TTTAATATATAAAAATGTTTTATATTTC
177237 TTT-ATCATATAAAAATGTTTTATATTTC
1 TTTAAT-ATATAAAAATGTTTTATATTTC
177265 TTTAATATA
1 TTTAATATA
177274 AATATTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
24 2 0.07
25 10 0.33
26 6 0.20
27 4 0.13
28 6 0.20
29 2 0.07
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56
Consensus pattern (28 bp):
TTTAATATATAAAAATGTTTTATATTTC
Found at i:177272 original size:26 final size:24
Alignment explanation
Indices: 177212--177287 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 24
177202 ATTTTTTTTA
*
177212 TTTAATATATAATTAGTTTTA-ATTT
1 TTTAATATA-AAAT-GTTTTATATTT
177237 TTTATCATATAAAAATGTTTTATATTT
1 TTTA--ATAT-AAAATGTTTTATATTT
*
177264 CTTTAATAT-AAATATTTTATATTT
1 -TTTAATATAAAATGTTTTATATTT
177288 AAAATATTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
24 14 0.32
25 4 0.09
26 10 0.23
27 11 0.25
28 5 0.11
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (24 bp):
TTTAATATAAAATGTTTTATATTT
Found at i:177327 original size:18 final size:18
Alignment explanation
Indices: 177282--177356 Score: 55
Period size: 17 Copynumber: 4.1 Consensus size: 18
177272 TAAATATTTT
*
177282 ATATTTA-AAATATTAAAA
1 ATATTTATAAA-AGTAAAA
*
177300 ATAATT-TAAAAGTAAAA
1 ATATTTATAAAAGTAAAA
177317 ATATTTATAAAAAGTCAAATA
1 ATATTTAT-AAAAGT-AAA-A
* * *
177338 ATATTCAAAAAATTAAAA
1 ATATTTATAAAAGTAAAA
177356 A
1 A
177357 ATCAAAACGA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
17 11 0.24
18 11 0.24
19 9 0.20
20 8 0.17
21 7 0.15
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
ATATTTATAAAAGTAAAA
Found at i:177329 original size:19 final size:18
Alignment explanation
Indices: 177282--177356 Score: 64
Period size: 19 Copynumber: 4.1 Consensus size: 18
177272 TAAATATTTT
* *
177282 ATATTTAAAATATTAAAA
1 ATATTTAAAAAAGTAAAA
177300 ATAATTT--AAAAGTAAAA
1 AT-ATTTAAAAAAGTAAAA
177317 ATATTTATAAAAAGTCAAATA
1 ATATTTA-AAAAAGT-AAA-A
* *
177338 ATATTCAAAAAATTAAAA
1 ATATTTAAAAAAGTAAAA
177356 A
1 A
177357 ATCAAAACGA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
16 4 0.09
17 10 0.21
18 4 0.09
19 13 0.28
20 9 0.19
21 7 0.15
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
ATATTTAAAAAAGTAAAA
Found at i:177349 original size:21 final size:19
Alignment explanation
Indices: 177307--177349 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
177297 AAAATAATTT
* *
177307 AAAAGTAAAAATATTTATA
1 AAAAGTAAAAATATTCAAA
177326 AAAAGTCAAATAATATTCAAA
1 AAAAGT-AAA-AATATTCAAA
177347 AAA
1 AAA
177350 TTAAAAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 3 0.15
21 11 0.55
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
AAAAGTAAAAATATTCAAA
Found at i:187588 original size:22 final size:25
Alignment explanation
Indices: 187563--187608 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
187553 CAATAGTAAA
187563 AATATA-AT-TTTATAA-TTTTAAT
1 AATATATATCTTTATAACTTTTAAT
*
187585 AATATATGTCTTTATAACTTTTAA
1 AATATATATCTTTATAACTTTTAA
187609 AAGATTAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 1 0.05
24 7 0.35
25 6 0.30
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (25 bp):
AATATATATCTTTATAACTTTTAAT
Found at i:199991 original size:22 final size:22
Alignment explanation
Indices: 199956--199997 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
199946 TTTTGATATA
* *
199956 AATAAAATATAAATCAAAAGTT
1 AATAAAAAACAAATCAAAAGTT
*
199978 AATAAAAAACAAATGAAAAG
1 AATAAAAAACAAATCAAAAG
199998 AGCAATTACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.69, C:0.05, G:0.07, T:0.19
Consensus pattern (22 bp):
AATAAAAAACAAATCAAAAGTT
Found at i:202809 original size:47 final size:46
Alignment explanation
Indices: 202696--202829 Score: 151
Period size: 47 Copynumber: 2.9 Consensus size: 46
202686 GTTGTAGACA
* * *
202696 GTAGTTTGGAAAATATTCATCTGAAATCTTTTAGTTCTGTTACACT
1 GTAGTTTGGAAAATGTTCATCTGAAATCTTATAGTACTGTTACACT
* * * * **
202742 ATAGTTTGGAAAATGCTCATCTGAAATCTTATGGTACTTTTTATGCT
1 GTAGTTTGGAAAATGTTCATCTGAAATCTTATAGTAC-TGTTACACT
* * *
202789 GTAGTTTGGGAAATGTTCATCTCAAATCTTATAGTATTGTT
1 GTAGTTTGGAAAATGTTCATCTGAAATCTTATAGTACTGTT
202830 TAGATCTAAT
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
46 34 0.48
47 37 0.52
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (46 bp):
GTAGTTTGGAAAATGTTCATCTGAAATCTTATAGTACTGTTACACT
Found at i:206034 original size:23 final size:22
Alignment explanation
Indices: 205999--206086 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 22
205989 CACTACGTAA
*
205999 TCACACTTAATCATATGAATATT
1 TCACA-TTTATCATATGAATATT
* *
206022 TCATCATTTATCATATCACGTATT
1 TCA-CATTTATCATATGA-ATATT
*
206046 AATCACATTTAGTCACATGAATATT
1 --TCACATTTA-TCATATGAATATT
206071 TCAGCATTTATCATAT
1 TCA-CATTTATCATAT
206087 ATACATTAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
23 21 0.40
24 12 0.23
25 10 0.19
26 9 0.17
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (22 bp):
TCACATTTATCATATGAATATT
Found at i:206066 original size:49 final size:48
Alignment explanation
Indices: 205996--206108 Score: 156
Period size: 49 Copynumber: 2.3 Consensus size: 48
205986 AACCACTACG
* * * *
205996 TAATCACACTTAATCATATGAATATTTCATCATTTATCATAT-CACGTAT
1 TAATCACATTTAGTCACATGAATATTTCAGCATTTATCATATACAC--AT
*
206045 TAATCACATTTAGTCACATGAATATTTCAGCATTTATCATATATACAT
1 TAATCACATTTAGTCACATGAATATTTCAGCATTTATCATATACACAT
206093 TAATCACATTTAGTCA
1 TAATCACATTTAGTCA
206109 AATTACGTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
48 18 0.31
49 38 0.66
50 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (48 bp):
TAATCACATTTAGTCACATGAATATTTCAGCATTTATCATATACACAT
Found at i:206070 original size:25 final size:25
Alignment explanation
Indices: 206042--206108 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 25
206032 TCATATCACG
206042 TATTAATCACATTTAGTCACATGA-A
1 TATTAATCACATTTAGTCACAT-ATA
*
206067 TATT--TCAGCATTTA-TCATATATA
1 TATTAATCA-CATTTAGTCACATATA
*
206090 CATTAATCACATTTAGTCA
1 TATTAATCACATTTAGTCA
206109 AATTACGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
22 1 0.03
23 12 0.34
24 12 0.34
25 10 0.29
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.40
Consensus pattern (25 bp):
TATTAATCACATTTAGTCACATATA
Found at i:217172 original size:25 final size:26
Alignment explanation
Indices: 217139--217199 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
217129 TATAAATGAC
*
217139 ATAAA-TATAAAATTT-CAAAAATGT
1 ATAAATTATAAAATTTACAAAAATAT
* *
217163 ATAAATTATAGAATTTATAAAAATAT
1 ATAAATTATAAAATTTACAAAAATAT
217189 -TAAATTA-AAAA
1 ATAAATTATAAAA
217200 GATTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 8 0.26
25 16 0.52
26 7 0.23
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (26 bp):
ATAAATTATAAAATTTACAAAAATAT
Found at i:222243 original size:25 final size:25
Alignment explanation
Indices: 222188--222243 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
222178 TATTTATGAA
* ** *
222188 TATATTTTAAAAAATATTATTTATT
1 TATATTTTAAAAAATATCATAAACT
* *
222213 TGTATTTTAAATAATATCATAAACT
1 TATATTTTAAAAAATATCATAAACT
222238 TATATT
1 TATATT
222244 AATTATTAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (25 bp):
TATATTTTAAAAAATATCATAAACT
Found at i:222862 original size:12 final size:12
Alignment explanation
Indices: 222842--222875 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
222832 ATAACTTTAA
*
222842 AGAGGTAGAGAC
1 AGAGATAGAGAC
222854 AGAGATAGAGAC
1 AGAGATAGAGAC
*
222866 AGAGAGAGAG
1 AGAGATAGAG
222876 GAGGAGGGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.06, G:0.41, T:0.06
Consensus pattern (12 bp):
AGAGATAGAGAC
Found at i:239833 original size:2 final size:2
Alignment explanation
Indices: 239826--239851 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
239816 TTTAATTGTA
239826 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
239852 GTGTGTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:240003 original size:24 final size:25
Alignment explanation
Indices: 239976--240022 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
239966 TAATTATAGG
*
239976 TTAACCCATTATA-TTTTATTTTAA
1 TTAACCAATTATATTTTTATTTTAA
*
240000 TTAACCAATTTTATTTTTATTTT
1 TTAACCAATTATATTTTTATTTT
240023 TATAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.60
Consensus pattern (25 bp):
TTAACCAATTATATTTTTATTTTAA
Found at i:244670 original size:65 final size:65
Alignment explanation
Indices: 244566--244694 Score: 249
Period size: 65 Copynumber: 2.0 Consensus size: 65
244556 TATAAATCTT
*
244566 GAGATCGAATTCAGATACCAATGATTGACGAATAAATATAATCTCATAAGCTAAAAGACTTGCGC
1 GAGATCGAATTCAGATACCAATGATCGACGAATAAATATAATCTCATAAGCTAAAAGACTTGCGC
244631 GAGATCGAATTCAGATACCAATGATCGACGAATAAATATAATCTCATAAGCTAAAAGACTTGCG
1 GAGATCGAATTCAGATACCAATGATCGACGAATAAATATAATCTCATAAGCTAAAAGACTTGCG
244695 TATATAAAGA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (65 bp):
GAGATCGAATTCAGATACCAATGATCGACGAATAAATATAATCTCATAAGCTAAAAGACTTGCGC
Found at i:248406 original size:31 final size:31
Alignment explanation
Indices: 248341--248431 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 31
248331 TTTTTAAATC
* **
248341 TGAATAATAAAAGAATTAAATTTTTAA-A-A
1 TGAAAAATAAAAGAATTAAATTTCAAATATA
248370 T-AAAAATAAAA-AGATTAAATTTCAAATATA
1 TGAAAAATAAAAGA-ATTAAATTTCAAATATA
*
248400 TGAAAAATAAAGGAATTAAATTTCAAATATA
1 TGAAAAATAAAAGAATTAAATTTCAAATATA
248431 T
1 T
248432 TTTAACCATT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.02
28 20 0.38
29 2 0.04
30 2 0.04
31 27 0.51
32 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (31 bp):
TGAAAAATAAAAGAATTAAATTTCAAATATA
Found at i:249323 original size:9 final size:8
Alignment explanation
Indices: 249298--249350 Score: 54
Period size: 9 Copynumber: 6.2 Consensus size: 8
249288 TTTTGCTTGT
249298 GAAGAAAA
1 GAAGAAAA
249306 GGAAGGAAAA
1 -GAA-GAAAA
249316 GATAGAAAA
1 GA-AGAAAA
*
249325 GAAGAAAG
1 GAAGAAAA
249333 GAA-AAAA
1 GAAGAAAA
249340 GAAGGAAAA
1 GAA-GAAAA
249349 GA
1 GA
249351 GTAGCAGTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 6 0.16
8 8 0.21
9 18 0.47
10 6 0.16
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (8 bp):
GAAGAAAA
Found at i:249339 original size:24 final size:26
Alignment explanation
Indices: 249298--249350 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 26
249288 TTTTGCTTGT
249298 GAAGAAAAGGAAGGAAAAGATA-GAAAA
1 GAAGAAAAGGAA-GAAAAGA-AGGAAAA
249325 GAAG-AAAGGAA-AAAAGAAGGAAAA
1 GAAGAAAAGGAAGAAAAGAAGGAAAA
249349 GA
1 GA
249351 GTAGCAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 1 0.04
24 13 0.52
26 7 0.28
27 4 0.16
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (26 bp):
GAAGAAAAGGAAGAAAAGAAGGAAAA
Found at i:264059 original size:6 final size:6
Alignment explanation
Indices: 264048--264078 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
264038 AGTAATTTAG
264048 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA G
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA G
264079 ATGTCAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:272926 original size:14 final size:14
Alignment explanation
Indices: 272904--272953 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
272894 ACGAGAGAAA
*
272904 TTTCATTTACTTT-T
1 TTTCTTTTA-TTTCT
272918 TTTCTTTTATTTCT
1 TTTCTTTTATTTCT
272932 CTTT-TTTTATTTCT
1 -TTTCTTTTATTTCT
272946 TTTCTTTT
1 TTTCTTTT
272954 CTTCTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 6 0.19
14 23 0.72
15 3 0.09
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTCTTTTATTTCT
Found at i:272970 original size:8 final size:8
Alignment explanation
Indices: 272913--272970 Score: 62
Period size: 8 Copynumber: 6.8 Consensus size: 8
272903 ATTTCATTTA
272913 CTTTTTTT
1 CTTTTTTT
272921 CTTTTATTTCT
1 C-TTT-TTT-T
272932 CTTTTTTT
1 CTTTTTTT
*
272940 ATTTCTTTT
1 CTTT-TTTT
*
272949 CTTTTCTT
1 CTTTTTTT
272957 CTTTTTTT
1 CTTTTTTT
272965 CTTTTT
1 CTTTTT
272971 GACAAGGCGG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 21 0.50
9 13 0.31
10 6 0.14
11 2 0.05
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (8 bp):
CTTTTTTT
Found at i:273037 original size:5 final size:5
Alignment explanation
Indices: 273027--273055 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
273017 TTGACAAGGC
273027 GGAGG GGAGG GGAGG GGAGG GGAGG GGAG
1 GGAGG GGAGG GGAGG GGAGG GGAGG GGAG
273056 AAGGGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.79, T:0.00
Consensus pattern (5 bp):
GGAGG
Found at i:273079 original size:11 final size:11
Alignment explanation
Indices: 273063--273088 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
273053 GAGAAGGGAG
273063 AGAAAAATAAA
1 AGAAAAATAAA
273074 AGAAAAATAAA
1 AGAAAAATAAA
273085 AGAA
1 AGAA
273089 CCCTACCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.08
Consensus pattern (11 bp):
AGAAAAATAAA
Found at i:273891 original size:23 final size:23
Alignment explanation
Indices: 273834--273901 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 23
273824 AATAAATCGA
*
273834 AATTAAATTATAATTTTTATAAT
1 AATTAAATTATATTTTTTATAAT
*
273857 AA-TAATAATATATTTTTT-TAAAT
1 AATTAA-ATTATATTTTTTAT-AAT
273880 AATTAAATTATAATTTTATTAT
1 AATTAAATTAT-ATTTT-TTAT
273902 TTTTAAGAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
22 4 0.11
23 21 0.58
24 8 0.22
25 2 0.06
26 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATTAAATTATATTTTTTATAAT
Found at i:273905 original size:31 final size:31
Alignment explanation
Indices: 273865--273938 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
273855 ATAATAATAA
* *
273865 TATATTTTTTTAA-ATAATTAAATTATAATTT
1 TATA-TTTTTTAAGAGAATTAAAATATAATTT
273896 TAT-TATTTTTAAGAGAATTAAAATATAATTT
1 TATAT-TTTTTAAGAGAATTAAAATATAATTT
*
273927 TATATTTATTAA
1 TATATTTTTTAA
273939 TTTAAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 1 0.03
30 7 0.19
31 28 0.76
32 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (31 bp):
TATATTTTTTAAGAGAATTAAAATATAATTT
Found at i:274729 original size:17 final size:18
Alignment explanation
Indices: 274703--274737 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
274693 TAATTAGATG
274703 AAAATATAATTAT-TAAA
1 AAAATATAATTATGTAAA
*
274720 AAAATTTAATTATGTAAA
1 AAAATATAATTATGTAAA
274738 TGTATTTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
AAAATATAATTATGTAAA
Found at i:277781 original size:37 final size:40
Alignment explanation
Indices: 277731--277817 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 40
277721 AAAAATTATA
277731 TTTAATATAATAAAATATTTATTATATTT-ATTT-GT-AT
1 TTTAATATAATAAAATATTTATTATATTTAATTTAGTGAT
*
277768 TTTAATATGATAAAATATTTATTATATTTAATTTAGTGAT
1 TTTAATATAATAAAATATTTATTATATTTAATTTAGTGAT
277808 TTTAATATAA
1 TTTAATATAA
277818 ATACTCTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
37 28 0.62
38 4 0.09
39 2 0.04
40 11 0.24
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (40 bp):
TTTAATATAATAAAATATTTATTATATTTAATTTAGTGAT
Found at i:278623 original size:17 final size:16
Alignment explanation
Indices: 278603--278636 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
278593 TATTTTGTAT
278603 ATAAAAATACTTTTAAA
1 ATAAAAATA-TTTTAAA
*
278620 ATAATAATATTTTAAA
1 ATAAAAATATTTTAAA
278636 A
1 A
278637 AAATGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAAAATATTTTAAA
Found at i:278637 original size:17 final size:16
Alignment explanation
Indices: 278589--278636 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
278579 TATGTATATT
* *
278589 ATAATATTTTGTATATA
1 ATAATATTTT-AAAATA
*
278606 AAAATACTTTTAAAATA
1 ATAATA-TTTTAAAATA
278623 ATAATATTTTAAAA
1 ATAATATTTTAAAA
278637 AAATGAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 8 0.31
17 14 0.54
18 4 0.15
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
ATAATATTTTAAAATA
Found at i:281125 original size:32 final size:32
Alignment explanation
Indices: 281076--281173 Score: 169
Period size: 32 Copynumber: 3.1 Consensus size: 32
281066 ATGACAACAA
*
281076 AAGCTTCTATTAGTCCTAATGTAAATGAAGGT
1 AAGCTTCTATTAATCCTAATGTAAATGAAGGT
* *
281108 AAGCTTCTAGTAATCCTAATGTAAGTGAAGGT
1 AAGCTTCTATTAATCCTAATGTAAATGAAGGT
281140 AAGCTTCTATTAATCCTAATGTAAATGAAGGT
1 AAGCTTCTATTAATCCTAATGTAAATGAAGGT
281172 AA
1 AA
281174 CTATGGCTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (32 bp):
AAGCTTCTATTAATCCTAATGTAAATGAAGGT
Found at i:284884 original size:45 final size:45
Alignment explanation
Indices: 284835--284924 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
284825 ACGTTACATA
284835 TAAGCTAATTTTGGATGCCATATATTTACATAAACATGAAAATTT
1 TAAGCTAATTTTGGATGCCATATATTTACATAAACATGAAAATTT
284880 TAAGCTAATTTTGGATGCCATATATTTACATAAACATGAAAATTT
1 TAAGCTAATTTTGGATGCCATATATTTACATAAACATGAAAATTT
284925 AATGTTATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (45 bp):
TAAGCTAATTTTGGATGCCATATATTTACATAAACATGAAAATTT
Done.