Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold154
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: 1945843
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 156 characters in sequence are not A, C, G, or T
File 11 of 12
Found at i:1624765 original size:13 final size:13
Alignment explanation
Indices: 1624747--1624772 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1624737 AATTTTTTTA
1624747 TGTATCGATACAT
1 TGTATCGATACAT
1624760 TGTATCGATACAT
1 TGTATCGATACAT
1624773 ACTTTGTGTA
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:1625554 original size:20 final size:20
Alignment explanation
Indices: 1625529--1625569 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1625519 CTTAATCAAG
1625529 TAATTCATATCAAAAATTTA
1 TAATTCATATCAAAAATTTA
1625549 TAATTCATATCAAAAATTTA
1 TAATTCATATCAAAAATTTA
1625569 T
1 T
1625570 TTGCACATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (20 bp):
TAATTCATATCAAAAATTTA
Found at i:1626905 original size:21 final size:20
Alignment explanation
Indices: 1626876--1626918 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1626866 GACTAGTGTG
* *
1626876 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGATCGTGACCT
*
1626897 GGGAGTGCCGATCGTGACCT
1 GGGACTGCCGATCGTGACCT
1626917 GG
1 GG
1626919 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.12, C:0.26, G:0.42, T:0.21
Consensus pattern (20 bp):
GGGACTGCCGATCGTGACCT
Found at i:1629494 original size:15 final size:15
Alignment explanation
Indices: 1629474--1629504 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1629464 ATTTCGTTTG
*
1629474 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1629489 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1629504 G
1 G
1629505 GATATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1631022 original size:21 final size:21
Alignment explanation
Indices: 1630993--1631037 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1630983 AAGTTTTTAT
*
1630993 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1631013 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1631035 TTT
1 TTT
1631038 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1632955 original size:32 final size:30
Alignment explanation
Indices: 1632919--1632977 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
1632909 GAAATCAAAT
1632919 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
1632951 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
1632978 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:1633266 original size:13 final size:13
Alignment explanation
Indices: 1633248--1633273 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1633238 AATTTTTTTG
1633248 TGTATCGATACAT
1 TGTATCGATACAT
1633261 TGTATCGATACAT
1 TGTATCGATACAT
1633274 ACTTTGTGTA
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:1636606 original size:46 final size:46
Alignment explanation
Indices: 1636510--1636611 Score: 116
Period size: 46 Copynumber: 2.2 Consensus size: 46
1636500 TTCCAAAATG
** * *
1636510 TATCGATACATGTTTCTATGTATCGATACATCTGGAAAATTCAATG
1 TATCGATACATCATTCTATGTATCGATACATCTGGAAAATACAATA
* * * *
1636556 TATCGATACATCATTCTTTGTATCGATACAT-TGTATTAATACACTA
1 TATCGATACATCATTCTATGTATCGATACATCTGGA-AAATACAATA
1636602 TATCGATACA
1 TATCGATACA
1636612 GGGGGATTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 3 0.06
46 44 0.94
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (46 bp):
TATCGATACATCATTCTATGTATCGATACATCTGGAAAATACAATA
Found at i:1645152 original size:20 final size:20
Alignment explanation
Indices: 1645117--1645157 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
1645107 CAAAATTCTT
1645117 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
1645139 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
1645158 TTCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:1653747 original size:13 final size:13
Alignment explanation
Indices: 1653709--1653748 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
1653699 ACAATATTCC
*
1653709 TTGTATCGATACC
1 TTGTATCGATACA
1653722 TTGTATCGATACA
1 TTGTATCGATACA
1653735 TTGTATCGATACA
1 TTGTATCGATACA
1653748 T
1 T
1653749 GGGTAACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1656274 original size:13 final size:13
Alignment explanation
Indices: 1656256--1656280 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1656246 ACACCCAGAA
1656256 GTATCGATACATT
1 GTATCGATACATT
1656269 GTATCGATACAT
1 GTATCGATACAT
1656281 GTTCATTGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1656289 original size:19 final size:19
Alignment explanation
Indices: 1656264--1656320 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1656254 AAGTATCGAT
*
1656264 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
1656283 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
*
1656302 ACAATGGTATCGATACATG
1 AC-ATTGTATCGATACATG
1656321 AAACTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:1656383 original size:13 final size:13
Alignment explanation
Indices: 1656365--1656417 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1656355 CGATACATGG
1656365 TACATTGTATCGA
1 TACATTGTATCGA
*
1656378 TACATTGTATCTA
1 TACATTGTATCGA
1656391 TACA-TG-AT-G-
1 TACATTGTATCGA
1656400 -A-ATTGTATCGA
1 TACATTGTATCGA
1656411 TACATTG
1 TACATTG
1656418 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 1 0.03
11 2 0.06
12 3 0.09
13 20 0.62
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1656394 original size:33 final size:33
Alignment explanation
Indices: 1656349--1656417 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1656339 CTACCACTAT
*
1656349 TTGTATCGATACATGGT-ACATTGTATCGATACA
1 TTGTATCGATACATGATGA-ATTGTATCGATACA
*
1656382 TTGTATCTATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTGTATCGATACA
1656415 TTG
1 TTG
1656418 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTGTATCGATACA
Found at i:1660759 original size:17 final size:18
Alignment explanation
Indices: 1660711--1660759 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
1660701 TCAACTGCAC
1660711 ATTTATCTTAATAAATTAT
1 ATTTATC-TAATAAATTAT
*
1660730 ATTTATCTCATAAA-TAT
1 ATTTATCTAATAAATTAT
1660747 AATTT-TCTAATAA
1 -ATTTATCTAATAA
1660760 TTACAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 10 0.37
18 10 0.37
19 7 0.26
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTATCTAATAAATTAT
Found at i:1661163 original size:9 final size:9
Alignment explanation
Indices: 1661149--1661207 Score: 59
Period size: 10 Copynumber: 6.6 Consensus size: 9
1661139 TTTATACGTT
1661149 AAAAATTAA
1 AAAAATTAA
1661158 AAAAATTAAA
1 AAAAATT-AA
1661168 AAAAATTAA
1 AAAAATTAA
**
1661177 AAAGTTTTAA
1 AAA-AATTAA
*
1661187 ATAAATT-A
1 AAAAATTAA
1661195 AAAAA-TAA
1 AAAAATTAA
1661203 AAAAA
1 AAAAA
1661208 AAGAACTCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
7 1 0.02
8 11 0.27
9 14 0.34
10 15 0.37
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (9 bp):
AAAAATTAA
Found at i:1661171 original size:19 final size:19
Alignment explanation
Indices: 1661149--1661208 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
1661139 TTTATACGTT
1661149 AAAAATTAAAAAAATTAAA
1 AAAAATTAAAAAAATTAAA
** *
1661168 AAAAATTAAAAAGTTTTAA
1 AAAAATTAAAAAAATTAAA
*
1661187 ATAAATT-AAAAAA-TAAA
1 AAAAATTAAAAAAATTAAA
1661204 AAAAA
1 AAAAA
1661209 AGAACTCGCA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
17 7 0.21
18 4 0.12
19 22 0.67
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAAATTAAAAAAATTAAA
Found at i:1661291 original size:2 final size:2
Alignment explanation
Indices: 1661261--1661357 Score: 75
Period size: 2 Copynumber: 51.5 Consensus size: 2
1661251 TAGATATAAC
* * * *
1661261 AT AT AT A- AT AT TT AT -T A- AT AT AA AT AT AT AT A- AG AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1661299 AT AT AT CAT AT AT A- AT A- AT AT AT AT AT AGT AT AT AT AT AG AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
1661341 A- AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1661358 ACTTATAATA
Statistics
Matches: 78, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
1 8 0.10
2 66 0.85
3 4 0.05
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1661311 original size:11 final size:11
Alignment explanation
Indices: 1661278--1661357 Score: 85
Period size: 11 Copynumber: 7.3 Consensus size: 11
1661268 ATATTTATTA
1661278 ATATA-AATAT
1 ATATATAATAT
*
1661288 ATATA-AGAGAT
1 ATATATA-ATAT
*
1661299 ATATATCATAT
1 ATATATAATAT
1661310 ATA-ATAATAT
1 ATATATAATAT
*
1661320 ATATATAGTAT
1 ATATATAATAT
1661331 ATATATAGATAAT
1 ATATATA-AT-AT
1661344 ATATATAATAT
1 ATATATAATAT
1661355 ATA
1 ATA
1661358 ACTTATAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
10 15 0.25
11 32 0.54
12 3 0.05
13 9 0.15
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (11 bp):
ATATATAATAT
Found at i:1661314 original size:45 final size:45
Alignment explanation
Indices: 1661254--1661358 Score: 117
Period size: 45 Copynumber: 2.3 Consensus size: 45
1661244 TATGTTATAG
* * *
1661254 ATATAACATATATAAT-ATTTATTAATATAA-ATATATATAAGA-GAT
1 ATATATCATATATAATAATATA-T-ATATAATATATATAT-AGATAAT
*
1661299 ATATATCATATATAATAATATATATATAGTATATATATAGATAAT
1 ATATATCATATATAATAATATATATATAATATATATATAGATAAT
*
1661344 ATATATAATATATAA
1 ATATATCATATATAA
1661359 CTTATAATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
44 8 0.15
45 40 0.77
46 4 0.08
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (45 bp):
ATATATCATATATAATAATATATATATAATATATATATAGATAAT
Found at i:1661331 original size:9 final size:8
Alignment explanation
Indices: 1661261--1661357 Score: 75
Period size: 7 Copynumber: 12.9 Consensus size: 8
1661251 TAGATATAAC
1661261 ATATATA-
1 ATATATAT
*
1661268 ATATTTAT
1 ATATATAT
1661276 -TA-ATAT
1 ATATATAT
*
1661282 AAATATAT
1 ATATATAT
* *
1661290 ATA-AGAG
1 ATATATAT
1661297 ATATATAT
1 ATATATAT
1661305 CATATATA-
1 -ATATATAT
1661313 ATA-ATAT
1 ATATATAT
1661320 ATATATAGT
1 ATATATA-T
1661329 ATATATAT
1 ATATATAT
*
1661337 AGATA-AT
1 ATATATAT
1661344 ATATATA-
1 ATATATAT
1661351 ATATATA
1 ATATATA
1661358 ACTTATAATA
Statistics
Matches: 71, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
6 6 0.08
7 33 0.46
8 17 0.24
9 15 0.21
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (8 bp):
ATATATAT
Found at i:1661738 original size:89 final size:89
Alignment explanation
Indices: 1661443--1662107 Score: 616
Period size: 89 Copynumber: 7.4 Consensus size: 89
1661433 TTATTAGATT
* * **** * * *
1661443 AGATTCCTTCTGACAGAACAGAAAATATTT-AGTTAATATAAAATAAAATTCTTGAAACCCAAAA
1 AGATTCCTTCTGACACAACAGAAAATATTTGA-CTAATGCCTAATAAATTTCTTGGAACCCGAAA
* *
1661507 GATGTGACAGATGCATGCGAGTATC
65 GATGTGACAGATGCATGTGGGTATC
* * * * ** **** * *
1661532 AAATTCTTTTTGGCATGACAGAAAATATTTGACTAATATAAAATAAAATTCTTGAAACCACCCGA
1 AGATTCCTTCTGACACAACAGAAAATATTTGACTAATGCCTAATAAATTTCTTG-GA--ACCCGA
* *
1661597 AAGATGTGACAGATGTATGCGGGTATC
63 AAGATGTGACAGATGCATGTGGGTATC
* * * * * * * **
1661624 AGATTCCTTTTTACACGACAAAAAATATTTGACTAGTGCCTAATAAGTTTCTTGAAACTTGAAAT
1 AGATTCCTTCTGACACAACAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACCCGAAA-
* * *
1661689 G-TGTTACAGATGTATGCGGGTATC
65 GATGTGACAGATGCATGTGGGTATC
* * *
1661713 AGATTCCTTCTAACACAATAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACCCGAAAT
1 AGATTCCTTCTGACACAACAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACCCGAAAG
* *
1661778 ATGTTACAGATGCATGTAGGTATC
66 ATGTGACAGATGCATGTGGGTATC
* * * * * ***
1661802 AGATTCCTTCTGATACGACAGAAAATATTTGACTAATACCGAATAAATTTCTTGAAACTTAAAAG
1 AGATTCCTTCTGACACAACAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACCCGAAAG
* * ** *
1661867 ATGTGATAGATGTACATAGGTATC
66 ATGTGACAGATGCATGTGGGTATC
* * * ** *
1661891 AAAGTCATTCTGACATGAGAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACCCGAAAG
1 AGATTCCTTCTGACACAACAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACCCGAAAG
*
1661956 ATGTGACATATGCATGTGGGTATC
66 ATGTGACAGATGCATGTGGGTATC
* * *
1661980 AAATTCCTTCTGACACGAA-AGAAAATATTTGACTAATACTTAATAAATTTCTTGGAACCCGAAA
1 AGATTCCTTCTGACAC-AACAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACCCGAAA
*
1662044 GATGTGACAAATGCATGTGGGTATC
65 GATGTGACAGATGCATGTGGGTATC
* * * *
1662069 AGATTCCTTATAACACGACTGAAAAATATTTGACTAATG
1 AGATTCCTTCTGACACAACAG-AAAATATTTGACTAATG
1662108 ATAGGACAGA
Statistics
Matches: 480, Mismatches: 87, Indels: 17
0.82 0.15 0.03
Matches are distributed among these distances:
88 1 0.00
89 385 0.80
90 21 0.04
91 2 0.00
92 71 0.15
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (89 bp):
AGATTCCTTCTGACACAACAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACCCGAAAG
ATGTGACAGATGCATGTGGGTATC
Found at i:1665758 original size:13 final size:13
Alignment explanation
Indices: 1665740--1665764 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1665730 ACACACAGTA
1665740 TGTATCGATACAT
1 TGTATCGATACAT
1665753 TGTATCGATACA
1 TGTATCGATACA
1665765 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1665783 original size:33 final size:32
Alignment explanation
Indices: 1665720--1665787 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
1665710 GTAGCCAAAC
**
1665720 TTGTATCGATACACACAGTATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
* *
1665752 TTGTATCGATACACCATAAAATGTATTGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
1665785 TTG
1 TTG
1665788 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:1668398 original size:33 final size:33
Alignment explanation
Indices: 1668361--1668427 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1668351 TTCAACGATT
*
1668361 TGTATTGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1668394 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1668427 T
1 T
1668428 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1668399 original size:13 final size:13
Alignment explanation
Indices: 1668381--1668405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1668371 CATAAAATGT
1668381 TGTATCGATACAA
1 TGTATCGATACAA
1668394 TGTATCGATACA
1 TGTATCGATACA
1668406 TATTTTTTTG
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:1668486 original size:13 final size:13
Alignment explanation
Indices: 1668468--1668492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1668458 ATTACTCAAA
1668468 TGTATCGATACAT
1 TGTATCGATACAT
1668481 TGTATCGATACA
1 TGTATCGATACA
1668493 CCGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1668557 original size:52 final size:52
Alignment explanation
Indices: 1668501--1668672 Score: 326
Period size: 52 Copynumber: 3.3 Consensus size: 52
1668491 CACCGATCTT
1668501 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1668553 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
* *
1668605 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1668657 TGTATCGATACATGCA
1 TGTATCGATACATGCA
1668673 AGTAACTTTT
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 118 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:1675652 original size:13 final size:13
Alignment explanation
Indices: 1675634--1675672 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1675624 ACAGTATTCT
1675634 TTGTATCGATACA
1 TTGTATCGATACA
1675647 TTGTATCGATACA
1 TTGTATCGATACA
*
1675660 CTGTATCGATACA
1 TTGTATCGATACA
1675673 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1675839 original size:20 final size:20
Alignment explanation
Indices: 1675804--1675844 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
1675794 CAAATTTCTT
1675804 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
1675826 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
1675845 TTCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:1678219 original size:19 final size:20
Alignment explanation
Indices: 1678195--1678245 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1678185 TAGCCAAACT
**
1678195 TGTATCGATACA-CACAGTA
1 TGTATCGATACACCACAAAA
*
1678214 TGTATCGATACACCATAAAA
1 TGTATCGATACACCACAAAA
1678234 TGTATCGATACA
1 TGTATCGATACA
1678246 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (20 bp):
TGTATCGATACACCACAAAA
Found at i:1679137 original size:22 final size:20
Alignment explanation
Indices: 1679108--1679152 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1679098 AAACTTAACG
*
1679108 AAAAAAAATACAAAACTAAAA
1 AAAAAAAATA-AAAACGAAAA
*
1679129 AAAATAAAATAAAACCGAAAA
1 AAAA-AAAATAAAAACGAAAA
1679150 AAA
1 AAA
1679153 TTACAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.80, C:0.09, G:0.02, T:0.09
Consensus pattern (20 bp):
AAAAAAAATAAAAACGAAAA
Found at i:1679252 original size:2 final size:2
Alignment explanation
Indices: 1679245--1679422 Score: 106
Period size: 2 Copynumber: 97.0 Consensus size: 2
1679235 TATTATATGT
* *
1679245 TA TA TA TA T- TA TG TA TA TA T- TA TA TG T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1679284 TA CA CA CTA TGA TA T- TA T- TA TA T- TA TA TA T- TA TA TA T- TA
1 TA TA TA -TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1679323 TA AA T- TA T- TA TA T- TA T- TA TA TA TA TA GA TG T- TCA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* *
1679361 TA TT TA TA T- TA -A TA TA -A TA TA TA TA TA TA -A TA TA -A CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1679398 TA TA -A TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1679423 AGTTACATTG
Statistics
Matches: 139, Mismatches: 15, Indels: 44
0.70 0.08 0.22
Matches are distributed among these distances:
1 19 0.14
2 116 0.83
3 4 0.03
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1679252 original size:11 final size:12
Alignment explanation
Indices: 1679234--1679422 Score: 77
Period size: 11 Copynumber: 16.2 Consensus size: 12
1679224 AATAAACAAA
1679234 ATAT-TATATGTT
1 ATATATATATG-T
1679246 ATATATATTATGT
1 ATATATA-TATGT
1679259 ATATATTATATGT
1 ATATA-TATATGT
*
1679272 -TATATATATAT
1 ATATATATATGT
* *
1679283 ATACACACTATG-
1 ATATATA-TATGT
1679295 ATATTATTATAT-T
1 ATA-TA-TATATGT
*
1679308 ATATAT-TATAT
1 ATATATATATGT
*
1679319 AT-TATAAAT-T
1 ATATATATATGT
1679329 AT-TATATTAT-T
1 ATATATA-TATGT
1679340 ATATATATAGATGT
1 ATATATAT--ATGT
*
1679354 -TCATATATATTT
1 AT-ATATATATGT
*
1679366 ATAT-TA-ATAT
1 ATATATATATGT
*
1679376 A-ATATATATAT
1 ATATATATATGT
**
1679387 ATA-ATATA-AC
1 ATATATATATGT
*
1679397 ATATA-ATATAT
1 ATATATATATGT
1679408 ATATATATATGT
1 ATATATATATGT
1679420 ATA
1 ATA
1679423 AGTTACATTG
Statistics
Matches: 141, Mismatches: 13, Indels: 46
0.70 0.06 0.23
Matches are distributed among these distances:
9 2 0.01
10 26 0.18
11 37 0.26
12 35 0.25
13 27 0.19
14 14 0.10
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50
Consensus pattern (12 bp):
ATATATATATGT
Found at i:1679270 original size:27 final size:26
Alignment explanation
Indices: 1679234--1679364 Score: 113
Period size: 27 Copynumber: 4.8 Consensus size: 26
1679224 AATAAACAAA
1679234 ATATTATATGTTATATATATTATGTAT
1 ATATTATATGTTATATATATTAT-TAT
*
1679261 ATATTATATGTTATATATA-TATATAC
1 ATATTATATGTTATATATATTAT-TAT
* * *
1679287 ACACTATGATATTATTATATTATATATTAT
1 ATATTAT-ATGTTA-TATA-TAT-TATTAT
**
1679317 ATATTATAAATTAT-TATATTATTAT
1 ATATTATATGTTATATATATTATTAT
*
1679342 ATATATAGATGTTCATATATATT
1 ATAT-TATATGTT-ATATATATT
1679365 TATATTAATA
Statistics
Matches: 84, Mismatches: 12, Indels: 15
0.76 0.11 0.14
Matches are distributed among these distances:
25 10 0.12
26 18 0.21
27 28 0.33
28 11 0.13
29 7 0.08
30 7 0.08
31 3 0.04
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (26 bp):
ATATTATATGTTATATATATTATTAT
Found at i:1679313 original size:37 final size:37
Alignment explanation
Indices: 1679261--1679348 Score: 103
Period size: 37 Copynumber: 2.5 Consensus size: 37
1679251 TATTATGTAT
* * *
1679261 ATATTA-TATGTTATATA-TATATA-TACACACTATG
1 ATATTATTATATTATATATTATATATTATAAACTATG
* *
1679295 ATATTATTATATTATATATTATATATTATAAATTATT
1 ATATTATTATATTATATATTATATATTATAAACTATG
1679332 ATATTATTATA-TATATA
1 ATATTATTATATTATATA
1679349 GATGTTCATA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
34 6 0.13
35 10 0.22
36 12 0.26
37 18 0.39
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.51
Consensus pattern (37 bp):
ATATTATTATATTATATATTATATATTATAAACTATG
Found at i:1679414 original size:25 final size:24
Alignment explanation
Indices: 1679356--1679414 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 24
1679346 ATAGATGTTC
* *
1679356 ATATATAT-TTATATTAATATAAT
1 ATATATATATAATATAAATATAAT
1679379 ATATATATATAATATAACATATAAT
1 ATATATATATAATATAA-ATATAAT
1679404 ATATATATATA
1 ATATATATATA
1679415 TATGTATAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 8 0.25
24 6 0.19
25 18 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATATATATATAATATAAATATAAT
Found at i:1679831 original size:97 final size:97
Alignment explanation
Indices: 1679665--1679858 Score: 370
Period size: 97 Copynumber: 2.0 Consensus size: 97
1679655 ATTATCAACT
1679665 CTCTAGTCTAAGTAAAATACCGTTTCAACTAGGACAAGGTTTATCTACCTTACTATAGTATGCCC
1 CTCTAGTCTAAGTAAAATACCGTTTCAACTAGGACAAGGTTTATCTACCTTACTATAGTATGCCC
1679730 TAATTTAGACATTATCTTATAAGATAATCTTA
66 TAATTTAGACATTATCTTATAAGATAATCTTA
* *
1679762 CTCTAGTCTAAGTAAAATACCGTTTCAACTAGGACAAGGTTTATCTGCTTTACTATAGTATGCCC
1 CTCTAGTCTAAGTAAAATACCGTTTCAACTAGGACAAGGTTTATCTACCTTACTATAGTATGCCC
1679827 TAATTTAGACATTATCTTATAAGATAATCTTA
66 TAATTTAGACATTATCTTATAAGATAATCTTA
1679859 TTAATCATGT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.37
Consensus pattern (97 bp):
CTCTAGTCTAAGTAAAATACCGTTTCAACTAGGACAAGGTTTATCTACCTTACTATAGTATGCCC
TAATTTAGACATTATCTTATAAGATAATCTTA
Found at i:1680302 original size:21 final size:20
Alignment explanation
Indices: 1680278--1680328 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1680268 TAACAAATTA
* *
1680278 TATCAATACAATAGGGTAATG
1 TATCGATACAAAAGGG-AATG
*
1680299 TATCGATACAAAAGTGAATG
1 TATCGATACAAAAGGGAATG
1680319 TATCGATACA
1 TATCGATACA
1680329 TGTTGGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
TATCGATACAAAAGGGAATG
Found at i:1680461 original size:51 final size:52
Alignment explanation
Indices: 1680385--1680523 Score: 201
Period size: 52 Copynumber: 2.7 Consensus size: 52
1680375 TCTGGAATGA
*
1680385 AAATGTATCGATACAGTT-TTCATTGTATCGATACATTATGGG-TTTTAACCT
1 AAATGTATCGATACA-TTCTTCATTGTATCGATACATTATGGGTTTTTAACCC
* * *
1680436 AAATGTATCGATGCATTCTTCATTGTATCGATACATTTTGGGTTTTTGACCC
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTATGGGTTTTTAACCC
* *
1680488 AAATGTATCGATACATTCTTCAATGTATCAATACAT
1 AAATGTATCGATACATTCTTCATTGTATCGATACAT
1680524 GCAGGCAAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
50 2 0.03
51 37 0.47
52 40 0.51
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.40
Consensus pattern (52 bp):
AAATGTATCGATACATTCTTCATTGTATCGATACATTATGGGTTTTTAACCC
Found at i:1682918 original size:98 final size:97
Alignment explanation
Indices: 1682733--1682923 Score: 233
Period size: 98 Copynumber: 2.0 Consensus size: 97
1682723 TCTAATCCCG
* * ** *
1682733 TTTTTAAACTTATCAAGATCTAAATCTTATTTTTACTTAAATTGTCATCATCGAGGATACTCTAA
1 TTTTTAAACTTATCAAGATCTAAATCTTAATTTCACCAAAATTATCATCATCGAGGATACTCTAA
** ** *
1682798 CCTTATTCTTCTAAGAGGATACTCCAACATTA
66 CCCCATTCACCGAAGAGGATACTCCAACATTA
* *
1682830 TTTTTAAACTTATCAAGATTTAAATCTTAATTTCACCCAAAATTATCATCTTCG-GGAATACTCT
1 TTTTTAAACTTATCAAGATCTAAATCTTAATTTCA-CCAAAATTATCATCATCGAGG-ATACTCT
1682894 AACCCCATTCCACCGAA-AGGATACTCCAAC
64 AACCCCATT-CACCGAAGAGGATACTCCAAC
1682924 CCCGTTTTTC
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
97 34 0.43
98 41 0.52
99 4 0.05
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (97 bp):
TTTTTAAACTTATCAAGATCTAAATCTTAATTTCACCAAAATTATCATCATCGAGGATACTCTAA
CCCCATTCACCGAAGAGGATACTCCAACATTA
Found at i:1682932 original size:98 final size:97
Alignment explanation
Indices: 1682719--1682932 Score: 225
Period size: 98 Copynumber: 2.2 Consensus size: 97
1682709 TTTTGAGGGA
* * * * ** *
1682719 ATACTCTAATCCCGTTTTTAAACTTATCAAGATCTAAATCTTATTTTTACTTAAATTGTCATCAT
1 ATACTCCAACCCCGTTTTTAAACTTATCAAGATCTAAATCTTAATTTCACCAAAATTATCATCAT
** ** *
1682784 CGAGGATACTCTAACCTTATTCTTCTAAGAGG
66 CGAGGATACTCTAACCCCATTCACCGAAGAGG
**** * *
1682816 ATACTCCAACATTATTTTTAAACTTATCAAGATTTAAATCTTAATTTCACCCAAAATTATCATCT
1 ATACTCCAACCCCGTTTTTAAACTTATCAAGATCTAAATCTTAATTTCA-CCAAAATTATCATCA
1682881 TCG-GGAATACTCTAACCCCATTCCACCGAA-AGG
65 TCGAGG-ATACTCTAACCCCATT-CACCGAAGAGG
1682914 ATACTCCAACCCCGTTTTT
1 ATACTCCAACCCCGTTTTT
1682933 CAACCAAAAA
Statistics
Matches: 92, Mismatches: 22, Indels: 5
0.77 0.18 0.04
Matches are distributed among these distances:
97 42 0.46
98 46 0.50
99 4 0.04
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.36
Consensus pattern (97 bp):
ATACTCCAACCCCGTTTTTAAACTTATCAAGATCTAAATCTTAATTTCACCAAAATTATCATCAT
CGAGGATACTCTAACCCCATTCACCGAAGAGG
Found at i:1689123 original size:52 final size:50
Alignment explanation
Indices: 1689043--1689179 Score: 150
Period size: 52 Copynumber: 2.7 Consensus size: 50
1689033 ATTTAACTGG
* * * * * *
1689043 ATGTATCGATACATTGAAGAATATATCGATACATTTGGGTGAAAAACCTAGA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTGGAT--AAAACCCAAA
* *
1689095 ATGTATCGATCCAATGAAAAATGTATCGATACATTTGGATCAAACCCAAA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTGGATAAAACCCAAA
* * *
1689145 ATATATCGATATAAT-AAAAATGTATTGATACATTT
1 ATGTATCGATACAATGAAAAATGTATCGATACATTT
1689180 TCTTTTCAGA
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
49 19 0.26
50 19 0.26
52 35 0.48
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (50 bp):
ATGTATCGATACAATGAAAAATGTATCGATACATTTGGATAAAACCCAAA
Found at i:1689285 original size:21 final size:20
Alignment explanation
Indices: 1689236--1689289 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1689226 CATTTCAAAC
*
1689236 ATGTATTGATACATTCACTT
1 ATGTATCGATACATTCACTT
*
1689256 ATATATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
*
1689276 GTTGTATCGATACA
1 -ATGTATCGATACA
1689290 AATTGTAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:1696539 original size:31 final size:31
Alignment explanation
Indices: 1696503--1696567 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
1696493 TCTAAAATAA
1696503 AATTAAGTGTTTACAATAATTATTATATCTT
1 AATTAAGTGTTTACAATAATTATTATATCTT
*
1696534 AATTAAGTGTTTATAATAATTATTATATCTT
1 AATTAAGTGTTTACAATAATTATTATATCTT
1696565 AAT
1 AAT
1696568 GCATCAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (31 bp):
AATTAAGTGTTTACAATAATTATTATATCTT
Found at i:1696555 original size:17 final size:17
Alignment explanation
Indices: 1696499--1696555 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 17
1696489 TCAATCTAAA
1696499 ATAA-AATTAAGTGTTT
1 ATAATAATTAAGTGTTT
* *
1696515 ACAATAATT-A-T-TAT
1 ATAATAATTAAGTGTTT
**
1696529 ATCTTAATTAAGTGTTT
1 ATAATAATTAAGTGTTT
1696546 ATAATAATTA
1 ATAATAATTA
1696556 TTATATCTTA
Statistics
Matches: 29, Mismatches: 8, Indels: 7
0.66 0.18 0.16
Matches are distributed among these distances:
14 8 0.28
15 2 0.07
16 5 0.17
17 14 0.48
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (17 bp):
ATAATAATTAAGTGTTT
Found at i:1697147 original size:40 final size:43
Alignment explanation
Indices: 1697031--1697152 Score: 101
Period size: 48 Copynumber: 2.8 Consensus size: 43
1697021 TTTATATTAC
*
1697031 TTATAT-TATTATTTATAATTAATAAAAAATAATTTTATATTAATAT
1 TTATATAT-TTATTTA-AATAAATAAAAAAT-ATTTTATA-TAATAT
* *
1697077 TTATATATTATCAATTAAATTTAAAT-AAAAATATTTT-TA-ATTAT
1 TTATATATT-T-ATTTAAA--TAAATAAAAAATATTTTATATAATAT
*
1697121 TTA-ATATTTATTTAAATAAATAAAAAAAATTT
1 TTATATATTTATTTAAATAAATAAAAAATATTT
1697153 ATCTAAGATC
Statistics
Matches: 65, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
39 5 0.08
40 9 0.14
41 6 0.09
42 1 0.02
43 5 0.08
44 7 0.11
46 9 0.14
47 9 0.14
48 10 0.15
49 4 0.06
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (43 bp):
TTATATATTTATTTAAATAAATAAAAAATATTTTATATAATAT
Found at i:1697481 original size:12 final size:13
Alignment explanation
Indices: 1697460--1697488 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1697450 AGAAAAATAC
1697460 TTTTTAACGTAAA
1 TTTTTAACGTAAA
1697473 TTTTT-ACGTAAA
1 TTTTTAACGTAAA
1697485 TTTT
1 TTTT
1697489 GAATTCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (13 bp):
TTTTTAACGTAAA
Found at i:1698013 original size:6 final size:6
Alignment explanation
Indices: 1698004--1698052 Score: 57
Period size: 6 Copynumber: 8.0 Consensus size: 6
1697994 ATAATAAAAA
1698004 AAATAT AAATAT -AATAT AAATAAT AAATATTT AAATAT -AATAT AAATAT
1 AAATAT AAATAT AAATAT AAAT-AT AAATA--T AAATAT AAATAT AAATAT
1698053 TTAATATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
5 10 0.26
6 16 0.42
7 6 0.16
8 6 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
AAATAT
Found at i:1698019 original size:11 final size:11
Alignment explanation
Indices: 1698005--1698052 Score: 60
Period size: 11 Copynumber: 4.0 Consensus size: 11
1697995 TAATAAAAAA
1698005 AATATAAATAT
1 AATATAAATAT
1698016 AATATAAATAAT
1 AATATAAAT-AT
1698028 AAATATTTAAATAT
1 -AATA--TAAATAT
1698042 AATATAAATAT
1 AATATAAATAT
1698053 TTAATATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 16 0.48
12 2 0.06
13 8 0.24
14 2 0.06
15 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATATAAATAT
Found at i:1698026 original size:15 final size:15
Alignment explanation
Indices: 1698008--1698051 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 15
1697998 TAAAAAAAAT
1698008 ATAAATATAATATAA
1 ATAAATATAATATAA
1698023 AT-AATA-AATAT--
1 ATAAATATAATATAA
*
1698034 TTAAATATAATATAA
1 ATAAATATAATATAA
1698049 ATA
1 ATA
1698052 TTTAATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 8
0.70 0.06 0.24
Matches are distributed among these distances:
11 1 0.04
12 4 0.17
13 10 0.43
14 4 0.17
15 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAAATATAATATAA
Found at i:1698038 original size:26 final size:27
Alignment explanation
Indices: 1697996--1698080 Score: 95
Period size: 26 Copynumber: 3.2 Consensus size: 27
1697986 TGAACATGAT
* *
1697996 AATAAAAAAAATA-TAAATATAATATA
1 AATAATAAATATATTAAATATAATATA
1698022 AATAATAAATAT-TTAAATATAATATA
1 AATAATAAATATATTAAATATAATATA
* *
1698048 AATATTTAATATATTAAA-ATATATATCA
1 AATAATAAATATATTAAATATA-ATAT-A
1698076 AATAA
1 AATAA
1698081 ATTATTAGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
26 36 0.72
27 9 0.18
28 5 0.10
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (27 bp):
AATAATAAATATATTAAATATAATATA
Found at i:1698071 original size:19 final size:19
Alignment explanation
Indices: 1698016--1698071 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
1698006 ATATAAATAT
1698016 AATATAAATAATAAATATTTA
1 AATAT-AATAA-AAATATTTA
*
1698037 AATATAATATAAATATTT-
1 AATATAATAAAAATATTTA
*
1698055 AATATATTAAAATATAT
1 AATATAATAAAA-ATAT
1698072 ATCAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 10 0.32
19 12 0.39
20 4 0.13
21 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATAATAAAAATATTTA
Found at i:1700782 original size:14 final size:14
Alignment explanation
Indices: 1700763--1700798 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
1700753 CTAACAGTTG
1700763 CCTTTGAACTCATT
1 CCTTTGAACTCATT
1700777 CCTTTGTGAACTCATT
1 CC-TT-TGAACTCATT
1700793 CCTTTG
1 CCTTTG
1700799 TTTCCATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.20
15 4 0.20
16 12 0.60
ACGTcount: A:0.17, C:0.28, G:0.11, T:0.44
Consensus pattern (14 bp):
CCTTTGAACTCATT
Found at i:1700788 original size:16 final size:16
Alignment explanation
Indices: 1700767--1700799 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1700757 CAGTTGCCTT
1700767 TGAACTCATTCCTTTG
1 TGAACTCATTCCTTTG
1700783 TGAACTCATTCCTTTG
1 TGAACTCATTCCTTTG
1700799 T
1 T
1700800 TTCCATAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.45
Consensus pattern (16 bp):
TGAACTCATTCCTTTG
Found at i:1701865 original size:11 final size:11
Alignment explanation
Indices: 1701849--1701873 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1701839 TAATCAAACA
1701849 AAAATAAAAAT
1 AAAATAAAAAT
1701860 AAAATAAAAAT
1 AAAATAAAAAT
1701871 AAA
1 AAA
1701874 TAATTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:1702807 original size:23 final size:22
Alignment explanation
Indices: 1702777--1702821 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
1702767 GACAGGCTTG
*
1702777 AAATATTTAAATTATTATTTAAA
1 AAATATTTAAAATATT-TTTAAA
1702800 AAATATTTAAAATATTTTTAAA
1 AAATATTTAAAATATTTTTAAA
1702822 TTAATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATATTTAAAATATTTTTAAA
Found at i:1702852 original size:32 final size:30
Alignment explanation
Indices: 1702816--1702892 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 30
1702806 TTAAAATATT
*
1702816 TTTAAATTAATTTATTTATTT-TTATAATTAAA
1 TTTAAATTAAATTATTT-TTTATT-T-ATTAAA
*
1702848 TTTAAATAAAATTATTTTTTATTTATTAAA
1 TTTAAATTAAATTATTTTTTATTTATTAAA
*
1702878 TAATAAATTAAATTA
1 T-TTAAATTAAATTA
1702893 AATTAATTCG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
30 7 0.18
31 15 0.38
32 17 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TTTAAATTAAATTATTTTTTATTTATTAAA
Found at i:1702896 original size:36 final size:36
Alignment explanation
Indices: 1702817--1702897 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 36
1702807 TAAAATATTT
1702817 TTAAATTAATTTATTTATTTTTATAATTAAATTTAAA
1 TTAAATT-ATTTATTTATTTTTATAATTAAATTTAAA
*
1702854 TAAAATTATTT-TTTATTTATTA-AATAATAAA-TTAAA
1 TTAAATTATTTATTTATTT-TTATAAT--TAAATTTAAA
1702890 TTAAATTA
1 TTAAATTA
1702898 ATTCGAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
35 10 0.26
36 19 0.49
37 10 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (36 bp):
TTAAATTATTTATTTATTTTTATAATTAAATTTAAA
Found at i:1704686 original size:21 final size:20
Alignment explanation
Indices: 1704655--1704694 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1704645 TAAAATATTA
1704655 AATTTTATTTT-TATATTAAT
1 AATTTTATTTTATA-ATTAAT
1704675 AATTTATATTTTATAATTAA
1 AATTT-TATTTTATAATTAA
1704695 ATTGTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 11 0.61
22 2 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
AATTTTATTTTATAATTAAT
Found at i:1705503 original size:18 final size:17
Alignment explanation
Indices: 1705474--1705517 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1705464 ATGTCGAGAA
* *
1705474 TTTCTCTCTCTTTCTCC
1 TTTCTTTCTCTTGCTCC
*
1705491 TTCTCTTTCTCTTGCTCG
1 TT-TCTTTCTCTTGCTCC
1705509 TTTCTTTCT
1 TTTCTTTCT
1705518 TTCTTTGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.00, C:0.34, G:0.05, T:0.61
Consensus pattern (17 bp):
TTTCTTTCTCTTGCTCC
Found at i:1706161 original size:24 final size:22
Alignment explanation
Indices: 1706134--1706184 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1706124 TTTAAAAATT
*
1706134 TAAAATATAAGTATATTAATATTA
1 TAAAATAT-AGTATA-TAATAATA
*
1706158 TAAAA-ATATTATATAATAATA
1 TAAAATATAGTATATAATAATA
1706179 TAAAAT
1 TAAAAT
1706185 TAAAATTTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 12 0.50
22 5 0.21
23 2 0.08
24 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
TAAAATATAGTATATAATAATA
Found at i:1706465 original size:21 final size:22
Alignment explanation
Indices: 1706436--1706485 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1706426 GTGCAAGATT
*
1706436 TGAAAAAAAGCAA-GCCAATTAA
1 TGAAAAAAGGCAAGGCCAA-TAA
*
1706458 TGAAAAAAGGGAAGGCCAATAA
1 TGAAAAAAGGCAAGGCCAATAA
1706480 TGAAAA
1 TGAAAA
1706486 GAAATATGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.58, C:0.10, G:0.20, T:0.12
Consensus pattern (22 bp):
TGAAAAAAGGCAAGGCCAATAA
Found at i:1708815 original size:28 final size:28
Alignment explanation
Indices: 1708754--1708832 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
1708744 CAAATGCCAC
1708754 CTTTTGTATTTGTCAAATATGGTGGTTT
1 CTTTTGTATTTGTCAAATATGGTGGTTT
*
1708782 CCTTTGTATTTGTCAAATATGGTGGTTAT
1 CTTTTGTATTTGTCAAATATGGTGGTT-T
* *
1708811 -TTTTG--TTTGTAAAAAATGGTGG
1 CTTTTGTATTTGTCAAATATGGTGG
1708833 CTTGTTGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
26 15 0.33
28 30 0.65
29 1 0.02
ACGTcount: A:0.22, C:0.06, G:0.23, T:0.49
Consensus pattern (28 bp):
CTTTTGTATTTGTCAAATATGGTGGTTT
Found at i:1708849 original size:24 final size:24
Alignment explanation
Indices: 1708790--1708858 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
1708780 TTCCTTTGTA
* * *
1708790 TTTGTCAAATATGGTGGTTATTTTTG
1 TTTGTCAAAAATGGTGG--CTTGTTG
*
1708816 TTTGTAAAAAATGGTGGCTTGTTG
1 TTTGTCAAAAATGGTGGCTTGTTG
*
1708840 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAAATGGTGGCT
1708859 AATTTTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 22 0.59
26 15 0.41
ACGTcount: A:0.22, C:0.06, G:0.26, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAAATGGTGGCTTGTTG
Found at i:1711413 original size:21 final size:22
Alignment explanation
Indices: 1711384--1711429 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1711374 TGTTCAGACA
** *
1711384 AGTAGTACTCCGTAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1711406 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1711427 AGT
1 AGT
1711430 TTCAATAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:1712167 original size:41 final size:41
Alignment explanation
Indices: 1712122--1712206 Score: 143
Period size: 41 Copynumber: 2.1 Consensus size: 41
1712112 GCAGTGGTAC
1712122 AAGCGATTTGATAGCTTTATGAGAAGGCAAAAGTACACCAG
1 AAGCGATTTGATAGCTTTATGAGAAGGCAAAAGTACACCAG
* * *
1712163 AAGCGATTTGATAGCTTTATGAGATGGCAGAAGTACATCAG
1 AAGCGATTTGATAGCTTTATGAGAAGGCAAAAGTACACCAG
1712204 AAG
1 AAG
1712207 TAAATACGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.24
Consensus pattern (41 bp):
AAGCGATTTGATAGCTTTATGAGAAGGCAAAAGTACACCAG
Found at i:1713436 original size:28 final size:28
Alignment explanation
Indices: 1713374--1713428 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1713364 CAAATGCCAC
1713374 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
1713402 CCTTTGTATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
1713429 ATTTTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.11, G:0.22, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:1723349 original size:52 final size:52
Alignment explanation
Indices: 1723201--1723329 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1723191 CGAAATATGA
1723201 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
1723253 AAATTTGCCTGTATGTATCGATATATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1723305 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1723330 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1723356 original size:13 final size:13
Alignment explanation
Indices: 1723338--1723362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1723328 CAAAGATCAG
1723338 TGTATCGATACAA
1 TGTATCGATACAA
1723351 TGTATCGATACA
1 TGTATCGATACA
1723363 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:1723425 original size:13 final size:13
Alignment explanation
Indices: 1723407--1723490 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
1723397 AGCTTCGTAG
1723407 CGATACATTGTAT
1 CGATACATTGTAT
1723420 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1723439 CGATACATTGTAT
1 CGATACATTGTAT
1723452 CGATACAAAACTTATGTAT
1 CGATAC---A--T-TGTAT
1723471 CGATACATTGTAT
1 CGATACATTGTAT
1723484 CGATACA
1 CGATACA
1723491 ACACTTATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 28 0.47
14 1 0.02
15 2 0.03
16 4 0.07
17 2 0.03
18 1 0.02
19 21 0.36
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1723439 original size:19 final size:19
Alignment explanation
Indices: 1723415--1723511 Score: 101
Period size: 19 Copynumber: 5.7 Consensus size: 19
1723405 AGCGATACAT
1723415 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
1723434 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
1723447 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
1723466 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
1723479 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
1723498 TGTATCGATACAAA
1 TGTATCGATACAAA
1723512 TCGTTGAAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 22 0.34
14 2 0.03
16 4 0.06
18 2 0.03
19 35 0.54
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1723448 original size:32 final size:32
Alignment explanation
Indices: 1723407--1723509 Score: 197
Period size: 32 Copynumber: 3.2 Consensus size: 32
1723397 AGCTTCGTAG
1723407 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1723439 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
1723471 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1723503 CGATACA
1 CGATACA
1723510 AATCGTTGAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1724549 original size:43 final size:44
Alignment explanation
Indices: 1724441--1724997 Score: 575
Period size: 49 Copynumber: 12.1 Consensus size: 44
1724431 CAAGACGGAA
* **
1724441 AAGGTGCCAATATGTTGATTCAAGGCCAGCGCTATTGGACTTAAAGGTG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A---G
* * * * *
1724490 AAGATGCCAATATGCTGATTCATGGCCAACGATATTGGGCTT-G
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAG
* *
1724533 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--AG
1724579 ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 ---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--AG
* *
1724628 TTAAAAGTGCTAATATGCTGATTCAAGGCCAGCTATATTGGACTTA-
1 ---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAG
* * * *
1724674 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--AG
* *
1724720 ATAAAGGTGTCAATATGCTGATTCAAGGCCAGCTATATTGGACCTA-
1 ---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAG
* *
1724766 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--AG
1724812 ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA-
1 ---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAG
* *
1724858 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAG
* *
1724901 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--AG
* *
1724947 ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAG
1 ---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAG
1724994 AAGG
1 AAGG
1724998 GTTGCCACCG
Statistics
Matches: 442, Mismatches: 42, Indels: 53
0.82 0.08 0.10
Matches are distributed among these distances:
43 193 0.44
44 4 0.01
45 3 0.01
46 1 0.00
47 5 0.01
49 236 0.53
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (44 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAG
Found at i:1724598 original size:92 final size:88
Alignment explanation
Indices: 1724393--1725004 Score: 586
Period size: 92 Copynumber: 6.6 Consensus size: 88
1724383 TATTGGGCTT
* * * *
1724393 GTGCTAATATGCTGATTCAAGGCCAGCTACATTGGACTCAAGACGGAAAAGGTGCCAATATGTTG
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACT---TA--G-AAAGGTGCCAATATGCTG
*
1724458 ATTCAAGGCCAGC-GCTATTGGACTTAAAGGTG
60 ATTCAAGGCCAGCTAC-ATTGGACTTAAA---G
* * * * *
1724490 AAGATGCCAATATGCTGATTCATGGCCAACGATATTGGGCTT-G-AAGGTGCCAATGTGCTGATT
1 --G-TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGAAAGGTGCCAATATGCTGATT
1724553 CAAGGCCAGCTACATTGGACTTAAAGATAAAG
63 CAAGGCCAGCTACATTGGAC-T-----TAAAG
* * * *
1724585 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGTTAAAAGTGCTAATATGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT--AG--AAAGGTGCCAATATGCTGAT
*
1724650 TCAAGGCCAGCTATATTGGACTTAAAG
62 TCAAGGCCAGCTACATTGGACTTAAAG
* * *
1724677 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGTCAATATGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT--AG--AAAGGTGCCAATATGCTGAT
* *
1724742 TCAAGGCCAGCTATATTGGACCTAAAG
62 TCAAGGCCAGCTACATTGGACTTAAAG
* *
1724769 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT--AG--AAAGGTGCCAATATGCTGAT
*
1724834 TCAAGGCCAGCTATATTGGACTTAAAG
62 TCAAGGCCAGCTACATTGGACTTAAAG
* * *
1724861 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT--AAAGGTGCCAATGTGCTGATTCAA
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGAAAGGTGCCAATATGCTGATTCAA
1724924 GGCCAGCTACATTGGACTTAAAGATAAAG
66 GGCCAGCTACATTGGAC-T-----TAAAG
* * *
1724953 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAGAAGGGTTGCCA
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGAAAGG-TGCCA
1725005 CCGACTTGTG
Statistics
Matches: 452, Mismatches: 38, Indels: 50
0.84 0.07 0.09
Matches are distributed among these distances:
86 39 0.09
87 1 0.00
92 324 0.72
93 3 0.01
94 5 0.01
95 7 0.02
97 1 0.00
98 40 0.09
99 1 0.00
100 31 0.07
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (88 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGAAAGGTGCCAATATGCTGATTCAA
GGCCAGCTACATTGGACTTAAAG
Found at i:1724643 original size:141 final size:141
Alignment explanation
Indices: 1724259--1724979 Score: 652
Period size: 141 Copynumber: 5.2 Consensus size: 141
1724249 CGAAGAATGA
* * * * * * **
1724259 CAATGTGCTGATTCATGGCTAGCGACATTGGACTTGAAGA-AGAA--TGCCAATGTGTTGAGACA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATGCTGATTCA
* * * **
1724321 AGGTCAGCGACT-TTGGGCTTAGGAATGTTAAAGATGCCAATATGCTGATTCGCGGCCAACGATA
65 AGGCCAGCTA-TATTGGACTTA--AA-GTTAAAGATGCCAATATGCTGATTCAAGGCCAACGATA
*
1724385 TTGGGCTT----GTGC
126 TTGGACTTGAAGGTGC
* * * *
1724397 TAATATGCTGATTCAAGGCCAGCTACATTGGACTCAAGACGGA-AAAGGTGCCAATATGTTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAA-A--GATAAAGGTGCCAATATGCTGATT
** * * *
1724461 CAAGGCCAGCGCTATTGGACTTAAAGGTGAAGATGCCAATATGCTGATTCATGGCCAACGATATT
63 CAAGGCCAGCTATATTGGACTTAAAGTTAAAGATGCCAATATGCTGATTCAAGGCCAACGATATT
*
1724526 GGGCTTGAAGGTGC
128 GGACTTGAAGGTGC
1724540 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
* * *
1724605 GGCCAGCTATATTGGACTTAAAGTTAAA-AGTGCTAATATGCTGATTCAAGGCCAGCTATATTGG
66 GGCCAGCTATATTGGACTTAAAGTTAAAGA-TGCCAATATGCTGATTCAAGGCCAACGATATTGG
*
1724669 ACTTAAAGGTGC
130 ACTTGAAGGTGC
* * *
1724681 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGTCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
* * * * *
1724746 GGCCAGCTATATTGGACCTAAAG-----G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
66 GGCCAGCTATATTGGACTTAAAGTTAAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGA
1724805 CTTAAAGATAAAGGTGC
131 CTT---G---AAGGTGC
* * *
1724822 CAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----TAAAGGTGCCAATGTGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
* * * * *
1724881 GGCCAGCTACATTGGACTTAAAG-----G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
66 GGCCAGCTATATTGGACTTAAAGTTAAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGA
1724940 CTTAAAGATAAAGGTGC
131 CTT---G---AAGGTGC
*
1724957 CAATATGCTGATTCAAGGCCAGC
1 CAATGTGCTGATTCAAGGCCAGC
1724980 GATATTGGGC
Statistics
Matches: 517, Mismatches: 47, Indels: 41
0.85 0.08 0.07
Matches are distributed among these distances:
135 155 0.30
138 30 0.06
139 43 0.08
140 8 0.02
141 211 0.41
142 32 0.06
143 38 0.07
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (141 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAAGTTAAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGA
CTTGAAGGTGC
Found at i:1724882 original size:21 final size:21
Alignment explanation
Indices: 1724858--1724925 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
1724848 ATTGGACTTA
1724858 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATGTGCTGATTC
* * *
1724879 AAGGCCAGCTACAT-TG--GACTTA
1 AAGG--TGCCA-ATGTGCTGA-TTC
1724901 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATGTGCTGATTC
1724922 AAGG
1 AAGG
1724926 CCAGCTACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 12 0.35
22 8 0.24
23 5 0.15
24 2 0.06
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (21 bp):
AAGGTGCCAATGTGCTGATTC
Found at i:1724904 original size:22 final size:22
Alignment explanation
Indices: 1724879--1724946 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
1724869 GTGCTGATTC
1724879 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTACATTGGACTTA
* * *
1724901 AAGG--TGCCA-ATGTGCTGA-TTC
1 AAGGCCAGCTACAT-TG--GACTTA
1724922 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTACATTGGACTTA
1724944 AAG
1 AAG
1724947 ATAAAGGTGC
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 11 0.33
23 5 0.15
24 2 0.06
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.24
Consensus pattern (22 bp):
AAGGCCAGCTACATTGGACTTA
Found at i:1725036 original size:33 final size:33
Alignment explanation
Indices: 1724985--1725092 Score: 186
Period size: 33 Copynumber: 3.4 Consensus size: 33
1724975 CCAGCGATAT
1724985 TGGGC-TTAGA-AG-GGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGTGGTTGCCACCGACTTGTG
1725015 TGGGCTTTAGAGAGTGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGTGGTTGCCACCGACTTGTG
*
1725048 TGGGCTTTAGAGAATGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGTGGTTGCCACCGACTTGTG
1725081 TGGGCTTTAGAG
1 TGGGCTTTAGAG
1725093 GGGGTGCCAC
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
30 5 0.07
31 5 0.07
32 2 0.03
33 62 0.84
ACGTcount: A:0.17, C:0.18, G:0.36, T:0.30
Consensus pattern (33 bp):
TGGGCTTTAGAGAGTGGTTGCCACCGACTTGTG
Found at i:1725111 original size:31 final size:32
Alignment explanation
Indices: 1724985--1725111 Score: 179
Period size: 33 Copynumber: 4.0 Consensus size: 32
1724975 CCAGCGATAT
1724985 TGGGC-TTAGA-AGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1725015 TGGGCTTTAGAGAGTGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAG-GGTTGCCACCGACTTGTG
*
1725048 TGGGCTTTAGAGAATGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTG
* * *
1725081 TGGGCTTTAGAG-GGGGTGCCACGGAATTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1725112 GACTTTAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
30 5 0.06
31 20 0.23
32 2 0.02
33 60 0.68
34 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.38, T:0.28
Consensus pattern (32 bp):
TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
Found at i:1725135 original size:35 final size:35
Alignment explanation
Indices: 1725096--1725358 Score: 327
Period size: 35 Copynumber: 7.6 Consensus size: 35
1725086 TTTAGAGGGG
*
1725096 GTGCCACGGAATTGTGGACTTTAAAAAGAAAAAGA
1 GTGCCACGGAATTGTGGGCTTTAAAAAGAAAAAGA
* *
1725131 GTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGA
1 GTGCCACGGAATTGTGGGCTTTAAAAAGAAAAAGA
* * *
1725166 GTGCCACGGAGTGGTGGACTTTAAAAAGAAAAAGA
1 GTGCCACGGAATTGTGGGCTTTAAAAAGAAAAAGA
* * *
1725201 GTGCCACGGAATGGTGGGCTTTAAAAATAAAAAGG
1 GTGCCACGGAATTGTGGGCTTTAAAAAGAAAAAGA
* * *
1725236 GTGCCACGAAATTATGGGCTTTGAAAAGAAAAAG-
1 GTGCCACGGAATTGTGGGCTTTAAAAAGAAAAAGA
* * *
1725270 GTGCCACGGAGTTGTGGGCTTT--GAAGAAAAAGG
1 GTGCCACGGAATTGTGGGCTTTAAAAAGAAAAAGA
* * *
1725303 GTGCCATGGAATTGTAGGCTTTGAAAAGAAAAAG-
1 GTGCCACGGAATTGTGGGCTTTAAAAAGAAAAAGA
*
1725337 GTGCCACGGAGTTGTGGGCTTT
1 GTGCCACGGAATTGTGGGCTTT
1725359 GAAGAAAAGA
Statistics
Matches: 203, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
32 9 0.04
33 19 0.09
34 38 0.19
35 137 0.67
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.21
Consensus pattern (35 bp):
GTGCCACGGAATTGTGGGCTTTAAAAAGAAAAAGA
Found at i:1725183 original size:70 final size:67
Alignment explanation
Indices: 1725096--1725396 Score: 338
Period size: 70 Copynumber: 4.4 Consensus size: 67
1725086 TTTAGAGGGG
* *
1725096 GTGCCACGGAATTGTGGACTTTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAAGAA
1 GTGCCACGGAATTGTGGACTTTGAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTT--AAAGAA
1725161 AAAGA
63 AAAGA
* * * * * *
1725166 GTGCCACGGAGTGGTGGACTTTAAAAAGAAAAAGAGTGCCACGGAATGGTGGGCTTTAAAAATAA
1 GTGCCACGGAATTGTGGACTTTGAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTT--AAAGAA
*
1725231 AAAGG
63 AAAGA
* * * *
1725236 GTGCCACGAAATTATGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAGAAAAA
1 GTGCCACGGAATTGTGGACTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAGAAAAA
*
1725301 GG
66 GA
* *
1725303 GTGCCATGGAATTGTAGG-CTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAG-AAA
1 GTGCCACGGAATTGT-GGACTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAGAAAA
1725366 AGA
65 AGA
** * *
1725369 -TGCCATTGAGTCGTGGACTTTGAAAAGA
1 GTGCCACGGAATTGTGGACTTTGAAAAGA
1725397 GATTGCCAAT
Statistics
Matches: 205, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
64 2 0.01
65 22 0.11
66 5 0.02
67 63 0.31
68 2 0.01
69 20 0.10
70 91 0.44
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.21
Consensus pattern (67 bp):
GTGCCACGGAATTGTGGACTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAGAAAAA
GA
Found at i:1725467 original size:30 final size:30
Alignment explanation
Indices: 1725338--1725481 Score: 139
Period size: 31 Copynumber: 4.7 Consensus size: 30
1725328 AAGAAAAAGG
* * * * *
1725338 TGCCACGGAGTTGTGGGCTTTGAAGAAAAGA
1 TGCCACTGAGTCGTGGACTTTG-GGAAAAAA
*
1725369 TGCCATTGAGTCGTGGACTTT--GAAAAGAGA
1 TGCCACTGAGTCGTGGACTTTGGGAAAA-A-A
* *
1725399 TTGCCAATGAGTTGTGGACTTTGGAGAAAAAA
1 -TGCCACTGAGTCGTGGACTTTGG-GAAAAAA
* *
1725431 TTCCACTGAGTCGTGGACTTTGGGACAAAA
1 TGCCACTGAGTCGTGGACTTTGGGAAAAAA
1725461 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
1725482 AAGAAGGTAT
Statistics
Matches: 95, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
28 5 0.05
30 27 0.28
31 56 0.59
32 1 0.01
33 1 0.01
34 5 0.05
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (30 bp):
TGCCACTGAGTCGTGGACTTTGGGAAAAAA
Found at i:1726506 original size:15 final size:16
Alignment explanation
Indices: 1726481--1726515 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1726471 CTCACCGAGA
*
1726481 TTTTCTGTTTTGTTTT
1 TTTTCTGTTTTCTTTT
1726497 TTTTCT-TTTTCTTTT
1 TTTTCTGTTTTCTTTT
1726512 TTTT
1 TTTT
1726516 TGTGTTTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.86
Consensus pattern (16 bp):
TTTTCTGTTTTCTTTT
Found at i:1738259 original size:52 final size:51
Alignment explanation
Indices: 1738118--1738266 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
1738108 CGAAATATGA
*
1738118 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
1738170 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* **
1738222 AAATTTGTCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
1738267 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:1738273 original size:13 final size:13
Alignment explanation
Indices: 1738255--1738279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1738245 CAAAGATCAG
1738255 TGTATCGATACAA
1 TGTATCGATACAA
1738268 TGTATCGATACA
1 TGTATCGATACA
1738280 TTTAAGTGAT
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:1738357 original size:33 final size:33
Alignment explanation
Indices: 1738320--1738386 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1738310 AGTAGCTTAA
1738320 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1738353 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1738386 A
1 A
1738387 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1738360 original size:13 final size:13
Alignment explanation
Indices: 1738342--1738366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1738332 CAAAAAAATA
1738342 TGTATCGATACAT
1 TGTATCGATACAT
1738355 TGTATCGATACA
1 TGTATCGATACA
1738367 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1739950 original size:64 final size:64
Alignment explanation
Indices: 1739871--1739997 Score: 245
Period size: 64 Copynumber: 2.0 Consensus size: 64
1739861 AAGAAAAATG
1739871 AGGCGTAATATGAAAATGCAAACGTAGGTGACAATGTTCGCACATTATCACTTACGTAACTATA
1 AGGCGTAATATGAAAATGCAAACGTAGGTGACAATGTTCGCACATTATCACTTACGTAACTATA
*
1739935 AGGCGTAATATGAAAATGCAAACGTAGGTGACGATGTTCGCACATTATCACTTACGTAACTAT
1 AGGCGTAATATGAAAATGCAAACGTAGGTGACAATGTTCGCACATTATCACTTACGTAACTAT
1739998 GATGAATGAG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (64 bp):
AGGCGTAATATGAAAATGCAAACGTAGGTGACAATGTTCGCACATTATCACTTACGTAACTATA
Found at i:1754982 original size:69 final size:69
Alignment explanation
Indices: 1754865--1755013 Score: 217
Period size: 69 Copynumber: 2.2 Consensus size: 69
1754855 AGGAATGGGG
* * * *
1754865 TTGGAATATCCCCGACAATGATAATTTGGACAAAATAAGACTTGAATTTTGATGAGTTTAAAAAC
1 TTGGAATATCCACGACAATGATAATTTAGACAAAATAAGACTTAAATTTCGATGAGTTTAAAAAC
1754930 GGGA
66 GGGA
* * *
1754934 TTGGAGTATCCACGACAATGATAATTTAGACAAAATAAGATTTAAATTTCGATGAGTTTAAAAAT
1 TTGGAATATCCACGACAATGATAATTTAGACAAAATAAGACTTAAATTTCGATGAGTTTAAAAAC
*
1754999 GGGG
66 GGGA
*
1755003 TTGGACTATCC
1 TTGGAATATCC
1755014 CCTCAGAGGA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.30
Consensus pattern (69 bp):
TTGGAATATCCACGACAATGATAATTTAGACAAAATAAGACTTAAATTTCGATGAGTTTAAAAAC
GGGA
Found at i:1756068 original size:19 final size:19
Alignment explanation
Indices: 1756013--1756069 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
1756003 GGCTGATGTG
*
1756013 GTTGCT-GTTGCTGCTGGA
1 GTTGCTCGTGGCTGCTGGA
**
1756031 GTTGCTTC-TGGCTATTGGA
1 GTTGC-TCGTGGCTGCTGGA
1756050 GTTGCTCGTGGCTGCTGGA
1 GTTGCTCGTGGCTGCTGGA
1756069 G
1 G
1756070 GCTGCTGAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 7 0.23
19 24 0.77
ACGTcount: A:0.07, C:0.18, G:0.39, T:0.37
Consensus pattern (19 bp):
GTTGCTCGTGGCTGCTGGA
Found at i:1756840 original size:14 final size:15
Alignment explanation
Indices: 1756792--1756846 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 15
1756782 GATTTTTTTG
*
1756792 TTTAATTTTCATTAACT
1 TTTAATTTTGATT-A-T
*
1756809 TTTATTTTTTGATTAT
1 TTTA-ATTTTGATTAT
1756825 TTTAATTTTG-TTAT
1 TTTAATTTTGATTAT
1756839 TTTAATTT
1 TTTAATTT
1756847 ATTTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 12 0.35
15 5 0.15
16 5 0.15
17 5 0.15
18 7 0.21
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.69
Consensus pattern (15 bp):
TTTAATTTTGATTAT
Found at i:1756841 original size:41 final size:43
Alignment explanation
Indices: 1756787--1756867 Score: 98
Period size: 41 Copynumber: 1.9 Consensus size: 43
1756777 ATTTTGATTT
*
1756787 TTTTGTTTAATTTTCATTAACTTTT-A-TTTTTTGATTATTTTAA
1 TTTTGTTTAATTTTAATTAA-TTTTAATTTTTTTGA-TATTTTAA
*
1756830 TTTTG-TT-ATTTTAATTTATTTTAATTTTTTTGATATTT
1 TTTTGTTTAATTTTAATTAATTTTAATTTTTTTGATATTT
1756868 GATGTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
40 4 0.12
41 15 0.44
42 10 0.29
43 5 0.15
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.70
Consensus pattern (43 bp):
TTTTGTTTAATTTTAATTAATTTTAATTTTTTTGATATTTTAA
Found at i:1757596 original size:61 final size:61
Alignment explanation
Indices: 1757501--1757619 Score: 159
Period size: 61 Copynumber: 2.0 Consensus size: 61
1757491 GAAGATGATA
* * *
1757501 AAGAAGAGTGATAAAGATGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTTAAAGAT
1 AAGAAGAGTGATAAAGATGCCAATATGCTAATTCAAGACCAGCGATATTAGACTTAAAGAT
* * * *
1757562 AAGAAG-GATGATAAAGGTGCCAATATGTTGATTCAAGACCGGCGATATTAGACTTAAA
1 AAGAAGAG-TGATAAAGATGCCAATATGCTAATTCAAGACCAGCGATATTAGACTTAAA
1757620 AGTGCTAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 1 0.02
61 49 0.98
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (61 bp):
AAGAAGAGTGATAAAGATGCCAATATGCTAATTCAAGACCAGCGATATTAGACTTAAAGAT
Found at i:1757895 original size:49 final size:49
Alignment explanation
Indices: 1757576--1758231 Score: 426
Period size: 52 Copynumber: 12.9 Consensus size: 49
1757566 AGGATGATAA
* * * *
1757576 AGGTGCCAATATGTTGATTCAAGACCGGCGATATTAGACTT-AA-A---
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATGG
* ** * * *
1757620 A-GTGCTAATGTATTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAA
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATG---G
* * * ** * * *
1757671 ATGCGCCAATATGCTGATTCAAGGTGAGCGATATTGGGCTTAAAGGTGCG
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATG-G
* * * * **
1757721 AAGAATGCCAATGTGCTGATTCACGGCCAGCGACATTAGACTTGAAGATAAAA
1 -AG-GTGCCAATGTGCTGATTCAAGGCCAGCGATATTAGACTTAAAGAT--GG
* * ** *
1757774 AGAATGCCAATGTGCTGATTCAAGGCCAGCGACATT-GATCTTAGGGATGTTAA
1 AG-GTGCCAATGTGCTGATTCAAGGCCAGCGATATTAGA-CTTAAAGATG---G
* * * * **
1757827 AGATGCCAATATGCTGATTCAAGGCCAGTGATATCAGACCAAAAGATGG
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATGG
* *
1757876 AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGG
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATGG
* * * * * *
1757925 AGGTGCCAATGTGCTAATTCAAGACTAGTGATATTGGACTTAAAGATGA
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATGG
* * *
1757974 AGGTGCCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGACGG
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATGG
* * * ** *
1758023 AGGTGCTAATGTGCTAATTCAAGGCTAGCGACGTTGGACTTAAATTTCGAGGATGATG
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTAGACTT-AA-----A-GATG--G
* * * * *
1758081 AAGGTGCCAATATGTTGTTTCAAGGCCAACGATATTAGGCTTAAAGATGACAG
1 -AGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATG---G
* * *
1758134 AATGTGCCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGATGG
1 -AGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATGG
* * *
1758184 CAAAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTAGATTTAAAG
1 ---AGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTAGACTTAAAG
1758232 GTGCCAATGT
Statistics
Matches: 481, Mismatches: 100, Indels: 54
0.76 0.16 0.09
Matches are distributed among these distances:
43 32 0.07
44 3 0.01
45 1 0.00
49 161 0.33
50 3 0.01
51 4 0.01
52 190 0.40
53 50 0.10
55 1 0.00
56 3 0.01
58 3 0.01
59 30 0.06
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (49 bp):
AGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATGG
Found at i:1757970 original size:98 final size:99
Alignment explanation
Indices: 1757576--1758231 Score: 452
Period size: 98 Copynumber: 6.5 Consensus size: 99
1757566 AGGATGATAA
* * * * * **
1757576 AGGTGCCAATATGTTGATTCAAGACCGGCGATATTAGACTT--A-A--A-A-GTGCTAATGTATT
1 AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAGAGGTGCCAATGTGCT
* *
1757634 GATTCAAGGCCAGCGACATTGGACTTAAAGATGACAA
66 GATTCAAGGCCAGCGACATTAGACTTAAAGATG---G
* * ** * * * *
1757671 ATGCGCCAATATGCTGATTCAAGGTGAGCGATATTGGGCTTAAAGGTGCGAAGAATGCCAATGTG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAG-AG-GTGCCAATGTG
* * **
1757736 CTGATTCACGGCCAGCGACATTAGACTTGAAGATAAAA
64 CTGATTCAAGGCCAGCGACATTAGACTTAAAGAT--GG
* * * ** * * *
1757774 AGAATGCCAATGTGCTGATTCAAGGCCAGCGACATT-GATCTTAGGGATGTTAAAGATGCCAATA
1 AG-GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA-CTTAAAGATG--AGAGGTGCCAATG
* * * **
1757838 TGCTGATTCAAGGCCAGTGATATCAGACCAAAAGATGG
62 TGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGG
1757876 AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG-GAGGTGCCAATGTGCT
1 AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAGAGGTGCCAATGTGCT
* * * * * * *
1757940 AATTCAAGACTAGTGATATTGGACTTAAAGATGA
66 GATTCAAGGCCAGCGACATTAGACTTAAAGATGG
* * * * * *
1757974 AGGTGCCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGACG-GAGGTGCTAATGTGCT
1 AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAGAGGTGCCAATGTGCT
* * * *
1758038 AATTCAAGGCTAGCGACGTTGGACTTAAATTTCGAGGATGATG
66 GATTCAAGGCCAGCGACATTAGACTT-AA-----A-GATG--G
* * * *
1758081 AAGGTGCCAATATGTTGTTTCAAGGCCAACGATATTAGG-CTTAAAGATGACAGAATGTGCCAAT
1 -AGGTGCCAATATGCTGATTCAAGGCCAGCGATATT-GGACTTAAAGATG--AG-AGGTGCCAAT
*
1758145 GTGCTGATTCAAGGCCAACGACATTAGACTTAAAGATGG
61 GTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGG
* * *
1758184 CAAAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTAGATTTAAAG
1 ---AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1758232 GTGCCAATGT
Statistics
Matches: 439, Mismatches: 88, Indels: 58
0.75 0.15 0.10
Matches are distributed among these distances:
95 32 0.07
97 1 0.00
98 119 0.27
99 2 0.00
101 38 0.09
102 5 0.01
103 4 0.01
104 111 0.25
105 48 0.11
106 1 0.00
108 40 0.09
109 1 0.00
111 3 0.01
112 34 0.08
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (99 bp):
AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAGAGGTGCCAATGTGCT
GATTCAAGGCCAGCGACATTAGACTTAAAGATGG
Found at i:1758028 original size:147 final size:151
Alignment explanation
Indices: 1757635--1758231 Score: 427
Period size: 147 Copynumber: 3.9 Consensus size: 151
1757625 TAATGTATTG
* * * * * * ** *
1757635 ATTCAAGGCCAGCGACATT-GGACTTAAAGATGACAAATGCGCCAATATGCTGATTCAAGGTGAG
1 ATTCAAGACCAACGATATTAGG-CTTAAAGATGACAGA-GTGCCAATGTGCTGATTCAAGGCCAA
* * * * * * * * *
1757699 CGATATTGGGCTTAAAGGTGCGAAGAATGCCAATGTGCTGATTCACGGCCAGCGACATTAGACTT
64 CGACATTAGACTTAAAGATG-G-AG-GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * * * *
1757764 GAAGATAAAAAGAATGCCAATGTGCTG
126 AAAGATGAGAAG-GTGCCAATATGCTA
* * * * ** * *
1757791 ATTCAAGGCCAGCGACATT-GATCTTAGGGATGTTAAAGA-TGCCAATATGCTGATTCAAGGCCA
1 ATTCAAGACCAACGATATTAG-GCTTAAAGATG--ACAGAGTGCCAATGTGCTGATTCAAGGCCA
** * * **
1757854 GTGATATCAGACCAAAAGATGGAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
63 ACGACATTAGACTTAAAGATGGAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
*
1757919 AGATG-G-AGGTGCCAATGTGCTA
128 AGATGAGAAGGTGCCAATATGCTA
* **
1757941 ATTCAAGACTAGTGATATT-GGACTTAAAGATGA-AG-GTGCCAATGTGCTGATTCAAGGCCAAC
1 ATTCAAGACCAACGATATTAGG-CTTAAAGATGACAGAGTGCCAATGTGCTGATTCAAGGCCAAC
* * * * * **
1758003 GACATTAGACTTAAAGACGGAGGTGCTAATGTGCTAATTCAAGGCTAGCGACGTTGGACTTAAAT
65 GACATTAGACTTAAAGATGGAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-
* *
1758068 TTCGAGGATGATGAAGGTGCCAATATGTTG
128 ----A-GATGA-GAAGGTGCCAATATGCTA
* *
1758098 TTTCAAGGCCAACGATATTAGGCTTAAAGATGACAGAATGTGCCAATGTGCTGATTCAAGGCCAA
1 ATTCAAGACCAACGATATTAGGCTTAAAGATGACAG-A-GTGCCAATGTGCTGATTCAAGGCCAA
* * *
1758163 CGACATTAGACTTAAAGATGGCAAAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTAGATTT
64 CGACATTAGACTTAAAGATGG---AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1758228 AAAG
126 AAAG
1758232 GTGCCAATGT
Statistics
Matches: 354, Mismatches: 64, Indels: 45
0.76 0.14 0.10
Matches are distributed among these distances:
147 75 0.21
148 3 0.01
150 36 0.10
151 2 0.01
153 40 0.11
154 6 0.02
155 1 0.00
156 64 0.18
157 39 0.11
158 8 0.02
161 46 0.13
163 2 0.01
164 32 0.09
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (151 bp):
ATTCAAGACCAACGATATTAGGCTTAAAGATGACAGAGTGCCAATGTGCTGATTCAAGGCCAACG
ACATTAGACTTAAAGATGGAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
TGAGAAGGTGCCAATATGCTA
Found at i:1758156 original size:53 final size:52
Alignment explanation
Indices: 1758081--1758231 Score: 203
Period size: 53 Copynumber: 2.9 Consensus size: 52
1758071 GAGGATGATG
* * *
1758081 AAGGTGCCAATATGTTGTTTCAAGGCCAACGATATTAGGCTTAAAGATGACA
1 AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTAGACTTAAAGATGACA
* * * *
1758133 GAATGTGCCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGATGGCA
1 -AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTAGACTTAAAGATGACA
* * *
1758186 AAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTAGATTTAAAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTAGACTTAAAG
1758232 GTGCCAATGT
Statistics
Matches: 85, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
52 40 0.47
53 45 0.53
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (52 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTAGACTTAAAGATGACA
Found at i:1758419 original size:33 final size:32
Alignment explanation
Indices: 1758280--1758539 Score: 315
Period size: 32 Copynumber: 8.0 Consensus size: 32
1758270 TAGAAGGAAA
* *
1758280 TGCCACCAACTTGTGTGGGCTTTTCAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAAGGT
** * *
1758312 TGCCACTGACTTGTGTTGGC-TTTAAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAA-AAGGT
* * * *
1758344 TGCCACCAACTTGTCTAGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAAGGT
1758376 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAA-AAGGT
* * *
1758409 TGCCATCAACTTGTGTGGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAAGGT
*
1758441 TGCCACCAACTTATGTGGGCTTTTGAAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTG-AAAAGGT
*
1758474 TGCCATCAACTTGTGTGGGCTTTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAA-AAGGT
* * *
1758507 TGCCATCAGCTTGTGTGGGCTTTAGAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAAGGT
1758539 T
1 T
1758540 TCTCCACTGG
Statistics
Matches: 196, Mismatches: 27, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
31 5 0.03
32 99 0.51
33 92 0.47
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTTGAAAAGGT
Found at i:1758431 original size:65 final size:65
Alignment explanation
Indices: 1758280--1758539 Score: 344
Period size: 65 Copynumber: 4.0 Consensus size: 65
1758270 TAGAAGGAAA
** ** * *
1758280 TGCCACCAACTTGTGTGGGCTTTTCAAAGGGTTGCCACTGACTTGTGTTGGC-TTTAAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
* *
1758344 TGCCACCAACTTGTCTAGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
* * *
1758409 TGCCATCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAACTTATGTGGGCTTTTGAAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
* * * * * *
1758474 TGCCATCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCATCAGCTTGTGTGGGCTTTAGAA-AAGG
1 TGCCACCAACTTGTGTGGGCTTTAGAA-AGGGTTGCCACCAACTTGTGTGGGCTTTTGAAGAAGG
1758538 T
65 T
1758539 T
1 T
1758540 TCTCCACTGG
Statistics
Matches: 175, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
64 45 0.26
65 103 0.59
66 27 0.15
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (65 bp):
TGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
Found at i:1758701 original size:27 final size:27
Alignment explanation
Indices: 1758670--1758724 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1758660 CTTTAGAAGG
**
1758670 GGGTGCCATTGAGTTGTGGACTTAAAA
1 GGGTGCCACAGAGTTGTGGACTTAAAA
*
1758697 GGGTGCCACAGAGTTGTGGATTTAAAA
1 GGGTGCCACAGAGTTGTGGACTTAAAA
1758724 G
1 G
1758725 AAAAAGATGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.27, C:0.11, G:0.35, T:0.27
Consensus pattern (27 bp):
GGGTGCCACAGAGTTGTGGACTTAAAA
Found at i:1758778 original size:34 final size:33
Alignment explanation
Indices: 1758693--1759397 Score: 170
Period size: 33 Copynumber: 21.9 Consensus size: 33
1758683 TTGTGGACTT
*
1758693 AAAAG-GGTGCCACAGAGTTGTGGA-TTTAAAA
1 AAAAGAGGTGCCACGGAGTTGTGGACTTTAAAA
* ** *
1758724 GAAAA-AGATGCCACAAAGTTGTGGGCTTTGAAAA
1 -AAAAGAGGTGCCACGGAGTTGTGGACTTT-AAAA
* ** **
1758758 AAAAGAGGTGCCATGGAGTTGCAGACTTTGAAGG
1 AAAAGAGGTGCCACGGAGTTGTGGACTTT-AAAA
* * * *
1758792 AAAATA--TGCCACAGAGTTGTGGGTCTTGAAAA
1 AAAAGAGGTGCCACGGAGTTGT-GGACTTTAAAA
*
1758824 GAAAA-AGGTGCCACGGAGTTATGGAC-TT----
1 -AAAAGAGGTGCCACGGAGTTGTGGACTTTAAAA
1758852 AAAAG-GGTGCCACGGAGTTGTGGAC-TTAAAA
1 AAAAGAGGTGCCACGGAGTTGTGGACTTTAAAA
* * *
1758883 GGAAAAGA--TACCACAGAGTTGTGGGCTTTAAAA
1 --AAAAGAGGTGCCACGGAGTTGTGGACTTTAAAA
* * *
1758916 AGAAAAAGGTGCCATGGAGTTATGGAC-TTAAAA
1 A-AAAGAGGTGCCACGGAGTTGTGGACTTTAAAA
* * * *
1758949 GGAACA-AGGTGCCCCGGAGTTATGGACTTTGAAAG
1 --AAAAGAGGTGCCACGGAGTTGTGGACTTT-AAAA
* * ** ** *
1758984 AAATG-GATGCCACTAAGTCATGGAC-TT-AGA
1 AAAAGAGGTGCCACGGAGTTGTGGACTTTAAAA
* ** * *
1759014 AAAAG-GATGCCACTAAGTAGTGGACTTTTAAGA
1 AAAAGAGGTGCCACGGAGTTGTGGAC-TTTAAAA
* * * * *
1759047 AAAAG-GGCGCCACTGAGTCGTGGA-ATT-AGA
1 AAAAGAGGTGCCACGGAGTTGTGGACTTTAAAA
* * * * *
1759077 AAAAG-GATGCCACTGAGTCGTGAACTTTGAAGA
1 AAAAGAGGTGCCACGGAGTTGTGGACTTT-AAAA
* * * *
1759110 AAAAG-GATGCCACTGAGTCGTGGACTTTTAAGA
1 AAAAGAGGTGCCACGGAGTTGTGGAC-TTTAAAA
* ** * *
1759143 AAAAGA-ATGCCAATGAGTCGTGGACTTTGAAGA
1 AAAAGAGGTGCCACGGAGTTGTGGACTTT-AAAA
* * *
1759176 AAAAG-GATGCCACTGAGTCGTGGACTTTTAAGAA
1 AAAAGAGGTGCCACGGAGTTGTGGAC-TTTAA-AA
* ** * * *
1759210 AAAA-A--TGTCACTAAGTCGTAGACTTTTAAA
1 AAAAGAGGTGCCACGGAGTTGTGGACTTTAAAA
* ** * *
1759240 AAAAG-GATGCCACTAAGTAGTGGACTTTGAAGA
1 AAAAGAGGTGCCACGGAGTTGTGGACTTT-AAAA
* * * *
1759273 AAAAG-GATGCCACTGAGTCGTGGACTTTGAAGA
1 AAAAGAGGTGCCACGGAGTTGTGGACTTT-AAAA
* * ** * *
1759306 AAAAG-GATGCTATTGAGTAGTGGACTTTGAAGA
1 AAAAGAGGTGCCACGGAGTTGTGGACTTT-AAAA
* ** * *
1759339 AAAAG-GATGCCACTCAGTCGTGGACTTT-GAA
1 AAAAGAGGTGCCACGGAGTTGTGGACTTTAAAA
* * * *
1759370 GAAA-AGGTGTCACAGAGTAGTGGACTTT
1 AAAAGAGGTGCCACGGAGTTGTGGACTTT
1759398 GAAGAAAATG
Statistics
Matches: 540, Mismatches: 90, Indels: 87
0.75 0.13 0.12
Matches are distributed among these distances:
27 25 0.05
30 53 0.10
31 31 0.06
32 94 0.17
33 264 0.49
34 69 0.13
35 4 0.01
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.22
Consensus pattern (33 bp):
AAAAGAGGTGCCACGGAGTTGTGGACTTTAAAA
Found at i:1758861 original size:93 final size:93
Alignment explanation
Indices: 1758758--1758950 Score: 280
Period size: 93 Copynumber: 2.1 Consensus size: 93
1758748 GCTTTGAAAA
* ** * * *
1758758 AAAAGAGGTGCCATGGAGTTGCAGACTTTGAAGGAAAATATGCCACAGAGTTGTGGG-TCTTGAA
1 AAAAG-GGTGCCACGGAGTTGCAGACTTAAAAGGAAAAGATACCACAGAGTTGTGGGCT-TTAAA
1758822 AAGAAAAAGGTGCCACGGAGTTATGGACTT
64 AAGAAAAAGGTGCCACGGAGTTATGGACTT
**
1758852 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGATACCACAGAGTTGTGGGCTTTAAAAA
1 AAAAGGGTGCCACGGAGTTGCAGACTTAAAAGGAAAAGATACCACAGAGTTGTGGGCTTTAAAAA
*
1758917 GAAAAAGGTGCCATGGAGTTATGGACTT
66 GAAAAAGGTGCCACGGAGTTATGGACTT
1758945 AAAAGG
1 AAAAGG
1758951 AACAAGGTGC
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
93 83 0.93
94 6 0.07
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.21
Consensus pattern (93 bp):
AAAAGGGTGCCACGGAGTTGCAGACTTAAAAGGAAAAGATACCACAGAGTTGTGGGCTTTAAAAA
GAAAAAGGTGCCACGGAGTTATGGACTT
Found at i:1758863 original size:27 final size:27
Alignment explanation
Indices: 1758825--1758884 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
1758815 TCTTGAAAAG
*
1758825 AAAAAGGTGCCACGGAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTATGGACTT
*
1758852 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTATGGACTT
1758879 AAAAGG
1 AAAAGG
1758885 AAAAGATACC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.20
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTATGGACTT
Found at i:1758996 original size:159 final size:159
Alignment explanation
Indices: 1758671--1758986 Score: 404
Period size: 159 Copynumber: 2.0 Consensus size: 159
1758661 TTTAGAAGGG
** * * *
1758671 GGTGCCATTGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGATTTAAAAGAAAAAGATGCC
1 GGTGCCACGGAGTTATGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAAAAAGATACC
* * ** *
1758736 ACAAAGTTGTGGGCTTTGAAAAAAAAGAGGTGCCATGGAGTTGCAGACTTTGAAGGAAAATATGC
66 ACAAAGTTGTGGGCTTTGAAAAAAAAAAGGTGCCATGGAGTTACAGACTTAAAAGGAAAAGATGC
* *
1758801 CACAGAGTTGTGGGTCTTGAAAAGAAAAA
131 CACAGAGTTATGGCTCTTGAAAAGAAAAA
* *
1758830 GGTGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGATACC
1 GGTGCCACGGAGTTATGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAAAAAGATACC
* ** *
1758895 ACAGAGTTGTGGGCTTT-AAAAAGAAAAAGGTGCCATGGAGTTATGGACTTAAAAGGAACAAGGT
66 ACAAAGTTGTGGGCTTTGAAAAA-AAAAAGGTGCCATGGAGTTACAGACTTAAAAGGAA-AAGAT
* *
1758959 GCCCCGGAGTTATGGACT-TTG-AAAGAAA
129 GCCACAGAGTTATGG-CTCTTGAAAAGAAA
1758987 TGGATGCCAC
Statistics
Matches: 134, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
158 5 0.04
159 110 0.82
160 18 0.13
161 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.30, T:0.22
Consensus pattern (159 bp):
GGTGCCACGGAGTTATGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAAAAAGATACC
ACAAAGTTGTGGGCTTTGAAAAAAAAAAGGTGCCATGGAGTTACAGACTTAAAAGGAAAAGATGC
CACAGAGTTATGGCTCTTGAAAAGAAAAA
Found at i:1759007 original size:33 final size:33
Alignment explanation
Indices: 1758971--1759405 Score: 532
Period size: 33 Copynumber: 13.5 Consensus size: 33
1758961 CCCGGAGTTA
* * *
1758971 TGGACTTTGAA-AGAAATGGATGCCACTAAGTCA
1 TGGACTTTGAAGA-AAAAGGATGCCACTGAGTCG
* *
1759004 TGGAC-TT--AGAAAAAGGATGCCACTAAGTAG
1 TGGACTTTGAAGAAAAAGGATGCCACTGAGTCG
* **
1759034 TGGACTTTTAAGAAAAAGGGCGCCACTGAGTCG
1 TGGACTTTGAAGAAAAAGGATGCCACTGAGTCG
*
1759067 TGGA-ATT--AGAAAAAGGATGCCACTGAGTCG
1 TGGACTTTGAAGAAAAAGGATGCCACTGAGTCG
*
1759097 TGAACTTTGAAGAAAAAGGATGCCACTGAGTCG
1 TGGACTTTGAAGAAAAAGGATGCCACTGAGTCG
* * *
1759130 TGGACTTTTAAGAAAAAGAATGCCAATGAGTCG
1 TGGACTTTGAAGAAAAAGGATGCCACTGAGTCG
1759163 TGGACTTTGAAGAAAAAGGATGCCACTGAGTCG
1 TGGACTTTGAAGAAAAAGGATGCCACTGAGTCG
* * * *
1759196 TGGACTTTTAAGAAAAA-AATGTCACTAAGTCG
1 TGGACTTTGAAGAAAAAGGATGCCACTGAGTCG
* * * *
1759228 TAGACTTTTAA-AAAAAGGATGCCACTAAGTAG
1 TGGACTTTGAAGAAAAAGGATGCCACTGAGTCG
1759260 TGGACTTTGAAGAAAAAGGATGCCACTGAGTCG
1 TGGACTTTGAAGAAAAAGGATGCCACTGAGTCG
* * *
1759293 TGGACTTTGAAGAAAAAGGATGCTATTGAGTAG
1 TGGACTTTGAAGAAAAAGGATGCCACTGAGTCG
*
1759326 TGGACTTTGAAGAAAAAGGATGCCACTCAGTCG
1 TGGACTTTGAAGAAAAAGGATGCCACTGAGTCG
* * *
1759359 TGGACTTTGAAG-AAAAGG-TGTCACAGAGTAG
1 TGGACTTTGAAGAAAAAGGATGCCACTGAGTCG
1759390 TGGACTTTGAAGAAAA
1 TGGACTTTGAAGAAAA
1759406 TGAGTCCCAG
Statistics
Matches: 350, Mismatches: 42, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
30 47 0.13
31 31 0.09
32 56 0.16
33 216 0.62
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.23
Consensus pattern (33 bp):
TGGACTTTGAAGAAAAAGGATGCCACTGAGTCG
Found at i:1759007 original size:159 final size:159
Alignment explanation
Indices: 1758686--1759051 Score: 400
Period size: 159 Copynumber: 2.3 Consensus size: 159
1758676 CATTGAGTTG
* *
1758686 TGGACTTAAAAGGGTGCCACAGAGTTGTGGATTTAAAAGAAAAAGATGCCACAAAGTTGTGGGCT
1 TGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAAAAAGATACCACAAAGTTGTGGGCT
* * ** * * *
1758751 TTGAAAAAAAAGAGGTGCCATGGAGTTGCAGACTTTGAAGGAAAATATGCCACAGAGTTGTGGGT
66 TTGAAAAAAAAAAGGTGCCATGGAGTTACAGACTTAAAAGGAAAAGATGCCACAGAGTTATGGCT
* *
1758816 CTTGAAAAGAAAAAGGTGCCACGGAGTTA
131 CTTGAAAAGAAAAAGGTGCCACGAAGTCA
* * *
1758845 TGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGATACCACAGAGTTGTGGGCT
1 TGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAAAAAGATACCACAAAGTTGTGGGCT
** * * *
1758910 TT-AAAAAGAAAAAGGTGCCATGGAGTTATGGACTTAAAAGGAACAAGGTGCCCCGGAGTTATGG
66 TTGAAAAA-AAAAAGGTGCCATGGAGTTACAGACTTAAAAGGAA-AAGATGCCACAGAGTTATGG
* *
1758974 ACT-TTG-AAAG-AAATGGATGCCACTAAGTCA
129 -CTCTTGAAAAGAAAAAGG-TGCCACGAAGTCA
* * **
1759004 TGGACTTAGAAAAAGGATGCCACTA-AGTAGTGGACTTTTAAGAAAAAG
1 TGGACTT---AAAAGGGTGCCAC-AGAGTTGTGGACTTAAAAGAAAAAG
1759052 GGCGCCACTG
Statistics
Matches: 172, Mismatches: 27, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
158 10 0.06
159 112 0.65
160 18 0.10
161 1 0.01
162 31 0.18
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.22
Consensus pattern (159 bp):
TGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAAAAAGATACCACAAAGTTGTGGGCT
TTGAAAAAAAAAAGGTGCCATGGAGTTACAGACTTAAAAGGAAAAGATGCCACAGAGTTATGGCT
CTTGAAAAGAAAAAGGTGCCACGAAGTCA
Found at i:1759282 original size:163 final size:162
Alignment explanation
Indices: 1759011--1759374 Score: 523
Period size: 163 Copynumber: 2.2 Consensus size: 162
1759001 TCATGGACTT
* ** * * *
1759011 AGAAAAAGGATGCCACTAAGTAGTGGACTTTTAAGAAAAAGGGCGCCACTGAGTCGTGGAATTAG
1 AGAAAAAGGATGCCACTAAGTCGTGGACTTTTAAGAAAAAGAACGCCACTAAGTCGTAGAATTAA
* * *
1759076 AAAAAGGATGCCACTGAGTCGTGAACTTTGAAGAAAAAGGATGCCACTGAGTCGTGGACTTTTAA
66 AAAAAGGATGCCACTAAGTAGTGAACTTTGAAGAAAAAGGATGCCACTGAGTCGTGGACTTTGAA
*
1759141 GAAAAAGAATGCCAATGAGTCGTGGACTTTGA
131 GAAAAAGAATGCCAATGAGTAGTGGACTTTGA
* * * *
1759173 AGAAAAAGGATGCCACTGAGTCGTGGACTTTTAAGAAAAA-AATGTCACTAAGTCGTAGACTTTT
1 AGAAAAAGGATGCCACTAAGTCGTGGACTTTTAAGAAAAAGAACGCCACTAAGTCGTAGA--ATT
*
1759237 AAAAAAAGGATGCCACTAAGTAGTGGACTTTGAAGAAAAAGGATGCCACTGAGTCGTGGACTTTG
64 AAAAAAAGGATGCCACTAAGTAGTGAACTTTGAAGAAAAAGGATGCCACTGAGTCGTGGACTTTG
* * *
1759302 AAGAAAAAGGATGCTATTGAGTAGTGGACTTTGA
129 AAGAAAAAGAATGCCAATGAGTAGTGGACTTTGA
* *
1759336 AGAAAAAGGATGCCACTCAGTCGTGGACTTTGAAGAAAA
1 AGAAAAAGGATGCCACTAAGTCGTGGACTTTTAAGAAAA
1759375 GGTGTCACAG
Statistics
Matches: 180, Mismatches: 20, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
161 13 0.07
162 38 0.21
163 129 0.72
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.23
Consensus pattern (162 bp):
AGAAAAAGGATGCCACTAAGTCGTGGACTTTTAAGAAAAAGAACGCCACTAAGTCGTAGAATTAA
AAAAAGGATGCCACTAAGTAGTGAACTTTGAAGAAAAAGGATGCCACTGAGTCGTGGACTTTGAA
GAAAAAGAATGCCAATGAGTAGTGGACTTTGA
Found at i:1765455 original size:69 final size:69
Alignment explanation
Indices: 1765366--1765516 Score: 212
Period size: 69 Copynumber: 2.2 Consensus size: 69
1765356 AGAGGAATGG
* * * *
1765366 GGTTGGAGTATCCCCGACAATGATAATTCGGACAAAATAAGACTTGAATTTCTATGAGCTTAAAA
1 GGTTGGAGTATCCCCAACAATGATAATTCAGACAAAATAAGACTTAAATTTCAATGAGCTTAAAA
1765431 ACAA
66 ACAA
* * * *
1765435 GGTTGGACTATCCCCAACAATGATAATTTAGACAAAATAAGATTTAAATTTCAATGAGTTTAAAA
1 GGTTGGAGTATCCCCAACAATGATAATTCAGACAAAATAAGACTTAAATTTCAATGAGCTTAAAA
**
1765500 ACGG
66 ACAA
1765504 GGTTGGAGTATCC
1 GGTTGGAGTATCC
1765517 ACTCGAAGGA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (69 bp):
GGTTGGAGTATCCCCAACAATGATAATTCAGACAAAATAAGACTTAAATTTCAATGAGCTTAAAA
ACAA
Found at i:1766550 original size:19 final size:19
Alignment explanation
Indices: 1766526--1766568 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1766516 GAGCTACTGT
*
1766526 TGGAGTTGTTCCTGGCTGC
1 TGGAGTTGCTCCTGGCTGC
*
1766545 TGGAGTTGCTCGTGGCTGC
1 TGGAGTTGCTCCTGGCTGC
1766564 TGGAG
1 TGGAG
1766569 GCTGCTATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.07, C:0.19, G:0.42, T:0.33
Consensus pattern (19 bp):
TGGAGTTGCTCCTGGCTGC
Found at i:1767941 original size:20 final size:20
Alignment explanation
Indices: 1767916--1767966 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1767906 CAGTTTCTTA
**
1767916 TATCGATACAATTGTCCATG
1 TATCGATACAATTGAACATG
*
1767936 TATCGATACAA-TGAATATG
1 TATCGATACAATTGAACATG
1767955 TATCGATACAAT
1 TATCGATACAAT
1767967 GTATCGATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (20 bp):
TATCGATACAATTGAACATG
Found at i:1767970 original size:13 final size:13
Alignment explanation
Indices: 1767952--1767978 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1767942 TACAATGAAT
1767952 ATGTATCGATACA
1 ATGTATCGATACA
1767965 ATGTATCGATACA
1 ATGTATCGATACA
1767978 A
1 A
1767979 AGCATCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1767974 original size:32 final size:33
Alignment explanation
Indices: 1767933--1767994 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
1767923 ACAATTGTCC
*
1767933 ATGTATCGATACAATGAAT-ATGTATCGATACA
1 ATGTATCGATACAAAGAATCATGTATCGATACA
*
1767965 ATGTATCGATACAAAGCATCATGTATCGAT
1 ATGTATCGATACAAAGAATCATGTATCGAT
1767995 TCATCTGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATCATGTATCGATACA
Found at i:1776564 original size:20 final size:20
Alignment explanation
Indices: 1776539--1776612 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
1776529 GTTACAAGCA
* *
1776539 ATGTATTGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
1776559 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
*
1776579 ATGTATCGATACAATGTACA
1 ATGTATCGATACAATGTACC
1776599 ATGTATCGATACAA
1 ATGTATCGATACAA
1776613 ATAGTGGTAG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
20 49 0.98
21 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:1777178 original size:16 final size:17
Alignment explanation
Indices: 1777159--1777217 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
1777149 TTTCATTAAC
1777159 TTTTATTT-TTTGATTA
1 TTTTATTTATTTGATTA
1777175 TTTTAATTTATTT--TTA
1 TTTT-ATTTATTTGATTA
* *
1777191 TTTTTTTTATATTTGATTT
1 -TTTTATT-TATTTGATTA
1777210 TTTTATTT
1 TTTTATTT
1777218 TTTTATCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
16 9 0.26
17 14 0.41
18 9 0.26
19 2 0.06
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTATTTATTTGATTA
Found at i:1777203 original size:27 final size:27
Alignment explanation
Indices: 1777137--1777221 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
1777127 TAATTTTGGT
* * *
1777137 TTTTTATTTA-ATTTTCATTAACTTTTA
1 TTTTT-TTTATATTTTAATTTATTTTTA
*
1777164 -TTTTTTGATTATTTTAATTTATTTTTA
1 TTTTTTTTA-TATTTTAATTTATTTTTA
*
1777191 TTTTTTTTATA-TTTGA-TT-TTTTTA
1 TTTTTTTTATATTTTAATTTATTTTTA
1777215 TTTTTTT
1 TTTTTTT
1777222 ATCAAAGATA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
24 13 0.27
25 5 0.10
26 8 0.16
27 16 0.33
28 7 0.14
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (27 bp):
TTTTTTTTATATTTTAATTTATTTTTA
Found at i:1777204 original size:21 final size:23
Alignment explanation
Indices: 1777175--1777223 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1777165 TTTTTGATTA
1777175 TTTTA-ATTT-ATTTTTAT-TTT
1 TTTTATATTTGATTTTTATATTT
*
1777195 TTTTATATTTGATTTTTTTATTT
1 TTTTATATTTGATTTTTATATTT
1777218 TTTTAT
1 TTTTAT
1777224 CAAAGATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 5 0.20
21 4 0.16
22 7 0.28
23 9 0.36
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (23 bp):
TTTTATATTTGATTTTTATATTT
Found at i:1779785 original size:8 final size:8
Alignment explanation
Indices: 1779772--1779813 Score: 84
Period size: 8 Copynumber: 5.2 Consensus size: 8
1779762 CAAGCTAAGA
1779772 TGCCAATG
1 TGCCAATG
1779780 TGCCAATG
1 TGCCAATG
1779788 TGCCAATG
1 TGCCAATG
1779796 TGCCAATG
1 TGCCAATG
1779804 TGCCAATG
1 TGCCAATG
1779812 TG
1 TG
1779814 TCGAAACTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (8 bp):
TGCCAATG
Found at i:1779994 original size:49 final size:49
Alignment explanation
Indices: 1779837--1780022 Score: 178
Period size: 52 Copynumber: 3.7 Consensus size: 49
1779827 CCAATGAAAC
* * *
1779837 TGATTCACGGCCAGCGACATTAGACTTGAAGATGAGAAGAATGCCAATGTGC
1 TGATTCAAGGCCAGCGACATTAGACTTAAAGAT--GAAG-ATGCCAATGTGT
* * * * *
1779889 TGATTCAAGGCCAGGGACATTAGGCTTAGGAATGTTAAAGATGCCAATATGT
1 TGATTCAAGGCCAGCGACATTAGACTTA--AA-GATGAAGATGCCAATGTGT
* * * *
1779941 TGATTCAAGGCCAGCGATATCAGACTTAAAGATGAAGGTGCCAATGCGT
1 TGATTCAAGGCCAGCGACATTAGACTTAAAGATGAAGATGCCAATGTGT
* *
1779990 TGATTCAAGGCCAGTG--ATTGGACTTAAAGATGA
1 TGATTCAAGGCCAGCGACATTAGACTTAAAGATGA
1780023 GAAGGATGAT
Statistics
Matches: 111, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
47 15 0.14
49 29 0.26
50 2 0.02
52 58 0.52
53 3 0.03
54 2 0.02
55 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (49 bp):
TGATTCAAGGCCAGCGACATTAGACTTAAAGATGAAGATGCCAATGTGT
Found at i:1780027 original size:49 final size:49
Alignment explanation
Indices: 1779930--1780022 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
1779920 ATGTTAAAGA
*
1779930 TGCCAATATGTTGATTCAAGGCCAGCGATATCAGACTTAAAGATGAAGG
1 TGCCAATACGTTGATTCAAGGCCAGCGATATCAGACTTAAAGATGAAGG
* * *
1779979 TGCCAATGCGTTGATTCAAGGCCAGTGAT-T-GGACTTAAAGATGA
1 TGCCAATACGTTGATTCAAGGCCAGCGATATCAGACTTAAAGATGA
1780023 GAAGGATGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 13 0.32
48 1 0.03
49 26 0.65
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (49 bp):
TGCCAATACGTTGATTCAAGGCCAGCGATATCAGACTTAAAGATGAAGG
Done.