Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold173
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: 2040036
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 9 of 16
Found at i:1114522 original size:2 final size:2
Alignment explanation
Indices: 1114515--1114539 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1114505 ACATGTAGAT
1114515 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1114540 AACATTAGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1116674 original size:2 final size:2
Alignment explanation
Indices: 1116669--1116696 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1116659 ATTCTCTCCA
1116669 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1116697 ACACACACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1117565 original size:29 final size:31
Alignment explanation
Indices: 1117532--1117595 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 31
1117522 ATATAATACG
*
1117532 AAAATGATATAATTAAATAAT-TAAA-ATAT
1 AAAATAATATAATTAAATAATATAAATATAT
*
1117561 AAAATAATATAATTATATAATATAAATATAT
1 AAAATAATATAATTAAATAATATAAATATAT
1117592 AAAA
1 AAAA
1117596 ATATTAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 19 0.61
30 4 0.13
31 8 0.26
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (31 bp):
AAAATAATATAATTAAATAATATAAATATAT
Found at i:1117574 original size:21 final size:21
Alignment explanation
Indices: 1117538--1117593 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1117528 TACGAAAATG
* *
1117538 ATATAATTAAATAATTA-A-A
1 ATATAAATATATAATTATATA
1117557 ATATAAAATAATATAATTATATA
1 ATAT-AAAT-ATATAATTATATA
1117580 ATATAAATATATAA
1 ATATAAATATATAA
1117594 AAATATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 4 0.13
20 3 0.10
21 14 0.45
22 5 0.16
23 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATAAATATATAATTATATA
Found at i:1117582 original size:13 final size:13
Alignment explanation
Indices: 1117564--1117593 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1117554 AAAATATAAA
*
1117564 ATAATATAATTAT
1 ATAATATAAATAT
1117577 ATAATATAAATAT
1 ATAATATAAATAT
1117590 ATAA
1 ATAA
1117594 AAATATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATATAAATAT
Found at i:1119768 original size:15 final size:16
Alignment explanation
Indices: 1119748--1119781 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1119738 ATCTATAAAT
*
1119748 ATATTT-TTTTATTAA
1 ATATTTATTATATTAA
1119763 ATATTTATTATATTAA
1 ATATTTATTATATTAA
1119779 ATA
1 ATA
1119782 ACGTTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATATTTATTATATTAA
Found at i:1120255 original size:13 final size:14
Alignment explanation
Indices: 1120221--1120276 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
1120211 TAATCCGTAT
**
1120221 TATATTTTTTAATT
1 TATATTTTTTAAAA
1120235 TA-ATTTTTTTAAAA
1 TATA-TTTTTTAAAA
1120249 -ATATTTTTTAAAA
1 TATATTTTTTAAAA
* *
1120262 TTTAATTTTTAAAA
1 TATATTTTTTAAAA
1120276 T
1 T
1120277 TTAATAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 12 0.34
14 23 0.66
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATATTTTTTAAAA
Found at i:1120272 original size:27 final size:26
Alignment explanation
Indices: 1120222--1120275 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
1120212 AATCCGTATT
1120222 ATATTTTTTAATTTAATTTTTTTAAAA
1 ATATTTTTTAATTTAA-TTTTTTAAAA
1120249 ATATTTTTTAAAATTTAA-TTTTTAAAA
1 ATATTTTTT--AATTTAATTTTTTAAAA
1120276 TTTAATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 18 0.72
29 7 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
ATATTTTTTAATTTAATTTTTTAAAA
Found at i:1120370 original size:21 final size:21
Alignment explanation
Indices: 1120327--1120385 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
1120317 AATATTTTTA
* *
1120327 ATATTTATATTATAATATCATAT
1 ATATTTAT-TT-TTATATAATAT
1120350 ATATTTATTTTTATATAATAT
1 ATATTTATTTTTATATAATAT
*
1120371 A-AATTATTTTTATAT
1 ATATTTATTTTTATAT
1120386 GATAAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.39
21 10 0.30
22 2 0.06
23 8 0.24
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATTTATTTTTATATAATAT
Found at i:1120379 original size:20 final size:19
Alignment explanation
Indices: 1120354--1120396 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
1120344 TCATATATAT
1120354 TTATTTTTATATAATATAAA
1 TTATTTTTATATAATA-AAA
*
1120374 TTATTTTTATATGATAAAA
1 TTATTTTTATATAATAAAA
1120393 TTAT
1 TTAT
1120397 ATAATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTTTTATATAATAAAA
Found at i:1120423 original size:21 final size:21
Alignment explanation
Indices: 1120398--1120442 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1120388 TAAAATTATA
1120398 TAATATATATAAATATAAAAT
1 TAATATATATAAATATAAAAT
* * *
1120419 TAATATATATTATTATATAAT
1 TAATATATATAAATATAAAAT
1120440 TAA
1 TAA
1120443 AAATAAATCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATATATATAAATATAAAAT
Found at i:1120518 original size:18 final size:17
Alignment explanation
Indices: 1120492--1120557 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 17
1120482 TAAAACTCAC
1120492 TTTATTTTTAAATAAAT
1 TTTATTTTTAAATAAAT
* *
1120509 TTTATATTTTAAAAAAAC
1 TTTAT-TTTTAAATAAAT
*
1120527 TTAATTTTTAAATTAATAT
1 TTTATTTTTAAA-TAA-AT
*
1120546 TTT-TATTTAAAT
1 TTTATTTTTAAAT
1120558 TATTTTAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
17 13 0.33
18 23 0.59
19 3 0.08
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTATTTTTAAATAAAT
Found at i:1120764 original size:19 final size:20
Alignment explanation
Indices: 1120740--1120782 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1120730 CAGTAGCTTG
*
1120740 CTTTTAGCTT-TGCTGCATC
1 CTTTTAGCTTGTGCTGCATA
*
1120759 CTTTTAGCTTGTTCTGCATA
1 CTTTTAGCTTGTGCTGCATA
1120779 CTTT
1 CTTT
1120783 CAACATGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.12, C:0.23, G:0.14, T:0.51
Consensus pattern (20 bp):
CTTTTAGCTTGTGCTGCATA
Found at i:1123110 original size:20 final size:21
Alignment explanation
Indices: 1123074--1123112 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1123064 CTGGACATGT
1123074 TAAAATGCATAGAACATGGCA
1 TAAAATGCATAGAACATGGCA
1123095 TAAAATGCAT-GAACATGG
1 TAAAATGCATAGAACATGG
1123113 GCTATTAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.21
Consensus pattern (21 bp):
TAAAATGCATAGAACATGGCA
Found at i:1124182 original size:21 final size:20
Alignment explanation
Indices: 1124135--1124188 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
1124125 CATTTCAAGC
*
1124135 ATGTATCGATGCATTCACTT
1 ATGTATCGATACATTCACTT
1124155 ATGTATCGATACATT-ACCTT
1 ATGTATCGATACATTCA-CTT
1124175 ATTGTATCGATACA
1 A-TGTATCGATACA
1124189 AATTGTAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 1 0.03
20 18 0.58
21 12 0.39
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:1128946 original size:83 final size:83
Alignment explanation
Indices: 1128806--1128960 Score: 213
Period size: 83 Copynumber: 1.9 Consensus size: 83
1128796 AGAATTAAAT
* * *
1128806 TTTAAACTTTGATGCATTTAAAAACGGGGTTGGAGTATCCTCTCGGAGGAATGGGGTTAAAGTGT
1 TTTAAACTTTGATACATTTAAAAACGGGGTTGGAGTATCCTCTCGGAGGAATAGGGTTAAAGTAT
1128871 CCCCGATGATGACAAAGA
66 CCCCGATGATGACAAAGA
** * * **
1128889 TTTAAACTTTGATATGTTTGAAAGCGGGGTTGGAGTATCC-CTTCGGAGGAATAGGGTTGGAGTA
1 TTTAAACTTTGATACATTTAAAAACGGGGTTGGAGTATCCTC-TCGGAGGAATAGGGTTAAAGTA
1128953 TCCCCGAT
65 TCCCCGAT
1128961 AAATAAAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
82 1 0.02
83 61 0.98
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (83 bp):
TTTAAACTTTGATACATTTAAAAACGGGGTTGGAGTATCCTCTCGGAGGAATAGGGTTAAAGTAT
CCCCGATGATGACAAAGA
Found at i:1131498 original size:14 final size:15
Alignment explanation
Indices: 1131479--1131508 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1131469 CGTATTGCAC
1131479 TCCTTTT-TTTTTTT
1 TCCTTTTCTTTTTTT
1131493 TCCTTTTCTTTTTTT
1 TCCTTTTCTTTTTTT
1131508 T
1 T
1131509 ATATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TCCTTTTCTTTTTTT
Found at i:1132408 original size:25 final size:24
Alignment explanation
Indices: 1132361--1132409 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1132351 TTTAATTTAT
*
1132361 ACTAAAAAAAACTTAATTAATTTC
1 ACTAAAAAAAACTTAATAAATTTC
1132385 ACTAAAAAAAAGC-TAATAACATTTC
1 ACTAAAAAAAA-CTTAATAA-ATTTC
1132410 TATTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (24 bp):
ACTAAAAAAAACTTAATAAATTTC
Found at i:1135897 original size:2 final size:2
Alignment explanation
Indices: 1135892--1135918 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1135882 TGGGTGTGTG
1135892 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1135919 TTAGAGGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1137320 original size:89 final size:89
Alignment explanation
Indices: 1137167--1138159 Score: 679
Period size: 89 Copynumber: 10.9 Consensus size: 89
1137157 GTTCTAATAA
* * * * * * * *
1137167 AATAAAATTCTTAGAACTCAAAAGATGTGACAGATGTATATGGGCATCAGATTCTTTCTAACACG
1 AATAAATTTCTTGGAACCCAAAAGATGTGACAGATGCATGTGGGTATCAGATTCCTTCTGACACG
1137232 ACGAAAAATATTTGACTAATGCCT
66 ACGAAAAATATTTGACTAATGCCT
* * *
1137256 AATAAATTTTTTGGAACACAAAAGATGTGATAGATGCATGTGGGTATCAGATTCCTTCTGACACG
1 AATAAATTTCTTGGAACCCAAAAGATGTGACAGATGCATGTGGGTATCAGATTCCTTCTGACACG
** * * *
1137321 ACGGGAAATATTTGACCAATACTT
66 ACGAAAAATATTTGACTAATGCCT
*
1137345 AATAAATTTTTTGGAACCCGAAAA-ATGTGACAGATGCATGTGGGTATCAGATTCCTTCTGACAC
1 AATAAATTTCTTGGAACCC-AAAAGATGTGACAGATGCATGTGGGTATCAGATTCCTTCTGACAC
* * *
1137409 GATGAAAAATATTTAACTAATGTCT
65 GACGAAAAATATTTGACTAATGCCT
* * * * *
1137434 AATAAATTTCTTGAAACTCGAAAGATGTGACAGATACATGTGGGTATCAGATTCTTTCTGACACG
1 AATAAATTTCTTGGAACCCAAAAGATGTGACAGATGCATGTGGGTATCAGATTCCTTCTGACACG
*
1137499 AC-AGAAAATATTTGACTAATACCT
66 ACGA-AAAATATTTGACTAATGCCT
* * *
1137523 AATAAATTTCTTGGAACCCGAAAGATGTGACAAATGCATGTGGGTATCAGATTCTTTCTGACACG
1 AATAAATTTCTTGGAACCCAAAAGATGTGACAGATGCATGTGGGTATCAGATTCCTTCTGACACG
* * * *
1137588 ATGGAAAATATTTAACTAATGTCT
66 ACGAAAAATATTTGACTAATGCCT
* ** * * * * * * *
1137612 AATAAATTTCTTAGAACCTGAAAGATATAATAGATGCATATAGGTATTAAATTCCTTCTGACACG
1 AATAAATTTCTTGGAACCCAAAAGATGTGACAGATGCATGTGGGTATCAGATTCCTTCTGACACG
* *
1137677 ACGAAAAATATTTTACTATTGCCT
66 ACGAAAAATATTTGACTAATGCCT
* * * * * * ** *
1137701 AATAAATTTCTTGCAGATTCCTTCTAACACGACG-GAAATATTTG-ACTAATGCCTAAT-AAATT
1 AATAAATTTCTTG--GA-ACC--C-AA-AAGATGTGACAGA--TGCA-T-GTGGGT-ATCAGATT
* * * *
1137763 TCTT-GGA-AC--CCAAAAGATATTATAGA-TGTATG--T
54 CCTTCTGACACGACGAAAA-ATATT-T-GACT-AATGCCT
* * *** * * * * * ***
1137796 AGGTATCAGATTTCTTCTAGCACGATGAAAAAAATTTGATTA-TTGCCTAATAAATTTCT-TGCA
1 A---AT-AAATTTC-T-T-GGA--ACCCAAAAGATGTGA-CAGATG-C--AT--GTGGGTAT-CA
* * * *
1137859 GATTTCTTTTGACACGATGAAAAATATTTGATTAATGCCT
50 GATTCCTTCTGACACGACGAAAAATATTTGACTAATGCCT
* ** * * * * * *
1137899 AATAAAATTCTTAAAACTCGAAAGATATGACAGATGCATGTAGGTATCAGATTCTTTCTGACACA
1 AATAAATTTCTTGGAACCCAAAAGATGTGACAGATGCATGTGGGTATCAGATTCCTTCTGACACG
1137964 ACG-AAAATATTTGACTAATGCCT
66 ACGAAAAATATTTGACTAATGCCT
* * * * * **
1137987 AATAAAATTCTTGAAACCCAAAAGTTATGACAAATGCATGTAAGTATCAGATTCCTTCTGACACG
1 AATAAATTTCTTGGAACCCAAAAGATGTGACAGATGCATGTGGGTATCAGATTCCTTCTGACACG
* *
1138052 AC-AGAAAATATTTGATTAATGTCT
66 ACGA-AAAATATTTGACTAATGCCT
* * *
1138076 AAGAAAATTCTTGAAACCCAAAAGATGTGACAGATGCATGTGGGTATCAGATTCCTTCTGACACG
1 AATAAATTTCTTGGAACCCAAAAGATGTGACAGATGCATGTGGGTATCAGATTCCTTCTGACACG
1138141 AC-AGAAAATATTTGACTAA
66 ACGA-AAAATATTTGACTAA
1138160 CAATACAATA
Statistics
Matches: 718, Mismatches: 138, Indels: 96
0.75 0.14 0.10
Matches are distributed among these distances:
88 82 0.11
89 498 0.69
90 5 0.01
91 4 0.01
92 2 0.00
93 2 0.00
94 16 0.02
95 11 0.02
96 11 0.02
97 11 0.02
98 19 0.03
99 15 0.02
100 18 0.03
101 8 0.01
102 5 0.01
103 7 0.01
104 4 0.01
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (89 bp):
AATAAATTTCTTGGAACCCAAAAGATGTGACAGATGCATGTGGGTATCAGATTCCTTCTGACACG
ACGAAAAATATTTGACTAATGCCT
Found at i:1137758 original size:54 final size:55
Alignment explanation
Indices: 1137662--1137767 Score: 169
Period size: 54 Copynumber: 1.9 Consensus size: 55
1137652 TAGGTATTAA
* * *
1137662 ATTCCTTCTGACACGACGAAAAATATTTTACTATTGCCTAATAAATTTCTTGCAG
1 ATTCCTTCTAACACGACGAAAAATATTTGACTAATGCCTAATAAATTTCTTGCAG
*
1137717 ATTCCTTCTAACACGACG-GAAATATTTGACTAATGCCTAATAAATTTCTTG
1 ATTCCTTCTAACACGACGAAAAATATTTGACTAATGCCTAATAAATTTCTTG
1137768 GAACCCAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 30 0.64
55 17 0.36
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (55 bp):
ATTCCTTCTAACACGACGAAAAATATTTGACTAATGCCTAATAAATTTCTTGCAG
Found at i:1137840 original size:143 final size:143
Alignment explanation
Indices: 1137570--1137999 Score: 533
Period size: 143 Copynumber: 3.0 Consensus size: 143
1137560 ATGTGGGTAT
* * * *
1137570 CAGATTCTTTCTGACACGATGGAAAATATTTAACTAATGTCTAATAAATTTCTTAGAACCTGAAA
1 CAGATTCCTTCTGACACGATGG-AAATATTTGACTAATGCCTAATAAATTTCTTAGAACCCGAAA
* * * * *
1137635 GATATAATAGATGCATATAGGTATTAAATTCCTTCTGACACGACGAAAAATATTTTACTATTGCC
65 GATATAATAGATGCATGTAGGTATCAGATTTCTTCTGACACGACGAAAAATATTTGACTATTGCC
1137700 TAATAAATTTCTTG
130 TAATAAATTTCTTG
* * * *
1137714 CAGATTCCTTCTAACACGACGGAAATATTTGACTAATGCCTAATAAATTTCTTGGAACCCAAAAG
1 CAGATTCCTTCTGACACGATGGAAATATTTGACTAATGCCTAATAAATTTCTTAGAACCCGAAAG
* * * * *
1137779 ATATTATAGATGTATGTAGGTATCAGATTTCTTCT-AGCACGATGAAAAAAATTTGATTATTGCC
66 ATATAATAGATGCATGTAGGTATCAGATTTCTTCTGA-CACGACGAAAAATATTTGACTATTGCC
1137843 TAATAAATTTCTTG
130 TAATAAATTTCTTG
* * * * * * *
1137857 CAGATTTCTTTTGACACGATGAAAAATATTTGATTAATGCCTAATAAAATTCTTAAAACTCGAAA
1 CAGATTCCTTCTGACACGATG-GAAATATTTGACTAATGCCTAATAAATTTCTTAGAACCCGAAA
* * * *
1137922 GATATGACAGATGCATGTAGGTATCAGA-TTCTTTCTGACACAACG-AAAATATTTGACTAATGC
65 GATATAATAGATGCATGTAGGTATCAGATTTC-TTCTGACACGACGAAAAATATTTGACTATTGC
*
1137985 CTAATAAAATTCTTG
129 CTAATAAATTTCTTG
1138000 AAACCCAAAA
Statistics
Matches: 244, Mismatches: 38, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
142 1 0.00
143 153 0.63
144 89 0.36
145 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (143 bp):
CAGATTCCTTCTGACACGATGGAAATATTTGACTAATGCCTAATAAATTTCTTAGAACCCGAAAG
ATATAATAGATGCATGTAGGTATCAGATTTCTTCTGACACGACGAAAAATATTTGACTATTGCCT
AATAAATTTCTTG
Found at i:1137875 original size:55 final size:55
Alignment explanation
Indices: 1137802--1137910 Score: 166
Period size: 55 Copynumber: 2.0 Consensus size: 55
1137792 ATGTAGGTAT
* *
1137802 CAGATTTCTTCTAGCACGATGAAAAAAATTTGATTATTGCCTAATAAATTTCTTG
1 CAGATTTCTTCTAGCACGATGAAAAAAATTTGATTAATGCCTAATAAAATTCTTG
* *
1137857 CAGATTTCTT-TTGACACGATGAAAAATATTTGATTAATGCCTAATAAAATTCTT
1 CAGATTTCTTCTAG-CACGATGAAAAAAATTTGATTAATGCCTAATAAAATTCTT
1137911 AAAACTCGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 2 0.04
55 47 0.96
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.39
Consensus pattern (55 bp):
CAGATTTCTTCTAGCACGATGAAAAAAATTTGATTAATGCCTAATAAAATTCTTG
Found at i:1141276 original size:10 final size:10
Alignment explanation
Indices: 1141261--1141327 Score: 59
Period size: 10 Copynumber: 6.9 Consensus size: 10
1141251 AAAAACTTAC
1141261 TTAAAAAAAT
1 TTAAAAAAAT
1141271 TTAAAAAAA-
1 TTAAAAAAAT
* *
1141280 CT-AAAAACT
1 TTAAAAAAAT
* *
1141289 ATAAAATAA-
1 TTAAAAAAAT
1141298 TTATAAAAAAT
1 TTA-AAAAAAT
1141309 TTAAAAAAAT
1 TTAAAAAAAT
*
1141319 TGAAAAAAA
1 TTAAAAAAA
1141328 ATGAATCTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
8 5 0.11
9 4 0.09
10 33 0.73
11 3 0.07
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.25
Consensus pattern (10 bp):
TTAAAAAAAT
Found at i:1141278 original size:9 final size:9
Alignment explanation
Indices: 1141264--1141326 Score: 54
Period size: 9 Copynumber: 6.7 Consensus size: 9
1141254 AACTTACTTA
1141264 AAAAAATTT
1 AAAAAATTT
**
1141273 AAAAAAACT
1 AAAAAATTT
* *
1141282 AAAAACTAT
1 AAAAAATTT
1141291 AAAATAATTAT
1 AAAA-AATT-T
1141302 AAAAAATTT
1 AAAAAATTT
*
1141311 AAAAAAATTG
1 -AAAAAATTT
1141321 AAAAAA
1 AAAAAA
1141327 AATGAATCTG
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
9 24 0.56
10 14 0.33
11 5 0.12
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (9 bp):
AAAAAATTT
Found at i:1141573 original size:28 final size:28
Alignment explanation
Indices: 1141522--1141584 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
1141512 TTATAAATGA
*
1141522 TTAAA-AATAAAAATTATAACAAAAATT
1 TTAAATAATAAAAATTATAAAAAAAATT
* *
1141549 TTGAATAATAAAAATTGA-AAAAAAAGTT
1 TTAAATAATAAAAATT-ATAAAAAAAATT
1141577 TTAAATAA
1 TTAAATAA
1141585 ATTATAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 4 0.13
28 25 0.83
29 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (28 bp):
TTAAATAATAAAAATTATAAAAAAAATT
Found at i:1141589 original size:51 final size:53
Alignment explanation
Indices: 1141532--1141656 Score: 139
Period size: 58 Copynumber: 2.3 Consensus size: 53
1141522 TTAAAAATAA
* *
1141532 AAATTATAACAAAAATTTTGAAT-A-AT-AAAAATTGAAAAAAAAGTTTTAAAT
1 AAATTATAACAAAAATTTTAAATAATATGAAAAAATGAAAAAAAA-TTTTAAAT
*
1141583 AAATTATAAATCGAAAAGTTTTAAATAAATTATGAAAAAATGAAAAAAAATTTTAAAT
1 AAATTAT-AA-C-AAAAATTTTAAAT-AA-TATGAAAAAATGAAAAAAAATTTTAAAT
*
1141641 AAATTATAAAAAAAAT
1 AAATTATAACAAAAAT
1141657 GAAAAAAAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
51 7 0.11
52 2 0.03
53 1 0.02
54 11 0.18
55 5 0.08
56 1 0.02
57 2 0.03
58 17 0.28
59 15 0.25
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (53 bp):
AAATTATAACAAAAATTTTAAATAATATGAAAAAATGAAAAAAAATTTTAAAT
Found at i:1141592 original size:11 final size:11
Alignment explanation
Indices: 1141530--1141698 Score: 94
Period size: 11 Copynumber: 14.5 Consensus size: 11
1141520 GATTAAAAAT
1141530 AAAAATTATAA
1 AAAAATTATAA
1141541 CAAAAATTTTGAATAA
1 -AAAAA--TT--ATAA
1141557 TAAAAATTGA-AA
1 -AAAAATT-ATAA
*
1141569 AAAAAGTTTTAA
1 AAAAA-TTATAA
*
1141581 ATAAATTATAA
1 AAAAATTATAA
*
1141592 ATCGAAAAGTTTTAA
1 A---AAAA-TTATAA
* *
1141607 ATAAATTATGA
1 AAAAATTATAA
*
1141618 AAAAATGA-AA
1 AAAAATTATAA
*
1141628 AAAAATTTTAA
1 AAAAATTATAA
*
1141639 ATAAATTATAAA
1 AAAAATTAT-AA
*
1141651 AAAAATGA-AA
1 AAAAATTATAA
*
1141661 AAAAATTTTAA
1 AAAAATTATAA
1141672 AAAAATTATAA
1 AAAAATTATAA
1141683 AAAAATTGA-AA
1 AAAAATT-ATAA
1141694 AAAAA
1 AAAAA
1141699 AACACCAATT
Statistics
Matches: 121, Mismatches: 22, Indels: 29
0.70 0.13 0.17
Matches are distributed among these distances:
10 15 0.12
11 56 0.46
12 27 0.22
13 1 0.01
14 7 0.06
15 6 0.05
16 9 0.07
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:1141654 original size:22 final size:22
Alignment explanation
Indices: 1141530--1141699 Score: 94
Period size: 23 Copynumber: 7.2 Consensus size: 22
1141520 GATTAAAAAT
1141530 AAAAATTATAACAAAAATTTTGAATAA
1 AAAAATTATAA-AAAAA--TT--ATAA
*
1141557 TAAAAATTGA-AAAAAAAGTTTTAA
1 -AAAAATT-ATAAAAAAA-TTATAA
* *
1141581 ATAAATTATAAATCGAAAAGTTTTAA
1 AAAAATTATAAA---AAAA-TTATAA
* * *
1141607 ATAAATTATGAAAAAATGA-AA
1 AAAAATTATAAAAAAATTATAA
* *
1141628 AAAAATTTTAAATAAATTATAAA
1 AAAAATTATAAAAAAATTAT-AA
* *
1141651 AAAAATGA-AAAAAAATTTTAA
1 AAAAATTATAAAAAAATTATAA
*
1141672 AAAAATTATAAAAAAATTGAAAA
1 AAAAATTATAAAAAAATT-ATAA
1141695 AAAAA
1 AAAAA
1141700 ACACCAATTG
Statistics
Matches: 115, Mismatches: 18, Indels: 23
0.74 0.12 0.15
Matches are distributed among these distances:
21 25 0.22
22 20 0.17
23 28 0.24
24 3 0.03
26 24 0.21
27 5 0.04
28 9 0.08
29 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (22 bp):
AAAAATTATAAAAAAATTATAA
Found at i:1141659 original size:33 final size:33
Alignment explanation
Indices: 1141596--1141698 Score: 163
Period size: 33 Copynumber: 3.2 Consensus size: 33
1141586 TTATAAATCG
* *
1141596 AAAAGTTTTAAATAAATTAT-GAAAAAATGAAA
1 AAAAATTTTAAATAAATTATAAAAAAAATGAAA
1141628 AAAAATTTTAAATAAATTATAAAAAAAATGAAA
1 AAAAATTTTAAATAAATTATAAAAAAAATGAAA
* *
1141661 AAAAATTTTAAAAAAATTATAAAAAAATTGAAA
1 AAAAATTTTAAATAAATTATAAAAAAAATGAAA
1141694 AAAAA
1 AAAAA
1141699 AACACCAATT
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 19 0.29
33 47 0.71
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (33 bp):
AAAAATTTTAAATAAATTATAAAAAAAATGAAA
Found at i:1142130 original size:2 final size:2
Alignment explanation
Indices: 1142119--1142152 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1142109 TATATTCTTT
*
1142119 TA TA TC TA TA TA TA TA TA TA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1142153 GGGTTTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1142145 original size:13 final size:13
Alignment explanation
Indices: 1142127--1142152 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1142117 TTTATATCTA
1142127 TATATATATATAT
1 TATATATATATAT
1142140 TATATATATATAT
1 TATATATATATAT
1142153 GGGTTTTGAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:1144353 original size:32 final size:34
Alignment explanation
Indices: 1144306--1144398 Score: 97
Period size: 36 Copynumber: 2.8 Consensus size: 34
1144296 CAATACTATC
*
1144306 TTTC-AAGGATAAGATAGAAACCTCTT-TATC-T
1 TTTCAAAGGCTAAGATAGAAACCTCTTCTATCTT
**
1144337 TTTCACGGGCTAAGATAG-AACCTCTCTCCATATCTT
1 TTTCAAAGGCTAAGATAGAAACCTCT-T-C-TATCTT
1144373 TTTCAAAGGCTAAGATA-AAACCTCTT
1 TTTCAAAGGCTAAGATAGAAACCTCTT
1144399 AATCACTTAG
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
31 11 0.22
32 11 0.22
35 5 0.10
36 23 0.46
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (34 bp):
TTTCAAAGGCTAAGATAGAAACCTCTTCTATCTT
Found at i:1144854 original size:19 final size:19
Alignment explanation
Indices: 1144830--1144889 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
1144820 GGGCTCAATG
1144830 TATCGATACTATTTACATA
1 TATCGATACTATTTACATA
*
1144849 TATCGATAC-----A-ATG
1 TATCGATACTATTTACATA
1144862 TATCGATACTATTTACATA
1 TATCGATACTATTTACATA
1144881 TATCGATAC
1 TATCGATAC
1144890 AATGTATCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
13 11 0.33
14 1 0.03
18 1 0.03
19 20 0.61
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (19 bp):
TATCGATACTATTTACATA
Found at i:1144866 original size:32 final size:32
Alignment explanation
Indices: 1144825--1144902 Score: 156
Period size: 32 Copynumber: 2.4 Consensus size: 32
1144815 CTGTTGGGCT
1144825 CAATGTATCGATACTATTTACATATATCGATA
1 CAATGTATCGATACTATTTACATATATCGATA
1144857 CAATGTATCGATACTATTTACATATATCGATA
1 CAATGTATCGATACTATTTACATATATCGATA
1144889 CAATGTATCGATAC
1 CAATGTATCGATAC
1144903 ATAAATAGTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (32 bp):
CAATGTATCGATACTATTTACATATATCGATA
Found at i:1146112 original size:155 final size:154
Alignment explanation
Indices: 1145351--1146268 Score: 888
Period size: 155 Copynumber: 5.9 Consensus size: 154
1145341 ACTAAAGAAA
* * * * * *
1145351 GGATGAACCTATCCTAAATGCCCAACTTCGGCATAAAAGCGGACCCAGTGACAACCTAATAGTTG
1 GGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGAACCCGGTGACAACCTAAGACTTG
* * * * * * **
1145416 GTTCTAGAAAATTACGAAAATACCCTACAGGTATACCTTTGATGTAAAAGTATCATGACAACCCT
66 GTTCTAAAAAATTACGAAAATGCCCTA-AGGGATACCTTCGACGTAAAAGTATCCTG-GTACCCT
* *
1145481 AAAGGATTTAAAAA-GACTAGAGAAA-
129 AAAGGACTTAAAAAGGACTACA-AAAG
* * * * * * *
1145506 GGATGAACCCATCCTAAATGCCCACCTTTGGCATAAAAGCGGATCCGGTGACAACCTAGGAGTTG
1 GGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGAACCCGGTGACAACCTAAGACTTG
** * * * *
1145571 GTTCTTGAAAATTATGAAAATGCCCCTACGGGTATACCTTCGACGTAAAAGTATCATGGCAACCC
66 GTTCTAAAAAATTACGAAAATG-CCCTAAGGG-ATACCTTCGACGTAAAAGTATCCTGG-TACCC
* * *
1145636 TAAAGGACTTAAAAA-GACTAGAGATG
128 TAAAGGACTTAAAAAGGACTACAAAAG
* * * * * *
1145662 GGATAAACCTATCCTAAATACCCACCTTCGGCATAAAAACAAACCCGATGACGACCTAAGACTCG
1 GGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGAACCCGGTGACAACCTAAGACTTG
* **
1145727 GTTCTAAAAAATTACGAAAATGACCCTAAGGGATACTTTCGAC-T-TGAGTAT-CTCGGTACCCC
66 GTTCTAAAAAATTACGAAAATG-CCCTAAGGGATACCTTCGACGTAAAAGTATCCT-GGTA-CCC
* * *
1145789 TAATGGACTTAAAAAGGACTATAAAAT
128 TAAAGGACTTAAAAAGGACTACAAAAG
** * * * *
1145816 GGATGAACCTATCCTAAATACCCACCTTCGATATAAAAGAGGACCTGGTGACGACCTAAGACTTG
1 GGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGAACCCGGTGACAACCTAAGACTTG
* *
1145881 GTTCTAAAAAATTACGAAAATGCCCCTAAGGGATACCTTCAACGTGAAAGTAT-CTCGGTACCTC
66 GTTCTAAAAAATTACGAAAATG-CCCTAAGGGATACCTTCGACGTAAAAGTATCCT-GGTACC-C
* *
1145945 CAAAGGATTTAAAAAGGACTACAAAAG
128 TAAAGGACTTAAAAAGGACTACAAAAG
**
1145972 GGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGAACCCGGTGGTAACCT-AGACTTA
1 GGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGAACCCGGTGACAACCTAAGACTT-
* * * * *
1146036 GCTT-TAAAAAATTACGAAAATGCTCATAGGGGATACCTTTGACGTGAAAGTATCCTGGTACCCT
65 GGTTCTAAAAAATTACGAAAATGC-CCTAAGGGATACCTTCGACGTAAAAGTATCCTGGTACCC-
*
1146100 TCAAGGACTTAAAAAGGACTACAAAAG
128 TAAAGGACTTAAAAAGGACTACAAAAG
* * * * * * * * *
1146127 AGATGAACATATCCTAAATATCTACCCTCGGCAT-AAAGTGAACTCGGTGATAACCTAAGACTCG
1 GGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGAACCCGGTGACAACCTAAGACTTG
** * * * * *
1146191 GTTGAAAAAAATTACGAAAATG-CTTATAGGAGATACCCTCGATGTAAAAGTA-CCCGATACCCC
66 GTTCTAAAAAATTACGAAAATGCCCTA-AGG-GATACCTTCGACGTAAAAGTATCCTGGTA-CCC
1146254 TAAAGGACTTAAAAA
128 TAAAGGACTTAAAAA
1146269 AGATATGGAT
Statistics
Matches: 642, Mismatches: 102, Indels: 39
0.82 0.13 0.05
Matches are distributed among these distances:
152 2 0.00
153 27 0.04
154 148 0.23
155 243 0.38
156 222 0.35
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (154 bp):
GGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGAACCCGGTGACAACCTAAGACTTG
GTTCTAAAAAATTACGAAAATGCCCTAAGGGATACCTTCGACGTAAAAGTATCCTGGTACCCTAA
AGGACTTAAAAAGGACTACAAAAG
Found at i:1148091 original size:20 final size:17
Alignment explanation
Indices: 1148050--1148109 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
1148040 ATTACTGCTG
*
1148050 TTGCTGGTGTCTTCTTC
1 TTGCTGCTGTCTTCTTC
1148067 TTGCTGCTGTCTTCTTC
1 TTGCTGCTGTCTTCTTC
* *
1148084 TTACTGCTGTCTTTTTC
1 TTGCTGCTGTCTTCTTC
*
1148101 TTGCAGCTG
1 TTGCTGCTG
1148110 GTGCTGGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.03, C:0.25, G:0.20, T:0.52
Consensus pattern (17 bp):
TTGCTGCTGTCTTCTTC
Found at i:1148609 original size:15 final size:16
Alignment explanation
Indices: 1148577--1148611 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1148567 TTTTTTTTGC
1148577 TTCTTCTCATCCTTTT
1 TTCTTCTCATCCTTTT
*
1148593 TTCTTCTC-TCTTTTT
1 TTCTTCTCATCCTTTT
1148608 TTCT
1 TTCT
1148612 CCTTCTCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.69
Consensus pattern (16 bp):
TTCTTCTCATCCTTTT
Found at i:1150372 original size:22 final size:23
Alignment explanation
Indices: 1150333--1150381 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1150323 AAAGAAAAAA
* * *
1150333 TATATAAAAATTTATATTTGTGT
1 TATAAAAAAATTTATATTCGAGT
1150356 TATAAAAAAATTT-TATTCGAGT
1 TATAAAAAAATTTATATTCGAGT
1150378 TATA
1 TATA
1150382 TTCTAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (23 bp):
TATAAAAAAATTTATATTCGAGT
Found at i:1150488 original size:21 final size:21
Alignment explanation
Indices: 1150462--1150517 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
1150452 TTGTAATTTA
1150462 TTATTATGATTAAATTTAATT-
1 TTATTATGATTAAATTT-ATTG
* * *
1150483 TTATTATAATTAAGTTTTTTG
1 TTATTATGATTAAATTTATTG
1150504 TTATTATTGATTAA
1 TTATTA-TGATTAA
1150518 GGTATAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.07
21 21 0.72
22 6 0.21
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (21 bp):
TTATTATGATTAAATTTATTG
Found at i:1150739 original size:20 final size:18
Alignment explanation
Indices: 1150702--1150741 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
1150692 AACAGAGAAA
1150702 TTTTTTTATATCTAATTT
1 TTTTTTTATATCTAATTT
*
1150720 TTTTGTTTATAATTTAATTT
1 TTTT-TTTAT-ATCTAATTT
1150740 TT
1 TT
1150742 ATATTAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 5 0.26
20 10 0.53
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTTTTATATCTAATTT
Found at i:1150975 original size:2 final size:2
Alignment explanation
Indices: 1150970--1151320 Score: 217
Period size: 2 Copynumber: 200.0 Consensus size: 2
1150960 AATATTAATA
1150970 AT AT AT A- AT A- AT AT AT AT A- AT AT AT A- AT A- AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1151006 AA AT AT AT A- AC AT AT AT AT -T AT AT GT -T AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1151044 AT AT -T AT -T AT AT AT -T AT AT GT -T AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1151081 A- AT AT -T AT AT AT AT -T AT AT AT AT AT GT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1151119 AT AT AT AT -T AT AT GT -T AT AT AT AT -T A- AT AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1151155 AT GT -T AT AT AT AA AT AT GT -T AC AT AT -T A- AT AT AGT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
1151193 AT GT -T AT AT A- AT AT AT AT -T AT AT AT -T AT -T AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1151229 AT TT AT -T AT AT AT AT -T AT AT AT -T GT AT AT A- AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1151266 A- AT AT A- AT A- AT AT GT -T AT AT AT -T AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1151302 -T AT AT AT AT A- AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
1151321 GTCGCTACGT
Statistics
Matches: 280, Mismatches: 18, Indels: 102
0.70 0.05 0.25
Matches are distributed among these distances:
1 50 0.18
2 228 0.81
3 2 0.01
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1150977 original size:7 final size:7
Alignment explanation
Indices: 1150967--1151320 Score: 181
Period size: 7 Copynumber: 51.3 Consensus size: 7
1150957 AAAAATATTA
1150967 ATAATAT
1 ATAATAT
1150974 ATAATA-
1 ATAATAT
1150980 AT-ATAT
1 ATAATAT
1150986 ATAATAT
1 ATAATAT
1150993 ATAATA-
1 ATAATAT
1150999 AT-ATAT
1 ATAATAT
*
1151005 AAAATAT
1 ATAATAT
1151012 ATAACATAT
1 AT-A-ATAT
*
1151021 ATATTAT
1 ATAATAT
**
1151028 ATGTTAT
1 ATAATAT
*
1151035 ATATTAT
1 ATAATAT
1151042 AT-ATATT
1 ATAATA-T
*
1151049 ATTATAT
1 ATAATAT
*
1151056 ATTATAT
1 ATAATAT
*
1151063 GTTATATAT
1 -ATA-ATAT
1151072 ATAATAT
1 ATAATAT
1151079 ATAATAT
1 ATAATAT
1151086 -T-ATAT
1 ATAATAT
*
1151091 ATATTAT
1 ATAATAT
1151098 AT-ATAT
1 ATAATAT
*
1151104 AT-GTAT
1 ATAATAT
*
1151110 ATATTAT
1 ATAATAT
1151117 AT-ATAT
1 ATAATAT
*
1151123 ATATTAT
1 ATAATAT
**
1151130 ATGTTAT
1 ATAATAT
1151137 AT-ATAT
1 ATAATAT
1151143 -TAATAT
1 ATAATAT
1151149 AATAATAT
1 -ATAATAT
* *
1151157 GTTATAT
1 ATAATAT
1151164 ATAAATAT
1 AT-AATAT
*
1151172 GTTACATAT
1 -ATA-ATAT
1151181 -TAATAT
1 ATAATAT
1151187 AGTAATAT
1 A-TAATAT
*
1151195 GT--TAT
1 ATAATAT
1151200 ATAATAT
1 ATAATAT
*
1151207 ATATTAT
1 ATAATAT
1151214 AT-AT-T
1 ATAATAT
*
1151219 ATTATAT
1 ATAATAT
* *
1151226 ATTATTT
1 ATAATAT
1151233 ATTATATAT
1 A-TA-ATAT
*
1151242 ATTATAT
1 ATAATAT
**
1151249 ATTGTAT
1 ATAATAT
1151256 ATAATAT
1 ATAATAT
1151263 ATTAATAT
1 A-TAATAT
1151271 AATAATAT
1 -ATAATAT
*
1151279 GT--TAT
1 ATAATAT
*
1151284 ATATTAT
1 ATAATAT
1151291 ATAATAT
1 ATAATAT
*
1151298 ATATTAT
1 ATAATAT
1151305 AT-ATAT
1 ATAATAT
1151311 AATAATAT
1 -ATAATAT
1151319 AT
1 AT
1151321 GTCGCTACGT
Statistics
Matches: 275, Mismatches: 38, Indels: 68
0.72 0.10 0.18
Matches are distributed among these distances:
5 22 0.08
6 43 0.16
7 147 0.53
8 43 0.16
9 20 0.07
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.50
Consensus pattern (7 bp):
ATAATAT
Found at i:1151012 original size:9 final size:9
Alignment explanation
Indices: 1150958--1151023 Score: 80
Period size: 9 Copynumber: 7.1 Consensus size: 9
1150948 AATTTAATAA
1150958 AAAATAT-T
1 AAAATATAT
1150966 AATAATATAT
1 AA-AATATAT
1150976 AATAATATAT
1 AA-AATATAT
*
1150986 ATAATATAT
1 AAAATATAT
1150995 AATAATATAT
1 AA-AATATAT
1151005 AAAATATAT
1 AAAATATAT
*
1151014 AACATATAT
1 AAAATATAT
1151023 A
1 A
1151024 TTATATGTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
8 2 0.04
9 29 0.56
10 21 0.40
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (9 bp):
AAAATATAT
Found at i:1153678 original size:20 final size:20
Alignment explanation
Indices: 1153627--1153701 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
1153617 AAAAAGACAT
* * *
1153627 AATGCATCGATACATTGAAG
1 AATGTATCGATACATTCAAA
* * *
1153647 AATATATTGATACATTCACA
1 AATGTATCGATACATTCAAA
* * *
1153667 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCAAA
1153687 AATGTATCGATACAT
1 AATGTATCGATACAT
1153702 CTGGGTAAAA
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:1154373 original size:29 final size:29
Alignment explanation
Indices: 1154312--1155325 Score: 1163
Period size: 28 Copynumber: 35.3 Consensus size: 29
1154302 GACACGTGTA
* * *
1154312 GGCTTTGAAAAGAGTTACTACTGGCTTGTG
1 GGCTTTGAAAAGAG-TGCCACTGACTTGTG
*
1154342 GGCTTTGAAAAGAGTGTCACTGACTTGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
*
1154371 GGCTTTAAAAAG-GTGCCACTGACTTGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
*
1154399 GGCTTT-AAAAG-GATGCCACTAACTTGTG
1 GGCTTTGAAAAGAG-TGCCACTGACTTGTG
*
1154427 GGCTTTGAAAA-AGTTCCACTGACTTGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
1154455 GGC-TTGAAAA-AGTGCCACTGACTTGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
**
1154482 GGC-TTGAAAAG-GTGCCACTGACTCATG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
* **
1154509 GGATTTGAAAAG-GTGCCACTGACTCATG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
* *
1154537 GGCTTTGAAAGGAGTGCCATTGACTTGCGTG
1 GGCTTTGAAAAGAGTGCCACTGACTT--GTG
* * *
1154568 GGCTTTGAAAGGAGTGCCACTAATTTGCGTG
1 GGCTTTGAAAAGAGTGCCACTGACTT--GTG
*
1154599 GGCTTT-AAAAGGGTGCCACTGACTTGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
* *
1154627 GGCTTTGAAAGGA-TGCCACTAACTTGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
* *
1154655 GGCTTTGAAAA-AGTACCACTGACTTATG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
1154683 GGC-TTGAAAA-AGTGCCACTGACTTGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
**
1154710 GGC-TTGAAAAG-GTGCCACTGACTCATG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
* **
1154737 GGCTTT-AAAAGGGTGCCACTGACTCATG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
*
1154765 GGCTTTGAAAGGAGTGCCACTGACTTGCGTG
1 GGCTTTGAAAAGAGTGCCACTGACTT--GTG
*
1154796 GGCTTTGACAAGAGTGCCACTGACTTACGTG
1 GGCTTTGAAAAGAGTGCCACTGACTT--GTG
* *
1154827 GGCTTT-AAAAGGGTGGCACTGACTTGCGTG
1 GGCTTTGAAAAGAGTGCCACTGACTT--GTG
* *
1154857 GGCTTTGAAAGGA-TGCCATTGACTTGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
* *
1154885 GGCTTTG-AAAGAGTGCCATTGACTCGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
1154913 GGC-TTGAAAAG-GTGCCACTGACTTGCGTG
1 GGCTTTGAAAAGAGTGCCACTGACTT--GTG
*
1154942 GGCTTTAAAAAG-GTGCCA-TAGACTTGCGTG
1 GGCTTTGAAAAGAGTGCCACT-GACTT--GTG
*
1154972 GGCTTTGAAAGGA-TGCCACTGACTTGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
*
1155000 GGCTTTGAAAAG-GTGCCACTGACTCGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
*
1155028 GGCTTTGAAAAG-GTGCCACTGACTCGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
* *
1155056 GGC-TTG-AAAGGGTGCCACTGACTCGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
* *
1155083 GGCTTTGAAAAGAGTGCCACCGACTTGTT
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
*
1155112 GGCTTTGAAATGAGTTGCCACTGACTTGTGTG
1 GGCTTTGAAAAGAG-TGCCACTGAC-T-TGTG
*
1155144 GGCTTTGAAAGGAGTGCCACTGACTTGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
* *
1155173 GGCTTTG-AAAGGGTGCCACTAACTTGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
*
1155201 GGCTTTGAAAAGAGTGCCACTGATTTGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
1155230 GGCTTTGAAAAGAGTGCCACTGACTTGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
* *
1155259 GGCTTTG-AAAGGGTGCCACTGACTCGTG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
* *
1155287 GGCTTTGAAAAGAGTGCTACTGACTTATG
1 GGCTTTGAAAAGAGTGCCACTGACTTGTG
1155316 GGCTTTGAAA
1 GGCTTTGAAA
1155326 GGGATGAACA
Statistics
Matches: 869, Mismatches: 81, Indels: 69
0.85 0.08 0.07
Matches are distributed among these distances:
26 4 0.00
27 150 0.17
28 307 0.35
29 186 0.21
30 118 0.14
31 88 0.10
32 16 0.02
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (29 bp):
GGCTTTGAAAAGAGTGCCACTGACTTGTG
Found at i:1154765 original size:228 final size:227
Alignment explanation
Indices: 1154312--1155327 Score: 1277
Period size: 228 Copynumber: 4.4 Consensus size: 227
1154302 GACACGTGTA
* * * *
1154312 GGCTTTGAAAAGAGTTACTACTGGCTT-GTGGGCTTTGAAAAGAGTGTCACTGACTT-GTGGGCT
1 GGCTTTGAAAAGAG-TGCCACTGACTTCGTGGGCTTTGAAAAGAGTGCCACTGA-TTCGTGGGCT
* *
1154375 TTAAAAAGGTGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAG
64 TTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAG
*
1154440 TTCCACTGACTTGTGGGCTTGAAAAAGTGCCACTGACTTGTGGGC-TTGAAAAGGTGCCACTGAC
129 TGCCACTGACTTGTGGGCTTGAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGAC
*
1154504 TCATGGGATTTGAAAA-GGTGCCACTGACTCATG
194 TCATGGGCTTTGAAAAGGGTGCCACTGACTCATG
* * * *
1154537 GGCTTTGAAAGGAGTGCCATTGACTTGCGTGGGCTTTGAAAGGAGTGCCACTAATTTGCGTGGGC
1 GGCTTTGAAAAGAGTGCCACTGACTT-CGTGGGCTTTGAAAAGAGTGCCACTGA-TT-CGTGGGC
1154602 TTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAA
63 TTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAA
* *
1154667 GTACCACTGACTTATGGGCTTGAAAAAGTGCCACTGACTTGTGGGC-TTGAAAAGGTGCCACTGA
128 GTGCCACTGACTTGTGGGCTTGAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGA
1154731 CTCATGGGCTTT-AAAAGGGTGCCACTGACTCATG
193 CTCATGGGCTTTGAAAAGGGTGCCACTGACTCATG
* *
1154765 GGCTTTGAAAGGAGTGCCACTGACTTGCGTGGGCTTTGACAAGAGTGCCACTGACTTACGTGGGC
1 GGCTTTGAAAAGAGTGCCACTGACTT-CGTGGGCTTTGAAAAGAGTGCCACTGA-TT-CGTGGGC
* * *
1154830 TTTAAAAGGGTGGCACTGACTTGCGTGGGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTGAAA
63 TTTAAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAA
* * * * *
1154895 GAGTGCCATTGACTCGTGGGCTTGAAAAGGTGCCACTGACTTGCGTGGGCTTTAAAAAGGTGCCA
126 AAGTGCCACTGACTTGTGGGCTTGAAAAAGTGCCACTGACTT--GTGGGCTTTGAAAAGGTGCCA
* * **
1154960 -TAGACTTGCGTGGGCTTTG-AAAGGATGCCACTGACTTGTG
189 CT-GAC-T-CATGGGCTTTGAAAAGGGTGCCACTGACTCATG
*
1155000 GGCTTTGAAAAG-GTGCCACTGAC-TCGTGGGCTTTGAAAAG-GTGCCACTGACTCGTGGGC-TT
1 GGCTTTGAAAAGAGTGCCACTGACTTCGTGGGCTTTGAAAAGAGTGCCACTGATTCGTGGGCTTT
* * * ** * *
1155061 GAAAGGGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCACCGACTTGTTGGCTTTGAAATGAG
66 AAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGCTTTGAAA-AAG
* *
1155126 TTGCCACTGACTTGTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
129 -TGCCACTGAC-T-TGTGGGC-TTGAAA-AAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCA
* ** * * **
1155191 CTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTG
189 CTGACTCATGGGCTTTGAAAAGGGTGCCACTGACTCATG
* *
1155230 GGCTTTGAAAAGAGTGCCACTGACTT-GTGGGCTTTG-AAAGGGTGCCACTGACTCGTGGGCTTT
1 GGCTTTGAAAAGAGTGCCACTGACTTCGTGGGCTTTGAAAAGAGTGCCACTGATTCGTGGGCTTT
* * *
1155293 GAAAAGAGTGCTACTGACTTATGGGCTTTGAAAGG
66 -AAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG
1155328 GATGAACATT
Statistics
Matches: 702, Mismatches: 61, Indels: 48
0.87 0.08 0.06
Matches are distributed among these distances:
224 8 0.01
225 13 0.02
226 40 0.06
227 26 0.04
228 260 0.37
229 26 0.04
230 112 0.16
231 77 0.11
232 32 0.05
233 58 0.08
234 12 0.02
235 38 0.05
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (227 bp):
GGCTTTGAAAAGAGTGCCACTGACTTCGTGGGCTTTGAAAAGAGTGCCACTGATTCGTGGGCTTT
AAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAGTG
CCACTGACTTGTGGGCTTGAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTC
ATGGGCTTTGAAAAGGGTGCCACTGACTCATG
Found at i:1156581 original size:17 final size:17
Alignment explanation
Indices: 1156560--1156604 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
1156550 TTTTTTGCTA
1156560 TTTTTTCTTGGTTTTTTG
1 TTTTTT-TTGGTTTTTTG
*
1156578 TTTTTTTTGTTTTTTTG
1 TTTTTTTTGGTTTTTTG
1156595 TTTTTTTTGG
1 TTTTTTTTGG
1156605 GTGTAAAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (17 bp):
TTTTTTTTGGTTTTTTG
Found at i:1156582 original size:8 final size:8
Alignment explanation
Indices: 1156561--1156601 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
1156551 TTTTTGCTAT
1156561 TTTTTCTTG
1 TTTTT-TTG
*
1156570 GTTTTTTG
1 TTTTTTTG
1156578 TTTTTTTTG
1 -TTTTTTTG
1156587 TTTTTTTG
1 TTTTTTTG
1156595 TTTTTTT
1 TTTTTTT
1156602 TGGGTGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 18 0.62
9 11 0.38
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.85
Consensus pattern (8 bp):
TTTTTTTG
Found at i:1160502 original size:13 final size:13
Alignment explanation
Indices: 1160484--1160554 Score: 70
Period size: 13 Copynumber: 5.0 Consensus size: 13
1160474 TTCAACGATT
1160484 TGTATCGATACAA
1 TGTATCGATACAA
1160497 TGTATCGATACATAA
1 TGTATCGATAC--AA
1160512 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
1160529 TGTATCGCTACAA
1 TGTATCGATACAA
*
1160542 TGTATCGCTACAA
1 TGTATCGATACAA
1160555 AGCTACTGCC
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
13 36 0.71
15 2 0.04
17 2 0.04
19 11 0.22
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1160610 original size:13 final size:13
Alignment explanation
Indices: 1160592--1160617 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1160582 CATTATTCCA
1160592 TGTATCGATACAT
1 TGTATCGATACAT
1160605 TGTATCGATACAT
1 TGTATCGATACAT
1160618 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1161027 original size:1 final size:1
Alignment explanation
Indices: 1161023--1161088 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
1161013 ATTTTTTTTC
* * * * * * * * *
1161023 AAAAAAAAAAACAAAAAACATAACAAAAAAAAAACAAAAAACAAAACAAAGAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1161088 A
1 A
1161089 GAAGAATCTG
Statistics
Matches: 47, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.02
Consensus pattern (1 bp):
A
Found at i:1161039 original size:12 final size:12
Alignment explanation
Indices: 1161022--1161088 Score: 75
Period size: 12 Copynumber: 5.6 Consensus size: 12
1161012 CATTTTTTTT
1161022 CAAAAAAAAAAA
1 CAAAAAAAAAAA
* *
1161034 CAAAAAACATAA
1 CAAAAAAAAAAA
1161046 C-AAAAAAAAAA
1 CAAAAAAAAAAA
*
1161057 CAAAAAACAAAA
1 CAAAAAAAAAAA
1161069 CAAAGAAAAAAGAA
1 CAAA-AAAAAA-AA
1161083 -AAAAAA
1 CAAAAAA
1161089 GAAGAATCTG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
11 9 0.20
12 27 0.59
13 8 0.17
14 2 0.04
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.01
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:1161050 original size:23 final size:23
Alignment explanation
Indices: 1161024--1161086 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1161014 TTTTTTTTCA
*
1161024 AAAAAAAAAACAAAAAACATAAC
1 AAAAAAAAAACAAAAAACAAAAC
1161047 AAAAAAAAAACAAAAAACAAAAC
1 AAAAAAAAAACAAAAAACAAAAC
* *
1161070 AAAGAAAAAAGAAAAAA
1 AAAAAAAAAACAAAAAA
1161087 AAGAAGAATC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.86, C:0.10, G:0.03, T:0.02
Consensus pattern (23 bp):
AAAAAAAAAACAAAAAACAAAAC
Found at i:1161086 original size:7 final size:7
Alignment explanation
Indices: 1161023--1161068 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
1161013 ATTTTTTTTC
1161023 AAAAA-A
1 AAAAACA
1161029 AAAAACA
1 AAAAACA
1161036 AAAAACA
1 AAAAACA
*
1161043 TAACAAAAA
1 -AA-AAACA
1161052 AAAAACA
1 AAAAACA
1161059 AAAAACA
1 AAAAACA
1161066 AAA
1 AAA
1161069 CAAAGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 5 0.14
7 22 0.63
8 4 0.11
9 4 0.11
ACGTcount: A:0.87, C:0.11, G:0.00, T:0.02
Consensus pattern (7 bp):
AAAAACA
Found at i:1161089 original size:16 final size:16
Alignment explanation
Indices: 1161023--1161091 Score: 63
Period size: 16 Copynumber: 4.5 Consensus size: 16
1161013 ATTTTTTTTC
1161023 AAAAA-AAAAAACAAA
1 AAAAAGAAAAAACAAA
* * *
1161038 AAACA-TAACAA-AAA
1 AAAAAGAAAAAACAAA
*
1161052 AAAAACAAAAAACAAA
1 AAAAAGAAAAAACAAA
* *
1161068 ACAAAGAAAAAAGAAA
1 AAAAAGAAAAAACAAA
1161084 AAAAAGAA
1 AAAAAGAA
1161092 GAATCTGCTT
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
14 7 0.17
15 12 0.29
16 23 0.55
ACGTcount: A:0.86, C:0.09, G:0.04, T:0.01
Consensus pattern (16 bp):
AAAAAGAAAAAACAAA
Found at i:1162299 original size:60 final size:59
Alignment explanation
Indices: 1162145--1162395 Score: 281
Period size: 60 Copynumber: 4.4 Consensus size: 59
1162135 TTCCTTTCAC
* *
1162145 CCTTTAGTCCTCAAAGAGCAGGACACCTTT-C----AATGCCCACACAAGTTGGTGGCA
1 CCTTTAGTCCTCAAAGAGCAGGACACCTTTCCTTTTAAAGCCCACACAAGCTGGTGGCA
*
1162199 CCTTTCAGTCCTCAAAGAGCAGG--A---TGCCTTTTAAAGCCCACACAAGCTGGTGGCA
1 CCTTT-AGTCCTCAAAGAGCAGGACACCTTTCCTTTTAAAGCCCACACAAGCTGGTGGCA
*
1162254 CCTTTAGTCCTCAAAGAGCAGGACACCTTCTCCTTTTAAATCCCACACAAGCTGGTGGCA
1 CCTTTAGTCCTCAAAGAGCAGGACACCTT-TCCTTTTAAAGCCCACACAAGCTGGTGGCA
* * * * * *
1162314 CCTTCAGTCCTCAAAGAGTAGGACACCTTCTTCTTTTAAAGCCCATAAAAGTTGGTGGCA
1 CCTTTAGTCCTCAAAGAGCAGGACACCTT-TCCTTTTAAAGCCCACACAAGCTGGTGGCA
*
1162374 -CTTCCTAGCCCTCAAAGAGCAG
1 CCTT--TAGTCCTCAAAGAGCAG
1162396 TACGCTCTCT
Statistics
Matches: 168, Mismatches: 15, Indels: 21
0.82 0.07 0.10
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
53 1 0.01
54 22 0.13
55 43 0.26
56 1 0.01
59 4 0.02
60 81 0.48
61 14 0.08
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.24
Consensus pattern (59 bp):
CCTTTAGTCCTCAAAGAGCAGGACACCTTTCCTTTTAAAGCCCACACAAGCTGGTGGCA
Found at i:1162566 original size:61 final size:60
Alignment explanation
Indices: 1162411--1162790 Score: 360
Period size: 61 Copynumber: 6.5 Consensus size: 60
1162401 TCTCTCCTTT
* *
1162411 CACCCTTTAATTCTCAAAGAGCAGGACGCCTTTC-----AAAGCCCACACAAGTTGGTGG
1 CACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCTTTTTAAAGCCCACACAAGTTGGTGG
* * *
1162466 CA-CCTTTCAGTCCTTAAAGAGTAGGACG-C---C-TTTTAAAGCCCACACGAGTTGGTGG
1 CACCCTTT-AGTCCTCAAAGAGCAGGACGCCTTTCTTTTTAAAGCCCACACAAGTTGGTGG
* *
1162521 CACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTTAAAGCCCACATAAGCTGGTGG
1 CACCCTTTAGTCCTCAAAGAGCAGGACGCC-TTTCTTTTTAAAGCCCACACAAGTTGGTGG
* * * *
1162582 CA-CCTTCAGTCCTCAAAGAGTAGGACGCCTTTTTCTTTTAAATCCCACACAAGTTGGTGG
1 CACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCT-TTTTAAAGCCCACACAAGTTGGTGG
** * *
1162642 CACTTTTTAGTCCTCAAAGAGGAGGATG-CTTTCTTTTTGCAAAGCCCACACAAGTTGGTGG
1 CACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCTTTTT--AAAGCCCACACAAGTTGGTGG
* * * * * *
1162703 CATCTCC--CAATCCTCAAAGGGCAGGACCCCTTTTCTTTTCAAAGCCCACACGAGTTGGTGG
1 CA-C-CCTTTAGTCCTCAAAGAGCAGGACGCC-TTTCTTTTTAAAGCCCACACAAGTTGGTGG
* *
1162764 CA-CTTTTCAGTCCTCAAAGAGCGGGAC
1 CACCCTTT-AGTCCTCAAAGAGCAGGAC
1162791 ACACTTCCTT
Statistics
Matches: 264, Mismatches: 38, Indels: 40
0.77 0.11 0.12
Matches are distributed among these distances:
51 1 0.00
54 6 0.02
55 58 0.22
56 6 0.02
58 1 0.00
59 8 0.03
60 55 0.21
61 119 0.45
62 2 0.01
63 8 0.03
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (60 bp):
CACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCTTTTTAAAGCCCACACAAGTTGGTGG
Found at i:1162654 original size:121 final size:119
Alignment explanation
Indices: 1162423--1162790 Score: 443
Period size: 121 Copynumber: 3.1 Consensus size: 119
1162413 CCCTTTAATT
*
1162423 CTCAAAGAGCAGGACGCCTTTC-----AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTTAA
1 CTCAAAGAGCAGGACGCCTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAA
**
1162483 AGAGTAGGACG-C----CTTTTAAAGCCCACACGAGTTGGTGGCACCCTTTAGTC
65 AGAGTAGGACGCCTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACTTTTTAGTC
* *
1162533 CTCAAAGAGCAGGACGCCTTTTCTTTTTAAAGCCCACATAAGCTGGTGGCACCTTCAGTCCTCAA
1 CTCAAAGAGCAGGACGCC-TTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAA
* *
1162598 AGAGTAGGACGCCTTTTTCTTTTAAATCCCACACAAGTTGGTGGCACTTTTTAGTC
65 AGAGTAGGACGCC-TTTTCTTTTAAAGCCCACACGAGTTGGTGGCACTTTTTAGTC
* * * * *
1162654 CTCAAAGAGGAGGATG-CTTTCTTTTTGCAAAGCCCACACAAGTTGGTGGCATCTCCCAATCCTC
1 CTCAAAGAGCAGGACGCCTTTCTTTTT--AAAGCCCACACAAGTTGGTGGCACCT-TCAGTCCTC
* * * *
1162718 AAAGGGCAGGACCCCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTC
63 AAAGAGTAGGACGCCTTTTCTTTT-AAAGCCCACACGAGTTGGTGGCACTTTTTAGTC
*
1162776 CTCAAAGAGCGGGAC
1 CTCAAAGAGCAGGAC
1162791 ACACTTCCTT
Statistics
Matches: 219, Mismatches: 23, Indels: 20
0.84 0.09 0.08
Matches are distributed among these distances:
110 18 0.08
111 4 0.02
115 22 0.10
116 24 0.11
119 9 0.04
120 1 0.00
121 80 0.37
122 61 0.28
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (119 bp):
CTCAAAGAGCAGGACGCCTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAA
GAGTAGGACGCCTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACTTTTTAGTC
Found at i:1162750 original size:182 final size:176
Alignment explanation
Indices: 1162440--1162784 Score: 442
Period size: 182 Copynumber: 1.9 Consensus size: 176
1162430 AGCAGGACGC
* *
1162440 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTTAAAGAGTAGGACGCCTTTTAAAGC
1 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGGAGGACGCCTTTTAAAGC
* * * * *
1162505 CCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTTAAAGCCCAC
66 CCACACAAGTTGGTGGCACCC-TCAATCCTCAAAGAGCAGGACCCCTTTTCTTTTCAAAGCCCAC
*
1162570 ATAAGCTGGTGGCAC-CTTCAGTCCTCAAAGAGTAGGACGCCTTTTT
130 ACAAGCTGGTGGCACTCTTCAGTCCTCAAAGAGTAGGACGCCTTTTT
* * * * *
1162616 CTTTTAAATCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGGAGGATGCTTTCTTTTTG
1 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGGAGGACGC---C-TTTT-
*
1162681 CAAAGCCCACACAAGTTGGTGGCATCTCC-CAATCCTCAAAGGGCAGGACCCCTTTTCTTTTCAA
61 -AAAGCCCACACAAGTTGGTGGCA-C-CCTCAATCCTCAAAGAGCAGGACCCCTTTTCTTTTCAA
* * *
1162745 AGCCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAG
123 AGCCCACACAAGCTGGTGGCACTCTTCAGTCCTCAAAGAG
1162785 CGGGACACAC
Statistics
Matches: 143, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
176 48 0.34
179 1 0.01
180 4 0.03
182 71 0.50
183 17 0.12
184 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.28
Consensus pattern (176 bp):
CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGGAGGACGCCTTTTAAAGC
CCACACAAGTTGGTGGCACCCTCAATCCTCAAAGAGCAGGACCCCTTTTCTTTTCAAAGCCCACA
CAAGCTGGTGGCACTCTTCAGTCCTCAAAGAGTAGGACGCCTTTTT
Found at i:1162894 original size:42 final size:42
Alignment explanation
Indices: 1162807--1162910 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 42
1162797 CCTTCCCTTA
* *
1162807 TTTTCTCTTTTGTCCTCAAAGAGCAGGATGCACTTTATTTTCC
1 TTTT-TCTTTTGTCCTCAAAGAGCAGGACGCACTTTATTTCCC
* * * *
1162850 TTTTTCTTTTATCCTCAGAGAGCAGGACGTA-TTTCGTTTCCC
1 TTTTTCTTTTGTCCTCAAAGAGCAGGACGCACTTT-ATTTCCC
*
1162892 TTTTTCCTTTGTCCTCAAA
1 TTTTTCTTTTGTCCTCAAA
1162911 AAATGGGACG
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 3 0.06
42 44 0.86
43 4 0.08
ACGTcount: A:0.17, C:0.24, G:0.13, T:0.45
Consensus pattern (42 bp):
TTTTTCTTTTGTCCTCAAAGAGCAGGACGCACTTTATTTCCC
Found at i:1162951 original size:119 final size:117
Alignment explanation
Indices: 1162815--1163036 Score: 265
Period size: 119 Copynumber: 1.9 Consensus size: 117
1162805 TATTTTCTCT
* * *
1162815 TTTGTCCTCAAAGAGCAGGATGCACTTT-ATTTTCCTT-T-TTCTTTTATCCTC-AGAGAGCAGG
1 TTTGTCCTCAAAGAGCAGGA--CACTTTCATTTT-CTTCTCTTCCTTCATCCTCAAG-GAGCAAG
* *
1162876 ACGTATTTCGTTTCCCTTTTTCCTTTGTCCTCAAAAAATGGGACGTACTCTTTTTCAC
62 ACCTATTTC-ATTCCC-TTTTCCTTTGTCCTCAAAAAATGGGACGTACTCTTTTTCAC
* *
1162934 TTTGTCCTC-AAGAAGCAGGACACTTTCCTTTTCTTCTCTTCCTTCGTCCTCAAGGAGCAAGACC
1 TTTGTCCTCAAAG-AGCAGGACACTTTCATTTTCTTCTCTTCCTTCATCCTCAAGGAGCAAGACC
* *
1162998 TATTTCATTCTCTTTTCCTTTGTCCTCAAAAAGTGGGAC
65 TATTTCATTCCCTTTTCCTTTGTCCTCAAAAAATGGGAC
1163037 ACCCCTTCCA
Statistics
Matches: 89, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
117 35 0.39
118 12 0.13
119 40 0.45
120 2 0.02
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.39
Consensus pattern (117 bp):
TTTGTCCTCAAAGAGCAGGACACTTTCATTTTCTTCTCTTCCTTCATCCTCAAGGAGCAAGACCT
ATTTCATTCCCTTTTCCTTTGTCCTCAAAAAATGGGACGTACTCTTTTTCAC
Found at i:1163023 original size:40 final size:42
Alignment explanation
Indices: 1162927--1163026 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 42
1162917 GACGTACTCT
* *
1162927 TTTTCACTTTGTCCTCAAGAAGCAGGACACTTTCCTTTTCTTC
1 TTTTC-CTTTGTCCTCAAGAAGCAAGACACTTTCCTATTCTTC
* * * *
1162970 TCTTCCTTCGTCCTCAAGGAGCAAGAC-CTATTTC-ATTC-TC
1 TTTTCCTTTGTCCTCAAGAAGCAAGACACT-TTCCTATTCTTC
1163010 TTTTCCTTTGTCCTCAA
1 TTTTCCTTTGTCCTCAA
1163027 AAAGTGGGAC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
40 17 0.35
41 5 0.10
42 22 0.46
43 4 0.08
ACGTcount: A:0.18, C:0.30, G:0.11, T:0.41
Consensus pattern (42 bp):
TTTTCCTTTGTCCTCAAGAAGCAAGACACTTTCCTATTCTTC
Found at i:1166311 original size:79 final size:79
Alignment explanation
Indices: 1166175--1166350 Score: 246
Period size: 79 Copynumber: 2.2 Consensus size: 79
1166165 TTTCATAATC
* * *
1166175 GGGGGTACTCCAACCCTGGTTTTATTCCTAAAACACTAATTTTCCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTCCTAAAACACTAATTTTCCACAATCGGGGATACTCCAAC
* *
1166240 CTCGTTATTTCCAA
66 CCCATTATTTCCAA
* *
1166254 GGGGATACTCCAACCCCGGTTTTATTCCTAAAATATTAA-TTTCTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTATTCCTAAAACACTAATTTTC-CACAATCGGGGATACTCCAA
* **
1166318 CCCCATTATTTTCGT
65 CCCCATTATTTCCAA
1166333 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1166351 TTATTTTTGA
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
78 4 0.05
79 82 0.95
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGGTTTTATTCCTAAAACACTAATTTTCCACAATCGGGGATACTCCAAC
CCCATTATTTCCAA
Found at i:1166345 original size:28 final size:28
Alignment explanation
Indices: 1166305--1166376 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
1166295 TCTCACAATC
*
1166305 GGGGATACTCCAACCCCATTATTTTCGT
1 GGGGATACTCCAACCCCATTATTTTCGA
* *
1166333 GGGGATACTCCAACCCCGTTATTTTTGA
1 GGGGATACTCCAACCCCATTATTTTCGA
*
1166361 AGGGATACTCCAACCC
1 GGGGATACTCCAACCC
1166377 TGATTTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (28 bp):
GGGGATACTCCAACCCCATTATTTTCGA
Found at i:1166417 original size:79 final size:79
Alignment explanation
Indices: 1166334--1166509 Score: 237
Period size: 79 Copynumber: 2.2 Consensus size: 79
1166324 TATTTTCGTG
** * *
1166334 GGGATACTCCAACCCCGTTATTTTTGAA-GGGATACTCCAACCCTGATTTTATTTTCAGAACACC
1 GGGATACTCCAACCCCGTTA-TTTCCAATGGGATACTCCAACCCCGATTTTATTTCCAGAACACC
* *
1166398 AATTTTCTATAATTA
65 AATTTTCCATAATCA
** *
1166413 GGGATACTCCAACCCTATTATTTCCAATGGGATACTCCAACCCCGATTTTATTTCCAGAACACCG
1 GGGATACTCCAACCCCGTTATTTCCAATGGGATACTCCAACCCCGATTTTATTTCCAGAACACCA
1166478 ATTTTCCATAATCA
66 ATTTTCCATAATCA
* *
1166492 GGGGTACTCCAGCCCCGT
1 GGGATACTCCAACCCCGT
1166510 CGTCATCTCC
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
78 5 0.06
79 78 0.94
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (79 bp):
GGGATACTCCAACCCCGTTATTTCCAATGGGATACTCCAACCCCGATTTTATTTCCAGAACACCA
ATTTTCCATAATCA
Found at i:1174637 original size:20 final size:19
Alignment explanation
Indices: 1174608--1174682 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
1174598 AAAAAGAAAT
1174608 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
1174627 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
1174648 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
1174668 AATGTATCGATACAT
1 AATGTATCGATACAT
1174683 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:1175454 original size:29 final size:29
Alignment explanation
Indices: 1175247--1175985 Score: 846
Period size: 29 Copynumber: 24.9 Consensus size: 29
1175237 AAAAAAAGGG
* *
1175247 GTGCCACTAACTTATGTGGGCCTTGAAAAGA
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAAGA
* *
1175278 GTTGCCACCGACTCGTGTGGGCTTTAAAAAGA
1 G-TGCCACTGACT--TGTGGGCTTTGAAAAGA
** * *
1175310 GTTATCACTGGCTTGTGGGCTTTAAAAAG-
1 G-TGCCACTGACTTGTGGGCTTTGAAAAGA
*
1175339 GTGCCACTGACTTGTGGGCTTTG-GAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1175367 GTGCCACTGATTTGTGTGGGCTTTGAAAAGA
1 GTGCCACTGA-CT-TGTGGGCTTTGAAAAGA
*
1175398 GTGCCATTGACTCGTGTGGGCTTTGAAAAGA
1 GTGCCACTGACT--TGTGGGCTTTGAAAAGA
*
1175429 GTGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1175458 GTGCCACTGACTTGCGTGGGCTTTGAAAGGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
* *
1175489 GTGCCACTGACTTGTGGGCTTTGAAAGGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1175518 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1175546 GTGCCATTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1175575 GTTGCCACCGACTCGTGTGGGCTTTGAAAAGA
1 G-TGCCACTGACT--TGTGGGCTTTGAAAAGA
*
1175607 GTGCCACTGACTTGTAGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
1175636 GTGCCACTAACTTGCGTGCGCTTTGAAAGGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
1175667 GTGCCACTGACTTGTGGGCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1175695 GTGCCACTGACTTGTGGGCTTTG-AAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1175723 GGTGCCACTAACTTGTGGGCTTTG-AAAGG
1 -GTGCCACTGACTTGTGGGCTTTGAAAAGA
1175752 GTGCCACTGACTTGCGTGGGCTTTGAAAAGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
* *
1175783 GTTGCCACCGACTCGTGTGGGCTTTGAAAAAA
1 G-TGCCACTGACT--TGTGGGCTTTGAAAAGA
* *
1175815 GTGCCACTGACTTGTGGACTTTGAGAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1175844 GTGCCACTGACTTGCATGGGCTTTGAAAGGG
1 GTGCCACTGACTTG--TGGGCTTTGAAAAGA
*
1175875 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
1175903 GTGCCACTAACTTGTGGGCTTTGAAAGGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1175932 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1175960 GTGCCACTGACTTATGGGCTTGGAAA
1 GTGCCACTGACTTGTGGGCTTTGAAA
1175986 GGGTTTGAAC
Statistics
Matches: 622, Mismatches: 59, Indels: 56
0.84 0.08 0.08
Matches are distributed among these distances:
27 7 0.01
28 140 0.23
29 207 0.33
30 47 0.08
31 144 0.23
32 76 0.12
34 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (29 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:1175457 original size:60 final size:58
Alignment explanation
Indices: 1175247--1175985 Score: 846
Period size: 60 Copynumber: 12.4 Consensus size: 58
1175237 AAAAAAAGGG
* * * *
1175247 GTGCCACTAACTTATGTGGGCCTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTAAAAAGA
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAAGAG-TGCCACTGACT--TGTGGGCTTTGAAAAGA
** * * *
1175310 GTTATCACTGGCTTGTGGGCTTTAAAAAG-GTGCCACTGACTTGTGGGCTTTG-GAAGA
1 G-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1175367 GTGCCACTGATTTGTGTGGGCTTTGAAAAGAGTGCCATTGACTCGTGTGGGCTTTGAAAAGA
1 GTGCCACTGA-CT-TGTGGGCTTTGAAAAGAGTGCCACTGACT--TGTGGGCTTTGAAAAGA
* * *
1175429 GTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGCGTGGGCTTTGAAAGGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAAGA
* * *
1175489 GTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1175546 GTGCCATTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGACT--TGTGGGCTTTGAAAAGA
* * * * *
1175607 GTGCCACTGACTTGTAGGCTTTGAAAAGAGTGCCACTAACTTGCGTGCGCTTTGAAAGGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAAGA
1175667 GTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTG-AAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1175723 GGTGCCACTAACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAAGA
1 -GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAAGA
* * * *
1175783 GTTGCCACCGACTCGTGTGGGCTTTGAAAAAAGTGCCACTGACTTGTGGACTTTGAGAAGA
1 G-TGCCACTGACT--TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
1175844 GTGCCACTGACTTGCATGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTG--TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
1175903 GTGCCACTAACTTGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1175960 GTGCCACTGACTTATGGGCTTGGAAA
1 GTGCCACTGACTTGTGGGCTTTGAAA
1175986 GGGTTTGAAC
Statistics
Matches: 590, Mismatches: 60, Indels: 58
0.83 0.08 0.08
Matches are distributed among these distances:
56 13 0.02
57 147 0.25
58 49 0.08
59 50 0.08
60 209 0.35
61 60 0.10
62 38 0.06
63 18 0.03
64 6 0.01
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (58 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:1175846 original size:208 final size:205
Alignment explanation
Indices: 1175241--1175985 Score: 1030
Period size: 208 Copynumber: 3.6 Consensus size: 205
1175231 TTTTTTAAAA
* * * *
1175241 AAAGGGGTGCCACTAACTTATGTGGGCCTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTAAA
1 AAAGGGGTGCCACTGAC-T-TGTGGGCTTTGAAAAG-G-TGCCACTGACT--TGTGGGCTTT-GA
* ** * * * *
1175306 AAGAGTTATCACTGGCTTGTGGGCTTTAAAAAGGTGCCACTGACTTGTGGGCTTTG-GAAGAG-T
59 AAGAGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTT
* * * *
1175369 GCCACTGATTTGTGTGGGCTTTGAAAAGAGTGCCATTGACTCGTGTGGGCTTTGAAAAGAGTGCC
124 GCCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACT--TGT-GGCTTTGAAAAGAGTGCC
1175434 ACTAACTT--GTGGGCTTTG
186 ACTAACTTGCGTGGGCTTTG
* * * *
1175452 AAAAGAGTGCCACTGACTTGCGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGG
1 AAAGGGGTGCCACTGACTT--GTGGGCTTTGAAA-AGGTGCCACTGACTTGTGGGCTTTGAAAGA
*
1175517 GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCATTGACTTGTGGGCTTTGAAAAGAGTTGCCA
63 GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCA
1175582 CCGACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTAGGCTTTGAAAAGAGTGCCACTAAC
128 CCGACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGT-GGCTTTGAAAAGAGTGCCACTAAC
*
1175647 TTGCGTGCGCTTTG
192 TTGCGTGGGCTTTG
1175661 AAAGGGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGGT
1 AAAGGGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGGT
*
1175726 GCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAAGAGTTGCCAC
66 GCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAAGAGTTGCCAC
* * *
1175791 CGACTCGTGTGGGCTTTGAAAAAAGTGCCACTGACTTGTGGACTTTGAGAAGAGTGCCACTGACT
129 CGACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG-CTTTGAAAAGAGTGCCACTAACT
*
1175856 TGCATGGGCTTTG
193 TGCGTGGGCTTTG
* * *
1175869 AAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGGGT
1 AAAGGGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGGT
* *
1175934 GCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGCTTGGAAA
66 GCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
1175986 GGGTTTGAAC
Statistics
Matches: 485, Mismatches: 39, Indels: 25
0.88 0.07 0.05
Matches are distributed among these distances:
206 79 0.16
207 93 0.19
208 209 0.43
209 65 0.13
210 11 0.02
211 27 0.06
212 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (205 bp):
AAAGGGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGGT
GCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCG
ACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGCTTTGAAAAGAGTGCCACTAACTTGC
GTGGGCTTTG
Found at i:1177210 original size:1 final size:1
Alignment explanation
Indices: 1177206--1177259 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
1177196 TTTTTTGCTA
* * * * **
1177206 TTTTTTTTGTTTTTTTGTTTTGTTTTTTTTTGTTTTTTTTTTTTGGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1177260 GGGTGTAAAG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:1177226 original size:13 final size:12
Alignment explanation
Indices: 1177196--1177259 Score: 76
Period size: 12 Copynumber: 5.2 Consensus size: 12
1177186 GACCCTTCTA
* *
1177196 TTTTTTGCTATT
1 TTTTTTGTTTTT
1177208 TTTTTTGTTTTT
1 TTTTTTGTTTTT
1177220 TTGTTTTGTTTTT
1 TT-TTTTGTTTTT
1177233 TTTTGTT-TTTTT
1 TTTT-TTGTTTTT
*
1177245 TTTTTGGTTTTT
1 TTTTTTGTTTTT
1177257 TTT
1 TTT
1177260 GGGTGTAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
11 1 0.02
12 31 0.67
13 14 0.30
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.86
Consensus pattern (12 bp):
TTTTTTGTTTTT
Found at i:1177226 original size:14 final size:13
Alignment explanation
Indices: 1177206--1177259 Score: 69
Period size: 13 Copynumber: 4.3 Consensus size: 13
1177196 TTTTTTGCTA
1177206 TTTTTTTTGTTTT
1 TTTTTTTTGTTTT
*
1177219 TTTGTTTTG---T
1 TTTTTTTTGTTTT
1177229 TTTTTTTTGTTTT
1 TTTTTTTTGTTTT
1177242 TTTTTTTTGGTTTT
1 TTTTTTTT-GTTTT
1177256 TTTT
1 TTTT
1177260 GGGTGTAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
10 9 0.26
13 17 0.49
14 9 0.26
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (13 bp):
TTTTTTTTGTTTT
Found at i:1177233 original size:15 final size:14
Alignment explanation
Indices: 1177208--1177259 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
1177198 TTTTGCTATT
1177208 TTTTTTGTTTTTTTG
1 TTTTTT-TTTTTTTG
1177223 TTTTGTTTTTTTTTG
1 TTTT-TTTTTTTTTG
*
1177238 TTTTTTTTTTTTGG
1 TTTTTTTTTTTTTG
1177252 TTTTTTTT
1 TTTTTTTT
1177260 GGGTGTAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
14 17 0.49
15 16 0.46
16 2 0.06
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTTTTG
Found at i:1177236 original size:23 final size:23
Alignment explanation
Indices: 1177206--1177260 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
1177196 TTTTTTGCTA
*
1177206 TTTTTTTTGTTTTTTTGTTTTGT
1 TTTTTTTTGTTTTTTTGTTTTGG
*
1177229 TTTTTTTTGTTTTTTTTTTTTGG
1 TTTTTTTTGTTTTTTTGTTTTGG
1177252 TTTTTTTTG
1 TTTTTTTTG
1177261 GGTGTAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (23 bp):
TTTTTTTTGTTTTTTTGTTTTGG
Found at i:1177261 original size:10 final size:9
Alignment explanation
Indices: 1177206--1177260 Score: 60
Period size: 10 Copynumber: 6.0 Consensus size: 9
1177196 TTTTTTGCTA
1177206 TTTTTTTTG
1 TTTTTTTTG
1177215 -TTTTTTTG
1 TTTTTTTTG
1177223 TTTTGTTTT-
1 TTTT-TTTTG
*
1177232 TTTTTGTTTT
1 TTTTT-TTTG
1177242 TTTTTTTTGG
1 TTTTTTTT-G
1177252 TTTTTTTTG
1 TTTTTTTTG
1177261 GGTGTAAAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
8 9 0.22
9 14 0.35
10 17 0.43
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:1187917 original size:20 final size:19
Alignment explanation
Indices: 1187892--1187963 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
1187882 AGACATAATG
1187892 TATCGATACATTGAAGAATA
1 TATCGATACATTGAA-AATA
* * *
1187912 TATCGATACATTCATACATG
1 TATCGATACATTGA-AAATA
* *
1187932 TATCGATATATTGAAAAATT
1 TATCGATACATTG-AAAATA
1187952 TATCGATACATT
1 TATCGATACATT
1187964 TAGGTAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 40 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (19 bp):
TATCGATACATTGAAAATA
Found at i:1187945 original size:40 final size:39
Alignment explanation
Indices: 1187885--1187963 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 39
1187875 GGTAAAAAGA
*
1187885 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1187924 CATACATGTATCGATATATTGAAAAATTTATCGATACATT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACATT
1187964 TAGGTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1189105 original size:52 final size:52
Alignment explanation
Indices: 1189042--1189289 Score: 349
Period size: 52 Copynumber: 4.8 Consensus size: 52
1189032 AGATGAAGGT
* * *
1189042 GCCAATGTGCTGATTCAGGGCCAGCGACATTGGACTTAAAGATGACAAAGAC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGAC
* *
1189094 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAAGGC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGAC
**
1189146 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGAC
* * * * *
1189195 GCCAATATGCTGATTGAAGGCCAGCAATATTGGACTTAGAGGTGCCAAAGAC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGAC
*
1189247 GCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAGAAGA
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGA
1189290 AGATGCCACC
Statistics
Matches: 175, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
49 44 0.25
52 129 0.74
53 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.22
Consensus pattern (52 bp):
GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGAC
Found at i:1189225 original size:101 final size:102
Alignment explanation
Indices: 1189037--1189289 Score: 346
Period size: 101 Copynumber: 2.5 Consensus size: 102
1189027 GTTAAAGATG
* * * *
1189037 AAGGTGCCAATGTGCTGATTCAGGGCCAGCGACATTGGACTTAAAGATGACAAAGACGCCAATAT
1 AAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG--AAAGACGCCAATAT
*
1189102 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAA
64 GCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAA
**
1189141 AAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG-AAGGTGCCAATATGC
1 AAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAGACGCCAATATGC
* * * **
1189205 TGATTGAAGGCCAGCAATATTGGACTTAGAGGTGCCA
66 TGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAA
* *
1189242 AAGACGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAGAAGA
1 AAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGA
1189290 AGATGCCACC
Statistics
Matches: 134, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
101 85 0.63
102 4 0.03
104 45 0.34
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (102 bp):
AAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAGACGCCAATATGC
TGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAA
Found at i:1189366 original size:28 final size:28
Alignment explanation
Indices: 1189306--1189542 Score: 298
Period size: 28 Copynumber: 8.3 Consensus size: 28
1189296 CACCAACTTG
*
1189306 TGTGGGCTTTTGAAAGGTTTG-CA-TCAACT
1 TGTGGGCTTTT-AAAGG-TTGCCACT-GACT
* * * *
1189335 TGTGTGCTTTTGAAGGTTGCTACTGACC
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
*
1189363 TGTGGGCTTTTAAAGATTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
1189391 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
*
1189419 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* *
1189447 TGTGGGCTTTTCAAGATTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
1189475 TGTGGGCTTTTTAAAGGTTGCCACTGACT
1 TGTGGGC-TTTTAAAGGTTGCCACTGACT
* * *
1189504 TATGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTT--AAAGGTTGCCACTGACT
1189534 TGTGGGCTT
1 TGTGGGCTT
1189543 AAAAGGAAAA
Statistics
Matches: 183, Mismatches: 20, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
27 3 0.02
28 121 0.66
29 36 0.20
30 23 0.13
ACGTcount: A:0.18, C:0.17, G:0.28, T:0.36
Consensus pattern (28 bp):
TGTGGGCTTTTAAAGGTTGCCACTGACT
Found at i:1189602 original size:34 final size:34
Alignment explanation
Indices: 1189516--1189605 Score: 101
Period size: 34 Copynumber: 2.6 Consensus size: 34
1189506 TGGGCTTTTG
* * *
1189516 AAAAGGGTGCCACTA-ACTTGTGGGCTTAAAAGGA
1 AAAAGAGTGCCAC-AGAGTTGTGAGCTTAAAAGGA
* ** *
1189550 AAAAGAGTGCTATGGAGTTGTGAGCTTACAAGGA
1 AAAAGAGTGCCACAGAGTTGTGAGCTTAAAAGGA
1189584 AAAAGAGTGCCACAGAGTTGTG
1 AAAAGAGTGCCACAGAGTTGTG
1189606 GACTTTGGAA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.21
Consensus pattern (34 bp):
AAAAGAGTGCCACAGAGTTGTGAGCTTAAAAGGA
Found at i:1189625 original size:29 final size:28
Alignment explanation
Indices: 1189582--1189698 Score: 137
Period size: 29 Copynumber: 4.0 Consensus size: 28
1189572 AGCTTACAAG
*
1189582 GAAAAAGAGTGCCACAGAGTTGTGGACTTT
1 GAAAAAGA-TGCCACAGACTTGTGG-CTTT
* *
1189612 GGAAAAGATGCCACCGACTTGTAGGCTTT
1 GAAAAAGATGCCACAGACTTGT-GGCTTT
*
1189641 GAAAAAGATGCCACTGACTTGTGGGCTTT
1 GAAAAAGATGCCACAGACTTGT-GGCTTT
1189670 GAAAAAGATGCCACTA-ACTTGTGGGCTTT
1 GAAAAAGATGCCAC-AGACTTGT-GGCTTT
1189699 TGAAGGGTGA
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
29 69 0.88
30 9 0.12
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (28 bp):
GAAAAAGATGCCACAGACTTGTGGCTTT
Found at i:1191178 original size:6 final size:6
Alignment explanation
Indices: 1191136--1191222 Score: 67
Period size: 6 Copynumber: 14.7 Consensus size: 6
1191126 ATCCGGACCC
* * *
1191136 TTTTTG TTGTTG TTGTTG TTTTTTT TTCTTCTG TTTTTG TTTTT- TTTTTG
1 TTTTTG TTTTTG TTTTTG -TTTTTG TT-TT-TG TTTTTG TTTTTG TTTTTG
*
1191186 TTTTT- TTTGT- TTTTTG TTTTTTG TTTTT- TTTTT- TTTT
1 TTTTTG TTTTTG TTTTTG -TTTTTG TTTTTG TTTTTG TTTT
1191223 GCGGAGGACG
Statistics
Matches: 69, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
5 22 0.32
6 30 0.43
7 14 0.20
8 3 0.04
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:1191178 original size:20 final size:19
Alignment explanation
Indices: 1191145--1191222 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 19
1191135 CTTTTTGTTG
*
1191145 TTGTTGTTGTTTTTTTTTCT
1 TTGTTTTTGTTTTTTTTT-T
1191165 TCTGTTTTTGTTTTTTTTTT
1 T-TGTTTTTGTTTTTTTTTT
*
1191185 GTTTTTTTTGTTTTTTGTTTT
1 -TTGTTTTTGTTTTTT-TTTT
1191206 TTGTTTTT-TTTTTTTTT
1 TTGTTTTTGTTTTTTTTT
1191223 GCGGAGGACG
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
18 3 0.06
19 6 0.12
20 22 0.42
21 21 0.40
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.86
Consensus pattern (19 bp):
TTGTTTTTGTTTTTTTTTT
Found at i:1191184 original size:27 final size:25
Alignment explanation
Indices: 1191136--1191220 Score: 98
Period size: 27 Copynumber: 3.2 Consensus size: 25
1191126 ATCCGGACCC
*
1191136 TTTTTGTTGTTGTTGTTGTTTTTTTTT
1 TTTTTGTTTTTGTT-TT-TTTTTTTTT
* *
1191163 CTTCTGTTTTTGTTTTTTTTTTGTTT
1 TTTTTGTTTTTGTTTTTTTTTT-TTT
1191189 TTTTTGTTTTTTGTTTTTTGTTTTTTT
1 TTTTTG-TTTTTGTTTTTT-TTTTTTT
1191216 TTTTT
1 TTTTT
1191221 TTGCGGAGGA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
25 6 0.12
26 9 0.18
27 31 0.62
28 4 0.08
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (25 bp):
TTTTTGTTTTTGTTTTTTTTTTTTT
Found at i:1191222 original size:41 final size:41
Alignment explanation
Indices: 1191136--1191221 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
1191126 ATCCGGACCC
1191136 TTTTTGTTGTTGTTGTTGTTTTTTTTTCTTCTGTTTTTGTT
1 TTTTTGTTGTTGTTGTTGTTTTTTTTTCTTCTGTTTTTGTT
* * * *
1191177 TTTTTTTTGTTTTTTTTGTTTTTTGTTT-TT-TGTTTTTTTT
1 TTTTTGTTGTTGTTGTTGTTTTTT-TTTCTTCTGTTTTTGTT
1191217 TTTTT
1 TTTTT
1191222 TGCGGAGGAC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 14 0.35
41 23 0.57
42 3 0.08
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (41 bp):
TTTTTGTTGTTGTTGTTGTTTTTTTTTCTTCTGTTTTTGTT
Found at i:1191239 original size:1 final size:1
Alignment explanation
Indices: 1191154--1191222 Score: 66
Period size: 1 Copynumber: 69.0 Consensus size: 1
1191144 GTTGTTGTTG
* * * * * * * *
1191154 TTTTTTTTTCTTCTGTTTTTGTTTTTTTTTTGTTTTTTTTGTTTTTTGTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1191219 TTTT
1 TTTT
1191223 GCGGAGGACG
Statistics
Matches: 52, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:1205161 original size:52 final size:52
Alignment explanation
Indices: 1205013--1205141 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
1205003 TGAAATATGA
*
1205013 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCCATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1205065 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1205117 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1205142 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:1205168 original size:13 final size:13
Alignment explanation
Indices: 1205150--1205174 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1205140 CAAAGATCAG
1205150 TGTATCGATACAA
1 TGTATCGATACAA
1205163 TGTATCGATACA
1 TGTATCGATACA
1205175 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1205253 original size:13 final size:13
Alignment explanation
Indices: 1205235--1205262 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1205225 TACAAAACTT
1205235 ATGTATCGATACA
1 ATGTATCGATACA
1205248 ATGTATCGATACA
1 ATGTATCGATACA
1205261 AT
1 AT
1205263 ATTTTATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1205275 original size:33 final size:32
Alignment explanation
Indices: 1205217--1205281 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
1205207 TAGCTTAAAT
1205217 TGTATCGATACAAAACTTATGTATCGATACAA
1 TGTATCGATACAAAACTTATGTATCGATACAA
**
1205249 TGTATCGATACAATATTTTATGTATCGATACAA
1 TGTATCGATACAA-AACTTATGTATCGATACAA
1205282 ATCGTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.43
33 17 0.57
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAA
Found at i:1207612 original size:28 final size:27
Alignment explanation
Indices: 1207513--1207641 Score: 138
Period size: 27 Copynumber: 4.9 Consensus size: 27
1207503 AAAGCCACCC
* *
1207513 TTTGTGTTTGTAAAAAATGGTGGTTAT
1 TTTGTATTTGTCAAAAATGGTGGTTAT
*
1207540 TTTGTATTTGCCAAAAATGGTGGTTAT
1 TTTGTATTTGTCAAAAATGGTGGTTAT
**
1207567 TTTGTATTTGTCAAAAATGGTGGATCCT
1 TTTGTATTTGTCAAAAATGGTGG-TTAT
* * *
1207595 TTTTTATTTGTCAAAAATTGTGGCT-T
1 TTTGTATTTGTCAAAAATGGTGGTTAT
* *
1207621 GTTG--TTTGTCAAAATTGGTGG
1 TTTGTATTTGTCAAAAATGGTGG
1207642 CTAATTTTTA
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
24 15 0.17
26 3 0.03
27 46 0.53
28 23 0.26
ACGTcount: A:0.24, C:0.06, G:0.23, T:0.47
Consensus pattern (27 bp):
TTTGTATTTGTCAAAAATGGTGGTTAT
Found at i:1212137 original size:27 final size:26
Alignment explanation
Indices: 1212106--1212207 Score: 100
Period size: 27 Copynumber: 3.9 Consensus size: 26
1212096 AAAGCCACCC
*
1212106 TTTGTGTTTGTCAAAAATGGTGGTTAT
1 TTTGTGTTTGTCAAAAATGGTGG-TCT
* *
1212133 TTTGTATTTGTCAAAAATGGTAGATCCT
1 TTTGTGTTTGTCAAAAATGGT-GGT-CT
* *
1212161 TTTTTGTTTGTCAAAAATTGTGG-CT
1 TTTGTGTTTGTCAAAAATGGTGGTCT
* *
1212186 TGT-TGTTTGTCAAAATTGGTGG
1 TTTGTGTTTGTCAAAAATGGTGG
1212208 CTAATTTTTA
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
24 17 0.27
25 4 0.06
27 22 0.35
28 20 0.32
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.47
Consensus pattern (26 bp):
TTTGTGTTTGTCAAAAATGGTGGTCT
Found at i:1212192 original size:24 final size:24
Alignment explanation
Indices: 1212164--1212209 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1212154 AGATCCTTTT
1212164 TTGTTTGTCAAAAATT-GTGGCTTG
1 TTGTTTGTC-AAAATTGGTGGCTTG
1212188 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTCAAAATTGGTGGCT
1212210 AATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.20, C:0.09, G:0.26, T:0.46
Consensus pattern (24 bp):
TTGTTTGTCAAAATTGGTGGCTTG
Found at i:1213439 original size:21 final size:21
Alignment explanation
Indices: 1213406--1213453 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
1213396 GGTTTATAAA
*
1213406 AAAATTATTTAAAT-TTAATTAT
1 AAAA-TATATAAATATTAA-TAT
1213428 AAAATATATAAATATTAATAT
1 AAAATATATAAATATTAATAT
1213449 AAAAT
1 AAAAT
1213454 TATTTGTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATATATAAATATTAATAT
Found at i:1214672 original size:17 final size:17
Alignment explanation
Indices: 1214626--1214667 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1214616 AACATAAAAA
*
1214626 ATAAT-TAAAATATAAT
1 ATAATATAAAAAATAAT
1214642 ATAATATAAAAAATAAT
1 ATAATATAAAAAATAAT
1214659 ATAAATATA
1 AT-AATATA
1214668 TAAATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.22
17 12 0.52
18 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAATATAAAAAATAAT
Found at i:1215530 original size:6 final size:6
Alignment explanation
Indices: 1215519--1215557 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1215509 ATTTTGGTTG
* * *
1215519 TTTTGC TTTTGC TTTTGC TTCTGC TTCTAC TTTTGC TTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTT
1215558 AAAAGCATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.03, C:0.21, G:0.13, T:0.64
Consensus pattern (6 bp):
TTTTGC
Found at i:1217622 original size:31 final size:33
Alignment explanation
Indices: 1217587--1217648 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
1217577 AAAACAAACT
* *
1217587 AAAATTGATAATTA-AATTT-TTTATTTTATAA
1 AAAATTAATAATTACAATTTGATTATTTTATAA
1217618 AAAATTAATAATTACAATTTGATTATTTTAT
1 AAAATTAATAATTACAATTTGATTATTTTAT
1217649 TTTTAGTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 13 0.48
32 5 0.19
33 9 0.33
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (33 bp):
AAAATTAATAATTACAATTTGATTATTTTATAA
Found at i:1218634 original size:21 final size:21
Alignment explanation
Indices: 1218608--1218650 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1218598 AAGTCAAATT
1218608 TATTATTATAATTTAATTTAA
1 TATTATTATAATTTAATTTAA
* * *
1218629 TATTATTTTATTTTTATTTAA
1 TATTATTATAATTTAATTTAA
1218650 T
1 T
1218651 TGAATTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTATTATAATTTAATTTAA
Found at i:1218639 original size:26 final size:26
Alignment explanation
Indices: 1218610--1218660 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1218600 GTCAAATTTA
*
1218610 TTATTATAATTTAATTTAATATTATT
1 TTATTATAATTTAATTGAATATTATT
* * *
1218636 TTATTTTTATTTAATTGAATTTTAT
1 TTATTATAATTTAATTGAATATTAT
1218661 CATAAAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTATTATAATTTAATTGAATATTATT
Found at i:1220320 original size:2 final size:2
Alignment explanation
Indices: 1220315--1220346 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1220305 GCGAGTGATC
1220315 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1220347 TTATTTATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1221163 original size:2 final size:2
Alignment explanation
Indices: 1221156--1221186 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1221146 TTTAATTATG
1221156 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1221187 CATTATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1224306 original size:17 final size:17
Alignment explanation
Indices: 1224280--1224312 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1224270 ATTTTCAATC
1224280 AAAATAAAAATTAAATG
1 AAAATAAAAATTAAATG
*
1224297 AAAATTAAAATTAAAT
1 AAAATAAAAATTAAAT
1224313 TTGTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAATAAAAATTAAATG
Found at i:1224897 original size:6 final size:6
Alignment explanation
Indices: 1224886--1224915 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1224876 CTTAGCTTGG
1224886 AACCAT AACCAT AACCAT AACCAT AACCAT
1 AACCAT AACCAT AACCAT AACCAT AACCAT
1224916 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (6 bp):
AACCAT
Found at i:1225262 original size:15 final size:15
Alignment explanation
Indices: 1225242--1225274 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1225232 GTTGTGTTGG
1225242 TTTTGGATTGAGTCA
1 TTTTGGATTGAGTCA
*
1225257 TTTTGGATTGAGTTA
1 TTTTGGATTGAGTCA
1225272 TTT
1 TTT
1225275 CAGATTTTAA
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:0.18, C:0.03, G:0.24, T:0.55
Consensus pattern (15 bp):
TTTTGGATTGAGTCA
Found at i:1225324 original size:16 final size:17
Alignment explanation
Indices: 1225289--1225326 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1225279 TTTTAAAATT
* *
1225289 TTCGGTTTATTTTTGAG
1 TTCGGGTTATTTTCGAG
1225306 TTCGGGTTA-TTTCGAG
1 TTCGGGTTATTTTCGAG
1225322 TTCGG
1 TTCGG
1225327 ATAATCGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.11, C:0.11, G:0.29, T:0.50
Consensus pattern (17 bp):
TTCGGGTTATTTTCGAG
Found at i:1226149 original size:16 final size:16
Alignment explanation
Indices: 1226128--1226164 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1226118 AGTTTAAGTC
1226128 ATTTCAGGTTCGGGTG
1 ATTTCAGGTTCGGGTG
*
1226144 ATTTCAGGTTCGGGTT
1 ATTTCAGGTTCGGGTG
1226160 ATTTC
1 ATTTC
1226165 GGGCTCGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.14, C:0.14, G:0.30, T:0.43
Consensus pattern (16 bp):
ATTTCAGGTTCGGGTG
Found at i:1230568 original size:33 final size:33
Alignment explanation
Indices: 1230530--1230593 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
1230520 GACAATTTAA
1230530 ATATAACATAAAAAATAATTAAAATATAATAAT
1 ATATAACATAAAAAATAATTAAAATATAATAAT
*
1230563 ATATAATATAAAAAATAATTAAAATATAATA
1 ATATAACATAAAAAATAATTAAAATATAATA
1230594 TAATAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (33 bp):
ATATAACATAAAAAATAATTAAAATATAATAAT
Found at i:1230571 original size:5 final size:5
Alignment explanation
Indices: 1230552--1230623 Score: 53
Period size: 5 Copynumber: 14.6 Consensus size: 5
1230542 AAATAATTAA
* *
1230552 AATAT AATA- ATATAT AATAT AA-A- AA-AT AATTAA AATAT AATAT AATAA
1 AATAT AATAT A-ATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT
* *
1230600 AAAAT AATAT AAATAT ATTAT AAT
1 AATAT AATAT -AATAT AATAT AAT
1230624 TATATAAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
3 3 0.06
4 4 0.08
5 37 0.70
6 9 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
AATAT
Found at i:1230573 original size:26 final size:25
Alignment explanation
Indices: 1230544--1230623 Score: 92
Period size: 26 Copynumber: 3.2 Consensus size: 25
1230534 AACATAAAAA
*
1230544 ATAATTAAAATATAATAATATATAAT
1 ATAA-TAAAATATAATAAAATATAAT
*
1230570 ATAA-AAAATA-ATTAAAATATAAT
1 ATAATAAAATATAATAAAATATAAT
* *
1230593 ATAATAAAAAATAATATAAATATATT
1 ATAATAAAATATAATA-AAATATAAT
1230619 ATAAT
1 ATAAT
1230624 TATATAAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
23 15 0.33
24 11 0.24
25 3 0.07
26 17 0.37
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
ATAATAAAATATAATAAAATATAAT
Found at i:1230576 original size:23 final size:22
Alignment explanation
Indices: 1230544--1230616 Score: 89
Period size: 23 Copynumber: 3.4 Consensus size: 22
1230534 AACATAAAAA
*
1230544 ATAAT-TAAAATATAATAATAT
1 ATAATATAAAAAATAATAATAT
*
1230565 ATAATATAAAAAATAATTAAAAT
1 ATAATATAAAAAATAA-TAATAT
1230588 ATAATATAATAAAA-AATAATAT
1 ATAATATAA-AAAATAATAATAT
1230610 A-AATATA
1 ATAATATA
1230617 TTATAATTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
21 11 0.24
22 15 0.33
23 16 0.35
24 4 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAATATAAAAAATAATAATAT
Found at i:1230627 original size:11 final size:11
Alignment explanation
Indices: 1230607--1230688 Score: 52
Period size: 10 Copynumber: 8.0 Consensus size: 11
1230597 TAAAAAATAA
1230607 TATAAATATAT
1 TATAAATATAT
1230618 TAT-AAT-TA-
1 TATAAATATAT
*
1230626 TATAAATATGT
1 TATAAATATAT
*
1230637 TA-AAATTTA-
1 TATAAATATAT
*
1230646 TATAATATAAAT
1 TATAA-ATATAT
*
1230658 TATTAATATA-
1 TATAAATATAT
* *
1230668 TAAAAATTTA-
1 TATAAATATAT
1230678 TATAAATATAT
1 TATAAATATAT
1230689 AATACATTAA
Statistics
Matches: 52, Mismatches: 12, Indels: 14
0.67 0.15 0.18
Matches are distributed among these distances:
8 3 0.06
9 7 0.13
10 26 0.50
11 12 0.23
12 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (11 bp):
TATAAATATAT
Found at i:1230655 original size:33 final size:31
Alignment explanation
Indices: 1230612--1230687 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 31
1230602 AATAATATAA
* * *
1230612 ATATATTATAATTATATAAATATGTTAAAATTT
1 ATATAATATAATTAT-T-AATATATAAAAATTT
1230645 ATATAATATAAATTATTAATATATAAAAATTT
1 ATATAATAT-AATTATTAATATATAAAAATTT
1230677 ATATAAATATA
1 ATAT-AATATA
1230688 TAATACATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
32 18 0.47
33 14 0.37
34 6 0.16
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (31 bp):
ATATAATATAATTATTAATATATAAAAATTT
Found at i:1230667 original size:20 final size:21
Alignment explanation
Indices: 1230644--1230692 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
1230634 TGTTAAAATT
1230644 TATATAATATAAATTAT-T-AA
1 TATATAATA-AAATTATATAAA
*
1230664 TATATAA-AAATTTATATAAA
1 TATATAATAAAATTATATAAA
1230684 TATATAATA
1 TATATAATA
1230693 CATTAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.24
19 2 0.08
20 16 0.64
21 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATATAATAAAATTATATAAA
Found at i:1230705 original size:27 final size:27
Alignment explanation
Indices: 1230645--1230714 Score: 65
Period size: 27 Copynumber: 2.6 Consensus size: 27
1230635 GTTAAAATTT
*
1230645 ATATAATATAAAT-TATTAATATA-TAA
1 ATATTATATAAATATA-TAATATATTAA
* *
1230671 AAATTTATATAAATATATAATACATTAA
1 ATA-TTATATAAATATATAATATATTAA
1230699 ATATTATA-ATAATATA
1 ATATTATATA-AATATA
1230715 AAAATAAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
26 3 0.08
27 26 0.72
28 7 0.19
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
ATATTATATAAATATATAATATATTAA
Found at i:1230720 original size:28 final size:27
Alignment explanation
Indices: 1230543--1230721 Score: 78
Period size: 28 Copynumber: 6.6 Consensus size: 27
1230533 TAACATAAAA
1230543 AATAAT-TAAAATATAA-T-AATA-TAT
1 AATAATATAAAA-ATAATTAAATATTAT
*
1230567 AAT-ATA-AAAAATAATTAAAATATAAT
1 AATAATATAAAAATAATT-AAATATTAT
1230593 -ATAATA-AAAAATAATATAAATA-TAT
1 AATAATATAAAAATAAT-TAAATATTAT
* * *
1230618 TATAATTATATAAATATGTTAAA-ATT-T
1 AATAA-TATAAAAATA-ATTAAATATTAT
* *
1230645 ATATAATATAAATTATTAATATATAAAAATT-T
1 A-ATAATATAAA--AAT-A-AT-TAAATATTAT
*
1230677 ATATAA-ATATATAATACATTAAATATTAT
1 A-ATAATATA-AAAATA-ATTAAATATTAT
1230706 AATAATATAAAAATAA
1 AATAATATAAAAATAA
1230722 AACAAACATG
Statistics
Matches: 121, Mismatches: 13, Indels: 39
0.70 0.08 0.23
Matches are distributed among these distances:
22 4 0.03
23 7 0.06
24 3 0.02
25 8 0.07
26 23 0.19
27 11 0.09
28 31 0.26
29 11 0.09
30 5 0.04
31 7 0.06
32 11 0.09
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.38
Consensus pattern (27 bp):
AATAATATAAAAATAATTAAATATTAT
Found at i:1231490 original size:6 final size:6
Alignment explanation
Indices: 1231479--1231517 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1231469 ATTTTGGTTG
* * *
1231479 TTTTGC TTTTGC TTTTGC TTCTGC TTCTAC TTTTGC TTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTT
1231518 AAAAGTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.03, C:0.21, G:0.13, T:0.64
Consensus pattern (6 bp):
TTTTGC
Found at i:1238703 original size:18 final size:18
Alignment explanation
Indices: 1238655--1238752 Score: 98
Period size: 18 Copynumber: 5.7 Consensus size: 18
1238645 GATCAGCATC
*
1238655 AATCATAGATTTTCTAAG
1 AATCATAGATTTTTTAAG
1238673 AATC--AGA--TTTT-AG
1 AATCATAGATTTTTTAAG
*
1238686 AAATCATAGATTTTTTAGG
1 -AATCATAGATTTTTTAAG
* *
1238705 AATCACAAATTTTTTAAG
1 AATCATAGATTTTTTAAG
* *
1238723 AATCTTAGATTTTCTAAG
1 AATCATAGATTTTTTAAG
1238741 AATCATAGATTT
1 AATCATAGATTT
1238753 CTAGGATCAT
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
13 2 0.03
14 7 0.11
16 6 0.09
18 48 0.75
19 1 0.02
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (18 bp):
AATCATAGATTTTTTAAG
Found at i:1238763 original size:16 final size:16
Alignment explanation
Indices: 1238655--1238802 Score: 88
Period size: 18 Copynumber: 8.8 Consensus size: 16
1238645 GATCAGCATC
1238655 AATCATAGATTTTCTAAG
1 AATCATAGA-TTTCT-AG
1238673 AATC--AGATTT-TAG
1 AATCATAGATTTCTAG
*
1238686 AAATCATAGATTTTTTAGG
1 -AATCATAGA-TTTCTA-G
* * *
1238705 AATCACAAATTTTTTAAG
1 AATCATAGA-TTTCT-AG
*
1238723 AATCTTAGATTTTCTAAG
1 AATCATAGA-TTTCT-AG
1238741 AATCATAGATTTCTAG
1 AATCATAGATTTCTAG
* *
1238757 GATCATATATTTCT-G
1 AATCATAGATTTCTAG
*
1238772 TAATCATAGATTTCTAT
1 -AATCATAGATTTCTAG
*
1238789 AATTATAGAATTTC
1 AATCATAG-ATTTC
1238803 AACTATAATA
Statistics
Matches: 107, Mismatches: 13, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
13 2 0.02
14 5 0.05
15 4 0.04
16 39 0.36
17 13 0.12
18 42 0.39
19 2 0.02
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (16 bp):
AATCATAGATTTCTAG
Done.