Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold326
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: 1352760
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 7 of 8
Found at i:1081186 original size:20 final size:19
Alignment explanation
Indices: 1081161--1081214 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
1081151 CTACCACTGT
1081161 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGAG-A-A
1081181 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGA-GAA
1081201 TTGTATCGATACAT
1 TTGTATCGATACAT
1081215 TGCTTCAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:1082715 original size:82 final size:83
Alignment explanation
Indices: 1082623--1082788 Score: 316
Period size: 83 Copynumber: 2.0 Consensus size: 83
1082613 ACTCTATATT
*
1082623 ATTTTTTTCCTATCATTTTCAA-TAAAGCAAGTCTCTTATACTTAGTTTACTGTAGAAAACTAAG
1 ATTTTTTTCCTATCATTTTCAATTAAAACAAGTCTCTTATACTTAGTTTACTGTAGAAAACTAAG
1082687 TATAAGAAAGATATTGTC
66 TATAAGAAAGATATTGTC
1082705 ATTTTTTTCCTATCATTTTCAATTAAAACAAGTCTCTTATACTTAGTTTACTGTAGAAAACTAAG
1 ATTTTTTTCCTATCATTTTCAATTAAAACAAGTCTCTTATACTTAGTTTACTGTAGAAAACTAAG
1082770 TATAAGAAAGATATTGTC
66 TATAAGAAAGATATTGTC
1082788 A
1 A
1082789 CTCATTAAGG
Statistics
Matches: 82, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 22 0.27
83 60 0.73
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.40
Consensus pattern (83 bp):
ATTTTTTTCCTATCATTTTCAATTAAAACAAGTCTCTTATACTTAGTTTACTGTAGAAAACTAAG
TATAAGAAAGATATTGTC
Found at i:1086627 original size:20 final size:20
Alignment explanation
Indices: 1086602--1086655 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
1086592 CTACCACTGT
*
1086602 TTGTATCGATACATGACA-CA
1 TTGTATCGATACATGA-AGAA
1086622 TTGTATCGATACATGAAGAA
1 TTGTATCGATACATGAAGAA
1086642 TTGTATCGATACAT
1 TTGTATCGATACAT
1086656 TGTCCCAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATGAAGAA
Found at i:1088266 original size:15 final size:15
Alignment explanation
Indices: 1088246--1088278 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1088236 AACCATCAAA
1088246 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
1088261 GATGATGATGATAAT
1 GATGATGAAGATAAT
1088276 GAT
1 GAT
1088279 AATGTTGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:1096856 original size:15 final size:15
Alignment explanation
Indices: 1096836--1096880 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1096826 ATTCCGCCAA
1096836 ATCCACCACAAAATC
1 ATCCACCACAAAATC
** *
1096851 ATCCACCACCTAATT
1 ATCCACCACAAAATC
*
1096866 ACCCACCACAAAATC
1 ATCCACCACAAAATC
1096881 GTTAATACAC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (15 bp):
ATCCACCACAAAATC
Found at i:1104072 original size:26 final size:26
Alignment explanation
Indices: 1104004--1104076 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
1103994 CAAGAAATGG
* * *
1104004 TTGTCAAGAAATTATCGTCAAGAACT
1 TTGTCAAGAAATTTTCATCAAAAACT
* *
1104030 TT-TACCCAG-AATGTTCATCAAAAACT
1 TTGT--CAAGAAATTTTCATCAAAAACT
1104056 TTGTCAAGAAATTTTCATCAA
1 TTGTCAAGAAATTTTCATCAA
1104077 TACAATCCTT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
25 4 0.11
26 28 0.78
27 4 0.11
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (26 bp):
TTGTCAAGAAATTTTCATCAAAAACT
Found at i:1104139 original size:28 final size:28
Alignment explanation
Indices: 1104087--1105363 Score: 1355
Period size: 28 Copynumber: 45.5 Consensus size: 28
1104077 TACAATCCTT
* *
1104087 TTTCAAAAGCCCATAAGTCAATGGCATCC
1 TTTC-AAAGCCCACAAGTCAGTGGCATCC
* *
1104116 TTTCAAAGCCCACAACTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
1104144 TTTCAAAGCCCACAAGTCAATGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1104171 CTTCAAAGCCCACAAGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * * *
1104199 TTTCAAAGACCACAAGTTAATGGCCTCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
1104227 TTTCAAAGCCCACAAGTTAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1104254 TTTCAATGCCCATAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
**
1104281 TTTTCAAAGCCCTTAAGTCAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1104310 TTTCAAAGCCCACAAGTCAATGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1104338 TTTCAAAACCCACAAGTCAGTGCCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1104365 CTTCAAAGCCCATAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
1104392 TTTTCAAAGCCCACAAGTTAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
1104421 TTTTAAAGCCCATAAGTCAGTAGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* **
1104449 TTTCAAATCCCATGAG-CTAGTGGCA-CC
1 TTTCAAAGCCCACAAGTC-AGTGGCATCC
*
1104476 TTTTCAAAGCCCACGAGTCAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
1104505 TTTTAAAGCCCATAAGTCAGTAGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* ** *
1104533 TTTCAAATCCCATGAG-CTAGGGGCA-CC
1 TTTCAAAGCCCACAAGTC-AGTGGCATCC
*
1104560 TTTTCAAAGCCCACGAGTCAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
*
1104589 TTTCAAAAGCCCACGAGTCAGTGGCA-CTC
1 TTTC-AAAGCCCACAAGTCAGTGGCATC-C
* * *
1104618 TTTCAAAACCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1104646 TTTCAAAGCCCACGAGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
1104674 TTTTTCAAAGCCCACAAGTCAGTGACATCC
1 --TTTCAAAGCCCACAAGTCAGTGGCATCC
*
1104704 TTTTAAAGCCCACAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
1104731 CTTCAAAGCTCACAAGTTAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1104759 TTTCAAAGCCCATAAGTCAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
1104787 TTTCAAAGCCCACAAGTTAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1104814 CTTCAAAGCCCACAAGTCAGTGGCA-CAT
1 TTTCAAAGCCCACAAGTCAGTGGCATC-C
* *
1104842 TTTCAAAGCACACAAGTCAGTGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
1104870 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * ** *
1104898 TTTTAAATCCCATGAGTTAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1104925 TTTTCAAAGCCCACAAGTTAGTGGCATTC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
1104954 TTTCAAAGCCCATAAGTTAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
1104982 TTTCAAAGCCCACAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
1105009 ATTCAAAACCCACAAGTTAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1105037 TTTCAAAGCCCATAAGTCAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1105065 TTTCAAAGCCCATAAGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
1105093 TTTTAAATCCCACGAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* ** *
1105121 TTTCCAAAGCCTACAAGTTGGTGGCACCC
1 TTT-CAAAGCCCACAAGTCAGTGGCATCC
* * * *
1105150 TTTCAAAACTCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1105178 TTTCAAAGCCCACGAGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1105206 TTTTTAAAGCCCACAAGTCAGTGGCACCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
1105235 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1105263 TTTTTCAAAGCCTACAAGTTAGTGGCA-CC
1 --TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1105292 TTTTCAAAGCCCA-TAGTCAGTGGCATCT
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * * *
1105320 TTTTAAAGCCCACAAATCGGTGGGAACC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
1105348 TCTTCTAAAGCCCACA
1 T-TTC-AAAGCCCACA
1105364 CAAGCCGGTG
Statistics
Matches: 1058, Mismatches: 158, Indels: 63
0.83 0.12 0.05
Matches are distributed among these distances:
27 173 0.16
28 735 0.69
29 92 0.09
30 58 0.05
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:1104231 original size:83 final size:84
Alignment explanation
Indices: 1104087--1105363 Score: 1371
Period size: 83 Copynumber: 15.2 Consensus size: 84
1104077 TACAATCCTT
* * *
1104087 TTTCAAAAGCCCATAAGTCAATGGCATCCTTTCAAAGCCCACAACTTAGTGGCATCC-TTTCAAA
1 TTTC-AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCA-CCTTTTCAAA
*
1104151 GCCCACAAGTCAATGGCA-CC
64 GCCCACAAGTCAGTGGCATCC
* * * *
1104171 CTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGACCACAAGTTAATGGC-CTCTTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCAC-CTTTTCAAAG
*
1104235 CCCACAAGTTAGTGGCA-CC
65 CCCACAAGTCAGTGGCATCC
* * ** *
1104254 TTTCAATGCCCATAAGTCAGTGGCA-CCTTTTCAAAGCCCTTAAGTCAGTGGCATCC-TTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTTAGTGGCA-CCTTTTCAAA
* *
1104317 GCCCACAAGTCAATGGCATCT
64 GCCCACAAGTCAGTGGCATCC
* * * * *
1104338 TTTCAAAACCCACAAGTCAGTGCCA-CCCTTCAAAGCCCATAAGTCAGTGGCACCTTTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGC
*
1104402 CCACAAGTTAGTGGCATCC
66 CCACAAGTCAGTGGCATCC
* * * * ** *
1104421 TTTTAAAGCCCATAAGTCAGTAGCATCCTTTCAAATCCCATGAGCTAGTGGCACCTTTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGC
*
1104486 CCACGAGTCAGTGGCATCC
66 CCACAAGTCAGTGGCATCC
* * * * ** * *
1104505 TTTTAAAGCCCATAAGTCAGTAGCATCCTTTCAAATCCCATGAGCTAGGGGCACCTTTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGC
*
1104570 CCACGAGTCAGTGGCATCC
66 CCACAAGTCAGTGGCATCC
* * *
1104589 TTTCAAAAGCCCACGAGTCAGTGGCA-CTCTTTCAAAACCCACAAGTTAGTGGCACCCTTTCAAA
1 TTTC-AAAGCCCACAAGTCAGTGGCATC-CTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAA
* *
1104653 GCCCACGAGTTAGTGGCATCC
64 GCCCACAAGTCAGTGGCATCC
* * * *
1104674 TTTTTCAAAGCCCACAAGTCAGTGACATCCTTTTAAAGCCCACAAGTCAGTGGCACC-CTTCAAA
1 --TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAA
* * *
1104738 GCTCACAAGTTAGTGGCATCT
64 GCCCACAAGTCAGTGGCATCC
* * *
1104759 TTTCAAAGCCCATAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCACC-CTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGC
*
1104823 CCACAAGTCAGTGGCA-CAT
66 CCACAAGTCAGTGGCATC-C
* * * *
1104842 TTTCAAAGCACACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCATCCTTTT-AAAT
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCA-CCTTTTCAAAG
** *
1104906 CCCATGAGTTAGTGGCA-CC
65 CCCACAAGTCAGTGGCATCC
* * * *
1104925 TTTTCAAAGCCCACAAGTTAGTGGCATTCTTTCAAAGCCCATAAGTTAGTGGCATCTTTTCAAAG
1 -TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAG
1104990 CCCACAAGTCAGTGGCA-CC
65 CCCACAAGTCAGTGGCATCC
* * * * * * *
1105009 ATTCAAAACCCACAAGTTAGTGGCATCTTTTCAAAGCCCATAAGTCAGTGGCATCTTTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGC
* *
1105074 CCATAAGTTAGTGGCATCC
66 CCACAAGTCAGTGGCATCC
* * * * * * *
1105093 TTTTAAATCCCACGAGTCAGTGGCATCCTTTCCAAAGCCTACAAGTTGGTGGCACCCTTTCAAAA
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTT-CAAAGCCCACAAGTTAGTGGCACCTTTTCAAAG
* * *
1105158 CTCACAAGTTAGTGGCACCC
65 CCCACAAGTCAGTGGCATCC
* * * * *
1105178 TTTCAAAGCCCACGAGTTAGTGGCATCCTTTTTAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAG
1105243 CCCACAAGTCAGTGGCATCC
65 CCCACAAGTCAGTGGCATCC
* * * * * *
1105263 TTTTTCAAAGCCTACAAGTTAGTGGCA-CCTTTTCAAAGCCCA-TAGTCAGTGGCATCTTTTTAA
1 --TTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAA
* * * *
1105326 AGCCCACAAATCGGTGGGAACC
63 AGCCCACAAGTCAGTGGCATCC
1105348 TCTTCTAAAGCCCACA
1 T-TTC-AAAGCCCACA
1105364 CAAGCCGGTG
Statistics
Matches: 1031, Mismatches: 137, Indels: 49
0.85 0.11 0.04
Matches are distributed among these distances:
81 1 0.00
82 6 0.01
83 401 0.39
84 282 0.27
85 252 0.24
86 61 0.06
87 28 0.03
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (84 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGC
CCACAAGTCAGTGGCATCC
Found at i:1105373 original size:32 final size:32
Alignment explanation
Indices: 1105323--1105450 Score: 131
Period size: 31 Copynumber: 4.1 Consensus size: 32
1105313 GGCATCTTTT
*
1105323 TAAAGCCCACA-AA-TCGGTGGGAACCTCTTC
1 TAAAGCCCACACAAGTCGGTGGTAACCTCTTC
* *
1105353 TAAAGCCCACACAAGCCGGTGGTAACC-CTTT
1 TAAAGCCCACACAAGTCGGTGGTAACCTCTTC
* *
1105384 TAAAGCCCACACAAGTTGGTGGTAA-CTTTCTC
1 TAAAGCCCACACAAGTCGGTGGTAACCTCT-TC
* ** *
1105416 TAAAGCCCACACGAGTTAGTGGAAACC-CTTC
1 TAAAGCCCACACAAGTCGGTGGTAACCTCTTC
1105447 TAAA
1 TAAA
1105451 CCTAATGTCA
Statistics
Matches: 82, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
30 12 0.15
31 35 0.43
32 34 0.41
33 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (32 bp):
TAAAGCCCACACAAGTCGGTGGTAACCTCTTC
Found at i:1105443 original size:63 final size:61
Alignment explanation
Indices: 1105320--1105450 Score: 147
Period size: 63 Copynumber: 2.1 Consensus size: 61
1105310 AGTGGCATCT
* *
1105320 TTTTAAAGCCCACAAATCGGTGGGAACCTCTTCTAAAGCCCACACAAGCCGGTGGTAACCC
1 TTTTAAAGCCCACAAATCGGTGGGAACCTCTTCTAAAGCCCACACAAGCCAGTGGAAACCC
* * * * **
1105381 TTTTAAAGCCCACACAAGTTGGTGGTAA-CTTTCTCTAAAGCCCACACGAGTTAGTGGAAACCC
1 TTTTAAAGCCCACA-AA-TCGGTGGGAACCTCT-TCTAAAGCCCACACAAGCCAGTGGAAACCC
*
1105444 TTCTAAA
1 TTTTAAA
1105451 CCTAATGTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
61 14 0.24
62 5 0.09
63 39 0.67
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (61 bp):
TTTTAAAGCCCACAAATCGGTGGGAACCTCTTCTAAAGCCCACACAAGCCAGTGGAAACCC
Found at i:1106536 original size:31 final size:30
Alignment explanation
Indices: 1106473--1106548 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 30
1106463 TGAACAGTAC
*
1106473 ATGTATCGATACATTCTATTTTTTACCCAG
1 ATGTATCGATATATTCTATTTTTTACCCAG
* *
1106503 ATGTATCGATATATTCTATTTTTTTATCGAG
1 ATGTATCGATATATTCTA-TTTTTTACCCAG
1106534 ATGTATCGATATATT
1 ATGTATCGATATATT
1106549 TTTCAATGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 17 0.40
31 25 0.60
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (30 bp):
ATGTATCGATATATTCTATTTTTTACCCAG
Found at i:1107511 original size:12 final size:12
Alignment explanation
Indices: 1107494--1107518 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1107484 ATGTCCAGCA
1107494 TCTCATTAAATG
1 TCTCATTAAATG
1107506 TCTCATTAAATG
1 TCTCATTAAATG
1107518 T
1 T
1107519 TATTCATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TCTCATTAAATG
Found at i:1109263 original size:51 final size:51
Alignment explanation
Indices: 1109197--1109308 Score: 136
Period size: 51 Copynumber: 2.2 Consensus size: 51
1109187 AACGGGGTTA
* * * *
1109197 AAGTATTCCCAATTGTGAGAAATTGGTGTTTTG-GAACTAAAATCAGAGTTG
1 AAGTATCCCCAATTGTGAAAAATTGGT-ATTTGAGAAATAAAATCAGAGTTG
* * *
1109248 AAGTATCCCCGATTGTGAAAAATTGGTATTTGAGAAATAAAATCGGGGTTG
1 AAGTATCCCCAATTGTGAAAAATTGGTATTTGAGAAATAAAATCAGAGTTG
*
1109299 GAGTATCCCC
1 AAGTATCCCC
1109309 TCGGAAATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
50 4 0.08
51 48 0.92
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.30
Consensus pattern (51 bp):
AAGTATCCCCAATTGTGAAAAATTGGTATTTGAGAAATAAAATCAGAGTTG
Found at i:1109525 original size:52 final size:53
Alignment explanation
Indices: 1109465--1109596 Score: 162
Period size: 52 Copynumber: 2.5 Consensus size: 53
1109455 ATTGATAATA
* * *
1109465 TAGAAATAAAATCGGAGTTGGAGTATCCCCCGATTATG-GAAAATGGGTGTTT
1 TAGAAATAAAATCGGAGTTGGAGTATCCCCCGATTAAGAAAAAATGGATGTTT
** *
1109517 TAGAAATAAAATCGGAGTTAAAGTAT-CCCCGATTAAGAAAAAATTGATGTTT
1 TAGAAATAAAATCGGAGTTGGAGTATCCCCCGATTAAGAAAAAATGGATGTTT
* *
1109569 TGGAAATGAAATCGG-GATTGGAGTATCC
1 TAGAAATAAAATCGGAG-TTGGAGTATCC
1109597 TTGAGATGAA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
51 11 0.16
52 55 0.82
53 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (53 bp):
TAGAAATAAAATCGGAGTTGGAGTATCCCCCGATTAAGAAAAAATGGATGTTT
Found at i:1111954 original size:20 final size:19
Alignment explanation
Indices: 1111890--1112034 Score: 92
Period size: 20 Copynumber: 6.8 Consensus size: 19
1111880 AAAAATGCCT
* *
1111890 AAATGTATCGGTACATTGTA
1 AAATGTATCGATACAATG-A
*
1111910 AAATGTATCGATGCAATGA
1 AAATGTATCGATACAATGA
*
1111929 GCAATGTATCGATACAATGCA
1 -AAATGTATCGATACAATG-A
* *
1111950 AAATGTATTGATACATCTGGGTAAA
1 AAATGTATCGATACA-AT--G---A
1111975 CCCAGAATGTATCGATACAATGA
1 ---A-AATGTATCGATACAATGA
*
1111998 GCAATGTATCGATACAATGA
1 -AAATGTATCGATACAATGA
1112018 ACAATGTATCGATACAA
1 A-AATGTATCGATACAA
1112035 ATTATGAAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
19 1 0.01
20 77 0.78
21 2 0.02
23 2 0.02
25 1 0.01
26 1 0.01
28 2 0.02
29 13 0.13
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (19 bp):
AAATGTATCGATACAATGA
Found at i:1115402 original size:34 final size:36
Alignment explanation
Indices: 1115359--1115789 Score: 164
Period size: 35 Copynumber: 12.3 Consensus size: 36
1115349 GTCTTTGTTA
* * *
1115359 AAATATCCTTAAGAGAGG-TTTTAAAA-TTTGGTTG
1 AAATATCCTTAAGAAAGGCTTTAAAAATTTTGGATG
1115393 AAATATCCTTGAA-AAAGGCTTTAAAAATTTTTGGATG
1 AAATATCCTT-AAGAAAGGCTTTAAAAA-TTTTGGATG
* * ** *
1115430 AAATATCTTTAAGAAAGGCTCTGGAAGTCTTT-GAT-
1 AAATATCCTTAAGAAAGGCTTTAAAAAT-TTTGGATG
* * * *
1115465 AAATATCTTTGAGAGAAGG-TTTAGAGATTTT---TG
1 AAATATCCTTAAGA-AAGGCTTTAAAAATTTTGGATG
** * * **
1115498 AAATATCCTCTAA-AGTGGCTTTGAAAGTTTTTAATG
1 AAATATCCT-TAAGAAAGGCTTTAAAAATTTTGGATG
** * * *
1115534 AAATATCCACAAGAGAA-GCTTTGAAAGATTTT-GTTA
1 AAATATCCTTAAGA-AAGGCTTT-AAAAATTTTGGATG
** **
1115570 AAATATCCTTAAGAAAGGCTTTGGAGGTTTT-GATG
1 AAATATCCTTAAGAAAGGCTTTAAAAATTTTGGATG
* *
1115605 AAATATCCTCAA-AAGAGGCTTT-AAAATTTTGGTTG
1 AAATATCCTTAAGAA-AGGCTTTAAAAATTTTGGATG
* ** * * * *
1115640 AAAAATCCTCGAGAAAGGCTTCAAAGATTATGGATC
1 AAATATCCTTAAGAAAGGCTTTAAAAATTTTGGATG
* * * **
1115676 AAATGT-C-TAAAAATAAGCTTTAAAAA-TTTGTTTG
1 AAATATCCTTAAGAA-AGGCTTTAAAAATTTTGGATG
* ** * * * *
1115710 AAATATCATCGAGAGATGCTCTAAAGATTTTGGATG
1 AAATATCCTTAAGAAAGGCTTTAAAAATTTTGGATG
* * * * *
1115746 AAATATACTCAA-AGAGGCTTT-AAAATGTTGGATA
1 AAATATCCTTAAGAAAGGCTTTAAAAATTTTGGATG
1115780 AAATATCCTT
1 AAATATCCTT
1115790 TAGAGAGGTT
Statistics
Matches: 289, Mismatches: 83, Indels: 50
0.68 0.20 0.12
Matches are distributed among these distances:
32 3 0.01
33 17 0.06
34 56 0.19
35 102 0.35
36 76 0.26
37 35 0.12
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.34
Consensus pattern (36 bp):
AAATATCCTTAAGAAAGGCTTTAAAAATTTTGGATG
Found at i:1115519 original size:105 final size:105
Alignment explanation
Indices: 1115344--1115583 Score: 240
Period size: 105 Copynumber: 2.3 Consensus size: 105
1115334 AGAGATTTTG
*
1115344 TGGAAGTCTTTGTTAAAATATCCTTAAGAGAGGTTTTAAAATTTGGTTGAAATATCCTTGAAAAA
1 TGGAAGTCTTTGATAAAATATCCTTAAGAGAGGTTTTAAAATTT-GTTGAAATATCCTTGAAAAA
*
1115409 GGCTTTAAAAATTTTTGGATGAAATATCTTTAAGAAAGGCTC
65 GGCTTTAAAAATTTTT-AATGAAATATCTTTAAGAAAGGCTC
* * *
1115451 TGGAAGTCTTTGAT-AAATATCTTTGAGAGAAGG-TTTAGAGATTT-TTGAAATATCCTCT-AAA
1 TGGAAGTCTTTGATAAAATATCCTTAAGAG-AGGTTTTA-AAATTTGTTGAAATATCCT-TGAAA
** * * *** *
1115512 GTGGCTTTGAAAGTTTTTAATGAAATATCCACAAGAGAA-GCTT
63 AAGGCTTTAAAAATTTTTAATGAAATATCTTTAAGA-AAGGCTC
* *
1115555 TGAAAGAT-TTTGTTAAAATATCCTTAAGA
1 TGGAAG-TCTTTGATAAAATATCCTTAAGA
1115584 AAGGCTTTGG
Statistics
Matches: 110, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
104 27 0.25
105 44 0.40
106 18 0.16
107 21 0.19
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (105 bp):
TGGAAGTCTTTGATAAAATATCCTTAAGAGAGGTTTTAAAATTTGTTGAAATATCCTTGAAAAAG
GCTTTAAAAATTTTTAATGAAATATCTTTAAGAAAGGCTC
Found at i:1115609 original size:35 final size:35
Alignment explanation
Indices: 1115359--1115626 Score: 133
Period size: 36 Copynumber: 7.6 Consensus size: 35
1115349 GTCTTTGTTA
* ** * * *
1115359 AAATATCCTTAAGAGAGG-TTTTAAAATTTGGTTG
1 AAATATCCTTAAGAAAGGCTTTGGAGATTTTGATG
** *
1115393 AAATATCCTTGAA-AAAGGCTTTAAAAATTTTTGGATG
1 AAATATCCTT-AAGAAAGGCTTTGGAGA-TTTT-GATG
* *
1115430 AAATATCTTTAAGAAAGGCTCTGGA-AGTCTTTGAT-
1 AAATATCCTTAAGAAAGGCTTTGGAGA-T-TTTGATG
* * *
1115465 AAATATCTTTGAGAGAAGG-TTTAGAGATTTT--TG
1 AAATATCCTTAAGA-AAGGCTTTGGAGATTTTGATG
** * * *
1115498 AAATATCCTCTAA-AGTGGCTTTGAAAGTTTTTAATG
1 AAATATCCT-TAAGAAAGGCTTTG-GAGATTTTGATG
** * * *
1115534 AAATATCCACAAGAGAA-GCTTTGAAAGATTTTGTTA
1 AAATATCCTTAAGA-AAGGCTTTG-GAGATTTTGATG
*
1115570 AAATATCCTTAAGAAAGGCTTTGGAGGTTTTGATG
1 AAATATCCTTAAGAAAGGCTTTGGAGATTTTGATG
*
1115605 AAATATCCTCAA-AAGAGGCTTT
1 AAATATCCTTAAGAA-AGGCTTT
1115627 AAAATTTTGG
Statistics
Matches: 182, Mismatches: 34, Indels: 35
0.73 0.14 0.14
Matches are distributed among these distances:
32 3 0.02
33 12 0.07
34 27 0.15
35 57 0.31
36 59 0.32
37 24 0.13
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.35
Consensus pattern (35 bp):
AAATATCCTTAAGAAAGGCTTTGGAGATTTTGATG
Found at i:1115766 original size:70 final size:69
Alignment explanation
Indices: 1115597--1115770 Score: 181
Period size: 70 Copynumber: 2.5 Consensus size: 69
1115587 GCTTTGGAGG
* *
1115597 TTTT-GATGAAATATCCTCAAAAGAGGCTTTAAAATTTTGGTTGAAAAATCCTCGAGAAAGGCTT
1 TTTTGGATGAAATAT-CTC-AAAGAGGCTTTAAAAATTTGGTTGAAAAATCATCGAGAAAGGCTT
1115661 CAAAGA
64 CAAAGA
* * * * * * * * * *
1115667 TTATGGATCAAATGTCTAAAAATAAGCTTTAAAAATTTGTTTGAAATATCATCGAGAGATGC-TC
1 TTTTGGATGAAATATCT-CAAAGAGGCTTTAAAAATTTGGTTGAAAAATCATCGAGAAAGGCTTC
1115731 TAAAGA
65 -AAAGA
1115737 TTTTGGATGAAATATACTCAAAGAGGCTTTAAAA
1 TTTTGGATGAAATAT-CTCAAAGAGGCTTTAAAA
1115771 TGTTGGATAA
Statistics
Matches: 82, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
69 2 0.02
70 70 0.85
71 10 0.12
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (69 bp):
TTTTGGATGAAATATCTCAAAGAGGCTTTAAAAATTTGGTTGAAAAATCATCGAGAAAGGCTTCA
AAGA
Found at i:1116351 original size:16 final size:16
Alignment explanation
Indices: 1116332--1116376 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1116322 CCAATGTAGG
* *
1116332 TGAATATGAATGCACA
1 TGAATATAAATACACA
*
1116348 TGAATGTAAATACACA
1 TGAATATAAATACACA
*
1116364 TGAGTATAAATAC
1 TGAATATAAATAC
1116377 CTATGAGTGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (16 bp):
TGAATATAAATACACA
Found at i:1117820 original size:19 final size:18
Alignment explanation
Indices: 1117788--1117823 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1117778 TTAGAATGTC
*
1117788 TTTTTTTTTTGTTTTTTG
1 TTTTTTTTTGGTTTTTTG
1117806 TTTTCTTTTTGGTTTTTT
1 TTTT-TTTTTGGTTTTTT
1117824 TGGGTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.86
Consensus pattern (18 bp):
TTTTTTTTTGGTTTTTTG
Found at i:1117857 original size:24 final size:24
Alignment explanation
Indices: 1117830--1117876 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1117820 TTTTTGGGTT
*
1117830 TTTTTTGCATCT-GTGTTTTCTTTA
1 TTTTGTGCATCTAG-GTTTTCTTTA
*
1117854 TTTTGTGCTTCTAGGTTTTCTTT
1 TTTTGTGCATCTAGGTTTTCTTT
1117877 TTCATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.06, C:0.13, G:0.15, T:0.66
Consensus pattern (24 bp):
TTTTGTGCATCTAGGTTTTCTTTA
Found at i:1121138 original size:22 final size:23
Alignment explanation
Indices: 1121100--1121143 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1121090 CTTGAACATA
*
1121100 AAAATTGAATTTGTTAT-TGAAT
1 AAAATTGAAATTGTTATATGAAT
1121122 AAAATT-AAATTGATTATATGAA
1 AAAATTGAAATTG-TTATATGAA
1121144 AATTTATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 10 0.53
23 4 0.21
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (23 bp):
AAAATTGAAATTGTTATATGAAT
Found at i:1121222 original size:15 final size:14
Alignment explanation
Indices: 1121168--1121225 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
1121158 ATATAATTTT
*
1121168 TAATTTTTATAATT
1 TAATTTTTATAATA
*
1121182 TAATCCTTTA-AAT-
1 TAAT-TTTTATAATA
1121195 TAATTTTTATAATA
1 TAATTTTTATAATA
1121209 TAATTTTATATAATA
1 TAATTTT-TATAATA
1121224 TA
1 TA
1121226 TACAAATATC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
12 4 0.11
13 7 0.18
14 14 0.37
15 13 0.34
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TAATTTTTATAATA
Found at i:1122039 original size:21 final size:20
Alignment explanation
Indices: 1122015--1122058 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
1122005 TACTATGTGA
*
1122015 TTTTATGCATTTTTAAACATG
1 TTTTAGGCATTTTT-AACATG
1122036 TTTTAGGCATTTTTAACAT-
1 TTTTAGGCATTTTTAACATG
1122055 TTTT
1 TTTT
1122059 TCTTCTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.18
20 5 0.23
21 13 0.59
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.57
Consensus pattern (20 bp):
TTTTAGGCATTTTTAACATG
Found at i:1123939 original size:28 final size:29
Alignment explanation
Indices: 1123906--1123977 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 29
1123896 AATAAAATCA
1123906 GGGTTGGAGTATCCCCT-CAAAAATAACG
1 GGGTTGGAGTATCCCCTGCAAAAATAACG
*
1123934 GGGTTGGAGTAT-CCCTGCGAAAATAACG
1 GGGTTGGAGTATCCCCTGCAAAAATAACG
1123962 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
1123978 GATTGTGAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 4 0.10
28 34 0.83
29 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (29 bp):
GGGTTGGAGTATCCCCTGCAAAAATAACG
Found at i:1124026 original size:51 final size:51
Alignment explanation
Indices: 1123960--1124079 Score: 204
Period size: 51 Copynumber: 2.4 Consensus size: 51
1123950 GCGAAAATAA
*
1123960 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGGAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAAC
*
1124011 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAAC
* *
1124062 TGGGTTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
1124080 TCGGAAATAA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 65 1.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAAC
Found at i:1124058 original size:158 final size:158
Alignment explanation
Indices: 1123859--1124234 Score: 388
Period size: 158 Copynumber: 2.4 Consensus size: 158
1123849 ACGAAGGGGC
* ** * * *
1123859 TGGAGTA-CCCCTGATTATGGAAAATCGGTGTTCTAGAAATAAAATCAGGGTTGGAGTATCCCCT
1 TGGAGTATCCCC-GATTATAGAAAATCAATATTTTGGAAATAAAATCAGGGTTGGAGTATCCCCT
* * *
1123923 CAAAAATAACGGGGTTGGAGTATCCCTGCGA-AAATAACGGGGTTGGAGTATCCCCGATTGTGAG
65 CAAAAATAACGGGGTTGGAGTATCCC--CGATAAATAACGGGGTTAGAGTATCCCCGATTATGAA
* *
1123987 AAATCAATAT-TTT-AGGAATAAAACCGGGGT
128 AAATCAATATGTTTGA-AAATAAAACCGGAGT
* *
1124017 TGGAGTATCCCCGATTAT-GAGAAATCAATATTTTAGG-AAT-AAAGCTGGGTTTGGAGTATCCC
1 TGGAGTATCCCCGATTATAGA-AAATCAATATTTT-GGAAATAAAATCAGGG-TTGGAGTATCCC
** * * *
1124079 CTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTAGAGTATCTCCGATTATGAA
63 CTCAAAAATAACGGGGTTGGAGTATCCCCGATAAATAACGGGGTTAGAGTATCCCCGATTATGAA
*** * *
1124144 AAATTGGTGTGTTTGAAAATAAAATCGGAGT
128 AAATCAATATGTTTGAAAATAAAACCGGAGT
*** * *
1124175 TGGAGTATCCCCGATTATAGAAAATTGGTGTTTTGGAAATAAAATCAGAGTTGGAGTATC
1 TGGAGTATCCCCGATTATAGAAAATCAATATTTTGGAAATAAAATCAGGGTTGGAGTATC
1124235 TCCGATTATA
Statistics
Matches: 179, Mismatches: 29, Indels: 20
0.79 0.13 0.09
Matches are distributed among these distances:
156 3 0.02
157 44 0.25
158 118 0.66
159 14 0.08
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (158 bp):
TGGAGTATCCCCGATTATAGAAAATCAATATTTTGGAAATAAAATCAGGGTTGGAGTATCCCCTC
AAAAATAACGGGGTTGGAGTATCCCCGATAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAA
TCAATATGTTTGAAAATAAAACCGGAGT
Found at i:1124404 original size:153 final size:154
Alignment explanation
Indices: 1124117--1124401 Score: 407
Period size: 153 Copynumber: 1.9 Consensus size: 154
1124107 CGATGATTAA
* *
1124117 CGGGGTTAGAGTATCTCCGATTATGAAAAATTGGTGTGTTTGAAAATAAAATCGGAGTTGGAGTA
1 CGGGGTTAGAGTATCCCCGATTATGAAAAATTGGTGTGTTCGAAAATAAAATCGGAGTTGGAGTA
* * * *
1124182 TCCCCGATTATAGAAAATTGGTGTTTTGGAAATAAAATCAGAGTTGGAGTATCTCCGATTATAGA
66 TCCCCGATTATAGAAAATTAGTGTTTTAGAAATAAAACCAGAGTTGGAGTATCCCCGATTATAGA
1124247 AAATTGATGTTTTGAAAATAAAAT
131 AAATTGATGTTTTGAAAATAAAAT
* * * *
1124271 CGGGGTTGGAGTATCCCCGGTTGTGGAAAATTGGTGT-TTCGAAAATAAAATCGGAGTTGGAGTA
1 CGGGGTTAGAGTATCCCCGATTATGAAAAATTGGTGTGTTCGAAAATAAAATCGGAGTTGGAGTA
* * *
1124335 TCCCTGATTGTGGAAAATTAGTGTTTTAGAAATAAAACC-GAGATTGGAGTA-CCCCTGATTAT-
66 TCCCCGATTATAGAAAATTAGTGTTTTAGAAATAAAACCAGAG-TTGGAGTATCCCC-GATTATA
1124397 GAAAA
129 GAAAA
1124402 ATTAAGAAAC
Statistics
Matches: 116, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
152 11 0.09
153 73 0.63
154 32 0.28
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (154 bp):
CGGGGTTAGAGTATCCCCGATTATGAAAAATTGGTGTGTTCGAAAATAAAATCGGAGTTGGAGTA
TCCCCGATTATAGAAAATTAGTGTTTTAGAAATAAAACCAGAGTTGGAGTATCCCCGATTATAGA
AAATTGATGTTTTGAAAATAAAAT
Found at i:1124405 original size:51 final size:51
Alignment explanation
Indices: 1124125--1124404 Score: 336
Period size: 51 Copynumber: 5.5 Consensus size: 51
1124115 AACGGGGTTA
*
1124125 GAGTATCTCCGATTATGAAAAATTGGTGTGTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAAAATTGGTGT-TTTGAAAATAAAATCGGAGTTG
* *
1124177 GAGTATCCCCGATTAT-AGAAAATTGGTGTTTTGGAAATAAAATCAGAGTTG
1 GAGTATCCCCGATTATGA-AAAATTGGTGTTTTGAAAATAAAATCGGAGTTG
* * *
1124228 GAGTATCTCCGATTAT-AGAAAATTGATGTTTTGAAAATAAAATCGGGGTTG
1 GAGTATCCCCGATTATGA-AAAATTGGTGTTTTGAAAATAAAATCGGAGTTG
* * * *
1124279 GAGTATCCCCGGTTGTGGAAAATTGGTGTTTCGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAATCGGAGTTG
* * * * *
1124330 GAGTATCCCTGATTGTGGAAAATTAGTGTTTT-AGAAATAAAA-CCGAGATTG
1 GAGTATCCCCGATTATGAAAAATTGGTGTTTTGA-AAATAAAATCGGAG-TTG
1124381 GAGTA-CCCCTGATTATGAAAAATT
1 GAGTATCCCC-GATTATGAAAAATT
1124405 AAGAAACTTA
Statistics
Matches: 200, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
50 8 0.04
51 166 0.83
52 26 0.13
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (51 bp):
GAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAATCGGAGTTG
Found at i:1126812 original size:21 final size:21
Alignment explanation
Indices: 1126786--1126827 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1126776 GTATCGATAC
1126786 AATGTATCAATACACTTCCTT
1 AATGTATCAATACACTTCCTT
* *
1126807 AATGTATCGATACATTTCCTT
1 AATGTATCAATACACTTCCTT
1126828 GGCAGTAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.40
Consensus pattern (21 bp):
AATGTATCAATACACTTCCTT
Found at i:1126862 original size:13 final size:13
Alignment explanation
Indices: 1126844--1126927 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
1126834 AGCTTCGTAG
1126844 CGATACATTGTAT
1 CGATACATTGTAT
1126857 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1126876 CGATACATTGTAT
1 CGATACATTGTAT
1126889 CGATACAAAACTTATGTAT
1 CGATAC---A--T-TGTAT
1126908 CGATACATTGTAT
1 CGATACATTGTAT
1126921 CGATACA
1 CGATACA
1126928 ACACTTATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 28 0.47
14 1 0.02
15 2 0.03
16 4 0.07
17 2 0.03
18 1 0.02
19 21 0.36
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1126876 original size:19 final size:19
Alignment explanation
Indices: 1126852--1126969 Score: 98
Period size: 19 Copynumber: 6.7 Consensus size: 19
1126842 AGCGATACAT
1126852 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
1126871 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
1126884 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
1126903 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
1126916 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
** *
1126935 TGTATCGATACATTTACTATT
1 TGTATCGATACA-AAACT-TA
1126956 TGTATCGATACAAA
1 TGTATCGATACAAA
1126970 TTGTTTGAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 27
0.71 0.04 0.24
Matches are distributed among these distances:
13 22 0.28
14 2 0.03
16 4 0.05
18 2 0.03
19 34 0.43
20 3 0.04
21 13 0.16
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1126885 original size:32 final size:32
Alignment explanation
Indices: 1126844--1126948 Score: 201
Period size: 32 Copynumber: 3.3 Consensus size: 32
1126834 AGCTTCGTAG
1126844 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1126876 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
1126908 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1126940 CGATACATT
1 CGATACATT
1126949 TACTATTTGT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 72 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1127811 original size:42 final size:42
Alignment explanation
Indices: 1127724--1127818 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
1127714 CCCGTTTTTC
* * *
1127724 GAGGACAAAGGAAAAAGGGAAACGAAATACGTCCTGTTCTCT
1 GAGGACAAAAGAAAAAGGGAAAAGAAATACGTCCTGCTCTCT
* * * *
1127766 GAGGACAAAAGAAAAA-GGAAAATAAAGTGCGTCTTGCTCTTT
1 GAGGACAAAAGAAAAAGGGAAAAGAAA-TACGTCCTGCTCTCT
1127808 GAGGACTAAAA
1 GAGGAC-AAAA
1127819 AGTGCCACCA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 8 0.18
42 32 0.73
43 4 0.09
ACGTcount: A:0.43, C:0.14, G:0.25, T:0.18
Consensus pattern (42 bp):
GAGGACAAAAGAAAAAGGGAAAAGAAATACGTCCTGCTCTCT
Found at i:1128013 original size:55 final size:55
Alignment explanation
Indices: 1127802--1128381 Score: 619
Period size: 55 Copynumber: 10.3 Consensus size: 55
1127792 GTGCGTCTTG
* * ** * *
1127802 CTCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTGAAAAGGAAAGGTGTCCTG
1 CTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCT--TTA--AAAGGCGTCCTA
** * *
1127861 CTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTG
1 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT--AAA-AG---GCGTCCTA
* * *
1127922 CTCTTTGAGGACTGGAAAATGCCACCGACTTATGTGGGCTTCAAAAGGCGTCCTA
1 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTA
* * * *
1127977 CTCTTTGAAGACTGGAAAATGCCATCAACTTGTGTGGGCTTTAAAAGGTGTCCTG
1 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTA
* *
1128032 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTG
1 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTA
* * *
1128087 CTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTG
1 CTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTA
* * * *
1128142 CTCTTTGAGGACTGGAAAATGCCACTAACTTATGTGGGCTTTAAGAGACGTCCTA
1 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTA
* *
1128197 CTCTTTGAGGACTGGAAAATGCCACCAACCTGTGTGTGCTTTAAAAAGAAAAG-GTTTCCTA
1 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAAG----GCG--TCCTA
* * * * *
1128258 CTCTTTGAGGATTAGAAAATGCCACCAACTCGTATGGGCTTTAAAAGGAGTCCTA
1 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTA
* * * *
1128313 CTCTTTGAGGACT-GAAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGCATCCTA
1 CTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTA
1128368 CTCTTTGAGGACTG
1 CTCTTTGAGGACTG
1128382 AAGGGTGAAA
Statistics
Matches: 448, Mismatches: 54, Indels: 41
0.83 0.10 0.08
Matches are distributed among these distances:
54 8 0.02
55 295 0.66
56 9 0.02
57 3 0.01
58 4 0.01
59 38 0.08
60 7 0.02
61 84 0.19
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (55 bp):
CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTA
Found at i:1128102 original size:26 final size:26
Alignment explanation
Indices: 1128073--1128155 Score: 69
Period size: 26 Copynumber: 3.1 Consensus size: 26
1128063 GTGTGGGCTT
1128073 TGAAAGGCGTCCTGCTCTTTGAGGAC
1 TGAAAGGCGTCCTGCTCTTTGAGGAC
* ** * * *
1128099 TGAAAGGTG-CCACCAACTTGTGTGGGC
1 TGAAAGGCGTCCTGC-TCTT-TGAGGAC
1128126 TTTGAAAGGCGTCCTGCTCTTTGAGGAC
1 --TGAAAGGCGTCCTGCTCTTTGAGGAC
1128154 TG
1 TG
1128156 GAAAATGCCA
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
25 3 0.08
26 13 0.32
27 5 0.12
28 5 0.12
29 11 0.28
30 3 0.08
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (26 bp):
TGAAAGGCGTCCTGCTCTTTGAGGAC
Found at i:1128278 original size:226 final size:220
Alignment explanation
Indices: 1127802--1128381 Score: 775
Period size: 226 Copynumber: 2.6 Consensus size: 220
1127792 GTGCGTCTTG
** *
1127802 CTCTTTGAGGACTA-AAAAGTGCCACCAACTCGTGTGGGCTGAAAAGGAAAGGTGTCCTGCTCTT
1 CTCTTTGAGGACTAGAAAA-TGCCACCAACTCGTGTGGGCT----TTGAAAGGAGTCCTGCTCTT
*
1127866 TGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTCTTTGAG
61 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG--AA-AG---GCATCCTGCTCTTTGAG
* *
1127931 GACTGGAAAATGCCACCGACTTATGTGGGCTTCAAAAGGCGTCCTACTCTTTGAAGACTGGAAAA
120 GACTGGAAAATGCCACCAACTTATGTGGGCTTCAAAAGACGTCCTACTCTTTGAAGACTGGAAAA
* * *
1127996 TGCCATCAACTTGTGTGGGCTTTAAAAGGTGTCCTG
185 TGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTA
* * *
1128032 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGG
1 CTCTTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGAGTCCTGCTCTTTGAGG
*
1128097 ACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGGAAAAT
66 ACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTGGAAAAT
* * * *
1128162 GCCACTAACTTATGTGGGCTTTAAGAGACGTCCTACTCTTTGAGGACTGGAAAATGCCACCAACC
131 GCCACCAACTTATGTGGGCTTCAAAAGACGTCCTACTCTTTGAAGACTGGAAAATGCCACCAACC
* *
1128227 TGTGTGTGCTTTAAAAAGAAAAGGTTTCCTA
196 TGTGTGGGCTTT------AAAAGGTGTCCTA
* * * *
1128258 CTCTTTGAGGATTAGAAAATGCCACCAACTCGTATGGGCTTTAAAAGGAGTCCTACTCTTTGAGG
1 CTCTTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGAGTCCTGCTCTTTGAGG
* *
1128323 ACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGCATCCTACTCTTTGAGGACTG
66 ACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTG
1128382 AAGGGTGAAA
Statistics
Matches: 315, Mismatches: 28, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
220 95 0.30
223 2 0.01
224 2 0.01
226 179 0.57
230 33 0.10
231 4 0.01
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (220 bp):
CTCTTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGAGTCCTGCTCTTTGAGG
ACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTGGAAAAT
GCCACCAACTTATGTGGGCTTCAAAAGACGTCCTACTCTTTGAAGACTGGAAAATGCCACCAACC
TGTGTGGGCTTTAAAAGGTGTCCTA
Found at i:1141946 original size:28 final size:27
Alignment explanation
Indices: 1141915--1141987 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 27
1141905 AATAAAATCA
* * *
1141915 AGGTTGGAGTGTCCCCTCAAAAATAATG
1 AGGTTGGAGTATCCCCGCAAAAATAA-C
*
1141943 AGGTTGGAGTATCCCCGCGAAAATAAC
1 AGGTTGGAGTATCCCCGCAAAAATAAC
1141970 AGGGTTGGAGTATCCCCG
1 A-GGTTGGAGTATCCCCG
1141988 ATTGTGAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 1 0.03
28 39 0.98
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.22
Consensus pattern (27 bp):
AGGTTGGAGTATCCCCGCAAAAATAAC
Found at i:1142027 original size:79 final size:78
Alignment explanation
Indices: 1141944--1142147 Score: 327
Period size: 79 Copynumber: 2.6 Consensus size: 78
1141934 AAAATAATGA
* *
1141944 GGTTGGAGTATCCCCGCGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTT
1 GGTTGGAGTATCCCCTCGAAAATAAC-GGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTT
1142009 AAGAATAAAACCGG
65 AAGAATAAAACCGG
1142023 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTT
1 GGTTGGAGTATCCCCTCGAAAATAAC-GGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTT
* **
1142088 AGGAATAAAGTCGG
65 AAGAATAAAACCGG
*
1142102 GGTTAGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCCCGAT
1 GGTTGGAGTATCCCCTCGAAAATAACGGG-TTGGAGTATCCCCGAT
1142148 GATTAATGAG
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
78 3 0.03
79 114 0.97
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (78 bp):
GGTTGGAGTATCCCCTCGAAAATAACGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTA
AGAATAAAACCGG
Found at i:1142204 original size:186 final size:185
Alignment explanation
Indices: 1141868--1142223 Score: 407
Period size: 186 Copynumber: 1.9 Consensus size: 185
1141858 ACGACCGGGC
* * * *
1141868 TGGAGTACCCCTGATTATGAAAAATCAGTGTTTTGGAAATAAAATCAAGGTTGGAGTGTCCCCTC
1 TGGAGTACCCCTGATTATGAAAAATCAATATTTTGGAAATAAAATCAAGGTTAGAGTATCCCCTC
* * *
1141933 AAAAATAATGAGGTTGGAGTATCCCCGCGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAGAA
66 AAAAATAACGAGGTTGGAGTATCCCCGCGAAAAT-ACAGGGTTGGAGTATCCCCGATTATGAAAA
*
1141998 ATCAATATTTTAAGAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGT
130 ATCAATATTTTAAGAATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGT
* * **
1142054 TGGAGTATCCCC-GATTATGAGAAATCAATATTTTAGG-AATAAAGTCGGGGTTAGAGTATCCCC
1 TGGAGTA-CCCCTGATTATGAAAAATCAATATTTT-GGAAATAAAATCAAGGTTAGAGTATCCCC
* * * *
1142117 TCGAAAATAACG-GGATTGGAGTATCCCCGATGATTAAT-GA-GGTTGGAGTATCCCCGATTATG
64 TCAAAAATAACGAGG-TTGGAGTATCCCCG-CGA-AAATACAGGGTTGGAGTATCCCCGATTATG
*** * ** *
1142179 AAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
126 AAAAATCAATATTTTAAG-AATAAAACCGGAGTTGGAGTATCCCC
1142224 GATTATAGAA
Statistics
Matches: 141, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
185 34 0.24
186 96 0.68
187 8 0.06
188 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (185 bp):
TGGAGTACCCCTGATTATGAAAAATCAATATTTTGGAAATAAAATCAAGGTTAGAGTATCCCCTC
AAAAATAACGAGGTTGGAGTATCCCCGCGAAAATACAGGGTTGGAGTATCCCCGATTATGAAAAA
TCAATATTTTAAGAATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGT
Found at i:1142267 original size:51 final size:51
Alignment explanation
Indices: 1142158--1142490 Score: 465
Period size: 51 Copynumber: 6.5 Consensus size: 51
1142148 GATTAATGAG
* *
1142158 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAAAATTGGTG-TTTTGAAAATAAAATCGGA
* * *
1142210 GTTGGAGTATCCCCGATTATAGAAAATTGGTGTTTTGGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTTGAAAATAAAATCGGA
* * *
1142261 GTTGGAGTATCCCCGATTATAGAAAATTGGTGTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTTGAAAATAAAATCGGA
* * *
1142312 GTTGGAGTATCCCTGATTGTGGAAAATTGGTGTTTCGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTTGAAAATAAAATCGGA
*
1142363 GTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTCGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTTGAAAATAAAATCGGA
* * *
1142414 GTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTT-AGAAATAAAACCAGG-
1 GTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTTGA-AAATAAAATC-GGA
*
1142465 GTTGGAGTA-CCCTCGATTATGAAAAA
1 GTTGGAGTATCCC-CGATTATGGAAAA
1142491 CTGAGAAACT
Statistics
Matches: 257, Mismatches: 21, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
50 4 0.02
51 221 0.86
52 32 0.12
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTTGAAAATAAAATCGGA
Found at i:1142388 original size:153 final size:154
Alignment explanation
Indices: 1142157--1142490 Score: 512
Period size: 153 Copynumber: 2.2 Consensus size: 154
1142147 TGATTAATGA
* * *
1142157 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCC
1 GGTTGGAGTATCCCTGATTATGAAAAATTGGTGTTTTCGAAAATAAAATCGGAGTTGGAGTATCC
* *
1142222 CCGATTATAGAAAATTGGTGTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTATAGAAAA
66 CCGATTATAGAAAATTGGTGTTTCGAAAATAAAATCAGAGTTGGAGTATCCCCGATTATAGAAAA
* *
1142287 TTGGTGTTTT-GAAAATAAAACCGG
131 TTAGTGTTTTAG-AAATAAAACCAG
* *
1142311 GGTTGGAGTATCCCTGATTGTGGAAAATTGGTG-TTTCGAAAATAAAATCGGAGTTGGAGTATCC
1 GGTTGGAGTATCCCTGATTATGAAAAATTGGTGTTTTCGAAAATAAAATCGGAGTTGGAGTATCC
* * * *
1142375 CCGATTATGGAAAATTGGTGTTTCGAAAATAAAATCGGAGTTGGAGTATCCCCGATTGTGGAAAA
66 CCGATTATAGAAAATTGGTGTTTCGAAAATAAAATCAGAGTTGGAGTATCCCCGATTATAGAAAA
1142440 TTAGTGTTTTAGAAATAAAACCAG
131 TTAGTGTTTTAGAAATAAAACCAG
1142464 GGTTGGAGTA-CCCTCGATTATGAAAAA
1 GGTTGGAGTATCCCT-GATTATGAAAAA
1142491 CTGAGAAACT
Statistics
Matches: 163, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
152 4 0.02
153 128 0.79
154 31 0.19
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.30
Consensus pattern (154 bp):
GGTTGGAGTATCCCTGATTATGAAAAATTGGTGTTTTCGAAAATAAAATCGGAGTTGGAGTATCC
CCGATTATAGAAAATTGGTGTTTCGAAAATAAAATCAGAGTTGGAGTATCCCCGATTATAGAAAA
TTAGTGTTTTAGAAATAAAACCAG
Found at i:1144867 original size:13 final size:13
Alignment explanation
Indices: 1144849--1144874 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1144839 ACAAAGATCG
1144849 ATGTATCGATACA
1 ATGTATCGATACA
1144862 ATGTATCGATACA
1 ATGTATCGATACA
1144875 CTTCCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1144885 original size:21 final size:21
Alignment explanation
Indices: 1144861--1144902 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1144851 GTATCGATAC
1144861 AATGTATCGATACACTTCCTT
1 AATGTATCGATACACTTCCTT
* *
1144882 AATGTATCGATATATTTCCTT
1 AATGTATCGATACACTTCCTT
1144903 GACAGTAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
AATGTATCGATACACTTCCTT
Found at i:1144951 original size:19 final size:20
Alignment explanation
Indices: 1144927--1144980 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
1144917 AGTGATACAT
1144927 TGTATCGATACAAAACT-TA
1 TGTATCGATACAAAACTGTA
** *
1144946 TGTATCGATACATTTACTGTT
1 TGTATCGATACA-AAACTGTA
1144967 TGTATCGATACAAA
1 TGTATCGATACAAA
1144981 TTGTTTGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTATCGATACAAAACTGTA
Found at i:1144987 original size:19 final size:19
Alignment explanation
Indices: 1144926--1144987 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
1144916 TAGTGATACA
1144926 TTGTATCGATACAAAACT-T
1 TTGTATCGATAC-AAACTGT
* *
1144945 ATGTATCGATACATTTACTGT
1 TTGTATCGATACA--AACTGT
*
1144966 TTGTATCGATACAAATTGT
1 TTGTATCGATACAAACTGT
1144985 TTG
1 TTG
1144988 AAATTCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 1 0.03
19 18 0.51
20 3 0.09
21 13 0.37
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.42
Consensus pattern (19 bp):
TTGTATCGATACAAACTGT
Found at i:1145044 original size:21 final size:21
Alignment explanation
Indices: 1145018--1145073 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
1145008 GTTGGGACCT
1145018 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATTCTAGAAA
1145039 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATTCTAGAAA
1145060 TGTATCGATACATT
1 TGTATCGATACATT
1145074 TGGATAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTCTAGAAA
Found at i:1148648 original size:16 final size:15
Alignment explanation
Indices: 1148629--1148677 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
1148619 CTCTTCAAAT
1148629 AAAAAACAAGAATAAA
1 AAAAAACAAGAA-AAA
1148645 AAAAAACAA-AAAAA
1 AAAAAACAAGAAAAA
*
1148659 AACAAAAAAAGAGAAAA
1 AA-AAAACAAGA-AAAA
1148676 AA
1 AA
1148678 GAATGAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 5 0.17
15 8 0.28
16 10 0.34
17 6 0.21
ACGTcount: A:0.86, C:0.06, G:0.06, T:0.02
Consensus pattern (15 bp):
AAAAAACAAGAAAAA
Found at i:1148677 original size:10 final size:10
Alignment explanation
Indices: 1148642--1148668 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1148632 AAACAAGAAT
1148642 AAAAAAAAAC
1 AAAAAAAAAC
1148652 AAAAAAAAAC
1 AAAAAAAAAC
1148662 AAAAAAA
1 AAAAAAA
1148669 GAGAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:1149010 original size:11 final size:12
Alignment explanation
Indices: 1148994--1149023 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
1148984 AAGTAATCAA
1148994 AAAAAAAAAAG-
1 AAAAAAAAAAGC
1149005 AAAAAAAAAAGC
1 AAAAAAAAAAGC
1149017 AAAAAAA
1 AAAAAAA
1149024 TGGAAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGC
Found at i:1149500 original size:111 final size:112
Alignment explanation
Indices: 1149296--1149518 Score: 340
Period size: 111 Copynumber: 2.0 Consensus size: 112
1149286 AACTTGAAAG
* * * *
1149296 AACATCAAATTTGTCTGATTTTTAGAGAAATTCATATTTTATATGACCTGATCCATTCGTGCCTA
1 AACATCAAATTTGTCTGATTTTTAAAAAAATTCATATTTCATATGACCTGATCCATTCATGCCTA
* *
1149361 GGAAAATAAGGCATGTATTTTATTAGTTTTGAAATTTTTGAGCCAAT
66 GGAAAATAAGGCATGTATCTTATCAGTTTTGAAATTTTTGAGCCAAT
* *
1149408 AACATCAAATTTGTCTGA-TTTTAAAAAAATTCATGTTTCATATGACTTGATCCATTCATGCCTA
1 AACATCAAATTTGTCTGATTTTTAAAAAAATTCATATTTCATATGACCTGATCCATTCATGCCTA
* **
1149472 GGAAACTGGGGCATGTATCTTATCAGTTTTGAAATTTTTGAGCCAAT
66 GGAAAATAAGGCATGTATCTTATCAGTTTTGAAATTTTTGAGCCAAT
1149519 TAAAATTTTT
Statistics
Matches: 100, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
111 82 0.82
112 18 0.18
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (112 bp):
AACATCAAATTTGTCTGATTTTTAAAAAAATTCATATTTCATATGACCTGATCCATTCATGCCTA
GGAAAATAAGGCATGTATCTTATCAGTTTTGAAATTTTTGAGCCAAT
Found at i:1150194 original size:88 final size:88
Alignment explanation
Indices: 1150003--1150194 Score: 206
Period size: 88 Copynumber: 2.2 Consensus size: 88
1149993 TATCATCTGT
* * * *
1150003 ATTTACATTATTTTACGTGCATCTACATCATTAGATGACATTGGTATTTACATCATCTCATGTGT
1 ATTTACA-TATTTCACGTACATCTACATCATTAGATGACATTGGTATTTACATCATCTCATATAT
** *
1150068 ATTTGCCTTTTTATTAATGCTTGT
65 ATTTGCCACTTTATTAATGCTTGC
* * * * * * * *
1150092 ATTTGCGTAGTTTCACGTACATCTGCA-CTTTAGATGATATTGGTATTTGCATTATTTCATATAT
1 ATTTACATA-TTTCACGTACATCTACATCATTAGATGACATTGGTATTTACATCATCTCATATAT
*
1150156 ATTTGCCACTTTATTGATGCTTGC
65 ATTTGCCACTTTATTAATGCTTGC
1150180 ATTTACATCATTTCA
1 ATTTACAT-ATTTCA
1150195 GTGCATTTGC
Statistics
Matches: 83, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
88 63 0.76
89 20 0.24
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.46
Consensus pattern (88 bp):
ATTTACATATTTCACGTACATCTACATCATTAGATGACATTGGTATTTACATCATCTCATATATA
TTTGCCACTTTATTAATGCTTGC
Found at i:1151127 original size:66 final size:63
Alignment explanation
Indices: 1151053--1151234 Score: 159
Period size: 64 Copynumber: 2.8 Consensus size: 63
1151043 AACAATACTG
* * * *
1151053 GTTTCACCTCATTTAACCTTTTTTTTACTTAGGTTTCATCCTAGTCACCTTTAGTTGACTACATT
1 GTTTCACCT-AATTAACC-TTTTTTCACTTAGGTTTC-TCCTGGTCACCTTTAGTTGACTACACT
1151118 A
63 A
** * * * * * * *
1151119 GTTTCACCTTGGTCAACC-TTTTTGACTTAGGTTTTGTCTTGGACACTTTTAGTTGACTATACTA
1 GTTTCACC-TAATTAACCTTTTTTCACTTAGG-TTTCTCCTGGTCACCTTTAGTTGACTACACTA
*
1151183 GTTTCATCCTAACTAACCCTTTTTTCACTTAGGTTTCTCCCTGGTCACCTTT
1 GTTTCA-CCTAATTAA-CCTTTTTTCACTTAGGTTTCT-CCTGGTCACCTTT
1151235 TGTAGGTTCA
Statistics
Matches: 90, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
64 43 0.48
65 11 0.12
66 35 0.39
67 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.12, T:0.46
Consensus pattern (63 bp):
GTTTCACCTAATTAACCTTTTTTCACTTAGGTTTCTCCTGGTCACCTTTAGTTGACTACACTA
Found at i:1151181 original size:130 final size:131
Alignment explanation
Indices: 1150966--1151234 Score: 294
Period size: 130 Copynumber: 2.1 Consensus size: 131
1150956 CTTGTCTTTA
** * * * *
1150966 TCACCTTTAGTTGACTGTATTGGTTTTACCCTAGTCATCCTCTTTCGATTTAGGTTTTGCCTTGG
1 TCACCTTTAGTTGACTACATTAGTTTCACCCTAGTCAACCTCTTTCGACTTAGGTTTTGCCTTGG
* * ** * *
1151031 TCAACCTTAGATAACAATACTGGTTTCA-CCTCATTTAACCTTTTTTTTACTTAGGTTTCAT-CC
66 ACAACCTTAGATAACAATACTAGTTTCATCCT-AACTAACCCTTTTTTCACTTAGGTTTC-TCCC
1151094 TAG
129 TAG
* * * *
1151097 TCACCTTTAGTTGACTACATTAGTTTCACCTTGGTCAACCT-TTTTGACTTAGGTTTTGTCTTGG
1 TCACCTTTAGTTGACTACATTAGTTTCACCCTAGTCAACCTCTTTCGACTTAGGTTTTGCCTTGG
* * * *
1151161 AC-ACTTTTAGTTGACTATACTAGTTTCATCCTAACTAACCCTTTTTTCACTTAGGTTTCTCCCT
66 ACAAC-CTTAGATAACAATACTAGTTTCATCCTAACTAACCCTTTTTTCACTTAGGTTTCTCCCT
*
1151225 GG
130 AG
1151227 TCACCTTT
1 TCACCTTT
1151235 TGTAGGTTCA
Statistics
Matches: 114, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
129 3 0.03
130 74 0.65
131 37 0.32
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.44
Consensus pattern (131 bp):
TCACCTTTAGTTGACTACATTAGTTTCACCCTAGTCAACCTCTTTCGACTTAGGTTTTGCCTTGG
ACAACCTTAGATAACAATACTAGTTTCATCCTAACTAACCCTTTTTTCACTTAGGTTTCTCCCTA
G
Found at i:1151976 original size:107 final size:104
Alignment explanation
Indices: 1151630--1152262 Score: 331
Period size: 107 Copynumber: 5.9 Consensus size: 104
1151620 CCATTTGTTA
* * * * * ** ** *
1151630 ACTTGTATGGTTTTATCTTGGTCAACCCCTCTAGCTTATTGGTTAATACAGTTTCATCCTAATTA
1 ACTTGTATGGTTTCATCTTGGTCAACCCCTCTAACTTGTCGGTTCATATGGTTTTGTCCTAACTA
* * *
1151695 ACTCCTTTTT-GACTTAGATTTCACTCTGGTCACCTTTCGTTG
66 ACT-CTTTTTCGACTTAGGTTT-AC-CTAGTCACCCTTC-TTG
* * * * * * * * * * ** * * *
1151737 ACTTATATGGTTTTATCTTAGTTAATCTCTCTCACTTGT-TGTATCGTATAGTTTCATCATAGCC
1 ACTTGTATGGTTTCATCTTGGTCAACCCCTCTAACTTGTCGGT-TCATATGGTTTTGTCCTAACT
* ** * *
1151801 AATTCTTTTTTAACTTAGGTTTCACTCTAGTCACCCTTTGTTT
65 AACTCTTTTTCGACTTAGGTTT-AC-CTAGTCACCC-TTCTTG
* ** * * ** * *
1151844 AATTGTATGGTTTTGTCCCT-ATCAACCTTTTTAACTTGTCAGTTCATATGGTTTTGTCCTAACT
1 ACTTGTATGGTTTCAT-CTTGGTCAACCCCTCTAACTTGTCGGTTCATATGGTTTTGTCCTAACT
*
1151908 AACTCTTTTTCGACTAAGGGTTTACCTTAGTCACCCTTCATTG
65 AACTCTTTTTCGACTTA-GGTTTACC-TAGTCACCCTTC-TTG
* * * * ** * * * * *
1151951 ATTTGTATGGTTTCATCTTTGTCAACCCCTCTAATTTGTTGGTTTGTTTGGTTTTTTCCCAGCAA
1 ACTTGTATGGTTTCATCTTGGTCAACCCCTCTAACTTGTCGGTTCATATGGTTTTGTCCTAACTA
* ** * **
1152016 ACTCTTTTTTGACTTAGGTTCTGTC-ATGCTTACTTTTTCTTG
66 ACTCTTTTTCGACTTAGGTT-TACCTA-G-TCAC-CCTTCTTG
* * * * * * * *
1152058 ACTCGTATGGTTTCATCTCGGTCAACCCTTCTAACTTGTTGGTTCGTATGGCTTTATCCTAACCA
1 ACTTGTATGGTTTCATCTTGGTCAACCCCTCTAACTTGTCGGTTCATATGGTTTTGTCCTAACTA
*
1152123 ACTCTTTTTTAGA-TTAGGTTTCACCTAGTCACCCTTCGTTG
66 ACTC-TTTTTCGACTTAGGTTT-ACCTAGTCACCCTTC-TTG
* * * * * * **
1152164 GCTTGTATGGTTTCATCTTGGTTAACCTCTTTAACTTATCGATTCATATGGTTTTGTCCTAGTTA
1 ACTTGTATGGTTTCATCTTGGTCAACCCCTCTAACTTGTCGGTTCATATGGTTTTGTCCTAACTA
* *
1152229 ATTCCTTTTCGACTTAGGTTTTATCCTAGTCACC
66 ACTCTTTTTCGACTTAGG-TTTA-CCTAGTCACC
1152263 TTTTATTAAC
Statistics
Matches: 396, Mismatches: 110, Indels: 40
0.73 0.20 0.07
Matches are distributed among these distances:
105 10 0.03
106 83 0.21
107 281 0.71
108 22 0.06
ACGTcount: A:0.18, C:0.21, G:0.14, T:0.46
Consensus pattern (104 bp):
ACTTGTATGGTTTCATCTTGGTCAACCCCTCTAACTTGTCGGTTCATATGGTTTTGTCCTAACTA
ACTCTTTTTCGACTTAGGTTTACCTAGTCACCCTTCTTG
Found at i:1152282 original size:213 final size:212
Alignment explanation
Indices: 1152058--1152545 Score: 479
Period size: 213 Copynumber: 2.3 Consensus size: 212
1152048 CTTTTTCTTG
* *
1152058 ACTCGTATGGTTTCATCTCGGTCAACCCTTCTAACTTGTTGGTTCGTATGGCTTTATCCTAACCA
1 ACTCGTATGGTTTTATC-CAGTCAACCCTTCTAACTTGTT-GTTCGTATGGCTTTATCCTAACCA
* * * ** * *
1152123 ACTCTTT-TTTAGATTAGGTTTCACC-TAGTCACCCTTCGTTGGCTTGTATGGTTTCATCTTGGT
64 ACTCTTTGTTTACA-TAGGTTTCACCTTAGTCACCCTTCATTGACAAGTATGGTTTCATCCTAGT
* * * * *
1152186 -TAACCTCTTTAACTTATCGATTCATATGGTTTTGTCCTAG-TTAATTCCTTTTCGACTTAGGTT
128 CAAACC-CTTTAACTTATCGATTCACATGGTTTTGT-CTAGACTAATTCCTTTTCGACTTAAGAT
* * *
1152249 TTATCCT-AGTCACCTTTTATTA
191 TCATCCTGA-TCACCCTTCATTA
* * * * * * ** *
1152271 ACTCATATGGTTTTATCACAATCAA-CCTCTCGAATTTGTTGTTCGCACGG-TTTCATCCTGGCG
1 ACTCGTATGGTTTTATC-CAGTCAACCCT-TCTAACTTGTTGTTCGTATGGCTTT-ATCCTAACC
*
1152334 AACTCTTTGTTTACATAGGTTTCACCTTGGTCACCCTTCATTGACAAGTATGGTTTCATCCTAGT
63 AACTCTTTGTTTACATAGGTTTCACCTTAGTCACCCTTCATTGACAAGTATGGTTTCATCCTAGT
* * * * * *
1152399 CAAACCCTTTAATTTATTGGTTCACATGGTTTTGTCTCGACTAATTTCTTTTTGACTTAAGATTC
128 CAAACCCTTTAACTTATCGATTCACATGGTTTTGTCTAGACTAATTCCTTTTCGACTTAAGATTC
* *
1152464 ATTCTGATCACCCTTCATTT
193 ATCCTGATCACCCTTCATTA
* *
1152484 ACTCGTATGGTTTTATCCTAGTCAACCAC-TCTAACTTGTTAGTTCATATGGCTTCATCCTAA
1 ACTCGTATGGTTTTATCC-AGTCAACC-CTTCTAACTTGTT-GTTCGTATGGCTTTATCCTAA
1152546 GTAACTTCTT
Statistics
Matches: 217, Mismatches: 46, Indels: 23
0.76 0.16 0.08
Matches are distributed among these distances:
211 3 0.01
212 40 0.18
213 153 0.71
214 18 0.08
215 3 0.01
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.42
Consensus pattern (212 bp):
ACTCGTATGGTTTTATCCAGTCAACCCTTCTAACTTGTTGTTCGTATGGCTTTATCCTAACCAAC
TCTTTGTTTACATAGGTTTCACCTTAGTCACCCTTCATTGACAAGTATGGTTTCATCCTAGTCAA
ACCCTTTAACTTATCGATTCACATGGTTTTGTCTAGACTAATTCCTTTTCGACTTAAGATTCATC
CTGATCACCCTTCATTA
Found at i:1153076 original size:107 final size:106
Alignment explanation
Indices: 1152965--1153238 Score: 280
Period size: 107 Copynumber: 2.6 Consensus size: 106
1152955 TTTCGTCCTG
* * * * * *
1152965 GCCAACTCATTTTTTACATAGGTTTTGC-CTTGATCATCTTTCATTGACTTGTATGGTTTCGTCC
1 GCCAACTC-TTTTTAACATAGCTTTTGCAC-TGATCACCCTTCATTGACTTATATGGTTTCGGCC
** *
1153029 TGGTTAACCCTTCTAACTTGTTAGTTCGTAGGGTTTCATCCCA
64 CCGTTAACCCTTCTAACTTGTTAGTTCATAGGGTTTCATCCCA
* * * * *
1153072 GCCAACTCCTTTTCAACTTAGCTTTTGCACTGGTCACCCTTCGTTGACTTATATGGTTTTGGCCC
1 GCCAACT-CTTTTTAACATAGCTTTTGCACTGATCACCCTTCATTGACTTATATGGTTTCGGCCC
* *
1153137 CGTTAACCCTTCTAACTTGTTAGTTCATATGGTTTCATCCTA
65 CGTTAACCCTTCTAACTTGTTAGTTCATAGGGTTTCATCCCA
* * * * * * * * *
1153179 ACCAACTCTTTTTCGACTTAGATTTTTCCCTGGTCACACTTCATTGACTCATATGGTTTC
1 GCCAACTCTTTTT-AACATAGCTTTTGCACTGATCACCCTTCATTGACTTATATGGTTTC
1153239 ATCCTAGTCA
Statistics
Matches: 138, Mismatches: 26, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
106 5 0.04
107 131 0.95
108 2 0.01
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.42
Consensus pattern (106 bp):
GCCAACTCTTTTTAACATAGCTTTTGCACTGATCACCCTTCATTGACTTATATGGTTTCGGCCCC
GTTAACCCTTCTAACTTGTTAGTTCATAGGGTTTCATCCCA
Found at i:1153299 original size:107 final size:106
Alignment explanation
Indices: 1153188--1153487 Score: 293
Period size: 106 Copynumber: 2.8 Consensus size: 106
1153178 AACCAACTCT
* *
1153188 TTTTCGACTTAGATTTTTCCC-TGGTCACACTTCATTGACTCATATGGTTTCATCCTAGTCAACC
1 TTTTCAACTTAGA-TTTTCCCGTGGTCA-ACTTCATTGACTCATATGATTTCATCCTAGTCAACC
1153252 TCTTTTAA-TTATTGGTTCGTATAGTTTTATTCCAACTAACTTC
64 TC-TTTAACTTATTGGTTCGTATAGTTTTATTCCAACTAACTTC
* * * * *
1153295 TTTTCAACTTAGATTTTCCCGTGGTCATCTTTATTGACTTATATGATTTCATCTTGGTCAACCTC
1 TTTTCAACTTAGATTTTCCCGTGGTCAACTTCATTGACTCATATGATTTCATCCTAGTCAACCTC
* * * * * *
1153360 TTTAACTTGTTGGTTCGTATAGTTTTGTCCCAGCCAACTTT
66 TTTAACTTATTGGTTCGTATAGTTTTATTCCAACTAACTTC
* * * * * ** * * *
1153401 TTTTCAACTGA-AGGTTTCACCTTGGTC-ACTTCGTTAACTTGTATGTTTTCATCCTAATTAACC
1 TTTTCAACTTAGA-TTTTC-CCGTGGTCAACTTCATTGACTCATATGATTTCATCCTAGTCAACC
* **
1153464 TCTCTAACTTATTGACTCGTATAG
64 TCTTTAACTTATTGGTTCGTATAG
1153488 CTCTCTATTA
Statistics
Matches: 159, Mismatches: 30, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
105 6 0.04
106 128 0.81
107 25 0.16
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.45
Consensus pattern (106 bp):
TTTTCAACTTAGATTTTCCCGTGGTCAACTTCATTGACTCATATGATTTCATCCTAGTCAACCTC
TTTAACTTATTGGTTCGTATAGTTTTATTCCAACTAACTTC
Found at i:1153374 original size:106 final size:106
Alignment explanation
Indices: 1153004--1153409 Score: 388
Period size: 107 Copynumber: 3.8 Consensus size: 106
1152994 TTGATCATCT
* * * **
1153004 TTCATTGACTTGTATGGTTTCGTCCTGGTTAACCCTTCTAACTTGTTAGTTCGTAGGGTTTCATC
1 TTCATTGACTTATATGGTTTCATCCTGGTCAACCCTTCTAACTTGTTAGTTCGTATAGTTTCATC
* * * * *
1153069 CCAGCCAACTCCTTTTCAACTTAGCTTTTGCACTGGTCACCC
66 CCAACCAACTTCTTTTCAACTTAGATTTT-CCCTGGTCACTC
* *** ** * * *
1153111 TTCGTTGACTTATATGGTTTTGGCCCCGTTAACCCTTCTAACTTGTTAGTTCATATGGTTTCATC
1 TTCATTGACTTATATGGTTTCATCCTGGTCAACCCTTCTAACTTGTTAGTTCGTATAGTTTCATC
* * *
1153176 CTAACCAAC-TCTTTTTCGACTTAGATTTTTCCCTGGTCACAC
66 CCAACCAACTTC-TTTTCAACTTAGA-TTTTCCCTGGTCACTC
* * * * * *
1153218 TTCATTGACTCATATGGTTTCATCCTAGTCAACCTCTTTTAA-TTATTGGTTCGTATAGTTTTAT
1 TTCATTGACTTATATGGTTTCATCCTGGTCAACC-CTTCTAACTTGTTAGTTCGTATAGTTTCAT
* *
1153282 TCCAACTAACTTCTTTTCAACTTAGATTTTCCCGTGGTCA-TC
65 CCCAACCAACTTCTTTTCAACTTAGATTTTCCC-TGGTCACTC
* * * * **
1153324 TTTATTGACTTATATGATTTCATCTTGGTCAACCTCTT-TAACTTGTTGGTTCGTATAGTTTTGT
1 TTCATTGACTTATATGGTTTCATCCTGGTCAACC-CTTCTAACTTGTTAGTTCGTATAGTTTCAT
* *
1153388 CCCAGCCAACTTTTTTTCAACT
65 CCCAACCAACTTCTTTTCAACT
1153410 GAAGGTTTCA
Statistics
Matches: 248, Mismatches: 45, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
105 3 0.01
106 80 0.32
107 153 0.62
108 12 0.05
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (106 bp):
TTCATTGACTTATATGGTTTCATCCTGGTCAACCCTTCTAACTTGTTAGTTCGTATAGTTTCATC
CCAACCAACTTCTTTTCAACTTAGATTTTCCCTGGTCACTC
Found at i:1153472 original size:106 final size:106
Alignment explanation
Indices: 1153141--1153487 Score: 283
Period size: 106 Copynumber: 3.3 Consensus size: 106
1153131 TGGCCCCGTT
* * * * * * * * *
1153141 AACC-CTTCTAACTTGTTAGTTCATATGGTTTCATCCTAACCAAC-TCTTTTTCGACTTAGATTT
1 AACCTCTT-TAACTTATTGGTTCGTATAGTTTTATCCCAACCAACTTC-TTTTCAACTAAGA-GT
* * * *
1153204 TTCCC-TGGTCACACTTCATTGACTCATATGGTTTCATCCTAGTC
63 TTCCCGTGGTCA-TCTTCATTAACTTATATGATTTCATCCTAGTC
* * * *
1153248 AACCTCTTTTAA-TTATTGGTTCGTATAGTTTTATTCCAACTAACTTCTTTTCAACTTAGATTTT
1 AACCTC-TTTAACTTATTGGTTCGTATAGTTTTATCCCAACCAACTTCTTTTCAACTAAGAGTTT
* * * *
1153312 CCCGTGGTCATCTTTATTGACTTATATGATTTCATCTTGGTC
65 CCCGTGGTCATCTTCATTAACTTATATGATTTCATCCTAGTC
* * * *
1153354 AACCTCTTTAACTTGTTGGTTCGTATAGTTTTGTCCCAGCCAACTTTTTTTCAACTGAAG-GTTT
1 AACCTCTTTAACTTATTGGTTCGTATAGTTTTATCCCAACCAACTTCTTTTCAACT-AAGAGTTT
* * * * * *
1153418 CACCTTGGTCA-CTTCGTTAACTTGTATGTTTTCATCCTAATT
65 C-CCGTGGTCATCTTCATTAACTTATATGATTTCATCCTAGTC
* **
1153460 AACCTCTCTAACTTATTGACTCGTATAG
1 AACCTCTTTAACTTATTGGTTCGTATAG
1153488 CTCTCTATTA
Statistics
Matches: 196, Mismatches: 37, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
105 5 0.03
106 127 0.65
107 56 0.29
108 6 0.03
109 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (106 bp):
AACCTCTTTAACTTATTGGTTCGTATAGTTTTATCCCAACCAACTTCTTTTCAACTAAGAGTTTC
CCGTGGTCATCTTCATTAACTTATATGATTTCATCCTAGTC
Found at i:1153554 original size:41 final size:41
Alignment explanation
Indices: 1153509--1153619 Score: 125
Period size: 41 Copynumber: 2.7 Consensus size: 41
1153499 TTAACCCCTT
* * *
1153509 TAACTCATTAACTCGTATGGTTTTAT-TCTGATCAACCATTC
1 TAACTCATTGACTCGTATGGTTTCATCTCAG-TCAACCATTC
* *
1153550 TAACTCATTGACTAGTATGGTTTCATCTCAGTCAACCTTTC
1 TAACTCATTGACTCGTATGGTTTCATCTCAGTCAACCATTC
* ** *
1153591 TAACTTATTGGTTCGTATGGTTTCGTCTC
1 TAACTCATTGACTCGTATGGTTTCATCTC
1153620 GGCCAACAAC
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 56 0.95
42 3 0.05
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.42
Consensus pattern (41 bp):
TAACTCATTGACTCGTATGGTTTCATCTCAGTCAACCATTC
Found at i:1153851 original size:81 final size:82
Alignment explanation
Indices: 1153706--1153863 Score: 196
Period size: 81 Copynumber: 1.9 Consensus size: 82
1153696 ATTAAGCCTC
* * * ** *
1153706 TAACTCATTGACTCATATAGTTTCATACCGGTCAACCCTTCTAACTCATTGGTTTGTATGGTTTC
1 TAACTCATTGACTCATACAGTTTCATACCGATCAACCCTTCTAACTCATTGATTCATATAGTTTC
1153771 AT-CTCAGTCAACTTGTT
66 ATAC-CAGTCAACTTGTT
* * *
1153788 TAACTCATTGACTCGTACGGTTTCAT-CTCGATTAACCC-TCTAACTCATTGATTCATATAGTTT
1 TAACTCATTGACTCATACAGTTTCATAC-CGATCAACCCTTCTAACTCATTGATTCATATAGTTT
1153851 CATACCAGTCAAC
65 CATACCAGTCAAC
1153864 CCTTCTAACT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
81 33 0.51
82 32 0.49
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (82 bp):
TAACTCATTGACTCATACAGTTTCATACCGATCAACCCTTCTAACTCATTGATTCATATAGTTTC
ATACCAGTCAACTTGTT
Found at i:1153892 original size:41 final size:41
Alignment explanation
Indices: 1153677--1153895 Score: 173
Period size: 41 Copynumber: 5.4 Consensus size: 41
1153667 CTTGTATGGT
* * * *
1153677 TTCATACGGTTTCATCTCAATTAAGCC-TCTAACTCATTGA
1 TTCATATGGTTTCATCTCAGTCAACCCTTCTAACTCATTGA
* * * *
1153717 CTCATATAGTTTCATAC-CGGTCAACCCTTCTAACTCATTGG
1 TTCATATGGTTTCAT-CTCAGTCAACCCTTCTAACTCATTGA
** * *
1153758 TTTGTATGGTTTCATCTCAGTCAA-CTTGTTTAACTCATTGA
1 TTCATATGGTTTCATCTCAGTCAACCCT-TCTAACTCATTGA
* * * *
1153799 CTCGTACGGTTTCATCTC-GATTAACCC-TCTAACTCATTGA
1 TTCATATGGTTTCATCTCAG-TCAACCCTTCTAACTCATTGA
* * *
1153839 TTCATATAGTTTCATAC-CAGTCAACCCTTCTAACTTATTGTT
1 TTCATATGGTTTCAT-CTCAGTCAACCCTTCTAACTCATTG-A
1153881 TTC-TATGGTTTCATC
1 TTCATATGGTTTCATC
1153896 CTAGCCAACC
Statistics
Matches: 139, Mismatches: 30, Indels: 20
0.74 0.16 0.11
Matches are distributed among these distances:
40 53 0.38
41 82 0.59
42 4 0.03
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (41 bp):
TTCATATGGTTTCATCTCAGTCAACCCTTCTAACTCATTGA
Found at i:1155202 original size:23 final size:23
Alignment explanation
Indices: 1155179--1155221 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1155169 TTGAACATTA
*
1155179 AAACTAAATTTATTAT-TGAATT
1 AAACTAAATTGATTATATGAATT
*
1155201 AAATTAAATTGATTATATGAA
1 AAACTAAATTGATTATATGAA
1155222 ATATTATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (23 bp):
AAACTAAATTGATTATATGAATT
Found at i:1155428 original size:8 final size:8
Alignment explanation
Indices: 1155399--1155438 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1155389 AATCAAAATC
1155399 AAAATTAA
1 AAAATTAA
* * *
1155407 AATATCAC
1 AAAATTAA
1155415 AAAATTAA
1 AAAATTAA
1155423 AAAATTAA
1 AAAATTAA
1155431 AAAATTAA
1 AAAATTAA
1155439 GGAAAATCAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (8 bp):
AAAATTAA
Found at i:1157677 original size:39 final size:40
Alignment explanation
Indices: 1157633--1157713 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 40
1157623 TTTTTTAAAA
*
1157633 GGGGAGAATGCATAAATTTGCTAAAATTACCTTA-TTAAG
1 GGGGAGAATGCACAAATTTGCTAAAATTACCTTAGTTAAG
* * * *
1157672 GGGGAGAATGTACGAATTTGTTAAAATTACTTTAGTTAAG
1 GGGGAGAATGCACAAATTTGCTAAAATTACCTTAGTTAAG
1157712 GG
1 GG
1157714 AGAAAGAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 29 0.81
40 7 0.19
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (40 bp):
GGGGAGAATGCACAAATTTGCTAAAATTACCTTAGTTAAG
Found at i:1158356 original size:13 final size:13
Alignment explanation
Indices: 1158338--1158363 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1158328 TACACAAAGT
1158338 ATGTATCGATACA
1 ATGTATCGATACA
1158351 ATGTATCGATACA
1 ATGTATCGATACA
1158364 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1158362 original size:32 final size:33
Alignment explanation
Indices: 1158320--1158383 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1158310 TAGCCAAACT
* **
1158320 TGTATTGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1158352 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1158384 TTGGCTTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1159629 original size:15 final size:15
Alignment explanation
Indices: 1159609--1159643 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1159599 AACCATCAAA
1159609 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
1159624 GATGATGATGATAAT
1 GATGATGAAGATAAT
1159639 GATGA
1 GATGA
1159644 AGTTGACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:1161017 original size:40 final size:40
Alignment explanation
Indices: 1160962--1161045 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
1160952 AAGGCATGAA
1160962 AGTAGTTTTTGAATCACAAAATTGTCACATAATTGATGTT
1 AGTAGTTTTTGAATCACAAAATTGTCACATAATTGATGTT
1161002 AGTAGTTTTTGAATCACAAAATTGTCACATAATTGATGTT
1 AGTAGTTTTTGAATCACAAAATTGTCACATAATTGATGTT
1161042 AGTA
1 AGTA
1161046 ATAATAAATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (40 bp):
AGTAGTTTTTGAATCACAAAATTGTCACATAATTGATGTT
Found at i:1166773 original size:19 final size:20
Alignment explanation
Indices: 1166749--1166801 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1166739 CATATCTAGA
* *
1166749 TGTATCAATACATGT-TCAT
1 TGTATCGATACATGTATAAT
1166768 TGTATCGATACATGTATAAT
1 TGTATCGATACATGTATAAT
1166788 TGTATCGATACATG
1 TGTATCGATACATG
1166802 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATGTATAAT
Found at i:1166855 original size:20 final size:19
Alignment explanation
Indices: 1166830--1166883 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
1166820 CTACCACTGT
1166830 TTGTATCGATACAT-AGCACA
1 TTGTATCGATACATAAG-A-A
1166850 TTGTATCGATACATAAAGAA
1 TTGTATCGATACAT-AAGAA
1166870 TTGTATCGATACAT
1 TTGTATCGATACAT
1166884 TGTCCCAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 29 0.91
21 1 0.03
22 2 0.06
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (19 bp):
TTGTATCGATACATAAGAA
Found at i:1167861 original size:51 final size:49
Alignment explanation
Indices: 1167715--1167872 Score: 183
Period size: 51 Copynumber: 3.1 Consensus size: 49
1167705 TTCTAGAAAA
* * * *
1167715 AAATGTATCGATACACTTTT-ATTGTATCAATACATTTTGGGTTTGATCT
1 AAATGTATCGATACA-TTTTCATTGTATCAATACATTCTGGTTTTGACCC
* *
1167764 AATTGTATTGATACATTTTCATTGTATCAATACATTCTAGGTTTTTGACCC
1 AAATGTATCGATACATTTTCATTGTATCAATACATTCT-GG-TTTTGACCC
* * *
1167815 AAATGTATCGATACATTATTCACTATATCGATACATTCTGGATTTTGACCC
1 AAATGTATCGATACATT-TTCATTGTATCAATACATTCTGG-TTTTGACCC
1167866 AAATGTA
1 AAATGTA
1167873 ATAATTCACT
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
48 4 0.04
49 30 0.32
50 2 0.02
51 39 0.42
52 18 0.19
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (49 bp):
AAATGTATCGATACATTTTCATTGTATCAATACATTCTGGTTTTGACCC
Found at i:1167886 original size:51 final size:52
Alignment explanation
Indices: 1167788--1167905 Score: 143
Period size: 51 Copynumber: 2.3 Consensus size: 52
1167778 ATTTTCATTG
* * * * *
1167788 TATCAATACATTCTAGGTTTTTGACCCAAATGTATCGATACATTATTCACTA
1 TATCGATACATTCTAGGATTTTGACCCAAATGTATCAATACACTATTCAATA
* *
1167840 TATCGATACATTCT-GGATTTTGACCCAAATGTAAT-AATTCACTATTCAATG
1 TATCGATACATTCTAGGATTTTGACCCAAATGT-ATCAATACACTATTCAATA
1167891 TATCGATACA-TCTAG
1 TATCGATACATTCTAG
1167906 TTAAATTTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
50 3 0.05
51 39 0.68
52 15 0.26
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (52 bp):
TATCGATACATTCTAGGATTTTGACCCAAATGTATCAATACACTATTCAATA
Found at i:1174219 original size:16 final size:16
Alignment explanation
Indices: 1174200--1174275 Score: 89
Period size: 16 Copynumber: 4.8 Consensus size: 16
1174190 GACTCGAAAT
* *
1174200 CCGAAATAACCTGAAC
1 CCGAAATGACCCGAAC
*
1174216 CCGAAATGACCCAAAC
1 CCGAAATGACCCGAAC
*
1174232 CCAAAATGACCCGAAC
1 CCGAAATGACCCGAAC
* *
1174248 CCGAAATGATCCGAAA
1 CCGAAATGACCCGAAC
*
1174264 CCAAAATGACCC
1 CCGAAATGACCC
1174276 AAACAATTAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.43, C:0.34, G:0.13, T:0.09
Consensus pattern (16 bp):
CCGAAATGACCCGAAC
Found at i:1174253 original size:32 final size:32
Alignment explanation
Indices: 1174203--1174275 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
1174193 TCGAAATCCG
* *
1174203 AAATAACCTGAACCCGAAATGA-CCCAAACCCA
1 AAATGACCCGAACCCGAAATGATCCCAAA-CCA
*
1174235 AAATGACCCGAACCCGAAATGATCCGAAACCA
1 AAATGACCCGAACCCGAAATGATCCCAAACCA
1174267 AAATGACCC
1 AAATGACCC
1174276 AAACAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 32 0.86
33 5 0.14
ACGTcount: A:0.45, C:0.33, G:0.12, T:0.10
Consensus pattern (32 bp):
AAATGACCCGAACCCGAAATGATCCCAAACCA
Found at i:1174803 original size:16 final size:16
Alignment explanation
Indices: 1174784--1174850 Score: 71
Period size: 16 Copynumber: 4.2 Consensus size: 16
1174774 CCCGAATCTG
*
1174784 AAATGACCCAAACCCA
1 AAATAACCCAAACCCA
* * *
1174800 AAATGATCCAAACCCG
1 AAATAACCCAAACCCA
* *
1174816 AAATAATCCAAACCCG
1 AAATAACCCAAACCCA
*
1174832 AAATAACCCGAACCCA
1 AAATAACCCAAACCCA
1174848 AAA
1 AAA
1174851 ATATTCGAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.51, C:0.33, G:0.07, T:0.09
Consensus pattern (16 bp):
AAATAACCCAAACCCA
Found at i:1174846 original size:32 final size:32
Alignment explanation
Indices: 1174773--1174846 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 32
1174763 AACCCGATTG
* * * *
1174773 ACCCGAATCTGAAATGACCCAAACCCAAAATG
1 ACCCGAACCCGAAATAACCCAAACCCAAAATA
* * * *
1174805 ATCCAAACCCGAAATAATCCAAACCCGAAATA
1 ACCCGAACCCGAAATAACCCAAACCCAAAATA
1174837 ACCCGAACCC
1 ACCCGAACCC
1174847 AAAAATATTC
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.45, C:0.35, G:0.09, T:0.11
Consensus pattern (32 bp):
ACCCGAACCCGAAATAACCCAAACCCAAAATA
Found at i:1175307 original size:149 final size:152
Alignment explanation
Indices: 1174965--1175308 Score: 376
Period size: 152 Copynumber: 2.3 Consensus size: 152
1174955 CTACCCAAAT
* * * *
1174965 CAATTAAATTGCTGCAAAATCTTGTAATTAGTTGTTGCTTAAAGAAAAACACCACGCATGTACTT
1 CAATTAAATTGTTGCAAAATCTTTTAATTAATTGTTGCTTAAAGAAAAACACCACGCATATACTT
* **
1175030 TTGAAAAAAAAATTGTTAAATGTAATAAAAGTGTTGCAATAACTATAAAAAATATGGCTTTTACT
66 TTGAAAAAAAAATTGCTAAATGTAATAAAAACGTTGCAATAACTATAAAAAATATGGCTTTTACT
* *
1175095 TTCGAATAAATGTTTCCTAAAA
131 TTCAAATAAATGATTCCTAAAA
* * * * *
1175117 CAATTAAATTGTTGCAAAATCTTTTAATTATTTATTTCTTAAAGAAAAA-ACCATTGCATATAGT
1 CAATTAAATTGTTGCAAAATCTTTTAATTAATTGTTGCTTAAAGAAAAACACCA-CGCATATACT
** * ** * * *
1175181 TTT-AAAAAAACGTTGCTAAATGTAATAAAAACGTTGCTAA-ATCT-TTTAATATGGTTGCTTTT
65 TTTGAAAAAAAAATTGCTAAATGTAATAAAAACGTTGC-AATAACTATAAAAAAT-ATGGCTTTT
* *
1175243 CCTTT-AAATAAAT-ATTGCTAAAA
128 ACTTTCAAATAAATGATTCCTAAAA
* * *
1175266 CAATTAAATTATTGCAAAATCTTTTTATTAATCGTTGCTTAAA
1 CAATTAAATTGTTGCAAAATCTTTTAATTAATTGTTGCTTAAA
1175309 ATATGTTGCA
Statistics
Matches: 160, Mismatches: 29, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
149 45 0.28
150 12 0.08
151 47 0.29
152 56 0.35
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (152 bp):
CAATTAAATTGTTGCAAAATCTTTTAATTAATTGTTGCTTAAAGAAAAACACCACGCATATACTT
TTGAAAAAAAAATTGCTAAATGTAATAAAAACGTTGCAATAACTATAAAAAATATGGCTTTTACT
TTCAAATAAATGATTCCTAAAA
Found at i:1177011 original size:30 final size:31
Alignment explanation
Indices: 1176958--1177016 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1176948 AAAAGGGAAG
1176958 TTGCTACCTTAGCCACTAAAAGATAGAGAAA
1 TTGCTACCTTAGCCACTAAAAGATAGAGAAA
* *
1176989 TTGCTATCTTAGCCTC-AAAAGATAGAGA
1 TTGCTACCTTAGCCACTAAAAGATAGAGA
1177017 TGATAGAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (31 bp):
TTGCTACCTTAGCCACTAAAAGATAGAGAAA
Found at i:1183432 original size:78 final size:77
Alignment explanation
Indices: 1183311--1183466 Score: 260
Period size: 78 Copynumber: 2.0 Consensus size: 77
1183301 AAAGAAAGAC
* *
1183311 AAGAAAAAAAAAAGAAAAAATGAAAATTTTGATTGTAACATTGTGTGATTAAAATATTTAAAATG
1 AAGAAAAAAAAAAGAAAAAATGAAAATATTGATTATAACATTGTGTGATTAAAATATTTAAAATG
1183376 ATTTTAAAAAAA
66 ATTTTAAAAAAA
1183388 AAGAAGAAAAAAAAGAAAAAATGGAAAA-ATTGATTATAACATTGTGTGATTAAAATATTTAAAA
1 AAGAA-AAAAAAAAGAAAAAAT-GAAAATATTGATTATAACATTGTGTGATTAAAATATTTAAAA
*
1183452 TGATTTTTAAAAAA
64 TGATTTTAAAAAAA
1183466 A
1 A
1183467 GAACCTTTTT
Statistics
Matches: 74, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
77 5 0.07
78 64 0.86
79 5 0.07
ACGTcount: A:0.58, C:0.01, G:0.12, T:0.29
Consensus pattern (77 bp):
AAGAAAAAAAAAAGAAAAAATGAAAATATTGATTATAACATTGTGTGATTAAAATATTTAAAATG
ATTTTAAAAAAA
Found at i:1191389 original size:2 final size:2
Alignment explanation
Indices: 1191384--1191412 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1191374 AATGAATCTG
1191384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1191413 ACAAATTTGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1193201 original size:3 final size:3
Alignment explanation
Indices: 1193184--1193230 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
1193174 AAATTCATTA
1193184 ATT A-T ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1193230 A
1 A
1193231 AATAGAAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1194885 original size:18 final size:18
Alignment explanation
Indices: 1194862--1194898 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1194852 TATTCGCCTC
1194862 TTTCCTGCCCCTCTTTAT
1 TTTCCTGCCCCTCTTTAT
1194880 TTTCCTGCCCCTCTTTAT
1 TTTCCTGCCCCTCTTTAT
1194898 T
1 T
1194899 AGTGATCCGT
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:0.05, C:0.38, G:0.05, T:0.51
Consensus pattern (18 bp):
TTTCCTGCCCCTCTTTAT
Found at i:1196053 original size:28 final size:28
Alignment explanation
Indices: 1196022--1196092 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 28
1196012 CAATAAAAAA
*
1196022 TAAATTGAAAAAAAAAAAACTTTAAAGT
1 TAAATTGAAAAAAAAAAAACTCTAAAGT
* * *
1196050 TAAAACTCAAAAAAAAAAAAGTCTAAAGT
1 T-AAATTGAAAAAAAAAAAACTCTAAAGT
* *
1196079 AAAATAAGAAAAAA
1 TAAAT-TGAAAAAA
1196093 TTTTTATGAC
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.69, C:0.06, G:0.07, T:0.18
Consensus pattern (28 bp):
TAAATTGAAAAAAAAAAAACTCTAAAGT
Found at i:1196092 original size:29 final size:29
Alignment explanation
Indices: 1196027--1196082 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1196017 AAAAATAAAT
*
1196027 TGAAAAAAAAAAAACTTTAAAGTTAAAAC
1 TGAAAAAAAAAAAACTCTAAAGTTAAAAC
* *
1196056 TCAAAAAAAAAAAAGTCTAAAG-TAAAA
1 TGAAAAAAAAAAAACTCTAAAGTTAAAA
1196083 TAAGAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.18
Consensus pattern (29 bp):
TGAAAAAAAAAAAACTCTAAAGTTAAAAC
Found at i:1197325 original size:50 final size:51
Alignment explanation
Indices: 1197230--1197652 Score: 384
Period size: 50 Copynumber: 8.4 Consensus size: 51
1197220 TCATCAATTC
* **
1197230 AAAAATTTCAAAATATATTTTATATTCAAT-TTCAAATTAAAATTTAAAAATAAT
1 AAAAATTT-AAAA-ATA-TTTATATTAAATCTT-AAATTACTATTTAAAAATAAT
* * *
1197284 AAAAA-TT-AAAATATTTGTATTAGATCTAAAATTACCTATTTAAAAATAAT
1 AAAAATTTAAAAATATTTATATTAAATCTTAAATTA-CTATTTAAAAATAAT
* *
1197334 AAAAAGTTTAAAAAATATTTTGTATTAAATTCTGAAA-TACTA-TT--AAATAAT
1 AAAAA-TTT-AAAAATA-TTTATATTAAA-TCTTAAATTACTATTTAAAAATAAT
*
1197385 AAAAATTTAAAAATATTTCATATTAAATCTTGAATTACTATTTAAAAAGTAAT
1 AAAAATTTAAAAATATTT-ATATTAAATCTTAAATTACTATTTAAAAA-TAAT
*
1197438 AAAAATTTAAAAATATTTATATT-AATCTTAAATTACTATTTAAAAA-CAT
1 AAAAATTTAAAAATATTTATATTAAATCTTAAATTACTATTTAAAAATAAT
* * *
1197487 AAAAAATAAAAAATATTTTATATTAAATCTTGAATTA-TAATTTTAAAAA-AAT
1 AAAAATTTAAAAATA-TTTATATTAAATCTTAAATTACT-A-TTTAAAAATAAT
*
1197539 AAAAAATTT-AAAA-ATTTATATTAAATCCTAAATTACTATCTT-AAAA-AAT
1 -AAAAATTTAAAAATATTTATATTAAATCTTAAATTACTAT-TTAAAAATAAT
* * *
1197588 ---AA---AAAAATATTTGATATTGAATCTTGAATTACTGTTTAAAAATAAT
1 AAAAATTTAAAAATATTT-ATATTAAATCTTAAATTACTATTTAAAAATAAT
1197634 AAAAAATTTAAAAATATTT
1 -AAAAATTTAAAAATATTT
1197653 TATACTATAA
Statistics
Matches: 311, Mismatches: 25, Indels: 67
0.77 0.06 0.17
Matches are distributed among these distances:
43 4 0.01
44 6 0.02
45 24 0.08
46 3 0.01
48 8 0.03
49 57 0.18
50 60 0.19
51 51 0.16
52 24 0.08
53 42 0.14
54 14 0.05
55 12 0.04
56 6 0.02
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (51 bp):
AAAAATTTAAAAATATTTATATTAAATCTTAAATTACTATTTAAAAATAAT
Found at i:1197510 original size:102 final size:102
Alignment explanation
Indices: 1197230--1197652 Score: 414
Period size: 102 Copynumber: 4.2 Consensus size: 102
1197220 TCATCAATTC
* ** *
1197230 AAAAATTTCAAAATATATTTTATATTCAAT-TTCAAATTAAAATTT-AAAAATAATAAAA-ATTA
1 AAAAATTT-AAAA-ATA-TTTATATTAAATCTT-AAATTACTATTTAAAAAATAA-AAAATA-AA
* * **
1197292 AAATA-TTTGTATTAGATCTAAAATTACCTATTTAAAAATAATA
60 AAATATTTTATATTAAATCTTGAATTA-CTATTTAAAAATAATA
* * * * * *
1197335 AAAAGTTTAAAAAATATTTTGTATTAAATTCTGAAA-TACTA-TTAAATAATAAAAATTTAAAAA
1 AAAAATTT-AAAAATA-TTTATATTAAA-TCTTAAATTACTATTTAAAAAATAAAAAATAAAAAA
*
1197398 TATTTCATATTAAATCTTGAATTACTATTTAAAAAGTAAT-
63 TATTTTATATTAAATCTTGAATTACTATTTAAAAA-TAATA
1197438 AAAAATTTAAAAATATTTATATT-AATCTTAAATTACTATTTAAAAACATAAAAAATAAAAAATA
1 AAAAATTTAAAAATATTTATATTAAATCTTAAATTACTATTTAAAAA-ATAAAAAATAAAAAATA
1197502 TTTTATATTAAATCTTGAATTA-TAATTTTAAAAA-AATA
65 TTTTATATTAAATCTTGAATTACT-A-TTTAAAAATAATA
*
1197540 AAAAATTT-AAAA-ATTTATATTAAATCCTAAATTACTATCTTAAAAAAT-----A-AAAAAATA
1 AAAAATTTAAAAATATTTATATTAAATCTTAAATTACTAT-TTAAAAAATAAAAAATAAAAAATA
* * *
1197597 TTTGATATTGAATCTTGAATTACTGTTTAAAAATAATA
65 TTTTATATTAAATCTTGAATTACTATTTAAAAATAATA
1197635 AAAAATTTAAAAATATTT
1 AAAAATTTAAAAATATTT
1197653 TATACTATAA
Statistics
Matches: 273, Mismatches: 27, Indels: 44
0.79 0.08 0.13
Matches are distributed among these distances:
94 8 0.03
95 40 0.15
96 6 0.02
97 4 0.01
99 6 0.02
100 16 0.06
101 38 0.14
102 59 0.22
103 37 0.14
104 43 0.16
105 15 0.05
106 1 0.00
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (102 bp):
AAAAATTTAAAAATATTTATATTAAATCTTAAATTACTATTTAAAAAATAAAAAATAAAAAATAT
TTTATATTAAATCTTGAATTACTATTTAAAAATAATA
Found at i:1197620 original size:45 final size:42
Alignment explanation
Indices: 1197548--1197768 Score: 134
Period size: 42 Copynumber: 5.1 Consensus size: 42
1197538 TAAAAAATTT
1197548 AAAAATTTATATTAAATCCTAAATTACTATCTTAAAAAATAA-A
1 AAAAATTTATATTAAATCCTAAATTACTAT-TT-AAAAATAATA
* * * *
1197591 AAAATATTTGATATTGAATCTTGAATTACTGTTTAAAAATAATA
1 AAAA-ATTT-ATATTAAATCCTAAATTACTATTTAAAAATAATA
** **
1197635 AAAAATTTA-A--AAATATTTTA-TACTA--TAAAAATTAAAGATA
1 AAAAATTTATATTAAATCCTAAATTACTATTTAAAAA-T--A-ATA
* ** * *
1197675 AAAATATATTTTCGATTAAATATTCAATTACCATTT-AAAATAATAA
1 AAAA-AT-TTAT--ATTAAATCCTAAATTACTATTTAAAAATAAT-A
* *
1197721 AAAAATTTATATTAAATCCTGAATTGCTATTTAAAAATAATA
1 AAAAATTTATATTAAATCCTAAATTACTATTTAAAAATAATA
1197763 AAAAAT
1 AAAAAT
1197769 AAAAAATATT
Statistics
Matches: 140, Mismatches: 19, Indels: 39
0.71 0.10 0.20
Matches are distributed among these distances:
36 6 0.04
37 1 0.01
38 4 0.03
39 7 0.05
40 7 0.05
41 3 0.02
42 27 0.19
43 24 0.17
44 14 0.10
45 23 0.16
46 6 0.04
47 8 0.06
48 5 0.04
49 4 0.03
50 1 0.01
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (42 bp):
AAAAATTTATATTAAATCCTAAATTACTATTTAAAAATAATA
Found at i:1197665 original size:128 final size:126
Alignment explanation
Indices: 1197533--1197783 Score: 294
Period size: 128 Copynumber: 2.0 Consensus size: 126
1197523 ATAATTTTAA
* * *
1197533 AAAAATAAAAAATTTAAAA-AT-TTAT-ATTAAATCCTAAATTACTATCTTAAAA-AATAAAAAA
1 AAAAATAAAAAA-TAAAAATATATTATCATTAAATACTAAATTACCAT-TTAAAATAAT-AAAAA
* * * *
1197594 ATATTTGATATTGAATCTTGAATTACTGTTTAAAAATAATAAAAAATTTAAAAATATTTTATACT
63 A-ATTT-ATATTAAATCCTGAATTACTATTTAAAAATAATAAAAAA-TAAAAAATATTTTATACT
1197659 AT
125 AT
* * * * *
1197661 AAAAATTAAAGATAAAAATATATTTTCGATTAAATATTCAATTACCATTTAAAATAATAAAAAAA
1 AAAAATAAAAAATAAAAATATATTATC-ATTAAATACTAAATTACCATTTAAAATAATAAAAAAA
*
1197726 TTTATATTAAATCCTGAATTGCTATTTAAAAATAATAAAAAATAAAAAATATTTTATA
65 TTTATATTAAATCCTGAATTACTATTTAAAAATAATAAAAAATAAAAAATATTTTATA
1197784 TTAAATCTAA
Statistics
Matches: 105, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
127 20 0.19
128 47 0.45
129 7 0.07
130 12 0.11
131 19 0.18
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.37
Consensus pattern (126 bp):
AAAAATAAAAAATAAAAATATATTATCATTAAATACTAAATTACCATTTAAAATAATAAAAAAAT
TTATATTAAATCCTGAATTACTATTTAAAAATAATAAAAAATAAAAAATATTTTATACTAT
Found at i:1197668 original size:95 final size:93
Alignment explanation
Indices: 1197384--1197648 Score: 259
Period size: 95 Copynumber: 2.7 Consensus size: 93
1197374 TATTAAATAA
* * *
1197384 TAAAAATTTAAAAATATTTCATATTAAATCTTGAATTACTA-TTTAAAAAGTAAT-AAAAATTTA
1 TAAAAAATAAAAAATATTTGATATTAAATCTTGAATTA-TAGTTTAAAAA--AATAAAAAATTT-
** *
1197447 AAAATATTTATATT-AATCTTAAATTACTATTTAAAAACA
62 AAAA-ATTTATATTAAATCAAAAATTACTA--T-----CT
* *
1197486 TAAAAAATAAAAAATATTTTATATTAAATCTTGAATTATAATTTTAAAAAAATAAAAAATTTAAA
1 TAAAAAATAAAAAATATTTGATATTAAATCTTGAATTAT-AGTTTAAAAAAATAAAAAATTTAAA
**
1197551 AATTTATATTAAATCCTAAATTACTATCT
65 AATTTATATTAAATCAAAAATTACTATCT
*
1197580 TAAAAAATAAAAAAATATTTGATATTGAATCTTGAATTACT-GTTTAAAAATAATAAAAAATTTA
1 TAAAAAAT-AAAAAATATTTGATATTAAATCTTGAATTA-TAGTTTAAAAA-AATAAAAAATTTA
1197644 AAAAT
63 AAAAT
1197649 ATTTTATACT
Statistics
Matches: 148, Mismatches: 8, Indels: 21
0.84 0.05 0.12
Matches are distributed among these distances:
94 17 0.11
95 46 0.31
96 1 0.01
99 1 0.01
100 9 0.06
101 22 0.15
102 44 0.30
103 8 0.05
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (93 bp):
TAAAAAATAAAAAATATTTGATATTAAATCTTGAATTATAGTTTAAAAAAATAAAAAATTTAAAA
ATTTATATTAAATCAAAAATTACTATCT
Found at i:1197815 original size:49 final size:51
Alignment explanation
Indices: 1197710--1197833 Score: 141
Period size: 49 Copynumber: 2.5 Consensus size: 51
1197700 AATTACCATT
* *
1197710 TAAAATAATAAAAAA-A-TTTATATTAAATCCTGAATTGCTATTTAAAAATAA
1 TAAAA-AATAAAAAATATTTTATATTAAATCCTAAATTACTATTT-AAAATAA
*
1197761 TAAAAAATAAAAAATATTTTATATTAAAT-CTAAAATTACTATTT-AAA-GA
1 TAAAAAATAAAAAATATTTTATATTAAATCCT-AAATTACTATTTAAAATAA
* *
1197810 TAAAAATTTAAAAATATTTTATAT
1 TAAAAAATAAAAAATATTTTATAT
1197834 ATGCATTGGG
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
49 23 0.35
50 12 0.18
51 8 0.12
52 22 0.34
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (51 bp):
TAAAAAATAAAAAATATTTTATATTAAATCCTAAATTACTATTTAAAATAA
Found at i:1198448 original size:37 final size:37
Alignment explanation
Indices: 1198384--1198454 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
1198374 AAGAAATAAG
*
1198384 TTTTCTTTTTTAATTTATTATTTTTTTAGTTTAACAA
1 TTTTCTTTTTTAATTTATTATTTTTTTAATTTAACAA
* *
1198421 TTTTCTTTTTTGATTTGTT-TATTTTTTAATTTAA
1 TTTTCTTTTTTAATTTATTAT-TTTTTTAATTTAA
1198455 AAGTTAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 1 0.03
37 29 0.97
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.70
Consensus pattern (37 bp):
TTTTCTTTTTTAATTTATTATTTTTTTAATTTAACAA
Found at i:1201649 original size:25 final size:25
Alignment explanation
Indices: 1201608--1201687 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
1201598 AAAATCTTTT
* *
1201608 TATTTTATTATATTTATATTTTATTA
1 TATTTTAAT-TATTTATATTATATTA
* *
1201634 TATTTTAATTATTTATGTAATATTA
1 TATTTTAATTATTTATATTATATTA
* *
1201659 TATTTTTATTATATA-ATTATATTA
1 TATTTTAATTATTTATATTATATTA
1201683 TATTT
1 TATTT
1201688 AAAATCTATG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
24 12 0.26
25 26 0.57
26 8 0.17
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (25 bp):
TATTTTAATTATTTATATTATATTA
Found at i:1201681 original size:13 final size:11
Alignment explanation
Indices: 1201608--1201688 Score: 62
Period size: 10 Copynumber: 7.5 Consensus size: 11
1201598 AAAATCTTTT
1201608 TATTT-TATTA
1 TATTTATATTA
*
1201618 TATTTATATTT
1 TATTTATATTA
*
1201629 TA-TTATATTT
1 TATTTATATTA
*
1201639 TAATTAT-TTA
1 TATTTATATTA
* *
1201649 T-GTAATATTA
1 TATTTATATTA
*
1201659 TATTTTTATTA
1 TATTTATATTA
1201670 TATAATTATATTA
1 TAT--TTATATTA
1201683 TATTTA
1 TATTTA
1201689 AAATCTATGA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
9 3 0.05
10 22 0.39
11 22 0.39
13 10 0.18
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (11 bp):
TATTTATATTA
Found at i:1201684 original size:5 final size:5
Alignment explanation
Indices: 1201608--1201686 Score: 56
Period size: 5 Copynumber: 15.8 Consensus size: 5
1201598 AAAATCTTTT
* * * * *
1201608 TATTT TATTA TATTTA TATTT TATTA TATTT TAATTA T-TTA TGTAA TATTA
1 TATTA TATTA TA-TTA TATTA TATTA TATTA T-ATTA TATTA TATTA TATTA
*
1201659 TATTTT TATTA TA-TA -ATTA TATTA TATT
1 TA-TTA TATTA TATTA TATTA TATTA TATT
1201687 TAAAATCTAT
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
3 1 0.02
4 8 0.14
5 36 0.62
6 13 0.22
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (5 bp):
TATTA
Found at i:1203016 original size:26 final size:27
Alignment explanation
Indices: 1202987--1203046 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
1202977 TAAGAATTTT
* *
1202987 TTAATATTTATATATATTTAA-TTAAA
1 TTAATATTTACATAAATTTAAGTTAAA
*
1203013 TTAATAATTACATAAATTTAAGTTAAA
1 TTAATATTTACATAAATTTAAGTTAAA
1203040 TT-ATATT
1 TTAATATT
1203047 AAATAAGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 22 0.76
27 7 0.24
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (27 bp):
TTAATATTTACATAAATTTAAGTTAAA
Found at i:1203094 original size:18 final size:20
Alignment explanation
Indices: 1203041--1203087 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1203031 TAAGTTAAAT
*
1203041 TATA-TTAAATAA-GTATTA
1 TATATTTAAATAATTTATTA
1203059 TATATTTAAATAATTTATTA
1 TATATTTAAATAATTTATTA
1203079 TAT-TTTAAA
1 TATATTTAAA
1203088 ATTTTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 4 0.15
19 14 0.54
20 8 0.31
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TATATTTAAATAATTTATTA
Found at i:1203097 original size:17 final size:17
Alignment explanation
Indices: 1203041--1203096 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
1203031 TAAGTTAAAT
1203041 TATA-TTAAATAAGTATTA
1 TATATTTAAATAA-T-TTA
1203059 TATATTTAAATAATTTA
1 TATATTTAAATAATTTA
*
1203076 TTATATTTTAA-AATTT-
1 -TATATTTAAATAATTTA
1203092 TATAT
1 TATAT
1203097 AAATAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
15 5 0.14
17 8 0.23
18 14 0.40
19 8 0.23
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TATATTTAAATAATTTA
Found at i:1203744 original size:25 final size:28
Alignment explanation
Indices: 1203697--1203747 Score: 72
Period size: 25 Copynumber: 1.9 Consensus size: 28
1203687 AAAATATAAA
1203697 ATAAATCAAAATAAAATACAAACACATC
1 ATAAATCAAAATAAAATACAAACACATC
*
1203725 ATAAAT-AAAA-AAATTA-AAACACA
1 ATAAATCAAAATAAAATACAAACACA
1203748 AAAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 5 0.23
27 4 0.18
28 6 0.27
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.18
Consensus pattern (28 bp):
ATAAATCAAAATAAAATACAAACACATC
Found at i:1203879 original size:22 final size:23
Alignment explanation
Indices: 1203853--1203935 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 23
1203843 TAAATATACG
1203853 AAAAATAATAT-AAACATGATAT
1 AAAAATAATATAAAACATGATAT
* *
1203875 AAAAATAAT-TAAAACATAATACA
1 AAAAATAATATAAAACATGATA-T
** *
1203898 AAAAATAA-ATGTAACACGAATAT
1 AAAAATAATATAAAACATG-ATAT
*
1203921 AAAAATAGTATAAAA
1 AAAAATAATATAAAA
1203936 ATATGTGTAA
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
21 1 0.02
22 18 0.39
23 20 0.43
24 7 0.15
ACGTcount: A:0.66, C:0.06, G:0.05, T:0.23
Consensus pattern (23 bp):
AAAAATAATATAAAACATGATAT
Found at i:1203879 original size:23 final size:22
Alignment explanation
Indices: 1203848--1203901 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
1203838 CACTTTAAAT
*
1203848 ATACGAAAAATAA-TATAAACATG
1 ATAC-AAAAATAATTA-AAACATA
*
1203871 ATATAAAAATAATTAAAACATA
1 ATACAAAAATAATTAAAACATA
1203893 ATACAAAAA
1 ATACAAAAA
1203902 ATAAATGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (22 bp):
ATACAAAAATAATTAAAACATA
Found at i:1203893 original size:11 final size:12
Alignment explanation
Indices: 1203853--1203935 Score: 52
Period size: 11 Copynumber: 7.3 Consensus size: 12
1203843 TAAATATACG
1203853 AAAA-ATAATAT
1 AAAACATAATAT
*
1203864 -AAACATGATAT
1 AAAACATAATAT
1203875 AAAA-ATAAT-T
1 AAAACATAATAT
*
1203885 AAAACATAATAC
1 AAAACATAATAT
*
1203897 AAAAAATAA-AT
1 AAAACATAATAT
** *
1203908 GTAACACGAATAT
1 AAAACA-TAATAT
*
1203921 AAAA-ATAGTAT
1 AAAACATAATAT
1203932 AAAA
1 AAAA
1203936 ATATGTGTAA
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
10 8 0.15
11 27 0.51
12 14 0.26
13 4 0.08
ACGTcount: A:0.66, C:0.06, G:0.05, T:0.23
Consensus pattern (12 bp):
AAAACATAATAT
Found at i:1204296 original size:42 final size:41
Alignment explanation
Indices: 1204250--1204340 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 41
1204240 ATATAATTGT
*
1204250 ATTTTCATGTCGTAATCGTGTCAACACAGTTTATGGCACAAA
1 ATTTTCATGTCGTAATCGTGTCAACAC-GTTTATGACACAAA
** * **
1204292 ATTTTTGTGTCGTAATCGTTTCAACACGTTTATGACATGAA
1 ATTTTCATGTCGTAATCGTGTCAACACGTTTATGACACAAA
1204333 ATTTTCAT
1 ATTTTCAT
1204341 ATCATAAACG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 17 0.41
42 24 0.59
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (41 bp):
ATTTTCATGTCGTAATCGTGTCAACACGTTTATGACACAAA
Found at i:1205193 original size:16 final size:15
Alignment explanation
Indices: 1205172--1205201 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1205162 ATGTTATACT
1205172 TAGAATAGTAATATAG
1 TAGAATAG-AATATAG
1205188 TAGAATAGAATATA
1 TAGAATAGAATATA
1205202 AAGTTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (15 bp):
TAGAATAGAATATAG
Found at i:1205410 original size:8 final size:8
Alignment explanation
Indices: 1205389--1205430 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
1205379 GCTTATTTTG
1205389 AAAAATATA
1 AAAAATA-A
1205398 AAAAATAA
1 AAAAATAA
1205406 GAAAAA-AA
1 -AAAAATAA
1205414 CAAAAATAA
1 -AAAAATAA
1205423 AAAAATAA
1 AAAAATAA
1205431 GAAGAGAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 16 0.53
9 14 0.47
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:1211134 original size:20 final size:20
Alignment explanation
Indices: 1211105--1211181 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
1211095 GTAAAAAGAC
* *
1211105 AGAATATATCGATACATTGA
1 AGAATGTATCGATACATTAA
*
1211125 AGAATGTATCGATACATTCAT
1 AGAATGTATCGATACATT-AA
*
1211146 A-CATGTATCGATACATTAA
1 AGAATGTATCGATACATTAA
* *
1211165 AAAATGTATCAATACAT
1 AGAATGTATCGATACAT
1211182 CTAGGTACTT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.04
20 45 0.94
21 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTAA
Found at i:1212537 original size:22 final size:21
Alignment explanation
Indices: 1212512--1212577 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
1212502 TTTCAATTAA
1212512 AATATTACTATATTTTTTAATT
1 AATATTA-TATATTTTTTAATT
* *
1212534 AATA--ATATTTTTATTTAA-A
1 AATATTATATATTT-TTTAATT
1212553 AATATTATTATATTTTTTTAATT
1 AATATTA-TATA-TTTTTTAATT
1212576 AA
1 AA
1212578 CGGCGTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
19 10 0.29
20 6 0.18
21 1 0.03
22 12 0.35
23 5 0.15
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
AATATTATATATTTTTTAATT
Found at i:1212543 original size:17 final size:17
Alignment explanation
Indices: 1212521--1212558 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1212511 AAATATTACT
*
1212521 ATATTTTTTAATTAATA
1 ATATTTTTTAATTAAAA
*
1212538 ATA-TTTTTATTTAAAA
1 ATATTTTTTAATTAAAA
1212554 ATATT
1 ATATT
1212559 ATTATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTTTTAATTAAAA
Found at i:1213503 original size:6 final size:6
Alignment explanation
Indices: 1213463--1213509 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
1213453 TTTTTTCCTT
* * * *
1213463 TAATTT TAATTC TAATCC TAATAC TAATAC TAATTC TAATTC -AATTC
1 TAATTC TAATTC TAATTC TAATTC TAATTC TAATTC TAATTC TAATTC
1213510 CCACTTCATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (6 bp):
TAATTC
Found at i:1215247 original size:20 final size:20
Alignment explanation
Indices: 1215222--1215274 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
1215212 GTTTGGCATA
1215222 ATGTATCGATACAAT-TCTTC
1 ATGTATCGATACAATGTC-TC
1215242 ATGTATCGATACAATGTCTC
1 ATGTATCGATACAATGTCTC
1215262 ATGTATCGATACA
1 ATGTATCGATACA
1215275 TTTCACTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATGTCTC
Found at i:1215347 original size:20 final size:20
Alignment explanation
Indices: 1215324--1215396 Score: 146
Period size: 20 Copynumber: 3.6 Consensus size: 20
1215314 ACAATTGAGT
1215324 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAAAGCATA
1215344 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAAAGCATA
1215364 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAAAGCATA
1215384 ATGTATCGATACA
1 ATGTATCGATACA
1215397 TCTGGGTGTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (20 bp):
ATGTATCGATACAAAGCATA
Found at i:1215414 original size:40 final size:39
Alignment explanation
Indices: 1215304--1215415 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 39
1215294 TGCTAGTTTC
1215304 ATGTATCGATACAATTGAGTATGTATCGATACAAAGCATA
1 ATGTATCGATAC-ATTGAGTATGTATCGATACAAAGCATA
**
1215344 ATGTATCGATACAAAGCA-TAATGTATCGATACAAAGCATA
1 ATGTATCGATACATTG-AGT-ATGTATCGATACAAAGCATA
* * *
1215384 ATGTATCGATACATCTGGGTGTGTAACGATAC
1 ATGTATCGATACAT-TGAGTATGTATCGATAC
1215416 TTTCTAAGCT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
39 3 0.05
40 56 0.92
41 2 0.03
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (39 bp):
ATGTATCGATACATTGAGTATGTATCGATACAAAGCATA
Found at i:1217743 original size:21 final size:19
Alignment explanation
Indices: 1217696--1217743 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
1217686 TTTGTTGATG
1217696 ATTTTGATGAAAAACAGAA
1 ATTTTGATGAAAAACAGAA
1217715 AGTTTTGATGTAAATAACA-AGA
1 A-TTTTGATG-AAA-AACAGA-A
1217737 ATTTTGA
1 ATTTTGA
1217744 AAAGGATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 1 0.04
20 8 0.32
21 10 0.40
22 6 0.24
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (19 bp):
ATTTTGATGAAAAACAGAA
Found at i:1224156 original size:19 final size:19
Alignment explanation
Indices: 1224113--1224168 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1224103 CTGCTAGTTT
1224113 CATGTAT-TGATACAATTGAG
1 CATGTATCT-ATACAA-TGAG
*
1224133 TATGTATCTATACAATGAG
1 CATGTATCTATACAATGAG
*
1224152 CATGTATCGATACAATG
1 CATGTATCTATACAATG
1224169 TATCGATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.59
20 12 0.38
21 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (19 bp):
CATGTATCTATACAATGAG
Found at i:1224171 original size:13 final size:13
Alignment explanation
Indices: 1224153--1224184 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1224143 TACAATGAGC
1224153 ATGTATCGATACA
1 ATGTATCGATACA
1224166 ATGTATCGATACA
1 ATGTATCGATACA
1224179 ATGTAT
1 ATGTAT
1224185 AATGTATCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1224178 original size:32 final size:33
Alignment explanation
Indices: 1224134--1224198 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1224124 ACAATTGAGT
* *
1224134 ATGTATCTATACAATG-AGCATGTATCGATACA
1 ATGTATCGATACAATGTAGAATGTATCGATACA
*
1224166 ATGTATCGATACAATGTATAATGTATCGATACA
1 ATGTATCGATACAATGTAGAATGTATCGATACA
1224199 TCTAGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAATGTAGAATGTATCGATACA
Found at i:1230540 original size:15 final size:15
Alignment explanation
Indices: 1230518--1230560 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1230508 CAAGAAAAAA
1230518 AAGAAAAAAAAAGAC
1 AAGAAAAAAAAAGAC
* ** *
1230533 ATGAAAAAGTAAGAG
1 AAGAAAAAAAAAGAC
1230548 AAGAAAAAAAAAG
1 AAGAAAAAAAAAG
1230561 CTATGAATAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (15 bp):
AAGAAAAAAAAAGAC
Found at i:1233771 original size:113 final size:114
Alignment explanation
Indices: 1233571--1233797 Score: 330
Period size: 113 Copynumber: 2.0 Consensus size: 114
1233561 ATTACTAAAT
* * *
1233571 ATTATCCATTACAATCATGACTAATTGTTTGGAAGTATAACTAATTTAATGCATGCTTATCTTTT
1 ATTATCCATTACAATCATGACTAATTGTTTGGAAGTATAACTAATTGAATACATGCTCATCTTTT
*
1233636 TATGAAAGTAAAAATTAGAAAAAAAATCAAAGCAAAATAATATAAAAAA
66 TATGAAAGTAAAAATTAAAAAAAAAATCAAAGCAAAATAATATAAAAAA
* * * *** *
1233685 ATTATCCATTATAATCGTGACTAATTG-TTGGAATTATCTTTAATTGCATACATGCTCATCTTTT
1 ATTATCCATTACAATCATGACTAATTGTTTGGAAGTATAACTAATTGAATACATGCTCATCTTTT
* *
1233749 TATGAAAGTAATAATTAAAAAAAAAATCAAAGTAAAATAATATAAAAAA
66 TATGAAAGTAAAAATTAAAAAAAAAATCAAAGCAAAATAATATAAAAAA
1233798 TCATTCCTCT
Statistics
Matches: 100, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
113 75 0.75
114 25 0.25
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (114 bp):
ATTATCCATTACAATCATGACTAATTGTTTGGAAGTATAACTAATTGAATACATGCTCATCTTTT
TATGAAAGTAAAAATTAAAAAAAAAATCAAAGCAAAATAATATAAAAAA
Done.